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Reagor CC, Velez-Angel N, Hudspeth AJ. Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference. PNAS NEXUS 2023; 2:pgad113. [PMID: 37113980 PMCID: PMC10129065 DOI: 10.1093/pnasnexus/pgad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023]
Abstract
Identifying the causal interactions in gene-regulatory networks requires an accurate understanding of the time-lagged relationships between transcription factors and their target genes. Here we describe DELAY (short for Depicting Lagged Causality), a convolutional neural network for the inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. We show that combining supervised deep learning with joint probability matrices of pseudotime-lagged trajectories allows the network to overcome important limitations of ordinary Granger causality-based methods, for example, the inability to infer cyclic relationships such as feedback loops. Our network outperforms several common methods for inferring gene regulation and, when given partial ground-truth labels, predicts novel regulatory networks from single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data sets. To validate this approach, we used DELAY to identify important genes and modules in the regulatory network of auditory hair cells, as well as likely DNA-binding partners for two hair cell cofactors (Hist1h1c and Ccnd1) and a novel binding sequence for the hair cell-specific transcription factor Fiz1. We provide an easy-to-use implementation of DELAY under an open-source license at https://github.com/calebclayreagor/DELAY.
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Affiliation(s)
| | - Nicolas Velez-Angel
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065, USA
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2
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Wang J, Zheng J, Wang H, He H, Li S, Zhang Y, Wang Y, Xu X, Wang S. Gene therapy: an emerging therapy for hair cells regeneration in the cochlea. Front Neurosci 2023; 17:1177791. [PMID: 37207182 PMCID: PMC10188948 DOI: 10.3389/fnins.2023.1177791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Sensorineural hearing loss is typically caused by damage to the cochlear hair cells (HCs) due to external stimuli or because of one's genetic factors and the inability to convert sound mechanical energy into nerve impulses. Adult mammalian cochlear HCs cannot regenerate spontaneously; therefore, this type of deafness is usually considered irreversible. Studies on the developmental mechanisms of HC differentiation have revealed that nonsensory cells in the cochlea acquire the ability to differentiate into HCs after the overexpression of specific genes, such as Atoh1, which makes HC regeneration possible. Gene therapy, through in vitro selection and editing of target genes, transforms exogenous gene fragments into target cells and alters the expression of genes in target cells to activate the corresponding differentiation developmental program in target cells. This review summarizes the genes that have been associated with the growth and development of cochlear HCs in recent years and provides an overview of gene therapy approaches in the field of HC regeneration. It concludes with a discussion of the limitations of the current therapeutic approaches to facilitate the early implementation of this therapy in a clinical setting.
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Affiliation(s)
- Jipeng Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianwei Zheng
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haiyan Wang
- Department of Otolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoying He
- Department of Neurology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Shuang Li
- Department of Otolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ya Zhang
- Department of Otolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - You Wang
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- *Correspondence: You Wang,
| | - Xiaoxiang Xu
- Department of Otolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Xiaoxiang Xu,
| | - Shuyi Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Shuyi Wang,
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3
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Connolly K, Gonzalez-Cordero A. Modelling inner ear development and disease using pluripotent stem cells - a pathway to new therapeutic strategies. Dis Model Mech 2022; 15:dmm049593. [PMID: 36331565 PMCID: PMC10621662 DOI: 10.1242/dmm.049593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
The sensory epithelia of the mammalian inner ear enable sound and movement to be perceived. Damage to these epithelia can cause irreversible sensorineural hearing loss and vestibular dysfunction because they lack regenerative capacity. The human inner ear cannot be biopsied without causing permanent damage, significantly limiting the tissue samples available for research. Investigating disease pathology and therapeutic developments have therefore traditionally relied on animal models, which often cannot completely recapitulate the human otic systems. These challenges are now being partly addressed using induced pluripotent stem cell-derived cultures, which generate the sensory epithelial-like tissues of the inner ear. Here, we review how pluripotent stem cells have been used to produce two-dimensional and three-dimensional otic cultures, the strengths and limitations of these new approaches, and how they have been employed to investigate genetic and acquired forms of audiovestibular dysfunction. This Review provides an overview of the progress in pluripotent stem cell-derived otic cultures thus far, focusing on their applications in disease modelling and therapeutic trials. We survey their current limitations and future directions, highlighting their prospective utility for high-throughput drug screening and developing personalised medicine approaches.
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Affiliation(s)
- Keeva Connolly
- Stem Cell Medicine Group, Children's Medical Research Institute, Westmead, 2145 NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145 NSW, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children's Medical Research Institute, Westmead, 2145 NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145 NSW, Australia
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4
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Ren H, Hu B, Jiang G. Advancements in prevention and intervention of sensorineural hearing loss. Ther Adv Chronic Dis 2022; 13:20406223221104987. [PMID: 35782345 PMCID: PMC9243368 DOI: 10.1177/20406223221104987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Abstract
The inner ear is a complex and difficult organ to study, and sensorineural hearing loss (SNHL) is a multifactorial sensorineural disorder with characteristics of impaired speech discrimination, recognition, sound detection, and localization. Till now, SNHL is recognized as an incurable disease because the potential mechanisms underlying SNHL have not been elucidated. The risk of developing SNHL is no longer viewed as primarily due to environmental factors. Instead, SNHL seems to result from a complicated interplay of genetic and environmental factors affecting numerous fundamental cellular processes. The complexity of SNHL is presented as an inability to make an early diagnosis at the earliest stages of the disease and difficulties in the management of symptoms during the process. To date, there are no treatments that slow the neurodegenerative process. In this article, we review the recent advances about SHNL and discuss the complexities and challenges of prevention and intervention of SNHL.
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Affiliation(s)
- Hongmiao Ren
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, P.R. China
| | - Bing Hu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Guangli Jiang
- Otorhinolaryngology Hospital, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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5
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Deafness-in-a-dish: modeling hereditary deafness with inner ear organoids. Hum Genet 2021; 141:347-362. [PMID: 34342719 PMCID: PMC9035009 DOI: 10.1007/s00439-021-02325-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/24/2021] [Indexed: 12/27/2022]
Abstract
Sensorineural hearing loss (SNHL) is a major cause of functional disability in both the developed and developing world. While hearing aids and cochlear implants provide significant benefit to many with SNHL, neither targets the cellular and molecular dysfunction that ultimately underlies SNHL. The successful development of more targeted approaches, such as growth factor, stem cell, and gene therapies, will require a yet deeper understanding of the underlying molecular mechanisms of human hearing and deafness. Unfortunately, the human inner ear cannot be biopsied without causing significant, irreversible damage to the hearing or balance organ. Thus, much of our current understanding of the cellular and molecular biology of human deafness, and of the human auditory system more broadly, has been inferred from observational and experimental studies in animal models, each of which has its own advantages and limitations. In 2013, researchers described a protocol for the generation of inner ear organoids from pluripotent stem cells (PSCs), which could serve as scalable, high-fidelity alternatives to animal models. Here, we discuss the advantages and limitations of conventional models of the human auditory system, describe the generation and characteristics of PSC-derived inner ear organoids, and discuss several strategies and recent attempts to model hereditary deafness in vitro. Finally, we suggest and discuss several focus areas for the further, intensive characterization of inner ear organoids and discuss the translational applications of these novel models of the human inner ear.
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Nourbakhsh A, Colbert BM, Nisenbaum E, El-Amraoui A, Dykxhoorn DM, Koehler KR, Chen ZY, Liu XZ. Stem Cells and Gene Therapy in Progressive Hearing Loss: the State of the Art. J Assoc Res Otolaryngol 2021; 22:95-105. [PMID: 33507440 PMCID: PMC7943682 DOI: 10.1007/s10162-020-00781-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Progressive non-syndromic sensorineural hearing loss (PNSHL) is the most common cause of sensory impairment, affecting more than a third of individuals over the age of 65. PNSHL includes noise-induced hearing loss (NIHL) and inherited forms of deafness, among which is delayed-onset autosomal dominant hearing loss (AD PNSHL). PNSHL is a prime candidate for genetic therapies due to the fact that PNSHL has been studied extensively, and there is a potentially wide window between identification of the disorder and the onset of hearing loss. Several gene therapy strategies exist that show potential for targeting PNSHL, including viral and non-viral approaches, and gene editing versus gene-modulating approaches. To fully explore the potential of these therapy strategies, a faithful in vitro model of the human inner ear is needed. Such models may come from induced pluripotent stem cells (iPSCs). The development of new treatment modalities by combining iPSC modeling with novel and innovative gene therapy approaches will pave the way for future applications leading to improved quality of life for many affected individuals and their families.
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Affiliation(s)
- Aida Nourbakhsh
- Department of Otolaryngology–Head and Neck Surgery, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL 33136 USA
| | - Brett M. Colbert
- Department of Otolaryngology–Head and Neck Surgery, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL 33136 USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Eric Nisenbaum
- Department of Otolaryngology–Head and Neck Surgery, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL 33136 USA
| | - Aziz El-Amraoui
- Unit Progressive Sensory Disorders, Institut Pasteur, INSERM-UMRS1120, Sorbonne Université, 25 rue du Dr. Roux, 75015 Paris, France
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Karl Russell Koehler
- Department of Otolaryngology-Head and Neck Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Zheng-yi Chen
- Department of Otology and Laryngology, Harvard Medical School and Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA 02114 USA
| | - Xue Z. Liu
- Department of Otolaryngology–Head and Neck Surgery, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL 33136 USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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Zine A, Messat Y, Fritzsch B. A human induced pluripotent stem cell-based modular platform to challenge sensorineural hearing loss. STEM CELLS (DAYTON, OHIO) 2021; 39:697-706. [PMID: 33522002 PMCID: PMC8359331 DOI: 10.1002/stem.3346] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/16/2022]
Abstract
The sense of hearing depends on a specialized sensory organ in the inner ear, called the cochlea, which contains the auditory hair cells (HCs). Noise trauma, infections, genetic factors, side effects of ototoxic drugs (ie, some antibiotics and chemotherapeutics), or simply aging lead to the loss of HCs and their associated primary neurons. This results in irreversible sensorineural hearing loss (SNHL) as in mammals, including humans; the inner ear lacks the capacity to regenerate HCs and spiral ganglion neurons. SNHL is a major global health problem affecting millions of people worldwide and provides a growing concern in the aging population. To date, treatment options are limited to hearing aids and cochlear implants. A major bottleneck for development of new therapies for SNHL is associated to the lack of human otic cell bioassays. Human induced pluripotent stem cells (hiPSCs) can be induced in two-dimensional and three-dimensional otic cells in vitro models that can generate inner ear progenitors and sensory HCs and could be a promising preclinical platform from which to work toward restoring SNHL. We review the potential applications of hiPSCs in the various biological approaches, including disease modeling, bioengineering, drug testing, and autologous stem cell based-cell therapy, that offer opportunities to understand the pathogenic mechanisms of SNHL and identify novel therapeutic strategies.
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Affiliation(s)
- Azel Zine
- Laboratory of Bioengineering and Nanoscience, LBN, University of Montpellier, Montpellier, France
| | - Yassine Messat
- Laboratory of Bioengineering and Nanoscience, LBN, University of Montpellier, Montpellier, France
| | - Bernd Fritzsch
- Department of Biology, CLAS, University of Iowa, Iowa City, Iowa, USA
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8
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Fu Y, Yuan SS, Zhang LJ, Ji ZL, Quan XJ. Atonal bHLH transcription factor 1 is an important factor for maintaining the balance of cell proliferation and differentiation in tumorigenesis. Oncol Lett 2020; 20:2595-2605. [PMID: 32782577 PMCID: PMC7400680 DOI: 10.3892/ol.2020.11833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022] Open
Abstract
Establishing the link between cellular processes and oncogenesis may aid the elucidation of targeted and effective therapies against tumor cell proliferation and metastasis. Previous studies have investigated the mechanisms involved in maintaining the balance between cell proliferation, differentiation and migration. There is increased interest in determining the conditions that allow cancer stem cells to differentiate as well as the identification of molecules that may serve as novel drug targets. Furthermore, the study of various genes, including transcription factors, which serve a crucial role in cellular processes, may present a promising direction for future therapy. The present review described the role of the transcription factor atonal bHLH transcription factor 1 (ATOH1) in signaling pathways in tumorigenesis, particularly in cerebellar tumor medulloblastoma and colorectal cancer, where ATOH1 serves as an oncogene or tumor suppressor, respectively. Additionally, the present review summarized the associated therapeutic interventions for these two types of tumors and discussed novel clinical targets and approaches.
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Affiliation(s)
- Ying Fu
- Key Laboratory of Diabetes Prevention and Research, Endocrinology Center, Lu He Hospital, Capital Medical University, Beijing 101149, P.R. China
| | - Sha-Sha Yuan
- Key Laboratory of Diabetes Prevention and Research, Endocrinology Center, Lu He Hospital, Capital Medical University, Beijing 101149, P.R. China
| | - Li-Jie Zhang
- Key Laboratory of Diabetes Prevention and Research, Endocrinology Center, Lu He Hospital, Capital Medical University, Beijing 101149, P.R. China
| | - Zhi-Li Ji
- Key Laboratory of Diabetes Prevention and Research, Endocrinology Center, Lu He Hospital, Capital Medical University, Beijing 101149, P.R. China
| | - Xiao-Jiang Quan
- Key Laboratory of Diabetes Prevention and Research, Endocrinology Center, Lu He Hospital, Capital Medical University, Beijing 101149, P.R. China.,Laboratory of Brain Development, Institut du Cerveau et de la Moelle Épinière, Hôpital Pitié-Salpêtrière, 75013 Paris, France
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9
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Tang PC, Hashino E, Nelson RF. Progress in Modeling and Targeting Inner Ear Disorders with Pluripotent Stem Cells. Stem Cell Reports 2020; 14:996-1008. [PMID: 32442531 PMCID: PMC7355141 DOI: 10.1016/j.stemcr.2020.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
Sensorineural hearing loss and vestibular dysfunction are caused by damage to neurons and mechanosensitive hair cells, which do not regenerate to any clinically relevant extent in humans. Several protocols have been devised to direct pluripotent stem cells (PSCs) into inner ear hair cells and neurons, which display many properties of their native counterparts. The efficiency, reproducibility, and scalability of these protocols are enhanced by incorporating knowledge of inner ear development. Modeling human diseases in vitro through genetic manipulation of PSCs is already feasible, thereby permitting the elucidation of mechanistic understandings of a wide array of disease etiologies. Early studies on transplantation of PSC-derived otic progenitors have been successful in certain animal models, yet restoration of function and long-term cell survival remain unrealized. Through further research, PSC-based approaches will continue to revolutionize our understanding of inner ear biology and contribute to the development of therapeutic treatments for inner ear disorders.
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Affiliation(s)
- Pei-Ciao Tang
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eri Hashino
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rick F Nelson
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Zhao D, Chen S, Horie T, Gao Y, Bao H, Liu X. Comparison of differentiation gene batteries for migratory mechanosensory neurons across bilaterians. Evol Dev 2020; 22:438-450. [PMID: 32078235 DOI: 10.1111/ede.12331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In embryos of distantly related bilaterian phyla, their lateral neural borders give rise to the peripheral nervous system elements, including various mechanosensory cells derived from migratory precursors, such as hair cells and dorsal root ganglion (DRG) neurons in vertebrates, bipolar tail neuron (BTN) in Ciona, chordotonal organ in Drosophila, and AVM/PVM in Caenorhabditis elegans. Developmental genetics studies had revealed a couple of transcription factors (TFs) regulating differentiation of mechanosensory cells shared by vertebrates and arthropods. However, unbiased systematic profiling of regulators is needed to demonstrate conservation of differentiation gene batteries for mechanosensory cells across bilaterians. At first, we observed that in both C. elegans Q neuroblasts and Drosophila lateral neuroectoderm, conserved NPB specifier Msx/vab-15 regulates Atoh1/lin-32, supporting the homology of mechanosensory neuron development in lateral neural border lineage of Ecdysozia. So we used C. elegans as a protostomia model. Single-cell resolution expression profiling of TFs and genetic analysis revealed a differentiation gene battery (Atonh1/lin-32, Drg11/alr-1, Gfi1/pag-3, Lhx5/mec-3, and Pou4/unc-86) for AVM/PVM mechanosensory neurons. The worm-gene battery significantly overlaps with both that of placode-derived Atonh1/lin-32-dependent hair cells and that of NPB-derived Neurogenin-dependent DRG neurons in vertebrates, supporting the homology of molecular mechanisms underlying the differentiation of neural border-derived mechanosensory cells between protostome and deuterostome. At last, Ciona BTN, the homolog of vertebrate DRG, also expresses Atonh1/lin-32, further supporting the homology notion and indicating a common origin of hair cells and DRG in vertebrate lineage.
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Affiliation(s)
- Di Zhao
- School of Life Sciences, Capital Normal University, Beijing, China.,Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siyu Chen
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Yimeng Gao
- School of Life Sciences, Capital Normal University, Beijing, China
| | - Hongcun Bao
- Department of Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Liu
- School of Life Sciences, Capital Normal University, Beijing, China.,Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
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