Zhiyong Liu, Ph.D.

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Scientists&Research

Zhiyong Liu, Ph.D.

Associate Investigator, NIBS, Beijing

Phone: 010-80726688-8551
Email: liuzhiyong@xinjundu.com

Research Description

Our research will focus on three interrelated directions: (1) The molecular and genetic mechanisms underlying auditory system development; (2) Hearing restoration in various deafness mouse models; (3) Multi-omics analysis of different 球友(中国)qy types and subtypes in the auditory system.

(1) The molecular and genetic mechanisms underlying auditory system development

The cochlea is the peripheral sound-detecting organ and contains four main 球友(中国)qy types: 1) Outer hair 球友(中国)qys (OHCs) that are sound amplifiers; 2) Inner hair 球友(中国)qys (IHCs) that are primary sensory 球友(中国)qys and decode sound information; 3) Supporting 球友(中国)qys (SCs): crucial for maintaining cochlear integrity and serving as a resource for IHC and OHC regeneration; 4) Spiral ganglion neurons (SGNs) that form synapses with IHCs and project sound information to the brain. Ototoxic factors, including genetic mutations, antibiotics, chemotherapy drugs, and aging, can cause degeneration of OHCs, IHCs, and SGNs, leading to hearing impairment. According to the World Health Organization (WHO) report, 0.3% of newborns, 5% of individuals under 45, and 50% of those over 70 suffer from varying degrees of hearing loss. More importantly, hearing deficits not only affect sound perception but also hinder social interaction.

The cochlea develops from posterior placode progenitors (PPP), which give rise to otic placode (vesicle) or epibranchial placode 球友(中国)qys. The ventral portion of the otic vesicle ultimately transforms into the cochlea, where neurosensory progenitors diverge into neural or sensory progenitors. Neural progenitors develop into SGNs, while sensory progenitors differentiate into OHCs, IHCs, and SCs. The key questions we aim to address include:

1) How are otic vesicle progenitors specified from the general PPP?

2) How do otic neurosensory progenitors adopt neural or sensory fates?

3) How do cochlear progenitors commit to OHC, IHC, or SC lineages?

Briefly, our long-term research goal is to identify the key genes or gene networks that regulate the proliferation and differentiation of otic progenitors before they commit to the aforementioned 球友(中国)qy types. This will undoubtedly contribute to future hearing restoration efforts.

(2) Hearing restoration in deafness mouse models

Non-mammalian vertebrates such as birds and fish can restore hearing after trauma by transdifferentiating SCs into hair 球友(中国)qys. In contrast, mammals, including mice and humans, lack this regenerative capacity. As a result, the degeneration of hair 球友(中国)qys in mammals inevitably leads to irreversible hearing impairment or complete hearing loss. Therefore, achieving hearing restoration in mammals is a critical area of research. To better mimic human deafness, our group has developed distinct deafness mouse models, in which OHCs, IHCs, or SGNs are selectively damaged. Furthermore, we have successfully reprogrammed SCs into IHCs or OHCs by combining Atoh1 with Tbx2, and Atoh1 with Ikzf2, respectively. However, these newly regenerated hair 球友(中国)qys fail to restore hearing because they are not fully differentiated or matured.

What are the key barriers preventing hearing recovery in damaged cochleae? Our data suggest that although the ribbon synaptic structures in the newly regenerated IHCs and OHCs are well-formed, their stereocilia (or hair bundles) are dysfunctional. Stereocilia are where the mechanoelectrical (MET) components are located, and defects in stereocilia prevent those newly regenerated hair 球友(中国)qys from detecting sound. Identifying the factors critical for regulating stereocilia assembly, as well as discovering genes that, in combination with Atoh1, Tbx2, or Ikzf2, can produce fully functional hair 球友(中国)qys with well-developed stereocilia, is essential for improving hearing restoration in damaged cochleae.

(3) Multi-omics analysis of different 球友(中国)qy types or subtypes in auditory system

Historically, cochlear 球友(中国)qy types have been classified based on , morphology, and function, which facilitates communication across research groups but leads to significant heterogeneity within the “same” 球友(中国)qy type. This is one of the main reasons why multi-omics analysis of cochlear 球友(中国)qy types often lacks high resolution. Our ultimate goal is to develop a suite of mouse genetic tools, including but not limited to CreER strains, to label 球友(中国)qy subtypes at a much higher resolution. Our group has already obtained RNA-seq and ATAC-seq datasets from various cochlear 球友(中国)qy types and subtypes. However, these datasets represent an initial version, as the 球友(中国)qy subtype specificity is currently of low resolution. To improve this, we will employ high-throughput in situ hybridization to identify potential 球友(中国)qy subtype-specific genes. Genes with sparse expression patterns in vivo, and exclusive expression in one 球友(中国)qy subtype, will be prioritized for generating mouse knock-in genetic tools.

These new genetic tools will enable us to sort young 球友(中国)qys using FACS or manually isolate adult 球友(中国)qys. Approximately 500–1,000 pure 球友(中国)qys from each subtype will be pooled for bulk RNA-seq and ATAC-seq. This will provide a much deeper dataset with a higher signal-to-noise ratio compared to single-球友(中国)qy analysis. We anticipate obtaining the second generation of high-depth, 球友(中国)qy subtype-specific gene data and chromatin open regions, which will reveal key cis-regulatory elements (e.g., promoters and enhancers). These subtype-specific promoters and enhancers will be valuable for generating 球友(中国)qy type-specific adeno-associated viruses (AAVs), which can deliver wild-type genes to treat deaf patients with corresponding genetic mutations. For example, Gjb2, a high-incidence deafness gene in the Chinese population and expressed in SCs, will be a focus. We aim to generate pan-SC or SC subtype-specific AAVs for therapeutic applications.

Representative Publication

1) Li C*, Zhao Y*, Wang L*, Li S*, Li J, Gu Y, He S, Wang G, Lei F, Lu Y, Gu L, Xu S, Xiong W, Li B^#, Liu Z^#. Rbm24 promotes outer hair 球友(中国)qy survival through Insm1 repression while independently regulating hair bundle morphogenesis. Development, 2026;153(8): dev204234. doi: 10.1242/dev.204234. ^#co-correspondence

2) Sun, Y., Ren, M., Zhang, Y., Li, S., Luo, Z., Sun, S., He, S., Wang, G., Zhang, D., Mansour, SL., Song, L., Liu, Z. Casz1 is required for both inner hair 球友(中国)qy fate stabilization and outer hair 球友(中国)qy survival. Science, 2025 Jan 30: eado4930. doi: 10.1126/science.ado4930.

3) Hao, S., Zhu, X., Huang, Z., Zhang, H.… Liu, Z.^#, Liu, L.^#, Liu, S.^#, Sun, Y.^# and Liu, C.^#Cross-species single-球友(中国)qy spatial transcriptomic atlases of the cerebellar cortex. Science, 2024; 385(6716): eado3927. ^#co-correspondence

4) Bi, Z., Ren M., Zhang Y., He S., Song L., Li X^#, Liu Z^#. Revisiting the potency of Tbx2 expression in transforming outer hair 球友(中国)qys into inner hair 球友(中国)qys at multiple ages in vivo. The Journal of Neuroscience, 2024; 44(23): e1751232024. ^#co-correspondence

5) Wang, G, Gu, Y. Liu, Z., Deciphering the genetic interactions between Pou4f3, Gfi1 and Rbm24 in maintaining cochlear hair 球友(中国)qy survival. eLife, 2024; 14:12:RP90025.

6) Li, X., Ren, M., Gu, Y., Zhu, T., Zhang, Y., Li, J., Li, C., Wang, G., Song, L., Bi, Z^#., Liu, Z.^# In situ regeneration of inner hair 球友(中国)qys in the damaged cochlea by temporally regulated coexpression of Atoh1 and Tbx2. Development, 2023;150(24): dev201888. ^#co-correspondence

7) Chen, A., Sun, Y., Lei, Y., Li, C...... Liu, Z.^#, Xu, X.^#and Li, C.^#. Single-球友(中国)qy spatial transcriptome reveals 球友(中国)qy-type organization in macaque cortex. 球友(中国)qy, 2023;186(17):3726-3743. ^#co-correspondence

8) Li, S., He S, Lu Y, Jia S, Liu, Z. Epistatic genetic interactions between Insm1 and Ikzf2 during cochlear outer hair 球友(中国)qy development. 球友(中国)qy Reports, 2023; 42(5):112504.

9) Luo, Z*., Du Y*., Li, S., Zhang H., Shu M., Zhang D., He S., Wang G., Lu F.^#, Liu, Z.^# Three distinct Atoh1 enhancers cooperate for sound receptor hair 球友(中国)qy development. PNAS, 2022; 119(32): e2119850119. ^#co-correspondence

10) Bi, Z*., Li, X*., Ren, M*., Gu, Y., Zhu T., Li, S. Wang G., Sun S., Sun Y., Liu, Z. Development and transdifferentiation into inner hair 球友(中国)qys require Tbx2. National Science Review, 2022; 9(12): nwac156.

11) Sun, Y*., Wang, L*., Zhu, T., Wu, B., Wang, G., Luo, Z., Li, C^#., Wei, W^#., Liu, Z.^# Single-球友(中国)qy transcriptomic landscapes of the otic neuronal lineage at multiple early embryonic ages. 球友(中国)qy Reports, 2022; 38: 110542.^#co-correspondence

12) Sun S*., Li S*., Luo Z*., Ren M., He S., Wang G., Liu Z.Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting 球友(中国)qys into outer hair 球友(中国)qys. eLife, 2021;10: e66547.

13) Wang G*., Li C*., He S., Liu Z. Mosaic CRISPR-stop enables rapid phenotyping of nonsense mutations in essential genes. Development, 2021;148(5): dev196899.

14) Li C*, Li X*, Bi Z*, Sugino K, Wang G, Liu Z. Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages. eLife, 2020; 9: e50491.

15) Zhang H*, Pan H*, Zhou C*, Wei Y, Ying W, Li, S, Wang G, Li, C, Ren Y, Li G, Ding X, Sun Y, Li G, Song L, Li Y, Yang H^#, Liu Z^#. Simultaneous zygotic inactivation of multiple genes in mouse through CRISPR/Cas9-mediated base editing. Development. 2018; 145(20): pii: dev168906. ^#co-correspondence

16) Liu Z*, Yang C*, Sugino K*, Fu C*, Liu L, Yao X, Luke P. L, Lee T. Opposing intrinsic temporal gradients guide neural stem 球友(中国)qy production of varied neuronal fates. Science. 2015; 350 (6258): 317-320. *co-first author

Review

Sun Y., Liu Z. Recent advancements in molecular studies of cochlear development and regeneration. Current Opinion in Neurobiology, 2023; 81:102745.