Xiangyu Ma

All Publications

• Characterization of 3,3'-iminodipropionitrile (IDPN) damaged utricle transcriptome in the adult mouse utricle. Frontiers in molecular neuroscience Tian, M., Huang, J., Xiao, H., Jiang, P., Ma, X., Lin, Y., Tang, X., Wang, Y., Dai, M., Tong, W., Ye, Z., Sheng, X., Chai, R., Zhang, S. 2024; 17: 1487364

  Abstract

  Utricle is an important vestibular sensory organ for maintaining balance. 3,3'-iminodipropionitrile (IDPN), a prototype nitrile toxin, has been reported to be neurotoxic and vestibulotoxic, and can be used to establish an in vivo damage model of vestibular dysfunction. However, the mechanism of utricular HCs damage caused by IDPN is unclear. Here, we first studied mice balance behavior and HCs damage in IDPN utricle damage model, and found that IDPN injection in vivo can cause vestibular dysfunction and HCs damage, which is more pronounced than neomycin damage model. Then we used RNA-seq to characterize the transcriptome of IDPN damaged utricle in detail to identify genes and pathways that play roles in this process. We found 1,165 upregulated genes and 1,043 downregulated genes in IDPN damaged utricles, and identified that NF-κB pathway and TNF pathway may play important roles in IDPN damage model. Our study provides details of transcriptome of IDPN utricle damage model for further study of vestibular dysfunction.

  View details for DOI 10.3389/fnmol.2024.1487364

  View details for PubMedID 39764513

  View details for PubMedCentralID PMC11701596

• Molecular insights into the activation mechanism of GPR156 in maintaining auditory function. Nature communications Ma, X., Chen, L. N., Liao, M., Zhang, L., Xi, K., Guo, J., Shen, C., Shen, D. D., Cai, P., Shen, Q., Qi, J., Zhang, H., Zang, S. K., Dong, Y. J., Miao, L., Qin, J., Ji, S. Y., Li, Y., Liu, J., Mao, C., Zhang, Y., Chai, R. 2024; 15 (1): 10601

  Abstract

  The class C orphan G-protein-coupled receptor (GPCR) GPR156, which lacks the large extracellular region, plays a pivotal role in auditory function through Gi2/3. Here, we firstly demonstrate that GPR156 with high constitutive activity is essential for maintaining auditory function, and further reveal the structural basis of the sustained role of GPR156. We present the cryo-EM structures of human apo GPR156 and the GPR156-Gi3 complex, unveiling a small extracellular region formed by extracellular loop 2 (ECL2) and the N-terminus. The GPR156 dimer in both apo state and Gi3 protein-coupled state adopt a transmembrane (TM)5/6-TM5/6 interface, indicating the high constitutive activity of GPR156 in the apo state. Furthermore, C-terminus in G-bound subunit of GPR156 plays a dual role in promoting G protein binding within G-bound subunit while preventing the G-free subunit from binding to additional G protein. Together, these results explain how GPR156 constitutive activity is maintained through dimerization and provide a mechanistic insight into the sustained role of GPR156 in maintaining auditory function.

  View details for DOI 10.1038/s41467-024-54681-5

  View details for PubMedID 39638804

  View details for PubMedCentralID PMC11621567

• Isolation and Comprehensive Analysis of Cochlear Tissue-Derived Small Extracellular Vesicles. Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jiang, P., Ma, X., Wang, X., Huang, J., Wang, Y., Ai, J., Xiao, H., Dai, M., Lin, Y., Shao, B., Tang, X., Tong, W., Ye, Z., Chai, R., Zhang, S. 2024: e2408964

  Abstract

  Small extracellular vesicles (sEVs) act as a critical mediator in intercellular communication. Compared to sEVs derived from in vitro sources, tissue-derived sEVs can reflect the in vivo signals released from specific tissues more accurately. Currently, studies on the role of sEVs in the cochlea have relied on studying sEVs from in vitro sources. This study evaluates three cochlear tissue digestion and cochlear tissue-derived sEV (CDsEV) isolation methods, and first proposes that the optimal approach for isolating CDsEVs using collagenase D and DNase І combined with sucrose density gradient centrifugation. Furthermore, it comprehensively investigates CDsEV contents and cell origins. Small RNA sequencing and proteomics are performed to analyze the miRNAs and proteins of CDsEVs. The miRNAs and proteins of CDsEVs are crucial for maintaining normal auditory function. Among them, FGFR1 in CDsEVs may mediate the survival of cochlear hair cells via sEVs. Finally, the joint analysis of single CDsEV sequencing and single-cell RNA sequencing data is utilized to trace cellular origins of CDsEVs. The results show that different types of cochlear cells secrete different amounts of CDsEVs, with Kölliker's organ cells and supporting cells secrete the most. The findings are expected to enhance the understanding of CDsEVs in the cochlea.

  View details for DOI 10.1002/advs.202408964

  View details for PubMedID 39497619

• The single-cell transcriptomic landscape of the topological differences in mammalian auditory receptors. Science China. Life sciences Ma, X., Chen, X., Che, Y., Zhu, S., Wang, X., Gao, S., Wu, J., Kong, F., Cheng, C., Wu, Y., Guo, J., Qi, J., Chai, R. 2024; 67 (11): 2398-2410

  Abstract

  Mammalian hair cells (HCs) are arranged spirally along the cochlear axis and correspond to different frequency ranges. Serving as primary sound detectors, HCs spatially segregate component frequencies into a topographical map. HCs display significant diversity in anatomical and physiological characteristics, yet little is known about the organization of the cochleotopic map of HCs or the molecules involved in this process. Using single-cell RNA sequencing, we determined the distinct molecular profiles of inner hair cells and outer hair cells, and we identified numerous position-dependent genes that were expressed as gradients. Newly identified genes such as Ptn, Rxra, and Nfe2l2 were found to be associated with tonotopy. We employed the SCENIC algorithm to predict the transcription factors that potentially shape these tonotopic gradients. Furthermore, we confirmed that Nfe2l2, a tonotopy-related transcription factor, is critical in mice for sensing low-to-medium sound frequencies in vivo. the analysis of cell-cell communication revealed potential receptor-ligand networks linking inner hair cells to spiral ganglion neurons, including pathways such as BDNF-Ntrk and PTN-Scd4, which likely play essential roles in tonotopic maintenance. Overall, these findings suggest that molecular gradients serve as the organizing principle for maintaining the selection of sound frequencies by HCs.

  View details for DOI 10.1007/s11427-024-2672-1

  View details for PubMedID 39083201

  View details for PubMedCentralID 5937676

• Advance and Application of Single-cell Transcriptomics in Auditory Research. Neuroscience bulletin Ma, X., Guo, J., Tian, M., Fu, Y., Jiang, P., Zhang, Y., Chai, R. 2024; 40 (7): 963-980

  Abstract

  Hearing loss and deafness, as a worldwide disability disease, have been troubling human beings. However, the auditory organ of the inner ear is highly heterogeneous and has a very limited number of cells, which are largely uncharacterized in depth. Recently, with the development and utilization of single-cell RNA sequencing (scRNA-seq), researchers have been able to unveil the complex and sophisticated biological mechanisms of various types of cells in the auditory organ at the single-cell level and address the challenges of cellular heterogeneity that are not resolved through by conventional bulk RNA sequencing (bulk RNA-seq). Herein, we reviewed the application of scRNA-seq technology in auditory research, with the aim of providing a reference for the development of auditory organs, the pathogenesis of hearing loss, and regenerative therapy. Prospects about spatial transcriptomic scRNA-seq, single-cell based genome, and Live-seq technology will also be discussed.

  View details for DOI 10.1007/s12264-023-01149-z

  View details for PubMedID 38015350

  View details for PubMedCentralID PMC11250760

• G protein-coupled receptors in cochlea: Potential therapeutic targets for hearing loss. Frontiers in molecular neuroscience Ma, X., Guo, J., Fu, Y., Shen, C., Jiang, P., Zhang, Y., Zhang, L., Yu, Y., Fan, J., Chai, R. 2022; 15: 1028125

  Abstract

  The prevalence of hearing loss-related diseases caused by different factors is increasing worldwide year by year. Currently, however, the patient's hearing loss has not been effectively improved. Therefore, there is an urgent need to adopt new treatment measures and treatment techniques to help improve the therapeutic effect of hearing loss. G protein-coupled receptors (GPCRs), as crucial cell surface receptors, can widely participate in different physiological and pathological processes, particularly play an essential role in many disease occurrences and be served as promising therapeutic targets. However, no specific drugs on the market have been found to target the GPCRs of the cochlea. Interestingly, many recent studies have demonstrated that GPCRs can participate in various pathogenic process related to hearing loss in the cochlea including heredity, noise, ototoxic drugs, cochlear structure, and so on. In this review, we comprehensively summarize the functions of 53 GPCRs known in the cochlea and their relationships with hearing loss, and highlight the recent advances of new techniques used in cochlear study including cryo-EM, AI, GPCR drug screening, gene therapy vectors, and CRISPR editing technology, as well as discuss in depth the future direction of novel GPCR-based drug development and gene therapy for cochlear hearing loss. Collectively, this review is to facilitate basic and (pre-) clinical research in this area, and provide beneficial help for emerging GPCR-based cochlear therapies.

  View details for DOI 10.3389/fnmol.2022.1028125

  View details for PubMedID 36311029

  View details for PubMedCentralID PMC9596917

• Transcriptomic and epigenomic analyses explore the potential role of H3K4me3 in neomycin-induced cochlear Lgr5+ progenitor cell regeneration of hair cells. Human cell Ma, X., Zhang, S., Qin, S., Guo, J., Yuan, J., Qiang, R., Zhou, S., Cao, W., Yang, J., Ma, F., Chai, R. 2022; 35 (4): 1030-1044

  Abstract

  Currently, adult cochlear hair cells (HCs) lack the capacity to regenerate, particularly the hearing damage caused by the HC damage are hard to recover. Remarkably, Lgr5+ inner ear progenitor cells can be activated to proliferate and regenerate hair cells (HCs) in response to injury, but the epigenetic regulatory roles in HC regeneration from Lgr5+ progenitor cells remain unresolved to date. We here investigate the possible roles of H3K4me3 modification in Lgr5+ progenitor cell proliferation and HC regeneration, and identify these differentially expressed genes associated with different binding regions between untreated Lgr5+ progenitor cells (ULPs) and neomycin-treated Lgr5+ progenitor cells (NLPs). Especially, H3K4me3 modification drives 12 genes involved in regulating proliferation and HC regeneration. Interestingly, we find that transcription factors Zeb1, Fev and Prdm5 are enriched in distinct peaks, implying their probable important roles in modulating neomycin-induced Lgr5+ progenitor cell proliferation and HC regeneration. Overall, our study demonstrates the underlying roles of H3k4me3 modification in Lgr5+ progenitor cell proliferation and HCs regeneration, and provides candidate H3K4me3 modification targets and regulators for subsequent studies.

  View details for DOI 10.1007/s13577-022-00727-z

  View details for PubMedID 35668241

  View details for PubMedCentralID 5658794

• Dync1li1 is required for the survival of mammalian cochlear hair cells by regulating the transportation of autophagosomes. PLoS genetics Zhang, Y., Zhang, S., Zhou, H., Ma, X., Wu, L., Tian, M., Li, S., Qian, X., Gao, X., Chai, R. 2022; 18 (6): e1010232

  Abstract

  Dync1li1, a subunit of cytoplasmic dynein 1, is reported to play important roles in intracellular retrograde transport in many tissues. However, the roles of Dync1li1 in the mammalian cochlea remain uninvestigated. Here we first studied the expression pattern of Dync1li1 in the mouse cochlea and found that Dync1li1 is highly expressed in hair cells (HCs) in both neonatal and adult mice cochlea. Next, we used Dync1li1 knockout (KO) mice to investigate its effects on hearing and found that deletion of Dync1li1 leads to early onset of progressive HC loss via apoptosis and to subsequent hearing loss. Further studies revealed that loss of Dync1li1 destabilizes dynein and alters the normal function of dynein. In addition, Dync1li1 KO results in a thinner Golgi apparatus and the accumulation of LC3+ autophagic vacuoles, which triggers HC apoptosis. We also knocked down Dync1li1 in the OC1 cells and found that the number of autophagosomes were significantly increased while the number of autolysosomes were decreased, which suggested that Dync1li1 knockdown leads to impaired transportation of autophagosomes to lysosomes and therefore the accumulation of autophagosomes results in HC apoptosis. Our findings demonstrate that Dync1li1 plays important roles in HC survival through the regulation of autophagosome transportation.

  View details for DOI 10.1371/journal.pgen.1010232

  View details for PubMedID 35727824

  View details for PubMedCentralID PMC9249241

• Controllable growth of spiral ganglion neurons by magnetic colloidal nanochains NANO TODAY Xia, L., Zhao, X., Ma, X., Hu, Y., Zhang, Y., Li, S., Wang, J., Zhao, Y., Chai, R. 2022; 44

  View details for DOI 10.1016/j.nantod.2022.101507

  View details for Web of Science ID 000811188000001

• Characterization of the microRNA transcriptomes and proteomics of cochlear tissue-derived small extracellular vesicles from mice of different ages after birth. Cellular and molecular life sciences : CMLS Jiang, P., Ma, X., Han, S., Ma, L., Ai, J., Wu, L., Zhang, Y., Xiao, H., Tian, M., Tao, W. A., Zhang, S., Chai, R. 2022; 79 (3): 154

  Abstract

  The cochlea is an important sensory organ for both balance and sound perception, and the formation of the cochlea is a complex developmental process. The development of the mouse cochlea begins on embryonic day (E)9 and continues until postnatal day (P)21 when the hearing system is considered mature. Small extracellular vesicles (sEVs), with a diameter ranging from 30 to 200 nm, have been considered a significant medium for information communication in both physiological and pathological processes. However, there are no studies exploring the role of sEVs in the development of the cochlea. Here, we isolated tissue-derived sEVs from the cochleae of FVB mice at P3, P7, P14, and P21 by ultracentrifugation. These sEVs were first characterized by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Next, we used small RNA-seq and mass spectrometry to characterize the microRNA transcriptomes and proteomes of cochlear sEVs from mice at different ages. Many microRNAs and proteins were discovered to be related to inner ear development, anatomical structure development, and auditory nervous system development. These results all suggest that sEVs exist in the cochlea and are likely to be essential for the normal development of the auditory system. Our findings provide many sEV microRNA and protein targets for future studies of the roles of cochlear sEVs.

  View details for DOI 10.1007/s00018-022-04164-x

  View details for PubMedID 35218422

  View details for PubMedCentralID PMC11072265

• Effects of superparamagnetic iron oxide nanoparticles and static magnetic fields on neural stem cell differentiation by transcriptomic techniques STEMedicine Li, D., Ma, X., Tang, M. 2022

  View details for DOI 10.37175/stemedicine.v3i3.139

• The Expression and Roles of the Super Elongation Complex in Mouse Cochlear Lgr5+ Progenitor Cells. Frontiers in cellular neuroscience Chen, Y., Qiang, R., Zhang, Y., Cao, W., Wu, L., Jiang, P., Ai, J., Ma, X., Dong, Y., Gao, X., Li, H., Lu, L., Zhang, S., Chai, R. 2021; 15: 735723

  Abstract

  The super elongation complex (SEC) has been reported to play a key role in the proliferation and differentiation of mouse embryonic stem cells. However, the expression pattern and function of the SEC in the inner ear has not been investigated. Here, we studied the inner ear expression pattern of three key SEC components, AFF1, AFF4, and ELL3, and found that these three proteins are all expressed in both cochlear hair cells (HCs)and supporting cells (SCs). We also cultured Lgr5+ inner ear progenitors in vitro for sphere-forming assays and differentiation assays in the presence of the SEC inhibitor flavopiridol. We found that flavopiridol treatment decreased the proliferation ability of Lgr5+ progenitors, while the differentiation ability of Lgr5+ progenitors was not affected. Our results suggest that the SEC might play important roles in regulating inner ear progenitors and thus regulating HC regeneration. Therefore, it will be very meaningful to further investigate the detailed roles of the SEC signaling pathway in the inner ear in vivo in order to develop effective treatments for sensorineural hearing loss.

  View details for DOI 10.3389/fncel.2021.735723

  View details for PubMedID 34658793

  View details for PubMedCentralID PMC8519586

• Characterization of Strip1 Expression in Mouse Cochlear Hair Cells. Frontiers in genetics Zhang, S., Dong, Y., Qiang, R., Zhang, Y., Zhang, X., Chen, Y., Jiang, P., Ma, X., Wu, L., Ai, J., Gao, X., Wang, P., Chen, J., Chai, R. 2021; 12: 625867

  Abstract

  Striatin-interacting protein 1 (Strip1) is a core component of the striatin interacting phosphatase and kinase (STRIPAK) complex, which is involved in embryogenesis and development, circadian rhythms, type 2 diabetes, and cancer progression. However, the expression and role of Strip1 in the mammalian cochlea remains unclear. Here we studied the expression and function of Strip1 in the mouse cochlea by using Strip1 knockout mice. We first found that the mRNA and protein expression of Strip1 increases as mice age starting from postnatal day (P) 3 and reaches its highest expression level at P30 and that the expression of Strip1 can be detected by immunofluorescent staining starting from P14 only in cochlear HCs, and not in supporting cells (SCs). Next, we crossed Strip1 heterozygous knockout (Strip +/-) mice to obtain Strip1 homozygous knockout (Strip1-/-) mice for studying the role of Strip1 in cochlear HCs. However, no Strip1-/- mice were obtained and the ratio of Strip +/- to Strip1+/+ mice per litter was about 2:1, which suggested that homozygous Strip1 knockout is embryonic lethal. We measured hearing function and counted the HC number in P30 and P60 Strip +/- mice and found that they had normal hearing ability and HC numbers compared to Strip1+/+ mice. Our study suggested that Strip1 probably play important roles in HC development and maturation, which needs further study in the future.

  View details for DOI 10.3389/fgene.2021.625867

  View details for PubMedID 33889175

  View details for PubMedCentralID PMC8056008

• Knockdown of Foxg1 in Sox9+ supporting cells increases the trans-differentiation of supporting cells into hair cells in the neonatal mouse utricle. Aging Zhang, Y., Zhang, S., Zhang, Z., Dong, Y., Ma, X., Qiang, R., Chen, Y., Gao, X., Zhao, C., Chen, F., He, S., Chai, R. 2020; 12 (20): 19834-19851

  Abstract

  Foxg1 plays important roles in regeneration of hair cell (HC) in the cochlea of neonatal mouse. Here, we used Sox9-CreER to knock down Foxg1 in supporting cells (SCs) in the utricle in order to investigate the role of Foxg1 in HC regeneration in the utricle. We found Sox9 an ideal marker of utricle SCs and bred Sox9CreER/+Foxg1loxp/loxp mice to conditionally knock down Foxg1 in utricular SCs. Conditional knockdown (cKD) of Foxg1 in SCs at postnatal day one (P01) led to increased number of HCs at P08. These regenerated HCs had normal characteristics, and could survive to at least P30. Lineage tracing showed that a significant portion of newly regenerated HCs originated from SCs in Foxg1 cKD mice compared to the mice subjected to the same treatment, which suggested SCs trans-differentiate into HCs in the Foxg1 cKD mouse utricle. After neomycin treatment in vitro, more HCs were observed in Foxg1 cKD mice utricle compared to the control group. Together, these results suggest that Foxg1 cKD in utricular SCs may promote HC regeneration by inducing trans-differentiation of SCs. This research therefore provides theoretical basis for the effects of Foxg1 in trans-differentiation of SCs and regeneration of HCs in the mouse utricle.

  View details for DOI 10.18632/aging.104009

  View details for PubMedID 33099273

  View details for PubMedCentralID PMC7655167

• Stress-Induced Metabolic Disorder in Peripheral CD4+ T Cells Leads to Anxiety-like Behavior. Cell Fan, K. Q., Li, Y. Y., Wang, H. L., Mao, X. T., Guo, J. X., Wang, F., Huang, L. J., Li, Y. N., Ma, X. Y., Gao, Z. J., Chen, W., Qian, D. D., Xue, W. J., Cao, Q., Zhang, L., Shen, L., Zhang, L., Tong, C., Zhong, J. Y., Lu, W., Lu, L., Ren, K. M., Zhong, G., Wang, Y., Tang, M., Feng, X. H., Chai, R. J., Jin, J. 2019; 179 (4): 864-879.e19

  Abstract

  Physical or mental stress leads to neuroplasticity in the brain and increases the risk of depression and anxiety. Stress exposure causes the dysfunction of peripheral T lymphocytes. However, the pathological role and underlying regulatory mechanism of peripheral T lymphocytes in mood disorders have not been well established. Here, we show that the lack of CD4+ T cells protects mice from stress-induced anxiety-like behavior. Physical stress-induced leukotriene B4 triggers severe mitochondrial fission in CD4+ T cells, which further leads to a variety of behavioral abnormalities including anxiety, depression, and social disorders. Metabolomic profiles and single-cell transcriptome reveal that CD4+ T cell-derived xanthine acts on oligodendrocytes in the left amygdala via adenosine receptor A1. Mitochondrial fission promotes the de novo synthesis of purine via interferon regulatory factor 1 accumulation in CD4+ T cells. Our study implicates a critical link between a purine metabolic disorder in CD4+ T cells and stress-driven anxiety-like behavior.

  View details for DOI 10.1016/j.cell.2019.10.001

  View details for PubMedID 31675497

• The amphioxus ERK2 gene is involved in innate immune response to LPS stimulation. Fish & shellfish immunology Ma, X., Peng, S., Zhou, X., Li, S., Jin, P. 2019; 86: 64-69

  Abstract

  The ERK2 gene is a member of the MAPK family, which plays very important roles in responses to external environmental pressures. However, the ERK2 has yet not been identified in amphioxus to date. To further illuminate the function and evolutionary mechanism of the ERK2 gene, in this present study, we have cloned the full length of the ERK2 gene of Branchiostoma belcheri (designed as AmphiERK2), which is highly homologous to these vertebrate ERK2 genes. The AmphiERK2 protein contains the conserved S_TKc domain and the TEY motif, and its 3D structure is also highly similar to human ERK2 protein. Taken together, our results indicate that the AmphiERK2 gene belongs to a member of the ERK2 gene family. We further use qRT-PCR technology to detect an ubiquitous expression of AmphiERK2 gene in all five investigated tissues (muscle, notochord, gill, hepatic caecum and intestine), and the expression level of AmphiERK2 in both notochord and muscle is significantly higher than the other three tissues. Meanwhile our results also demonstrate that LPS stimulation can induce the up-regulation expression of AmphiERK2 gene and significantly increase the phosphorylation level of AmphiERK2 protein, which seems to imply that the AmphiERK2 may be involved in amphioxus innate immune responses. Overall, our findings provide an important insight into amphioxus innate immune function and evolution of the ERK2 gene family.

  View details for DOI 10.1016/j.fsi.2018.11.018

  View details for PubMedID 30439498

• LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs. Database : the journal of biological databases and curation Pian, C., Zhang, G., Tu, T., Ma, X., Li, F. 2018; 2018

  Abstract

  Long non-coding RNAs (lncRNAs) are endogenous molecules longer than 200 nucleotides, and lack coding potential. LncRNAs that interact with microRNAs (miRNAs) are known as a competing endogenous RNAs (ceRNAs) and have the ability to regulate the expression of target genes. The ceRNAs play an important role in the initiation and progression of various cancers. However, until now, there is no a database including a collection of experimentally verified, human ceRNAs. We developed the LncCeRBase database, which encompasses 432 lncRNA-miRNA-mRNA interactions, including 130 lncRNAs, 214 miRNAs and 245 genes from 300 publications. In addition, we compiled the signaling pathways associated with the included lncRNA-miRNA-mRNA interactions as a tool to explore their functions. LncCeRBase is useful for understanding the regulatory mechanisms of lncRNA.Database URL: http://lnccerbase.it1004.com.

  View details for DOI 10.1093/database/bay061

  View details for PubMedID 29961817

  View details for PubMedCentralID PMC6014130