Suppressing DBNDD2 promotes neuron growth and axon regeneration in adult mammals

Abstract

Effective axon regeneration is essential for the successful restoration of nerve functions in patients suffering from axon injury-associated neurological diseases. Certain self-regeneration occurs in injured peripheral axonal branches of dorsal root ganglion (DRG) neurons but does not occur in their central axonal branches. By performing rat sciatic nerve or dorsal root axotomy, we determined the expression of the dysbindin domain containing 2 (DBNDD2) in the DRGs after the regenerative peripheral axon injury or the non-regenerative central axon injury, respectively, and found that DBNDD2 is down-regulated in the DRGs after peripheral axon injury but up-regulated after central axon injury. Furthermore, we found that DBNDD2 expression differs in neonatal and adult rat DRGs and is gradually increased during development. Functional analysis through DBNDD2 knockdown revealed that silencing DBNDD2 promotes the outgrowth of neurites in both neonatal and adult rat DRG neurons and stimulates robust axon regeneration in adult rats after sciatic nerve crush injury. Bioinformatic analysis data showed that transcription factor estrogen receptor 1 (ESR1) interacts with DBNDD2, exhibits a similar expression trend as DBNDD2 after axon injury, and may targets DBDNN2. These studies indicate that reduced level of DBNDD2 after peripheral axon injury and low abundance of DBNDD2 in neonates contribute to axon regeneration and thus suggest the manipulation of DBNDD2 expression as a promising therapeutic approach for improving recovery after axon damage.

Keywords

axon damage / peripheral axon injury / central axon injury / RNA sequencing / development / single-cell sequencing / DBNDD2 / DRG neuron / neuron growth / axon regeneration

References

[1] Winter CC, He Z, Jacobi A. Axon regeneration: a subcellular extension in multiple dimensions. Cold Spring Harb Perspect Biol 2022; 14(3): a040923

[2] Williams PR, Benowitz LI, Goldberg JL, He Z. Axon regeneration in the mammalian optic nerve. Annu Rev Vis Sci 2020; 6(1): 195–213

[3] Saijilafu BY, Zhang FQ. Signaling pathways that regulate axon regeneration. Neurosci Bull 2013; 29(4): 411–420

[4] He Z, Jin Y. Intrinsic control of axon regeneration. Neuron 2016; 90(3): 437–451

[5] Uyeda A, Muramatsu R. Molecular mechanisms of central nervous system axonal regeneration and remyelination: a review. Int J Mol Sci 2020; 21(21): 8116

[6] Li F, Sami A, Noristani HN, Slattery K, Qiu J, Groves T, Wang S, Veerasammy K, Chen YX, Morales J, Haynes P, Sehgal A, He Y, Li S, Song Y. Glial metabolic rewiring promotes axon regeneration and functional recovery in the central nervous system. Cell Metab 2020; 32(5): 767–785.e7

[7] Bradke F. Mechanisms of axon growth and regeneration: moving between development and disease. J Neurosci 2022; 42(45): 8393–8405

[8] Montero AM, Huang AH. The regenerative capacity of neonatal tissues. Development 2022; 149(12): dev199819

[9] Wang D, Zheng T, Zhou S, Liu M, Liu Y, Gu X, Mao S, Yu B. Promoting axon regeneration by inhibiting RNA N6-methyladenosine demethylase ALKBH5. Elife 2023; 12: e85309

[10] Mahar M, Cavalli V. Intrinsic mechanisms of neuronal axon regeneration. Nat Rev Neurosci 2018; 19(6): 323–337

[11] Robinson LR. Traumatic injury to peripheral nerves. Muscle Nerve 2022; 66(6): 661–670

[12] Hutson TH, Kathe C, Palmisano I, Bartholdi K, Hervera A, De Virgiliis F, McLachlan E, Zhou L, Kong G, Barraud Q, Danzi MC, Medrano-Fernandez A, Lopez-Atalaya JP, Boutillier AL, Sinha SH, Singh AK, Chaturbedy P, Moon LDF, Kundu TK, Bixby JL, Lemmon VP, Barco A, Courtine G, Di Giovanni S. Cbp-dependent histone acetylation mediates axon regeneration induced by environmental enrichment in rodent spinal cord injury models. Sci Transl Med 2019; 11(487): eaaw2064

[13] Zhao Q, Jiang C, Zhao L, Dai X, Yi S. Unleashing axonal regeneration capacities: neuronal and non-neuronal changes after injuries to dorsal root ganglion neuron central and peripheral axonal branches. Mol Neurobiol 2024; 61(1): 423–433

[14] Avraham O, Feng R, Ewan EE, Rustenhoven J, Zhao G, Cavalli V. Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair. eLife 2021; 10: e68457

[15] Kong G, Zhou L, Serger E, Palmisano I, De Virgiliis F, Hutson TH, McLachlan E, Freiwald A, La Montanara P, Shkura K, Puttagunta R, Di Giovanni S. AMPK controls the axonal regenerative ability of dorsal root ganglia sensory neurons after spinal cord injury. Nat Metab 2020; 2(9): 918–933

[16] Palmisano I, Danzi MC, Hutson TH, Zhou L, McLachlan E, Serger E, Shkura K, Srivastava PK, Hervera A, Neill NO, Liu T, Dhrif H, Wang Z, Kubat M, Wuchty S, Merkenschlager M, Levi L, Elliott E, Bixby JL, Lemmon VP, Di Giovanni S. Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons. Nat Neurosci 2019; 22(11): 1913–1924

[17] Hervera A, Zhou L, Palmisano I, McLachlan E, Kong G, Hutson TH, Danzi MC, Lemmon VP, Bixby JL, Matamoros-Angles A, Forsberg K, De Virgiliis F, Matheos DP, Kwapis J, Wood MA, Puttagunta R, Del Río JA, Di Giovanni S. PP4-dependent HDAC3 dephosphorylation discriminates between axonal regeneration and regenerative failure. EMBO J 2019; 38(13): e101032

[18] Yin H, Laguna KA, Li G, Kuret J. Dysbindin structural homologue CK1BP is an isoform-selective binding partner of human casein kinase-1. Biochemistry 2006; 45(16): 5297–5308

[19] Elsholz L, Wasser Y, Ziegler P, Habib P, Voigt A. CK1BP reduces α-synuclein oligomerization and aggregation independent of serine 129 phosphorylation. Cells 2021; 10(11): 2830

[20] Mao S, Chen Y, Feng W, Zhou S, Jiang C, Zhang J, Liu X, Qian T, Liu K, Wang Y, Yao C, Gu X, Yu B. RSK1 promotes mammalian axon regeneration by inducing the synthesis of regeneration-related proteins. PLoS Biol 2022; 20(6): e3001653

[21] Cao HJ, Huang L, Zheng MR, Zhang T, Xu LC. Characterization of circular RNAs in dorsal root ganglia after central and peripheral axon injuries. Front Cell Neurosci 2022; 16: 1046050

[22] Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26(1): 139–140

[23] Zhang R, Chen S, Wang X, Gu X, Yi S. Cell populations in neonatal rat peripheral nerves identified by single-cell transcriptomics. Glia 2021; 69(3): 765–778

[24] Ma JJ, Ju X, Xu RJ, Wang WH, Luo ZP, Liu CM, Yang L, Li B, Chen JQ, Meng B, Yang HL, Zhou FQ. Telomerase reverse transcriptase and p53 regulate mammalian peripheral nervous system and CNS axon regeneration downstream of c-Myc. J Neurosci 2019; 39(46): 9107–9118

[25] Yi S, Zhang H, Gong L, Wu J, Zha G, Zhou S, Gu X, Yu B. Deep sequencing and bioinformatic analysis of lesioned sciatic nerves after crush injury. PLoS One 2015; 10(12): e0143491

[26] Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 2023; 51(D1): D638–D646

[27] Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O’Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res 2020; 48(D1): D489–D497

[28] Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Lemma RB, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res 2022; 50(D1): D165–D173

[29] Hu H, Miao YR, Jia LH, Yu QY, Zhang Q, Guo AY. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic Acids Res 2019; 47(D1): D33–D38

[30] Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. GTRD: an integrated view of transcription regulation. Nucleic Acids Res 2021; 49(D1): D104–D111

[31] Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR, Xia M, Guo AY. hTFtarget: a comprehensive database for regulations of human transcription factors and their targets. Genomics Proteomics Bioinformatics 2020; 18(2): 120–128

[32] Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009; 37(Web Server issue): W202–8

[33] Gordon T, Borschel GH. The use of the rat as a model for studying peripheral nerve regeneration and sprouting after complete and partial nerve injuries. Exp Neurol 2017; 287(Pt 3): 331–347

[34] Bobkiewicz A, Cwykiel J, Siemionow M. Anatomic variations of brachial and lumbosacral plexus models in different rat strains. Microsurgery 2017; 37(4): 327–333

[35] Smith GM, Falone AE, Frank E. Sensory axon regeneration: rebuilding functional connections in the spinal cord. Trends Neurosci 2012; 35(3): 156–163

[36] Zheng B, Lorenzana AO, Ma L. Understanding the axonal response to injury by in vivo imaging in the mouse spinal cord: a tale of two branches. Exp Neurol 2019; 318: 277–285

[37] Renthal W, Tochitsky I, Yang L, Cheng YC, Li E, Kawaguchi R, Geschwind DH, Woolf CJ. Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury. Neuron 2020; 108(1): 128–144.e9

[38] Li Y, He X, Kawaguchi R, Zhang Y, Wang Q, Monavarfeshani A, Yang Z, Chen B, Shi Z, Meng H, Zhou S, Zhu J, Jacobi A, Swarup V, Popovich PG, Geschwind DH, He Z. Microglia-organized scar-free spinal cord repair in neonatal mice. Nature 2020; 587(7835): 613–618

[39] Park KK, Liu K, Hu Y, Kanter JL, He Z. PTEN/mTOR and axon regeneration. Exp Neurol 2010; 223(1): 45–50

[40] Park KK, Liu K, Hu Y, Smith PD, Wang C, Cai B, Xu B, Connolly L, Kramvis I, Sahin M, He Z. Promoting axon regeneration in the adult CNS by modulation of the PTEN/mTOR pathway. Science 2008; 322(5903): 963–966

[41] Liu K, Lu Y, Lee JK, Samara R, Willenberg R, Sears-Kraxberger I, Tedeschi A, Park KK, Jin D, Cai B, Xu B, Connolly L, Steward O, Zheng B, He Z. PTEN deletion enhances the regenerative ability of adult corticospinal neurons. Nat Neurosci 2010; 13(9): 1075–1081

[42] Zhou LY, Han F, Qi SB, Ma JJ, Ma YX, Xie JL, Zhang HC, Fu XY, Chen JQ, Li B, Yang HL, Zhou F. Inhibition of PTEN activity promotes IB4-positive sensory neuronal axon growth. J Cell Mol Med 2020; 24(18): 11012–11017

[43] Chen H, Xiang J, Wu J, He B, Lin T, Zhu Q, Liu X, Zheng C. Expression patterns and role of PTEN in rat peripheral nerve development and injury. Neurosci Lett 2018; 676: 78–84

[44] Cong M, Li J, Wang L, Liu C, Zheng M, Zhou Q, Du M, Ye X, Feng M, Ye Y, Zhang S, Xu W, Lu Y, Wang C, Xia Y, Xie H, Zhang Y, He Q, Gong L, Gu Y, Sun H, Zhang Q, Zhao J, Ding F, Gu X, Zhou S. MircoRNA-25-3p in skin precursor cell-induced Schwann cell-derived extracellular vesicles promotes axon regeneration by targeting Tgif1. Exp Neurol 2024; 376: 114750

[45] Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U, Linnarsson S. Molecular architecture of the mouse nervous system. Cell 2018; 174(4): 999–1014.e22

[46] Dun XP, Parkinson DB. Transection and crush models of nerve injury to measure repair and remyelination in peripheral nerve. Methods Mol Biol 2018; 1791: 251–262

[47] Wang K, Wang S, Chen Y, Wu D, Hu X, Lu Y, Wang L, Bao L, Li C, Zhang X. Single-cell transcriptomic analysis of somatosensory neurons uncovers temporal development of neuropathic pain. Cell Res 2021; 31(8): 904–918

[48] Yi S, Zhang Y, Gu X, Huang L, Zhang K, Qian T, Gu X. Application of stem cells in peripheral nerve regeneration. Burns Trauma 2020; 8: tkaa002

[49] Lee JK, Zheng B. Role of myelin-associated inhibitors in axonal repair after spinal cord injury. Exp Neurol 2012; 235(1): 33–42

[50] Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet 2017; 18(9): 551–562

[51] Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. eLife 2014; 3: e02626

[52] Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The human transcription factors. Cell 2018; 172(4): 650–665

[53] Zhang Y, Zhao Q, Chen Q, Xu L, Yi S. Transcriptional control of peripheral nerve regeneration. Mol Neurobiol 2023; 60(1): 329–341

[54] Chandran V, Coppola G, Nawabi H, Omura T, Versano R, Huebner EA, Zhang A, Costigan M, Yekkirala A, Barrett L, Blesch A, Michaelevski I, Davis-Turak J, Gao F, Langfelder P, Horvath S, He Z, Benowitz L, Fainzilber M, Tuszynski M, Woolf CJ, Geschwind DH. A systems-level analysis of the peripheral nerve intrinsic axonal growth program. Neuron 2016; 89(5): 956–970

[55] Cheong RY, Czieselsky K, Porteous R, Herbison AE. Expression of ESR1 in glutamatergic and GABAergic neurons is essential for normal puberty onset, estrogen feedback, and fertility in female mice. J Neurosci 2015; 35(43): 14533–14543

[56] Hishida M, Nomoto S, Inokawa Y, Hayashi M, Kanda M, Okamura Y, Nishikawa Y, Tanaka C, Kobayashi D, Yamada S, Nakayama G, Fujii T, Sugimoto H, Koike M, Fujiwara M, Takeda S, Kodera Y. Estrogen receptor 1 gene as a tumor suppressor gene in hepatocellular carcinoma detected by triple-combination array analysis. Int J Oncol 2013; 43(1): 88–94

[57] Backes FJ, Walker CJ, Goodfellow PJ, Hade EM, Agarwal G, Mutch D, Cohn DE, Suarez AA. Estrogen receptor-alpha as a predictive biomarker in endometrioid endometrial cancer. Gynecol Oncol 2016; 141(2): 312–317

[58] Król MB, Galicki M, Grešner P, Wieczorek E, Jabłońska E, Reszka E, Morawiec Z, Wąsowicz W, Gromadzińska J. The ESR1 and GPX1 gene expression level in human malignant and non-malignant breast tissues. Acta Biochim Pol 2018; 65(1): 51–57

[59] Aresti U, Carrera S, Iruarrizaga E, Fuente N, Marrodan I, de Lobera AR, Muñoz A, Buque A, Condori E, Ugalde I, Calvo B, Vivanco GL. Estrogen receptor 1 gene expression and its combination with estrogen receptor 2 or aromatase expression predicts survival in non-small cell lung cancer. PLoS One 2014; 9(10): e109659

[60] Ge Q, Lu M, Ju L, Qian K, Wang G, Wu CL, Liu X, Xiao Y, Wang X. miR-4324-RACGAP1-STAT3–ESR1 feedback loop inhibits proliferation and metastasis of bladder cancer. Int J Cancer 2019; 144(12): 3043–3055

[61] Tu CC, Kumar VB, Day CH, Kuo WW, Yeh SP, Chen RJ, Liao CR, Chen HY, Tsai FJ, Wu WJ, Huang CY. Estrogen receptor α (ESR1) over-expression mediated apoptosis in Hep3B cells by binding with SP1 proteins. J Mol Endocrinol 2013; 51(1): 203–212

[62] Zhou J, Teng R, Xu C, Wang Q, Guo J, Xu C, Li Z, Xie S, Shen J, Wang L. Overexpression of ERα inhibits proliferation and invasion of MKN28 gastric cancer cells by suppressing β-catenin. Oncol Rep 2013; 30(4): 1622–1630

[63] Wang L, Cui M, Cheng D, Qu F, Yu J, Wei Y, Cheng L, Wu X, Liu X. miR-9–5p facilitates hepatocellular carcinoma cell proliferation, migration and invasion by targeting ESR1. Mol Cell Biochem 2021; 476(2): 575–583

[64] Li F, Chen Q, Yang Y, Li M, Zhang L, Yan Z, Zhang J, Wang K. ESR1 as a recurrence-related gene in intrahepatic cholangiocarcinoma: a weighted gene coexpression network analysis. Cancer Cell Int 2021; 21(1): 225

[65] Christie KJ, Krishnan A, Martinez JA, Purdy K, Singh B, Eaton S, Zochodne D. Enhancing adult nerve regeneration through the knockdown of retinoblastoma protein. Nat Commun 2014; 5(1): 3670

[66] Duraikannu A, Krishnan A, Chandrasekhar A, Zochodne DW. Beyond trophic factors: exploiting the intrinsic regenerative properties of adult neurons. Front Cell Neurosci 2019; 13: 128

[67] Meyer zu Reckendorf S, Moser D, Blechschmidt A, Joga VN, Sinske D, Hegler J, Deininger S, Catanese A, Vettorazzi S, Antoniadis G, Boeckers T, Knöll B. Motoneuron-specific PTEN deletion in mice induces neuronal hypertrophy and also regeneration after facial nerve injury. J Neurosci 2022; 42(12): 2474–2491

RIGHTS & PERMISSIONS

Higher Education Press