The peripheral branch of sensory dorsal root ganglion (DRG) neurons regenerates readily after injury unlike their central branch in the spinal cord. However, extensive regeneration and reconnection of sensory axons in the spinal cord can be driven by the expression of α9 integrin and its activator kindlin-1 (α9k1), which enable axons to interact with tenascin-C. To elucidate the mechanisms and downstream pathways affected by activated integrin expression and central regeneration, we conducted transcriptomic analyses of adult male rat DRG sensory neurons transduced with α9k1, and controls, with and without axotomy of the central branch. Expression of α9k1 without the central axotomy led to upregulation of a known PNS regeneration program, including many genes associated with peripheral nerve regeneration. Coupling α9k1 treatment with dorsal root axotomy led to extensive central axonal regeneration. In addition to the program upregulated by α9k1 expression, regeneration in the spinal cord led to expression of a distinctive CNS regeneration program, including genes associated with ubiquitination, autophagy, endoplasmic reticulum (ER), trafficking, and signaling. Pharmacological inhibition of these processes blocked the regeneration of axons from DRGs and human iPSC-derived sensory neurons, validating their causal contributions to sensory regeneration. This CNS regeneration-associated program showed little correlation with either embryonic development or PNS regeneration programs. Potential transcriptional drivers of this CNS program coupled to regeneration include Mef2a, Runx3, E2f4, and Yy1. Signaling from integrins primes sensory neurons for regeneration, but their axon growth in the CNS is associated with an additional distinctive program that differs from that involved in PNS regeneration.SIGNIFICANCE STATEMENT Restoration of neurologic function after spinal cord injury has yet to be achieved in human patients. To accomplish this, severed nerve fibers must be made to regenerate. Reconstruction of nerve pathways has not been possible, but recently, a method for stimulating long-distance axon regeneration of sensory fibers in rodents has been developed. This research uses profiling of messenger RNAs in the regenerating sensory neurons to discover which mechanisms are activated. This study shows that the regenerating neurons initiate a novel CNS regeneration program which includes molecular transport, autophagy, ubiquitination, and modulation of the endoplasmic reticulum (ER). The study identifies mechanisms that neurons need to activate to regenerate their nerve fibers.

Centre for Reconstructive Neuroscience Institute of Experimental Medicine Czech Academy of Science Prague Czech Republic

Department of Neurobiology and Behavior University of California Irvine California 92697

Department of Neurobiology Harvard Medical School; F M Kirby Neurobiology Center Boston Children's Hospital Boston Massachusetts 02115

John van Geest Centre for Brain Repair Department of Clinical Neurosciences University of Cambridge Cambridge CB2 0PY United Kingdom

Program in Neurogenetics Department of Neurology and Department of Human Genetics David Geffen School of Medicine University of California Los Angeles California 90095

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Abbi S, Ueda H, Zheng C, Cooper LA, Zhao J, Christopher R, Guan JL (2002) Regulation of focal adhesion kinase by a novel protein inhibitor FIP200. Mol Biol Cell 13:3178–3191. 10.1091/mbc.e02-05-0295 PubMed DOI PMC

Andrews MR, Czvitkovich S, Dassie E, Vogelaar CF, Faissner A, Blits B, Gage FH, Ffrench-Constant C, Fawcett JW (2009) Alpha9 integrin promotes neurite outgrowth on tenascin-C and enhances sensory axon regeneration. J Neurosci 29:5546–5557. 10.1523/JNEUROSCI.0759-09.2009 PubMed DOI PMC

Ayad NG, Lee JK, Lemmon VP (2016) Casein kinase signaling in axon regeneration. Neural Regen Res 11:210–211. 10.4103/1673-5374.177713 PubMed DOI PMC

Bradke F, Fawcett JW, Spira ME (2012) Assembly of a new growth cone after axotomy: the precursor to axon regeneration. Nat Rev Neurosci 13:183–193. 10.1038/nrn3176 PubMed DOI

Chandran V, et al. . (2016) A systems-level analysis of the peripheral nerve intrinsic axonal growth program. Neuron 89:956–970. 10.1016/j.neuron.2016.01.034 PubMed DOI PMC

Cheah M, Andrews MR, Chew DJ, Moloney EB, Verhaagen J, Fässler R, Fawcett JW (2016) Expression of an activated integrin promotes long-distance sensory axon regeneration in the spinal cord. J Neurosci 36:7283–7297. 10.1523/JNEUROSCI.0901-16.2016 PubMed DOI PMC

Cheah M, Fawcett JW, Andrews MR (2017) Dorsal root ganglion injection and dorsal root crush injury as a model for sensory axon regeneration. J Vis Exp (123):55535. PubMed PMC

Chen AI, de Nooij JC, Jessell TM (2006) Graded activity of transcription factor Runx3 specifies the laminar termination pattern of sensory axons in the developing spinal cord. Neuron 49:395–408. 10.1016/j.neuron.2005.12.028 PubMed DOI

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14:128. PubMed PMC

Cheng J, Fan YH, Xu X, Zhang H, Dou J, Tang Y, Zhong X, Rojas Y, Yu Y, Zhao Y, Vasudevan SA, Zhang H, Nuchtern JG, Kim ES, Chen X, Lu F, Yang J (2014) A small-molecule inhibitor of UBE2N induces neuroblastoma cell death via activation of p53 and JNK pathways. Cell Death Dis 5:e1079. 10.1038/cddis.2014.54 PubMed DOI PMC

Chierzi S, Ratto GM, Verma P, Fawcett JW (2005) The ability of axons to regenerate their growth cones depends on axonal type and age, and is regulated by calcium, cAMP and ERK. Eur J Neurosci 21:2051–2062. 10.1111/j.1460-9568.2005.04066.x PubMed DOI

Christie KJ, Martinez JA, Zochodne DW (2012) Disruption of E3 ligase NEDD4 in peripheral neurons interrupts axon outgrowth: linkage to PTEN. Mol Cell Neurosci 50:179–192. 10.1016/j.mcn.2012.04.006 PubMed DOI

Curcio M, Bradke F (2018) Axon regeneration in the central nervous system: facing the challenges from the inside. Annu Rev Cell Dev Biol 34:495–521. 10.1146/annurev-cellbio-100617-062508 PubMed DOI

de Angelis L, Zhao J, Andreucci JJ, Olson EN, Cossu G, McDermott JC (2005) Regulation of vertebrate myotome development by the p38 MAP kinase-MEF2 signaling pathway. Dev Biol 283:171–179. 10.1016/j.ydbio.2005.04.009 PubMed DOI

Deng T, et al. . (2023) Scalable generation of sensory neurons from human pluripotent stem cells. Stem Cell Reports 18:1030–1047. 10.1016/j.stemcr.2023.03.006 PubMed DOI PMC

Dikic I (2017) Proteasomal and autophagic degradation systems. Annu Rev Biochem 86:193–224. 10.1146/annurev-biochem-061516-044908 PubMed DOI

Dobbertin A, Czvitkovich S, Theocharidis U, Garwood J, Andrews MR, Properzi F, Lin R, Fawcett JW, Faissner A (2010) Analysis of combinatorial variability reveals selective accumulation of the fibronectin type III domains B and D of tenascin-C in injured brain. Exp Neurol 225:60–73. 10.1016/j.expneurol.2010.04.019 PubMed DOI

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. 10.1093/bioinformatics/bts635 PubMed DOI PMC

Drinjakovic J, Jung H, Campbell DS, Strochlic L, Dwivedy A, Holt CE (2010) E3 ligase Nedd4 promotes axon branching by downregulating PTEN. Neuron 65:341–357. 10.1016/j.neuron.2010.01.017 PubMed DOI PMC

Du J, Ren W, Yao F, Wang H, Zhang K, Luo M, Shang Y, O'Connell D, Bei Z, Wang H, Xiong R, Yang Y (2019) YY1 cooperates with TFEB to regulate autophagy and lysosomal biogenesis in melanoma. Mol Carcinog 58:2149–2160. 10.1002/mc.23105 PubMed DOI

El Bejjani R, Hammarlund M (2012) Notch signaling inhibits axon regeneration. Neuron 73:268–278. 10.1016/j.neuron.2011.11.017 PubMed DOI PMC

Eva R, Crisp S, Marland JR, Norman JC, Kanamarlapudi V, Ffrench-Constant C, Fawcett JW (2012) ARF6 directs axon transport and traffic of integrins and regulates axon growth in adult DRG neurons. J Neurosci 32:10352–10364. 10.1523/JNEUROSCI.1409-12.2012 PubMed DOI PMC

Fagoe ND, van Heest J, Verhaagen J (2014) Spinal cord injury and the neuron-intrinsic regeneration-associated gene program. Neuromolecular Med 16:799–813. 10.1007/s12017-014-8329-3 PubMed DOI

Fagoe ND, Attwell CL, Kouwenhoven D, Verhaagen J, Mason MR (2015) Overexpression of ATF3 or the combination of ATF3, c-Jun, STAT3 and Smad1 promotes regeneration of the central axon branch of sensory neurons but without synergistic effects. Hum Mol Genet 24:6788–6800. 10.1093/hmg/ddv383 PubMed DOI

Feng H, et al. . (2014) EGFR phosphorylation of DCBLD2 recruits TRAF6 and stimulates AKT-promoted tumorigenesis. J Clin Invest 124:3741–3756. 10.1172/JCI73093 PubMed DOI PMC

Golan N, Kauer S, Ehrlich DB, Ravindra N, van Dijk D, Cafferty WB (2021) Single-cell transcriptional profiling of the adult corticospinal tract reveals forelimb and hindlimb molecular specialization. bioRxiv 446653. 10.1101/2021.06.02.446653 DOI

Grafstein B, Murray M (1969) Transport of protein in goldfish optic nerve during regeneration. Exp Neurol 25:494–508. 10.1016/0014-4886(69)90093-4 PubMed DOI

Hamidi A, Song J, Thakur N, Itoh S, Marcusson A, Bergh A, Heldin CH, Landström M (2017) TGF-β promotes PI3K-AKT signaling and prostate cancer cell migration through the TRAF6-mediated ubiquitylation of p85α. Sci Signal 10:eaal4186. 10.1126/scisignal.aal4186 PubMed DOI

Hansen KD, Irizarry RA, Wu Z (2012) Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13:204–216. 10.1093/biostatistics/kxr054 PubMed DOI PMC

Hara T, Takamura A, Kishi C, Iemura S, Natsume T, Guan JL, Mizushima N (2008) FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol 181:497–510. 10.1083/jcb.200712064 PubMed DOI PMC

Harty M, Neff AW, King MW, Mescher AL (2003) Regeneration or scarring: an immunologic perspective. Dev Dyn 226:268–279. 10.1002/dvdy.10239 PubMed DOI

He M, Ding Y, Chu C, Tang J, Xiao Q, Luo ZG (2016) Autophagy induction stabilizes microtubules and promotes axon regeneration after spinal cord injury. Proc Natl Acad Sci U S A 113:11324–11329. 10.1073/pnas.1611282113 PubMed DOI PMC

Ho TS-Y, Hees JT, Xu Z, Kawaguchi R, Biscola NP, Taub DG, Chen K, Chen X, Barrett LB, Cheng L, Gabel CV, Havton LA, Geschwind DH, Woolf CJ (2021) Screening for axon regeneration promoting compounds with human iPSC-derived motor neurons. bioRxiv 466937. 10.1101/2021.11.02.466937 DOI

Hsia HE, Kumar R, Luca R, Takeda M, Courchet J, Nakashima J, Wu S, Goebbels S, An W, Eickholt BJ, Polleux F, Rotin D, Wu H, Rossner MJ, Bagni C, Rhee JS, Brose N, Kawabe H (2014) Ubiquitin E3 ligase Nedd4-1 acts as a downstream target of PI3K/PTEN-mTORC1 signaling to promote neurite growth. Proc Natl Acad Sci U S A 111:13205–13210. 10.1073/pnas.1400737111 PubMed DOI PMC

Humphries JD, Chastney MR, Askari JA, Humphries MJ (2019) Signal transduction via integrin adhesion complexes. Curr Opin Cell Biol 56:14–21. 10.1016/j.ceb.2018.08.004 PubMed DOI

Hynes RO (2002) Integrins: bidirectional, allosteric signaling machines. Cell 110:673–687. 10.1016/s0092-8674(02)00971-6 PubMed DOI

Kaplan A, Morquette B, Kroner A, Leong S, Madwar C, Sanz R, Banerjee SL, Antel J, Bisson N, David S, Fournier AE (2017) Small-molecule stabilization of 14-3-3 protein-protein interactions stimulates axon regeneration. Neuron 93:1082–1093.e5. 10.1016/j.neuron.2017.02.018 PubMed DOI

Kenific CM, Debnath J (2016) NBR1-dependent selective autophagy is required for efficient cell-matrix adhesion site disassembly. Autophagy 12:1958–1959. 10.1080/15548627.2016.1212789 PubMed DOI PMC

Kenific CM, Wittmann T, Debnath J (2016) Autophagy in adhesion and migration. J Cell Sci 129:3685–3693. PubMed PMC

Klar M, Fenske P, Vega FR, Dame C, Bräuer AU (2015) Transcription factor Yin-Yang 2 alters neuronal outgrowth in vitro. Cell Tissue Res 362:453–460. 10.1007/s00441-015-2268-7 PubMed DOI PMC

Ko SH, Apple EC, Liu Z, Chen L (2020) Age-dependent autophagy induction after injury promotes axon regeneration by limiting NOTCH. Autophagy 16:2052–2068. 10.1080/15548627.2020.1713645 PubMed DOI PMC

Kobayashi A, Kang MI, Okawa H, Ohtsuji M, Zenke Y, Chiba T, Igarashi K, Yamamoto M (2004) Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2. Mol Cell Biol 24:7130–7139. 10.1128/MCB.24.16.7130-7139.2004 PubMed DOI PMC

Koley S, Rozenbaum M, Fainzilber M, Terenzio M (2019) Translating regeneration: local protein synthesis in the neuronal injury response. Neurosci Res 139:26–36. 10.1016/j.neures.2018.10.003 PubMed DOI

Komatsu M, Waguri S, Chiba T, Murata S, Iwata JI, Tanida I, Ueno T, Koike M, Uchiyama Y, Kominami E, Tanaka K (2006) Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 441:880–884. 10.1038/nature04723 PubMed DOI

Koseki H, Donegá M, Lam BY, Petrova V, van Erp S, Yeo GS, Kwok JC, Ffrench-Constant C, Eva R, Fawcett JW (2017) Selective rab11 transport and the intrinsic regenerative ability of CNS axons. Elife 6:e26956. 10.7554/eLife.26956 PubMed DOI PMC

Ktistakis NT (2020) ER platforms mediating autophagosome generation. Biochim Biophys Acta Mol Cell Biol Lipids 1865:158433. 10.1016/j.bbalip.2019.03.005 PubMed DOI

Kuijpers M, Azarnia Tehran D, Haucke V, Soykan T (2021) The axonal endolysosomal and autophagic systems. J Neurochem 158:589–602. PubMed

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A (2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res 44:W90–W97. PubMed PMC

Kulkarni A, Chen J, Maday S (2018) Neuronal autophagy and intercellular regulation of homeostasis in the brain. Curr Opin Neurobiol 51:29–36. 10.1016/j.conb.2018.02.008 PubMed DOI

Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A (2010) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26:2438–2444. PubMed PMC

Lallemend F, Sterzenbach U, Hadjab-Lallemend S, Aquino JB, Castelo-Branco G, Sinha I, Villaescusa JC, Levanon D, Wang Y, Franck MC, Kharchenko O, Adameyko I, Linnarsson S, Groner Y, Turner E, Ernfors P (2012) Positional differences of axon growth rates between sensory neurons encoded by Runx3. EMBO J 31:3718–3729. 10.1038/emboj.2012.228 PubMed DOI PMC

Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559. 10.1186/1471-2105-9-559 PubMed DOI PMC

Langfelder P, Zhang B, Horvath S (2008) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24:719–720. 10.1093/bioinformatics/btm563 PubMed DOI

Lehman NL (2009) The ubiquitin proteasome system in neuropathology. Acta Neuropathol 118:329–347. 10.1007/s00401-009-0560-x PubMed DOI PMC

Lin MY, Lin YM, Kao TC, Chuang HH, Chen RH (2011) PDZ-RhoGEF ubiquitination by Cullin3-KLHL20 controls neurotrophin-induced neurite outgrowth. J Cell Biol 193:985–994. 10.1083/jcb.201103015 PubMed DOI PMC

Liu WQ, Martinez JA, Durand J, Wildering W, Zochodne DW (2009) RGD-mediated adhesive interactions are important for peripheral axon outgrowth in vivo. Neurobiol Dis 34:11–22. 10.1016/j.nbd.2008.11.012 PubMed DOI

Ma TC, Willis DE (2015) What makes a RAG regeneration associated? Front Mol Neurosci 8:43. 10.3389/fnmol.2015.00043 PubMed DOI PMC

Maday S, Holzbaur EL (2016) Compartment-specific regulation of autophagy in primary neurons. J Neurosci 36:5933–5945. 10.1523/JNEUROSCI.4401-15.2016 PubMed DOI PMC

Mallucci GR, Klenerman D, Rubinsztein DC (2020) Developing therapies for neurodegenerative disorders: insights from protein aggregation and cellular stress responses. Annu Rev Cell Dev Biol 36:165–189. 10.1146/annurev-cellbio-040320-120625 PubMed DOI

Mehta ST, Luo X, Park KK, Bixby JL, Lemmon VP (2016) Hyperactivated Stat3 boosts axon regeneration in the CNS. Exp Neurol 280:115–120. 10.1016/j.expneurol.2016.03.004 PubMed DOI PMC

Mowers EE, Sharifi MN, Macleod KF (2017) Autophagy in cancer metastasis. Oncogene 36:1619–1630. 10.1038/onc.2016.333 PubMed DOI PMC

Nacu E, Tanaka EM (2011) Limb regeneration: a new development? Annu Rev Cell Dev Biol 27:409–440. 10.1146/annurev-cellbio-092910-154115 PubMed DOI

Nazio F, Strappazzon F, Antonioli M, Bielli P, Cianfanelli V, Bordi M, Gretzmeier C, Dengjel J, Piacentini M, Fimia GM, Cecconi F (2013) mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol 15:406–416. 10.1038/ncb2708 PubMed DOI

Neumann S, Woolf CJ (1999) Regeneration of dorsal column fibers into and beyond the lesion site following adult spinal cord injury. Neuron 23:83–91. 10.1016/s0896-6273(00)80755-2 PubMed DOI

Nguyen VN, Huang KY, Weng JT, Lai KR, Lee TY (2016) UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. Database (Oxford) 2016:baw054. 10.1093/database/baw054 PubMed DOI PMC

Nguyen Hoang AT, Lee H, Lee SJ (2022) Casein kinase I inhibitor D4476 influences autophagy and apoptosis in chloroquine-induced adult retinal pigment epithelial-19 cells. Exp Eye Res 218:109004. 10.1016/j.exer.2022.109004 PubMed DOI

Nieuwenhuis B, Haenzi B, Andrews MR, Verhaagen J, Fawcett JW (2018) Integrins promote axonal regeneration after injury of the nervous system. Biol Rev Camb Philos Soc 93:1339–1362. 10.1111/brv.12398 PubMed DOI PMC

Oblinger MM, Brady ST, McQuarrie IG, Lasek RJ (1987) Cytotypic differences in the protein composition of the axonally transported cytoskeleton in mammalian neurons. J Neurosci 7:453–462. 10.1523/JNEUROSCI.07-02-00453.1987 PubMed DOI PMC

Oh E, Akopian D, Rape M (2018a) Principles of ubiquitin-dependent signaling. Annu Rev Cell Dev Biol 34:137–162. 10.1146/annurev-cellbio-100617-062802 PubMed DOI

Oh YM, Mahar M, Ewan EE, Leahy KM, Zhao G, Cavalli V (2018b) Epigenetic regulator UHRF1 inactivates REST and growth suppressor gene expression via DNA methylation to promote axon regeneration. Proc Natl Acad Sci U S A 115:E12417–E12426. PubMed PMC

Onishi K, Hollis E, Zou Y (2014) Axon guidance and injury-lessons from Wnts and Wnt signaling. Curr Opin Neurobiol 27:232–240. 10.1016/j.conb.2014.05.005 PubMed DOI PMC

Palmisano I, et al. . (2019) Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons. Nat Neurosci 22:1913–1924. 10.1038/s41593-019-0490-4 PubMed DOI

Patodia S, Raivich G (2012) Role of transcription factors in peripheral nerve regeneration. Front Mol. Neurosci 5:8. PubMed PMC

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419. 10.1038/nmeth.4197 PubMed DOI PMC

Petrova V, Pearson CS, Ching J, Tribble JR, Solano AG, Yang Y, Love FM, Watt RJ, Osborne A, Reid E, Williams PA, Martin KR, Geller HM, Eva R, Fawcett JW (2020) Protrudin functions from the endoplasmic reticulum to support axon regeneration in the adult CNS. Nat Commun 11:5614. 10.1038/s41467-020-19436-y PubMed DOI PMC

Plaisier SB, Taschereau R, Wong JA, Graeber TG (2010) Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res 38:e169. 10.1093/nar/gkq636 PubMed DOI PMC

Poplawski GHD, Kawaguchi R, Van Niekerk E, Lu P, Mehta N, Canete P, Lie R, Dragatsis I, Meves JM, Zheng B, Coppola G, Tuszynski MH (2020) Injured adult neurons regress to an embryonic transcriptional growth state. Nature 581:77–82. 10.1038/s41586-020-2200-5 PubMed DOI

Qiang L, Zhao B, Shah P, Sample A, Yang S, He YY (2016) Autophagy positively regulates DNA damage recognition by nucleotide excision repair. Autophagy 12:357–368. 10.1080/15548627.2015.1110667 PubMed DOI PMC

Raiborg C, Wenzel EM, Pedersen NM, Olsvik H, Schink KO, Schultz SW, Vietri M, Nisi V, Bucci C, Brech A, Johansen T, Stenmark H (2015) Repeated ER-endosome contacts promote endosome translocation and neurite outgrowth. Nature 520:234–238. 10.1038/nature14359 PubMed DOI

Rao K, Stone MC, Weiner AT, Gheres KW, Zhou C, Deitcher DL, Levitan ES, Rolls MM (2016) Spastin, atlastin, and ER relocalization are involved in axon but not dendrite regeneration. Mol Biol Cell 27:3245–3256. 10.1091/mbc.E16-05-0287 PubMed DOI PMC

Rao MV, Darji S, Stavrides PH, Goulbourne CN, Kumar A, Yang DS, Yoo L, Peddy J, Lee JH, Yuan A, Nixon RA (2023) Autophagy is a novel pathway for neurofilament protein degradation in vivo. Autophagy 19:1277–1292. 10.1080/15548627.2022.2124500 PubMed DOI PMC

Rauch U (2004) Extracellular matrix components associated with remodeling processes in brain. Cell Mol Life Sci 61:2031–2045. 10.1007/s00018-004-4043-x PubMed DOI PMC

Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J (2016) g: profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res 44:W83–W89. 10.1093/nar/gkw199 PubMed DOI PMC

Renthal W, Tochitsky I, Yang L, Cheng YC, Li E, Kawaguchi R, Geschwind DH, Woolf CJ (2020) Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury. Neuron 108:128–144.e9. 10.1016/j.neuron.2020.07.026 PubMed DOI PMC

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47. 10.1093/nar/gkv007 PubMed DOI PMC

Rosenbloom KR, et al. . (2012) ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res 40:D912–D917. PubMed PMC

Rousset M, Cens T, Menard C, Bowerman M, Bellis M, Brusés J, Raoul C, Scamps F, Charnet P (2015) Regulation of neuronal high-voltage activated Ca(V)2 Ca(2+) channels by the small GTPase RhoA. Neuropharmacology 97:201–209. 10.1016/j.neuropharm.2015.05.019 PubMed DOI

Rozenbaum M, Rajman M, Rishal I, Koppel I, Koley S, Medzihradszky KF, Oses-Prieto JA, Kawaguchi R, Amieux PS, Burlingame AL, Coppola G, Fainzilber M (2018) Translatome regulation in neuronal injury and axon regrowth. eNeuro 5:ENEURO.0276-17.2018. 10.1523/ENEURO.0276-17.2018 PubMed DOI PMC

Sakai Y, Hanafusa H, Shimizu T, Pastuhov SI, Hisamoto N, Matsumoto K (2021) BRCA1-BARD1 regulates axon regeneration in concert with the Gqα-DAG signaling network. J Neurosci 41:2842–2853. 10.1523/JNEUROSCI.1806-20.2021 PubMed DOI PMC

Sakamoto K, Ozaki T, Ko YC, Tsai CF, Gong Y, Morozumi M, Ishikawa Y, Uchimura K, Nadanaka S, Kitagawa H, Zulueta MML, Bandaru A, Tamura JI, Hung SC, Kadomatsu K (2019) Glycan sulfation patterns define autophagy flux at axon tip via PTPRσ-cortactin axis. Nat Chem Biol 15:699–709. 10.1038/s41589-019-0274-x PubMed DOI

Seifert AW, Cook AB, Shaw D (2019) Inhibiting fibroblast aggregation in skin wounds unlocks developmental pathway to regeneration. Dev Biol 455:60–72. 10.1016/j.ydbio.2019.07.001 PubMed DOI

Sharifi MN, Mowers EE, Drake LE, Collier C, Chen H, Zamora M, Mui S, Macleod KF (2016) Autophagy promotes focal adhesion disassembly and cell motility of metastatic tumor cells through the direct interaction of paxillin with LC3. Cell Rep 15:1660–1672. 10.1016/j.celrep.2016.04.065 PubMed DOI PMC

Singec I, Deng T, Simeonov A (2020) WO/2020/219811 - Nociceptor differentiation from human pluripotent stem cells. Available at https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2020219811&_cid=P21-KUMWLF-29547-1.

Smith TP, Sahoo PK, Kar AN, Twiss JL (2020) Intra-axonal mechanisms driving axon regeneration. Brain Res 1740:146864. 10.1016/j.brainres.2020.146864 PubMed DOI PMC

Stavoe AKH, Holzbaur ELF (2018) Axonal autophagy: mini-review for autophagy in the CNS. Neurosci Lett 697:17–23. PubMed PMC

Tedeschi A, Dupraz S, Laskowski CJ, Xue J, Ulas T, Beyer M, Schultze JL, Bradke F (2016) The calcium channel subunit alpha2delta2 suppresses axon regeneration in the adult CNS. Neuron 92:419–434. 10.1016/j.neuron.2016.09.026 PubMed DOI

Tuloup-Minguez V, Hamaï A, Greffard A, Nicolas V, Codogno P, Botti J (2013) Autophagy modulates cell migration and β1 integrin membrane recycling. Cell Cycle 12:3317–3328. 10.4161/cc.26298 PubMed DOI PMC

van Kesteren RE, Mason MR, MacGillavry HD, Smit AB, Verhaagen J (2011) A gene network perspective on axonal regeneration. Front Mol Neurosci 4:46. PubMed PMC

van Vliet AC, Lee J, van der Poel M, Mason MRJ, Noordermeer JN, Fradkin LG, Tannemaat MR, Malessy MJA, Verhaagen J, De Winter F (2021) Coordinated changes in the expression of Wnt pathway genes following human and rat peripheral nerve injury. PLoS One 16:e0249748. 10.1371/journal.pone.0249748 PubMed DOI PMC

Verma P, Chierzi S, Codd AM, Campbell DS, Meyer RL, Holt CE, Fawcett JW (2005) Axonal protein synthesis and degradation are necessary for efficient growth cone regeneration. J Neurosci 25:331–342. 10.1523/JNEUROSCI.3073-04.2005 PubMed DOI PMC

Vogelezang MG, Liu Z, Relvas JB, Raivich G, Scherer SS, Ffrench-Constant C (2001) Alpha4 integrin is expressed during peripheral nerve regeneration and enhances neurite outgrowth. J Neurosci 21:6732–6744. 10.1523/JNEUROSCI.21-17-06732.2001 PubMed DOI PMC

Vogl AM, Phu L, Becerra R, Giusti SA, Verschueren E, Hinkle TB, Bordenave MD, Adrian M, Heidersbach A, Yankilevich P, Stefani FD, Wurst W, Hoogenraad CC, Kirkpatrick DS, Refojo D, Sheng M (2020) Global site-specific neddylation profiling reveals that NEDDylated cofilin regulates actin dynamics. Nat Struct Mol Biol 27:210–220. 10.1038/s41594-019-0370-3 PubMed DOI

Wei X, Wang X, Zhan J, Chen Y, Fang W, Zhang L, Zhang H (2017) Smurf1 inhibits integrin activation by controlling Kindlin-2 ubiquitination and degradation. J Cell Biol 216:1455–1471. 10.1083/jcb.201609073 PubMed DOI PMC

Werner A, Willem M, Jones LL, Kreutzberg GW, Mayer U, Raivich G (2000a) Impaired axonal regeneration in α7 integrin-deficient mice. J Neurosci 20:1822–1830. 10.1523/JNEUROSCI.20-05-01822.2000 PubMed DOI PMC

Werner A, Willem M, Jones LL, Kreutzberg GW, Mayer U, Raivich G (2000b) Impaired axonal regeneration in alpha7 integrin-deficient mice. J Neurosci 20:1822–1830. 10.1523/JNEUROSCI.20-05-01822.2000 PubMed DOI PMC

Winckler B, Faundez V, Maday S, Cai Q, Guimas Almeida C, Zhang H (2018) The Endolysosomal system and proteostasis: from development to degeneration. J Neurosci 38:9364–9374. 10.1523/JNEUROSCI.1665-18.2018 PubMed DOI PMC

Yang WL, Wang J, Chan CH, Lee SW, Campos AD, Lamothe B, Hur L, Grabiner BC, Lin X, Darnay BG, Lin HK (2009) The E3 ligase TRAF6 regulates Akt ubiquitination and activation. Science 325:1134–1138. 10.1126/science.1175065 PubMed DOI PMC

Zinngrebe J, Montinaro A, Peltzer N, Walczak H (2014) Ubiquitin in the immune system. EMBO Rep 15:28–45. 10.1002/embr.201338025 PubMed DOI PMC

Neuronal maturation and axon regeneration: unfixing circuitry to enable repair