Primary cilia promote the differentiation of human neurons through the WNT signaling pathway.
Axon branching
Neuron differentiation
Primary cilia
Transcriptomics time-course
WNT signaling
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
27 Feb 2024
27 Feb 2024
Historique:
received:
18
07
2023
accepted:
12
02
2024
medline:
28
2
2024
pubmed:
28
2
2024
entrez:
27
2
2024
Statut:
epublish
Résumé
Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
Sections du résumé
BACKGROUND
BACKGROUND
Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce.
RESULTS
RESULTS
We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes.
CONCLUSIONS
CONCLUSIONS
We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
Identifiants
pubmed: 38413974
doi: 10.1186/s12915-024-01845-w
pii: 10.1186/s12915-024-01845-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
48Informations de copyright
© 2024. The Author(s).
Références
Joukov, De Nicolo. The Centrosome and the Primary Cilium: The Yin and Yang of a Hybrid Organelle. Cells. 2019;8:701.
Ishikawa H, Marshall WF. Ciliogenesis: building the cell’s antenna. Nat Rev Mol Cell Biol. 2011;12:222–34.
pubmed: 21427764
doi: 10.1038/nrm3085
De Stasio EA, Mueller KP, Bauer RJ, Hurlburt AJ, Bice SA, Scholtz SL, et al. An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons. Genetics. 2018;208:1083–97.
pubmed: 29301909
pmcid: 5844324
doi: 10.1534/genetics.117.300571
Piasecki BP, Burghoorn J, Swoboda P. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals. Proc Natl Acad Sci USA. 2010;107:12969–74.
pubmed: 20615967
pmcid: 2919930
doi: 10.1073/pnas.0914241107
Senti G, Swoboda P. Distinct Isoforms of the RFX Transcription Factor DAF-19 Regulate Ciliogenesis and Maintenance of Synaptic Activity. Mol Biol Cell. 2008;19:5517–28.
pubmed: 18843046
pmcid: 2592639
doi: 10.1091/mbc.e08-04-0416
Choksi SP, Lauter G, Swoboda P, Roy S. Switching on cilia: transcriptional networks regulating ciliogenesis. Development. 2014;141:1427–41.
pubmed: 24644260
doi: 10.1242/dev.074666
Harris HK, Nakayama T, Lai J, Zhao B, Argyrou N, Gubbels CS, et al. Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior. Genet Med. 2021;23:1028–40.
pubmed: 33658631
pmcid: 9472083
doi: 10.1038/s41436-021-01114-z
Sugiaman-Trapman D, Vitezic M, Jouhilahti E-M, Mathelier A, Lauter G, Misra S, et al. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics. 2018;19:181.
pubmed: 29510665
pmcid: 5838959
doi: 10.1186/s12864-018-4564-6
Bisgrove BW, Makova S, Yost HJ, Brueckner M. RFX2 is essential in the ciliated organ of asymmetry and an RFX2 transgene identifies a population of ciliated cells sufficient for fluid flow. Dev Biol. 2012;363:166–78.
pubmed: 22233545
doi: 10.1016/j.ydbio.2011.12.030
Chung M-I, Peyrot SM, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, et al. RFX2 is broadly required for ciliogenesis during vertebrate development. Dev Biol. 2012;363:155–65.
pubmed: 22227339
doi: 10.1016/j.ydbio.2011.12.029
Reiter JF, Leroux MR. Genes and molecular pathways underpinning ciliopathies. Nat Rev Mol Cell Biol. 2017;18:533–47.
pubmed: 28698599
pmcid: 5851292
doi: 10.1038/nrm.2017.60
Garcia G, Raleigh DR, Reiter JF. How the Ciliary Membrane Is Organized Inside-Out to Communicate Outside-In. Curr Biol. 2018;28:R421–34.
pubmed: 29689227
pmcid: 6434934
doi: 10.1016/j.cub.2018.03.010
Wheway G, Nazlamova L, Hancock JT. Signaling through the Primary Cilium. Front Cell Dev Biol. 2018;6:8.
pubmed: 29473038
pmcid: 5809511
doi: 10.3389/fcell.2018.00008
Steinhart Z, Angers S. Wnt signaling in development and tissue homeostasis. Development. 2018;145:dev146589.
pubmed: 29884654
doi: 10.1242/dev.146589
Flores-Hernández E, Velázquez DM, Castañeda-Patlán MC, Fuentes-García G, Fonseca-Camarillo G, Yamamoto-Furusho JK, et al. Canonical and non-canonical Wnt signaling are simultaneously activated by Wnts in colon cancer cells. Cell Signal. 2020;72:109636.
pubmed: 32283254
doi: 10.1016/j.cellsig.2020.109636
MacDonald BT, Tamai K, He X. Wnt/β-Catenin Signaling: Components, Mechanisms, and Diseases. Dev Cell. 2009;17:9–26.
pubmed: 19619488
pmcid: 2861485
doi: 10.1016/j.devcel.2009.06.016
Nishita M, Saji T, Minami Y. Non-canonical Wnt signaling and cellular responses. Clin Calcium. 2019;29:291–7.
pubmed: 30814373
Arredondo SB, Valenzuela-Bezanilla D, Mardones MD, Varela-Nallar L. Role of Wnt Signaling in Adult Hippocampal Neurogenesis in Health and Disease. Front Cell Dev Biol. 2020;8:860.
pubmed: 33042988
pmcid: 7525004
doi: 10.3389/fcell.2020.00860
Veland IR, Montjean R, Eley L, Pedersen LB, Schwab A, Goodship J, et al. Inversin/Nephrocystin-2 Is Required for Fibroblast Polarity and Directional Cell Migration. PLoS ONE. 2013;8:e60193.
pubmed: 23593172
pmcid: 3620528
doi: 10.1371/journal.pone.0060193
Simons M, Gloy J, Ganner A, Bullerkotte A, Bashkurov M, Krönig C, et al. Inversin, the gene product mutated in nephronophthisis type II, functions as a molecular switch between Wnt signaling pathways. Nat Genet. 2005;37:537–43.
pubmed: 15852005
pmcid: 3733333
doi: 10.1038/ng1552
Bengoa-Vergniory N, Gorroño-Etxebarria I, González-Salazar I, Kypta RM. A Switch From Canonical to Noncanonical Wnt Signaling Mediates Early Differentiation of Human Neural Stem Cells. Stem Cells. 2014;32:3196–208.
pubmed: 25100239
doi: 10.1002/stem.1807
Suciu SK, Caspary T. Cilia, neural development and disease. Semin Cell Dev Biol. 2021;110:34–42.
pubmed: 32732132
doi: 10.1016/j.semcdb.2020.07.014
Tereshko L, Turrigiano GG, Sengupta P. Primary cilia in the postnatal brain: Subcellular compartments for organizing neuromodulatory signaling. Curr Opin Neurobiol. 2022;74:102533.
pubmed: 35405626
pmcid: 9167775
doi: 10.1016/j.conb.2022.102533
Bieder A, Yoshihara M, Katayama S, Krjutškov K, Falk A, Kere J, et al. Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. Mol Neurobiol. 2020;57:2944–58.
pubmed: 32445086
pmcid: 7320047
doi: 10.1007/s12035-020-01905-6
Tammimies K, Bieder A, Lauter G, Sugiaman-Trapman D, Torchet R, Hokkanen M, et al. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs. FASEB J. 2016;30:3578–87.
pubmed: 27451412
pmcid: 5024701
doi: 10.1096/fj.201500124RR
Lauter G, Swoboda P, Tapia-Páez I. Cilia in Brain Development and Disease. In: Cilia: Development and Disease. CRC Press, Taylor & Francis Publ, Boca Raton, Florida, USA. 2018; ch. 1:pp. 1–35.
Lepanto P, Badano JL, Zolessi FR. Neuron’s little helper: The role of primary cilia in neurogenesis. Neurogenesis. 2016;3:e1253363.
pubmed: 28090545
pmcid: 5129898
doi: 10.1080/23262133.2016.1253363
Liu S, Trupiano MX, Simon J, Guo J, Anton ES. The essential role of primary cilia in cerebral cortical development and disorders. In: Current Topics in Developmental Biology. Elsevier; 2021. p. 99–146.
Matsumoto M, Sawada M, García-González D, Herranz-Pérez V, Ogino T, Bang Nguyen H, et al. Dynamic Changes in Ultrastructure of the Primary Cilium in Migrating Neuroblasts in the Postnatal Brain. J Neurosci. 2019;39:9967–88.
pubmed: 31685650
pmcid: 6978947
doi: 10.1523/JNEUROSCI.1503-19.2019
Stoufflet J, Chaulet M, Doulazmi M, Fouquet C, Dubacq C, Métin C, et al. Primary cilium-dependent cAMP/PKA signaling at the centrosome regulates neuronal migration. Sci Adv. 2020;6:eaba3992.
pubmed: 32917588
pmcid: 7467704
doi: 10.1126/sciadv.aba3992
Toro-Tapia G, Das RM. Primary cilium remodeling mediates a cell signaling switch in differentiating neurons. Sci Adv. 2020;6:eabb0601.
pubmed: 32494754
pmcid: 7252506
doi: 10.1126/sciadv.abb0601
Guo J, Otis JM, Suciu SK, Catalano C, Xing L, Constable S, et al. Primary Cilia Signaling Promotes Axonal Tract Development and Is Disrupted in Joubert Syndrome-Related Disorders Models. Dev Cell. 2019;51:759–774.e5.
pubmed: 31846650
pmcid: 6953258
doi: 10.1016/j.devcel.2019.11.005
Guadiana SM, Semple-Rowland S, Daroszewski D, Madorsky I, Breunig JJ, Mykytyn K, et al. Arborization of dendrites by developing neocortical neurons is dependent on primary cilia and type 3 adenylyl cyclase. J Neurosci. 2013;33:2626–38.
pubmed: 23392690
pmcid: 6619186
doi: 10.1523/JNEUROSCI.2906-12.2013
Guo J, Otis JM, Higginbotham H, Monckton C, Cheng J, Asokan A, et al. Primary Cilia Signaling Shapes the Development of Interneuronal Connectivity. Dev Cell. 2017;42:286–300.e4.
pubmed: 28787594
pmcid: 5571900
doi: 10.1016/j.devcel.2017.07.010
Kaech S, Huang C-F, Banker G. General Considerations for Live Imaging of Developing Hippocampal Neurons in Culture. Cold Spring Harb Protoc. 2012;2012(3):312–8.
pubmed: 22383651
pmcid: 4438674
Meka DP, Scharrenberg R, Calderon De Anda F. Emerging roles of the centrosome in neuronal development. Cytoskeleton. 2020;77:84–96.
pubmed: 31925901
doi: 10.1002/cm.21593
Meka DP, Kobler O, Hong S, Friedrich CM, Wuesthoff S, Henis M, et al. Centrosome-dependent microtubule modifications set the conditions for axon formation. Cell Rep. 2022;39:110686.
pubmed: 35443171
pmcid: 10150443
doi: 10.1016/j.celrep.2022.110686
Lauter G, Coschiera A, Yoshihara M, Sugiaman-Trapman D, Ezer S, Sethurathinam S, et al. Differentiation of ciliated human midbrain-derived LUHMES neurons. J Cell Sci. 2020;133:jcs249789.
pubmed: 33115758
doi: 10.1242/jcs.249789
Larkins CE, Aviles GDG, East MP, Kahn RA, Caspary T. Arl13b regulates ciliogenesis and the dynamic localization of Shh signaling proteins. Mol Biol Cell. 2011;22:4694–703.
pubmed: 21976698
pmcid: 3226485
doi: 10.1091/mbc.e10-12-0994
Mühlhans J, Brandstätter JH, Gießl A. The Centrosomal Protein Pericentrin Identified at the Basal Body Complex of the Connecting Cilium in Mouse Photoreceptors. PLoS ONE. 2011;6:e26496.
pubmed: 22031837
pmcid: 3198765
doi: 10.1371/journal.pone.0026496
Bell M, Bachmann S, Klimek J, Langerscheidt F, Zempel H. Axonal TAU Sorting Requires the C-terminus of TAU but is Independent of ANKG and TRIM46 Enrichment at the AIS. Neuroscience. 2021;461:155–71.
pubmed: 33556457
doi: 10.1016/j.neuroscience.2021.01.041
Coschiera A, Watts ME, Kere J, Tammimies K, Swoboda P. Human LUHMES and NES cells as models for studying primary cilia in neurons. Methods Cell Biol. 2023;176:27–41.
pubmed: 37164541
doi: 10.1016/bs.mcb.2022.12.012
Vasquez SSV, Van Dam J, Wheway G. An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. Mol Biol Cell. 2021;32:br13.
Cao Y, Park A, Sun Z. Intraflagellar Transport Proteins Are Essential for Cilia Formation and for Planar Cell Polarity. J Am Soc Nephrol. 2010;21:1326–33.
pubmed: 20576807
pmcid: 2938599
doi: 10.1681/ASN.2009091001
Ezer S, Yoshihara M, Katayama S, Daub C, Lohi H, Krjutskov K, et al. Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog. STAR Protocols. 2021;2:100995.
pubmed: 34950881
pmcid: 8672047
doi: 10.1016/j.xpro.2021.100995
Islam S, Kjällquist U, Moliner A, Zajac P, Fan J-B, Lönnerberg P, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 2011;21:1160–7.
pubmed: 21543516
pmcid: 3129258
doi: 10.1101/gr.110882.110
Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods. 2014;11:163–6.
pubmed: 24363023
doi: 10.1038/nmeth.2772
La Manno G, Gyllborg D, Codeluppi S, Nishimura K, Salto C, Zeisel A, et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell. 2016;167:566–580.e19.
pubmed: 27716510
pmcid: 5055122
doi: 10.1016/j.cell.2016.09.027
Hankey W, Chen Z, Bergman MJ, Fernandez MO, Hancioglu B, Lan X, et al. Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. Oncotarget. 2018;9:31214–30.
pubmed: 30131849
pmcid: 6101278
doi: 10.18632/oncotarget.25781
Hasenpusch-Theil K, Laclef C, Colligan M, Fitzgerald E, Howe K, Carroll E, et al. transient role of the ciliary gene Inpp5e in controlling direct versus indirect neurogenesis in cortical development. eLife. 2020;9:e58162.
pubmed: 32840212
pmcid: 7481005
doi: 10.7554/eLife.58162
Ma R, Kutchy NA, Chen L, Meigs DD, Hu G. Primary cilia and ciliary signaling pathways in aging and age-related brain disorders. Neurobiol Dis. 2022;163:105607.
pubmed: 34979259
doi: 10.1016/j.nbd.2021.105607
Inestrosa NC, Varela-Nallar L. Wnt signalling in neuronal differentiation and development. Cell Tissue Res. 2015;359:215–23.
pubmed: 25234280
doi: 10.1007/s00441-014-1996-4
Motono M, Ioroi Y, Ogura T, Takahashi J. WNT-C59, a Small-Molecule WNT Inhibitor, Efficiently Induces Anterior Cortex That Includes Cortical Motor Neurons From Human Pluripotent Stem Cells. Stem Cells Transl Med. 2016;5:552–60.
pubmed: 26941358
pmcid: 4798742
doi: 10.5966/sctm.2015-0261
Belgacem YH, Hamilton AM, Shim S, Spencer KA, Borodinsky LN. The Many Hats of Sonic Hedgehog Signaling in Nervous System Development and Disease. 2016;4:35.
Shang S, Hua F, Hu Z-W. The regulation of β-catenin activity and function in cancer: therapeutic opportunities. Oncotarget. 2017;8:33972–89.
pubmed: 28430641
pmcid: 5464927
doi: 10.18632/oncotarget.15687
Oh EC, Katsanis N. Context-Dependent Regulation of Wnt Signaling through the Primary Cilium. J Am Soc Nephrol. 2013;24:10–8.
pubmed: 23123400
doi: 10.1681/ASN.2012050526
May-Simera HL, Wan Q, Jha BS, Hartford J, Khristov V, Dejene R, et al. Primary Cilium-Mediated Retinal Pigment Epithelium Maturation Is Disrupted in Ciliopathy Patient Cells. Cell Rep. 2018;22:189–205.
pubmed: 29298421
pmcid: 6166245
doi: 10.1016/j.celrep.2017.12.038
Clarke A, McQueen PG, Fang HY, Kannan R, Wang V, McCreedy E, et al. Abl signaling directs growth of a pioneer axon in Drosophila by shaping the intrinsic fluctuations of actin. Mol Biol Cell. 2020;31:466–77.
pubmed: 31967946
pmcid: 7185895
doi: 10.1091/mbc.E19-10-0564
May-Simera HL, Kelley MW. Cilia, Wnt signaling, and the cytoskeleton. Cilia. 2012;1:7.
pubmed: 23351924
pmcid: 3555707
doi: 10.1186/2046-2530-1-7
Grumolato L, Liu G, Mong P, Mudbhary R, Biswas R, Arroyave R, et al. Canonical and noncanonical Wnts use a common mechanism to activate completely unrelated coreceptors. Genes Dev. 2010;24:2517–30.
pubmed: 21078818
pmcid: 2975928
doi: 10.1101/gad.1957710
Luo W, Lieu ZZ, Manser E, Bershadsky AD, Sheetz MP. Formin DAAM1 Organizes Actin Filaments in the Cytoplasmic Nodal Actin Network. PLoS ONE. 2016;11:e0163915.
pubmed: 27760153
pmcid: 5070803
doi: 10.1371/journal.pone.0163915
Vargas JY, Loria F, Wu Y-J, Córdova G, Nonaka T, Bellow S, et al. The Wnt/Ca2+ pathway is involved in interneuronal communication mediated by tunneling nanotubes. EMBO J. 2019;38:e101230.
pubmed: 31625188
pmcid: 6885744
doi: 10.15252/embj.2018101230
Harterink M, Vocking K, Pan X, Soriano Jerez EM, Slenders L, Fréal A, et al. TRIM46 Organizes Microtubule Fasciculation in the Axon Initial Segment. J Neurosci. 2019;39:4864–73.
pubmed: 30967428
pmcid: 6670255
doi: 10.1523/JNEUROSCI.3105-18.2019
Sohn PD, Tracy TE, Son H-I, Zhou Y, Leite REP, Miller BL, et al. Acetylated tau destabilizes the cytoskeleton in the axon initial segment and is mislocalized to the somatodendritic compartment. Mol Neurodegener. 2016;11:47.
pubmed: 27356871
pmcid: 4928318
doi: 10.1186/s13024-016-0109-0
Krneta-Stankic V, Corkins ME, Paulucci-Holthauzen A, Kloc M, Gladden AB, Miller RK. The Wnt/PCP formin Daam1 drives cell-cell adhesion during nephron development. Cell Rep. 2021;36:109340.
pubmed: 34233186
pmcid: 8629027
doi: 10.1016/j.celrep.2021.109340
Yamakawa K. Mutations of Voltage-Gated Sodium Channel Genes SCN1A and SCN2A in Epilepsy, Intellectual Disability, and Autism. In: Neuronal and Synaptic Dysfunction in Autism Spectrum Disorder and Intellectual Disability. Elsevier; 2016. p. 233–51.
Chia PH, Zhong FL, Niwa S, Bonnard C, Utami KH, Zeng R, et al. A homozygous loss-of-function CAMK2A mutation causes growth delay, frequent seizures and severe intellectual disability. eLife. 2018;7:e32451.
pubmed: 29784083
pmcid: 5963920
doi: 10.7554/eLife.32451
Yang R, Walder-Christensen KK, Kim N, Wu D, Lorenzo DN, Badea A, et al. ANK2 autism mutation targeting giant ankyrin-B promotes axon branching and ectopic connectivity. Proc Natl Acad Sci USA. 2019;116:15262–71.
pubmed: 31285321
pmcid: 6660793
doi: 10.1073/pnas.1904348116
Delprato A, Xiao E, Manoj D. Connecting DCX, COMT and FMR1 in social behavior and cognitive impairment. Behav Brain Funct. 2022;18:7.
pubmed: 35590332
pmcid: 9121553
doi: 10.1186/s12993-022-00191-7
Scholz D, Pöltl D, Genewsky A, Weng M, Waldmann T, Schildknecht S, et al. Rapid, complete and large-scale generation of post-mitotic neurons from the human LUHMES cell line. J Neurochem. 2011;119:957–71.
pubmed: 21434924
doi: 10.1111/j.1471-4159.2011.07255.x
Kasahara K, Inagaki M. Primary ciliary signaling: links with the cell cycle. Trends Cell Biol. 2021;31:954–64.
pubmed: 34420822
doi: 10.1016/j.tcb.2021.07.009
Arrighi N, Lypovetska K, Moratal C, Giorgetti-Peraldi S, Dechesne CA, Dani C, et al. The primary cilium is necessary for the differentiation and the maintenance of human adipose progenitors into myofibroblasts. Sci Rep. 2017;7:15248.
pubmed: 29127365
pmcid: 5681559
doi: 10.1038/s41598-017-15649-2
Wang W, Jack BM, Wang HH, Kavanaugh MA, Maser RL, Tran PV. Intraflagellar Transport Proteins as Regulators of Primary Cilia Length. Front Cell Dev Biol. 2021;9:661350.
pubmed: 34095126
pmcid: 8170031
doi: 10.3389/fcell.2021.661350
Kistler WS, Baas D, Lemeille S, Paschaki M, Seguin-Estevez Q, Barras E, et al. RFX2 Is a Major Transcriptional Regulator of Spermiogenesis. PLoS Genet. 2015;11:e1005368.
pubmed: 26162102
pmcid: 4498915
doi: 10.1371/journal.pgen.1005368
Shawlot W, Vazquez-Chantada M, Wallingford JB, Finnell RH. Rfx2 is required for spermatogenesis in the mouse. Genesis. 2015;53:604–11.
pubmed: 26248850
pmcid: 4744581
doi: 10.1002/dvg.22880
Wu Y, Hu X, Li Z, Wang M, Li S, Wang X, et al. Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis. Sci Rep. 2016;6:20435.
pubmed: 26853561
pmcid: 4745085
doi: 10.1038/srep20435
Akhshi T, Trimble WS. A non-canonical Hedgehog pathway initiates ciliogenesis and autophagy. J Cell Biol. 2021;220:e202004179.
pubmed: 33258871
doi: 10.1083/jcb.202004179
Tran FH, Zheng JJ. Modulating the wnt signaling pathway with small molecules. Protein Sci. 2017;26:650–61.
pubmed: 28120389
pmcid: 5368067
doi: 10.1002/pro.3122
Corbit KC, Shyer AE, Dowdle WE, Gaulden J, Singla V, Chen M-H, et al. Kif3a constrains beta-catenin-dependent Wnt signalling through dual ciliary and non-ciliary mechanisms. Nat Cell Biol. 2008;10:70–6.
pubmed: 18084282
doi: 10.1038/ncb1670
Ocbina PJR, Tuson M, Anderson KV. Primary cilia are not required for normal canonical Wnt signaling in the mouse embryo. PLoS ONE. 2009;4:e6839.
pubmed: 19718259
pmcid: 2729396
doi: 10.1371/journal.pone.0006839
Godoy JA, Espinoza-Caicedo J, Inestrosa NC. Morphological neurite changes induced by porcupine inhibition are rescued by Wnt ligands. Cell Commun Signal. 2021;19:87.
pubmed: 34399774
pmcid: 8369806
doi: 10.1186/s12964-021-00709-y
Janda CY, Dang LT, You C, Chang J, De Lau W, Zhong ZA, et al. Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Nature. 2017;545:234–7.
pubmed: 28467818
pmcid: 5815871
doi: 10.1038/nature22306
Kumamoto N, Gu Y, Wang J, Janoschka S, Takemaru K-I, Levine J, et al. A role for primary cilia in glutamatergic synaptic integration of adult-born neurons. Nat Neurosci. 2012;15:399–405.
pubmed: 22306608
pmcid: 3288565
doi: 10.1038/nn.3042
Park SM, Jang HJ, Lee JH. Roles of Primary Cilia in the Developing Brain. Front Cell Neurosci. 2019;13:218.
pubmed: 31139054
pmcid: 6527876
doi: 10.3389/fncel.2019.00218
Mercado-Gómez O, Hernández-Fonseca K, Villavicencio-Queijeiro A, Massieu L, Chimal-Monroy J, Arias C. Inhibition of Wnt and PI3K Signaling Modulates GSK-3β Activity and Induces Morphological Changes in Cortical Neurons: Role of Tau Phosphorylation. Neurochem Res. 2008;33:1599–609.
pubmed: 18461448
doi: 10.1007/s11064-008-9714-9
Zhang J, Shemezis JR, McQuinn ER, Wang J, Sverdlov M, Chenn A. AKT activation by N-cadherin regulates beta-catenin signaling and neuronal differentiation during cortical development. Neural Dev. 2013;8:7.
pubmed: 23618343
pmcid: 3658902
doi: 10.1186/1749-8104-8-7
Valente EM, Rosti RO, Gibbs E, Gleeson JG. Primary cilia in neurodevelopmental disorders. Nat Rev Neurol. 2014;10:27–36.
pubmed: 24296655
doi: 10.1038/nrneurol.2013.247
Massinen S, Hokkanen M-E, Matsson H, Tammimies K, Tapia-Páez I, Dahlström-Heuser V, et al. Increased Expression of the Dyslexia Candidate Gene DCDC2 Affects Length and Signaling of Primary Cilia in Neurons. PLoS ONE. 2011;6:e20580.
pubmed: 21698230
pmcid: 3116825
doi: 10.1371/journal.pone.0020580
Azzarelli R, Oleari R, Lettieri A, Andre’ V, Cariboni A. In Vitro, Ex Vivo and In Vivo Techniques to Study Neuronal Migration in the Developing Cerebral Cortex. Brain Sci. 2017;7:48.
pubmed: 28448448
pmcid: 5447930
doi: 10.3390/brainsci7050048
Shah RR, Cholewa-Waclaw J, Davies FCJ, Paton KM, Chaligne R, Heard E, et al. Efficient and versatile CRISPR engineering of human neurons in culture to model neurological disorders. Wellcome Open Res. 2016;1:13.
pubmed: 27976757
pmcid: 5146642
doi: 10.12688/wellcomeopenres.10011.1
Calamini B, Geyer N, Huss-Braun N, Bernhardt A, Harsany V, Rival P, et al. Development of a physiologically relevant and easily scalable LUHMES cell-based model of G2019S LRRK2-driven Parkinson’s disease. Dis Model Mech. 2021;14:dmm048017.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.
pubmed: 22743772
doi: 10.1038/nmeth.2019
Dummer A, Poelma C, DeRuiter MC, Goumans MJTH, Hierck BP. Measuring the primary cilium length: improved method for unbiased high-throughput analysis. Cilia. 2016;5:7.
pubmed: 26870322
pmcid: 4750300
doi: 10.1186/s13630-016-0028-2
Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE, et al. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell. 2013;154:1380–9.
pubmed: 23992846
pmcid: 3856256
doi: 10.1016/j.cell.2013.08.021
Stemmer M, Thumberger T, Del Sol KM, Wittbrodt J, Mateo JL. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE. 2015;10:e0124633.
pubmed: 25909470
pmcid: 4409221
doi: 10.1371/journal.pone.0124633
Livak KJ, Schmittgen TD. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods. 2001;25:402–8.
pubmed: 11846609
doi: 10.1006/meth.2001.1262
Kaur N, Chettiar S, Rathod S, Rath P, Muzumdar D, Shaikh ML, et al. Wnt3a mediated activation of Wnt/β-catenin signaling promotes tumor progression in glioblastoma. Mol Cell Neurosci. 2013;54:44–57.
pubmed: 23337036
doi: 10.1016/j.mcn.2013.01.001
Krjutškov K, Katayama S, Saare M, Vera-Rodriguez M, Lubenets D, Samuel K, et al. Single-cell transcriptome analysis of endometrial tissue. Hum Reprod. 2016;31:844–53.
pubmed: 26874359
pmcid: 4791917
doi: 10.1093/humrep/dew008
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15.
pubmed: 31375807
pmcid: 7605509
doi: 10.1038/s41587-019-0201-4
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
pubmed: 25690850
pmcid: 4643835
doi: 10.1038/nbt.3122
Töhönen V, Katayama S, Vesterlund L, Jouhilahti E-M, Sheikhi M, Madissoon E, et al. Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development. Nat Commun. 2015;6:8207.
pubmed: 26360614
doi: 10.1038/ncomms9207
Yoshihara M, Coschiera A, Kere J, Swoboda P. Time-course transcriptome analysis of a human neuronal cell line with RFX2 KO. BioStudies accession: E-MTAB-11546 (2024).
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44:W90–7.
pubmed: 27141961
pmcid: 4987924
doi: 10.1093/nar/gkw377
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell. 2010;38:576–89.
pubmed: 20513432
pmcid: 2898526
doi: 10.1016/j.molcel.2010.05.004
Nueda MJ, Tarazona S, Conesa A. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics. 2014;30:2598–602.
pubmed: 24894503
pmcid: 4155246
doi: 10.1093/bioinformatics/btu333
Korotkevich G, Sukhov V, Budin N, Shpak B, Artyomov MN, Sergushichev A. Fast gene set enrichment analysis. bioRxiv 2021. https://doi.org/10.1101/060012 .
La Manno G, Gyllborg D, Arenas E, Linnarsson S. Single Cell RNA-seq Study of Midbrain and Dopaminergic Neuron Development in Mouse, Human, and Stem Cells. NCBI GEO Accession: GSE76381 (2016).
Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20:163–72.
pubmed: 30643263
pmcid: 6340744
doi: 10.1038/s41590-018-0276-y