Cited by 1Genetics and Neurodevelopmental DisordersAxon Guidance and Neuronal SignalingAutism Spectrum Disorder Research

CYFIP1 governs the development of cortical axons by modulating calcium availability

Open access
Ricci, Carlotta, Midroit, Maëllie Julie, Caicci, Federico, Achsel, Tilmann, Domínguez-Iturza, Nuria, Bagni, Claudia·2025·Nature Communications

Abstract

The human CYFIP1 gene is linked to Autism Spectrum Disorder (ASD) and Schizophrenia (SCZ), both associated with brain connectivity defects and corpus callosum abnormalities. Previous studies demonstrated that Cyfip1 -heterozygous mice exhibit diminished bilateral functional connectivity and callosal defects—resembling observations in ASD and SCZ patients. Here, we demonstrate that CYFIP1 is crucial for cortical axonal development and identify insufficient calcium uptake as the pivotal mechanism. In vivo , Cyfip1 heterozygosity delays callosal axon growth and arborization. Additionally, Cyfip1 -deficient cortical neurons and axons have reduced intracellular calcium, along with impaired mitochondria morphology, activity, and motility. Mechanistically, CYFIP1 binds and stabilises the mRNA of specific voltage-gated calcium channel subunits, explaining the decreased calcium concentration in Cyfip1 +/- cells. Notably, elevating intracellular calcium rescues delayed axonal growth and mitochondrial defects in Cyfip1 -deficient neurons. These findings highlight that, by regulating mRNA metabolism, CYFIP1 ensures proper callosal development, offering insights into brain connectivity disruptions underlaying neurodevelopmental disorders.

AI snapshot

Written from the paper’s full text.

TL;DR

CYFIP1 is required for timely cortical callosal axon growth and arborization, and its reduction lowers intracellular and mitochondrial calcium, alters mitochondrial distribution/activity, and delays axonal development. CYFIP1 stabilizes mRNAs encoding specific voltage-gated calcium channel alpha-1 subunits via Hu proteins, and raising intracellular calcium rescues the axonal and mitochondrial phenotypes in Cyfip1+/- neurons.

Key findings

  • In vivo, Cyfip1 heterozygosity delayed callosal axon growth at P5 (invasion index, two-way ANOVA p = 0.0082; genotype effect p = 0.0594) and reduced P15 axonal arborization (primary p = 0.0015, secondary p = 0.00035, total p = 0.00029), with arborization comparable by P30.
  • Cyfip1+/- cortical neurons/axons showed reduced in vitro axonal growth rate (p = 0.0021), reduced axoplasmic Ca2+ (p = 0.0286), reduced mitochondrial Ca2+ (p = 0.0030), reduced TMRE in axons (p = 0.0001) and P5–6 corpus callosum (p = 0.0015), increased mitochondrial density (p = 0.0002), increased mitochondrial motility (p = 0.0414), and increased mitochondrial area (p = 0.0055) and major axis (p = 0.0398).
  • CYFIP1 RNA-IP enriched mCacna1c, mCacna1e, and mCacna1i mRNAs (p = 0.0054, 0.0078, 0.0009); in Cyfip1+/- DIV3 neurons, mCacna1e and mCacna1i mRNA levels were reduced (p = 0.0435, p = 0.0202), and CaV1.2, CaV2.3, and CaV3.3 proteins were reduced (p = 0.0338, p = 0.0281, p = 0.0129); mRNA decay after actinomycin D was enhanced at 4 h for mCacna1c, mCacna1e, and mCacna1i (p = 0.0010, p = 0.0003, p = 0.0454).
  • Elevating intracellular Ca2+ with ionomycin rescued axonal growth (Cyfip1+/- DMSO vs ionomycin p < 0.0001), mitochondrial motility (WT-ionomycin vs Cyfip1+/- ionomycin p > 0.9999), and mitochondrial membrane potential (WT-ionomycin vs Cyfip1+/- ionomycin p > 0.9999); the VGCC agonists Bay-K-8644 and Nefiracetam also rescued delayed axonal growth (p < 0.0001 each).

Methods

  • Mouse Cyfip1+/- line and WT C57Bl6 mice were used; in utero electroporation at E15.5 labeled callosal projection neurons with tdTomato ± human CYFIP1 WT, and brains were analyzed at P5, P15, and P30.
  • Primary E15.5 mouse cortical neurons were cultured in microfluidic chambers or dishes for DIV3/4/7/14 analyses, including axonal growth, Fluo-4 AM and mitoGCaMP5G calcium imaging, TMRE, ATP measurement, electron microscopy, mitochondrial density/motility, RNA-IP RT-qPCR, membrane-enriched Western blotting, and actinomycin D mRNA decay assays.
  • Binding-site prediction used RBPmap; statistics used GraphPad Prism 9 with tests listed in figure legends; both male and female mice were used.

Limitations

  • The paper does not state a dedicated limitations section.
  • Evident from the text: the Hu-protein mechanism is correlative—CYFIP1 co-IPs HuD/HuR and Hu binding to Cacna1c/Cacna1e is reduced in Cyfip1+/- neurons, but no direct manipulation of Hu proteins or mRNA stability is shown; mCacna1i binding to HuD/HuR was not significantly changed (p = 0.8857, p = 0.6289), and mCacna1c mRNA reduction was a trend (p = 0.0766).
  • Evident from the text: some phenotypes are stage-specific or not statistically significant (P15 axonal growth p = 0.0947; mitochondrial DNA copy number p = 0.7302), and the ionomycin/Bay-K-8644/Nefiracetam rescue experiments are in vitro, not in vivo; sex differences were not analyzed despite use of both sexes.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s41467-025-65801-0

Cites

121 of 121 references verified0 citation errors · 0 not checkable

Statistics

7 tests recomputed · 0 with the reported and recomputed p on opposite sides of .05

Claims the paper makes

39 of 53 cited sources checked · 18 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Nefiracetam targets both L- and N-type calcium channels.

    “whereas Nefiracetam has a broader effect, targeting both L- and N-type calcium channels.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [74] Trujillo, C. A. et al. Pharmacological reversal of synaptic and network pathology in human MECP2‐KO neurons and cortical organoids. EMBO Mol. Med. 13, e12523 (2021). source

      The Results section reports that nefiracetam increased calcium-transient frequency in MECP2-mosaic neurospheres, but it does not identify the calcium channels involved. Searches for L-type and N-type calcium channels found no passage in our copy stating that nefiracetam targets either channel type; page numbers are unavailable. (LLM, conf=0.74)

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  • Premisecitation

    Published nELAVL CLIP-seq data from human brain found that hCACNA1C, hCACNA1E and hCACNA1I are targets of nELAVL proteins.

    “a published nELAVL CLIP-seq experiment from human brain found that hCACNA1C, hCACNA1E and hCACNA1I are targets of nELAVL proteins66”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [66] Scheckel, C. et al. Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. eLife 5, e10421 (2016). source

      The Results section, “Identification of nELAVL targets in human brain” (page unavailable), confirms that the authors performed CLIP on human brain samples and identified nELAVL RNA-binding sites. The passages in our copy do not identify CACNA1C, CACNA1E, or CACNA1I as targets; searches for those gene names found no matching passage. Thus the experiment is supported, but the specific target list is not verified. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    CYFIP1 regulation of calcium channel subunits compromises intracellular calcium levels, resulting in delayed axonal development.

    “These findings support our model in which CYFIP1 regulation of calcium channel subunits compromise intracellular calcium levels, resulting in delayed axonal development10,84,85 (Fig. 7).”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [10] Purcell, S. M. et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature 506, 185–190 (2014). source

      The Extended Data table lists a disruptive CYFIP1 variant, and the ‘ARC, PSD-95 and calcium ion channel genes’ section reports mutations in calcium-channel subunits. The Discussion proposes altered calcium-dependent signaling as a possibility. Neither passage shows that CYFIP1 regulates those subunits, changes intracellular calcium levels, or delays axonal development; those links are the citing authors’ model, not findings established by this source. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [84] Ciccolini, F. et al. Local and Global Spontaneous Calcium Events Regulate Neurite Outgrowth and Onset of GABAergic Phenotype during Neural Precursor Differentiation. J. Neurosci. 23, 103–111 (2003). source

      The Results section (page not specified in our copy) reports that low-calcium conditions significantly shortened neurites in differentiating neural precursors. That supports the calcium–outgrowth link, but the paper does not establish that CYFIP1 regulates calcium-channel subunits or that this mechanism delays axonal development. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [85] Arjun McKinney, A., Petrova, R. & Panagiotakos, G. Calcium and activity-dependent signaling in the developing cerebral cortex. Development 149, dev198853 (2022). source

      The review’s “Mechanisms regulating intracellular calcium signaling” section explains that calcium-channel subunits regulate calcium entry. Its “Differentiation” section links intracellular calcium signaling to axonal pathfinding and neuronal activity to callosal axon outgrowth. It does not identify CYFIP1 as a regulator of those subunits or establish the proposed chain from CYFIP1 to altered calcium levels and delayed axonal development; the citing sentence labels that chain as the authors’ model. Page numbers were not available in our copy. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Premisecitation

    Abnormalities in the corpus callosum and interhemispheric connectivity are linked to many neurodevelopmental disorders, including ASD and SCZ.

    “a wealth of evidence links abnormalities in the corpus callosum and interhemispheric connectivity (driven by callosal projection neurons) to many neurodevelopmental disorders, among them ASD and SCZ2,3,111,112.”
    Quote in the paperSubstantial claim3 of 4 sources checked
    • cites [2] Heinsfeld, A. S., Franco, A. R., Craddock, R. C., Buchweitz, A. & Meneguzzi, F. Identification of autism spectrum disorder using deep learning and the ABIDE dataset. Neuroimage Clin. 17, 16–23 (2017). source

      The paper’s “Neural patterns: connectivity in the autistic brain” section reports disrupted anterior–posterior connectivity in ASD and links that theory to corpus callosum morphometry (page unavailable). It does not establish abnormal interhemispheric connectivity, a role for callosal projection neurons, or a link to schizophrenia or neurodevelopmental disorders generally. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [3] Hu, M.-L. et al. A Review of the Functional and Anatomical Default Mode Network in Schizophrenia. Neurosci. Bull. 33, 73–84 (2017). source

      The section “Functional Connectivity in the DMN in Schizophrenia” reports abnormal connectivity in schizophrenia, supporting that part of the claim. The paper does not link those findings to corpus callosum abnormalities or interhemispheric connectivity; the retrieved mention of autism is a reference entry, not evidence for the claimed link across ASD and other disorders. No page numbers are available in our copy. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [111] Urchs, S. G. W. et al. Functional connectivity subtypes associate robustly with ASD diagnosis. eLife 11, e56257 (2022). source

      The Results section reports functional-connectivity alterations associated with ASD diagnosis. But the passages do not identify those alterations as interhemispheric or callosal, and the paper's Discussion (Limitations) says its analysis focused on ASD rather than other disorders. The source therefore does not support the corpus-callosum or schizophrenia parts of the claim. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [112] Fenlon, L. R. & Richards, L. J. Contralateral targeting of the corpus callosum in normal and pathological brain function. Trends Neurosci. 38, 264–272 (2015). source
  • Findingown data

    mMap1b mRNA is significantly associated with CYFIP1, >1.5 fold compared to mHprt1 mRNA.

    “mMap1b mRNA, an mRNA previously identified in the CYFIP1 complex21, was significantly associated with CYFIP1, >1.5 fold compared to mHprt1 mRNA”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [21] Napoli, I. et al. The fragile X syndrome protein represses activity-dependent translation through CYFIP1, a new 4E-BP. Cell 134, 1042–1054 (2008). source
  • May combine two claims. 24
  • Classified as probably not a substantial claim. 24
  • May combine two claims.

    Premisecitation

    Cyfip1+/- mice have reduced bilateral functional connectivity and structural abnormalities in the corpus callosum.

    “previous work from our laboratory found that Cyfip1+/- mice have reduced bilateral functional connectivity and structural abnormalities in the corpus callosum28.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [28] Domínguez-Iturza, N. et al. The autism- and schizophrenia-associated protein CYFIP1 regulates bilateral brain connectivity and behaviour. Nat. Commun. 10, 3454 (2019). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Cytosolic Ca2+ fluctuations play a pivotal role in maintaining the structure and function of intracellular organelles.

    “Cytosolic Ca²⁺ fluctuations also play a pivotal role in maintaining the structure and function of intracellular organelles88,89.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [88] Clapham, D. E. Calcium Signaling. Cell 131, 1047–1058 (2007). source
    • cites [89] Bagur, R. & Hajnóczky, G. Intracellular Ca2+ Sensing: Its Role in Calcium Homeostasis and Signaling. Mol. Cell 66, 780–788 (2017). source

      The Calcium Homeostasis and Signaling section says cytosolic Ca2+ signals may regulate organelle-specific functions, including nuclear gene regulation and mitochondrial metabolism. Localization and compartmentalization also describes Ca2+-dependent mitochondrial positioning. These passages support a role in organelle function and distribution, but do not establish that cytosolic fluctuations maintain organelle structure generally; page numbers are unavailable in our copy. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Calcium enters neurons primarily through voltage-sensitive calcium (CaV) channels, ionotropic glutamate receptors, and transient receptor potential channels.

    “Calcium enters neurons primarily through voltage-sensitive calcium (CaV) channels, ionotropic glutamate receptors, and transient receptor potential channels79,91.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [79] Rosenberg, S. S. & Spitzer, N. C. Calcium Signaling in Neuronal Development. Cold Spring Harb. Perspect. Biol. 3, a004259 (2011). source
    • cites [91] Alves, V. S. et al. Calcium Signaling in Neurons and Glial Cells: Role of Cav1 channels. Neuroscience 421, 95–111 (2019). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Cytosolic calcium modulates mitochondrial morphology, promoting transitions between tubular and spherical shapes.

    “Notably, cytosolic calcium has been implicated in modulating mitochondrial morphology, promoting transitions between tubular and spherical shapes53,90.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [53] Nemani, N. et al. MIRO-1 Determines Mitochondrial Shape Transition upon GPCR Activation and Ca2+ Stress. Cell Rep. 23, 1005–1019 (2018). source
    • cites [90] Deheshi, S., Dabiri, B., Fan, S., Tsang, M. & Rintoul, G. L. Changes in mitochondrial morphology induced by calcium or rotenone in primary astrocytes occur predominantly through ros-mediated remodeling. J. Neurochem. 133, 684–699 (2015). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Deficits in callosal axonal development and arborization compromise synaptic transmission of adult mice in a 22q11.2 deletion model.

    “Mukai and colleagues, using a mouse model with 22q11.2 deletion, specifically designed for studying SCZ, found that deficits in callosal axonal development and arborization compromise synaptic transmission of adult mice108”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [108] Mukai, J. et al. Molecular substrates of altered axonal growth and brain connectivity in a mouse model of schizophrenia. Neuron 86, 680–695 (2015). source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The alpha-1 subunit of CaV channels is the pore-forming subunit and has a fundamental role in the selective gating and regulated entry of calcium ions into cells.

    “The alpha-1 subunit of CaV channels is the pore-forming subunit and has a fundamental role in the selective gating and regulated entry of calcium ions into cells55,56.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [55] Catterall, W. A. Voltage-gated calcium channels. Cold Spring Harb. Perspect. Biol. 3, a003947 (2011). source
    • cites [56] Gandini, M. A. & Zamponi, G. W. Voltage-gated calcium channel nanodomains: molecular composition and function. FEBS J. 289, 614–633 (2022). source
  • Classified as probably not a substantial claim.

    Premisecitation

    Cytosolic calcium plays a critical role in controlling axonal and dendritic growth and arborization.

    “Cytosolic calcium plays a critical role in controlling axonal and dendritic growth and arborization75–79.”
    Quote in the paperSubstantial claim3 of 5 sources checked
    • cites [75] Gomez, T. M. & Zheng, J. Q. The molecular basis for calcium-dependent axon pathfinding. Nat. Rev. Neurosci. 7, 115–125 (2006). source
    • cites [76] Zheng, J. Q. & Poo, M. M. Calcium Signaling in Neuronal Motility. Annu. Rev. Cell Dev. Biol. 23, 375–404 (2007). source
    • cites [77] Baudet, S. et al. Subcellular second messenger networks drive distinct repellent-induced axon behaviors. Nat. Commun. 14, 3809 (2023). source

      The Introduction states that Ca2+ is a critical regulator of axonal behavior and that localized Ca2+ signals orient axon outgrowth. The Results section on retinal axon arbors also discusses Ca2+ signaling in axon pathfinding. Our copy does not establish a role for calcium in dendritic growth or arborization, so it supports only the axonal part of the claim. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [78] Urrutia, P. J. & González-Billault, C. A Role for Second Messengers in Axodendritic Neuronal Polarity. J. Neurosci. 43, 2037–2052 (2023). source

      The Calcium section states that calcium regulates neurite growth and describes effects on axonal elongation and branching. The passages do not establish a role in dendritic growth or arborization specifically, so that part of the claim is not supported by our copy. Page numbers were not provided. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [79] Rosenberg, S. S. & Spitzer, N. C. Calcium Signaling in Neuronal Development. Cold Spring Harb. Perspect. Biol. 3, a004259 (2011). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Knocking out Cav1.2 reduces neurite length.

    “while knocking out Cav1.2 reduces neurite length95.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [95] Kamijo, S. et al. A Critical Neurodevelopmental Role for L-Type Voltage-Gated Calcium Channels in Neurite Extension and Radial Migration. J. Neurosci. 38, 5551–5566 (2018). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Brain connectivity mapping across 16 mouse models for autism reveals a spectrum of functional connectivity abnormalities across different etiologies.

    “brain connectivity mapping across 16 mouse models for autism reveals a spectrum of functional connectivity abnormalities across different etiologies110.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [110] Zerbi, V. et al. Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes. Mol. Psychiatry 26, 7610–7620 (2021). source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Embryonic deletion of CaV1.2 in cortical neurons disturbs spontaneous calcium activity, causing increased anxiety in mice.

    “embryonic deletion of CaV1.2 in cortical neurons disturbs spontaneous calcium activity, causing increased anxiety in mice96”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [96] Smedler, E. et al. Disrupted Cacna1c gene expression perturbs spontaneous Ca2+ activity causing abnormal brain development and increased anxiety. PNAS 119, e2108768119 (2022). source

      The Discussion (page unavailable) reports that forebrain-specific Cacna1c knockout mice had altered spontaneous calcium activity in the developing neocortex and increased anxiety-like behavior as adults. The Methods identify an Emx1-Cre forebrain-specific manipulation, while the Results measure calcium activity in neural progenitors at postnatal day 7. The copy therefore supports the central finding but not the claim’s more specific description of an embryonic deletion in cortical neurons. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Expression of Cav1.2 or Cav1.3 is sufficient to trigger spontaneous regenerative calcium transients in developing cortical neurons.

    “previous studies have shown that the expression of Cav1.2 or Cav1.3 (subunits of the L-type voltage-gated calcium channel) is sufficient to trigger spontaneous regenerative calcium transients in developing cortical neurons”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [95] Kamijo, S. et al. A Critical Neurodevelopmental Role for L-Type Voltage-Gated Calcium Channels in Neurite Extension and Radial Migration. J. Neurosci. 38, 5551–5566 (2018). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Connectivity defects are a common abnormality of ASD.

    “This highlights connectivity defects as a common abnormality of ASD”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [110] Zerbi, V. et al. Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes. Mol. Psychiatry 26, 7610–7620 (2021). source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Ca2+ activates mitochondrial metabolism and stimulates ATP synthesis.

    “Ca2+ activates mitochondrial metabolism and stimulates ATP synthesis”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [51] Datta, S. & Jaiswal, M. Mitochondrial calcium at the synapse. Mitochondrion 59, 135–153 (2021). source
    • cites [103] Rizzuto, R., De Stefani, D., Raffaello, A. & Mammucari, C. Mitochondria as sensors and regulators of calcium signalling. Nat. Rev. Mol. Cell Biol. 13, 566–578 (2012). source
    • cites [104] Walkon, L. L., Strubbe-Rivera, J. O. & Bazil, J. N. Calcium Overload and Mitochondrial Metabolism. Biomolecules 12, 1891 (2022). source

      Section 4 says calcium regulates TCA-cycle enzymes and links calcium homeostasis to ATP production. But the Introduction limits the beneficial effect to relatively low calcium levels; it says calcium overload impairs oxidative phosphorylation and inhibits ATP synthesis. The claim omits that condition and presents stimulation as an unqualified effect. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Premisecitation

    In cultured cortical neurons, the axon can be identified as the longest neurite, based on previous studies of neuronal polarity and axonal specification.

    “We identified the axon as the longest neurite based on previous studies describing the establishment of neuronal polarity and axonal specification in vitro119.”
    • Also stated in: § Immunofluorescence and mitochondrial density analysis · plain
      “We identified the axon as the longest neurite and counted the number of mitochondria present in each segment.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [119] Dotti, C. G., Sullivan, C. A. & Banker, G. A. The establishment of polarity by hippocampal neurons in culture. J. Neurosci. 8, 1454–1468 (1988). source

      In “Identification of axons and dendrites at early stages of development” (page unavailable), the paper says that the longer process was the axon in the cultured hippocampal neurons it followed. This supports the longest-neurite criterion, but the paper does not establish it for the citing study’s cultured cortical neurons. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Rbfox proteins associate with CaV2.2, regulating splicing of specific exons in peripheral neurons.

    “RNA-binding Fox (Rbfox) proteins associate with CaV2.2, regulating the splicing of specific exons in peripheral neurons99”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [99] Allen, S. E. et al. Cell-Specific RNA Binding Protein Rbfox2 Regulates CaV2.2 mRNA Exon Composition and CaV2.2 Current Size. eNeuro 4, e0332–16.2017 (2017). source

      The Introduction reports that Rbfox2 binds CaV2.2 pre-mRNA near exon e18a and suppresses its inclusion in early postnatal sympathetic neurons. The Discussion says the study directly demonstrates this for Rbfox2, while roles for Rbfox1 and Rbfox3 are not excluded—not established. The claim’s plural references to Rbfox proteins and specific exons therefore go beyond the evidence shown. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Mitochondria buffer cytosolic calcium.

    “mitochondria also buffer cytosolic calcium51,103,104.”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [51] Datta, S. & Jaiswal, M. Mitochondrial calcium at the synapse. Mitochondrion 59, 135–153 (2021). source
    • cites [103] Rizzuto, R., De Stefani, D., Raffaello, A. & Mammucari, C. Mitochondria as sensors and regulators of calcium signalling. Nat. Rev. Mol. Cell Biol. 13, 566–578 (2012). source
    • cites [104] Walkon, L. L., Strubbe-Rivera, J. O. & Bazil, J. N. Calcium Overload and Mitochondrial Metabolism. Biomolecules 12, 1891 (2022). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Splicing factor Nova controls alternative splicing in particular subtypes of CaV2 calcium channels.

    “the splicing factor Nova controls alternative splicing in particular subtypes of CaV2 calcium channels100.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [100] Allen, S. E., Darnell, R. B. & Lipscombe, D. The neuronal splicing factor Nova controls alternative splicing in N-type and P-type CaV2 calcium channels. Channels 4, 483–489 (2010). source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Excessive or prolonged activation of CaV channels leads to calcium overload in mitochondria, disrupting their normal function.

    “excessive or prolonged activation of CaV channels leads to calcium overload in mitochondria, disrupting their normal function at multiple levels and significantly impacting cellular development and homeostasis101,102.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [101] Stanika, R. I., Villanueva, I., Kazanina, G., Brian Andrews, S. & Pivovarova, N. B. Comparative Impact of Voltage-Gated Calcium Channels and NMDA Receptors on Mitochondria-Mediated Neuronal Injury. J. Neurosci. 32, 6642–6650 (2012). source

      The Results (‘VGCC-mediated calcium loading and mitochondrial dysfunction,’ Figs. 3–5) show that VGCC-mediated calcium entry can cause mitochondrial overload and damage, but this occurred in a minor subset of neurons; most showed little mitochondrial calcium accumulation or dysfunction. The cited passages do not establish an effect of prolonged activation or the sentence’s broader claim about cellular development and homeostasis. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [102] Walters, G. C. & Usachev, Y. M. Mitochondrial calcium cycling in neuronal function and neurodegeneration. Front. Cell Dev. Biol. 11, 1094356 (2023). source

      The Figure 3 caption in the neurological-diseases section links CaV2 and CaV3 channels, alongside NMDA and AMPA receptors, to mitochondrial calcium buildup during seizures; it says long or repeated seizures can cause mitochondrial overload and neuronal toxicity (page unavailable). The mPTP section explains how overload impairs mitochondrial function. The paper does not establish that excessive or prolonged CaV activation alone causes this outcome across cells generally. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Proper balance between motile and stationary mitochondria is crucial for maintaining high ATP levels required for proper axonal growth and branching.

    “Several studies over the last years suggest that a proper balance between motile and stationary mitochondria is crucial for maintaining the high ATP levels required for proper axonal growth and branching105,106.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [105] Sheng, Z.-H. The Interplay of Axonal Energy Homeostasis and Mitochondrial Trafficking and Anchoring. Trends Cell Biol. 27, 403–416 (2017). source
    • cites [106] Lanfranchi, M. et al. The AMPK-related kinase NUAK1 controls cortical axons branching by locally modulating mitochondrial metabolic functions. Nat. Commun. 15, 2487 (2024). source

      The Results section on mitochondrial recruitment (page unavailable) reports that local mitochondrial inactivation lowered the axonal ATP:ADP ratio and impaired branch growth and stabilization. It does not establish that a particular balance of motile and stationary mitochondria maintains high ATP levels for both axonal growth and branching; the Discussion also cautions that ATP alone is unlikely to suffice for branch stabilization. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Premisecitation

    Ca2+ is a key regulator of mitochondria motility and docking.

    “it has been largely described that Ca2+ is a key regulator of mitochondria motility and docking44–49,107.”
    Quote in the paperSubstantial claim6 of 7 sources checked
    • cites [44] Chen, Y. & Sheng, Z. H. Kinesin-1-syntaphilin coupling mediates activity-dependent regulation of axonal mitochondrial transport. J. Cell Biol. 202, 351–364 (2013). source
    • cites [45] Kang, J. S. et al. Docking of Axonal Mitochondria by Syntaphilin Controls Their Mobility and Affects Short-Term Facilitation. Cell 132, 137–148 (2008). source

      The Discussion reports that disrupting mitochondrial docking changes presynaptic Ca2+ dynamics—the reverse of the claimed regulatory direction. The Results identify syntaphilin-mediated docking and nerve growth factor signaling as influences on motility, but the searched passages do not say that Ca2+ regulates mitochondrial motility or docking. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [46] Russo, G. J. et al. Drosophila Miro is required for both anterograde and retrograde axonal mitochondrial transport. J. Neurosci. 29, 5443–5455 (2009). source

      The Introduction states that Ca2+ binding by Miro arrests bidirectional mitochondrial movement, supporting regulation of motility. It does not establish that Ca2+ regulates mitochondrial docking; the References list a separate study of docking by syntaphilin. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [47] Saotome, M. et al. Bidirectional Ca2 + -dependent control of mitochondrial dynamics by the Miro GTPase. PNAS 105, 20728–20733 (2008). source
    • cites [48] Chang, K. T., Niescier, R. F. & Min, K. T. Mitochondrial matrix Ca2+ as an intrinsic signal regulating mitochondrial motility in axons. PNAS 108, 15456–15461 (2011). source
    • cites [49] Wang, X. & Schwarz, T. L. The Mechanism of Ca2 + -Dependent Regulation of Kinesin-Mediated Mitochondrial Motility. Cell 136, 163–174 (2009). source
    • cites [107] Canty, J., Hensley, A., Aslan, M., Jack, A. & Yildiz, A. TRAK adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport. Nat. Commun. 14, 1376 (2023). source
  • May combine two claims.

    Findingown data

    The increase in mitochondrial density is evident along the whole axon and in proximal, medial, and distal axonal regions.

    “This increase was evident both along the whole axon and in different axonal regions (proximal, medial, and distal) (Fig. 2b)”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    At P15, axons of both WT and Cyfip1+/- mice have reached the target region, with length equivalent to ~95% of cortical thickness.

    “When we analyzed axonal invasion into the contralateral cortex at P15, we observed that the axons of both genotypes had nonetheless reached their target region (length equivalent to ∼95% of the cortical thickness, Fig. 1b)”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    mCacna1c mRNA exhibits a notable inclination toward reduction but does not reach statistical significance (p=0.0766) in Cyfip1+/- compared to WT.

    “The third target, mCacna1c, exhibits a notable inclination toward reduction but it did not reach statistical significance (p = 0.076626) (Fig. 4b) under the tested conditions.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Cyfip1-deficient axons have increased mitochondrial density and transport, but reduced calcium concentration and activity.

    “Here, we found that Cyfip1-deficient axons have increased mitochondrial density and transport, but reduced calcium concentration and activity (Figs. 2 and 3).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    The minor axis and roundness of mitochondria are comparable between WT and Cyfip1+/- axons.

    “In contrast, the minor axis and roundness were comparable between WT and Cyfip1+/- axonal mitochondria (Fig. 3e).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    mCacna1c, mCacna1e and mCacna1i mRNAs are significantly enriched and associated with the CYFIP1 complex.

    “Among the candidate mRNAs encoding protein subunits of Ca2+ channels, we found that mCacna1c, mCacna1e and mCacna1i mRNAs were significantly enriched, and therefore associated with the CYFIP1 complex.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    mHprt1 mRNA is highly stable and exhibits a prolonged half-life.

    “The highly stable mHprt1 mRNA exhibited a prolonged half-life”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    HuR/Elavl1 RNA-IP from DIV3 WT and Cyfip1+/- cortical neurons shows significant difference in enrichment of mCacna1c mRNA (p=0.0310), but not mCacna1e (p=0.2270) or mCacna1i (p=0.6289).

    “d HuR/Elavl1 RNA-IP from DIV 3 WT and Cyfip1+/- cortical neurons. Histograms represent calcium channel mRNAs enrichment, calculated as the ratio over the positive control (mDlg4) (mean ± SEM, Two-tailed Multiple Mann-Whitney test; mCacna1c mRNA p = 0.0310, mCacna1e mRNA p = 0.2270, mCacna1i mRNA p = 0.6289).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    BAPTA-AM treatment markedly decreased the growth rate in WT neurons and only marginally affected Cyfip1+/- neurons.

    “BAPTA-AM treatment markedly decreased the growth rate in WT neurons and only marginally affected Cyfip1+/- neurons, where the growth rate was already low (Fig. S5b).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    mArc mRNA shows great decay in both genotypes starting from 2 h of actinomycin-D treatment.

    “mArc mRNA, a transcript that is activity-regulated and described as unstable68–70, shows a great decay in both genotypes starting from 2 h of actinomycin-D treatment (Fig. S4f).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    HuD/Elavl4 RNA-IP from DIV3 WT and Cyfip1+/- cortical neurons shows significant differences in enrichment of mCacna1c and mCacna1e mRNAs (p=0.0285 for both), but not mCacna1i (p=0.8857).

    “c HuD/Elavl4 RNA immunoprecipitation (RNA-IP) from DIV 3 WT and Cyfip1+/- cortical neurons. Histograms represent calcium channel mRNAs enrichment, calculated as the ratio over the positive control (mDlg4) (WT n = 4 embryos, Cyfip1+/- n = 4 embryos; mean ± SEM, Two-tailed Multiple Mann-Whitney test; mCacna1c mRNA p = 0.0285, mCacna1e mRNA p = 0.0285, mCacna1i mRNA p = 0.8857).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Cyfip1 deficiency results in delayed axonal growth and arborization.

    “Altogether, our findings show that Cyfip1 deficiency results in delayed axonal growth and arborization”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Reduced levels of CYFIP1 compromise axonal distribution and transport of mitochondria.

    “These results demonstrate that reduced levels of CYFIP1 compromise axonal distribution and transport of mitochondria”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    CYFIP1 regulation of voltage gated calcium channels, leading to defects in intracellular calcium levels, may impact several aspects of axonal function, including mitochondrial distribution and activity, ultimately compromising axonal development.

    “Altogether, we propose that CYFIP1 regulation of voltage gated calcium channels, leading to defects in intracellular calcium levels, may impact several aspects of axonal function, among them mitochondrial distribution and activity, ultimately compromising axonal development.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Ionomycin treatment in Cyfip1+/- neurons rescued delayed axonal growth, increased motility, and reduced mitochondrial activity.

    “Remarkably, Ionomycin treatment in Cyfip1+/- neurons was able to rescue not only the delayed axonal growth but also the increased motility and reduced mitochondrial activity (Fig. 6).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The mechanism of regulation of CaV alpha-1 subunits by CYFIP1 may be at the level of mRNA stability.

    “and suggest that the mechanism of regulation may be at the level of mRNA stability”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: CYFIP1 has no putative RNA binding domains.
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    nELAVL proteins could regulate the stability, localization, or translation of these mRNAs.

    “which suggest that nELAVL proteins could regulate their stability, localization, or translation”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    CYFIP1 may regulate axonal development, ultimately contributing to brain connectivity.

    “provide insights into the molecular mechanisms by which CYFIP1 may regulate axonal development, ultimately contributing to brain connectivity.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    Delayed growth and arborization observed in Cyfip1+/- axons may impair target selection, ultimately affecting synaptic transmission and brain connectivity.

    “The delayed growth and arborization observed in Cyfip1+/- axons (Fig. 1) may impair target selection, ultimately affecting synaptic transmission and brain connectivity.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    Depletion of intracellular calcium in rat cortical neurons arrests axonal growth and reduces dendritic arborization.

    “depletion of intracellular calcium in rat cortical neurons arrests axonal growth and reduces dendritic arborization97.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [97] Ramakers, G. J. A. et al. The role of calcium signaling in early axonal and dendritic morphogenesis of rat cerebral cortex neurons under non-stimulated growth conditions. Brain Res. Dev. Brain Res. 126, 163–172 (2001). source
  • May combine two claims.

    Interpretationown data

    Reduction in CYFIP1, mimicking 15q11.2 copy number deletion, leads to reduced axonal growth, intracellular calcium concentration, and mitochondrial function.

    “We discovered that a reduction in CYFIP1, which mimics the psychiatric disorders seen with 15q11.2 copy number deletion, leads to reduced axonal growth, intracellular calcium concentration, and mitochondrial function.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: A reduction in CYFIP1 mimics the psychiatric disorders seen with 15q11.2 copy number deletion.
  • Probably not a substantial claim: may not pass S1 (asserted). May combine two claims.

    Interpretationreasoning

    Diminished intracellular calcium levels observed in Cyfip1+/- neurons may adversely impact both mitochondrial transport and activity, potentially contributing to delayed axonal growth phenotype.

    “Our hypothesis posits that the diminished intracellular calcium levels observed in Cyfip1+/- neurons may adversely impact both mitochondrial transport and activity, potentially contributing to the observed delayed axonal growth phenotype in these neurons.”
    Quote in the paperNot a substantial claim
42 of 42
  • The paper relies on this without support.

    Very little is known about how CYFIP1 regulates axonal development and circuit formation.

    “very little is known about how CYFIP1 regulates axonal development and circuit formation.”
  • The paper relies on this without support.

    CYFIP1 has no putative RNA binding domains.

    “While CYFIP1 has no putative RNA binding domains”
  • The paper relies on this without support.

    CACNA1C is an L-type calcium channel.

    “CACNA1C, the most affected channel in Cyfip1+/- cortical neurons, is an L-type calcium channel, and is therefore activated by both Bay-K-8644 and Nefiracetam.”
  • The paper relies on this without support.

    A reduction in CYFIP1 mimics the psychiatric disorders seen with 15q11.2 copy number deletion.

    “a reduction in CYFIP1, which mimics the psychiatric disorders seen with 15q11.2 copy number deletion”
  • The paper relies on this without support.

    mDlg4 is enriched in the Hu protein complex, making its enrichment rate suitable as a positive control for HuD/Elavl4 and HuR/Elavl1 RNA immunoprecipitation.

    “For HuD/Elavl4 and HuR/Elavl1 RNA-IP, the enrichment of the calcium channels mRNA is expressed as a ratio over the positive control mDlg4 enrichment rate, previously identified in the Hu protein complex and used as a positive control.”
5 of 5

Statistics that don’t add up

Each reported p-value recomputed from its test statistic and degrees of freedom.

  • Inconsistent p-value: F(2,30) = 5.8, p = .0070

    Minor

    The paper reports p = .007 here; recomputing from the test statistic and its degrees of freedom gives p = .007. The check cannot tell whether the statistic or the p-value is the misprint.

    Reported p = .007 · recomputed p = .007

1 of 1

Statistics recomputed

Every reported test result, recomputed from its test statistic and degrees of freedom. A result shows as not adding up only once an independent check has confirmed it.

  • Doesn’t add upF(2, 30) = 5.8reported p = .007 · recomputed p = .007

    “F(2,30) = 5.8, p = .0070”

  • ConsistentF(18, 144) = 2.108reported p = .0082 · recomputed p = .008

    “F(18, 144) = 2.108, p = .0082”

  • ConsistentF(2, 15) = 6.834reported p = .0078 · recomputed p = .008

    “F(2, 15) = 6.834, p = .0078”

  • ConsistentF(2, 15) = 6.697reported p = .0083 · recomputed p = .008

    “F(2, 15) = 6.697, p = .0083”

  • ConsistentF(2, 15) = 1.905reported p = .1831 · recomputed p = .183

    “F(2, 15) = 1.905, p = .1831”

  • ConsistentF(1, 22) = 4.326reported p = .0494 · recomputed p = .049

    “F(1,22) = 4.326, p = .0494”

  • ConsistentF(1, 12) = 16.87reported p = .0015 · recomputed p = .001

    “F(1,12) = 16.87, p = .0015”

7 of 7

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Mitochondrial DNA is described with two different denominators

    Minor

    The results call the measure a mitochondrial-to-total-DNA ratio, whereas the figure legend calls it mitochondrial DNA relative to nuclear DNA. Those are different ratios; the methods specify the nuclear-DNA denominator.

  • Axonal TMRE measurement is assigned to both DIV 3 and DIV 4

    Minor

    The results describe the axonal mitochondrial membrane-potential measurement in Fig. 3c as being from DIV 3 neurons, but the figure legend identifies those neurons as DIV 4.

2 of 2

Cites

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Cited by

Sorted by citations

Authors
Ricci, C., Midroit, M. J., Caicci, F., Achsel, T., Domínguez-Iturza, N., & Bagni, C.
Affiliations
  • University of Rome Tor Vergata (IT)
  • University of Lausanne (CH)
  • University of Padua (IT)
Corresponding author
Bagni, Claudia
Venue
Nature Communications
Published
2025-11-28
Volume
16
Issue
1
Pages
10764-10764
ISSN
2041-1723 (ISSN-L)
OpenAlex
W4416794578
Cited by
1
References
121
Citations by year
2026: 1
FWCI
0.55
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Cineca Institutional Research Information System (Tor Vergata University) (submittedVersion, cc-by)
  • IRIS (submittedVersion, cc-by)
  • Europe PMC (PubMed Central) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNSF 310030, 182651, 310030)
  • Fonds Wetenschappelijk Onderzoek (11Y2416N)
  • KU Leuven
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Axon Guidance and Neuronal Signaling
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
Keywords
CYFIP1, calcium availability, calcium uptake, mRNA stability, mitochondrial morphology, mitochondrial motility, corpus callosum, brain connectivity, autism spectrum disorder, schizophrenia, neurodevelopmental disorders
MeSH terms
Autism Spectrum Disorder, Animals, Axons, Calcium, Cerebral Cortex, Corpus Callosum, Female, Humans, Male, Mice, Inbred C57BL, Mitochondria, Neurons, RNA, Messenger, Schizophrenia, Mice, Knockout, Adaptor Proteins, Signal Transducing, Mice

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-27.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-27.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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