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Cited by 38PI3K/AKT/mTOR signaling in cancerTuberous Sclerosis Complex ResearchGenetics and Neurodevelopmental Disorders

Analysis of proteins that rapidly change upon mechanistic/mammalian target of rapamycin complex 1 (mTORC1) repression identifies parkinson protein 7 (PARK7) as a novel protein aberrantly expressed in tuberous sclerosis complex (TSC)

Open access
Niere, Farr, Namjoshi, Sanjeev, Song, Ehwang, Dilly, Geoffrey A., Schoenhard, Grant, Zemelman, Boris V., Mechref, Yehia, Raab-Graham, Kimberly F.·2016·Molecular & Cellular Proteomics
DOI 10.1074/mcp.m115.055079PMC PMC4739665
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Abstract

Many biological processes involve the mechanistic/mammalian target of rapamycin complex 1 (mTORC1). Thus, the challenge of deciphering mTORC1-mediated functions during normal and pathological states in the central nervous system is challenging. Because mTORC1 is at the core of translation, we have investigated mTORC1 function in global and regional protein expression. Activation of mTORC1 has been generally regarded to promote translation. Few but recent works have shown that suppression of mTORC1 can also promote local protein synthesis. Moreover, excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis. To determine the role of mTORC1 activation in protein expression, we have used an unbiased, large-scale proteomic approach. We provide evidence that a brief repression of mTORC1 activity in vivo by rapamycin has little effect globally, yet leads to a significant remodeling of synaptic proteins, in particular those proteins that reside in the postsynaptic density. We have also found that curtailing the activity of mTORC1 bidirectionally alters the expression of proteins associated with epilepsy, Alzheimer's disease, and autism spectrum disorder-neurological disorders that exhibit elevated mTORC1 activity. Through a protein-protein interaction network analysis, we have identified common proteins shared among these mTORC1-related diseases. One such protein is Parkinson protein 7, which has been implicated in Parkinson's disease, yet not associated with epilepsy, Alzheimers disease, or autism spectrum disorder. To verify our finding, we provide evidence that the protein expression of Parkinson protein 7, including new protein synthesis, is sensitive to mTORC1 inhibition. Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95. Our work offers a comprehensive view of mTORC1 and its role in regulating regional protein expression in normal and diseased states.

AI snapshot

Written from the paper’s full text.

TL;DR

A one-hour in vivo rapamycin treatment in rats produced little global proteomic change but rapidly remodeled the postsynaptic density proteome, including bidirectional changes in disease-associated proteins. Protein–protein interaction network analysis identified PARK7 as a shared hub for epilepsy, Alzheimer’s disease, and autism spectrum disorder, and PARK7 was elevated in dendrites and colocalized with PSD-95 in a Tsc1 knockout model of tuberous sclerosis complex.

Key findings

  • Systemic rapamycin (10 mg/kg) reduced mTORC1 activity in rat cortex within 1 h, measured as P-mTORC1/mTORC1 = 0.50 ± 0.14 and P-S6/S6 = 0.21 ± 0.08 of control.
  • The PSD fraction was highly labile: about 73–75% of PSD proteins changed expression profiles within 1 h; 50 proteins were no longer detected and 39 new proteins appeared after mTORC1 inhibition.
  • Among disease-associated proteins detected, there were 38 epilepsy, 15 Alzheimer’s disease, and 14 autism spectrum disorder proteins; rapamycin bidirectionally altered select proteins, with SNAP-25 new synthesis increasing to 2.18 ± 0.34 of control and GAP-43 new synthesis decreasing to 0.39 ± 0.08 of control.
  • PPI network analysis identified MAPK3, SUMO3, SNCA, and PARK7 as top common hubs; rapamycin reduced PSD PARK7 by about 75% (RAPA = 0.24 ± 0.10 vs. control = 1.00 ± 0.06, p < 0.002), while new PARK7 synthesis fell only to 0.76 ± 0.05 of control. In Tsc1 knockout neurons, dendritic PARK7 increased about 1.79-fold in culture and 1.97-fold in hippocampal slices, with increased PARK7/PSD-95 colocalization (PCC 0.10 ± 0.01 to 0.30 ± 0.03).

Methods

  • Three paired sibling male Sprague-Dawley rats (7–9 weeks old) received rapamycin (10 mg/kg i.p.) or DMSO and were sacrificed after 1 h; cortical lysates, synaptoneurosomes, TX-100-soluble fractions, and PSD fractions were analyzed by LC-MS/MS and Western blot.
  • Cultured hippocampal neurons were used for BONCAT-PLA and immunocytochemistry; Tsc1 conditional knockout mice and cultured neurons were used with Cre or GFP, including stereotaxic AAV-Cre/GFP injection into hippocampus, immunohistochemistry, and confocal imaging.
  • Quantitation used normalized spectral counts, MASCOT/Scaffold, DAVID/Enrichment Map/Cytoscape PPI networks, disease gene databases, Pearson’s correlation coefficient colocalization analysis, and t tests/ANOVA.

Limitations

  • The paper states that the precise subcellular targeting mechanisms remain to be determined, and that antibodies for synapsin and PSD-95 did not work after the BONCAT-PLA procedure.
  • Evident from the text: the proteomic and Western analyses used only three animals per condition, the in vivo manipulation was a single acute 1-h rapamycin time point in male rats, and the study did not test causal roles of PARK7 or behavioral/electrophysiological disease phenotypes.

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

Integrity signals

Registry

Crossref · 10.1074/mcp.m115.055079

Cites

102 of 102 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

28 of 45 cited sources checked · 7 supported · 2 flagged · accuracy not yet measured

  • Findingcitation

    Kv1.1 protein (Kcna1) was only detected in the soluble fraction when mTORC1 was repressed.

    “As expected, Kv1.1 protein (Kcna1) was only detected in the soluble fraction when mTORC1 was repressed, confirming our previous findings (31,34,35).”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [31] Sosanya, 2015, Rapamycin reveals an mTOR-independent repression of Kv1.1 expression during epileptogenesis, Neurobiol. Dis source
    • cites [34] Raab-Graham, 2006, Activity- and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites, Science source
    • cites [35] Sosanya, 2013, Degradation of high affinity HuD targets releases Kv1.1 mRNA from miR-129 repression by mTORC1, J. Cell Biol source

      The Results section on mTORC1 kinase activity reports that rapamycin inhibition approximately doubled Kv1.1 protein in synaptoneurosomes. It does not report detection specifically in a soluble fraction, and it measures Kv1.1 in the untreated condition too, so it does not support the claim that the protein was detected only when mTORC1 was repressed. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Premisecitation

    SNAP-25 has recently been shown to facilitate the removal of kainate receptors (KARs) from the membrane surface.

    “Moreover, SNAP-25 has recently been shown to facilitate the removal of kainate receptors (KARs), which are implicated in epileptogenesis, from the membrane surface (83, 90 -95).”
    Quote in the paperSubstantial claim5 of 7 sources checked
    • cites [83] Ovsepian, 2011, Dendritic SNAREs add a new twist to the old neuron theory, Proc. Natl. Acad. Sci. U.S.A source

      The section ‘Evidence for Specialization of Exocytotic Machinery for Dendritic Secretion’ discusses SNAP-25 localization and identifies SNAP-23 in dendritic fusion; it does not say SNAP-25 removes kainate receptors from the membrane. Searches for kainate receptors, receptor endocytosis, and epileptogenesis found no passage addressing the claimed effect. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [90] Selak, 2009, A role for SNAP25 in internalization of kainate receptors and synaptic plasticity, Neuron source
    • cites [91] Vincent, 2009, Kainate receptors in epilepsy and excitotoxicity, Neuroscience source
    • cites [92] Rizo, 2002, Snares and Munc18 in synaptic vesicle fusion, Nat. Rev. Neurosci source
    • cites [93] Catterall, 2008, Calcium channel regulation and presynaptic plasticity, Neuron source

      The Introduction (page unavailable) says SNARE proteins mediate the internalization of postsynaptic glutamate receptors. It does not identify SNAP-25 as facilitating that process or specify kainate receptors, so it does not support those parts of the claim. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [94] Lau, 2010, SNAP-25 is a target of protein kinase C phosphorylation critical to NMDA receptor trafficking, J. Neurosci source
    • cites [95] Tomasoni, 2013, SNAP-25 regulates spine formation through postsynaptic binding to p140Cap, Nat. Commun source
  • Findingown data

    There was a significant reduction in new GAP-43 in rapamycin-treated neurons relative to control neurons (0.39 ± 0.08 of control).

    “Indeed, there was a significant reduction in new GAP-43 in rapamycin-treated neurons relative to control neurons (0.39 Ϯ 0.08 of control; Fig. 4D-4F), supporting our previous report that mTORC1 inhibition reduces Gap-43 mRNA (35).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [35] Sosanya, 2013, Degradation of high affinity HuD targets releases Kv1.1 mRNA from miR-129 repression by mTORC1, J. Cell Biol source
  • Findingown data

    Protein expression of PARK7, including new protein synthesis, is sensitive to mTORC1 inhibition.

    “To verify our finding, we provide evidence that the protein expression of Parkinson protein 7, including new protein synthesis, is sensitive to mTORC1 inhibition.”
    Quote in the paperSubstantial claim
  • Findingown data

    In a mouse model of tuberous sclerosis complex, PARK7 protein is elevated in the dendrites.

    “Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: TSC is an mTORC1-related disease that has symptoms of epilepsy and autism.
  • Classified as probably not a substantial claim. 21
  • May combine two claims. 19
  • The quote only partly states this claim. 1

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In models of temporal lobe epilepsy there is a reduction in the expression of voltage-gated ion channels including Kv1.1.

    “Consistent with these results, in models of temporal lobe epilepsy there is a reduction in the expression of voltage-gated ion channels including Kv1.1 (30,31,36).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [30] Brewster, 2013, Rapamycin reverses status epilepticus-induced memory deficits and dendritic damage, PLoS One source

      The Results section (Figure 9) reports reduced levels of several hippocampal ion channels after status epilepticus, but explicitly states that Kv1.1 levels were not changed in the SE group. That contradicts the claim’s inclusion of Kv1.1 among the reduced channels. (LLM, conf=0.90)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [31] Sosanya, 2015, Rapamycin reveals an mTOR-independent repression of Kv1.1 expression during epileptogenesis, Neurobiol. Dis source
    • cites [36] Poolos, 2012, Dendritic ion channelopathy in acquired epilepsy, Epilepsia source

      The A-type K+ channels section (page unavailable) reports reduced Kv4.2 expression in chronically epileptic rats, and the HCN channels section reports diminished HCN1 expression in acquired epilepsy models. These support the general point that ion-channel expression is reduced in such models, but our copy does not report a reduction in Kv1.1 expression. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Reduction of SNAP-25 has been observed in age-related dementia including AD.

    “We focused our attention on SNAP-25 as reduction of SNAP-25 has been observed in age-related dementia including AD (75)(76)(77).”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [75] Honer, 2003, Pathology of presynaptic proteins in Alzheimer's disease: more than simple loss of terminals, Neurobiol. Aging source
    • cites [76] Honer, 2012, Cognitive reserve, presynaptic proteins, and dementia in the elderly, Transl. Psychiatry source

      The Results (Presynaptic proteins and dementia; page unavailable) say SNAP-25 levels were not associated with cognitive functioning. The Discussion likewise distinguishes unchanged associations for directly measured SNAP-25 levels from the SNAP-25/syntaxin interaction, which was associated with cognition. The paper does not report a reduction in SNAP-25 levels in age-related dementia or AD. (LLM, conf=0.85)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [77] Greber, 1999, Decreased levels of synaptosomal associated protein 25 in the brain of patients with Down syndrome and Alzheimer's disease, Electrophoresis source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Dysregulated mTORC1 signaling is implicated in epilepsy, Alzheimer's disease, and autism spectrum disorder.

    “Dysregulated mTORC1 signaling is implicated in many neurological disorders such as epilepsy, Alzheimer's disease (AD), and autism spectrum disorder (ASD) (11,12).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [11] Pei, 2008, mTOR-dependent signaling in Alzheimer's disease, J. Cell. Mol. Med source

      The Perspectives section (page unavailable) implicates altered mTOR-dependent signalling in Alzheimer’s disease, and the Introduction identifies mTORC1 as a distinct mTOR complex. The cited paper does not address epilepsy or autism spectrum disorder, so it supports only the Alzheimer’s disease portion of the attributed claim. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [12] Swiech, 2008, Role of mTOR in physiology and pathology of the nervous system, Biochim. Biophys. Acta source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    mTORC1 and its downstream targets are hyperactive in human brains diagnosed with Alzheimer's disease.

    “For example, mTORC1 and its downstream targets are hyperactive in human brains diagnosed with Alzheimer's disease (AD) (18 -20).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [18] An, 2003, Up-regulation of phosphorylated/activated p70 S6 kinase and its relationship to neurofibrillary pathology in Alzheimer's disease, Am. J. Pathol source

      The Abstract reports increased phosphorylated p70 S6 kinase in AD brains compared with controls, and the Discussion reports increased phosphorylated ribosomal S6, its downstream substrate. The paper identifies mTOR as upstream of p70 S6 kinase but does not show that mTORC1 itself is hyperactive in human AD brains. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [19] Li, 2005, Levels of mTOR and its downstream targets 4E-BP1, eEF2, and eEF2 kinase in relationships with tau in Alzheimer's disease brain, FEBS J source
    • cites [20] Yates, 2013, Dysfunction of the mTOR pathway is a risk factor for Alzheimer's disease, Acta Neuropathol. Commun source

      The Background (page unavailable) reports up-regulation of components downstream of mTORC1 in AD brains. It does not establish that mTORC1 itself is hyperactive; moreover, the Results section on advanced AD says most differentially expressed downstream genes changed in a direction consistent with mTOR inhibition. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In animal models of autism spectrum disorder, altered mTORC1 signaling contributes to synaptic dysfunction and aberrant network connectivity.

    “Additionally in animal models of autism spectrum disorder (ASD), altered mTORC1 signaling contributes to the observed synaptic dysfunction and aberrant network connectivity (13,15,(21)(22)(23)(24)(25)(26)(27).”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [13] Sharma, 2010, Dysregulation of mTOR signaling in fragile X syndrome, J. Neurosci source

      The Introduction (page not provided) links elevated mTOR signaling in Fmr1 knockout mice to exaggerated synaptic long-term depression; the Discussion identifies fragile X syndrome as a genetic cause of autism. This supports the synaptic-dysfunction part of the claim in one relevant animal model, but the paper does not report aberrant network connectivity or establish the claim across ASD animal models generally. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [15] Ricciardi, 2011, Reduced AKT/mTOR signaling and protein synthesis dysregulation in a Rett syndrome animal model, Hum. Mol. Genet source

      The Discussion (page unavailable) reports reduced AKT/mTOR signaling in Mecp2-mutant Rett syndrome brains and associates it with reduced synaptic connectivity and impaired network performance. It says the molecular defects might contribute to synapse loss, rather than establishing causation, and does not specifically identify mTORC1 or demonstrate the claim across ASD animal models. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [21] Zhou, 2009, Pharmacological inhibition of mTORC1 suppresses anatomical, cellular, and behavioral abnormalities in neural-specific Pten knock-out mice, J. Neurosci source

      The Results report altered dendritic spine density and mossy-fiber tract thickness in Pten-mutant mice, and the Discussion links mTORC1 inhibition to reduced ectopic axonal projections. These support a role for the pathway in neuronal structural abnormalities, but the paper does not establish synaptic dysfunction or aberrant network connectivity as functional outcomes. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Rapamycin is an FDA-approved, immunosuppressive drug that inhibits mTORC1 activity.

    “Rapamycin is an FDA-approved, immunosuppressive drug that inhibits mTORC1 activity (38).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [38] Seto, 2012, Rapamycin and mTOR: a serendipitous discovery and implications for breast cancer, Clin. Transl. Med source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    mTORC1 tightly coordinates LTP and LTD, the molecular correlates of learning and memory.

    “In the brain, mTORC1 tightly coordinates different synaptic plasticities -long-term potentiation (LTP) and long-term depression (LTD) -the molecular correlates of learning and memory (2)(3)(4)(5).”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [2] Tang, 2002, A rapamycin-sensitive signaling pathway contributes to long-term synaptic plasticity in the hippocampus, Proc. Natl. Acad. Sci. U.S.A source

      The Results report that rapamycin inhibited late-phase LTP in hippocampal slices but left early-phase LTP unaffected; the Discussion also links LTP to long-term information storage. The paper does not report an effect on LTD or establish that mTORC1 tightly coordinates both LTP and LTD. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [3] Hou, 2004, Activation of the phosphoinositide 3-kinase-Akt-mammalian target of rapamycin signaling pathway is required for metabotropic glutamate receptor-dependent long-term depression, J. Neurosci source

      The section “mTOR is required for protein synthesis-dependent forms of synaptic plasticity” reports that certain forms of LTP require mTOR and that this study found mTOR necessary for mGluR-LTD. The Introduction describes hippocampal LTD as a possible substrate for learning and memory. The paper does not specifically identify mTORC1 or establish that it tightly coordinates LTP and LTD generally. Page numbers were unavailable in our copy. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [4] Hay, 2004, Upstream and downstream of mTOR, Genes Dev source

      The section “mTOR function in synaptic plasticity, memory, and learning” (page unavailable) identifies LTP as a model of plasticity underlying learning and reports that rapamycin inhibits late LTP. It does not establish that mTORC1 tightly coordinates both LTP and LTD; the supplied passages and searches do not address LTD. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Pharmacological antagonism of NMDA receptors promotes the synthesis of Kv1.1 in dendrites.

    “Pharmacological antagonism of N-methyl-D-aspartate (NMDA) receptors, a subtype of glutamate receptors that lies upstream of mTOR activation, promotes the synthesis of the voltage-gated potassium channel, Kv1.1, in dendrites (34,35).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [34] Raab-Graham, 2006, Activity- and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites, Science source
    • cites [35] Sosanya, 2013, Degradation of high affinity HuD targets releases Kv1.1 mRNA from miR-129 repression by mTORC1, J. Cell Biol source

      The Introduction describes NMDAR/mTORC1-mediated suppression of local Kv1.1 translation in dendrites, and the Results report increased dendritic Kv1.1 protein after pharmacological inhibition of mTORC1 with rapamycin (page not provided). These passages support the direction of the proposed pathway, but they do not establish that pharmacological antagonism of NMDA receptors itself promotes dendritic Kv1.1 synthesis. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Suppressing mTORC1 activation can trigger local translation in neurons.

    “Emerging data, however, show that suppressing mTORC1 activation can trigger local translation in neurons (34,35).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [34] Raab-Graham, 2006, Activity- and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites, Science source
    • cites [35] Sosanya, 2013, Degradation of high affinity HuD targets releases Kv1.1 mRNA from miR-129 repression by mTORC1, J. Cell Biol source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Epilepsy, which is common in AD and ASD, has enhanced mTORC1 activity.

    “Furthermore, epilepsy, which is common in AD and ASD, has enhanced mTORC1 activity (28 -32).”
    Quote in the paperNot a substantial claim3 of 5 sources checked
    • cites [28] Pun, 2012, Excessive activation of mTOR in postnatally generated granule cells is sufficient to cause epilepsy, Neuron source

      The Introduction (page unavailable) says the mTOR pathway is activated in several models of epilepsy, and the Results report enhanced mTOR signaling in epileptic PTEN-knockout mice. The paper does not establish that epilepsy is common in AD or ASD, and the cited passages do not specifically identify mTORC1 activity. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [29] Wong, 2014, mTOR strikes again: mTORC1 activation causes epilepsy independent of overt pathological changes, Epilepsy Curr source
    • cites [30] Brewster, 2013, Rapamycin reverses status epilepticus-induced memory deficits and dendritic damage, PLoS One source

      The Results and Discussion report increased mTORC1 activity after status epilepticus in rats, supporting the mTORC1 portion of the claim. The paper does not establish that epilepsy is common in AD or ASD, and its finding is specific to status epilepticus rather than epilepsy generally. Page numbers are unavailable in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [31] Sosanya, 2015, Rapamycin reveals an mTOR-independent repression of Kv1.1 expression during epileptogenesis, Neurobiol. Dis source
    • cites [32] Crino, 2008, Do we have a cure for tuberous sclerosis complex?, Epilepsy Curr source

      The Abstract reports hyperactive mTOR signaling in resected tubers from patients with tuberous sclerosis complex (TSC) and epilepsy, and suggests a possible link to seizures. It does not establish enhanced mTORC1 activity in epilepsy generally or say that epilepsy is common in AD and ASD; its discussion of mTORC1 and mTORC2 does not make that broader claim. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In a model of focal neocortical epilepsy, overexpression of Kv1.1 blocked seizure activity.

    “Interestingly in a model of focal neocortical epilepsy, overexpression of Kv1.1 blocked seizure activity (37).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [37] Wykes, 2012, Optogenetic and potassium channel gene therapy in a rodent model of focal neocortical epilepsy, Sci. Transl. Med source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    GAP-43 is down-regulated in PSD with mTORC1 inhibition.

    “We selected GAP-43 protein as a control that is down-regulated in PSD with mTORC1 inhibition (79).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [79] Han, 2013, The novel caspase-3 substrate Gap43 is involved in AMPA receptor endocytosis and long-term depression, Mol. Cell. Proteomics source

      The section ‘Gap43 is Localized at the Postsynaptic Site’ reports that Gap43 was detected in the postsynaptic density (PSD) fraction. It does not report that mTORC1 inhibition down-regulates Gap43 there; searches for mTORC1 inhibition and rapamycin found no supporting passage in our copy. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    PARK7 is reported to be involved in transcriptional regulation and complexes with processing bodies (P-bodies).

    “PARK7 is reported to be involved in transcriptional regulation and complexes with processing bodies (P-bodies) suggesting that it may also play a central role in translational regulation as suggested by our PPI network (96,97).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [96] Ariga, 2013, Neuroprotective function of DJ-1 in Parkinson's disease, Oxid. Med. Cell Longev source

      Section 2 identifies DJ-1 (PARK7) as participating in transcriptional regulation, and Section 3 describes its regulation of transcription factors. Neither the supplied passages nor searches of our copy for processing bodies and translational regulation support the claim that it complexes with P-bodies. The suggestion about a central role in translational regulation is framed as the citing authors’ inference, not a finding attributed to this source. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [97] Miller-Fleming, 2014, Yeast DJ-1 superfamily members are required for diauxic-shift reprogramming and cell survival in stationary phase, Proc. Natl. Acad. Sci. U.S.A source

  • May combine two claims.

    Findingown data

    We detected 38 epilepsy, 15 AD, and 14 ASD-associated proteins in the MS/MS data.

    “We detected 38 epilepsy, 15 AD, and 14 ASD-associated proteins (Fig. 3; supplemental Table S8).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the PSD fraction, 401 proteins were quantified; 210 had positive log2 fold-change and 191 had negative log2 fold-change.

    “For PSD fraction: n ϭ 401 proteins, n log2 fold-change Ͼ 0 ϭ 210, n log2 fold-change Ͻ 0 ϭ 191.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In PSD, 50 proteins could no longer be detected and 39 new proteins were identified upon inhibiting mTORC1.

    “In PSD, 50 proteins could no longer be detected, whereas 39 new proteins were identified upon inhibiting mTORC1.”
    • Also stated in: § PSD Proteome is Labile During Brief Rapamycin Exposure and Contains More mTORC1-Responsive Proteins-Because · plain
      “DMSO column represents 50 proteins whose average spectral counts for the rapamycin treatment condition was zero. RAPA column represents 39 proteins whose average spectral counts for DMSO treatment condition was zero”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A one-hour reduction in mTORC1 signaling altered expression of select disease-related proteins bidirectionally, with ~23% increasing when mTORC1 is active and ~17% increasing when mTORC1 is inhibited (beyond ±0.5 log2 fold change).

    “A brief one hour reduction in mTORC1 signaling was sufficient to alter the expression of select proteins bidirectionally with ϳ23% (red) and ϳ17% (yellow) increasing their expression when mTORC1 is active and inhibited, respectively (beyond Ϯ 0.5 log 2 fold change; supplemental Table S8).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Rapamycin reduced the normalized PCC of PARK7 and PSD-95 from ~1.47 to 1.17 and of PARK7 and synapsin from ~1.00 to 0.67.

    “Remarkably, rapamycin reduced the normalized PCC of PARK7 and PSD-95 as well as PARK7 and synapsin from ϳ1.47 to 1.17 and ϳ1.00 to 0.67, respectively (Fig. 7D-7G).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Rapamycin-treated neurons expressed more SNAP-25 that colocalized with postsynaptic protein PSD-95, shifting normalized PCC from 1.6 ± 0.12 to 2.1 ± 0.07.

    “We found that rapamycin-treated neurons expressed more SNAP-25 that colocalized with the postsynaptic protein PSD-95, shifting its normalized PCC from 1.6 Ϯ 0.12 to 2.1 Ϯ 0.07 (Fig. 5A-5D).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    In the enrichment network comparing DMSO and rapamycin treatments for the lysate fraction, synaptic vesicle maturation was the biological process node with the most unique connections.

    “Green arrow indicates biological process of synaptic vesicle maturation, the node with the most unique connections.”
    • Also stated in: § DISCUSSION · plain
      “Enrichment network comparing differences in proteins GO clustering between DMSO and rapamycin treatments for the lysate fraction.”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    One hour after systemic rapamycin (10 mg/kg body weight), phosphorylated ribosomal S6 relative to S6 was reduced to 0.21 ± 0.08 of DMSO in mice (n = 3, p < 0.05).

    “One hour, systemic administration of rapamycin (10 mg/kg body weight) reduced mTORC1 activity as measured by densitometric analyses of phosphorylated mTORC1 (P-mTORC1, Ser2448) and its downstream target, phosphorylated ribosomal S6 (P-S6).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Immunostaining of hippocampi from Tsc1 cKO mice showed an increase in phospho-S6 ribosomal protein and typical increase in cell body size relative to control.

    “Immunostaining of hippocampi from these mice showed an increase in the downstream marker of mTORC1 activity, phospho-S6 ribosomal protein, along with the typical increase in cell body size relative to control (Fig. 8C and supplemental Fig. S6) (84).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [84] Tavazoie, 2005, Regulation of neuronal morphology and function by the tumor suppressors Tsc1 and Tsc2, Nat. Neurosci source
    • Rests on an assumption: In the Tsc1 conditional knockout mouse, expression of Cre recombinase virus elevates mTORC1 activity by knocking down the expression of TSC1 protein, an upstream repressor of mTOR.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The same threshold value was applied across all conditions using the threshold function in ImageJ.

    “The same threshold value was applied across all conditions using the threshold function in ImageJ.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    Replicate consistency was assessed by average standard errors and spectral count correlations across all proteins; correlations were r2 > 0.85 for PSD/DMSO, >0.88 for PSD/RAPA, >0.90 for SOL/DMSO, and >0.90 for SOL/RAPA.

    “Again, to assess consistency between rep-licates we measured the average standard errors and spectral count correlations across all proteins (supplemental Fig. S2A; PSD/DMSO ϭ 0.222 Ϯ 0.007, PSD/RAPA ϭ 0.198 Ϯ 0.006”
    • Also stated in: § mTORC1 Rapidly Shifts Expression of Disease Proteomes · plain
      “r 2 Ͼ 0.85 (PSD/DMSO), r 2 Ͼ 0.88 (PSD/RAPA); r 2 Ͼ 0.90 (SOL/DMSO), r 2 Ͼ 0.90 (SOL/RAPA)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Secondary dendrites (50 m long and 1 m thick) were used for analysis to minimize variability in dendritic caliber.

    “Secondary dendrites (50 m long and 1 m thick) were used for analysis to minimize variability in dendritic caliber.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    The TX-100-insoluble pellet fraction of synaptoneurosomes is enriched for PSD-95, and the TX-100-soluble supernatant is enriched for tubulin and synapsin 1.

    “As indicated by Western blot analysis, the pellet is enriched for PSD-95-a postsynaptic marker-and the supernatant is enriched for tubulin and synaptophysin 1-a presynaptic marker (Fig. 2B)”
    • Also stated in: § PSD Proteome is Labile During Brief Rapamycin Exposure and Contains More mTORC1-Responsive Proteins-Because · plain
      “B, By Western blot analysis, top, TX-100-insoluble pellet (P) was enriched in postsynaptic density-95 (PSD-95, postsynaptic marker) while bottom, TX-100-soluble supernatant (S) was enriched for synapsin 1 (SYN1, presynaptic marker) and tubulin.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    PLA and MAP2 signals were thresholded to at least thrice above background that remained constant within an experiment.

    “PLA and MAP2 signals were thresholded to at least thrice above background that remained constant within an experiment.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    The accepted proteins contain at least two identified peptides.

    “The accepted proteins contain at least two identified peptides.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The false discovery rate (FDR) was 0.2% for identification of peptides and proteins.

    “The false discovery rate (FDR) was 0.2% for identification of peptides and proteins.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisereasoning

    Both active and inactive mTORC1 permit protein synthesis.

    “Because both active and inactive mTORC1 permit protein synthesis, we sought to determine the proteins whose expression is altered when mTORC1 phosphorylation is reduced in vivo.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    In any given cell culture experiment, image acquisition across all conditions was performed on the same day using similar duration and intensity of excitation light.

    “In any given cell culture experiment, image acquisition across all conditions was performed on the same day using similar duration and intensity of excitation light.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    In the PSD fraction, rapamycin reduced phospho-S6 levels, indicating successful mTORC1 inhibition.

    “Furthermore, phospho-S6 (P-S6)-a downstream marker of mTORC1 activity-was reduced in the PSD, indicating that mTORC1 was successfully inhibited by rapamycin in this fraction (DMSO ϭ 1.00 Ϯ 0.31; RAPA ϭ 0.12 Ϯ 0.05)”
    • Also stated in: § PSD Proteome is Labile During Brief Rapamycin Exposure and Contains More mTORC1-Responsive Proteins-Because · plain
      “C, In the PSD, rapamycin reduces P-S6 level (DMSO ϭ 1.00 Ϯ 0.31; RAPA ϭ 0.12 Ϯ 0.05; n ϭ 3 animals per condition).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Peptide identifications were accepted with a MASCOT ion score greater than 20, whereas protein identifications were accepted with a probability greater than 99%.

    “Peptide identifications were accepted with a MASCOT ion score greater than 20, whereas protein identifications were accepted with a probability greater than 99%.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Phosphorylation of mTORC1, considered the active form, is generally regarded to promote protein synthesis.

    “Phosphorylation of mTORC1, considered the active form, is generally regarded to promote protein synthesis (33).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [33] Laplante, 2012, mTOR signaling in growth control and disease, Cell source

  • May combine two claims.

    Interpretationown data

    Changes in mTORC1 activity induce a rapid and dramatic remodeling of the synaptic proteome by increasing and decreasing syntheses of specific proteins and by altering the local expression of synaptic proteins.

    “Our work, overall, provides evidence that changes in mTORC1 activity induce a rapid and dramatic remodeling of the synaptic proteome by increasing and decreasing syntheses of specific proteins and by altering the local expression of synaptic proteins.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Inhibition of mTORC1 for one hour promotes new synthesis of SNAP-25 protein while reducing synthesis of new GAP-43.

    “Nevertheless, these data do suggest that inhibition of mTORC1 for one hour promotes new synthesis of SNAP-25 protein while reducing synthesis of new GAP-43.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Our results may help explain why in part rapamycin reduces seizure frequency in mTOR-related diseases, possibly through increased expression of SNAP-25 in the PSD and removal of KARs.

    “Our results may help explain why in part rapamycin reduces seizure frequency in mTOR-related diseases, possibly through the increased expression of SNAP-25 in the PSD and the removal of KARs.”
    Quote in the paperSubstantial claim
37 of 37

  • The paper relies on this without support.

    PARK7 is not associated with epilepsy, Alzheimer's disease, or autism spectrum disorder.

    “One such protein is Parkinson protein 7, which has been implicated in Parkinson's disease, yet not associated with epilepsy, Alzheimers disease, or autism spectrum disorder.”

  • The paper relies on this without support.

    TSC is an mTORC1-related disease that has symptoms of epilepsy and autism.

    “Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95.”

  • The paper relies on this without support.

    Excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis.

    “Moreover, excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis.”

  • The paper relies on this without support.

    Seizures are commonly observed in epilepsy, AD, and ASD.

    “Seizures are commonly observed in epilepsy, AD, and ASD.”

  • The paper relies on this without support.

    Tuberous sclerosis complex (TSC) is a disease that exhibits epilepsy and autistic behaviors.

    “we used a mouse model of tuberous sclerosis complex (TSC), a disease that exhibits epilepsy and autistic behaviors.”

  • The paper relies on this without support.

    In the Tsc1 conditional knockout mouse, expression of Cre recombinase virus elevates mTORC1 activity by knocking down the expression of TSC1 protein, an upstream repressor of mTOR.

    “In the Tsc1 conditional knockout (cKO) mouse, expression of Cre recombinase virus elevates mTORC1 activity by knocking down the expression of TSC1 protein, an upstream repressor of mTOR.”
6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • These findings suggest that mTORC1 and mTORC2 may be differentially regulated across hippocampal subregions and molecular layers.

    “These findings suggest that mTORC1 and mTORC2 may be differentially regulated across hippocampal subregions and molecular layers. 73 , 74”

    From Disruption of hippocampal upstream regulators of mTOR and insulin pathways in Down syndrome with Alzheimer's disease neuropathology: Preliminary observations (2026) · cites this paper as [73]

    The Discussion (page unavailable) reports region-specific changes in protein expression after mTORC1 repression, and the PARK7 results examine dendrites in the CA1 stratum radiatum. Neither those passages nor searches for mTORC2 and hippocampal subregions address whether mTORC1 and mTORC2 are differentially regulated across hippocampal subregions or molecular layers. (LLM, conf=0.75)

    Experimental — accuracy not yet measured

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.

  • Overlapping solvent-gradient steps specify different concentrations

    Minor

    The 10-65 minute ramp and the 55-90 minute ramp both apply from minute 55 through minute 65, but specify different solvent B concentrations during that interval.

  • Cultured-neuron PARK7 uncertainty values are reversed

    Minor

    The Results assign uncertainties of 0.22 to WT and 0.11 to KO, whereas the Figure 8B caption assigns 0.11 to WT and 0.22 to KO for the same reported means.

2 of 2

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Authors
Niere, F., Namjoshi, S., Song, E., Dilly, G. A., Schoenhard, G., Zemelman, B. V., Mechref, Y., & Raab-Graham, K. F.
Affiliations
  • The University of Texas at Austin (US)
  • Texas Tech University (US)
  • Cassava Sciences (United States) (US)
ORCID
Venue
Molecular & Cellular Proteomics
Publisher
Elsevier BV
Published
2016-02
Volume
15
Issue
2
Pages
412-430
ISSN
1535-9476 (ISSN-L)
DOI
10.1074/mcp.m115.055079
PMC
PMC4739665
OpenAlex
W2326642470
Cited by
38
References
101
Citations by year
2026: 4 · 2025: 3 · 2024: 4 · 2023: 3 · 2022: 1 · 2021: 4 · 2020: 4 · 2019: 4 · 2018: 4 · 2017: 4 · 2016: 3
FWCI
1.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular & Cellular Proteomics (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ThinkTech (Texas Tech University) (submittedVersion, cc-by)
  • Europe PMC (PubMed Central) (submittedVersion)
  • PubMed Central (submittedVersion)
Funders
  • National Science Foundation (1026527, 1355158, 1306528)
  • U.S. Department of Defense (W81XWH-14-1-0061)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › PI3K/AKT/mTOR signaling in cancer
  • Health Sciences › Medicine › Physiology › Tuberous Sclerosis Complex Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Keywords
mTORC1, tuberous sclerosis complex, rapamycin, synaptic protein expression, postsynaptic density, PSD-95, epilepsy, Alzheimer's disease, autism spectrum disorder, protein-protein interaction network, dendrites, neurodegenerative diseases
MeSH terms
Autism Spectrum Disorder, Protein Deglycase DJ-1, Mechanistic Target of Rapamycin Complex 1, Animals, Central Nervous System, Dendrites, Disease Models, Animal, Epilepsy, Humans, Parkinson Disease, Protein Biosynthesis, Tuberous Sclerosis, Signal Transduction, Oncogene Proteins, Proteomics, Multiprotein Complexes, Mice, Peroxiredoxins, TOR Serine-Threonine Kinases

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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