Distinct anterograde trafficking pathways of BACE1 and amyloid precursor protein from the TGN and the regulation of amyloid-β production
Open accessAbstract
The anterograde trafficking of BACE1 and the potential processing of amyloid precursor protein along the secretory pathway remain poorly defined. Our findings reveal that Golgi exit of BACE1 and APP in primary neurons is tightly regulated, resulting in their segregation along different transport routes, which limits APP processing.
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Written from the paper’s full text.
TL;DR
BACE1 and APP use distinct post-Golgi anterograde pathways: BACE1 exits the TGN directly to the plasma membrane via AP-1/Arf1/Arf4, whereas APP uses AP-4/Arl5b to early endosomes. Disrupting BACE1 export retains BACE1 in the TGN and increases BACE1 cleavage of APP and production of Aβ40 and Aβ42.
Key findings
- Newly synthesized BACE1 traffics from the TGN directly to the plasma membrane: BACE1-SBP-GFP reached the PM at ~22 min after biotin release, with TGN colocalization peaking at 43.8 ± 5.4% at 20 min and falling to 21.7 ± 4.1% at 30 min and 11.7 ± 2.2% at 60 min; recycling endosome signal rose to 25.9 ± 2.1% by 60 min.
- AP-1 depletion retained BACE1 in the TGN: BACE1-GFP colocalization with golgin-97 increased 3.0-fold, cell-surface BACE1 decreased by 19.8%, and the Golgi exit rate fell by 35%. In primary neurons, AP-1 depletion increased BACE1 colocalization with p230/golgin-245 from 10.4 ± 3.1% to 25.2 ± 5.6%, while AP-4 depletion had no significant effect.
- Arf1 and Arf4 depletion also retained BACE1 in the TGN: BACE1-GFP/golgin-97 colocalization rose from 8.1 ± 2.1% in controls to 21.1 ± 2.4% with Arf1 siRNA and 25.7 ± 2.9% with Arf4 siRNA; cell-surface BACE1 decreased by 36.3% and 39.3%, respectively. APP localization was not altered by AP-1, Arf1, or Arf4 depletion.
- Perturbing BACE1 export increased amyloidogenic processing: AP-1γ depletion increased secreted Aβ40 1.7-fold and β-CTF/C99 2.8-fold; Arf1, Arf4, and Arf1+4 depletion increased secreted Aβ40 2.7-, 4.5-, and 3.5-fold and β-CTF/C99 2.7-, 3.9-, and 4.1-fold. In primary neurons, AP-1 shRNA increased β-CTF/C99 1.88- and 1.94-fold and secreted Aβ40 and Aβ42 by 3.0- and 3.7-fold.
Methods
- Used the Retention Using Selective Hooks (RUSH) system to synchronize BACE1-SBP-GFP anterograde transport in HeLa cells, plus live imaging, TIRF, and fast acquisition; also generated HeLa-BACE1-GFP and HeLa-APP695wt stable lines and used primary mouse cortical neurons.
- Knockdowns were performed with siRNA in HeLa cells and lentiviral shRNA in primary neurons for AP-1γ, AP-4ε, GGA1, Arl5b, Arf1, and Arf4; readouts included confocal colocalization, flow cytometry for cell-surface BACE1/TfR, immunoblotting for β-CTF/C99 and α-CTF/C83, and Aβ40/Aβ42 ELISAs.
- Quantification used OBCOL, Imaris, Volocity/Manders’ coefficient, and Fiji/ImageJ; statistical tests included unpaired two-tailed Student’s t tests and one-way ANOVA with Tukey’s test.
Limitations
- Stated in the paper: direct evidence that AP-1μ interacts with the acidic cluster motif of BACE1 remains to be formally shown.
- Stated in the paper: after AP-1, Arf1, or Arf4 depletion, substantial BACE1 remained at the cell surface, which could be due to incomplete knockdown or transport by an AP-1–independent mechanism.
- Evident from the text: the main mechanistic work is in HeLa cells and primary mouse cortical neurons, with no in vivo Alzheimer’s disease model; conclusions rely on siRNA/shRNA knockdowns and tagged or overexpressed BACE1 constructs, although endogenous neuronal BACE1 distribution and AP-1 effects were also examined.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
38 of 67 cited sources checked · 23 supported · 0 flagged · accuracy not yet measured
- Premisecitation
Extended residency of BACE1 at early endosomes leads to an increase in Aβ production.
“an extended residency time of BACE1 at the early endosomes also leads to an increase in Aβ production (Toh et al., 2018).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2018 source
- Premisecitation
γ-secretase cleavage of C99 releases pathogenic amyloidogenic Aβ associated with Alzheimer's disease.
“The subsequent cleavage of C99 by γ-secretase leads to the release of the pathogenic amyloidogenic beta-amyloid peptide (Aβ) associated with Alzheimer’s disease (Qi-Takahara et al., 2005; Takami et al., 2009; Tomita, 2014).”
Quote in the paperSubstantial claim2 of 3 sources checked - Premisecitation
Highest BACE1 activity is detected in acidic compartments along the secretory and endocytic pathways including endosomes and trans-Golgi.
“which is consistent with highest BACE1 activity being detected in acidic compartments along the secretory and endocytic pathways including the endosomes and trans-Golgi (Bennett et al., 2000; Huse et al., 2000, 2002; Toh et al., 2017, 2018).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Bennett et al., 2000 source
- cites Huse et al., 2000 source
- cites Toh et al., 2017 source
The Introduction identifies early endosomes as a major site of APP processing by BACE1, and the Discussion says the slightly acidic trans-Golgi network provides favourable conditions for BACE1 cleavage. The paper supports activity in those compartments, but does not establish that BACE1 activity is highest there. (LLM, conf=0.84)
Experimental — accuracy not yet measured
- Premisecitation
Post-Golgi export of BACE1 is independent of the Arl5b/AP-4 sorting pathway.
“As the post-Golgi export of BACE1 is independent of the Arl5b/AP-4 sorting pathway”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2017 source
- Interpretationcitation
The presence of BACE1-SBP-GFP in late endosomes/lysosomes suggests turnover of BACE1 in the lysosomes.
“suggesting turnover of BACE1 in the lysosomes (Ye and Cai, 2014; Ye et al., 2017; Feng et al., 2017).”
Quote in the paperNot a substantial claim2 of 3 sources checked
- Premisecitation
Depletion of Arl5b or AP-4 leads to accumulation of APP, but not BACE1, in the TGN.
“The depletion of either Arl5b or AP-4 leads to the accumulation of APP, but not BACE1, in the TGN.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2017 source
- Premisecitation
Newly synthesized APP traffics directly from the TGN to early endosomes.
“We have previously shown that newly synthesized APP traffics directly from the TGN to the early endosomes (Toh et al., 2017)”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2017 source
- Premisecitation
APP TGN-to-early endosome transport is regulated by AP-4 and Arl5b.
“a transport step regulated by the adaptor AP-4 and the small G protein Arl5b (Burgos et al., 2010; Toh et al., 2017).”
Quote in the paperSubstantial claim2 of 2 sources checked - Premisecitation
Arl5b/AP-4 depletion increases APP processing by endogenous BACE1.
“Arl5b/AP-4 depletion also resulted in an increase in APP processing by endogenous BACE1”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2017 source
- Premisecitation
BACE1 cleavage of APP is the rate-limiting step along the amyloidogenic processing pathway.
“BACE1 cleavage of APP is the rate-limiting step along the amyloidogenic processing pathway (Thinakaran and Koo, 2008; Zhang et al., 2011)”
Quote in the paperSubstantial claim1 of 2 sources checked- cites Thinakaran and Koo, 2008 source
- cites Zhang et al., 2011 source
In Background > APP Processing, the paper identifies BACE1 cleavage as the first step in Aβ generation and says BACE1 activity is thought to be rate-limiting. The citing sentence presents that qualified assessment as an established fact. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation
The TGN is a major site for Aβ production along the secretory pathway.
“We and others have shown that the TGN is a major site for Aβ production along the secretory pathway (Burgos et al., 2010; Toh et al., 2017).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites Burgos et al., 2010 source
The Discussion (page not available in our copy) says the authors’ observations support Aβ production in the Golgi complex and/or late secretory pathway: reduced endosomal localization of APP was accompanied by increased Aβ secretion. It also says the precise site remains controversial and does not establish that the TGN specifically is a major site of production. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites Toh et al., 2017 source
The Discussion reports that blocking APP export from the TGN increases Aβ production and suggests that Aβ can be generated there. It calls the TGN a potentially important site, but does not establish that it is a major site of Aβ production along the secretory pathway under normal conditions. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Premisecitation
GGA1 is not required for post-Golgi export of BACE1.
“In contrast, GGA1, which is also found at the Golgi, is not required for the post-Golgi export of BACE1.”
Quote in the paperSubstantial claim1 of 3 sources checked- cites He et al., 2002
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites He et al., 2005
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Toh et al., 2018 source
The Results section on GGA1 depletion and the Discussion address BACE1 transport from early endosomes to recycling endosomes, not its export from the Golgi. A search for post-Golgi export and Golgi-to-plasma-membrane trafficking found no passage in our copy establishing whether GGA1 is required for that step. (LLM, conf=0.72)
Experimental — accuracy not yet measured
- Premisecitation
Depletion of Arf1 or Arf4 does not affect recruitment of AP-4 to the TGN.
“We have previously shown that depletion of Arf1 or Arf4 does not affect recruitment of AP-4 to the TGN (Toh et al., 2017).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Toh et al., 2017 source
- Findingown data
There were low levels of BACE1-SBP-GFP (10.2 ± 2.3%) in CD63-positive late endosome/lysosome at both 45 and 60 min.
“There were low levels of BACE1-SBP-GFP (10.2 ± 2.3%) in CD63-positive late endosome/lysosome at both the 45- and 60-min time points”
Quote in the paperNot a substantial claim - Findingown data
AP-1-depleted cells showed a 35% reduction in the slope of Golgi exit compared with control and AP-4 siRNA-treated cells.
“AP-1–depleted cells showed a 35% reduction in slope compared with control and AP-4 siRNA-treated cells (Figure 7E).”
Quote in the paperSubstantial claim - Findingown data
Colocalization of BACE1-GFP and golgin-97 increased from 8.1 ± 2.1% in control cells to 21.1 ± 2.4% in Arf1-depleted cells and 25.7 ± 2.9% in Arf4-depleted cells.
“Quantitation revealed that there was an increase in the colocalization of BACE1-GFP and golgin-97 from 8.1 ± 2.1% in control cells to 21.1 ± 2.4% and 25.7 ± 2.9% in Arf1- and Arf4-depleted cells, respectively (Figure 8D).”
Quote in the paperSubstantial claim - Findingown data
Secreted Aβ increased 1.7-fold from AP-1γ-depleted cells compared with control.
“There was a 1.7-fold increase in secreted Aβ from AP-1γ–depleted cells as compared with control cells (Figure 10A).”
Quote in the paperSubstantial claim - Findingown data
Cell surface expression of BACE1 was unaltered in AP-4ε- or Arl5b-depleted cells.
“cell surface expression of BACE1 was unaltered in either AP-4ε− or Arl5b-depleted cells (Figure 9, B and E).”
Quote in the paperSubstantial claim - Findingown data
In Arf1+Arf4-depleted cells, BACE1-GFP accumulated in the TGN to a lesser extent than after single depletion of Arf4.
“In Arf1+Arf4–depleted cells, BACE1-GFP accumulated in the TGN, as expected, but to a lesser extent than after single depletion of Arf4 (Figure 8, B and C).”
Quote in the paperSubstantial claim - Findingown data
Depletion of AP-1γ results in a decrease in the total cell pool of BACE1-GFP that overlapped with Rab11.
“Conversely, the depletion of AP-1γ resulted in a decrease in the total cell pool of BACE1-GFP that overlapped with Rab11 (Figure 5)”
Quote in the paperSubstantial claim - Findingown data
BACE1-SBP-GFP in the TGN decreased to 15.1 ± 2.5% at 45 min and 11.7 ± 2.2% at 60 min.
“the level of BACE1-SBP-GFP in the TGN decreased to 15.1 ± 2.5% at 45 min and 11.7 ± 2.2% at 60 min”
Quote in the paperSubstantial claim - Findingown data
Depletion of either AP-4 or Arl5b did not alter the distribution of BACE1-GFP at the Golgi.
“As expected, the depletion of either AP-4 or Arl5b in HeLa-BACE1-GFP also did not alter the distribution of BACE1-GFP at the Golgi (Figure 4, A–C).”
Quote in the paperSubstantial claim - Findingown data
Depletion of AP-1γ showed no significant change in cell surface TfR compared with control.
“the depletion of AP-1γ showed no significant change in the level of cell surface TfR from that in control cells (Supplemental Figure S6, A and C).”
Quote in the paperSubstantial claim - Findingown data
Newly synthesized BACE1 traffics directly from the TGN to the plasma membrane.
“We have demonstrated that newly synthesized BACE1 traffics from the TGN directly to the cell surface.”
- Also stated in: § Trafficking itinerary of newly synthesized BACE1 from the TGN · hedged
“Taken together, TIRF and fast-acquisition imaging data indicate that newly synthesized BACE1 traffics directly from the TGN to the PM.”
Quote in the paperSubstantial claim - Also stated in: § Trafficking itinerary of newly synthesized BACE1 from the TGN · hedged
- Findingown data
BACE1 mean fluorescence intensity decreased by 36.3% and 39.3% in Arf1 siRNA and Arf4 siRNA treated cells, respectively, compared with control.
“Quantitative analysis showed a very similar decrease in BACE1 mean fluorescence intensity by 36.3% and 39.3% in cells treated with Arf1 siRNA or Arf4 siRNA, respectively, compared with control conditions (Figure 9F).”
Quote in the paperSubstantial claim - Findingown data
BACE1 is transported from the trans-Golgi network to the plasma membrane in an AP-1- and Arf1/4-dependent manner.
“we show that BACE1 is transported from the trans-Golgi network to the plasma membrane in an AP-1- and Arf1/4-dependent manner.”
Quote in the paperSubstantial claim - Findingown data
Depletion of AP-1γ, Arf1, or Arf4 did not alter the localization of APP at the TGN compared with control siRNA.
“None of these knockdowns altered the localization of APP at the TGN from that in cells treated with control siRNA, as shown by quantitative analyses (Supplemental Figure S5).”
Quote in the paperSubstantial claim - Findingown data
In primary mouse cortical neurons, AP-1 depletion increases colocalization of endogenous BACE1 with the TGN marker p230/golgin-245 from 10.4 ± 3.1% to 25.2 ± 5.6%.
“Quantitative analyses of fluorescence intensities of 3D projections revealed an increase in colocalization of BACE1 with the TGN marker p230/golgin-245, from 10.4 ± 3.1% in nontransduced neurons to 25.2 ± 5.6% in AP-1–depleted neurons (Figure 6B).”
Quote in the paperSubstantial claim - Findingown data
AP-1γ-depleted HeLa-BACE1-GFP cells showed a reduction of cell surface BACE1 compared with control.
“AP-1γ–depleted HeLa-BACE1-GFP cells showed a reduction of cell surface BACE1 compared with control conditions (Figure 9A).”
Quote in the paperSubstantial claim - Findingown data
Depletion of Arf4 resulted in a greater accumulation of BACE1-GFP at the TGN than depletion of Arf1.
“Notably, the depletion of Arf4 resulted in a greater accumulation of BACE1-GFP at the TGN than the depletion of Arf1 (Figure 8D).”
Quote in the paperSubstantial claim - Findingown data
Quantitative analyses revealed a 3.0-fold increase in colocalization of BACE1-GFP with the TGN marker golgin-97 in AP-1γ-depleted cells compared with control siRNA-treated cells.
“Quantitative analyses revealed a 3.0-fold increase in colocalization of BACE1-GFP with the TGN marker golgin-97 in AP-1γ–depleted cells compared with control siRNA-treated cells (Figure 4D).”
Quote in the paperSubstantial claim - Findingown data
Depletion of AP-1γ in neurons did not alter the distribution of APP in the Golgi.
“depletion of AP-1γ in neurons did not alter the distribution of APP in the Golgi (Figure 6, C and D).”
Quote in the paperSubstantial claim - Findingown data
BACE1-GFP did not accumulate in the Golgi of cells expressing either the Arf1 or Arf4 rescue construct, confirming that BACE1-GFP accumulation in the TGN was specifically due to depletion of Arf1 and Arf4.
“BACE1-GFP did not accumulate in the Golgi of cells expressing either the Arf1 and Arf4 rescue construct, confirming that the accumulation of BACE1-GFP in the TGN was specifically due to the depletion of Arf1 and Arf4 (Figure 8, B, E, and F).”
Quote in the paperSubstantial claim - Findingown data
BACE1 exits the Golgi in HeLa cells and primary neurons by a pathway distinct from the trafficking pathway for APP.
“Here we demonstrate that BACE1 exits the Golgi in HeLa cells and primary neurons by a pathway distinct from the trafficking pathway for APP.”
Quote in the paperSubstantial claim - Findingown data
BACE1 mean fluorescence intensity decreased by 19.8% in AP-1γ-depleted cells compared with control siRNA-treated cells.
“There was a decrease in BACE1 mean fluorescence intensity of 19.8% in AP-1γ–depleted cells compared with control siRNA-treated cells (Figure 9D)”
Quote in the paperSubstantial claim - Findingown data
AP-4 depletion does not significantly change the colocalization of BACE1 with the TGN marker in primary neurons.
“following transduction of primary neurons with AP-4ε shRNA recombinant lentivirus (Supplemental Figure S4B), there was no significant change in the colocalization of BACE1 with the TGN marker in AP-4–depleted neurons (Figure 6B).”
Quote in the paperSubstantial claim - Findingown data
The Golgi exit of BACE1-SBP-GFP was delayed in AP-1-depleted cells compared with control cells and cells treated with AP-4ε siRNA.
“From these findings, we conclude that the Golgi exit of BACE1-SBP-GFP was delayed in AP-1–depleted cells compared with control cells and cells treated with AP-4ε siRNA”
Quote in the paperSubstantial claim - Findingown data
After 10 min of biotin addition, 11.5 ± 3.5% of BACE1-SBP-GFP colocalized with the TGN marker GCC88.
“After 10 min incubation with biotin, BACE1-SBP-GFP exhibited a juxtanuclear staining pattern with very little overlap with the ER marker KDEL (Supplemental Figure S1A) or endosomal markers (Figure 1C; Supplemental Figure S1C) and with 11.5 ± 3.5% of BACE1-SBP-GFP colocalized with the TGN marker GCC88 (Figure 1C; Supplemental Figure S1D)”
Quote in the paperSubstantial claim - Findingown data
A previously uncharacterized acidic cluster-sorting signal, DDFADDISLL, exists in the cytoplasmic tail of BACE1.
“we identified a previously uncharacterized acidic cluster–sorting signal in the cytoplasmic tail of BACE1.”
- Also stated in: § AP-1 is required for the post-Golgi sorting of BACE1 in HeLa cells · plain
“In the cytoplasmic tail of BACE1, we came across a previously undetected acidic cluster sequence, DDFADDISLL, a motif presenting an extension of the previously defined DDISLL and DISLL motifs that play a role in endocytosis and endocytic sorting (He et al., 2002, 2005; Toh et al., 2018).”
Quote in the paperSubstantial claim - Also stated in: § AP-1 is required for the post-Golgi sorting of BACE1 in HeLa cells · plain
- Findingown data
BACE1 is endocytosed to early and recycling endosomes.
“Subsequently, BACE1 is endocytosed to early and recycling endosomes.”
Quote in the paperSubstantial claim - Findingown data
AP-1 and the Arf small G proteins Arf1 and Arf4 are required for efficient Golgi export of BACE1 in both HeLa cells and primary neurons.
“We have demonstrated that AP-1 and the Arf small G proteins Arf1 and Arf4 are required for efficient Golgi export of BACE1 in both HeLa cells and primary neurons.”
Quote in the paperSubstantial claim - Findingown data
Depletion of either Arf1 or Arf4 accumulates BACE1-GFP in the juxtanuclear region that colocalizes extensively with the Golgi marker golgin-97 compared with control conditions.
“The depletion of either Arf1 or Arf4 accumulated BACE1-GFP in the juxtanuclear region that colocalizes extensively with the Golgi marker golgin-97, compared with control conditions (Figure 8B).”
Quote in the paperSubstantial claim - Findingown data
BACE1-GFP colocalization with golgin-97 increased from 8% in control cells to 17.1 ± 4.8% in Arf1+Arf4-depleted cells.
“Quantitation revealed an increase in BACE1-GFP colocalization with golgin-97 from 8% in control cells to 17.1 ± 4.8% in Arf1+Arf4–depleted cells (Figure 8D).”
Quote in the paperSubstantial claim - Findingown data
Depletion of either Arf1 or Arf4 in HeLa-BACE1-GFP resulted in decreased cell surface expression of BACE1.
“The depletion of either Arf1 or Arf4 in HeLa-BACE1-GFP resulted in a decrease in cell surface expression of BACE1, as shown by a leftward shift in the fluorescence intensity peaks of each knockdown condition from control conditions (Figure 9C).”
Quote in the paperSubstantial claim - Findingown data
The level of BACE1-GFP at the TGN was not altered in GGA1-depleted cells.
“On the other hand, the level of BACE1-GFP at the TGN was not altered in GGA1-depleted cells (Figure 4, C and D).”
Quote in the paperSubstantial claim - Findingown data
AP-1γ was depleted by 43-46% in neurons transduced with AP-1γ-shRNA1 and AP-1γ-shRNA2 lentivirus compared with nontransduced neurons.
“AP-1γ was depleted by 43–46% in neurons transduced with AP-1γ-shRNA1 and AP-1γ-shRNA2 lentivirus as compared with nontransduced neurons (Figure 11, A and B).”
Quote in the paperSubstantial claim - Findingown data
In AP-1-silenced neurons, there was a 3.0-fold increase for Aβ40 and a 3.7-fold increase for Aβ42.
“In AP-1–silenced neurons, there was an increase in levels of both Aβ species: a 3.0-fold increase for Aβ40 and a 3.7-fold increase for Aβ42.”
Quote in the paperSubstantial claim - Findingown data
In absence of DAPT, β-CTF/C99 and α-CTF/C83 were not detected in any neuronal extracts.
“In the absence of DAPT, β-CTF/C99 and α-CTF/C83 were not detected in any of the neuronal extracts (Figure 11A)”
Quote in the paperSubstantial claim - Findingown data
Newly synthesized BACE1 traffics from the TGN to the PM.
“newly synthesized BACE1 traffics from the TGN to the PM”
- Also stated in: § DISCUSSION · plain
“BACE1-SBP-GFP was transported to the Golgi within 10–15 min following release from the ER by addition of biotin, and then trafficked from the TGN to the PM.”
Quote in the paperSubstantial claim - Also stated in: § DISCUSSION · plain
- Findingown data
Depletion of either Arf1 or Arf4 resulted in accumulation of BACE1-GFP in the TGN.
“The depletion of either Arf1 or Arf4 resulted in the accumulation of BACE1-GFP in the TGN.”
Quote in the paperSubstantial claim - Findingown data
Depletion of AP-1, Arf1, or Arf4 resulted in reduction of BACE1 at cell surface.
“Depletion of AP-1, Arf1, or Arf4 resulted in a reduction of BACE1 at the cell surface.”
Quote in the paperSubstantial claim - Findingown data
No significant changes in α-CTF/C83 levels in AP-1γ-shRNA1- and AP-1γ-shRNA2-transduced neurons compared with nontransduced neurons.
“there were no significant changes in the level of α-CTF/C83 (** band) in AP-1γ-shRNA1– and AP-1γ-shRNA2–transduced neurons from that in nontransduced neurons (Figure 11, A and D).”
Quote in the paperSubstantial claim - Findingown data
In presence of DAPT, intracellular β-CTF/C99 increased 2.7-fold, 3.9-fold, and 4.1-fold in Arf1 siRNA, Arf4 siRNA, and Arf1+4 siRNAs treated cells, respectively, compared with control.
“In the presence of DAPT, there was also a 2.7-fold, 3.9-fold, and 4.1-fold increase in the level of intracellular β-CTF/C99 detected in cells treated with either Arf1 siRNA, Arf4 siRNA, or Arf1+4 siRNAs, respectively, from that in control siRNA-treated cells (Figure 10, D and E).”
Quote in the paperSubstantial claim - Findingown data
In presence of C3 and DAPT, the 11-kDa band was absent, confirming its identity as β-CTF/C99.
“In the presence of C3 and DAPT, the 11-kDa band (indicated by *) was absent (Figure 11A), confirming their identity as β-CTF/C99.”
Quote in the paperSubstantial claim- Rests on an assumption: The BACE1 inhibitor C3 specifically inhibits BACE1 without affecting other proteases.
- Findingreasoning
Only low levels of β-CTF/C99 were detectable in AP-1-/Arf1-/Arf4-depleted cells in absence of γ-secretase inhibitor.
“Only low levels of β-CTF/C99 were detectable in AP-1-/Arf1-/Arf4-depleted cells in the absence of the γ-secretase inhibitor”
Quote in the paperSubstantial claim - Findingown data
Aβ42 is generated via TGN-mediated processing of APP.
“the finding that Aβ42 is generated via TGN-mediated processing of APP is an important observation”
Quote in the paperSubstantial claim - Findingown data
BACE1-SBP-GFP-containing vesicles were transported from a juxtanuclear compartment directly to the distal edge of the cell.
“quantitative analysis of confocal live imaging, TIRF analysis, and fast image acquisition, which showed that BACE1-SBP-GFP–containing vesicles were transported from a juxtanuclear compartment directly to the distal edge of the cell.”
Quote in the paperSubstantial claim - Findingown data
Upon depletion of AP-1, Arf1, or Arf4, there was increased processing of APP, with 2.8- to 4.1-fold increase of intracellular β-CTF/C99 and 1.7- to 4.5-fold increase in secreted Aβ.
“Upon the depletion of either AP-1, Arf1, or Arf4, there was increased processing of APP, as demonstrated by a 2.8- to 4.1-fold increase of intracellular β-CTF/C99 and a 1.7- to 4.5-fold increase in secreted Aβ secretion compared with control conditions.”
Quote in the paperSubstantial claim - Findingown data
In presence of DAPT, intracellular β-CTF/C99 increased 1.88- and 1.94-fold in neurons transduced with AP-1γ-shRNA1 and AP-1γ-shRNA2, respectively, compared with nontransduced neurons.
“in the presence of DAPT, there were 1.88- and 1.94-fold increases in the level of intracellular β-CTF/C99 in neurons transduced with AP-1γ-shRNA1 and AP-1γ- shRNA2, respectively, compared with nontransduced neurons (Figure 11, A and C).”
Quote in the paperSubstantial claim - Findingown data
Greater increase in β-CTF/C99 was detected under Arf4-depleted conditions than under Arf1-depleted conditions.
“Notably, a greater increase in the level of β-CTF/C99 was detected under Arf4-depleted conditions than under Arf1-depleted conditions (Figure 10, D and E)”
Quote in the paperSubstantial claim - Findingown data
BACE1 was retained in the Golgi/TGN following AP-1 knockdown.
“BACE1 was retained in the Golgi/TGN following AP-1 knockdown, as revealed by localization studies of fixed cells with defined markers and by the analysis of the kinetics of BACE1 transport through the Golgi in live cells using RUSH.”
Quote in the paperSubstantial claim - Interpretationown data
Golgi exit of BACE1 and APP in primary neurons is tightly regulated, resulting in their segregation along different transport routes, which limits APP processing.
“These findings reveal that Golgi exit of BACE1 and APP in primary neurons is tightly regulated, resulting in their segregation along different transport routes, which limits APP processing.”
Quote in the paperSubstantial claim - Premisecitation
BACE1 is the primary β-secretase that initiates β-site cleavage of APP to generate the membrane-bound C99 fragment.
“BACE1 is the primary β-secretase for initiating the β-site cleavage of amyloid precursor protein (APP) to generate the membrane-bound C99 fragment (Hussain et al., 1999; Sinha et al., 1999; Yan et al., 1999; Bennett et al., 2000).”
Quote in the paperSubstantial claim0 of 3 sources checked - Interpretationown data
TIRF and fast-acquisition imaging data indicate that newly synthesized BACE1 traffics directly from the TGN to the plasma membrane.
“Taken together, TIRF and fast-acquisition imaging data indicate that newly synthesized BACE1 traffics directly from the TGN to the PM.”
Quote in the paperSubstantial claim - Study design and conductown data
Immunoblotting showed that AP-1γ and GGA1 levels were depleted by >90% and >80%, respectively, in HeLa-BACE1-GFP treated with AP-1γ or GGA1 siRNA.
“Immunoblotting showed that the levels of AP-1γ and GGA1 were depleted by >90% and >80%, respectively, in HeLa-BACE1-GFP treated with either AP-1γ or GGA1 small interfering RNA (siRNA) (Figure 4A).”
Quote in the paperSubstantial claim - Interpretationown data
The AP-1/Arf1/Arf4 sorting machinery is not required for APP export from the TGN.
“These data indicate that the AP-1/Arf1/Arf4 sorting machinery is not required for APP export from the TGN.”
Quote in the paperSubstantial claim - Premisecitation
APP processing requires convergence of BACE1 and APP to the same compartment.
“as both BACE1 and APP are membrane proteins, APP processing requires the convergence of these proteins to the same compartment (Kinoshita et al., 2003).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Kinoshita et al., 2003 source
- Interpretationown data
Cell surface levels of BACE1 are dependent on AP-1 mediated trafficking of BACE1 from the Golgi.
“Therefore, the cell surface levels of BACE1 are dependent on AP-1 mediated trafficking of BACE1 from the Golgi.”
Quote in the paperSubstantial claim - Interpretationown data
Cell surface expression of BACE1 is dependent on the Golgi AP-1 export pathway.
“These results show that cell surface expression of BACE1 is dependent on the Golgi AP-1 export pathway.”
Quote in the paperSubstantial claim - Interpretationown data
Segregation of BACE1 and APP into distinct pathways at the TGN is relevant to the regulation of APP processing and Aβ production.
“Our findings also demonstrate that the segregation of BACE1 and APP into distinct pathways at the TGN is relevant to the regulation of APP processing and Aβ production.”
Quote in the paperSubstantial claim - Interpretationown data
Arf1 and Arf4 are required for trafficking of BACE1 to the cell surface.
“The decrease in cell surface expression of BACE1 demonstrates that Arf1 and Arf4 are also required for the trafficking of BACE1 to the cell surface.”
Quote in the paperSubstantial claim - Premisecitation
Redirecting the BACE1 plasma membrane recycling pathway via the TGN using a chimeric BACE1/TGN38 construct leads to increased Aβ production.
“redirecting the BACE1 plasma membrane recycling pathway via the trans-Golgi network (TGN), using a chimeric BACE1/TGN38 construct (TGN38 is known to traffic from the endosomes to the TGN), leads to increased Aβ production (Chia et al., 2013).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Chia et al., 2013 source
- Interpretationown data
Increase in Aβ production indicates enhanced processing of APP by endogenous BACE1 at the TGN following depletion of AP-1, Arf1, and Arf4 sorting machinery.
“The increase in Aβ production indicates enhanced processing of APP by endogenous BACE1 at the TGN following the depletion of AP-1, Arf1, and Arf4 sorting machinery.”
Quote in the paperSubstantial claim - Interpretationreasoning
BACE1-SBP-GFP detected in early endosomes at 30 min likely represents arrival of internalized BACE1 from the plasma membrane.
“Rather, the BACE1-SBP-GFP detected in the early endosomes at 30 min likely represents the arrival of internalized BACE1 from the PM.”
Quote in the paperSubstantial claim - Premisecitation
Enhanced APP cleavage was detected at TGN upon redirection of BACE1 recycling to this compartment using BACE1/TGN38 chimera.
“our earlier study where enhanced APP cleavage was detected at the TGN upon the redirection of BACE1 recycling to this compartment using a BACE1/TGN38 chimera (Chia et al., 2013).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Chia et al., 2013 source
- Interpretationown data
Post-Golgi trafficking of APP is independent of the AP-1-/Arf1-/Arf4-regulated pathway.
“the post-Golgi trafficking of APP is independent of the AP-1-/Arf1-/Arf4-regulated pathway”
Quote in the paperSubstantial claim - Interpretationreasoning
Increase in convergence between BACE1 and APP in TGN leads to increased processing of APP by BACE1 in this compartment.
“The increase in convergence between BACE1 and APP in the TGN then leads to increased processing of APP by BACE1 in this compartment.”
Quote in the paperSubstantial claim - Interpretationown data
AP-1 pathway is critical for regulating processing events under physiological conditions.
“These findings demonstrate that the AP-1 pathway is critical for regulating processing events under physiological conditions.”
Quote in the paperSubstantial claim - Interpretationreasoning
Requirement for distinct transport machinery for post-Golgi transport of APP and BACE1 provides a mechanism to sort and segregate APP and BACE1 into separate pathways.
“The requirement for distinct transport machinery for post-Golgi transport of APP and BACE1 provides a mechanism to sort and segregate APP and BACE1 into separate pathways.”
Quote in the paperSubstantial claim - Interpretationreasoning
Cargo that interacts selectively with AP-1 at TGN may be transported from Golgi directly to PM.
“cargo that interacts selectively with AP-1 at the TGN may be transported from the Golgi directly to the PM.”
Quote in the paperSubstantial claim - Interpretationreasoning
Liberation of Aβ peptide from β-CTF/C99 by γ-secretase is likely to occur in the TGN.
“the liberation of Aβ peptide from β-CTF/C99 by γ-secretase is also likely to occur in the TGN.”
Quote in the paperSubstantial claim - Interpretationcitation
Arrival of BACE1 at early and recycling endosomes at 30 min most likely represents internalized BACE1 from the PM.
“Arrival of BACE1 at the early and recycling endosomes at the 30-min time point most likely represents internalized BACE1 from the PM (Chia et al., 2013).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Chia et al., 2013 source
- Interpretationcitation
Combination of AP-1 and GGA is likely to regulate sorting of cargoes to endosomes from TGN.
“These studies suggest that the combination of AP-1 and GGA is likely to regulate the sorting of cargoes to the endosomes from the TGN.”
Quote in the paperNot a substantial claim - Interpretationown data
Golgi-associated APP processing events in primary neurons result in generation of cytotoxic Aβ42 species.
“Therefore, the Golgi-associated APP processing events in primary neurons result in the generation of the cytotoxic Aβ42 species.”
Quote in the paperSubstantial claim - Interpretationreasoning
Trafficking of BACE1 to PM via AP-1 pathway may serve as regulatory mechanism to segregate BACE1 from APP at TGN, limiting amyloidogenic processing of APP in this compartment.
“The trafficking of BACE1 to the PM via the AP-1 pathway may serve as a regulatory mechanism to segregate BACE1 from APP at the TGN, thus limiting the amyloidogenic processing of APP in this compartment.”
Quote in the paperSubstantial claim - Interpretationown data
AP-1, Arf1, and Arf4 trafficking machinery is relevant to regulation of amyloidogenic processing of APP at the TGN.
“Collectively, these findings highlight the relevance of AP-1, Arf1, and Arf4 trafficking machinery on the regulation of the amyloidogenic processing of APP at the TGN.”
Quote in the paperSubstantial claim - Interpretationreasoning
Trafficking of APP from TGN is independent of AP-1/Arf1/Arf4 pathway.
“the trafficking of APP from the TGN is independent of this pathway.”
Quote in the paperSubstantial claim - Interpretationown data
AP-1 is required for efficient post-Golgi sorting of BACE1 in both HeLa cells and neurons.
“A key finding of this work is that AP-1 is required for the efficient post-Golgi sorting of BACE1 in both HeLa cells and neurons.”
Quote in the paperSubstantial claim - Interpretationown data
BACE1 is transported directly from the TGN to the PM.
“Our data strongly indicate that BACE1 is transported directly from the TGN to the PM.”
Quote in the paperSubstantial claim - Premisecitation
γ-secretase is localized in the Golgi compartment.
“γ-secretase is also localized in the Golgi compartment (Rechards et al., 2003)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Rechards et al., 2003 source
- Premisereasoning
Trafficking of APP from TGN is regulated by AP-4/Arl5b transport machinery directly to endosomal pathway.
“the trafficking of APP from the TGN is regulated by the AP-4/Arl5b transport machinery directly to the endosomal pathway.”
Quote in the paperSubstantial claim - Premiseown data
Newly synthesized APP is transported from the TGN directly to early endosomes by an AP-4-dependent pathway.
“We previously showed that newly synthesized APP is transported from the TGN directly to the early endosomes by an AP-4–dependent pathway.”
Quote in the paperSubstantial claim - Interpretationown data
γ-secretase processes β-CTF/C99 rapidly.
“indicating that γ-secretase processes β-CTF/C99 rapidly.”
Quote in the paperSubstantial claim - Interpretationown data
AP-1, Arf1, and Arf4 are essential for TGN-to-PM trafficking of BACE1.
“the AP complex, AP-1, and Arf1 and Arf4 small G proteins are essential for TGN-to-PM trafficking of BACE1”
Quote in the paperSubstantial claim - Interpretationown data
Post-Golgi sorting machinery and trafficking pathways that regulate APP and BACE1 differ.
“These findings further support the conclusion that the post-Golgi sorting machinery and trafficking pathways that regulate APP and BACE1 differ.”
Quote in the paperSubstantial claim - Interpretationown data
Post-Golgi transport pathways of BACE1 are common between HeLa cells and primary neurons.
“Confirmation of the findings in HeLa cells by the behavior of endogenous BACE1 in primary neurons demonstrates that the post-Golgi transport pathways of BACE1 are common between the cell types.”
Quote in the paperSubstantial claim - Interpretationown data
Depletion of AP1γ, Arf1, Arf4, or Arf1+4 enhances BACE1 cleavage of APP at the TGN.
“The increase in β-CTF/C99 production directly demonstrates that the depletion of AP1γ, Arf1, Arf4, or Arf1+4 enhances BACE1 cleavage of APP at the TGN.”
Quote in the paperSubstantial claim - Interpretationown data
Golgi export of endogenous BACE1 by AP-1 pathway is essential for regulation of amyloidogenic processing.
“Using stably transfected HeLa-APP695wt cells, we showed that Golgi export of endogenous BACE1 by the AP-1 pathway is essential for the regulation of amyloidogenic processing.”
Quote in the paperSubstantial claim - Interpretationnone given
A functional AP-1/Arf1/Arf4 pathway is required for export of BACE1 from Golgi directly to PM.
“In conclusion, a functional AP-1/Arf1/Arf4 pathway is required for the export of BACE1 from the Golgi directly to the PM.”
Quote in the paperSubstantial claim - Interpretationown data
Arf4 is likely the major small G protein regulating post-Golgi trafficking of BACE1.
“These results again indicate that Arf4 is likely to be the major small G protein regulating the post-Golgi trafficking of BACE1.”
Quote in the paperSubstantial claim - Interpretationown data
Depletion of either AP-1, Arf1, or Arf4 enhanced amyloidogenic processing of APP.
“the depletion of either AP-1, Arf1, or Arf4 enhanced the amyloidogenic processing of APP”
Quote in the paperSubstantial claim - Interpretationown data
Reduced levels of BACE1 at cell surface in AP-1 knockdown cells are consistent with retention of BACE1 in the Golgi.
“the reduced levels of BACE1 at the cell surface in AP-1 knockdown cells, as assessed by FACS of nonpermeabilized cells, are also consistent with the retention of BACE1 in the Golgi.”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 25
- May combine two claims. 43
Classified as probably not a substantial claim.
PremisecitationRecruitment of AP-1 to TGN membranes is regulated by Arf1 and Arf4 small G proteins.
“Given that the recruitment of AP-1 to TGN membranes has been reported to be regulated by both Arf1 (Stamnes and Rothman, 1993; Le Borgne and Hoflack, 1997; Lee et al., 2008) and Arf4 (Lowery et al., 2013; Nakai et al., 2013) small G proteins”
Quote in the paperSubstantial claim2 of 3 sources checkedClassified as probably not a substantial claim.
PremisecitationA previous study showed that Arf1 depletion caused Arf4 levels to increase.
“A previous study showed that Arf1 depletion caused Arf4 levels to increase (Reiling et al., 2013)”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Reiling et al., 2013 source
Probably not a substantial claim: may not pass S3 (load-bearing).
FindingcitationDepletion of Arf1 resulted in an increase in Arf4 levels by approximately 20%.
“In addition, the depletion of Arf1 resulted in an increase in Arf4 levels by ∼20%, consistent with a previous report (Reiling et al., 2013; Figure 8A).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Reiling et al., 2013 source
The Results section (‘Compensatory ARF upregulation in cells with downregulated ARF4 function’; page unavailable) reports that loss of ARF1 entailed the re-emergence of ARF4 expression. It does not quantify the change as approximately 20%, so the cited paper supports the direction of the effect but not the stated magnitude. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationBACE1 activity is optimal at acidic pH.
“As a type-1 transmembrane aspartyl protease, BACE1 activity is optimal at acidic pH (Shimizu et al., 2008)”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Shimizu et al., 2008 source
Classified as probably not a substantial claim. May combine two claims.
PremisecitationAP-1 is required for trafficking of transferrin receptor (TfR) to the basolateral PM in polarized MDCK cells and to the somatodendritic PM in rat hippocampal neurons.
“AP-1 has been shown to be required for the trafficking of transferrin receptor (TfR) to the basolateral PM in polarized Madin–Darby canine kidney (MDCK) epithelial cells (Gravotta et al., 2012) and the trafficking of TfR to the somatodendritic PM in rat hippocampal neurons (Farias et al., 2012).”
Quote in the paperSubstantial claim2 of 2 sources checkedClassified as probably not a substantial claim. May combine two claims.
PremisecitationInternalized BACE1 traffics to early endosomes and recycles back to the plasma membrane via recycling endosomes.
“The intracellular itinerary of internalized BACE1 to the early endosomes followed by the recycling of BACE1 back to the plasma membrane (PM) via the recycling endosomes has been established previously (Chia et al., 2013; Toh et al., 2018).”
Quote in the paperSubstantial claim1 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationGGA1 interacts with a DISLL motif in cytoplasmic tail of BACE1 and is required for endosomal sorting of BACE1.
“GGA1, which can interact with a DISLL motif in the cytoplasmic tail of BACE1, is required for the endosomal sorting of BACE1 (He et al., 2002, 2005; Toh et al., 2018).”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites He et al., 2002
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites He et al., 2005
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Toh et al., 2018 source
The Introduction places the DISLL motif in BACE1’s cytoplasmic tail, and the Discussion says GGA1 recognizes its phosphorylated form. The Discussion also describes a separate SNX4-dependent sorting pathway and reports that GGA1 silencing reduces transport to recycling endosomes by about 30%. Thus, GGA1 is required for the signal-dependent pathway, not for all endosomal sorting of BACE1. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationTfR is loaded into tubular carriers derived from the TGN in nonpolarized HeLa cells by an AP-1-independent process.
“which showed that TfR is loaded into tubular carriers derived from the TGN in nonpolarized HeLa cells by an AP-1–independent process (Chen et al., 2017).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Chen et al., 2017 source
The Results section ('Exit of LAMP1 and TfR in tubular carriers is independent of signal–adaptor interactions'; page unavailable) reports TfR incorporation into Golgi-derived tubular carriers in HeLa cells and says AP-complex knockout did not affect its exit in those carriers. The Discussion ('Molecular determinants of early Golgi segregation and Golgi export'; page unavailable) explicitly says this exit is AP-1-independent. The paper describes the carriers as Golgi-derived, but the cited passages do not establish the more specific claim that they originate from the TGN. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAP-1 regulates TGN-to-endosomal pathway for delivery of newly synthesized lysosomal enzymes bound to MPRs from TGN to late endosomes.
“AP-1 is known to regulate the TGN-to-endosomal pathway required for the delivery of newly synthesized lysosomal enzymes bound to mannose 6-phosphate receptors (MPRs) from the TGN to the late endosomes (Hille-Rehfeld, 1995; Meyer et al., 2000).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites Hille-Rehfeld, 1995 source
- cites Meyer et al., 2000 source
The Introduction describes AP-1 as mediating TGN-to-endosome transport, and “Effect of μ1A deficiency on M6P-receptor trafficking” says MPRs bind newly synthesized lysosomal enzymes at the TGN and transport them to endosomes/lysosomes via AP-1-containing vesicles. Our copy does not specify late endosomes as the destination of that forward route; its mention of late endosomes concerns transport back to the TGN. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
FindingcitationIn nontransduced neurons, secreted Aβ40:Aβ42 ratio was 5.3:1, consistent with Aβ40 being major species from neuronal tissues.
“In nontransduced neurons, the secreted Aβ40:Aβ42 ratio was 5.3:1, consistent with Aβ40 representing the major species from neuronal tissues (Schieb et al., 2011).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Schieb et al., 2011 source
The discussion reports that Aβ(1-40) was the predominant soluble variant and describes it as the main species in cell-culture supernatants. Table 5 gives an Aβ(1-42):Aβ(1-40) ratio of 0.19 in APP23 mouse CSF, approximately the inverse of 5.3:1. Neither passage reports a measured 5.3:1 ratio in secretions from nontransduced neurons. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationA previous study of a reovirus membrane protein reported transport to the plasma membrane from the Golgi by an AP-1-dependent pathway.
“a previous study of a reovirus membrane protein also reported transport to the plasma membrane from the Golgi by an AP-1–dependent pathway (Parmer and Duncan, 2016).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Parmer and Duncan, 2016 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAP-1 regulates retrograde transport in the Golgi in yeast cells.
“AP-1 has also been reported to regulate retrograde transport in the Golgi in yeast cells (Casler et al., 2019).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Casler et al., 2019 source
Classified as probably not a substantial claim.
PremisecitationThe basic patch of AP-1μ subunit is required for binding of acidic cluster sequences.
“The basic patch (Lys274, Lys298, Lys302, Arg303, and Arg304) of the AP-1μ subunit has been shown to be required for the binding of acidic cluster sequences (Navarro Negredo et al., 2017).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Navarro Negredo et al., 2017 source
The Results identify Lys274, Lys298, Lys302, Arg303, and Arg304 as the basic patch and report that mutating them reduces binding. The Discussion says the patch is required for optimal binding, not that binding cannot occur without it; the claim overstates its necessity. Page numbers are not available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationThe D495R mutation caused accumulation of D495R BACE1 mutant in the juxtanuclear region, suggesting the acidic D495 residue could also be important for post-Golgi trafficking of BACE1.
“an additional effect of the D495R mutation, which was not alluded to by these authors, was the accumulation of D495R BACE1 mutant in the juxtanuclear region of the cell (Prabhu et al., 2012), suggesting that the acidic D495 residue could also be important for the post-Golgi trafficking of BACE1.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Prabhu et al., 2012 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationGGA proteins are recruited to TGN by Arf1 and function cooperatively with AP-1 to regulate trafficking of cargoes from TGN to endosomes.
“The GGA proteins, which are also recruited to the TGN by Arf1, have been shown to function cooperatively with AP-1 to regulate the trafficking of cargoes from the TGN to the endosomes (Doray et al., 2002; Hirst et al., 2012).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites Doray et al., 2002 source
- cites Hirst et al., 2012 source
In the Conclusions, the paper proposes that GGAs act with AP-1 to move hydrolase–receptor complexes from a TGN/post-TGN compartment toward endosomes. The Coat Components and Accessory Factors section says ARF1 facilitates GGA recruitment onto membranes, and the Conclusions place GGAs mainly at the TGN. The claim is stronger and broader than the paper on cooperation: it says this function has been shown for cargoes generally, whereas the paper presents it as a proposal focused on hydrolase–receptor complexes. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationRecruitment of AP-1 to the TGN is mediated by Arf1 and Arf4 small G proteins.
“The recruitment of AP-1 to the TGN is known to be mediated by Arf1 and Arf4 small G proteins (Stamnes and Rothman, 1993; Lee et al., 2008; Nakai et al., 2013)”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites Stamnes and Rothman, 1993 source
- cites Lee et al., 2008 source
The Introduction describes Arf-1 as a primary docking site in the initial recruitment of AP-1 to the TGN. The Results and discussion also report Arf-1-dependent AP-1 recruitment in a liposome assay. The passages do not support the claim’s additional attribution to Arf4 (searched: Arf4 recruitment AP-1 TGN). (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Nakai et al., 2013 source
The Results report that depleting ARF1 and ARF4 reduces AP-1 at the TGN, suggesting that they participate in its recruitment. The Discussion calls their role a possibility, so the source does not establish the citing sentence’s stronger claim that recruitment is known to be mediated by them. Page numbers are not provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationD495 residue is essential for AP-2-mediated endocytosis of BACE1.
“A previous study analyzing the AP-2–mediated endocytosis of BACE1-mutated D495 in the acidic cluster motif (DDFAD495DISLL) in BACE1 to R495 showed that the D495 residue is essential for AP-2–mediated endocytosis of BACE1 (Prabhu et al., 2012).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Prabhu et al., 2012 source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductcitationThe HeLa cells used were authenticated and tested for mycoplasma.
“Authentic and mycoplasma-tested HeLa cells (Scherer et al., 1953) were maintained as semiconfluent monolayers in DMEM”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Scherer et al., 1953 source
The Cell Strain passage identifies the origin and cultivation of HeLa cells, so the citation supports the cell-line identification. It does not report authentication or mycoplasma testing of the cells used in the citing study. (LLM, conf=0.87)
Experimental — accuracy not yet measured
May combine two claims.
Findingown dataAt 45 and 60 min, BACE1-SBP-GFP colocalization with the early endosome marker remained steady at approximately 20%, while recycling endosome colocalization increased to 25.9 ± 2.1% by 60 min.
“After 45- and 60-min time points, the colocalization of BACE1-SBP-GFP with the early endosome (EEA1) marker remained steady at ∼20%, while the level of BACE1-SBP-GFP in the recycling endosome increased to 25.9 ± 2.1% by 60 min”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAt 20 min, 43.8 ± 5.4% of BACE1-SBP-GFP overlapped with GCC88 and showed minimum overlap (<5%) with EEA1, Rab11, and CD63.
“At 20 min, 43.8 ± 5.4% of BACE1-SBP-GFP overlapped with GCC88 and showed minimum overlap (<5%) with the endosomal/lysosomal markers EEA1, Rab11, and CD63”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn the absence of biotin, BACE1-SBP-GFP is retained in the ER, with limited overlap (<5%) with other organelle markers and no overlap with a plasma membrane marker.
“In the absence of biotin, BACE1-SBP-GFP displayed ER-like staining pattern (Figure 1B), which overlapped substantially with the ER-marker, KDEL (Supplemental Figure S1A), limited overlap (<5%) with other organelle markers (Figure 1, B and C), and no overlap with a plasma membrane marker (Supplemental Figure S1B)”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe intracellular levels of BACE1-SBP-GFP in early and recycling endosomes at 60 min are very similar to the steady-state distribution of BACE1, indicating that the wave of BACE1 cargo from the ER had established an equilibrium throughout the cell by 60 min.
“Furthermore, the intracellular levels of BACE1-SBP-GFP in the early endosomes and recycling endosomes at the 60-min time point are very similar to the steady-state distribution of BACE1, as quantified from transfected cells incubated in the continuous presence of biotin (Figure 1C), indicating that the wave of BACE1 cargo from the ER had established an equilibrium throughout the cell by 60 min.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataHigher level of secreted Aβ was detected from Arf4-depleted cells than from Arf1-depleted cells, consistent with greater BACE1 accumulation at TGN in Arf4-depleted cells.
“A higher level of secreted Aβ was detected from Arf4-depleted cells than from Arf1-depleted cells (Figure 10B), consistent with the finding that BACE1 showed a greater accumulation at the TGN in Arf4-depleted cells (Figure 8, B and D).”
Quote in the paperSubstantial claimMay combine two claims.
FindingcitationThe distribution of BACE1-GFP is very similar to the steady-state distribution of transiently expressed untagged BACE1 in HeLa cells and to the distribution of BACE1-SBP-GFP in the RUSH system in the continuous presence of biotin.
“This distribution of BACE1-GFP is very similar to the steady-state distribution of transiently expressed untagged BACE1 in HeLa cells (Chia et al., 2013) and to the distribution of BACE1-SBP-GFP in the RUSH system in the continuous presence of biotin (Table 1).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Chia et al., 2013 source
May combine two claims.
Findingown dataDouble knockdown of Arf1+Arf4 depleted Arf1 by 82% and Arf4 by 55%.
“The double knockdown of Arf1+Arf4 depleted Arf1 by 82%, whereas Arf4 was depleted by only 55%, as assessed by immunoblotting (Figure 8A).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataPerturbation of BACE1 post-Golgi trafficking results in increased BACE1 cleavage of APP and increased production of both Aβ40 and Aβ42.
“Perturbation of BACE1 post-Golgi trafficking results in an increase in BACE1 cleavage of APP and increased production of both Aβ40 and Aβ42.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn presence of DAPT, β-CTF/C99 was readily detected in control and AP-1γ siRNA samples; there was a 2.8-fold increase in intracellular β-CTF/C99 under AP-1γ-depleted conditions.
“in the presence of DAPT, β-CTF/C99 was readily detected in both control siRNA- and AP-1γ siRNA-treated samples. Moreover, there was a 2.8-fold increase in the level of intracellular β-CTF/C99 under AP-1γ–depleted conditions from that under control conditions (Figure 10, C and E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe steady-state distribution of BACE1-GFP in HeLa-BACE1-GFP cells is 8.5 ± 1.8% at the TGN, 30.6 ± 3.6% at recycling endosomes, 27.4 ± 2.7% at early endosomes, and 9.7 ± 2.5% at late endosomes/lysosomes.
“Quantitation of the steady-state distribution of BACE1-GFP revealed that 8.5 ± 1.8% localized with GCC88-marked TGN, 30.6 ± 3.6% localized with the Rab11-marked recycling endosomes, 27.4 ± 2.7% localized with the EEA1-marked early endosomes, and 9.7 ± 2.5% localized in the CD63-positive late endosomes/lysosomes (Figure 3, A and B).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAt 30 min, BACE1-SBP-GFP colocalization with the TGN marker decreased to 21.7 ± 4.1%, while early endosome colocalization increased to 16.7 ± 2.4% and recycling endosome colocalization was 11.7 ± 1.9%.
“At the 30-min time point, the level of BACE1-SBP-GFP that colocalized with the TGN marker had decreased to 21.7 ± 4.1%, whereas there was an increase in BACE1-SBP-GFP in the early endosome (16.7 ± 2.4%), marked by EEA1, and in the recycling endosome (11.7 ± 1.9%; Figure 1C; Supplemental Figure S1E).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataDepletion of Arf1 showed no change and Arf4 a minor increase in cell surface TfR compared with control.
“The depletion of Arf1 showed no change and that of Arf4 a minor increase in the level of cell surface TfR, compared with that in control cells (Supplemental Figure S6 B, and D).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataBACE1-SBP-GFP at the plasma membrane was first detected at 22 min after biotin addition, followed by a rapid increase in BACE1-SBP-GFP arriving at the plasma membrane.
“BACE1-SBP-GFP at the PM was first detected at 22 min after biotin addition followed by a rapid increase in BACE1-SBP-GFP arriving at the PM (Figure 2A and Supplemental Movie S1).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAfter 30 min of biotin addition, BACE1-SBP-GFP had begun to exit the TGN and some cargo had arrived at early and recycling endosomes.
“These data show that after 30 min of biotin addition, BACE1-SBP-GFP had begun to exit the TGN, and some cargo had arrived at the early and recycling endosomes.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataSecreted Aβ increased 2.7-fold, 4.5-fold, and 3.5-fold from Arf1-, Arf4-, and Arf1+4-depleted conditions, respectively, compared with control.
“there were 2.7-fold, 4.5-fold, and 3.5-fold increases in secreted Aβ from Arf1-, Arf4-, and Arf1+4-depleted conditions, respectively, as compared with control conditions (Figure 10B).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe majority of endogenous BACE1 in primary mouse cortical neurons colocalized with Rab11 and Rab4, with lower levels in late endosomes/lysosomes and Golgi.
“The majority of endogenous BACE1 colocalized with Rab11 and Rab4, and lower levels of endogenous BACE1 were detected in the late endosomes/lysosomes and Golgi (Figure 3, C and D).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe majority of BACE1-SBP-GFP had exited the TGN by 45-60 min and was not recycled back to the TGN.
“Thus, the majority of BACE1-SBP-GFP had exited the TGN by 45–60 min and was not recycled back to this compartment.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAP-1 depletion in primary neurons resulted in 1.9-fold increase in intracellular β-CTF/C99 and 3.1- and 3.7-fold increases in secreted Aβ40 and Aβ42.
“AP-1 depletion in primary neurons resulted in a 1.9-fold increase in the level of intracellular β-CTF/C99 and 3.1- and 3.7-fold increases in secreted Aβ40 and Aβ42, respectively.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataBACE1 was detected arriving at the plasma membrane 20 min after biotin addition, whereas it was first detected in recycling endosomes at 30 min.
“BACE1 was detected arriving at the plasma membrane 20 min after addition of biotin, whereas it was first detected in recycling endosomes at a later time point (30 min)”
Quote in the paperSubstantial claimMay combine two claims.
FindingreasoningTransduction efficiency was 35-50%, indicating depletion of AP-1 in GFP-positive neurons was ∼90%.
“Based on GFP-positive neurons, the transduction efficiency of the transduced neuronal population was 35–50%, indicating that the depletion of AP-1 in GFP-positive neurons was ∼90%.”
Quote in the paperSubstantial claim- Rests on an assumption: The observed phenotypes of AP-1, Arf1, and Arf4 depletion are due to specific knockdown of the targeted proteins and not off-target effects of siRNA or shRNA.
May combine two claims.
Interpretationown dataAP-1 is specifically required for the export of BACE1 from the TGN, and BACE1 and APP have distinct post-Golgi sorting machineries.
“Collectively, these results revealed that AP-1 is specifically required for the export of BACE1 from the TGN and that BACE1 and APP have distinct post-Golgi sorting machineries.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataDouble depletion of Arf1 and Arf4 did not result in a further increase in BACE1-GFP in the TGN compared with single knockdowns, indicating Arf1 and Arf4 are unlikely to have overlapping functions in regulating BACE1 export from the TGN.
“These data show that the double depletion of Arf1 and Arf4 did not result in a further increase in the level of BACE1-GFP in the TGN compared with single knockdowns, indicating that Arf1 and Arf4 are unlikely to have overlapping functions in regulating the export of BACE1 from the TGN.”
Quote in the paperSubstantial claimMay combine two claims.
Study design and conductown dataHeLa cell lines and the BACE1 RUSH system faithfully reflect the distribution of endogenous BACE1 in primary neurons.
“these data demonstrate that HeLa cell lines and the BACE1 RUSH system faithfully reflect the distribution of endogenous BACE1 in primary neurons.”
Quote in the paperSubstantial claimMay combine two claims.
Study design and conductown dataThere was no significant deviation between control, AP-1, and AP-4 siRNA groups in maximal Golgi intensity or time to maximum, indicating that BACE1-SBP-GFP expression level was similar and ER-to-Golgi trafficking of BACE1-SBP-GFP was not affected by siRNA treatment.
“There was no significant deviation between the groups, indicating that the level of BACE1-SBP-GFP expression was similar and the ER-to-Golgi trafficking of BACE1-SBP-GFP was not affected by the siRNA treatment (Figure 7, C and D).”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataAP-1 depletion specifically retains BACE1 but not APP in the TGN.
“AP-1 depletion specifically retains BACE1 but not APP in the TGN.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataAP-1, Arf1, and Arf4 are not required for trafficking of all membrane cargo to the PM; they are likely required for a subset of cargo including BACE1 from the TGN to the PM.
“These findings demonstrate that AP-1, Arf1, and Arf4 are not required for the trafficking of all membrane cargo to the PM; rather, these machineries are likely to be required for a subset of cargo, which includes BACE1, from the TGN to the PM.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAβ42 is more cytotoxic than Aβ40.
“Aβ42 is more cytotoxic than Aβ40 (Lane et al., 2018)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Lane et al., 2018 source
May combine two claims.
Premiseown dataThe DISLL motif is part of an acidic cluster (DDFADDISLL) in BACE1 cytoplasmic tail with properties similar to other acidic cluster sequences that associate with AP-1.
“the DISLL motif is part of an acidic cluster (DDFADDISLL) motif in the cytoplasmic tail BACE1 that has properties similar to those of other acidic cluster sequences in proteins that are known to associate with AP-1 (Table 2).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Table 2
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
InterpretationreasoningThere are multiple transport pathways to the PM, and the AP-1 pathway may be selective for a subset of membrane cargoes that includes BACE1.
“Thus, it is clear there are multiple transport pathways to the PM, and the AP-1 pathway may be selective for a subset of membrane cargoes that includes BACE1.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAll animal experiments were carried out in accordance with animal ethics guidelines approved by the Animal Ethics Committee, the University of Melbourne.
“All experiments carried out on animals (Ethics ID 1613960) were in accordance with animal ethics guidelines (approval number 1212502.1) approved by the Animal Ethics Committee, the University of Melbourne.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAll quantitative analyses were carried out on the indicated number of cells over three independent experiments.
“All analysis was carried out on the indicated number of cells over three independent experiments.”
- Also stated in: § Quantitative analyses · plain
“All analyses were carried out on the indicated number of cells over three independent experiments.”
Quote in the paperNot a substantial claim- Also stated in: § Quantitative analyses · plain
May combine two claims.
Interpretationown dataAP-1 depletion results in increased β-CTF/C99 but not α-CTF/C83, demonstrating that AP-1 depletion enhances amyloidogenic processing of APP by BACE1.
“Collectively, AP-1 depletion results in an increased level of β-CTF/C99, but not α-CTF/C83, demonstrating that AP-1 depletion enhances amyloidogenic processing of APP by BACE1.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningLoss of AP-1/Arf1/Arf4 transport machinery results in accumulation of BACE1 in TGN, causing loss of segregation of BACE1 from newly synthesized APP arriving at TGN.
“We propose that the loss of the AP-1/Arf1/Arf4 transport machinery results in accumulation of BACE1 in the TGN, which results in a loss in the segregation of BACE1 from newly synthesized APP arriving at the TGN (see Figure 11G).”
Quote in the paperSubstantial claimMay combine two claims.
Study design and conductcitationThe intracellular distribution of BACE1-SBP-GFP at an extended time point was very similar to steady-state distribution of BACE1 in stable or transiently transfected HeLa cells, with or without GFP tag, indicating SBP and GFP tags are unlikely to interfere with BACE1-SBP-GFP trafficking in RUSH.
“The intracellular distribution of BACE1-SBP-GFP at an extended time point was very similar to the steady-state distribution of BACE1 in either stable or transiently transfected HeLa cells, with or without a GFP tag (Chia et al., 2013), indicating that the SBP and GFP tags are unlikely to interfere with the trafficking of BACE1-SBP-GFP in the RUSH system.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Chia et al., 2013 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSecretion of Aβ peptide from the cell is proposed to occur through various anterograde trafficking pathways.
“The secretion of Aβ peptide from the cell is proposed to occur through various anterograde trafficking pathways (reviewed in Toh and Gleeson, 2016).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Toh and Gleeson, 2016 source
May combine two claims.
InterpretationreasoningSubstantial levels of BACE1 were present at the surface in depleted cells, which could be due to incomplete knockdown or AP-1-independent transport.
“substantial levels of BACE1 were present at the surface in these depleted cells, which could be due to either the incomplete knockdown of the transport machinery or transport by an AP-1–independent mechanism.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningConvergence between APP and BACE1 along anterograde pathway would be limited, minimizing amyloidogenic APP processing and Aβ production.
“Therefore, the convergence between APP and BACE1 along the anterograde pathway would be limited, which in turn would minimize the extent of amyloidogenic APP processing and Aβ production.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe HeLa-BACE1-GFP stable clones used were validated by immunofluorescence, immunoblotting, and flow cytometry.
“HeLa-BACE1-GFP stable clones were validated by immunofluorescence, immunoblotting, and flow cytometry.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataThe AP-1-/Arf1-/Arf4-dependent transport pathway is crucial for efficient export of BACE1 from the Golgi to the PM, which in turn limits processing of APP at the TGN.
“Collectively, our findings indicate that the AP-1-/Arf1-/Arf4-dependent transport pathway is crucial for the efficient export of BACE1 from the Golgi to the PM, which in turn limits the processing of APP at the TGN.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductnone givenLaser power and acquisition settings were chosen to avoid photobleaching and were identical for control and siRNA-treated samples.
“Laser power and acquisition settings were chosen to avoid photobleaching, and settings were identical for control and siRNA treated samples.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationAP-1B is important for transport of cargo from recycling endosomes to PM in a subset of polarized epithelial cells; AP-1B is absent in nonepithelial cells.
“AP-1B, which is a distinct isoform of AP-1 bearing a μ1B subunit, is important for transport of cargo from the recycling endosomes to the PM in a subset of polarized epithelial cells; however, AP-1B is absent in nonepithelial cells (see Tan and Gleeson, 2019a).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Tan and Gleeson, 2019a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Classified as probably not a substantial claim.
Study design and conductcitationThe current studies involved silencing in a stable cell line expressing only modest levels of BACE1-GFP, to minimize possibility of saturation of post-Golgi transport machinery.
“The current studies involved silencing of trafficking machinery in a stable cell line expressing only modest levels of BACE1-GFP, to minimize the possibility of saturation of the post-Golgi transport machinery (Chia et al., 2013).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Chia et al., 2013 source
May combine two claims.
InterpretationreasoningAP-1 is likely to interact with BACE1 via the acidic motif at the TGN and recruit BACE1 into a transport pathway directing it to the PM.
“Based on the findings in this paper, AP-1 is likely to interact with BACE1 via the acidic motif at the TGN and recruit this membrane cargo into a transport pathway that directs BACE1 to the PM.”
Quote in the paperSubstantial claim
The paper relies on this without support.
AP-1 is localized at the TGN.
“As AP-1 is localized at the TGN, we therefore investigated whether AP-1 may regulate the post-Golgi trafficking of BACE1.”
The paper relies on this without support.
The observed phenotypes of AP-1, Arf1, and Arf4 depletion are due to specific knockdown of the targeted proteins and not off-target effects of siRNA or shRNA.
“HeLa cells stably expressing BACE1-GFP were transfected with either control siRNA, AP-1γ siRNA, Arf1 siRNA, Arf4 siRNA, or Arf1+4 siRNAs for 72 h.”
“AP-1γ was depleted by 43–46% in neurons transduced with AP-1γ-shRNA1 and AP-1γ-shRNA2 lentivirus as compared with nontransduced neurons (Figure 11, A and B).”
The paper relies on this without support.
The BACE1 inhibitor C3 specifically inhibits BACE1 without affecting other proteases.
“treated with DMSO (carrier control), 2 μM DAPT, and/or 2 μM BACE1 inhibitor C3 in the last 16–20 h of transduction.”
The paper relies on this without support.
The DAPT treatment completely inhibits γ-secretase without affecting other cellular processes.
“treated with either DMSO (carrier control) or 250 nM γ-secretase inhibitor DAPT in the last 16 h of siRNA transfection.”
The paper relies on this without support.
The cell surface staining with anti-BACE1 antibodies in nonpermeabilized cells measures only cell surface BACE1.
“Cells were harvested and stained with anti-BACE1 antibodies on ice for 30 min and then fixed in 4% PFA, quenched in 50 mM NH4Cl, and blocked in 5% FCS/PBS without permeabilization.”
The paper relies on this without support.
The GFP-positive neurons represent the transduced population and their depletion level reflects the transduced neurons.
“Based on GFP-positive neurons, the transduction efficiency of the transduced neuronal population was 35–50%, indicating that the depletion of AP-1 in GFP-positive neurons was ∼90%.”
The paper relies on this without support.
Mouse anti-golgin-97 and rabbit anti-GCC88 antibodies are specific for their respective human antigens and do not cross-react with the mouse homologues.
“As mouse anti–golgin-97 and rabbit anti-GCC88 antibodies are specific for their respective human antigens, and do not cross-react with the mouse homologues, human autoantibodies to p230/golgin-245 were used for TGN staining in primary mouse cortical neurons.”
The paper relies on this without support.
Z-stack images are superior for image analysis.
“Owing to the superiority in image analysis of z-stack images, Imaris microscopy image analysis software (Oxford Instruments) was used over OBCOL to determine the colocalization of endogenous BACE1 with organelle markers in primary cortical neurons at steady-state.”
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.
Stable HeLa BACE1 distribution disagrees with Table 1
MajorThe prose assigns the stable HeLa BACE1-GFP cells values of 8.5%, 30.6%, 27.4%, and 9.7% across the four organelles. Table 1 instead lists 5.6%, 29.8%, 21.0%, and 9.1% for those cells; the prose values appear under the transient BACE1-SBP-GFP column.
“Quantitation of the steady-state distribution of BACE1-GFP revealed that 8.5 ± 1.8% localized with GCC88-marked TGN, 30.6 ± 3.6% localized with the Rab11-marked recycling endosomes, 27.4 ± 2.7% localized with the EEA1-marked early endosomes, and 9.7 ± 2.5% localized in the CD63-positive late endosomes/lysosomes”
“| HeLa cells (stable expression) BACE1-GFP | Primary mouse cortical neurons Endogenous BACE1 | | --- | --- | --- | --- | --- | | trans-Golgi network | 4.4% | 8.5% | 5.6% | 5.6% | | Recycling endosomes | 31.9% | 30.6% | 29.8% | 40.7% | | Early endosomes | 31.8% | 27.4% | 21.0% | 22.4% | | Late endosomes/lysosomes | 12.0% | 9.7% | 9.1% | 15.5% |”
Neuronal Aβ collection period is stated as both 16 and 20 hours
MinorFigure 11 says neuronal medium was collected 16 hours after it was changed, whereas the ELISA methods describe the mouse Aβ40 and Aβ42 measurements as using 20-hour conditioned medium.
“80 h after transduction the medium was changed and spent medium containing secreted Aβ was collected 16 h later”
“secreted mouse Aβ40 and Aβ42 levels in 20 h conditioned medium”
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Ye, X., & Cai, Q. (2014) · Cell Reports · doi:10.1016/j.celrep.2013.12.008 · Cited by 63 · see citing works
Toh, W. H., & Gleeson, P. A. (2016) · Biochemical Journal · doi:10.1042/bcj20160147 · Cited by 62 · see citing works
Self-citationYe, X., Feng, T., Tammineni, P., Chang, Q., Jeong, Y. Y., Margolis, D. J., Cai, H., Kusnecov, A. W., & Cai, Q. (2017) · Journal of Neuroscience · doi:10.1523/jneurosci.2851-16.2017 · Cited by 62 · see citing works
Toh, W. H., Chia, P. Z. C., Hossain, M. I., & Gleeson, P. A. (2018) · Molecular Biology of the Cell · doi:10.1091/mbc.e17-05-0270 · Cited by 61 · see citing works
Self-citationMolecular mechanism of intramembrane proteolysis by γ-secretase
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Presenilin‐1 Exists in Both Pre‐ and Post‐Golgi Compartments and Recycles Via COPI‐Coated Membranes
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Binding of cargo sorting signals to AP-1 enhances its association with ADP ribosylation factor 1–GTP
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Tan, J. Z. A., & Gleeson, P. A. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005222 · Cited by 52 · see citing works
Self-citationContribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting
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Automated organelle‐based colocalization in whole‐cell imaging
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Synchronizing Protein Transport in the Secretory Pathway
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Self-citationArl5b is a Golgi-localised small G protein involved in the regulation of retrograde transport
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The ADP-ribosylation factor 1 (Arf1) is involved in regulating copper uptake
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- Boncompain G, 2012, Curr Protoc Cell Biol
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Self-citation
- Authors
- Tan, J. Z. A., Fourriere, L., Wang, J., Perez, F., Boncompain, G., & Gleeson, P. A.
- Affiliations
- The University of Melbourne (AU)
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
- Centre National de la Recherche Scientifique (FR)
- Dynamics of Intracellular Organization Laboratory, Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, 75248 Paris, France
- Corresponding author
- Gleeson, Paul A.
- Venue
- Molecular Biology of the Cell
- Published
- 2020-01-01
- Volume
- 31
- Issue
- 1
- Pages
- 27-44
- ISSN
- 1059-1524 (ISSN-L)
- 1939-4586
- PMC
- PMC6938271
- OpenAlex
- W2990766601
- Semantic Scholar
- 735eae867e687a0fae4fbb4bc90e5cca26169ea8
- Cited by
- 37
- References
- 63
- Citations by year
- 2026: 7 · 2025: 3 · 2024: 8 · 2023: 5 · 2022: 5 · 2021: 6 · 2020: 3
- FWCI
- 2.39
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-sa
- Locations
- Molecular Biology of the Cell (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc-sa)
- Funders
- University of Melbourne
- Medical Research Council
- National Health and Medical Research Council (1163862)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Health Sciences › Medicine › Physiology › Lysosomal Storage Disorders Research
- Keywords
- BACE1, amyloid precursor protein, anterograde trafficking, Golgi network, AP-1, endocytosis, early endosomes, recycling endosomes, amyloid-beta production, APP processing, primary neurons, secretory pathway
- MeSH terms
- Alzheimer Disease, Cell Membrane, Cell Movement, Endocytosis, Golgi Apparatus, HeLa Cells, Humans, Neurons, Endosomes, Amyloid beta-Peptides, Aspartic Acid Endopeptidases, Amyloid beta-Protein Precursor, Protein Transport, trans-Golgi Network, Amyloid Precursor Protein Secretases
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 2026-11-04.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-04.
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