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Cited by 21Cholesterol and Lipid MetabolismLipoproteins and Cardiovascular HealthLipid metabolism and disorders

The DOI matches its Crossref record; 53 of the 54 references it cites were found in a registry or an index; 24 of the 56 sources its claims cite were checked for support.

Phosphatidylinositol-(4,5)-Bisphosphate Regulates Plasma Cholesterol Through LDL (Low-Density Lipoprotein) Receptor Lysosomal Degradation

Open access
Qin, Yuanyuan, Ting, Flora, Kim, Mee J., Strelnikov, Jacob, Harmon, Joseph, Gao, Feng, Dose, Andrea, Teng, Ba-Bie, Alipour, Mohsen Amir, Yao, Zemin, Crooke, Rosanne, Krauss, Ronald M., Medina, Marisa W.·2020·Arteriosclerosis, Thrombosis, and Vascular Biology
DOI 10.1161/atvbaha.120.314033PMC PMC7197750
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Abstract

Objective: TMEM55B (transmembrane protein 55B) is a phosphatidylinositol-(4,5)-bisphosphate (PI[4,5]P 2 ) phosphatase that regulates cellular cholesterol, modulates LDLR (low-density lipoprotein receptor) decay, and lysosome function. We tested the effects of Tmem55b knockdown on plasma lipids in mice and assessed the roles of LDLR lysosomal degradation and change in (PI[4,5]P 2 ) in mediating these effects. Approach and Results: Western diet–fed C57BL/6J mice were treated with antisense oligonucleotides against Tmem55b or a nontargeting control for 3 to 4 weeks. Hepatic Tmem55b transcript and protein levels were reduced by ≈70%, and plasma non-HDL (high-density lipoprotein) cholesterol was increased ≈1.8-fold ( P <0.0001). Immunoblot analysis of fast protein liquid chromatography (FPLC) fractions revealed enrichment of ApoE-containing particles in the LDL size range. In contrast, Tmem55b knockdown had no effect on plasma cholesterol in Ldlr −/− mice. In primary hepatocytes and liver tissues from Tmem55b knockdown mice, there was decreased LDLR protein. In the hepatocytes, there was increased lysosome staining and increased LDLR-lysosome colocalization. Impairment of lysosome function (incubation with NH 4 Cl or knockdown of the lysosomal proteins LAMP1 or RAB7 ) abolished the effect of TMEM55B knockdown on LDLR in HepG2 (human hepatoma) cells. Colocalization of the recycling endosome marker RAB11 (Ras-related protein 11) with LDLR in HepG2 cells was reduced by 50% upon TMEM55B knockdown. Finally, knockdown increased hepatic PI(4,5)P 2 levels in vivo and in HepG2 cells, while TMEM55B overexpression in vitro decreased PI(4,5)P 2 . TMEM55B knockdown decreased, whereas overexpression increased, LDL uptake in HepG2 cells. Notably, the TMEM55B overexpression effect was reversed by incubation with PI(4,5)P 2. Conclusions: These findings indicate a role for TMEM55B in regulating plasma cholesterol levels by affecting PI(4,5)P 2 -mediated LDLR lysosomal degradation.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

Hepatic Tmem55b knockdown in Western diet-fed mice raises plasma non-HDL cholesterol via an LDLR-dependent mechanism, with increased PI(4,5)P2 and enhanced lysosomal LDLR degradation. The findings link TMEM55B/PI(4,5)P2 to LDLR lysosomal trafficking and plasma cholesterol regulation.

Key findings

  • ASO-mediated hepatic Tmem55b knockdown reduced Tmem55b transcript and protein by ~70% and increased plasma non-HDL cholesterol ~1.8-fold (p<0.0001) in Western diet-fed C57BL/6J mice.
  • Tmem55b knockdown had no effect on plasma cholesterol in Ldlr−/− mice, and hepatic LDLR protein was reduced by 48% in T2 ASO-treated animals (p<0.05).
  • Tmem55b knockdown increased hepatic PI(4,5)P2 levels by 94% and increased LDLR-lysosome colocalization; LDLR-RAB11 colocalization was reduced by 50%.
  • TMEM55B overexpression increased LDL uptake in HepG2 cells, and this effect was reversed by incubation with PI(4,5)P2-containing liposomes.

Methods

  • Western diet-fed C57BL/6J and Ldlr−/− male and female mice were treated with antisense oligonucleotides against Tmem55b or non-targeting control for 3–4 weeks; plasma lipids, FPLC fractions, ion mobility, hepatic lipids, and PCSK9 were measured.
  • Primary hepatocytes and HepG2 cells were used with siRNA knockdown or overexpression of TMEM55B, plus knockdown of LAMP1, RAB7, or LDLRAP1, NH4Cl treatment, immunofluorescence/confocal microscopy, flow cytometry for Dil-LDL uptake, co-immunoprecipitation, and PI(4,5)P2 ELISA.
  • Statistical comparisons used t-tests or one-way ANOVA with Tukey’s post hoc test; p<0.05 was considered significant.

Limitations

  • The paper states that Western blot analysis may not be sufficiently sensitive to detect small increases in apoB and/or apoAI levels, and that further study is required to determine whether LDLR-dependent effects involve altered apoB/apoE secretion, uptake, or both.
  • The paper notes that the mechanism underlying TMEM55B specificity for LDLR is unclear, as no direct TMEM55B-LDLR binding or modulation of PCSK9, COMMD1, or MYLIP/IDOL was found; it also did not directly test phosphatase activity.
  • Evident from the text: the main in vivo evidence is from mouse models and cell lines, with no human clinical data; ASO treatment also reduced Tmem55b transcript in muscle and adipose tissue, so extrahepatic contributions are not fully excluded.

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

Integrity signals

Registry

Crossref · 10.1161/atvbaha.120.314033

Cites

53 of 53 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

24 of 56 cited sources checked · 11 supported · 1 flagged · accuracy not yet measured

  • Premisecitation

    TMEM55B knockdown in human hepatoma cells reduced total LDLR protein level.

    “We found that TMEM55B knockdown in human hepatoma cells decreased intracellular cholesterol level, reduced total LDLR protein level, impaired LDL uptake, and increased LDLR protein degradation6.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [6] Lo Surdo P, Bottomley MJ, Calzetta A, Settembre EC, Cirillo A, Pandit S, Ni YG, Hubbard B, Sitlani A and Carfi A. Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. EMBO Rep. 2011; 12: 1300– 5. 22081141 PMC3245695 source

      The Methods describe experiments on PCSK9 and LDLR proteins, and the Results and Discussion propose PCSK9-mediated LDLR downregulation; neither addresses TMEM55B knockdown in human hepatoma cells. Searches for TMEM55B knockdown and silencing found no passage reporting a change in total LDLR protein. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Premisecitation

    TMEM55B knockdown in human hepatoma cells decreased intracellular cholesterol level.

    “We found that TMEM55B knockdown in human hepatoma cells decreased intracellular cholesterol level, reduced total LDLR protein level, impaired LDL uptake, and increased LDLR protein degradation6.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [6] Lo Surdo P, Bottomley MJ, Calzetta A, Settembre EC, Cirillo A, Pandit S, Ni YG, Hubbard B, Sitlani A and Carfi A. Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. EMBO Rep. 2011; 12: 1300– 5. 22081141 PMC3245695 source

      The Methods describe experiments on PCSK9 and LDLR proteins, and the Results and Discussion address PCSK9-mediated LDLR downregulation. Searches for TMEM55B knockdown, hepatoma cells, and intracellular cholesterol found no passage in our copy reporting the claimed decrease. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    PI(4,5)P2 may modulate LDLR through its effect on LDLR lysosomal decay.

    “Inhibition of lysosome activity increases cell surface LDLRs10, suggesting that PI(4,5)P2 may modulate LDLR through its effect on LDLR lysosomal decay.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [10] Yan H, Ma YL, Gui YZ, Wang SM, Wang XB, Gao F and Wang YP. MG132, a proteasome inhibitor, enhances LDL uptake in HepG2 cells in vitro by regulating LDLR and PCSK9 expression. Acta Pharmacol Sin. 2014; 35: 994– 1004. 25042549 PMC4125719 source
  • Premisecitation

    TMEM55B knockdown in human hepatoma cells increased LDLR protein degradation.

    “We found that TMEM55B knockdown in human hepatoma cells decreased intracellular cholesterol level, reduced total LDLR protein level, impaired LDL uptake, and increased LDLR protein degradation6.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [6] Lo Surdo P, Bottomley MJ, Calzetta A, Settembre EC, Cirillo A, Pandit S, Ni YG, Hubbard B, Sitlani A and Carfi A. Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. EMBO Rep. 2011; 12: 1300– 5. 22081141 PMC3245695 source

      The Methods describe experiments on PCSK9 and LDLR proteins, and the Results and Discussion propose a mechanism for PCSK9-mediated LDLR degradation. Searches for TMEM55B knockdown and hepatoma-cell LDLR degradation found no passage addressing the claimed experiment; the PCSK9 mechanism does not establish its result. (LLM, conf=0.72)

      Experimental — accuracy not yet measured
  • Premisecitation

    TMEM55B modulates lysosome function.

    “TMEM55B is localized to the late endosome and lysosome7, and has been shown to impact lysosome function23, 28.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [23] Hashimoto Y, Shirane M and Nakayama KI. TMEM55B contributes to lysosomal homeostasis and amino acid-induced mTORC1 activation. Genes Cells. 2018; 23: 418– 434. 29644770 source
    • cites [28] Willett R, Martina JA, Zewe JP, Wills R, Hammond GRV and Puertollano R. TFEB regulates lysosomal positioning by modulating TMEM55B expression and JIP4 recruitment to lysosomes. Nat Commun. 2017; 8: 1580. 29146937 PMC5691037 source
  • Probably not a substantial claim. 24
  • It may state two separate claims as one. 23
  • The quote only partly states this claim. 1

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Intracellular localization of lysosomes regulates their ability to interact and fuse with vesicles such as autophagosomes or endosomes.

    “Notably, intracellular localization of lysosomes regulates their ability to interact and fuse with vesicles such as autophagosomes or endosomes31, 32, 47, 48.”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [31] Johnson DE, Ostrowski P, Jaumouille V and Grinstein S. The position of lysosomes within the cell determines their luminal pH. J Cell Biol. 2016; 212: 677– 92. 26975849 PMC4792074 source

      In Results, “Interaction of lysosomes with the plasma membrane and with endosomes” (Fig. 5; page unavailable), moving lysosomes toward the cell periphery produced no significant difference in the rate of endosome-to-lysosome fusion. That finding runs contrary to the claim that lysosome location regulates fusion with endosomes. The paper does not establish whether location affects fusion with autophagosomes. (LLM, conf=0.84)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [32] Pu J, Guardia CM, Keren-Kaplan T and Bonifacino JS. Mechanisms and functions of lysosome positioning. J Cell Sci. 2016; 129: 4329– 4339. 27799357 PMC5201012 source

      The Autophagy section states that juxtanuclear lysosome positioning facilitates fusion with autophagosomes and that disrupting this positioning reduces the probability of fusion. Figure 1 links lysosome movement to endocytic degradation, but the passages do not establish that positioning regulates lysosome fusion with endosomes specifically. Page numbers were not available in our copy. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [47] Korolchuk VI, Saiki S, Lichtenberg M, Siddiqi FH, Roberts EA, Imarisio S, Jahreiss L, Sarkar S, Futter M, Menzies FM, O’Kane CJ, Deretic V and Rubinsztein DC. Lysosomal positioning coordinates cellular nutrient responses. Nat Cell Biol. 2011; 13: 453– 60. 21394080 PMC3071334 source

      The Abstract states that lysosome positioning influences autophagosome–lysosome fusion rates and that perinuclear clustering facilitates fusion. The passages from our copy do not establish that lysosome positioning regulates fusion with endosomes; their mention of endosomal markers does not address that interaction. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [48] Pous C and Codogno P. Lysosome positioning coordinates mTORC1 activity and autophagy. Nat Cell Biol. 2011; 13: 342– 4. 21460804 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Other PI(4,5)P2 phosphatases and kinases impact trafficking and degradation of the epidermal growth factor receptor and the transferrin receptor.

    “Notably, other PI(4,5)P2 phosphatases (e.g. Lowe oculocerebrorenal syndrome protein (OCRL), also known as INPP5F) and kinases have been reported to impact trafficking and degradation of the epidermal growth factor receptor and the transferrin receptor, which are recycled and degraded in a manner similar to LDLR11–13.”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [11] Vicinanza M, Di Campli A, Polishchuk E, Santoro M, Di Tullio G, Godi A, Levtchenko E, De Leo MG, Polishchuk R, Sandoval L, Marzolo MP and De Matteis MA. OCRL controls trafficking through early endosomes via PtdIns4,5P(2)-dependent regulation of endosomal actin. EMBO J. 2011; 30: 4970– 85. 21971085 PMC3242071 source

      The Results section reports that OCRL depletion slows transferrin-receptor recycling and delays EGFR degradation. It also reports that reducing PIP5K levels affects transferrin uptake, but does not show a kinase effect on EGFR degradation or transferrin-receptor degradation. The cited paper therefore supports the trafficking claim, not all of its stated degradation effects. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [12] Ketel K, Krauss M, Nicot AS, Puchkov D, Wieffer M, Muller R, Subramanian D, Schultz C, Laporte J and Haucke V. A phosphoinositide conversion mechanism for exit from endosomes. Nature. 2016; 529: 408– 12. 26760201 source

      Section 1.4 reports that the kinase PI4K2α affects EGFR endosomal trafficking and TfR recycling, and section 1.2.2 describes a role for the PI(4,5)P2 phosphatase OCRL in endocytic membrane traffic. The copy does not establish that OCRL affects EGFR or TfR trafficking or degradation specifically. Its enzyme table also lists INPP5F as Sac2, not OCRL, while PI4K2α synthesizes PI(4)P rather than PI(4,5)P2. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [13] Choi S, Thapa N, Tan X, Hedman AC and Anderson RA. PIP kinases define PI4,5P(2)signaling specificity by association with effectors. Biochim Biophys Acta. 2015; 1851: 711– 23. 25617736 PMC4380618 source

      Section 4.1 reports that PIP kinase knockdown inhibits transferrin receptor endocytosis, and section 4.3 describes PIPKIγi5-dependent sorting of the EGF receptor toward the lysosomal pathway. The cited paper thus supports the kinase-related trafficking claim, but the passages do not establish an OCRL phosphatase role or degradation of the transferrin receptor. (LLM, conf=0.85)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Premisecitation

    PI(4,5)P2 impacts endocytosis, endosome trafficking, and lysosome function and reformation.

    “PI(4,5)P2 has been shown to impact many subcellular processes including endocytosis, endosome trafficking, and importantly, lysosome function and reformation8, 9.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [8] Tan X, Thapa N, Choi S and Anderson RA. Emerging roles of PtdIns(4,5)P2--beyond the plasma membrane. J Cell Sci. 2015; 128: 4047– 56. 26574506 PMC4712784 source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [9] Pryor PR, Mullock BM, Bright NA, Gray SR and Luzio JP. The role of intraorganellar Ca(2+) in late endosome-lysosome heterotypic fusion and in the reformation of lysosomes from hybrid organelles. J Cell Biol. 2000; 149: 1053– 62. 10831609 PMC2174832 source

      The Introduction describes Ca2+-dependent late endosome–lysosome fusion and lysosome reformation, but does not attribute either process to PI(4,5)P2. Searches for PI(4,5)P2, phosphatidylinositol, and phosphoinositides found no passage in our copy establishing its effects on the claimed processes. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    PIKfyve is vital in early embryonic development, and homozygous PIKfyve−/− animals are not viable or die shortly after birth.

    “PIKfyve is vital in early embryonic development, and homozygous PIKfyve−/− animals are not viable or die shortly after birth39.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [39] Ikonomov OC, Sbrissa D, Delvecchio K, Xie Y, Jin JP, Rappolee D and Shisheva A. The phosphoinositide kinase PIKfyve is vital in early embryonic development: preimplantation lethality of PIKfyve−/− embryos but normality of PIKfyve+/− mice. J Biol Chem. 2011; 286: 13404– 13. 21349843 PMC3075686 source

      The Results section, “Homozygous pikfyve Gene Deletion Is Lethal at Preimplantation Embryo Stage,” supports that homozygous PIKfyve-null mice are not viable; the Discussion also identifies preimplantation embryonic death. The source does not support the alternative that they die shortly after birth: none of the day 1–2 neonates tested had the knockout genotype. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim.

    Premisecitation

    Lysosome activity depends on its position within the cell.

    “Lysosome activity is dependent on its position within the cell31, 32.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [31] Johnson DE, Ostrowski P, Jaumouille V and Grinstein S. The position of lysosomes within the cell determines their luminal pH. J Cell Biol. 2016; 212: 677– 92. 26975849 PMC4792074 source
    • cites [32] Pu J, Guardia CM, Keren-Kaplan T and Bonifacino JS. Mechanisms and functions of lysosome positioning. J Cell Sci. 2016; 129: 4329– 4339. 27799357 PMC5201012 source

  • It may state two separate claims as one.

    Premisecitation

    TMEM55B knockdown in human hepatoma cell lines alters LDLR protein decay and cell surface LDLR protein levels.

    “We previously reported that TMEM55B knockdown in human hepatoma cell lines alters LDLR protein decay and cell surface LDLR protein levels5.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [5] Medina MW, Bauzon F, Naidoo D, Theusch E, Stevens K, Schilde J, Schubert C, Mangravite LM, Rudel LL, Temel RE, Runz H and Krauss RM. Transmembrane protein 55B is a novel regulator of cellular cholesterol metabolism. Arterioscler Thromb Vasc Biol. 2014; 34: 1917– 23. 25035345 PMC4141484 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    In the late endosome where pH decreases, LDLR disassociates from LDL, and then is either recycled back to the plasma membrane for reuse, or targeted to the lysosome for decay.

    “In the late endosome where the pH value decreases, LDLR disassociates from LDL, and then is either recycled back to the plasma membrane for reuse, or targeted to the lysosome for decay46.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [46] Goldstein JL and Brown MS. The LDL receptor. Arterioscler Thromb Vasc Biol. 2009; 29: 431– 8. 19299327 PMC2740366 source

      In “Receptor-Mediated Endocytosis: Origin of the Concept” (page unavailable), the paper says that LDL receptors dissociate from their ligands as pH falls in endosomes, then return to the cell surface for reuse. It does not specify late endosomes or describe LDL receptors being sent to lysosomes for degradation; the lysosomal degradation discussed in “The LDL Receptor Pathway and Cholesterol Homeostasis” concerns LDL, not its receptor. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    TMEM55B was first identified as a PI(4,5)P2 phosphatase by Ungewickell et al, but a recent study by Willett et al failed to detect PI(4,5)P2 hydrolysis activity of TMEM55B.

    “Although TMEM55B was first identified as a PI(4,5)P2 phosphatase by Ungewickell et al7, a recent study by Willett et al failed to detect PI(4,5)P2 hydrolysis activity of TMEM55B28.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [7] Ungewickell A, Hugge C, Kisseleva M, Chang SC, Zou J, Feng Y, Galyov EE, Wilson M and Majerus PW. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Proc Natl Acad Sci U S A. 2005; 102: 18854– 9. 16365287 PMC1323219 source
    • cites [28] Willett R, Martina JA, Zewe JP, Wills R, Hammond GRV and Puertollano R. TFEB regulates lysosomal positioning by modulating TMEM55B expression and JIP4 recruitment to lysosomes. Nat Commun. 2017; 8: 1580. 29146937 PMC5691037 source

  • It may state two separate claims as one.

    Findingown data

    There were no differences in plasma total cholesterol, HDL cholesterol, or non-HDL cholesterol between T1, T2, and T1+T2 ASO treatments.

    “There were no differences in any of these measurements between T1, T2, and T1+T2 ASO treatments (Fig. SIVB).”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    In Ldlr−/− mice treated with T1+T2 or NTC ASOs weekly for four weeks, Tmem55b mRNA was reduced by 85% and 62%, and TMEM55B protein by 88% and 78% in males and females, respectively.

    “After four weeks Tmem55b mRNA was reduced by 85% and 62%, and TMEM55B protein by 88% and 78% in males and females, respectively, (Fig. 4A, 4B, 4D, 4E).”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    Tmem55b knockdown did not change hepatic total cholesterol, free cholesterol or triglyceride levels.

    “Tmem55b knockdown did not alter plasma triglyceride levels in either male or female mice (Fig. 2B, 2D) nor did it change hepatic total cholesterol, free cholesterol or triglyceride levels, Fig. SIVD.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    TMEM55B knockdown increases PI(4,5)P2-LAMP1 colocalization in HepG2 cells, and overexpression has the opposite effect.

    “we found that TMEM55B knockdown increased PI(4,5)P2 -LAMP1 colocalization in HepG2 cells (Fig. 7B), with opposite effects observed after overexpression (Fig. 7D).”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    In Ldlr−/− mice, there were no statistically significant differences in plasma lipid levels or lipoprotein particle concentrations between Tmem55b knockdown and NTC mice in either sex.

    “Importantly, no statistically significant differences in plasma lipid levels or lipoprotein particle concentrations were observed between Tmem55b knockdown and NTC mice in either sex (Fig. 4C, 4F, SIXA–D).”
    • Also stated in: § Approach and Results: · plain
      “In contrast, Tmem55b knockdown had no effect on plasma cholesterol in Ldlr−/− mice.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Tmem55b knockdown did not alter whole body, liver or gonadal adipose weights, or whole-body fat mass, lean mass or adiposity in male or female mice.

    “Tmem55b knockdown did not alter whole body, liver or gonadal adipose weights (Fig. 2A, 2C, SIIA–D) in either male or female mice, or measures of whole-body fat mass, lean mass or adiposity as quantified by DEXA (Fig. SIIIA–C).”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    TMEM55B knockdown increases PI(4,5)P2 levels in HepG2 cells and primary murine hepatocytes, consistent with independent results in Raw 264.7 macrophages.

    “we found that TMEM55B knockdown increased PI(4,5)P2 levels in HepG2 cells and in primary murine hepatocytes, consistent with independent results observed in Raw 264.7 macrophages by Kailash et al21.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [21] Gulshan K, Brubaker G, Conger H, Wang S, Zhang R, Hazen SL and Smith JD. PI(4,5)P2 Is Translocated by ABCA1 to the Cell Surface Where It Mediates Apolipoprotein A1 Binding and Nascent HDL Assembly. Circ Res. 2016; 119: 827– 38. 27514935 PMC5026623 source

  • It may state two separate claims as one.

    Findingown data

    TMEM55B overexpression has opposite effects on LAMP1/lysotracker staining, lysosomal clustering, LDLR levels, and LDLR-lysosome colocalization.

    “We have shown here that TMEM55B knockdown increased LAMP1 and lysotracker staining, stimulated lysosomal clustering, reduced LDLR levels and increased LDLR-lysosome colocalization, with opposite effects observed after TMEM55B overexpression.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Upon binding of plasma LDLs, cell surface LDLRs are internalized and transported to endosomes, where low pH causes LDLR-LDL dissociation.

    “Upon binding of plasma LDLs, cell surface LDLRs are internalized and transported to endosomes, where low pH causes LDLR-LDL dissociation1.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [1] Brown MS and Goldstein JL. A receptor-mediated pathway for cholesterol homeostasis. Science. 1986; 232: 34– 47. 3513311 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    LDLRs are either transported to lysosomes for degradation or recycled to the cell surface for reuse.

    “LDLRs are then either transported to lysosomes for degradation or recycled to the cell surface for reuse2.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [2] Gao F, Ihn HE, Medina MW and Krauss RM. A common polymorphism in the LDL receptor gene has multiple effects on LDL receptor function. Hum Mol Genet. 2013; 22: 1424– 31. 23297366 PMC3596853 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    TMEM55B is a late endosome/lysosome-localized type I phosphatase that converts PI(4,5)P2 to PI5P.

    “TMEM55B was originally reported to be a late endosome/lysosome-localized type I phosphatase that converts phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] to PI5P7.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [7] Ungewickell A, Hugge C, Kisseleva M, Chang SC, Zou J, Feng Y, Galyov EE, Wilson M and Majerus PW. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Proc Natl Acad Sci U S A. 2005; 102: 18854– 9. 16365287 PMC1323219 source

  • Probably not a substantial claim.

    Premisecitation

    TMEM55B is a phosphatase that catalyzes the conversion of PI(4,5)P2 to PI5P.

    “TMEM55B was originally reported to be a phosphatase that catalyzes the conversion of PI(4,5)P2 to PI5P7.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [7] Ungewickell A, Hugge C, Kisseleva M, Chang SC, Zou J, Feng Y, Galyov EE, Wilson M and Majerus PW. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Proc Natl Acad Sci U S A. 2005; 102: 18854– 9. 16365287 PMC1323219 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    Grubb's test for outliers was used to identify statistical outliers from triplicate qPCR values.

    “Grubb’s test for outliers was used to identify statistical outliers from the triplicate values.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premiseown data

    TMEM55B modulates LDLR decay (previously reported).

    “We had previously reported that TMEM55B modulates LDLR decay”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    PIKfyve is a phosphoinositide kinase reported to be the major enzyme for generating the PI5P pool.

    “PIKfyve is a phosphoinositide kinase reported to be the major enzyme for generating the PI5P pool38.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [38] Zolov SN, Bridges D, Zhang Y, Lee WW, Riehle E, Verma R, Lenk GM, Converso-Baran K, Weide T, Albin RL, Saltiel AR, Meisler MH, Russell MW and Weisman LS. In vivo, Pikfyve generates PI(3,5)P2, which serves as both a signaling lipid and the major precursor for PI5P. Proc Natl Acad Sci U S A. 2012; 109: 17472– 7. 23047693 PMC3491506 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Plasma membrane PI(4,5)P2 promotes ApoA1-ABCA1 mediated lipid efflux from macrophages.

    “Plasma membrane PI(4,5)P2 has been shown to promote ApoA1-ABCA1 mediated lipid efflux from macrophages21”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Gulshan K, Brubaker G, Conger H, Wang S, Zhang R, Hazen SL and Smith JD. PI(4,5)P2 Is Translocated by ABCA1 to the Cell Surface Where It Mediates Apolipoprotein A1 Binding and Nascent HDL Assembly. Circ Res. 2016; 119: 827– 38. 27514935 PMC5026623 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    All imaging parameters and analyzing settings remained the same for all data acquisition within one experiment.

    “All imaging parameters and analyzing settings remained the same for all data acquisition within one experiment.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim.

    Premisecitation

    LDLR decay typically occurs after internalization, when LDLRs from the cell surface can be delivered to the lysosome for degradation or recycled back to the cell surface.

    “LDLR decay typically occurs after internalization, when LDLRs from the cell surface can be delivered to the lysosome for degradation or recycled back to the cell surface29.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [29] Maxfield FR and McGraw TE. Endocytic recycling. Nat Rev Mol Cell Biol. 2004; 5: 121– 32. 15040445 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductnone given

    Each experiment was repeated at least three times, with 3-6 replicates per assay.

    “At least 3 experiments were conducted with 3–6 replicates per assay, with specific replicate numbers indicated in figure legends.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Tmem55b regulates plasma cholesterol levels in vivo, an effect dependent on LDLR, and functions through PI(4,5)P2-mediated LDLR lysosomal degradation.

    “Here we report that Tmem55b also regulates plasma cholesterol levels in vivo, an effect that is dependent on LDLR, and functions through PI(4,5)P2-mediated LDLR lysosomal degradation.”
    • Also stated in: § DISCUSSION · boosted
      “In summary, we have shown that TMEM55B contributes to the dynamic regulation of lysosomal LDLR degradation and recycling, that this effect is mediated by PI(4,5)P2, and that it ultimately impacts plasma non-HDL cholesterol and apoE-enriched lipoprotein levels.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    PIP4K2A converts PI5P to PI(4,5)P2 and has been reported to regulate intracellular cholesterol transport through PI(4,5)P2.

    “Phosphatidylinositol 5-phosphate 4-kinase type-2 α (PIP4K2A), which converts PI5P to PI(4,5)P2, has been reported to regulate intracellular cholesterol transport through PI(4,5)P240.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Hu A, Zhao XT, Tu H, Xiao T, Fu T, Wang Y, Liu Y, Shi XJ, Luo J and Song BL. PIP4K2A regulates intracellular cholesterol transport through modulating PI(4,5)P2 homeostasis. J Lipid Res. 2018; 59: 507– 514. 29353240 PMC5832930 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    TMEM55B was identified as a novel regulator of cellular cholesterol metabolism through gene expression profiling and in vitro studies.

    “TMEM55B was identified as a novel regulator of cellular cholesterol metabolism through gene expression profiling and in vitro studies5.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [5] Medina MW, Bauzon F, Naidoo D, Theusch E, Stevens K, Schilde J, Schubert C, Mangravite LM, Rudel LL, Temel RE, Runz H and Krauss RM. Transmembrane protein 55B is a novel regulator of cellular cholesterol metabolism. Arterioscler Thromb Vasc Biol. 2014; 34: 1917– 23. 25035345 PMC4141484 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    When circulating LDL binds to LDLR, the LDLR-LDL complex is internalized in a clathrin-coated pit on the plasma membrane and trafficked through the endo/lysosomal pathway.

    “When circulating LDL binds to LDLR, the LDLR-LDL complex is internalized in a clathrin-coated pit on the plasma membrane and trafficked through the endo/lysosomal pathway45.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [45] Yamamoto T, Davis CG, Brown MS, Schneider WJ, Casey ML, Goldstein JL and Russell DW. The human LDL receptor: a cysteine-rich protein with multiple Alu sequences in its mRNA. Cell. 1984; 39: 27– 38. 6091915 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    TMEM55B impacts lysosome positioning in AREP-19 and HeLa cells.

    “very recently TMEM55B was reported to impact lysosome positioning in AREP-19 and HeLa cells28.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [28] Willett R, Martina JA, Zewe JP, Wills R, Hammond GRV and Puertollano R. TFEB regulates lysosomal positioning by modulating TMEM55B expression and JIP4 recruitment to lysosomes. Nat Commun. 2017; 8: 1580. 29146937 PMC5691037 source

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    LDLR can regulate apoB and apoE secretion as well as uptake.

    “Since LDLR can regulate apoB and apoE secretion as well as uptake42, 43”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [42] Blasiole DA, Oler AT and Attie AD. Regulation of ApoB secretion by the low density lipoprotein receptor requires exit from the endoplasmic reticulum and interaction with ApoE or ApoB. J Biol Chem. 2008; 283: 11374– 81. 18272520 PMC2431081 source
    • cites [43] Nassir F, Xie Y, Patterson BW, Luo J and Davidson NO. Hepatic secretion of small lipoprotein particles in apobec-1−/− mice is regulated by the LDL receptor. J Lipid Res. 2004; 45: 1649– 59. 15145984 source

      Checked before — its earlier verdict is held back until a new check runs.

  • It may state two separate claims as one.

    Interpretationown data

    TMEM55B regulates LDLR activity and plasma non-HDLc through changes in PI(4,5)P2.

    “Together, these results support the likelihood that TMEM55B regulates LDLR activity and thus plasma non-HDLc through changes in PI(4,5)P2.”
    • Also stated in: § DISCUSSION · hedged
      “Our finding that the effect of TMEM55B overexpression on LDL uptake is reversed by addition of exogenous PI(4,5)P2 provides evidence that TMEM55B regulates LDLR lysosomal degradation through PI(4,5)P2.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    PI(4,5)P2 is primarily concentrated at the plasma membrane but is also found on lysosomes.

    “Although PI(4,5)P2 is primarily concentrated at the plasma membrane, it is also found on lysosomes50.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [50] Hammond GR, Machner MP and Balla T. A novel probe for phosphatidylinositol 4-phosphate reveals multiple pools beyond the Golgi. J Cell Biol. 2014; 205: 113– 26. 24711504 PMC3987136 source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Lysosomal PI(4,5)P2 serves as a signaling molecule that regulates traffic from the lysosome and mediates lysosome reformation after autophagosome fusion.

    “Lysosomal PI(4,5)P2 serves as an important signaling molecule that regulates traffic from the lysosome51 and that mediates lysosome reformation after autophagosome fusion52.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [51] Sridhar S, Patel B, Aphkhazava D, Macian F, Santambrogio L, Shields D and Cuervo AM. The lipid kinase PI4KIIIbeta preserves lysosomal identity. EMBO J. 2013; 32: 324– 39. 23258225 PMC3567500 source
    • cites [52] Rong Y, Liu M, Ma L, Du W, Zhang H, Tian Y, Cao Z, Li Y, Ren H, Zhang C, Li L, Chen S, Xi J and Yu L. Clathrin and phosphatidylinositol-4,5-bisphosphate regulate autophagic lysosome reformation. Nat Cell Biol. 2012; 14: 924– 34. 22885770 source

  • Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.

    Interpretationnone given

    The present findings highlight that there are as yet unidentified molecular players that impact LDLR regulation and function.

    “However, the present findings highlight that there are as yet unidentified molecular players that impact LDLR regulation and function.”
    Quote in the paperNot a substantial claim
37 of 37

  • The paper relies on this without support.

    Hepatic LDLRs play an important role in determining plasma cholesterol levels and the risk for cardiovascular disease.

    “Hepatic low-density lipoprotein receptors (LDLRs), play an important role in determining plasma cholesterol levels and the risk for cardiovascular disease (CVD).”

  • The paper relies on this without support.

    The three conditions used to impair lysosome function (NH4Cl treatment, LAMP1 knockdown, Rab7 knockdown) effectively block lysosomal degradation of LDLR in HepG2 cells.

    “We next tested the effects of TMEM55B knockdown on LDLR levels under three conditions of impaired lysosome function in HepG2 cells: i) treatment with NH4Cl, which prevents acidification of intracellular vesicles, leading to dysfunction of the lysosome hydrolytic enzymes33, ii) knockdown of LAMP1, or iii) knockdown of Rab7, a late endosome/lysosome protein.”

  • The paper relies on this without support.

    PIKfyve+/− mice have reduced PI5P levels.

    “PIKfyve is a phosphoinositide kinase reported to be the major enzyme for generating the PI5P pool38. PIKfyve is vital in early embryonic development, and homozygous PIKfyve−/− animals are not viable or die shortly after birth39. Therefore, we tested whether plasma lipids differed in Western diet-fed PIKFyve+/− versus littermate controls and found no differences (Fig. SXVB).”
3 of 3

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?

  • TMEM55B regulates autophagosome-lysosome fusion, lysosomal repair, and TFE3 nuclear translocation under stress, interacts with amino-acid sensing complexes, and modulates cholesterol metabolism via PI(4,5)P2 phosphatase activity.

    “TMEM55B also regulates autophagosome-lysosome fusion, lysosomal repair, and TFE3 nuclear translocation under stress (Jeong et al. 2024), interacts with amino-acid sensing complexes (Hashimoto et al. 2018), and modulates cholesterol metabolism via PI(4,5)P2 phosphatase activity (Qin et al. 2020).”

    From TMEM55B downregulation promotes neurodegeneration in Alzheimer’s disease models (2026) · cites this paper as Qin et al. 2020

    The Results and Discussion report that TMEM55B regulates plasma cholesterol through changes in PI(4,5)P2 and LDLR lysosomal degradation. But the Discussion explicitly says the authors did not test TMEM55B’s phosphatase activity and that its effect on PI(4,5)P2 could be indirect, so the claimed mechanism is not established by this paper. The other functions in the sentence are attributed to different citations, not Qin et al. (LLM, conf=0.90)

    Experimental — accuracy not yet measured

  • TMEM55B associates with V-ATPase/Ragulator to regulate mTORC1 and controls PI(4,5)P2-dependent LDLR and cholesterol metabolism.

    “TMEM55B associates with V-ATPase/Ragulator to regulate mTORC1 (Hashimoto et al. 2018) and controls PI(4,5)P2-dependent LDLR and cholesterol metabolism (Qin et al. 2020).”

    From TMEM55B downregulation promotes neurodegeneration in Alzheimer’s disease models (2026) · cites this paper as Qin et al. 2020

  • TMEM55B regulates surface expression of low-density lipoprotein receptor but not transferrin receptor or lipoprotein receptor 1.

    “TMEM55B also regulates surface expression of low-density lipoprotein receptor but not transferrin receptor or lipoprotein receptor 1 (Medina et al., 2014;Qin et al., 2020) suggesting its role in receptor trafficking may be cargo specific.”

    From Hippocampal TMEM55B overexpression in the 5XFAD mouse model of Alzheimer's disease (2024) · cites this paper as Qin et al., 2020

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Metadata

Authors
Qin, Y., Ting, F., Kim, M. J., Strelnikov, J., Harmon, J., Gao, F., Dose, A., Teng, B.-B., Alipour, M. A., Yao, Z., Crooke, R., Krauss, R. M., & Medina, M. W.
Affiliations
  • University of California, San Francisco (US)
  • Children’s Hospital Oakland Research Institute, CA (M.J.K., J.S., J.H., F.G., A.D.)
  • The University of Texas Health Science Center at Houston (US)
  • University of Ottawa (CA)
  • Ionis Pharmaceuticals (United States) (US)
ORCID
Venue
Arteriosclerosis, Thrombosis, and Vascular Biology
Publisher
Ovid Technologies (Wolters Kluwer Health)
Published
2020-05
Volume
40
Issue
5
Pages
1311-1324
ISSN
  • 1079-5642 (ISSN-L)
  • 1524-4636
DOI
10.1161/atvbaha.120.314033
PMC
PMC7197750
OpenAlex
W3011519625
Semantic Scholar
a546500e0aefca0141c713b44e11a45787b876ef
Cited by
18
References
54
Citations by year
2026: 2 · 2025: 4 · 2024: 4 · 2023: 6 · 2022: 2
FWCI
0.82
Type
journal article
Language
en
Open access
Locations
  • Arteriosclerosis Thrombosis and Vascular Biology (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Heart, Lung, and Blood Institute (R01HL139902, R56HL132088)
  • National Institute of General Medical Sciences (P50GM115318)
  • National Institute of Diabetes and Digestive and Kidney Diseases (P30DK026743)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Cholesterol and Lipid Metabolism
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Lipoproteins and Cardiovascular Health
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Lipid metabolism and disorders
Keywords
phosphatidylinositol 4,5-bisphosphate, LDL receptor, lysosomal degradation, serum cholesterol, non-HDL cholesterol, LDL uptake, recycling endosomes, lysosomal function, hepatic lipid metabolism, antisense oligonucleotide knockdown, LAMP1, Rab7, Rab11
MeSH terms
Phosphoinositide Phosphatases, Animals, Cholesterol, Female, Humans, Liver, Lysosomes, Male, Mice, Inbred C57BL, Receptors, LDL, Down-Regulation, Mice, Knockout, Phosphatidylinositol 4,5-Diphosphate, Protein Transport, Hepatocytes, Vesicular Transport Proteins, Hep G2 Cells, Diet, High-Fat, Proteolysis

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.

A language model drew the claims from the paper on 2026-11-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).

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