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Cited by 163Parkinson's Disease Mechanisms and TreatmentsAutophagy in Disease and TherapyMicroRNA in disease regulation

miR-27a and miR-27b regulate autophagic clearance of damaged mitochondria by targeting PTEN-induced putative kinase 1 (PINK1)

Open access
Kim, Jaekwang, Fiesel, Fabienne C., Belmonte, Krystal C., Hudec, Roman, Wang, Wang-Xia, Kim, Chaeyoung, Nelson, Peter T., Springer, Wolfdieter +1 more·2016·Molecular Neurodegeneration
DOI 10.1186/s13024-016-0121-4PMC PMC4960690
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Abstract

BACKGROUND: Loss-of-function mutations in PINK1 and PARKIN are the most common causes of autosomal recessive Parkinson's disease (PD). PINK1 is a mitochondrial serine/threonine kinase that plays a critical role in mitophagy, a selective autophagic clearance of damaged mitochondria. Accumulating evidence suggests mitochondrial dysfunction is one of central mechanisms underlying PD pathogenesis. Therefore, identifying regulatory mechanisms of PINK1 expression may provide novel therapeutic opportunities for PD. Although post-translational stabilization of PINK1 upon mitochondrial damage has been extensively studied, little is known about the regulation mechanism of PINK1 at the transcriptional or translational levels. RESULTS: Here, we demonstrated that microRNA-27a (miR-27a) and miR-27b suppress PINK1 expression at the translational level through directly binding to the 3'-untranslated region (3'UTR) of its mRNA. Importantly, our data demonstrated that translation of PINK1 is critical for its accumulation upon mitochondrial damage. The accumulation of PINK1 upon mitochondrial damage was strongly regulated by expression levels of miR-27a and miR-27b. miR-27a and miR-27b prevent mitophagic influx by suppressing PINK1 expression, as evidenced by the decrease of ubiquitin phosphorylation, Parkin translocation, and LC3-II accumulation in damaged mitochondria. Consequently, miR-27a and miR-27b inhibit lysosomal degradation of the damaged mitochondria, as shown by the decrease of the delivery of damaged mitochondria to lysosome and the degradation of cytochrome c oxidase 2 (COX2), a mitochondrial marker. Furthermore, our data demonstrated that the expression of miR-27a and miR-27b is significantly induced under chronic mitophagic flux, suggesting a negative feedback regulation between PINK1-mediated mitophagy and miR-27a and miR-27b. CONCLUSIONS: We demonstrated that miR-27a and miR-27b regulate PINK1 expression and autophagic clearance of damaged mitochondria. Our data further support a novel negative regulatory mechanism of PINK1-mediated mitophagy by miR-27a and miR-27b. Therefore, our results considerably advance our understanding of PINK1 expression and mitophagy regulation and suggest that miR-27a and miR-27b may represent potential therapeutic targets for PD.

AI snapshot

Written from the paper’s full text.

TL;DR

This study shows that miR-27a and miR-27b directly target the PINK1 3′UTR to suppress PINK1 translation, limiting PINK1 accumulation, ubiquitin phosphorylation, Parkin translocation, and mitophagic clearance of damaged mitochondria. Chronic mitophagic flux induces miR-27a/b, suggesting a negative feedback loop.

Key findings

  • miR-27a/b directly regulate PINK1 via its 3′UTR: luciferase reporters containing the full-length human PINK1 3′UTR were suppressed by miR-27a/b, mutation of either seed site increased activity, and combined mutation of both sites abolished the miR-27a/b effect. Overexpression decreased PINK1 protein in HeLa and M17 cells, while anti-miR-27a/b increased PINK1 protein.
  • PINK1 translation is required for damage-induced accumulation: PINK1 mRNA was not altered by CCCP or oligomycin/antimycin, but cycloheximide completely abolished CCCP-induced PINK1 protein accumulation. miR-27a/b overexpression reduced PINK1 accumulation upon CCCP, whereas miR-27a/b inhibition increased it.
  • miR-27a/b suppress mitophagic events: they reduced CCCP-induced pUbS65 accumulation, Parkin translocation to mitochondria (biochemical fractionation and imaging with >1000 cells), LC3-II accumulation, lysosomal delivery of damaged mitochondria by mtKeima (>300 cells, 12 replicates), and COX2 degradation.
  • Chronic mitophagic flux increased miR-27a/b and miR-23a/b levels, but not several other miRNAs, supporting a proposed negative feedback role for miR-27a/b in PINK1-mediated mitophagy.

Methods

  • Cell models: human cervical HeLa cells, dopaminergic-like M17 cells, HeLa cells stably expressing GFP-Parkin, and HeLa cells stably expressing mitochondria-targeting Keima (mtKeima); treatments included CCCP, oligomycin/antimycin, and cycloheximide.
  • Assays: AGO2-specific RNA immunoprecipitation, qRT-PCR, dual-luciferase reporter assays with wild-type or mutated PINK1 3′UTR, Western blot, mitochondrial fractionation, high-content imaging, and mtKeima live imaging.
  • Statistics: two-tailed Student’s t-test for two groups; one-way or two-way ANOVA with Tukey’s post-hoc for multiple groups; sample sizes reported in figures include n = 4, 6, or 8 for several experiments and >1000 or >300 cells for imaging assays.

Limitations

  • Stated: miRNA profiling studies in PD brains show discrepancies and relatively small sample sizes, making it difficult to conclude whether miR-27a/b are dysregulated in PD; the role of PINK1 in neuronal mitophagy is controversial; further studies are needed in dopaminergic neurons and human brain.
  • Evident: the experimental work relies mainly on HeLa and M17 cell lines rather than primary neurons or in vivo PD models.
  • Evident: the miR-27a/b binding sites in the PINK1 3′UTR are conserved in primates but not rodents, limiting direct translation to rodent models; no direct PD patient tissue validation of the miR-27a/b–PINK1 axis is presented.

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

Integrity signals

Registry

Crossref · 10.1186/s13024-016-0121-4

Cites

70 of 70 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

27 of 37 cited sources checked · 13 supported · 1 flagged · accuracy not yet measured

  • Premisecitation

    miR-27a/b are expressed in SN of human midbrain.

    “miR-27a/b are expressed in SN of human midbrain (Additional file 2a) [34–36]”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [34] Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007;129(7):1401–14. source
    • cites [35] Kim J, Inoue K, Ishii J, Vanti WB, Voronov SV, Murchison E, et al. A MicroRNA feedback circuit in midbrain dopamine neurons. Science. 2007;317(5842):1220–4. source

      The expression-analysis passage (p. 2) describes human midbrain samples and a panel of miRNAs, but identifies miR-133b rather than miR-27a/b. Searches for miR-27a/b and substantia nigra expression found no passage in our copy establishing the claimed expression. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites [36] Cardo LF, Coto E, Ribacoba R, Menendez M, Moris G, Suarez E, et al. MiRNA profile in the substantia nigra of Parkinson’s disease and healthy subjects. J Mol Neurosci. 2014;54(4):830–6. source
  • Findingcitation

    miR-27a/b have multiple putative binding sites in the 3'UTR of human PINK1 mRNA with low binding free energies.

    “miR-27a/b have multiple putative binding sites in the 3′UTR of human PINK1 mRNA with low binding free energies (Additional file 2b) [37].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [37] Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA. 2004;10(10):1507–17. source

      The Introduction and 'Multiple hits per target' section describe RNAhybrid as a method for predicting multiple miRNA binding sites and their free energies. The paper does not report binding sites for miR-27a/b in the human PINK1 3′UTR, so it supports the prediction method but not the specific result attributed here. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Premisecitation

    miR-27a/b are expressed in human midbrain.

    “Several previous studies showed that miR-27a/b are expressed in human midbrain [34–36].”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [34] Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007;129(7):1401–14. source
    • cites [35] Kim J, Inoue K, Ishii J, Vanti WB, Voronov SV, Murchison E, et al. A MicroRNA feedback circuit in midbrain dopamine neurons. Science. 2007;317(5842):1220–4. source

      The expression-analysis passage (p. 2) describes a panel of approximately 230 miRNAs tested in human midbrain, but does not identify miR-27a or miR-27b. Searches for “miR-27a miR-27b human midbrain” and “miR-27” found no passage in our copy establishing their expression there. (LLM, conf=0.73)

      Experimental — accuracy not yet measured
    • cites [36] Cardo LF, Coto E, Ribacoba R, Menendez M, Moris G, Suarez E, et al. MiRNA profile in the substantia nigra of Parkinson’s disease and healthy subjects. J Mol Neurosci. 2014;54(4):830–6. source
  • Findingown data

    miR-27a/b also suppress PINK1 expression in human dopaminergic-like M17 cells.

    “miR-27a/b also suppressed PINK1 expression in human dopaminergic-like M17 cells (Fig. 2f, g).”
    Quote in the paperSubstantial claim
  • Findingown data

    miR-27a/b are commonly predicted by several algorithms to have seed match sequences in the 3'UTR of human PINK1 mRNA.

    “miR-27a/b are commonly predicted by several algorithms to have seed match sequences in the 3′UTR of human PINK1 mRNA (Fig. 2a and Additional file 2a)”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. 17
  • May combine two claims. 9

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

    Premisecitation

    pUbS65 accumulates with mitochondrial stress, age, and disease and serves as a specific signal for recognition by autophagy receptors.

    “Moreover, pUbS65 has been suggested to accumulate with mitochondrial stress, age, and disease [19] and to serve as a specific signal for recognition by autophagy receptors [20, 21].”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [19] Fiesel FC, Ando M, Hudec R, Hill AR, Castanedes-Casey M, Caulfield TR, et al. (Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. EMBO Rep. 2015;16(9):1114–30. source
    • cites [20] Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW. The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol Cell. 2015;60(1):7–20. source

      The citation to this paper concerns pUbS65 as a specific signal for autophagy-receptor recognition; the accumulation claim is attached to [19]. In the Results ("Focal localization of p-TBK1S172 with OPTN on depolarized mitochondria"), the authors conclude that p-S65 UB alone does not specify sites of adaptor recruitment. The Discussion likewise says p-S65 UB does not exclusively dictate those sites. (LLM, conf=0.88)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
    • cites [21] Lazarou M, Sliter DA, Kane LA, Sarraf SA, Wang C, Burman JL, et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature. 2015;524(7565):309–14. source

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

    Premisecitation

    Upon mitochondrial damage, PINK1 is quickly stabilized on damaged mitochondria, leading to translocation of cytosolic Parkin to damaged mitochondria.

    “Upon mitochondrial damage, PINK1 is quickly stabilized on damaged mitochondria, which leads to translocation of cytosolic Parkin to damaged mitochondria [11–13].”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [11] Springer W, Kahle PJ. Regulation of PINK1-Parkin-mediated mitophagy. Autophagy. 2011;7(3):266–78. source

      In “The PINK1-Parkin-Mediated Control of Mitochondrial Degradation” (page unavailable), the paper says full-length PINK1 is stabilized on depolarized mitochondria, resulting in Parkin recruitment, and describes Parkin as cytosolic. It does not support “quickly”: the same section says PINK1 levels gradually rise on depolarized mitochondria. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [12] Narendra DP, Jin SM, Tanaka A, Suen DF, Gautier CA, Shen J, et al. PINK1 is selectively stabilized on impaired mitochondria to activate Parkin. PLoS Biol. 2010;8(1):e1000298. source
    • cites [13] Matsuda N, Sato S, Shiba K, Okatsu K, Saisho K, Gautier CA, et al. PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy. J Cell Biol. 2010;189(2):211–21. source

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

    Premisecitation

    Both PINK1 and Parkin have neuroprotective roles against various insults, such as oxidative stress and PD-relevant toxins.

    “Beyond their roles in mitophagy, mounting evidence suggested that both PINK1 and Parkin have neuroprotective roles against various insults, such as oxidative stress and PD-relevant toxins, although the underlying mechanisms still remain elusive [22, 23].”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [22] Seirafi M, Kozlov G, Gehring K. Parkin structure and function. FEBS J. 2015;282(11):2076–88. source

      The Abstract calls both PINK1 and parkin neuroprotective, and “Other functions of parkin” says they work together to repair mitochondria in response to mild oxidative stress. The References include studies of parkin protecting neurons against toxins, but the paper does not establish comparable protection by PINK1 against PD-relevant toxins. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [23] Deas E, Plun-Favreau H, Wood NW. PINK1 function in health and disease. EMBO Mol Med. 2009;1(3):152–65. source

      The section “PINK1 protects cells against oxidative stress-induced apoptosis” reports that PINK1 protects against oxidative-stress-induced death and chemical insults including MPTP. The paper discusses Parkin’s role in the PINK1 pathway, but the passages found do not establish that Parkin protects neurons against oxidative stress or PD-relevant toxins. Thus the claim is supported for PINK1, not for both proteins. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

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

    Premisecitation

    PINK1 also phosphorylates ubiquitin at Ser65 (pUbS65) and PINK1-dependent phosphorylation of ubiquitin is required for translocation and activation of Parkin to initiate mitophagy.

    “Recently, several groups discovered that PINK1 also phosphorylates ubiquitin at Ser65 (pUbS65) and PINK1-dependent phosphorylation of ubiquitin is required for translocation and activation of Parkin to initiate mitophagy [16–18].”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [16] Kane LA, Lazarou M, Fogel AI, Li Y, Yamano K, Sarraf SA, et al. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J Cell Biol. 2014;205(2):143–53. source

      The Introduction identifies ubiquitin Ser65 as a PINK1 phosphorylation site, and the Results and discussion report that nonphosphorylatable UbS65A reduces Parkin translocation and inhibits its activation. Those findings support a role for ubiquitin phosphorylation, but the observed translocation decrease was greater than 50%, not complete; the paper does not establish the claim’s absolute requirement for translocation or directly demonstrate that this phosphorylation is required to initiate mitophagy. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [17] Kazlauskaite A, Kondapalli C, Gourlay R, Campbell DG, Ritorto MS, Hofmann K, et al. Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65. Biochem J. 2014;460(1):127–39. source

      The Introduction and Discussion show that PINK1 phosphorylates ubiquitin at Ser65 and that phosphorylated ubiquitin activates Parkin E3 ligase. The Introduction reports that PINK1 is required for Parkin recruitment to mitochondria, but our copy does not establish that ubiquitin phosphorylation is required for that translocation or for initiating mitophagy. No page numbers are available in the indexed passages. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [18] Koyano F, Okatsu K, Kosako H, Tamura Y, Go E, Kimura M, et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature. 2014;510(7503):162–6. source

  • Classified as probably not a substantial claim.

    Premisecitation

    PINK1 and Parkin functionally mediate stress-activated selective clearance of impaired mitochondria via autophagic degradation (mitophagy).

    “Together, they functionally mediate the stress-activated, selective clearance of impaired mitochondria via autophagic degradation (termed mitophagy) [11]”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [11] Springer W, Kahle PJ. Regulation of PINK1-Parkin-mediated mitophagy. Autophagy. 2011;7(3):266–78. source

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

    Premisecitation

    miR-137 inhibits mitophagy by targeting FUNC1 and NIX.

    “For example, miR-137 inhibits mitophagy by targeting FUNC1 and NIX [47].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [47] Li W, Zhang X, Zhuang H, Chen HG, Chen Y, Tian W, et al. MicroRNA-137 is a novel hypoxia-responsive microRNA that inhibits mitophagy via regulation of two mitophagy receptors FUNDC1 and NIX. J Biol Chem. 2014;289(15):10691–701. source

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

    Premisecitation

    miR-351 and miR-125a regulate mitophagy.

    “miR-351 and miR-125a are also known to regulate mitophagy [49].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [49] Barde I, Rauwel B, Marin-Florez RM, Corsinotti A, Laurenti E, Verp S, et al. A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science. 2013;340(6130):350–3. source

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

    Premisecitation

    miR-320a promotes mitophagy by targeting VDAC1.

    “miR-320a promotes mitophagy by targeting VDAC1 [48].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [48] Li QQ, Zhang L, Wan HY, Liu M, Li X, Tang H. CREB1-driven expression of miR-320a promotes mitophagy by down-regulating VDAC1 expression during serum starvation in cervical cancer cells. Oncotarget. 2015;6(33):34924–40. source

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

    Premisecitation

    AMBRA1 and ATG12 positively regulate mitophagy.

    “Although the role of ATG4A in mitophagy is unclear, AMBRA1 and ATG12 positively regulate mitophagy [56–58].”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [56] Van Humbeeck C, Cornelissen T, Hofkens H, Mandemakers W, Gevaert K, De Strooper B, et al. Parkin interacts with Ambra1 to induce mitophagy. J Neurosci. 2011;31(28):10249–61. source

      The Discussion (p. 10259) identifies Ambra1 as a key player in clearing depolarized mitochondria and says its activating role in mitophagy depends on Parkin. The cited paper does not establish the claim about ATG12 (searched: ATG12 and ATG12 positively regulates mitophagy). (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [57] Strappazzon F, Nazio F, Corrado M, Cianfanelli V, Romagnoli A, Fimia GM, et al. AMBRA1 is able to induce mitophagy via LC3 binding, regardless of PARKIN and p62/SQSTM1. Cell Death Differ. 2015;22(3):419–32. source

      The Abstract (page unavailable) identifies AMBRA1 as a mitophagy regulator and reports that directing it to the outer mitochondrial membrane triggers mitophagy. Our copy does not establish that ATG12 positively regulates mitophagy; a search for ATG12 found no passage supporting that part of the claim. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [58] Radoshevich L, Murrow L, Chen N, Fernandez E, Roy S, Fung C, et al. ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. Cell. 2010;142(4):590–600. source

      The Results (page unavailable) show that loss of ATG12 conjugation to ATG3 reduces mitochondrial targeting to autophagosomes during CCCP treatment, supporting a positive role for that complex in mitophagy. The paper does not address AMBRA1, so it does not support that part of the claim. (LLM, conf=0.90)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    PINK1 plays critical roles in mitochondrial quality control, particularly in induction of mitophagy.

    “PINK1 plays critical roles in mitochondrial quality control, particularly in induction of mitophagy [39].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [39] Pickrell AM, Youle RJ. The roles of PINK1, parkin, and mitochondrial fidelity in Parkinson’s disease. Neuron. 2015;85(2):257–73. source

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

    Premisecitation

    PINK1 plays crucial roles in mitochondria trafficking, spine morphogenesis, and vulnerability to excitotoxicity in neurons.

    “PINK1 also plays crucial roles in mitochondria trafficking, spine morphogenesis, and vulnerability to excitotoxicity in neurons [23].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [23] Deas E, Plun-Favreau H, Wood NW. PINK1 function in health and disease. EMBO Mol Med. 2009;1(3):152–65. source

      The “PINK1 and mitochondrial trafficking” section links PINK1 to a transport complex relevant to neurons. The “PINK1 in calcium signalling” section discusses susceptibility of PINK1-deficient dopaminergic neurons to cell death, but does not identify excitotoxicity as the cause. The passages do not support a role in spine morphogenesis. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

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

    Premisecitation

    miR-23a, miR-23b, and miR-24 suppress AMBRA1, ATG12, and ATG4A, respectively.

    “For example, miR-23a, miR-23b, and miR-24 suppress AMBRA1 [52], ATG12 [53, 54], and ATG4A [55], respectively.”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [52] Zhang JA, Zhou BR, Xu Y, Chen X, Liu J, Gozali M, et al. MiR-23a-depressed autophagy is a participant in PUVA- and UVB-induced premature senescence. Oncotarget. 2016. doi: 10.18632/oncotarget.9357 . source
    • cites [53] An Y, Zhang Z, Shang Y, Jiang X, Dong J, Yu P, et al. miR-23b-3p regulates the chemoresistance of gastric cancer cells by targeting ATG12 and HMGB2. Cell Death Dis. 2015;6:e1766. source
    • cites [54] Wang P, Zhang J, Zhang L, Zhu Z, Fan J, Chen L, et al. MicroRNA 23b regulates autophagy associated with radioresistance of pancreatic cancer cells. Gastroenterology. 2013;145(5):1133–43. e12. source
    • cites [55] Pan B, Chen Y, Song H, Xu Y, Wang R, Chen L. Mir-24-3p downregulation contributes to VP16-DDP resistance in small-cell lung cancer by targeting ATG4A. Oncotarget. 2015;6(1):317–31. source

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

    Premisecitation

    Loss of PINK1 is associated with mitochondrial dysfunction in Drosophila, mouse, and human.

    “Loss of PINK1 has been associated with mitochondrial dysfunction in Drosophila, mouse, and human, suggesting that the roles of PINK1 in mitochondrial quality control may be evolutionally conserved [50, 51].”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [50] Narendra DP, Youle RJ. Targeting mitochondrial dysfunction: role for PINK1 and Parkin in mitochondrial quality control. Antioxid Redox Signal. 2011;14(10):1929–38. source
    • cites [51] Cookson MR. Parkinsonism due to mutations in PINK1, parkin, and DJ-1 and oxidative stress and mitochondrial pathways. Cold Spring Harb Perspect Med. 2012;2(9):a009415. source

      The PATHWAYS TO PARKINSONISM section reports mitochondrial phenotypes in PINK1-deficient Drosophila and says the human PINK1 homolog rescues them. The BIOCHEMICAL FUNCTION IN THE PINK1/PARKIN PATHWAY section also links loss of PINK1 to altered mitochondrial shape and function in cells. The passages do not establish mitochondrial dysfunction specifically in PINK1-deficient mice, so the three-species claim is only partly supported. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Inhibition of endogenous miR-27a/b significantly increases luciferase activities from the reporter construct with WT PINK1 3'UTR, whereas combined mutations of both seed match sites block the anti-miR-27a/b-mediated induction of luciferase activities in HeLa cells.

    “Inhibition of endogenous miR-27a/b significantly increased luciferase activities from the reporter construct with WT PINK1 3′UTR, whereas combined mutations of both seed match sites blocked the anti-miR-27a/b-mediated induction of luciferase activities in HeLa cells (Fig. 3b).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Both putative binding sites of miR-27a/b in the 3'UTR of PINK1 mRNA are well conserved in primates, such as human, chimpanzee, and monkey, but not in rodents, such as rat and mouse.

    “Of note, both putative binding sites of miR-27a/b in the 3′UTR of PINK1 mRNA are well conserved in primates, such as human, chimpanzee, and monkey, but not in rodents, such as rat and mouse (Additional file 3)”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingnone given

    Human PINK1 mRNA has a long 3'UTR of approximately 840 nucleotides.

    “PINK1 mRNA (NM_032409) has a long 3′UTR, ~840 nucleotides, raising the possibility that its expression may be regulated by miRNAs which often target 3′UTR sequences.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Mutations in PARKIN and PINK1 are the leading causes of autosomal recessive Parkinson's disease.

    “Mutations in PARKIN and PINK1 are the leading causes of autosomal recessive PD [9, 10].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [9] Kitada T, Asakawa S, Hattori N, Matsumine H, Yamamura Y, Minoshima S, et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature. 1998;392(6676):605–8. source
    • cites [10] Valente EM, Abou-Sleiman PM, Caputo V, Muqit MM, Harvey K, Gispert S, et al. Hereditary early-onset Parkinson’s disease caused by mutations in PINK1. Science. 2004;304(5674):1158–60. source

  • Classified as probably not a substantial claim.

    Interpretationown data

    miR-27a/b may regulate PINK1 expression in dopaminergic neurons of the human midbrain.

    “Because we demonstrated that endogenous miR-27a/b regulate PINK1 expression in human dopaminergic-like M17 cells, our study raises the possibility that miR-27a/b may regulate PINK1 expression in dopaminergic neurons of the human midbrain.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    miR-27a and miR-27b regulate PINK1 expression and autophagic clearance of damaged mitochondria.

    “We demonstrated that miR-27a and miR-27b regulate PINK1 expression and autophagic clearance of damaged mitochondria.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    miR-27a/b are endogenous inhibitors of mitophagy and may function as a negative feedback loop under chronic mitophagic flux.

    “Taken together, miR-27a/b are endogenous inhibitors of mitophagy and may function as a negative feedback loop under chronic mitophagic flux (Fig. 9c).”
    Quote in the paperSubstantial claim

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

    Interpretationcitation

    Mitophagy is actively regulated by diverse miRNAs at multiple levels.

    “These studies suggest that mitophagy is actively regulated by diverse miRNAs at multiple levels.”
    Quote in the paperNot a substantial claim
21 of 21

  • The paper relies on this without support.

    Post-transcriptional regulation of human PINK1 by miRNAs is poorly defined.

    “However, post-transcriptional regulation of human PINK1 by miRNAs is poorly defined.”

  • The paper relies on this without support.

    PINK1 is maintained at low levels under normal physiological conditions.

    “PINK1, a mitochondrial serine/threonine kinase, is maintained at low levels under normal physiological conditions.”

  • The paper relies on this without support.

    PINK1 activates Parkin by phosphorylating it at Ser65.

    “PINK1 activates Parkin by phosphorylating it at Ser65.”
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?

  • Transfection of miR-27b caused impaired PRKN translocation.

    “transfection of miR-27b caused impaired PRKN translocation, in line with our previous description [32].”

    From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [32]

  • Of the five miRNAs experimentally confirmed to directly target PINK1, only miR-27b was among the top hits in the genome-wide screen.

    “However, of the five miRNAs that have been experimentally confirmed to directly target PINK1 [37–39], only miR-27b [32] was among the top hits in our genome-wide screen.”

    From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [32]

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.

  • Conflicting designation of the miR-27b gene cluster

    Minor

    The Results section places miR-27b in the miR-23b ~ 27b ~ 24-1 cluster, while the Discussion calls the same cluster miR-23b ~ 27b ~ 24-2.

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Authors
Kim, J., Fiesel, F. C., Belmonte, K. C., Hudec, R., Wang, W.-X., Kim, C., Nelson, P. T., Springer, W., & Kim, J.
Affiliations
  • Mayo Clinic (US)
  • University of Kentucky (US)
Corresponding author
  • Kim, Jaekwang
  • Kim, Jungsu
ORCID
Venue
Molecular Neurodegeneration
Publisher
Springer Science and Business Media LLC
Published
2016-07-26
Volume
11
Issue
1
Pages
55-55
ISSN
1750-1326 (ISSN-L)
DOI
10.1186/s13024-016-0121-4
PMC
PMC4960690
OpenAlex
W2504529755
Semantic Scholar
bb585ee0de9115f5d851f228e68e14e168788670
Cited by
163
References
70
Citations by year
2026: 12 · 2025: 24 · 2024: 15 · 2023: 19 · 2022: 20 · 2021: 28 · 2020: 14 · 2019: 11 · 2018: 12 · 2017: 5 · 2016: 3
FWCI
6.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Neurodegeneration (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • UKnowledge (University of Kentucky) (submittedVersion, cc-by)
Funders
  • National Institute on Aging (AG016574, AG005681, AG028383)
  • National Institute of Neurological Disorders and Stroke (NS085830, NS085070)
Topics
  • Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
Keywords
miR-27a, miR-27b, PINK1, mitophagy, autophagy, Parkinson's disease, microRNA regulation, 3' untranslated region, translational regulation, mitochondrial damage, Parkin, ubiquitin phosphorylation, LC3-II, lysosomal degradation, cyclooxygenase-2, negative feedback regulation, miRNA-based therapy, neuroprotection
MeSH terms
PTEN-Induced Putative Kinase, Autophagy, Cell Line, Fluorescent Antibody Technique, Gene Expression Regulation, Humans, Mitochondria, Parkinson Disease, Protein Kinases, Blotting, Western, MicroRNAs, Immunoprecipitation, Real-Time Polymerase Chain Reaction

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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.

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