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

In the paper

“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].”

What the sources say

• Supported

  Citation [19] is attached to the claim that pUbS65 accumulates with mitochondrial stress, age, and disease, not to the separate autophagy-receptor claim cited to [20, 21]. The Discussion (page not supplied) states that pS65-Ub accumulates with organelle damage, age, and disease; the Results (page not supplied) also report accumulation with age and disease in human brain. (LLM, conf=0.94)

  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
• Disputed

  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.

  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. sourceExperimental — accuracy not yet measured
• Supported

  This source is cited for the second clause, about recognition by autophagy receptors; the age-and-disease clause is cited to [19]. In “Ubiquitin phosphorylation in mitophagy” (page not available), OPTN and NDP52 preferentially bind phospho-mimetic Ser65 ubiquitin, and OPTN binds phosphorylated ubiquitin better than unphosphorylated ubiquitin in a cell-cytosol assay. (LLM, conf=0.90)

  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

In the paper

“Upon mitochondrial damage, PINK1 is quickly stabilized on damaged mitochondria, which leads to translocation of cytosolic Parkin to damaged mitochondria [11–13].”

What the sources say

• Partly supported

  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)

  cites [11] Springer W, Kahle PJ. Regulation of PINK1-Parkin-mediated mitophagy. Autophagy. 2011;7(3):266–78. sourceExperimental — accuracy not yet measured
• Supported

  The Introduction states that PINK1 is selectively stabilized on impaired mitochondria and that its accumulation recruits Parkin. The Results report PINK1 accumulation beginning within 30 minutes of depolarization and show Parkin increasing in the mitochondrial fraction while decreasing in the supernatant. Page numbers are not available in our copy. (LLM, conf=0.93)

  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
• Supported

  In Results and discussion, the paper reports that depolarization causes PINK1 to accumulate on mitochondria and that Parkin translocates to mitochondria after depolarization in control cells, but not in PINK1-knockout cells. Its Conclusion explicitly identifies PINK1 as a factor that recruits Parkin from the cytoplasm to damaged mitochondria. The copy does not give a precise time for stabilization, but the claim’s general sequence is supported. (LLM, conf=0.92)

  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

In the paper

“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].”

What the sources say

• Partly supported

  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)

  cites [22] Seirafi M, Kozlov G, Gehring K. Parkin structure and function. FEBS J. 2015;282(11):2076–88. sourceExperimental — accuracy not yet measured
• Partly supported

  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)

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

In the paper

“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].”

What the sources say

• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [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

In the paper

“Together, they functionally mediate the stress-activated, selective clearance of impaired mitochondria via autophagic degradation (termed mitophagy) [11]”

What the sources say

• Supported

  The Introduction states that PINK1 and PARKIN functionally cooperate in the selective degradation of damaged mitochondria via autophagy. The section “The PINK1-Parkin-Mediated Control of Mitochondrial Degradation” also describes autophagic clearance of depolarized mitochondria, supporting the stress-related aspect of the paraphrase. (LLM, conf=0.94)

  cites [11] Springer W, Kahle PJ. Regulation of PINK1-Parkin-mediated mitophagy. Autophagy. 2011;7(3):266–78. source

In the paper

“For example, miR-137 inhibits mitophagy by targeting FUNC1 and NIX [47].”

What the sources say

• Supported

  The Abstract states that miR-137 inhibits hypoxia-induced mitophagy by targeting FUNDC1 and NIX. The citing sentence spells FUNDC1 as “FUNC1,” but otherwise matches the finding. (LLM, conf=0.94)

  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

In the paper

“miR-351 and miR-125a are also known to regulate mitophagy [49].”

What the sources say

• Supported

  The paper reports that miR-351 overexpression caused erythroid cells to accumulate mitochondria, a phenotype reversed by restoring Bnip3L. It also reports that human miR-125a-5p overexpression reduced Nix expression and increased mitochondrial content. These passages support regulation of mitophagy by both miRNAs in the erythroid cells studied; page numbers are not provided in our copy. (LLM, conf=0.92)

  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

In the paper

“miR-320a promotes mitophagy by targeting VDAC1 [48].”

What the sources say

• Supported

  The Results section (‘miR-320a down-regulates VDAC1 expression to promote mitophagy in HeLa cells’; page not supplied) explicitly concludes that miR-320a promotes mitophagy by downregulating VDAC1. The finding was established in HeLa cells during serum starvation. (LLM, conf=0.94)

  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

In the paper

“Although the role of ATG4A in mitophagy is unclear, AMBRA1 and ATG12 positively regulate mitophagy [56–58].”

What the sources say

• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured

In the paper

“PINK1 plays critical roles in mitochondrial quality control, particularly in induction of mitophagy [39].”

What the sources say

• Supported

  The Introduction section “PINK1 and Parkin Mediate Mitophagy” says PINK1’s kinase activity is required for Parkin translocation and mitophagy, and describes the two proteins as performing a mitochondrial quality-control function. “PINK1 Detects Mitochondrial Damage via Selective Proteolysis” further describes how PINK1 flags damaged mitochondria for elimination. (LLM, conf=0.94)

  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

In the paper

“PINK1 also plays crucial roles in mitochondria trafficking, spine morphogenesis, and vulnerability to excitotoxicity in neurons [23].”

What the sources say

• Partly supported

  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)

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

In the paper

“For example, miR-23a, miR-23b, and miR-24 suppress AMBRA1 [52], ATG12 [53, 54], and ATG4A [55], respectively.”

What the sources say

• Supported

  The citation [52] is attached to the miR-23a–AMBRA1 pairing, not the other two pairings. In the Results section, the paper reports that miR-23a suppressed an AMBRA1 3′-UTR reporter and that reducing miR-23a increased AMBRA1 protein and mRNA levels in fibroblasts. (LLM, conf=0.94)

  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
• Supported

  The citation to this paper is attached to the miR-23b–ATG12 pairing, not the AMBRA1 or ATG4A pairings. The Results section, “ATG12 and HMGB2 are direct targets of miR-23b-3p” (page not supplied), reports that restoring miR-23b-3p inhibited ATG12 expression and identifies ATG12 as a direct target. (LLM, conf=0.94)

  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
• ?Not checked — no full text of the sourcecites [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
• Supported

  The citation to this paper is attached to the miR-24–ATG4A relationship, not the preceding miRNA–target pairs. The Results section, “Mir-24-3p suppressed autophagy by directly targeting ATG4A” (page not provided), reports that miR-24-3p directly targets ATG4A and that increasing it reduces ATG4A mRNA and protein levels. (LLM, conf=0.94)

  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

In the paper

“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].”

What the sources say

• Supported

  The Introduction reports that Pink1-null Drosophila have the same phenotype as Parkin-knockout flies, whose affected tissues show mitochondrial dysfunction. Its section on conservation in mammals reports progressive loss of mitochondrial function in Pink1-null mice and mitochondrial dysfunction in cells from patients with PINK1 loss-of-function mutations. (LLM, conf=0.90)

  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
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured

In the paper

“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).”

In the paper

“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)”

In the paper

“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.”

In the paper

“Mutations in PARKIN and PINK1 are the leading causes of autosomal recessive PD [9, 10].”

What the sources say

• ?Not checked — no full text of the sourcecites [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
• ?Not checked — no full text of the sourcecites [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

In the paper

“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.”

In the paper

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

In the paper

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

In the paper

“These studies suggest that mitophagy is actively regulated by diverse miRNAs at multiple levels.”