bims-tofagi 2023-11-05 papers

on Mitophagy

Issue of 2023–11–05
nine papers selected by
Michele Frison, University of Cambridge and Aitor Martínez Zarate, Euskal Herriko Unibertsitatea

DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress.
TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery.
Genome-wide association study identifies APOE and ZMIZ1 variants as mitophagy modifiers in Lewy body disease.
Parkin depletion prevents the age-related alterations in the FGF21 system and the decline in white adipose tissue thermogenic function in mice.
Mitophagy in tumor: foe or friend？.
CKLF induces microglial activation via triggering defective mitophagy and mitochondrial dysfunction.
Mitophagy and mitochondrion-related expression profiles in response to physiological and pathological hypoxia in the corneal epithelium.
A human mitofusin 2 mutation can cause mitophagic cardiomyopathy.
Mitochondrial regulation in stem cells.

Nat Commun. 2023 Oct 30. 14(1): 6900

DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress.

Gautham Yepuri, Lisa M Ramirez, Gregory G Theophall, Sergei V Reverdatto, Nosirudeen Quadri, Syed Nurul Hasan, Lei Bu, Devi Thiagarajan, Robin Wilson, Raquel López Díez, Paul F Gugger, Kaamashri Mangar, Navneet Narula, Stuart D Katz, Boyan Zhou, Huilin Li, Aleksandr B Stotland, Roberta A Gottlieb, Ann Marie Schmidt, Alexander Shekhtman, Ravichandran Ramasamy.

Inter-organelle contact and communication between mitochondria and sarco/endoplasmic reticulum (SR/ER) maintain cellular homeostasis and are profoundly disturbed during tissue ischemia. We tested the hypothesis that the formin Diaphanous-1 (DIAPH1), which regulates actin dynamics, signal transduction and metabolic functions, contributes to these processes. We demonstrate that DIAPH1 interacts directly with Mitofusin-2 (MFN2) to shorten mitochondria-SR/ER distance, thereby enhancing mitochondria-ER contact in cells including cardiomyocytes, endothelial cells and macrophages. Solution structure studies affirm the interaction between the Diaphanous Inhibitory Domain and the cytosolic GTPase domain of MFN2. In male rodent and human cardiomyocytes, DIAPH1-MFN2 interaction regulates mitochondrial turnover, mitophagy, and oxidative stress. Introduction of synthetic linker construct, which shorten the mitochondria-SR/ER distance, mitigated the molecular and functional benefits of DIAPH1 silencing in ischemia. This work establishes fundamental roles for DIAPH1-MFN2 interaction in the regulation of mitochondria-SR/ER contact networks. We propose that targeting pathways that regulate DIAPH1-MFN2 interactions may facilitate recovery from tissue ischemia.

DOI: https://doi.org/10.1038/s41467-023-42521-x
bioRxiv. 2023 Oct 20. pii: 2023.10.19.563195. [Epub ahead of print]

TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery.

Bhaskar Saha, Hallvard Olsvik, Geneva L Williams, Seeun Oh, Gry Evjen, Eva Sjøttem, Michael A Mandell.

Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α. Mitochondrial damage triggers TRIM5α's auto-ubiquitination and its interaction with ubiquitin-binding autophagy adaptors including NDP52, optineurin, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1. TRIM5α with intact ubiquitination function is required for the proper accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Additionally, we show that TRIM5α can directly recruit autophagy initiation machinery to damaged mitochondria. Our data support a model in which TRIM5α provides a self-amplifying, mitochondria-localized, ubiquitin-based, assembly platform for TBK1 and mitophagy adaptors that is ultimately required to recruit the core autophagy machinery.

DOI: https://doi.org/10.1101/2023.10.19.563195
medRxiv. 2023 Oct 16. pii: 2023.10.16.23297100. [Epub ahead of print]

Genome-wide association study identifies APOE and ZMIZ1 variants as mitophagy modifiers in Lewy body disease.

Xu Hou, Michael G Heckman, Fabienne C Fiesel, Shunsuke Koga, Alexandra I Soto-Beasley, Jens O Watzlawik, Jing Zhao, Rebecca R Valentino, Patrick W Johnson, Launia J White, Zachary S Quicksall, Joseph S Reddy, Jose Bras, Rita Guerreiro, Na Zhao, Guojun Bu, Dennis W Dickson, Owen A Ross, Wolfdieter Springer.

The PINK1-PRKN pathway mediates a critical quality control to maintain mitochondrial health and function. Together the kinase-ligase pair identifies and decorate damaged mitochondria with phosphorylated ubiquitin (p-S65-Ub). This selective label serves as the mitophagy tag and facilitates their degradation via autophagy-lysosome system. While complete loss of PINK1 or PRKN function causes early-onset Parkinson disease, much broader mitophagy impairments are emerging across neurodegenerative disorders. We previously found age- and disease-dependent accumulation of p-S65-Ub signal in the hippocampus of autopsy brains with Lewy body disease (LBD). However, the contribution of genetic variation to mitochondrial damage and p-S65-Ub levels remains unknown in LBD cases. To identify novel regulators of PINK1-PRKN mitophagy in LBD, we performed an unbiased genome-wide association study of hippocampal p-S65-Ub level with 1,012 autopsy confirmed LBD samples. Using an established, mostly automated workflow, hippocampal sections were immunostained for p-S65-Ub, scanned, and quantified with unbiased algorithms. Functional validation of the significant hit was performed in animal model and human induced pluripotent stem cells (hiPSCs). We identified a strong association with p-S65-Ub for APOE4 (rs429358; β : 0.50, 95% CI: 0.41 to 0.69; p =8.67x10 -25 ) and a genome-wide significant association for ZMIZ1 (rs6480922; β : -0.33, 95% CI: -0.45 to -0.22; p =1.42x10 -8 ). The increased p-S65-Ub levels in APOE4 -carrier may be mediated by both co-pathology-dependent and -independent mechanisms, which was confirmed in Apoe-targeted replacement mice and hiPSC-derived astrocytes. Intriguingly, ZMIZ1 rs6480922 also significantly associated with increased brain weight and reduced neuropathological burden indicating a potential role as a resilience factor. Our findings nominate novel mitophagy regulators in LBD brain ( ZMIZ1 locus) and highlight a strong association of APOE4 with mitophagy alteration. With APOE4 being the strongest known risk factor for clinical Alzheimer's disease and dementia with Lewy bodies, our findings suggest a common mechanistic link underscoring the importance of mitochondrial quality control.

DOI: https://doi.org/10.1101/2023.10.16.23297100
J Physiol Biochem. 2023 Nov 02.

Parkin depletion prevents the age-related alterations in the FGF21 system and the decline in white adipose tissue thermogenic function in mice.

Alejandro Delgado-Anglés, Albert Blasco-Roset, Francisco J Godoy-Nieto, Montserrat Cairó, Francesc Villarroya, Marta Giralt, Joan Villarroya.

  Parkin is an ubiquitin-E3 ligase that is involved in cellular mitophagy and was recently shown to contribute to controlling adipose tissue thermogenic plasticity. We found that Parkin expression is induced in brown (BAT) and white (WAT) adipose tissues of aged mice. We determined the potential role of Parkin in the aging-associated decline in the thermogenic capacity of adipose tissues by analyzing subcutaneous WAT, interscapular BAT, and systemic metabolic and physiological parameters in young (5 month-old) and aged (16 month-old) mice with targeted invalidation of the Parkin (Park2) gene, and their wild-type littermates. Our data indicate that suppression of Parkin prevented adipose accretion, increased energy expenditure and improved the systemic metabolic derangements, such as insulin resistance, seen in aged mice. This was associated with maintenance of browning and reduction of the age-associated induction of inflammation in subcutaneous WAT. BAT in aged mice was much less affected by Parkin gene invalidation. Such protection was associated with a dramatic prevention of the age-associated induction of fibroblast growth factor-21 (FGF21) levels in aged Parkin-invalidated mice. This was associated with a parallel reduction in FGF21 gene expression in adipose tissues and liver in aged Parkin-invalidated mice. Additionally, Parkin invalidation prevented the protein down-regulation of β-Klotho (a key co-receptor mediating FGF21 responsiveness in tissues) in aged adipose tissues. We conclude that Parkin down-regulation leads to improved systemic metabolism in aged mice, in association with maintenance of adipose tissue browning and FGF21 system functionality.

Keywords:  Adipose tissue; Aging; Fibroblast growth factor-21; Metabolism; Parkin

DOI:  https://doi.org/10.1007/s13105-023-00977-x
Endokrynol Pol. 2023 ;74(5): 511-519

Mitophagy in tumor: foe or friend？.

Li Li, Fei Hu.

  Mitophagy is a specific type of autophagy and a selective form of autophagy on a larger scale. It selectively eliminates damaged, misfolded, and surplus mitochondria, particularly those that are cytotoxic, by using autophagic lysosomes. This process is crucial for maintaining a balance of both the quality and quantity of mitochondria, which is necessary for normal cell function and tissue development. However, in certain abnormal situations, such as nutritional deficiencies and hypoxia, the function of mitophagy becomes impaired. This leads to a failure to clear damaged mitochondria in a timely manner, resulting in the production of a large number of reactive oxygen species. These reactive oxygen species further contribute to an inflammatory response and the release of factors that induce apoptosis. Moreover, abnormal mitophagy can also cause mitochondrial dysfunction, disrupt metabolic reprogramming during stress responses, alter cell fate decisions and differentiation, and consequently impact the development and progression of diseases, including cancer. Therefore, mitophagy plays a crucial role in controlling the quality of cancer cells, making it imperative to study its function and impact. Numerous proteins and molecules are involved in the regulation of mitophagy, with Parkin and PTEN-induced kinase 1 (PINK1) serving as key mediators, and the hypoxia-related proteins hypoxia-inducible factor la (HIF1a) and FUN14 domain-containing 1 (FUNDC1) also playing a role. Additionally, proteins such as chromatin licensing and DNA replication factor 1 (CDT-1), insulin-like growth factor 1 (IGF-1), caveolin 1 (Cav-1), and others contribute to the regulation of mitophagy in various ways. This article aims to explore the dual role of mitophagy in tumourigenesis by examining the factors and proteins associated with mitophagy and their regulatory effects. The objective of this review is to provide a new theoretical foundation and direction for cancer treatment.

Keywords:  mitophagy; treatment; tumour

DOI:  https://doi.org/10.5603/ep.95652
Autophagy. 2023 Oct 31.

CKLF induces microglial activation via triggering defective mitophagy and mitochondrial dysfunction.

Hongyun Wang, Junrui Ye, Ye Peng, Wenyu Ma, Haodong Chen, Hongshuo Sun, Zhongping Feng, Wenbin He, Gang Li, Shifeng Chu, Zhao Zhang, Naihong Chen.

  Although microglial activation is induced by an increase in chemokines, the role of mitophagy in this process remains unclear. This study aimed to elucidate the role of microglial mitophagy in CKLF/CKLF1 (chemokine-like factor 1)-induced microglial activation and neuroinflammation, as well as the underlying molecular mechanisms following CKLF treatment. This study determined that CKLF, an inducible chemokine in the brain, leads to an increase in mitophagy markers, such as DNM1L, PINK1 (PTEN induced putative kinase 1), PRKN, and OPTN, along with a simultaneous increase in autophagosome formation, as evidenced by elevated levels of BECN1 and MAP1LC3B (microtubule-associated protein 1 light chain 3 beta)-II. However, SQSTM1, a substrate of autophagy, was also accumulated by CKLF treatment, suggesting that mitophagy flux was reduced and mitophagosomes accumulated. These findings were confirmed by transmission electron microscopy and confocal microscopy. The defective mitophagy observed in our study was caused by impaired lysosomal function, including mitophagosome-lysosome fusion, lysosome generation, and acidification, resulting in the accumulation of damaged mitochondria in microglial cells. Further analysis revealed that pharmacological blocking or gene-silencing of mitophagy inhibited CKLF-mediated microglial activation, as evidenced by the expression of the microglial marker AIF1 (allograft inflammatory factor 1) and the mRNA of proinflammatory cytokines (Tnf and Il6). Ultimately, defective mitophagy induced by CKLF results in microglial activation, as observed in the brains of adult mice. In summary, CKLF induces defective mitophagy, microglial activation, and inflammation, providing a potential approach for treating neuroinflammatory diseases.

Keywords:  Chemokine-like factor 1; inflammation; lysosomal function; microglia; mitophagosome formation; neuroinflammatory diseases

DOI:  https://doi.org/10.1080/15548627.2023.2276639
Genomics. 2023 Oct 31. pii: S0888-7543(23)00183-0. [Epub ahead of print] 110739

Mitophagy and mitochondrion-related expression profiles in response to physiological and pathological hypoxia in the corneal epithelium.

Ming-Feng Wu, Xi Peng, Jiang-Lan Zhao, Ming-Chang Zhang, Hua-Tao Xie.

  To study the mitochondrial and cellular responses to physiological and pathological hypoxia, corneal epithelial cells were preconditioned under 21% O2, 8% O2 or 1% O2. The cell survival rate, mitochondrial fluorescence and mitophagy flux were quantified using flow cytometry. After RNA sequencing, gene set enrichment analysis (GSEA) was performed. When the oxygen level decreased from 21% to 8%, mitochondrial fluorescence decreased by 45% (p < 0.001), accompanied by an 80% increase in mitophagy flux (p < 0.001). When the oxygen level dropped to 1%, the cell survival rate and mitochondrial fluorescence decreased, while mitophagy flux further increased (each p < 0.001). Comparison of 1% O2 vs. 21% O2 revealed enrichment of the HYPOXIA hallmark. Most of the significantly enriched mitochondrion-related gene sets were involved in apoptosis. The corresponding foremost leading edge genes belonged to the BCL-2 family. Corneal epithelial cell fate decisions under hypoxia may involve noncanonical pathways of mitophagy.

Keywords:  Corneal epithelial cells; Gene set enrichment analysis; Hypoxia; Mitochondria; Mitophagy

DOI:  https://doi.org/10.1016/j.ygeno.2023.110739
Elife. 2023 Nov 01. pii: e84235. [Epub ahead of print]12

A human mitofusin 2 mutation can cause mitophagic cardiomyopathy.

Antonietta Franco, Jiajia Li, Daniel P Kelly, Ray E Hershberger, Ali J Marian, Renate M Lewis, Moshi Song, Xiawei Dang, Alina D Schmidt, Mary E Mathyer, John R Edwards, Cristina de Guzman Strong, Gerald W Dorn.

  Cardiac muscle has the highest mitochondrial density of any human tissue, but mitochondrial dysfunction is not a recognized cause of isolated cardiomyopathy. Here, we determined that the rare mitofusin (MFN) 2 R400Q mutation is 15-20× over-represented in clinical cardiomyopathy, whereas this specific mutation is not reported as a cause of MFN2 mutant-induced peripheral neuropathy, Charcot-Marie-Tooth disease type 2A (CMT2A). Accordingly, we interrogated the enzymatic, biophysical, and functional characteristics of MFN2 Q400 versus wild-type and CMT2A-causing MFN2 mutants. All MFN2 mutants had impaired mitochondrial fusion, the canonical MFN2 function. Compared to MFN2 T105M that lacked catalytic GTPase activity and exhibited normal activation-induced changes in conformation, MFN2 R400Q and M376A had normal GTPase activity with impaired conformational shifting. MFN2 R400Q did not suppress mitochondrial motility, provoke mitochondrial depolarization, or dominantly suppress mitochondrial respiration like MFN2 T105M. By contrast to MFN2 T105M and M376A, MFN2 R400Q was uniquely defective in recruiting Parkin to mitochondria. CRISPR editing of the R400Q mutation into the mouse Mfn2 gene induced perinatal cardiomyopathy with no other organ involvement; knock-in of Mfn2 T105M or M376V did not affect the heart. RNA sequencing and metabolomics of cardiomyopathic Mfn2 Q/Q400 hearts revealed signature abnormalities recapitulating experimental mitophagic cardiomyopathy. Indeed, cultured cardiomyoblasts and in vivo cardiomyocytes expressing MFN2 Q400 had mitophagy defects with increased sensitivity to doxorubicin. MFN2 R400Q is the first known natural mitophagy-defective MFN2 mutant. Its unique profile of dysfunction evokes mitophagic cardiomyopathy, suggesting a mechanism for enrichment in clinical cardiomyopathy.

Keywords:  cardiomyopathy; developmental biology; heart; mitochondria; mitofusins; mouse

DOI:  https://doi.org/10.7554/eLife.84235
Trends Cell Biol. 2023 Oct 31. pii: S0962-8924(23)00207-6. [Epub ahead of print]

Mitochondrial regulation in stem cells.

Yifei Wang, Marine Barthez, Danica Chen.

  Stem cells persist throughout the lifespan to repair and regenerate tissues due to their unique ability to self-renew and differentiate. Here we reflect on the recent discoveries in stem cells that highlight a mitochondrial metabolic checkpoint at the restriction point of the stem cell cycle. Mitochondrial activation supports stem cell proliferation and differentiation by providing energy supply and metabolites as signaling molecules. Concomitant mitochondrial stress can lead to loss of stem cell self-renewal and requires the surveillance of various mitochondrial quality control mechanisms. During aging, a mitochondrial protective program mediated by several sirtuins becomes dysregulated and can be targeted to reverse stem cell aging and tissue degeneration, giving hope for targeting the mitochondrial metabolic checkpoint for treating tissue degenerative diseases.

Keywords:  NAD; NLRP3; SIRT2; SIRT3; SIRT7; aging

DOI:  https://doi.org/10.1016/j.tcb.2023.10.003