bims-nenemi 2024-01-07 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2024–01–07
twelve papers selected by
Marco Tigano, Thomas Jefferson University

Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease.
Yeast EndoG prevents genome instability by degrading cytoplasmic DNA.
LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function.
CHCHD4-TRIAP1 regulation of innate immune signaling mediates skeletal muscle adaptation to exercise.
Nuclear DNA damage-triggered ATM-dependent AMPK activation regulates the mitochondrial radiation response.
The integrated stress response protects against ER stress but is not required for altered translation and lifespan from dietary restriction in Caenorhabditis elegans.
ATF4 Responds to Metabolic Stress in Drosophila.
Identification of a potent and specific retinoic acid-inducible gene 1 pathway activator as a Hepatitis B Virus antiviral through a novel cell-based reporter assay.
Mitochondria-derived reactive oxygen species are the likely primary trigger of mitochondrial retrograde signaling in Arabidopsis.
The DNA repair enzyme, aprataxin, plays a role in innate immune signaling.
Low-dose X-ray radiation induces an adaptive response: A potential countermeasure to galactic cosmic radiation exposure.
Engineering TALE-linked deaminases to facilitate precision adenine base editing in mitochondrial DNA.

Nat Commun. 2024 Jan 02. 15(1): 168

Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease.

Jun Dong, Li Chen, Fei Ye, Junhui Tang, Bing Liu, Jiacheng Lin, Pang-Hu Zhou, Bin Lu, Min Wu, Jia-Hong Lu, Jing-Jing He, Simone Engelender, Qingtao Meng, Zhiyin Song, He He.

Endoplasmic reticulum (ER)-mitochondria contacts are critical for the regulation of lipid transport, synthesis, and metabolism. However, the molecular mechanism and physiological function of endoplasmic reticulum-mitochondrial contacts remain unclear. Here, we show that Mic19, a key subunit of MICOS (mitochondrial contact site and cristae organizing system) complex, regulates ER-mitochondria contacts by the EMC2-SLC25A46-Mic19 axis. Mic19 liver specific knockout (LKO) leads to the reduction of ER-mitochondrial contacts, mitochondrial lipid metabolism disorder, disorganization of mitochondrial cristae and mitochondrial unfolded protein stress response in mouse hepatocytes, impairing liver mitochondrial fatty acid β-oxidation and lipid metabolism, which may spontaneously trigger nonalcoholic steatohepatitis (NASH) and liver fibrosis in mice. Whereas, the re-expression of Mic19 in Mic19 LKO hepatocytes blocks the development of liver disease in mice. In addition, Mic19 overexpression suppresses MCD-induced fatty liver disease. Thus, our findings uncover the EMC2-SLC25A46-Mic19 axis as a pathway regulating ER-mitochondria contacts, and reveal that impairment of ER-mitochondria contacts may be a mechanism associated with the development of NASH and liver fibrosis.

DOI: https://doi.org/10.1038/s41467-023-44057-6
bioRxiv. 2023 Dec 13. pii: 2023.12.13.571550. [Epub ahead of print]

Yeast EndoG prevents genome instability by degrading cytoplasmic DNA.

Yang Yu, Xin Wang, Jordan Fox, Ruofan Yu, Pilendra Thakre, Brenna McCauley, Nicolas Nikoloutsos, Qian Li, P J Hastings, Weiwei Dang, Kaifu Chen, Grzegorz Ira.

In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease. Cytoplasmic nucleases degrade these DNA species to limit inflammation. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nu clear mt DNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (∼45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.

DOI: https://doi.org/10.1101/2023.12.13.571550
RNA. 2023 Dec 20. pii: rna.079799.123. [Epub ahead of print]

LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function.

Benjamin M Lewis, Chae Yun Cho, Hsuan-Lin Her, Orel Mizrahi, Tony Hunter, Gene W Yeo.

  Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4's targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome proteins (MRPs) across multiple human cell lines. Through quantitative proteomics, we demonstrate that depletion of LARP4 leads to a significant reduction in RCCP and MRP protein levels. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and that LARP4 re-expression rescues this phenotype. Our findings shed light on a novel function for LARP4 as an RBP that binds to and positively regulates NEMmRNAs to promote mitochondrial respiratory function.

Keywords:  La module protein; Mitochondria; RNA binding protein; Translation; eCLIP

DOI:  https://doi.org/10.1261/rna.079799.123
Cell Rep. 2023 Dec 28. pii: S2211-1247(23)01637-6. [Epub ahead of print]43(1): 113626

CHCHD4-TRIAP1 regulation of innate immune signaling mediates skeletal muscle adaptation to exercise.

Jin Ma, Ping-Yuan Wang, Jie Zhuang, Annie Y Son, Alexander K Karius, Abu Mohammad Syed, Masahiro Nishi, Zhichao Wu, Mateus P Mori, Young-Chae Kim, Paul M Hwang.

  Exercise training can stimulate the formation of fatty-acid-oxidizing slow-twitch skeletal muscle fibers, which are inversely correlated with obesity, but the molecular mechanism underlying this transformation requires further elucidation. Here, we report that the downregulation of the mitochondrial disulfide relay carrier CHCHD4 by exercise training decreases the import of TP53-regulated inhibitor of apoptosis 1 (TRIAP1) into mitochondria, which can reduce cardiolipin levels and promote VDAC oligomerization in skeletal muscle. VDAC oligomerization, known to facilitate mtDNA release, can activate cGAS-STING/NFKB innate immune signaling and downregulate MyoD in skeletal muscle, thereby promoting the formation of oxidative slow-twitch fibers. In mice, CHCHD4 haploinsufficiency is sufficient to activate this pathway, leading to increased oxidative muscle fibers and decreased fat accumulation with aging. The identification of a specific mediator regulating muscle fiber transformation provides an opportunity to understand further the molecular underpinnings of complex metabolic conditions such as obesity and could have therapeutic implications.

Keywords:  CHCHD4; CP: Immunology; MyoD; TRIAP1; VDAC; cardiolipin; exercise adaptation; innate immune signaling; mitochondria; mtDNA; skeletal muscle

DOI:  https://doi.org/10.1016/j.celrep.2023.113626
Int J Radiat Biol. 2024 Jan 03. 1-11

Nuclear DNA damage-triggered ATM-dependent AMPK activation regulates the mitochondrial radiation response.

Tsutomu Shimura, Kenta Sunaga, Mayu Yamazaki, Nara Honoka, Megumi Sasatani, Kenji Kamiya, Akira Ushiyama.

   PURPOSE: AMP-activated protein kinase (AMPK) acts as a cellular energy sensor and is essential for controlling mitochondrial homeostasis. Here, we investigated the regulatory mechanisms involved in AMPK activation to elucidate how networks of intracellular signaling pathways respond to stress conditions.
MATERIALS AND METHODS: Inhibitors of ATM, DNA-PK, and AKT were tested in normal TIG-3 and MRC-5 human fibroblasts to determine which upstream kinases are responsible for AMPK activation. SV40 transformed-human ATM-deficient fibroblasts (AT5BIVA) and their ATM-complemented cells (i.e., AT5BIVA/ATMwt) were also used. Protein expression associated with AMPK signaling was examined by immunostaining and/or Western blotting.
RESULTS: Radiation-induced nuclear DNA damage activates ATM-dependent AMPK signaling pathways that regulate mitochondrial quality control. In contrast, hypoxia and glucose starvation caused ATP depletion and activated AMPK via a pathway independent of ATM. DNA-PK and AKT are not involved in AMPK-mediated mitochondrial signaling pathways.
CONCLUSION: Activation of the AMPK signaling pathway differs depending on the stimulus. Radiation activates AMPK through two pathways: depletion of ATP-mediated LKB1 signaling and nuclear DNA damage-induced ATM signaling. Nuclear DNA damage signaling to mitochondria therefore plays a pivotal role in determining the cell fates of irradiated cells.

Keywords:  AMPK; ATM; Mitochondria; glucose starvation; hypoxia; radiation

DOI:  https://doi.org/10.1080/09553002.2023.2295297
Front Cell Dev Biol. 2023 ;11 1263344

The integrated stress response protects against ER stress but is not required for altered translation and lifespan from dietary restriction in Caenorhabditis elegans.

Zhengxin Ma, Jordan Horrocks, Dilawar A Mir, Matthew Cox, Marissa Ruzga, Jarod Rollins, Aric N Rogers.

  The highly conserved integrated stress response (ISR) reduces and redirects mRNA translation in response to certain forms of stress and nutrient limitation. It is activated when kinases phosphorylate a key residue in the alpha subunit of eukaryotic translation initiation factor 2 (eIF2). General Control Nonderepressible-2 (GCN2) is activated to phosphorylate eIF2α by the presence of uncharged tRNA associated with nutrient scarcity, while protein kinase R-like ER kinase-1 (PERK) is activated during the ER unfolded protein response (UPRER). Here, we investigated the role of the ISR during nutrient limitation and ER stress with respect to changes in protein synthesis, translationally driven mRNA turnover, and survival in Caenorhabditis elegans. We found that, while GCN2 phosphorylates eIF2α when nutrients are restricted, the ability to phosphorylate eIF2α is not required for changes in translation, nonsense-mediated decay, or lifespan associated with dietary restriction (DR). Interestingly, loss of both GCN2 and PERK abolishes increased lifespan associated with dietary restriction, indicating the possibility of other substrates for these kinases. The ISR was not dispensable under ER stress conditions, as demonstrated by the requirement for PERK and eIF2α phosphorylation for decreased translation and wild type-like survival. Taken together, results indicate that the ISR is critical for ER stress and that other translation regulatory mechanisms are sufficient for increased lifespan under dietary restriction.

Keywords:  aging; dietary restriction; endoplasmic reticulum stress; integrated stress response; nonsense mediated decay

DOI:  https://doi.org/10.3389/fcell.2023.1263344
Front Biosci (Landmark Ed). 2023 Dec 26. 28(12): 344

ATF4 Responds to Metabolic Stress in Drosophila.

Soonhyuck Ok, Jung-Eun Park, Seunghee Byun, Kwonyoon Kang, Jaekyoung Son, Min-Ji Kang.

   BACKGROUND: Activating transcription factor 4 (ATF4) is a fundamental basic-leucine zipper transcription factor that plays a pivotal role in numerous stress responses, including endoplasmic reticulum (ER) stress and the integrated stress response. ATF4 regulates adaptive gene expression, thereby triggering stress resistance in cells.
METHODS: To characterize the metabolic status of atf4-⁣/- Drosophila larvae, we conducted both metabolomic and microarray analyses.
RESULTS: Metabolomic analysis demonstrated an increase in lactate levels in atf4-⁣/- mutants when compared to wild-type flies. However, there was a significant reduction in adenosine triphosphate (ATP) synthesis in the atf4-⁣/- flies, suggesting an abnormal energy metabolism in the mutant larvae. Microarray analysis unveiled that Drosophila ATF4 controls gene expression related to diverse biological processes, including lipase activity, oxidoreductase activity, acyltransferase, immune response, cell death, and transcription factor, particularly under nutrient-restricted conditions. In situ hybridization analysis further demonstrated specific augmentation of CG6283, classified as a gastric lipase, within the gastric caeca of nutrient-restricted flies. Moreover, overexpression of lipases, CG6283 and CG6295, made the flies resistant to starvation.
CONCLUSIONS: These findings underscore the role of Drosophila ATF4 in responding to metabolic fluctuations and modulating gene expression associated with metabolism and stress adaptation. Dysregulation of ATF4 may detrimentally impact the development and physiology of Drosophila.

Keywords:  ATF4; Drosophila; integrated stress response; lipase; microarray; nutrient restriction

DOI:  https://doi.org/10.31083/j.fbl2812344
J Virol Methods. 2024 Jan 02. pii: S0166-0934(23)00200-8. [Epub ahead of print] 114875

Identification of a potent and specific retinoic acid-inducible gene 1 pathway activator as a Hepatitis B Virus antiviral through a novel cell-based reporter assay.

Liping Shi, Guangyang Guo, Jinying Zhou, Zhanling Cheng, Ren Zhu, George Kukolj, Chris Li.

  Chronic Hepatitis B Virus (HBV) infection remains a global burden. To identify small molecule RIG-I agonists as antivirals against HBV, we developed an HBV-pgRNA-based interferon-β (IFN-β) luciferase reporter assay with high level of assay sensitivity, specificity and robustness. Through HTS screening, lead compound (JJ#1) was identified to activate RIG-I signaling pathway by inducing TBK1 phosphorylation. Knockdown experiments demonstrated that JJ#1-induced retinoic acid-inducible gene 1 (RIG-I) signaling pathway activation was MAVS-dependent. Furthermore, JJ#1 exhibited HBV antiviral potency in HBV-infected cell models by reducing HBV DNA and antigens (HBsAg and HBeAg).

Keywords:  Hepatitis B virus; RIG-I pathway; antiviral activity; cell-based reported assay; small molecule antivirals

DOI:  https://doi.org/10.1016/j.jviromet.2023.114875
Curr Biol. 2023 Dec 28. pii: S0960-9822(23)01660-3. [Epub ahead of print]

Mitochondria-derived reactive oxygen species are the likely primary trigger of mitochondrial retrograde signaling in Arabidopsis.

Kasim Khan, Huy Cuong Tran, Berivan Mansuroglu, Pinar Önsell, Stefano Buratti, Markus Schwarzländer, Alex Costa, Allan G Rasmusson, Olivier Van Aken.

  Besides their central function in respiration, plant mitochondria play a crucial role in maintaining cellular homeostasis during stress by providing "retrograde" feedback to the nucleus. Despite the growing understanding of this signaling network, the nature of the signals that initiate mitochondrial retrograde regulation (MRR) in plants remains unknown. Here, we investigated the dynamics and causative relationship of a wide range of mitochondria-related parameters for MRR, using a combination of Arabidopsis fluorescent protein biosensor lines, in vitro assays, and genetic and pharmacological approaches. We show that previously linked physiological parameters, including changes in cytosolic ATP, NADH/NAD+ ratio, cytosolic reactive oxygen species (ROS), pH, free Ca2+, and mitochondrial membrane potential, may often be correlated with-but are not the primary drivers of-MRR induction in plants. However, we demonstrate that the induced production of mitochondrial ROS is the likely primary trigger for MRR induction in Arabidopsis. Furthermore, we demonstrate that mitochondrial ROS-mediated signaling uses the ER-localized ANAC017-pathway to induce MRR response. Finally, our data suggest that mitochondrially generated ROS can induce MRR without substantially leaking into other cellular compartments such as the cytosol or ER lumen, as previously proposed. Overall, our results offer compelling evidence that mitochondrial ROS elevation is the likely trigger of MRR.

Keywords:  Arabidopsis; mitochondria; reactive oxygen species; retrograde signaling

DOI:  https://doi.org/10.1016/j.cub.2023.12.005
Front Aging Neurosci. 2023 ;15 1290681

The DNA repair enzyme, aprataxin, plays a role in innate immune signaling.

Helena B Madsen, Louise I Pease, Rebekah-Louise Scanlan, Mansour Akbari, Lene J Rasmussen, Daryl P Shanley, Vilhelm A Bohr.

  Ataxia with oculomotor apraxia type 1 (AOA1) is a progressive neurodegenerative disorder characterized by a gradual loss of coordination of hand movements, speech, and eye movements. AOA1 is caused by an inactivation mutation in the APTX gene. APTX resolves abortive DNA ligation intermediates. APTX deficiency may lead to the accumulation of 5'-AMP termini, especially in the mitochondrial genome. The consequences of APTX deficiency includes impaired mitochondrial function, increased DNA single-strand breaks, elevated reactive oxygen species production, and altered mitochondrial morphology. All of these processes can cause misplacement of nuclear and mitochondrial DNA, which can activate innate immune sensors to elicit an inflammatory response. This study explores the impact of APTX knockout in microglial cells, the immune cells of the brain. RNA-seq analysis revealed significant differences in the transcriptomes of wild-type and APTX knockout cells, especially in response to viral infections and innate immune pathways. Specifically, genes and proteins involved in the cGAS-STING and RIG-I/MAVS pathways were downregulated in APTX knockout cells, which suggests an impaired immune response to cytosolic DNA and RNA. The clinical relevance of these findings was supported by analyzing publicly available RNA-seq data from AOA1 patient cell lines. Comparisons between APTX-deficient patient cells and healthy control cells also revealed altered immune responses and dysregulated DNA- and RNA-sensing pathways in the patient cells. Overall, this study highlights the critical role of APTX in regulating innate immunity, particularly in DNA- and RNA-sensing pathways. Our findings contribute to a better understanding of the underlying molecular mechanisms of AOA1 pathology and highlights potential therapeutic targets for this disease.

Keywords:  APTX; DNA repair; DNA- and RNA-sensing pathways; ataxia; innate immunity; microglia; neurodegenerative diseases

DOI:  https://doi.org/10.3389/fnagi.2023.1290681
Exp Physiol. 2024 Jan 05.

Low-dose X-ray radiation induces an adaptive response: A potential countermeasure to galactic cosmic radiation exposure.

Siena Edwards, Jessica Adams, Anastasia Tchernikov, John G Edwards.

  Space exploration involves many dangers including galactic cosmic radiation (GCR). This class of radiation includes high-energy protons and heavy ionizing ions. NASA has defined GCR as a carcinogenic risk for long-duration space missions. To date, no clear strategy has been developed to counter chronic GCR exposure. We hypothesize that preconditioning cells with low levels of radiation will be protective from subsequent higher radiation exposures. H9C2 cells were pretreated with 0.1 to 1.0 Gy X-rays. The challenge radiation exposure consisted of either 8 Gy X-rays or 75 cGy of GCR, using a five-ion GCRsim protocol. A cell doubling time assay was used to determine cell viability. An 8 Gy X-ray challenge alone significantly (P < 0.05) increased cell doubling time compared to the no-radiation control group. Low-dose radiation pre-treatment ameliorated the 8 Gy X-ray-induced increases in cell doubling time. A 75 cGy GCR challenge alone significantly increased cell doubling time compared to the no-radiation group. Following the 75 cGy challenge, only the 0.5 and 1.0 Gy pre-treatment ameliorated the 75 cGy-induced increases in cell doubling time. DNA damage or pathological oxidant stress will delay replicative functions and increase cell doubling time. Our results suggested that pretreatment with low-dose X-rays induced an adaptive response which offered a small but significant protection against a following higher radiation challenge. Although perhaps not a practical countermeasure, these findings may serve to offer insight into cell signalling pathways activated in response to low-dose irradiation and targeted for countermeasure development.

Keywords:  DNA damage; cardiomyopathy; galactic cosmic radiation; space flight countermeasures

DOI:  https://doi.org/10.1113/EP091350
Cell. 2024 Jan 04. pii: S0092-8674(23)01321-1. [Epub ahead of print]187(1): 95-109.e26

Engineering TALE-linked deaminases to facilitate precision adenine base editing in mitochondrial DNA.

Sung-Ik Cho, Kayeong Lim, Seongho Hong, Jaesuk Lee, Annie Kim, Chae Jin Lim, Seungmin Ryou, Ji Min Lee, Young Geun Mok, Eugene Chung, Sanghun Kim, Seunghun Han, Sang-Mi Cho, Jieun Kim, Eun-Kyoung Kim, Ki-Hoan Nam, Yeji Oh, Minkyung Choi, Tae Hyeon An, Kyoung-Jin Oh, Seonghyun Lee, Hyunji Lee, Jin-Soo Kim.

  DddA-derived cytosine base editors (DdCBEs) and transcription activator-like effector (TALE)-linked deaminases (TALEDs) catalyze targeted base editing of mitochondrial DNA (mtDNA) in eukaryotic cells, a method useful for modeling of mitochondrial genetic disorders and developing novel therapeutic modalities. Here, we report that A-to-G-editing TALEDs but not C-to-T-editing DdCBEs induce tens of thousands of transcriptome-wide off-target edits in human cells. To avoid these unwanted RNA edits, we engineered the substrate-binding site in TadA8e, the deoxy-adenine deaminase in TALEDs, and created TALED variants with fine-tuned deaminase activity. Our engineered TALED variants not only reduced RNA off-target edits by >99% but also minimized off-target mtDNA mutations and bystander edits at a target site. Unlike wild-type versions, our TALED variants were not cytotoxic and did not cause developmental arrest of mouse embryos. As a result, we obtained mice with pathogenic mtDNA mutations, associated with Leigh syndrome, which showed reduced heart rates.

Keywords:  CRISPR-adenine base editor; Leigh syndrome; RNA off-target; TALE-linked adenine deaminase; TALED; genetic disease; in vivo genome editing; mitochondria; mitochondrial genome editing; mtDNA

DOI:  https://doi.org/10.1016/j.cell.2023.11.035