bims-nenemi 2024-12-08 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2024–12–08
nine papers selected by
Marco Tigano, Thomas Jefferson University

OPA1 and disease-causing mutants perturb mitochondrial nucleoid distribution.
OCIAD1 and prohibitins regulate the stability of the TIM23 protein translocase.
Aberrant METTL1-mediated tRNA m7G modification alters B-cell responses in systemic autoimmunity in humans and mice.
Palmitoylation acts as a checkpoint for MAVS aggregation to promote antiviral innate immune responses.
HRK downregulation and augmented BCL-xL binding to BAK confer apoptotic protection to therapy-induced senescent melanoma cells.
Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses.
Mitochondria dysfunction: A trigger for cardiovascular diseases in systemic lupus erythematosus.
IRF-1 Regulates Mitochondrial Respiration and Intrinsic Apoptosis Under Metabolic Stress through ATP Synthase Ancillary Factor TMEM70.
Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes.

Cell Death Dis. 2024 Nov 30. 15(11): 870

OPA1 and disease-causing mutants perturb mitochondrial nucleoid distribution.

J Macuada, I Molina-Riquelme, G Vidal, N Pérez-Bravo, C Vásquez-Trincado, G Aedo, D Lagos, P Yu-Wai-Man, R Horvath, T J Rudge, B Cartes-Saavedra, V Eisner.

Optic atrophy protein 1 (OPA1) mediates inner mitochondrial membrane (IMM) fusion and cristae organization. Mutations in OPA1 cause autosomal dominant optic atrophy (ADOA), a leading cause of blindness. Cells from ADOA patients show impaired mitochondrial fusion, cristae structure, bioenergetic function, and mitochondrial DNA (mtDNA) integrity. The mtDNA encodes electron transport chain subunits and is packaged into nucleoids spread within the mitochondrial population. Nucleoids interact with the IMM, and their distribution is tightly linked to mitochondrial fusion and cristae shaping. Yet, little is known about the physio-pathological relevance of nucleoid distribution. We studied the effect of OPA1 and ADOA-associated mutants on nucleoid distribution using high-resolution confocal microscopy. We applied a novel model incorporating the mitochondrial context, separating nucleoid distribution into the array in the mitochondrial population and intramitochondrial longitudinal distribution. Opa1-null cells showed decreased mtDNA levels and nucleoid abundance. Also, loss of Opa1 led to an altered distribution of nucleoids in the mitochondrial population, loss of cristae periodicity, and altered nucleoids to cristae proximity partly rescued by OPA1 isoform 1. Overexpression of WT OPA1 or ADOA-causing mutants c.870+5 G > A or c.2713 C > T in WT cells, showed perturbed nucleoid array in the mitochondria population associated with cristae disorganization, which was partly reproduced in Skeletal muscle-derived fibroblasts from ADOA patients harboring the same mutants. Opa1-null and cells overexpressing ADOA mutants accumulated mitochondria without nucleoids. Interestingly, intramitochondrial nucleoid distribution was only altered in Opa1-null cells. Altogether, our results highlight the relevance of OPA1 in nucleoid distribution in the mitochondrial landscape and at a single-organelle level and shed light on new components of ADOA etiology.

DOI: https://doi.org/10.1038/s41419-024-07165-9
Cell Rep. 2024 Dec 03. pii: S2211-1247(24)01389-5. [Epub ahead of print]43(12): 115038

OCIAD1 and prohibitins regulate the stability of the TIM23 protein translocase.

Praveenraj Elancheliyan, Klaudia K Maruszczak, Remigiusz Adam Serwa, Till Stephan, Ahmet Sadik Gulgec, Mayra A Borrero-Landazabal, Sonia Ngati, Aleksandra Gosk, Stefan Jakobs, Michal Wasilewski, Agnieszka Chacinska.

  Mitochondrial proteins are transported and sorted to the matrix or inner mitochondrial membrane by the presequence translocase TIM23. In yeast, this essential and highly conserved machinery is composed of the core subunits Tim23 and Tim17. The architecture, assembly, and regulation of the human TIM23 complex are poorly characterized. The human genome encodes two paralogs, TIMM17A and TIMM17B. Here, we describe an unexpected role of the ovarian cancer immunoreactive antigen domain-containing protein 1 (OCIAD1) and the prohibitin complex in the biogenesis of human TIM23. Prohibitins were required to stabilize both the TIMM17A- and TIMM17B-containing variants of the translocase. Interestingly, OCIAD1 assembled with the prohibitin complex to protect the TIMM17A variant from degradation by the YME1L protease. The expression of OCIAD1 was in turn regulated by the status of the TIM23 complex. We postulate that OCIAD1 together with prohibitins constitute a regulatory axis that differentially regulates variants of human TIM23.

Keywords:  CP: Cell biology; OCIAD1; TIM23 translocase; biogenesis; mitochondria; prohibitin

DOI:  https://doi.org/10.1016/j.celrep.2024.115038
Nat Commun. 2024 Dec 05. 15(1): 10599

Aberrant METTL1-mediated tRNA m7G modification alters B-cell responses in systemic autoimmunity in humans and mice.

Shuyi Wang, Hui Han, Yichao Qian, Xinyuan Ruan, Zhangmei Lin, Jin Li, Binfeng Chen, Yimei Lai, Zhaoyu Wang, Mengyuan Li, Jingping Wen, Xiaoyu Yin, Niansheng Yang, Shuibin Lin, Hui Zhang.

Upon activation, naive B cells exit their quiescent state and enter germinal center (GC) responses, a transition accompanied by increased protein synthesis. How protein translation efficiency is adequately adjusted to meet the increased demand requires further investigation. Here, we identify the methyltransferase METTL1 as a translational checkpoint during GC responses. Conditional knockout of Mettl1 in mouse B cells blocks GC entry and impairs GC formation, whereas conditional knock-in of Mettl1 promotes GC responses. Mechanistically, METTL1 catalyzes m7G modification in a specific subset of tRNAs to preferentially translate BCR signaling-related proteins, ensuring mitochondrial electron transporter chain activity and sufficient bioenergetics in B cells. Pathologically, METTL1-mediated tRNA m7G modification controls B-cell autoreactivity in SLE patients or lupus-prone mice, and deletion of Mettl1 alleviates dysregulated B-cell responses during autoimmune induction. Thus, these results support the function of METTL1 in orchestrating an effective B-cell response and reveal that aberrant METTL1-mediated tRNA m7G modification promotes autoreactive B cells in systemic autoimmunity.

DOI: https://doi.org/10.1038/s41467-024-54941-4
J Clin Invest. 2024 Dec 02. pii: e177924. [Epub ahead of print]134(23):

Palmitoylation acts as a checkpoint for MAVS aggregation to promote antiviral innate immune responses.

Liqiu Wang, Mengqiu Li, Guangyu Lian, Shuai Yang, Jing Cai, Zhe Cai, Yaoxing Wu, Jun Cui.

  Upon RNA virus infection, the signaling adaptor MAVS forms functional prion-like aggregates on the mitochondrial outer membrane, which serve as a central hub that links virus recognition to downstream antiviral innate immune responses. Multiple mechanisms regulating MAVS activation have been revealed; however, the checkpoint governing MAVS aggregation remains elusive. Here, we demonstrated that the palmitoylation of MAVS at cysteine 79 (C79), which is catalyzed mainly by the palmitoyl S-acyltransferase ZDHHC12, was essential for MAVS aggregation and antiviral innate immunity upon viral infection in macrophages. Notably, the systemic lupus erythematosus-associated mutation MAVS C79F was associated with defective palmitoylation, resulting in low type I interferon (IFN) production. Accordingly, Zdhhc12 deficiency apparently impaired RNA virus-induced type I IFN responses, and Zdhhc12-deficient mice were highly susceptible to lethal viral infection. These findings reveal a previously unknown mechanism by which the palmitoylation of MAVS is a checkpoint for its aggregation during viral infection to ensure timely activation of antiviral defense.

Keywords:  Cell biology; Immunology; Innate immunity; Molecular biology

DOI:  https://doi.org/10.1172/JCI177924
Cell Death Differ. 2024 Dec 03.

HRK downregulation and augmented BCL-xL binding to BAK confer apoptotic protection to therapy-induced senescent melanoma cells.

Clara Alcon, Marta Kovatcheva, Paula Morales-Sánchez, Vanessa López-Polo, Teresa Torres, Susana Puig, Albert Lu, Josep Samitier, Carlos Enrich, Manuel Serrano, Joan Montero.

Senescent cells are commonly detected in tumors after chemo and radiotherapy, leading to a characteristic cellular phenotype that resists apoptotic cell death. In this study, we used multiple melanoma cell lines, molecular markers, and therapies to investigate the key role of the BCL-2 family proteins in the survival of senescent cells. We first used BH3 profiling to assess changes in apoptotic priming upon senescence induction. Unexpectedly, not all cell types analyzed showed a decrease in apoptotic priming, BIM was downregulated, there was variability in BAX expression and BAK remained constant or increased. Therefore, there was not a clear pattern for pro-survival adaptation. Many studies have been devoted to find ways to eliminate senescent cells, leading to one of the most studied senolytic agents: navitoclax, a promiscuous BH3 mimetic that inhibits BCL-2, BCL-xL and BCL-W. While it is known that the BCL-2 family of proteins is commonly upregulated in senescent cells, the complexity of the apoptotic network has not been fully explored. Interestingly, we found distinct protein expression changes always leading to a BCL-xL mediated pro-survival adaptation, as assessed by BH3 profiling. When analyzing potential therapeutic strategies, we observed a stronger senolytic activity in these melanoma cell lines when specifically targeting BCL-xL using A-1331852, navitoclax or the PROTAC BCL-xL degrader DT2216. We found that the sensitizer protein HRK was systematically downregulated when senescence was induced, leading to an increased availability of BCL-xL. Furthermore, we identified that the main apoptotic inhibition was shaped by BCL-xL and BAK binding increase that prevented mitochondrial permeabilization and apoptosis. To our knowledge, this is the first time that the molecular basis for BCL-xL anti-apoptotic adaptation in senescence is described, paving the way for the development of new molecules that either prevent HRK downregulation or displace BCL-xL binding to BAK to be used as senolytics.

DOI: https://doi.org/10.1038/s41418-024-01417-z
EMBO Rep. 2024 Dec 02.

Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses.

Magdalena Shumanska, Dmitri Lodygin, Christine S Gibhardt, Christian Ickes, Ioana Stejerean-Todoran, Lena C M Krause, Kira Pahl, Lianne J H C Jacobs, Andrea Paluschkiwitz, Shuya Liu, Angela Boshnakovska, Niels Voigt, Tobias J Legler, Martin Haubrock, Miso Mitkovski, Gereon Poschmann, Peter Rehling, Sven Dennerlein, Jan Riemer, Alexander Flügel, Ivan Bogeski.

  T-cell receptor (TCR)-induced Ca2+ signals are essential for T-cell activation and function. In this context, mitochondria play an important role and take up Ca2+ to support elevated bioenergetic demands. However, the functional relevance of the mitochondrial-Ca2+-uniporter (MCU) complex in T-cells was not fully understood. Here, we demonstrate that TCR activation causes rapid mitochondrial Ca2+ (mCa2+) uptake in primary naive and effector human CD4+ T-cells. Compared to naive T-cells, effector T-cells display elevated mCa2+ and increased bioenergetic and metabolic output. Transcriptome and proteome analyses reveal molecular determinants involved in the TCR-induced functional reprogramming and identify signalling pathways and cellular functions regulated by MCU. Knockdown of MCUa (MCUaKD), diminishes mCa2+ uptake, mitochondrial respiration and ATP production, as well as T-cell migration and cytokine secretion. Moreover, MCUaKD in rat CD4+ T-cells suppresses autoimmune responses in an experimental autoimmune encephalomyelitis (EAE) multiple sclerosis model. In summary, we demonstrate that mCa2+ uptake through MCU is essential for proper T-cell function and has a crucial role in autoimmunity. T-cell specific MCU inhibition is thus a potential tool for targeting autoimmune disorders.

Keywords:  Autoimmunity; Calcium; MCU; Mitochondria; T-cell

DOI:  https://doi.org/10.1038/s44319-024-00313-4
Int Immunopharmacol. 2024 Dec 01. pii: S1567-5769(24)02244-6. [Epub ahead of print]144 113722

Mitochondria dysfunction: A trigger for cardiovascular diseases in systemic lupus erythematosus.

Haitao Wang, Rui Tang, Qinyu Pan, Qiuyan Yin, Jian Feng, Li Deng.

  Cardiovascular disease (CVD), including pericarditis, myocarditis, sudden cardiac death, coronary heart disease, and stroke, are leading contributors to morbidity and mortality in systemic lupus erythematosus (SLE) patients. Emerging evidence highlights mitochondrial dysfunction as a key driver of cardiovascular pathology in SLE, with impaired oxidative phosphorylation, altered membrane potential, and disrupted metabolic processes promoting oxidative stress, inflammatory activation, and endothelial dysfunction. This review critically examines mitochondrial contributions to CVD in SLE, comparing these mechanisms with those in non-SLE CVD to highlight SLE-specific mitochondrial vulnerabilities. Furthermore, we discuss preclinical and clinical findings supporting mitochondrial pathways as potential therapeutic targets, aiming to bridge gaps in current understanding and outline future research directions. By synthesizing current knowledge of mitochondrial dysregulation, this review proposes therapeutic strategies to improve cardiovascular outcomes and advance patient care in SLE.

Keywords:  Atherosclerosis; Cardiovascular disease; Mitochondrial dysfunction; Oxidative stress; Systemic lupus erythematosus; Therapeutic target

DOI:  https://doi.org/10.1016/j.intimp.2024.113722
Inflammation. 2024 Dec 06.

IRF-1 Regulates Mitochondrial Respiration and Intrinsic Apoptosis Under Metabolic Stress through ATP Synthase Ancillary Factor TMEM70.

ChongXiu Sun, Haotian Sun, Jiahao Wei, Xing Fan, Scott I Simon, Anthony G Passerini.

  Mitochondrial dysfunction, which can be caused by metabolic stressors such as oxidized low-density lipoprotein (oxLDL), sensitizes the endothelium to pathological changes. The transcription factor interferon regulatory factor 1 (IRF-1) is a master regulator of inflammation, previously shown to promote oxLDL-induced inflammatory pyroptosis in human aortic endothelial cells (HAEC). However, a presumed role for IRF-1 in regulating the intrinsic apoptotic pathway in response to metabolic stress has not been demonstrated. Here targeted deletion of IRF-1 by siRNA in HAEC aggravated oxLDL-induced, mitochondria-mediated intrinsic apoptosis, as evidenced by increased Caspase-3 and Caspase-9 activation, and chromosomal DNA breakage. The increased apoptosis was concomitant with accumulation of mitochondrial ROS, decrease in intracellular ATP production and respiratory oxygen consumption, and abnormal mitochondrial structure. RNA profiling of endothelial cells isolated from wild type and Irf1 knockout mice, followed by quantitative PCR, luciferase activity assay and chromatin immunoprecipitation (ChIP), revealed that IRF-1 directly regulated the expression of transmembrane protein 70 (TMEM70), an ancillary factor required for the assembly of ATP synthase and conversion of an electrochemical gradient to ATP synthesis. Mirroring the effect of IRF1 knockdown, depletion of TMEM70 in HAEC resulted in impaired mitochondrial function and enhanced cell apoptosis. In contrast, overexpression of TMEM70 rescued ATP biosynthesis and suppressed apoptosis in oxLDL-treated, IRF-1-deficient HAEC. These results reveal a novel homeostatic role for IRF-1 in the regulation of mitochondrial function and associated stress-induced apoptosis.

Keywords:  Apoptosis; IRF-1; Inflammation; Metabolism; Mitochondrial dysfunction; Reactive oxygen species; TMEM70

DOI:  https://doi.org/10.1007/s10753-024-02209-w
Nat Biomed Eng. 2024 Dec 04.

Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes.

Jiang-An Yin, Lukas Frick, Manuel C Scheidmann, Tingting Liu, Chiara Trevisan, Ashutosh Dhingra, Anna Spinelli, Yancheng Wu, Longping Yao, Dalila Laura Vena, Britta Knapp, Jingjing Guo, Elena De Cecco, Kathi Ging, Andrea Armani, Edward J Oakeley, Florian Nigsch, Joel Jenzer, Jasmin Haegele, Michal Pikusa, Joachim Täger, Salvador Rodriguez-Nieto, Vangelis Bouris, Rafaela Ribeiro, Federico Baroni, Manmeet Sakshi Bedi, Scott Berry, Marco Losa, Simone Hornemann, Martin Kampmann, Lucas Pelkmans, Dominic Hoepfner, Peter Heutink, Adriano Aguzzi.

Arrayed CRISPR libraries extend the scope of gene-perturbation screens to non-selectable cell phenotypes. However, library generation requires assembling thousands of vectors expressing single-guide RNAs (sgRNAs). Here, by leveraging massively parallel plasmid-cloning methodology, we show that arrayed libraries can be constructed for the genome-wide ablation (19,936 plasmids) of human protein-coding genes and for their activation and epigenetic silencing (22,442 plasmids), with each plasmid encoding an array of four non-overlapping sgRNAs designed to tolerate most human DNA polymorphisms. The quadruple-sgRNA libraries yielded high perturbation efficacies in deletion (75-99%) and silencing (76-92%) experiments and substantial fold changes in activation experiments. Moreover, an arrayed activation screen of 1,634 human transcription factors uncovered 11 novel regulators of the cellular prion protein PrPC, screening with a pooled version of the ablation library led to the identification of 5 novel modifiers of autophagy that otherwise went undetected, and 'post-pooling' individually produced lentiviruses eliminated template-switching artefacts and enhanced the performance of pooled screens for epigenetic silencing. Quadruple-sgRNA arrayed libraries are a powerful and versatile resource for targeted genome-wide perturbations.

DOI: https://doi.org/10.1038/s41551-024-01278-4