bims-mibica 2025-07-20 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2025–07–20
23 papers selected by
Kelsey Fisher-Wellman, Wake Forest University

Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments.
High mtDNA content identifies oxidative phosphorylation-driven acute myeloid leukemias and represents a therapeutic vulnerability.
Mitochondrial DNA: how does it leave mitochondria?
Lipoyl deglutarylation by ABHD11 regulates mitochondrial and T cell metabolism.
Riboflavin drives nucleotide biosynthesis and iron-sulfur metabolism to promote acute myeloid leukemia.
Deletion of AC8 in glioma cells elevates oxidative phosphorylation by system-wide remodeling of the mitochondrial proteome.
mtKO: A dedicated guide RNA library for mitochondria research.
Impaired mitochondrial metabolism is a critical cancer vulnerability for MYC inhibitors.
Targeting bone marrow mesenchymal stromal cells-derived IL-6 to overcome acute myeloid leukemia chemoresistance.
Mitochondrial respiration is necessary for CD8+ T cell proliferation and cell fate.
Nucleoside diphosphate kinase strongly promotes GDP and ADP metabolism in the cell and affects endogenous proton leak in mitochondria - the kinase is hampered by oxidative phosphorylation inhibitors.
Multi-site phosphorylation of BCL2L13 in a TBK1- and AMPK-dependent manner reveals new modes of mitophagy regulation.
Exploring the oncogenic impact of heteroplasmic de novo MT-ND5 truncating mutations.
Organic cation transporter 3 on neuronal mitochondria mediates MPP+-induced mitochondrial dysfunction and neurotoxicity in a TIMM22-dependent manner.
MICU proteins facilitate Ca2+-dependent mitochondrial metabolon formation to regulate cellular energetics - independent of MCU.
Dynamic assembly of malate dehydrogenase-citrate synthase multienzyme complex in the mitochondria.
Mitochondria dysfunction: cause or consequence of physiologic aging?
Specialized high-capacity mitochondria fuel cell invasion.
Respiratory complex III 2 assembles complex I via toxic intermediate in mitochondrial disease.
Paclitaxel-induced mitotic arrest results in a convergence of apoptotic dependencies that can be safely exploited by BCL-X L degradation to overcome cancer chemoresistance.
A Platform for Mitochondrial Profiling in Enriched Kidney Segments Under Thermodynamic Control.
Old mitochondria regulate niche renewal via α-ketoglutarate metabolism in stem cells.
Utility of IDH1/2 mutations as biomarkers for detection of measurable residual disease in acute myeloid leukemia.

bioRxiv. 2025 May 10. pii: 2025.05.09.653205. [Epub ahead of print]

Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments.

Sarah M Chang, Muhammad Bin Munim, Sonia E Trojan, Anna Shevzov-Zebrun, Keene L Abbott, Matthew G Vander Heiden.

The cell NAD+/NADH ratio can constrain biomass synthesis and influence proliferation in nutrient-limited environments. However, which cell processes regulate the NAD+/NADH ratio is not known. Here, we find that some cancer cells elevate the NAD+/NADH ratio in response to serine deprivation by increasing mitochondrial respiration. Cancer cells that elevate mitochondrial respiration have higher serine production and proliferation in serine limiting conditions than cells with no mitochondrial respiration response, independent of serine synthesis enzyme expression. Increases in mitochondrial respiration and the NAD+/NADH ratio promote serine synthesis regardless of whether serine is environmentally limiting. Lipid deprivation can also increase the NAD+/NADH ratio via mitochondrial respiration in some cells, including cells that do not increase respiration following serine deprivation. Thus, in cancer cells where lipid depletion raises the NAD+/NADH ratio, proliferation in serine depleted environments improves when lipids are also depleted. Taken together, these data suggest that changes in mitochondrial respiration in response to nutrient deprivation can influence the NAD+/NADH ratio in a cell-specific manner to impact oxidative biomass synthesis and proliferation. Given the complexity of tumor microenvironments, this work provides a metabolic framework for understanding how levels of more than one environmental nutrient affects cancer cell proliferation.

DOI: https://doi.org/10.1101/2025.05.09.653205
Signal Transduct Target Ther. 2025 Jul 14. 10(1): 222

High mtDNA content identifies oxidative phosphorylation-driven acute myeloid leukemias and represents a therapeutic vulnerability.

Diego A Pereira-Martins, Isabel Weinhäuser, Emmanuel Griessinger, Juan L Coelho-Silva, Douglas R Silveira, Dominique Sternadt, Ayşegül Erdem, Bruno Kosa L Duarte, Prodromos Chatzikyriakou, Lynn Quek, Antonio Bruno Alves-Silva, Fabiola Traina, Sara T Olalla Saad, Jacobien R Hilberink, Amanda Moreira-Aguiar, Maria L Salustiano-Bandeira, Marinus M Lima, Pedro L Franca-Neto, Marcos A Bezerra, Nisha K van der Meer, Emanuele Ammatuna, Eduardo M Rego, Gerwin Huls, Jan Jacob Schuringa, Antonio R Lucena-Araujo.

Metabolic reprogramming is a hallmark of cancer, with acute myeloid leukemia (AML) being no exception. Mitochondrial function, particularly its role in protecting tumor cells against chemotherapy, is of significant interest in AML chemoresistance. In this study, we identified mitochondrial DNA content (mtDNAc), measured by quantitative PCR, as a simple and precise marker to stratify the metabolic states of AML patients. We show that patients with high mtDNAc are associated with increased mitochondrial metabolism and a higher dependency on oxidative phosphorylation (OXPHOS), often correlating with chemoresistance. Clinically, patients receiving cytarabine and an anthracycline-based regimen (7 + 3 regimen) experienced inferior relapse-free survival and a higher overall rate of leukemia recurrence. Ex vivo experiments using primary AML samples confirmed cytarabine resistance in high mtDNAc patients, which could be overcome by inhibiting mitochondrial complex I. The FDA-approved drug metformin, which targets mitochondrial metabolism, significantly enhanced apoptosis in response to chemotherapy or targeted agents, such as venetoclax, in AML models. However, metformin-treated cells adapted by increasing glycolysis and NAD+ production, a resistance mechanism that could be bypassed by targeting the nicotinamide phosphoribosyltransferase (NAMPT) enzyme. In summary, we demonstrated that mtDNAc is an effective tool for assessing the metabolic state of AML cells. This method can be easily implemented in clinical practice to identify chemoresistant patients and guide personalized treatment strategies, including novel combination therapies for those with a high reliance on mitochondrial metabolism.

DOI: https://doi.org/10.1038/s41392-025-02303-x
Trends Cell Biol. 2025 Jul 10. pii: S0962-8924(25)00146-1. [Epub ahead of print]

Mitochondrial DNA: how does it leave mitochondria?

Vladimir Gogvadze, Boris Zhivotovsky.

  In recent years, studies have reported the presence of mitochondrial DNA (mtDNA) in the cytosol. However, a certain number of publications on the mechanisms of mtDNA release contain uncertainties. mtDNA is located in the mitochondrial matrix and cannot be released through the same pathways as intermembrane space proteins. This forum article aims to examine the assumptions and elucidate the processes underlying this phenomenon.

Keywords:  Bcl-2 family proteins; inner mitochondrial membrane; mitochondria; mtDNA; outer mitochondrial membrane

DOI:  https://doi.org/10.1016/j.tcb.2025.06.005
Nat Chem Biol. 2025 Jul 15.

Lipoyl deglutarylation by ABHD11 regulates mitochondrial and T cell metabolism.

Guinevere L Grice, Eleanor Minogue, Hudson W Coates, Mekdes Debela, Richard J Stopforth, Niek Wit, Zongyu Li, Joseph P Crowley, Arthur Kaser, Nicole Kaneider-Kaser, P Robin Antrobus, Marcia C Haigis, Randall S Johnson, James A Nathan.

Glutarate is an intermediate of amino acid catabolism and an important metabolite for reprogramming T cell immunity. Glutarate exerts its effects either by directly inhibiting metabolite-dependent enzymes or through conjugation to substrates. Intriguingly, glutarylation can occur on protein and nonprotein substrates, but our understanding of these distinct glutaryl modifications is in its infancy. Here we uncover ABHD11 as a noncanonical deglutarylating enzyme critical for maintaining the tricarboxylic acid (TCA) cycle. Mechanistically, we find ABHD11 removes glutaryl adducts from lipoate-an essential fatty acid modification required for the TCA cycle. Loss of ABHD11 results in the accumulation of glutaryl-lipoyl adducts that drive an adaptive program, involving 2-oxoglutarate accumulation, that rewires mitochondrial metabolism. Functionally, this role of ABHD11 influences the metabolic programming of human CD8+ T cells. Therefore, our findings reveal lipoyl glutarylation as a reversible modification that regulates the TCA cycle.

DOI: https://doi.org/10.1038/s41589-025-01965-6
bioRxiv. 2025 Jun 29. pii: 2025.06.26.661633. [Epub ahead of print]

Riboflavin drives nucleotide biosynthesis and iron-sulfur metabolism to promote acute myeloid leukemia.

Stefan Bjelosevic, Rahel Fauth, Brian T Do, Gabriela Alexe, Lucy A Merickel, Thomas D Jackson, Allen T Basanthakumar, Audrey Taillon, Silvi Salhotra, Birgitta Ryback, Constanze Schneider, Giulia DiGiovanni, Ryan Elbashir, Nils Burger, Muhammad Bin Munim, Shan Lin, Pere Puigserver, David E Root, Matthew G Vander Heiden, Kimberly Stegmaier.

Riboflavin is a diet-derived vitamin in higher organisms that serves as a precursor for flavin mononucleotide and flavin adenine dinucleotide, key cofactors that participate in oxidoreductase reactions. Here, using proteomic, metabolomic and functional genomics approaches, we describe a specific riboflavin dependency in acute myeloid leukemia and demonstrate that, in addition to energy production via oxidative phosphorylation, a key biological role of riboflavin is to enable nucleotide biosynthesis and iron-sulfur cluster metabolism. Genetic perturbation of riboflavin metabolism pathways or exogenous depletion in physiological culture medium induce nucleotide imbalance and DNA damage responses, as well as impair the stability and activity of proteins which utilize [4Fe-4S] iron-sulfur clusters as cofactors. We identify a window of therapeutic opportunity upon riboflavin starvation or chemical riboflavin metabolism perturbation and demonstrate that this strongly synergizes with BCL-2 inhibition. Our work identifies riboflavin as a critical metabolic dependency in leukemia, with functions beyond energy production.

DOI: https://doi.org/10.1101/2025.06.26.661633
Biochim Biophys Acta Bioenerg. 2025 Jul 14. pii: S0005-2728(25)00033-7. [Epub ahead of print] 149567

Deletion of AC8 in glioma cells elevates oxidative phosphorylation by system-wide remodeling of the mitochondrial proteome.

Emil Jakobsen, Jacob M Bech, Jens V Andersen, Emil W Westi, Martin R Larsen, Niels H Skotte, José M A Moreira, Blanca I Aldana, Lasse K Bak.

  The Warburg effect is the reprogramming of cancer cells towards glycolytic metabolism, likely producing and releasing lactate into the tumor microenvironment. This lactate has been suggested to partly drive tumor growth by signaling through the lactate receptor, GPR81. Thus, reprogramming cancer cells away from glycolytic activity may be beneficial for cancer treatment. Here, we show that deletion of ADCY8 (coding for adenylyl cyclase 8; AC8) employing the CRISPR-Cas9 technology in U87MG glioma cells, changes the proteome of these cells through a system-wide transformation in expression of mitochondrial proteins. These changes shift the metabolic balance towards oxidative phosphorylation, as shown by an increase in oxygen consumption, an elevation in tricarboxylic acid cycle flux, and a concomitant decrease in glycolytic flux. This metabolic shift is likely driven by the absence of AC8-mediated transcriptional regulation and may suggest that inhibition of AC8 activity could hold therapeutic potential in the treatment of cancer.

Keywords:  ADCY8; Cancer; Glycolysis; Metabolism; Mitochondria; Warburg

DOI:  https://doi.org/10.1016/j.bbabio.2025.149567
Proc Natl Acad Sci U S A. 2025 Jul 22. 122(29): e2502285122

mtKO: A dedicated guide RNA library for mitochondria research.

Karambir Kaur, Javeria Zaheer, Fengchao Lang, Diego Luis Ribeiro, Meili Zhang, Hua Song, Wei Zhang, Raj Chari, Hussam Alkaissi, Chunzhang Yang.

  Mitochondria are multifunctional organelles central to both physiological and pathological processes. In malignant cancer cells, mitochondrial reprogramming establishes the metabolic foundation to meet cellular demands, which is particularly important in tumor cells with existing metabolic perturbations. To identify key mitochondrial pathways supporting cancer development, we developed mitochondria Knockout (mtKO), a robust and unbiased CRISPR screening platform to pinpoint critical mitochondria-associated pathways. The mtKO screen revealed that the mitochondrial antioxidant enzyme SOD2 is essential for cells harboring IDH1 mutations. Mechanistically, SOD2 activity determines the disease manifestation of IDH1-mutated cancers, through maintaining redox homeostasis and mitochondrial fitness. This study introduces a powerful functional genomic tool to identify mitochondrial-centered pathways and reveals the selective mitochondrial vulnerability in Krebs cycle-deficient cancers for future therapeutic intervention.

Keywords:  CRISPR screen; IDH1; SOD2; metabolism; mitochondria

DOI:  https://doi.org/10.1073/pnas.2502285122
Sci Adv. 2025 Jul 18. 11(29): eadw5228

Impaired mitochondrial metabolism is a critical cancer vulnerability for MYC inhibitors.

William Yang, Qianyu Guo, Songhua Quan, Zachary R Chalmers, J Brandon Parker, Mihai Truica, Mary F Dufficy, Megan M Kerber, Karthik Vasan, Dikshat G Gupta, Adam W T Steffeck, Hao Pan, Mohammed Siddiqui, H Tran Pham, Gary E Schiltz, Debabrata Chakravarti, Navdeep S Chandel, Sarki A Abdulkadir.

MYC is a key driver in many aggressive and therapy-resistant cancers. We have developed and characterized a small-molecule MYC inhibitor named MYCi975. To uncover combination strategies for MYC inhibitors, we conducted a genome-wide CRISPR screen using MYCi975. This screen revealed a notable synthetic lethality when MYC inhibition was paired with disruption of mitochondrial complex I components, but not other complexes. Mechanistically, MYC inhibition reduced oxidative phosphorylation and glycolysis, triggering a compensatory up-regulation of complex I genes. Consequently, genetic or pharmacological targeting of complex I sensitized tumors to MYCi975 treatment, leading to increased purine catabolism and infiltration of CD8+ T cells and macrophages into tumors. Additionally, a wide range of tumor cells with lower complex I expression showed increased MYC dependency. These results indicate that metabolic adaptation to MYC inhibition exposes a targetable weakness at complex I and provide a rational strategy for combination therapy with emerging MYC inhibitors.

DOI: https://doi.org/10.1126/sciadv.adw5228
Blood Adv. 2025 Jul 16. pii: bloodadvances.2024015496. [Epub ahead of print]

Targeting bone marrow mesenchymal stromal cells-derived IL-6 to overcome acute myeloid leukemia chemoresistance.

Diyu Hou, Danni Cai, Wei Dai, Xinai Liao, Maoqing Tan, Xiaoming Zheng, Liuhuan Wang, Jingru Liu, Jin Wang, Xiaoting Wang, Qiang Fu, Huifang Huang.

In acute myeloid leukemia (AML), elevated IL-6 levels in the bone marrow (BM) are linked to poor prognosis. However, the mechanisms driving this elevation and its role in chemoresistance remain unclear. Using the Prrx1-Cre system, we selectively deleted Il6 in BM mesenchymal stromal cells (MSCs) and established an AML mouse model. Our results show that MSCs are a major source of IL-6 in AML BM. Importantly, Il6 deletion in MSCs reduced oxidative phosphorylation (OXPHOS) activity in AML cells, slowed disease progression, and enhanced the chemosensitivity to cytarabine (Ara-C). Similarly, the OXPHOS inhibitor IACS-010759 improved chemosensitivity in AML mice. Exogenous recombinant IL-6 reversed the chemosensitivity gains from Il6 deletion, confirming its role in chemoresistance. We further demonstrated that Il6 absence in MSCs inhibits mitochondria transfer to AML cells, dampening OXPHOS and enhancing Ara-C efficacy. In summary, our study underscores the critical role of Il6 from MSCs in AML progression and chemoresistance. Targeting IL-6 in MSCs may offer a promising therapeutic strategy for AML. NCT06486350.

DOI: https://doi.org/10.1182/bloodadvances.2024015496
Nat Immunol. 2025 Jul 16.

Mitochondrial respiration is necessary for CD8+ T cell proliferation and cell fate.

Elizabeth M Steinert, Beatriz Furtado Bruza, Veronika D Danchine, Rogan A Grant, Karthik Vasan, Arjun Kharel, Yuqi Zhang, Weiguo Cui, Marten Szibor, Samuel E Weinberg, Navdeep S Chandel.

Mitochondrial electron transport chain (ETC) function is linked to the generation of ATP, signaling molecules including reactive oxygen species (ROS), pyrimidines and tricarboxylic acid cycle metabolites1. Mitochondrial electron transport is required for T cell proliferation2-4. However, which mitochondrial ETC functions are necessary for each dynamic state of CD8+ T cell responses is unknown. Here we report that impairing mitochondrial complex III function, which diminishes respiration, proton pumping linked to ATP production and superoxide production, decreases peripheral naive numbers, antigen-induced CD8+ T cell proliferation and memory formation. Acute stimulation of mitochondrial complex III-deficient CD8+ T cells induced an exhausted-like phenotype. Expression of Ciona intestinalis alternative oxidase (AOX) in mitochondrial complex III-deficient CD8+ T cells restores respiration without generating ROS or proton pumping, and rescues proliferation and the exhausted phenotype but not naive or memory formation. Thus, T cell development, proliferation and memory formation have distinct requirements for mitochondrial complex III ROS.

DOI: https://doi.org/10.1038/s41590-025-02202-x
J Enzyme Inhib Med Chem. 2025 Dec;40(1): 2520611

Nucleoside diphosphate kinase strongly promotes GDP and ADP metabolism in the cell and affects endogenous proton leak in mitochondria - the kinase is hampered by oxidative phosphorylation inhibitors.

Andrzej M Woyda-Ploszczyca.

  Rapid GDP metabolism in mitochondria isolated from wild-type yeast is postulated. The hallmark of exogenous GDP is convergence with the effect of exogenous ADP, typically inducing oxidative phosphorylation (OXPHOS). The GDP-provoked changes in the presence of ATP, i.e. increased respiratory rate accompanied by decreased inner mitochondrial membrane electrical potential, were curtailed by OXPHOS inhibitors, such as carboxyatractyloside, which apparently merged the GDP effect with OXPHOS. However, all performed tests indicated that the response of mitochondria to GDP is indirect and involves two steps. First, GDP is transphosphorylated via nucleoside diphosphate kinase (NDPK), ATP + GDP → ADP + GTP, which is followed by ADP-induced OXPHOS. Importantly, in mitochondria isolated from mutant yeast with a deleted NDPK gene, the stimulatory effect of GDP was eliminated. Therefore, a prerequisite for GDP metabolic action is the cooperation of NDPK with the OXPHOS apparatus. This biological model can help elucidate the molecular basis of some diseases treatment, such as cancer.

Keywords:  ADP/ATP carrier; mitochondria; nucleoside-diphosphate kinase (NDPK); nucleotide metabolism; proton (H+) leak

DOI:  https://doi.org/10.1080/14756366.2025.2520611
bioRxiv. 2025 Jul 11. pii: 2025.07.10.663832. [Epub ahead of print]

Multi-site phosphorylation of BCL2L13 in a TBK1- and AMPK-dependent manner reveals new modes of mitophagy regulation.

Hoda Ahmed, Mack B Reynolds, Gary Kasof, Gerald S Shadel, Reuben Shaw.

Mitophagy is a selective autophagic process that eliminates damaged mitochondria via lysosomal degradation, playing a crucial role in maintaining cellular metabolic balance. Mitophagy can occur through two pathways: ubiquitin-dependent and ubiquitin-independent. Recently, we and others have shown that, upon mitochondrial stress, AMP-activated protein kinase (AMPK) contributes to Parkin-mediated, ubiquitin-dependent mitophagy. The ubiquitin-independent pathway involves multiple outer mitochondrial membrane (OMM) "mitophagy receptors" that contain LC3-interacting region (LIR) motifs, including BNIP3, NIX/ BNIP3L, FUNDC1, and BCL2L13. LIR motifs bind Atg8/LC3 family proteins, facilitating the recruitment of the autophagosome membrane to target damaged mitochondria for degradation. The kinase Unc-51 Like autophagy activating kinase 1 (ULK1) phosphorylates the serine preceding the LIR motif in BNIP3, NIX, and FUNDC1, enhancing their binding to LC3 and promoting mitophagy. However, while BCL2L13 has been identified as a ULK1 binding partner, its regulation by phosphorylation remains unclear. We utilized mass spectrometry (MS) to map phosphorylation sites in BCL2L13 following mitochondrial stress and developed phospho-specific antibodies against two sites, Ser261 and Ser275, which were induced after exposure to the mitochondrial uncoupler, CCCP. Endogenous BCL2L13 Ser261 and Ser275 were both phosphorylated in an AMPK-dependent manner in cells and tissues. As neither site matches the established AMPK substrate consensus motif, we sought to identify which kinases directly mediate their phosphorylation downstream of AMPK. Surprisingly, genetic studies revealed that ULK1 is not regulating either site, but instead, TBK1 is controlling Ser275. This work reveals that BCL2L13 is unique amongst mitophagy receptors in being activated by mitochondrial stress and innate immune stimuli in an AMPK- and TBK1-dependent manner.

DOI: https://doi.org/10.1101/2025.07.10.663832
Mitochondrial Commun. 2025 ;3 26-43

Exploring the oncogenic impact of heteroplasmic de novo MT-ND5 truncating mutations.

Yuanyuan Wu, Jiangbin Ye, Zhenglong Gu.

  Numerous mitochondrial DNA (mtDNA) variants are associated with cancers, yet the causal link remains inconclusive. Using DddA-derived cytosine base editors, we induced de novo truncating mutations in MT-ND5 in HEK293 cells, establishing heteroplasmy, the coexistence of mutant and wild-type mtDNA. This study aimed to investigate the full molecular etiology following these deleterious mtDNA mutations, particularly in oncogenesis. We found that low to moderate heteroplasmic levels of the mutants were sufficient to impair mitochondrial functions and alter cellular redox status. Cellular adaptation to elevated ROS (Reactive Oxygen Species), energy crisis, and altered redox status was observed across varying heteroplasmy levels. Increased oncogenic potential was confirmed through in vitro oncogenesis and in vivo xenograft assays. Transcriptomic analysis revealed upregulated migration, invasion, and genome instability pathways, and downregulated ROS scavenging pathways. Our results demonstrate that MT-ND5 mutations drive cancer progression by increasing cellular ROS and genome instability, and by altering the redox balance and epigenetic landscapes.

Keywords:  MT-ND5 variants; Mitochondrial dysfunction; Oncogenesis; mtDNA heteroplasmy

DOI:  https://doi.org/10.1016/j.mitoco.2025.03.001
BMC Biol. 2025 Jul 15. 23(1): 214

Organic cation transporter 3 on neuronal mitochondria mediates MPP+-induced mitochondrial dysfunction and neurotoxicity in a TIMM22-dependent manner.

Ao Guan, Sida Han, Suzhen Liang, Weiwei Shen, Min Guo, Mei Cui.

   BACKGROUND: Mitochondria play crucial roles in cellular metabolism, and metabolite compartmentalization significantly impacts mitochondrial function and disease pathophysiology. MPP+ accumulation in mitochondria, a key factor in MPTP-induced neurodegeneration, leads to mitochondrial dysfunction, such as respiratory chain inhibition, ultimately leading to neuronal death. However, the mechanisms underlying mitochondrial MPP+ accumulation remain poorly understood. Organic cation transporter 3 (OCT3), a passive transporter mediating MPP+ transport, has been observed on the mitochondrial membrane, but it remains unclear whether mitochondrial OCT3 is involved in MPP+ accumulation in mitochondria.
RESULTS: OCT3 was detected in the mitochondria fraction of SH-SY5Y cells, located on both the inner membrane and outer membrane. Following MPP+ incubation, there was a significant increase in mitochondrial uptake of MPP+, which was mitigated by OCT3 inhibition. Knockdown of the translocase of inner mitochondrial membrane 22 (TIMM22), an important component of the mitochondrial protein import apparatus, successfully reduced OCT3 levels on mitochondria without impairing mitochondrial morphology or mitochondrial membrane potential. TIMM22 knockdown reduced mitochondrial MPP+ uptake, which in turn rescued MPP+-induced mitochondrial fragmentation, complex I inhibition, and mitochondrial membrane potential reduction. Furthermore, TIMM22 knockdown suppressed caspase-9 and caspase-3 activation and reversed the alterations of BAX and BCL-xL induced by mitochondrial MPP+ accumulation.
CONCLUSIONS: Here we found that OCT3 on neuronal mitochondria serves as an effective MPP+ transporter, crucial for mitochondrial MPP+ uptake and MPP+-induced neurotoxicity. Furthermore, TIMM22 downregulation can selectively reduce mitochondrial OCT3 and reverse MPP+-induced mitochondrial dysfunction and neurotoxicity, highlighting TIMM22 and OCT3 as potential therapeutic targets for MPP+-associated neurodegeneration and diseases.

Keywords:  MPP+ ; Mitochondria; Neurodegeneration; Organic cation transporter 3; TIMM22

DOI:  https://doi.org/10.1186/s12915-025-02318-4
Res Sq. 2025 Jun 26. pii: rs.3.rs-6346822. [Epub ahead of print]

MICU proteins facilitate Ca2+-dependent mitochondrial metabolon formation to regulate cellular energetics - independent of MCU.

John Elrod, Henry Cohen, Benjamin Gottschalk, Carmen Choya-Foces, Adam Chatoff, Anya Wilkinson, Joanne Garbincius, Adyson Johnson, Tyler Stevens, Jordan Howe, Emily Megill, Jennyfer Ngo, Dhanendra Tomar, Nathaniel Snyder, Wolfgang Graier.

Mitochondrial matrix Ca2+ concentration ([matrixCa2+]) is theorized to be an essential regulator of mitochondrial metabolism by positively regulating key mitochondrial dehydrogenases. However, ablation or functional inhibition of the mitochondrial calcium uniporter channel (mtCU) fails to significantly perturb basal metabolism and is largely phenotypically silent in the absence of stress. This begs the question, what are the primary molecular mechanisms regulating calcium-dependent changes in metabolism? The primary function of MICU proteins (MICU1, MICU2, and MICU3) is reported to be gatekeeping of the mtCU and regulating mitochondrial Ca2+ uptake. Here, we demonstrate that MICU proteins function in coordination to impart Ca2+-dependent regulation to FADH2-dependent mitochondrial dehydrogenases through metabolon formation independent of the mtCU and [matrixCa2+]. Our results demonstrate that MICU proteins differentially localize to mitochondrial microdomains and form heterodimers and interactomes in response to intermembrane space Ca2+ binding their respective EF-hand domains. Utilizing an equimolar expression platform coupled with unbiased proteomics we reveal unique interactomes for MICU1/2 versus MICU1/3 heterodimers and demonstrate that MICU proteins control coupling of Mitochondrial Glycerol-3-Phosphate Dehydrogenase with Succinate Dehydrogenase/Complex II and impart Ca2+-dependent changes in activity. We propose that MICU-mediated mitochondrial metabolons are a fundamental system facilitating matching of mitochondrial energy production with cellular demand and is the primary physiological Ca2+ signaling mechanism regulating homeostatic energetics - not mtCU-dependent changes in [matrixCa2+].

DOI: https://doi.org/10.21203/rs.3.rs-6346822/v1
bioRxiv. 2025 Jun 20. pii: 2025.06.16.659985. [Epub ahead of print]

Dynamic assembly of malate dehydrogenase-citrate synthase multienzyme complex in the mitochondria.

Joy Omini, Inga Krassovskaya, Taiwo Dele-Osibanjo, Connor Pedersen, Toshihiro Obata.

The tricarboxylic acid (TCA) cycle enzymes, malate dehydrogenase (MDH1) and citrate synthase (CIT1), form a multienzyme complex called 'metabolon' that channels intermediate, oxaloacetate, between the reaction centers of the enzymes. Since the MDH1-CIT1 metabolon enhances the pathway reactions in vitro, it is postulated to regulate the TCA cycle flux through dynamic assembly in response to cellular metabolic demands. Here, we demonstrated that yeast mitochondrial MDH1 and CIT1 dissociated when aerobic respiration was suppressed by the Crabtree effect and associated when the pathway flux was enhanced by acetate. Pharmacological TCA cycle inhibitions dissociated the complex, while electron transport chain inhibition enhanced the interaction. The multienzyme complex assembly was related to the mitochondrial matrix acidification and oxidation, as well as cellular levels of malate, fumarate, and citrate. These factors significantly affected the MDH1-CIT1 complex affinity in vitro. Especially the buffer pH significantly changed the MDH1-CIT1 affinity within the pH range between 6.0 and 7.0, which is observed in the mitochondrial matrix under physiological conditions. These results show a dynamic association and dissociation of a metabolon in the mitochondria and its relationship with pathway flux, supporting the metabolon's role in metabolic regulation. Multiple factors, including pH and metabolite availabilities, possibly regulate MDH1-CIT1 interaction.

DOI: https://doi.org/10.1101/2025.06.16.659985
Genes Dev. 2025 Jul 11.

Mitochondria dysfunction: cause or consequence of physiologic aging?

G R Scott Budinger, Navdeep S Chandel.

  Mitochondria are no longer viewed solely as ATP- or metabolite-generating organelles but as key regulators of cellular signaling that shape physiologic aging. Contrary to earlier theories linking aging to mitochondrial DNA mutations and oxidative damage, current evidence shows that these factors do not causally limit physiologic aging. Instead, an evolving literature links age-related loss of mitochondrial signaling and function to important physiologic changes of aging. Moreover, mild inhibition of mitochondrial respiratory function with drugs like metformin promote health span. These findings open new paths for pharmacologically reprogramming mitochondrial signaling to extend healthy aging.

Keywords:  aging; mitochondria; senescence

DOI:  https://doi.org/10.1101/gad.353106.125
bioRxiv. 2025 May 03. pii: 2025.05.02.651978. [Epub ahead of print]

Specialized high-capacity mitochondria fuel cell invasion.

Isabel W Kenny-Ganzert, Lena P Basta, Lianzijun Wang, Qiuyi Chi, Caitlin Su, Katherine S Morton, Joel N Meyer, David R Sherwood.

Cell invasion through basement membrane (BM) is energetically intensive, and how an invading cell produces high ATP levels to power invasion is understudied. By generating 20 endogenously tagged mitochondrial proteins, we identified a specialized mitochondrial subpopulation within the C. elegans anchor cell (AC) that localizes to the BM breaching site and generates elevated ATP to fuel invasion. These ETC-enriched high-capacity mitochondria are compositionally unique, harboring increased protein import machinery and dense cristae enriched with ETC components. High-capacity mitochondria emerge at the time of AC specification and depend on the AC pro-invasive transcriptional program. Finally, we show that netrin signaling through a Src kinase directs microtubule polarization, which facilitates metaxin adaptor complex dependent ETC-enriched mitochondrial trafficking to the AC invasive front. Our studies reveal that an invasive cell produces high ATP by generating and localizing high-capacity mitochondria. This might be common strategy used by other cells to meet energy demanding processes.

DOI: https://doi.org/10.1101/2025.05.02.651978
bioRxiv. 2025 Jun 18. pii: 2025.06.17.660237. [Epub ahead of print]

Respiratory complex III 2 assembles complex I via toxic intermediate in mitochondrial disease.

Maria G Ayala-Hernandez, Anetzy Bermudez Torales, Hannah Camille Tan, Claire B Montgomery, Abhilash Padavannil, Gino Cortopassi, James A Letts.

Mutations in mitochondrial complex I can cause severe metabolic disease. Although no treatments are available for complex I deficiencies, chronic hypoxia improves lifespan and function in a mouse model of the severe mitochondrial disease Leigh syndrome caused by mutation of complex I subunit NDUFS4. To understand the molecular mechanism of NDUFS4 mutant pathophysiology and hypoxia rescue, we investigated the structure of complex I in respiratory supercomplexes isolated from NDUFS4 mutant mice. We identified complex I assembly intermediates bound to complex III 2 , proving the cooperative assembly model. Further, an accumulated complex I intermediate is structurally consistent with pathological oxygen-dependent reverse electron transfer, revealing unanticipated pathophysiology and hypoxia rescue mechanisms. Thus, the build-up of toxic intermediates and not simply decreases in complex I levels underlie mitochondrial disease.

DOI: https://doi.org/10.1101/2025.06.17.660237
bioRxiv. 2025 Jun 26. pii: 2025.06.24.661170. [Epub ahead of print]

Paclitaxel-induced mitotic arrest results in a convergence of apoptotic dependencies that can be safely exploited by BCL-X L degradation to overcome cancer chemoresistance.

Xingping Qin, Adam Presser, Lissah Johnson, Yusuke Matoba, Brendan S Shay, Weiyi Xu, Jonathan Choiniere, Cameron Fraser, Filip Garbicz, Johan Spetz, Stacey Yu, Mary H C Florido, Francesca Picucci, Yang Yang, Ronny Drapkin, Ruben Carrasco, Sarah J Hill, Joyce Liu, Ursula Matulonis, Joan Brugge, Bo R Rueda, Daohong Zhou, Elizabeth H Stover, Kristopher A Sarosiek.

Paclitaxel and other microtubule-targeting agents are cornerstone therapies for diverse cancers, including lung, breast, cervical, pancreatic, and ovarian malignancies. Paclitaxel induces tumor cell apoptosis during mitosis by disrupting microtubule dynamics required for chromosome segregation. However, despite initial responsiveness, many tumors develop resistance, limiting therapeutic durability. Here, we used high-grade serous ovarian carcinoma (HGSOC), the most common and lethal subtype of ovarian cancer, as a model to dissect the mechanisms underlying this resistance. We find that paclitaxel-induced mitotic arrest triggers degradation of the pro-survival protein MCL-1 and upregulation of BCL-XL, followed by inactivating phosphorylation of BCL-XL at Ser62 to promote apoptosis. In resistant cells, this MCL-1 downregulation is insufficient to commit cells to apoptosis but instead results in a transient convergence of apoptotic dependencies by forcing BCL-X L to sequester the pro-apoptotic proteins BIM, BAX, and BAK. During this state, BCL-XL inhibition induces synergistic apoptosis, even in chemoresistant cells. Surprisingly, we also discover that loss of substrate attachment recapitulates this apoptotic convergence both in vitro and in vivo, with HGSOC cells growing in metastasis-promoting malignant ascites displaying heightened apoptotic priming and dependence on BCL-XL relative to solid tumors. In HGSOC xenografts, targeted degradation of BCL-XL using the platelet-sparing proteolysis-targeting chimera (PROTAC) DT2216 matches the efficacy of paclitaxel monotherapy while avoiding the chronic thrombocytopenia induced by BCL-XL inhibitors such as navitoclax (ABT-263). Strikingly, combination therapy leveraging the synergy between paclitaxel and DT2216 leads to complete eradication of HGSOC cell line and patient-derived xenografts. Moreover, DT2216 treatment blunts the rapid apoptotic adaptation caused by other BCL-X L inhibitors, indicating that targeted degradation of pro-survival proteins may yield more durable responses than inhibition alone. These findings uncover a mechanistic framework for safely exploiting the apoptotic dependency convergence caused by mitotic arrest and substrate detachment and support the clinical development of BCL-XL-targeting PROTACs to overcome chemoresistance in ovarian cancer and other solid tumors.

DOI: https://doi.org/10.1101/2025.06.24.661170
bioRxiv. 2025 May 09. pii: 2025.05.05.652276. [Epub ahead of print]

A Platform for Mitochondrial Profiling in Enriched Kidney Segments Under Thermodynamic Control.

Stephen T Decker, Precious C Opurum, Ran Hee Choi, Venisia L Paula, Anu S Kurian, Deborah Stuart, Linda S Nikolova, Alejandro Sanchez, Laith Al-Rabadi, Nirupama Ramkumar, Kelsey H Fisher-Wellman, Katsuhiko Funai.

Mitochondrial function varies widely across kidney nephron segments, yet conventional approaches lack the resolution and control needed to assess cell-type-specific bioenergetics in situ. We present a methodological platform that enables segment-resolved profiling of mitochondrial respiration, conductance, and membrane potential in freshly isolated mouse nephron segments. Combining mechanical sieving and adhesion-based enrichment with permeabilized high-resolution respirometry, we adapted the creatine kinase clamp to quantify oxygen flux and mitochondrial membrane potential across defined free energies. Using this approach, we found that proximal tubules exhibit high respiratory conductance and dynamic mitochondrial polarization, while distal tubules and glomeruli maintain static membrane potential and low conductance. In a model of adenine-induced nephropathy, only proximal tubule mitochondria showed marked reductions in respiration and ATP production. This segment-specific dysfunction was not detectable in bulk mitochondrial isolates. Our approach provides thermodynamically anchored, segment-resolved insight into mitochondrial adaptation under physiological and pathological conditions. It is broadly applicable to other tissues with metabolic heterogeneity and compatible with disease models, genetic tools, and pharmacological interventions. This platform bridges a critical gap between conventional respirometry and functional mitochondrial phenotyping in native tissue structures.

DOI: https://doi.org/10.1101/2025.05.05.652276
Nat Metab. 2025 Jul 14.

Old mitochondria regulate niche renewal via α-ketoglutarate metabolism in stem cells.

Simon Andersson, Hien Bui, Arto Viitanen, Daniel Borshagovski, Ella Salminen, Sami Kilpinen, Angelika Gebhart, Emilia Kuuluvainen, Swetha Gopalakrishnan, Nina Peltokangas, Martyn James, Kaia Achim, Eija Jokitalo, Petri Auvinen, Ville Hietakangas, Pekka Katajisto.

Cellular metabolism is a key regulator of cell fate1, raising the possibility that the recently discovered metabolic heterogeneity between newly synthesized and chronologically old organelles may affect stem cell fate in tissues2,3. In the small intestine, intestinal stem cells (ISCs)4 produce metabolically distinct progeny5, including their Paneth cell (PC) niche6. Here we show that asymmetric cell division of mouse ISCs generates a subset enriched for old mitochondria (ISCmito-O), which are metabolically distinct, and form organoids independently of niche because of their ability to recreate the PC niche. ISCmito-O mitochondria produce more α-ketoglutarate, driving ten-eleven translocation-mediated epigenetic changes that promote PC formation. In vivo α-ketoglutarate supplementation enhanced PC turnover and niche renewal, aiding recovery from chemotherapy-induced damage in aged mice. Our results reveal a subpopulation of ISCs whose old mitochondria metabolically regulate cell fate, and provide proof of principle for metabolically promoted replacement of specific aged cell types in vivo.

DOI: https://doi.org/10.1038/s42255-025-01325-7
Blood Adv. 2025 Jul 17. pii: bloodadvances.2025016726. [Epub ahead of print]

Utility of IDH1/2 mutations as biomarkers for detection of measurable residual disease in acute myeloid leukemia.

Emma L Boertjes, Christian M Vonk, François G Kavelaars, Marie Engvall, Sofia Nordin, Lisanne Beugelink, Melissa Rijken, Jolinda Konijnenburg, Jurjen Versluis, Bob Löwenberg, Peter J M Valk.

Molecular measurable residual disease (MRD) assessment in acute myeloid leukemia (AML) patients has been established for only a few specific markers, i.e. mutant NPM1 and FLT3-ITD. Mutations in IDH1/2 are present in approximately 20% of AML patients. However, validation of mutant IDH1/2 MRD has been hampered by cohort size as well as the availability of highly sensitive and specific MRD detection assays. Here, we comprehensively investigate the impact of persisting IDH1/2 mutations in complete remission (CR) after intensive chemotherapy in a cohort of 163 newly diagnosed IDH-mutant AML patients enrolled in HOVON-SAKK clinical trials using a next-generation sequencing (NGS)-based approach, targeting all hotspot mutations in IDH1 (R132) and IDH2 (R140, R172). The high sensitivity (10-4) as well as the levels of persisting IDH1/2 mutations detected by the NGS-based approach were confirmed by an independent rolling circle amplification (superRCA) assay. We demonstrate that relapse risk was significantly increased in AML patients with measurable persisting IDH2 mutations (p=0.027, SHR:2.34), but not in patients with persisting mutant IDH1 (p=0.591, SHR:0.80). Moreover, the association of persistence of mutant IDH2 and increased risk of relapse was most pronounced in mutant IDH2 AML patients without concomitant NPM1 mutations or FLT3-ITD (p=0.011, SHR:5.29). Thus, mutant IDH2 appears a potentially useful novel molecular MRD marker with prognostic significance in AML.

DOI: https://doi.org/10.1182/bloodadvances.2025016726