bims-midysc 2025-02-09 papers

bims-midysc

Biomed News

on Mitochondria dysfunction in cancer

Issue of 2025–02–09
23 papers selected by
Papachristodoulou Lab

Revisiting the Role of Mitochondrial DNA Mutations in Aging: Bridging Theoretical Expectations with Empirical Observations.
JMJD6 Rewires ATF4-Dependent Glutathione Metabolism to Confer Ferroptosis Resistance in SPOP-Mutated Prostate Cancer.
Inhibition of cytosolic translation mitigates mitochondrial dysfunction in C. elegans.
Oncogenic TFE3 fusions drive OXPHOS and confer metabolic vulnerabilities in translocation renal cell carcinoma.
Metformin in overcoming enzalutamide resistance in castration-resistant prostate cancer.
Mitochondrial heterogeneity: subpopulations with distinct metabolic activities.
Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor.
MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects.
TGF-β secreted by cancer cells-platelets interaction activates cancer metastasis potential by inducing metabolic reprogramming and bioenergetic adaptation.
The prognostic and neuroendocrine implications of SLC25A29-mediated biomass signature in prostate cancer.
Mitochondria-targeting of oxidative phosphorylation inhibitors to alleviate hypoxia and enhance anticancer treatment efficacy.
Identification of mitochondrial carrier homolog 2 as an important therapeutic target of castration-resistant prostate cancer.
The mitochondrial DNAJC co-chaperone TCAIM reduces α-ketoglutarate dehydrogenase protein levels to regulate metabolism.
Protocol for the quantitative detection of mtDNA in the supernatants of activated human naive CD8+ T cells.
Activating AMPK improves pathological phenotypes due to mtDNA depletion.
DNA repair pathways in the mitochondria.
Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.
Integrative pan-cancer genomic analysis highlights mitochondrial protein p32 as a potential therapeutic target in Myc-driven tumorigenesis.
CREB1-BCL2 drives mitochondrial resilience in RAS GAP-dependent breast cancer chemoresistance.
High-purity CTC RNA sequencing identifies prostate cancer lineage phenotypes prognostic for clinical outcomes.
Oxidative Phosphorylation (OXPHOS) Promotes the Formation and Growth of Melanoma Lung and Brain Metastases.
Intranuclear TCA and mitochondrial overload: the nascent sprout of tumors metabolism.
CRIP1 inhibits cutaneous melanoma progression through TFAM-mediated mitochondrial biogenesis.

Aging Dis. 2025 Feb 01.

Revisiting the Role of Mitochondrial DNA Mutations in Aging: Bridging Theoretical Expectations with Empirical Observations.

Runyu Liang, Qiang Tang, Jia Chen, Yongyin Huang, Luwen Zhu.

Since the association between mitochondria and aging was first identified, significant efforts have been devoted to elucidating the role of mitochondrial DNA mutations in the aging process. Due to their age-dependent accumulation, intrinsically high mutation rates, and defective replication mechanisms, mtDNA mutations have often been regarded as pivotal drivers of aging. This has led to certain intuitive yet inherently limited conclusions. Aging, however, is a multifactorial process, and the role of mtDNA cannot be simply categorized in binary terms, as its influence emerges as a composite vector of numerous interconnected physiological processes. Adopting alternative perspectives may mitigate the discrepancies between theoretical expectations and empirical findings, offering new directions and insights for future research.

DOI: https://doi.org/10.14336/AD.2024.1469
Cancer Res. 2025 Feb 04.

JMJD6 Rewires ATF4-Dependent Glutathione Metabolism to Confer Ferroptosis Resistance in SPOP-Mutated Prostate Cancer.

Chuanjie Zhang, Jiawei Ding, Kiat Shenq Lim, Wenjie Zhou, Wenyu Miao, Siqi Wu, Hanqing Liu, Da Huang, Chufeng Chen, Hongchao He, Jun Xiao, Dan-Feng Xu, Yan Shen, Hai Huang, Yi Gao.

Ferroptosis inducers have shown therapeutic potential in prostate cancer (PCa), but tumor heterogeneity poses a barrier to their efficacy. Distinguishing the regulators orchestrating metabolic crosstalk between cancer cells could shed light on therapeutic strategies to more robustly activate ferroptosis. Here, we found that aberrant accumulation of jumonji domain containing 6 (JMJD6) proteins correlated with poorer prognosis of PCa patients. Mechanistically, PCa-associated speckle type BTB/POZ protein (SPOP) mutants impaired the proteasomal degradation of JMJD6 proteins. Elevated JMJD6 and ATF4 coordinated enhancer-promoter loop interactions to stimulate the glutathione biosynthesis pathway. Independent of androgen receptor, JMJD6 recruited mediator subunits (Med1/14) to assemble de novo enhancers mapping to pivotal genes associated with glutathione metabolism, including SLC7A11, GCLM, ME1, and others. SPOP mutations thus induced intrinsic resistance to ferroptosis, dependent on enhanced JMJD6-ATF4 activity. Consequently, targeting JMJD6 rendered SPOP-mutated PCa selectively sensitive to ferroptosis. The JMJD6 antagonist SKLB325 synergized with erastin in multiple pre-clinical PCa models. Together, this study identifies JMJD6 as a druggable vulnerability in SPOP-mutated PCa to increase sensitivity to ferroptosis inducers.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-2796
bioRxiv. 2025 Jan 23. pii: 2025.01.22.634344. [Epub ahead of print]

Inhibition of cytosolic translation mitigates mitochondrial dysfunction in C. elegans.

Avijit Mallick, Yunguang Du, Theresa Ramalho, Rui Li, Levi Ali, Sookyung Kim, Lihua Julie Zhu, Cole M Haynes.

The mitochondrial unfolded protein response (UPR mt ) is regulated by the bZIP protein ATFS-1 which promotes mitochondrial protein homeostasis (proteostasis) and mitochondrial biogenesis in Caenorhabditis elegans . Upon mitochondrial perturbation, the ATFS-1-dependent transcriptional program promotes gene expression, leading to mitochondrial recovery. Conversely, atfs-1 -deletion worms harbor dysfunctional mitochondria, are developmentally impaired, and short-lived. However, atfs-1 -deletion worms develop to adults suggesting the presence of other signaling pathways that promote mitochondrial function and biogenesis in the absence of atfs-1 . We hypothesized that additional transcription factors regulate, or promote, mitochondrial function in the absence of atfs-1 . Here, we screened for transcription factors that could reduce the decline in mitochondrial function in the atfs-1 mutants when inhibited. Here, we demonstrate that inhibition of the nuclear hormone receptor NHR-180 re-establishes a functional mitochondrial network in atfs-1(null) worms, increases mtDNA content, and improves the developmental rate of wildtype worms. NHR-180 increases transcription of genes required for cytosolic protein synthesis in response to mitochondrial perturbation. Inhibition of the S6 kinase homolog, rsks-1 , in atfs-1(null) worms leads to a recovery of the mitochondrial network and mtDNA content consistent with nhr-180 regulating expression of protein synthesis components. Consistent with the observations in C. elegans , S6 kinase inhibition also increased mitochondrial biogenesis in mammalian atf5 -knockout cells that harbor severely impaired mitochondria. Intriguingly, nhr-180 or S6 kinase inhibition also rescues mitochondrial dysfunction caused by mutations in multiple genes required for oxidative phosphorylation. Combined, these studies suggest that increased protein synthesis contributes to the mitochondrial dysfunction caused by perturbations in OXPHOS gene expression and suggest a relatively straightforward approach to reducing the impact of mitochondrial dysfunction.

DOI: https://doi.org/10.1101/2025.01.22.634344
Nat Metab. 2025 Feb 06.

Oncogenic TFE3 fusions drive OXPHOS and confer metabolic vulnerabilities in translocation renal cell carcinoma.

Jiao Li, Kaimeng Huang, Meha Thakur, Fiona McBride, Ananthan Sadagopan, Daniel S Gallant, Prateek Khanna, Yasmin Nabil Laimon, Bingchen Li, Razan Mohanna, Maolin Ge, Cary N Weiss, Mingkee Achom, Qingru Xu, Sayed Matar, Gwo-Shu Mary Lee, Kun Huang, Miao Gui, Chin-Lee Wu, Kristine M Cornejo, Toni K Choueiri, Birgitta A Ryback, Sabina Signoretti, Liron Bar-Peled, Srinivas R Viswanathan.

Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic nature of most other renal cancers. Reliance on this TFE3 fusion-driven OXPHOS programme renders tRCCs vulnerable to NADH reductive stress, a metabolic stress induced by an imbalance of reducing equivalents. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to this metabolic state, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1 compromises tRCC cell growth by stabilizing HIF-1α and promoting metabolic reprogramming away from OXPHOS, thus representing a vulnerability for OXPHOS-dependent tRCC cells. Our study defines tRCC as being dependent on a mitochondria-centred metabolic programme driven by TFE3 fusions and nominates EGLN1 inhibition as a therapeutic strategy in this cancer.

DOI: https://doi.org/10.1038/s42255-025-01218-9
J Pharmacol Exp Ther. 2025 Jan;pii: S0022-3565(24)00092-2. [Epub ahead of print]392(1): 100034

Metformin in overcoming enzalutamide resistance in castration-resistant prostate cancer.

Kendall Simpson, Derek B Allison, Daheng He, Jinpeng Liu, Chi Wang, Xiaoqi Liu.

  Androgen deprivation is the standard treatment for patients with prostate cancer. However, the disease eventually progresses as castration-resistant prostate cancer (CRPC). Enzalutamide, an androgen receptor inhibitor, is a typical drug for treating CRPC and with continuous reliance on the drug, can lead to enzalutamide resistance. This highlights the necessity for developing novel therapeutic targets to combat the gain of resistance. Metformin has been recently investigated for its potential antitumorigenic effects in many cancer types. In this study, we used enzalutamide and metformin in combination to explore the possible rescued efficacy of enzalutamide in the treatment of enzalutamide-resistant CRPC. We first tested the effects of this combination treatment on cell viability, drug synergy, and cell proliferation in enzalutamide-resistant CRPC cell lines. After combination treatment, we observed a decrease in cell proliferation and viability as well as a synergistic effect of both enzalutamide and metformin in vitro. Following these results, we sought to explore how combination treatment affected mitochondrial fitness using mitochondrial stress test analysis and mitochondrial membrane potential shifts due to metformin's action in inhibiting complex I of oxidative phosphorylation. We employed 2 different strategies for in vivo testing using 22Rv1 and LuCaP35CR xenograft models. Finally, RNA sequencing revealed a potential link in the downregulation of rat sarcoma-mitogen-activated protein kinase signaling following combination treatment. SIGNIFICANCE STATEMENT: Increasing evidence suggests that oxidative phosphorylation might play a critical role in the development of resistance to cancer therapy. This study showed that targeting oxidative phosphorylation with metformin can enhance the efficacy of enzalutamide in castration-resistant prostate cancer in vitro.

Keywords:  Enzalutamide resistance; Metformin; Prostate cancer

DOI:  https://doi.org/10.1124/jpet.124.002424
Signal Transduct Target Ther. 2025 Feb 07. 10(1): 36

Mitochondrial heterogeneity: subpopulations with distinct metabolic activities.

Fabian den Brave, Swadha Mishra, Thomas Becker.

DOI: https://doi.org/10.1038/s41392-025-02130-0
Structure. 2025 Jan 27. pii: S0969-2126(25)00008-5. [Epub ahead of print]

Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor.

Merve Demir, Laura Koepping, Ya Li, Lynn Fujimoto, Andrey Bobkov, Jianhua Zhao, Taro Hitosugi, Eduard Sergienko.

  Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The inhibition of breast cancer growth by cyclocreatine targeting CKs indicates dependence of cancer cells on the "energy shuttle" for cell growth and survival. Hence, understanding key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present mutational and structural investigations on understudied ubiquitous MtCK that showed closure of the loop comprising His61 is specific to and relies on creatine binding and mechanism of phosphoryl transfer depends on electrostatics of active site. We demonstrate that previously identified pan-CK covalent inhibitor CKi inhibit breast cancer cell proliferation; however, our biochemical and structural data indicated that inhibition by CKi is highly dependent on covalent link formation and conformational changes upon creatine binding are not observed.

Keywords:  Her2+ breast cancer; Mitochondrial creatine kinase; chemical probes; cryo-EM; energy homeostasis; enzyme mechanism; steady-state kinetics

DOI:  https://doi.org/10.1016/j.str.2025.01.008
bioRxiv. 2025 Jan 25. pii: 2025.01.22.634390. [Epub ahead of print]

MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects.

Devansh Shah, Kelly McCastlain, Ti-Cheng Chang, Gang Wu, Mondira Kundu.

Motivation: Human mitochondrial DNA (mtDNA) mutations are causally implicated in maternally inherited mitochondrial respiratory disorders; however, the role of somatic mtDNA mutations in both late-onset chronic diseases and cancer remains less clear. Although recent advances in mtDNA base editing technology have the potential to model and characterize many of these mutations, current editing approaches are complicated by the potential for multiple unintentional edits (bystanders) that are only identifiable through empirical 'trial and error', thereby sacrificing valuable time and effort towards suboptimal construct development.
Results: We developed MitoEdit, a novel tool that incorporates empirical base editor patterns to facilitate identification of optimal target windows and potential bystander edits. MitoEdit allows users to input DNA sequences in a text-based format, specifying the target base position and its desired modification. The program generates a list of candidate target windows with a predicted number of bystander edits and their functional impact, along with flanking nucleotide sequences designed to bind TALE (transcription activator-like effectors) array proteins. In silico evaluations indicate that MitoEdit can predict the majority of bystander edits, thereby reducing the number of constructs that need to be tested empirically. To the best of our knowledge, MitoEdit is the first tool to automate prediction of base edits.
Availability and implementation: MitoEdit is freely available at Kundu Lab GitHub ( https://github.com/Kundu-Lab/mitoedit ).
Contact: Corresponding email: Gang.Wu@stjude.org ; Mondira.Kundu@stjude.org.
Supplementary information: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1101/2025.01.22.634390
J Cancer. 2025 ;16(4): 1310-1323

TGF-β secreted by cancer cells-platelets interaction activates cancer metastasis potential by inducing metabolic reprogramming and bioenergetic adaptation.

Chunlian Zhong, Weiyu Wang, Yinyin Yao, Shu Lian, Xiaodong Xie, Judan Xu, Shanshan He, Lin Luo, ZhouZhou Ye, Jiajie Zhang, Mingqing Huang, Guihua Wang, Yanhong Wang, Yusheng Lu, Chengbin Fu.

  Metastasis is the leading cause of cancer-related deaths and poses a treatment challenge. Although studies have shown the importance of epithelial-mesenchymal transition (EMT) and metabolic reprogramming during cancer metastasis, the link between EMT and metabolic reprogramming, as well as the underlying molecular mechanisms by which both mediate cancer cell invasion and metastasis have not been elucidated. Here, we observed that interactions between platelets and cancer cells promote the secretion of TGF-β, thereby initiating EMT, promoting the invasion, and altering the metastatic and metabolic potential of colon cancer cells. TGF-β activates the AKT signaling pathway to enhance HK1 and HK2 expression in cancer cells, leading to increased glucose consumption, ATP production, and precise modulation of cell cycle distribution. In an energy-deficient model induced by oxidative phosphorylation (OXPHOS) inhibition with oligomycin A, TGF-β-induced highly metastatic HCT116 (H-HCT116) cells adapt by upregulating HK expression and glycolytic metabolism, while concurrently decreasing cell proliferation to conserve energy for survival. Mechanistically, H-HCT116 cells regulate cell division rates by downregulating CDK2, CDK4, and Cyclin D1 protein expression and upregulating p21 expression. Furthermore, H-HCT116 cells display enhanced motility, which is linked to increased mitochondrial metabolic activity. These findings indicated that cancer cells-platelets interaction secreted TGF-β activates cancer metastasis potential by inducing metabolic reprogramming and bioenergetic adaptation. The present study provides new insights into the adaptive strategies of highly metastatic cancer cells under adverse conditions and indicates that targeting glycolysis and metabolic reprogramming could serve as a viable approach to prevent cancer metastasis.

Keywords:  Cancer metastasis; bioenergetic adaptation; epithelial-to-mesenchymal transition (EMT); metabolic reprogramming; platelet-cancer cells interaction; transforming growth factor-β (TGF-β)

DOI:  https://doi.org/10.7150/jca.103757
Geroscience. 2025 Jan 31.

The prognostic and neuroendocrine implications of SLC25A29-mediated biomass signature in prostate cancer.

Chia-Chang Wu, Su-Wei Hu, Shao-Wei Dong, Kai-Yi Tzou, Chien Hsiu Li.

  Dysregulated solutes are linked to cancer progression, with associated carriers being potential targets for prognosis and treatment. Androgen deprivation therapy (ADT) is essential for prostate cancer (PCa) progression, but secondary resistance often leads to androgen-independent tumor growth, necessitating new prognostic biomarkers. Transcriptome-based datasets identify SLC25A29, an arginine carrier, as upregulated in PCa, correlating with metastatic features and serving as a high-risk prognostic factor, particularly in castration-resistant prostate cancer (CRPC). Molecular simulations indicate that SLC25A29-mediated pathways contribute to mitochondrial metabolism and redox homeostasis, implicating POLD1 regulation and suggesting a link to ferroptosis. Further analysis reveals that SLC25A29 may transactivate POLD1 via E2F1, as shown by RNA-seq profiling of E2F1 knockdown in CRPC-related cells, which demonstrated reduced POLD1 expression. Clinical and cellular studies confirm that SLC25A29, E2F1, and POLD1 levels positively correlate with pathological features, with their downstream effectors serving as prognosis signatures. The SLC25A29/E2F1/POLD1 axis is associated with neuroendocrine PCa (NEPC) development, indicating its role in response to androgen receptor inhibition. Downregulation of E2F1 not only decreases POLD1 levels but also reduces NEPC-related markers. These findings support the SLC25A29/E2F1/POLD1 axis as a prognostic tool for CRPC and NEPC, and targeting E2F1 may offer a therapeutic strategy to disrupt SLC25A29-mediated PCa progression.

Keywords:  E2F1; Neuroendocrine; POLD1; Prostate cancer; SLC25A29

DOI:  https://doi.org/10.1007/s11357-025-01538-4
Clin Cancer Res. 2025 Feb 03.

Mitochondria-targeting of oxidative phosphorylation inhibitors to alleviate hypoxia and enhance anticancer treatment efficacy.

Anne P M Beerkens, Sandra Heskamp, Flavia V Reinema, Gosse J Adema, Paul N Span, Johan Bussink.

Hypoxia is a common feature of solid tumors and is associated with a poor response to anticancer therapies. Hypoxia also induces metabolic changes, such as a switch to glycolysis. This glycolytic switch causes acidification of the tumor microenvironment (TME), thereby attenuating the anticancer immune response. A promising therapeutic strategy to reduce hypoxia and thereby sensitize tumors to irradiation and/or antitumor immune responses is pharmacological inhibition of oxidative phosphorylation (OXPHOS). Several OXPHOS inhibitors (OXPHOSi) have been tested in clinical trials. However, moderate responses and/or substantial toxicity has hampered clinical implementation. OXPHOSi tested in clinical trials inhibit the oxidative metabolism in tumor cells as well as healthy cells. Therefore, new strategies are needed to improve the efficacy of OXPHOSi while minimizing side effects. To enhance the therapeutic window, available OXPHOSi have, for instance, been conjugated to triphenylphosphonium (TPP+) to preferentially target the mitochondria of cancer cells, resulting in increased tumor uptake compared to healthy cells, as cancer cells have a higher mitochondrial membrane potential. However, OXPHOS inhibition also induces reactive oxygen species (ROS), and subsequent antioxidant responses, which may influence the efficacy of therapies, such as platinum-based chemotherapy and radiotherapy. Here, we review the limitations of the clinically tested OXPHOSi metformin, atovaquone, tamoxifen, BAY 87-2243 and IACS-010759 and the potential of mito-targeted OXPHOSi and their influence on ROS production. Furthermore, the effect of the mitochondria-targeting moiety TPP+ on mitochondria is discussed as this affects mitochondrial bioenergetics.

DOI: https://doi.org/10.1158/1078-0432.CCR-24-3296
Cell Death Dis. 2025 Feb 05. 16(1): 70

Identification of mitochondrial carrier homolog 2 as an important therapeutic target of castration-resistant prostate cancer.

Yankui Liu, Anjie Chen, Yufan Wu, Jiang Ni, Rong Wang, Yong Mao, Ning Sun, Yuanyuan Mi.

We here investigate the expression of the mitochondrial carrier homolog 2 (MTCH2) and its potential function in castration-resistant prostate cancer (CRPC). Bioinformatic analyses reveal that MTCH2 overexpression is associated with critical clinical parameters of prostate cancer. Single-cell sequencing data indicate elevated MTCH2 expression in the prostate cancer epithelium. MTCH2 is also upregulated in locally treated CRPC tissue and various primary human CRPC cells. Using genetic silencing via shRNA and knockout (KO) through the CRISPR-sgRNA approach, we showed that the depletion of MTCH2 impaired mitochondrial function, resulting in a reduced oxygen consumption rate, diminished complex I activity, and decreased ATP levels, mitochondrial depolarization, and increased reactive oxygen species production in primary CRPC cells. The silencing or KO of MTCH2 significantly inhibited cell viability, proliferation, and migration, together with a marked increase in apoptosis in the primary CRPC cells. In contrast, ectopic expression of MTCH2 provided CRPC cells with pro-tumorigenic properties, enhancing ATP production and promoting cell proliferation and migration. MTCH2 silencing also markedly inhibited the growth of subcutaneous xenografts of the primary CRPC cells in nude mice. The MTCH2-silenced xenografts exhibited increased apoptosis, elevated lipid peroxidation, and decreased ATP levels. These results provide new insights into the role of MTCH2 in supporting mitochondrial function and CRPC progression.

DOI: https://doi.org/10.1038/s41419-025-07406-5
Mol Cell. 2025 Feb 06. pii: S1097-2765(25)00036-X. [Epub ahead of print]85(3): 638-651.e9

The mitochondrial DNAJC co-chaperone TCAIM reduces α-ketoglutarate dehydrogenase protein levels to regulate metabolism.

Wang Jiahui, Yu Xiang, Zhong Youhuan, Ma Xiaomin, Gao Yuanzhu, Zhou Dejian, Wang Jie, Fu Yinkun, Fan Shi, Su Juncheng, Huang Masha, Haigis Marcia, Wang Peiyi, Xu Yingjie, Yang Wen.

  Mitochondrial heat shock proteins and co-chaperones play crucial roles in maintaining proteostasis by regulating unfolded proteins, usually without specific target preferences. In this study, we identify a DNAJC-type co-chaperone: T cell activation inhibitor, mitochondria (TCAIM), and demonstrate its specific binding to α-ketoglutarate dehydrogenase (OGDH), a key rate-limiting enzyme in mitochondrial metabolism. This interaction suppresses OGDH function and subsequently reduces carbohydrate catabolism in both cultured cells and murine models. Using cryoelectron microscopy (cryo-EM), we resolve the human OGDH-TCAIM complex and reveal that TCAIM binds to OGDH without altering its apo structure. Most importantly, we discover that TCAIM facilitates the reduction of functional OGDH through its interaction, which depends on HSPA9 and LONP1. Our findings unveil a role of the mitochondrial proteostasis system in regulating a critical metabolic enzyme and introduce a previously unrecognized post-translational regulatory mechanism.

Keywords:  DNAJC; OGDH; TCAIM; charperon; metabolism; mitochondria; protein degradation; protein interaction; single-particle cryo-EM; α-ketoglutarate dehydrogenase

DOI:  https://doi.org/10.1016/j.molcel.2025.01.006
STAR Protoc. 2025 Jan 31. pii: S2666-1667(25)00018-8. [Epub ahead of print]6(1): 103612

Protocol for the quantitative detection of mtDNA in the supernatants of activated human naive CD8+ T cells.

Linlin Li, Jun Jin.

  Here, we present a protocol for the quantitative characterization of human T cell aging. We describe steps for sample collection; peripheral blood mononuclear cell (PBMC) isolation; and the enrichment, assessment, and activation of naive CD8+ T cells. We then detail procedures for supernatant collection and quantification using the absolute copy number of mitochondrial DNA (mtDNA) released into the supernatants from in-vitro-activated naive CD8+ T cells. We also apply this approach to predict the occurrence of lung adenocarcinoma in middle-aged populations. For complete details on the use and execution of this protocol, please refer to Jin et al.1.

Keywords:  cell isolation; clinical protocol; health sciences; immunology; metabolism; molecular biology

DOI:  https://doi.org/10.1016/j.xpro.2025.103612
FEBS J. 2025 Feb 07.

Activating AMPK improves pathological phenotypes due to mtDNA depletion.

Gustavo Carvalho, Tran V H Nguyen, Bruno Repolês, Josefin M E Forslund, W M Ruchitha Rukmal Wijethunga, Farahnaz Ranjbarian, Isabela C Mendes, Choco Michael Gorospe, Namrata Chaudhari, Micol Falabella, Mara Doimo, Sjoerd Wanrooij, Robert D S Pitceathly, Anders Hofer, Paulina H Wanrooij.

  AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis that also plays a role in preserving mitochondrial function and integrity. Upon a disturbance in the cellular energy state that increases AMP levels, AMPK activity promotes a switch from anabolic to catabolic metabolism to restore energy homeostasis. However, the level of severity of mitochondrial dysfunction required to trigger AMPK activation is currently unclear, as is whether stimulation of AMPK using specific agonists can improve the cellular phenotype following mitochondrial dysfunction. Using a cellular model of mitochondrial disease characterized by progressive mitochondrial DNA (mtDNA) depletion and deteriorating mitochondrial metabolism, we show that mitochondria-associated AMPK becomes activated early in the course of the advancing mitochondrial dysfunction, before any quantifiable decrease in the ATP/(AMP + ADP) ratio or respiratory chain activity. Moreover, stimulation of AMPK activity using the specific small-molecule agonist A-769662 alleviated the mitochondrial phenotypes caused by the mtDNA depletion and restored normal mitochondrial membrane potential. Notably, the agonist treatment was able to partially restore mtDNA levels in cells with severe mtDNA depletion, while it had no impact on mtDNA levels of control cells. The beneficial impact of the agonist on mitochondrial membrane potential was also observed in cells from patients suffering from mtDNA depletion. These findings improve our understanding of the effects of specific small-molecule activators of AMPK on mitochondrial and cellular function and suggest a potential application for these compounds in disease states involving mtDNA depletion.

Keywords:  AMPK; AMP‐activated protein kinase; mitochondrial DNA depletion; polymerase ɣ

DOI:  https://doi.org/10.1111/febs.70006
DNA Repair (Amst). 2025 Feb 01. pii: S1568-7864(25)00010-2. [Epub ahead of print]146 103814

DNA repair pathways in the mitochondria.

Dillon E King, William C Copeland.

  Mitochondria contain their own small, circular genome that is present in high copy number. The mitochondrial genome (mtDNA) encodes essential subunits of the electron transport chain. Mutations in the mitochondrial genome are associated with a wide range of mitochondrial diseases and the maintenance and replication of mtDNA is crucial to cellular health. Despite the importance of maintaining mtDNA genomic integrity, fewer DNA repair pathways exist in the mitochondria than in the nucleus. However, mitochondria have numerous pathways that allow for the removal and degradation of DNA damage that may prevent accumulation of mutations. Here, we briefly review the DNA repair pathways present in the mitochondria, sources of mtDNA mutations, and discuss the passive role that mtDNA mutagenesis may play in cancer progression.

Keywords:  DNA repair; Mitochondria; MtDNA; Mutagenesis

DOI:  https://doi.org/10.1016/j.dnarep.2025.103814
Science. 2025 Feb 06. eadf2034

Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.

Emily M Walker, Gemma L Pearson, Nathan Lawlor, Ava M Stendahl, Anne Lietzke, Vaibhav Sidarala, Jie Zhu, Tracy Stromer, Emma C Reck, Jin Li, Elena Levi-D'Ancona, Mabelle B Pasmooij, Dre L Hubers, Aaron Renberg, Kawthar Mohamed, Vishal S Parekh, Irina X Zhang, Benjamin Thompson, Deqiang Zhang, Sarah A Ware, Leena Haataja, Nathan Qi, Stephen C J Parker, Peter Arvan, Lei Yin, Brett A Kaufman, Leslie S Satin, Lori Sussel, Michael L Stitzel, Scott A Soleimanpour.

Mitochondrial damage is a hallmark of metabolic diseases, including diabetes, yet the consequences of compromised mitochondria in metabolic tissues are often unclear. Here, we report that dysfunctional mitochondrial quality control engages a retrograde (mitonuclear) signaling program that impairs cellular identity and maturity in β-cells, hepatocytes, and brown adipocytes. Targeted deficiency throughout the mitochondrial quality control pathway, including genome integrity, dynamics, or turnover, impaired the oxidative phosphorylation machinery, activating the mitochondrial integrated stress response, eliciting chromatin remodeling, and promoting cellular immaturity rather than apoptosis to yield metabolic dysfunction. Indeed, pharmacologic blockade of the integrated stress response in vivo restored β-cell identity following loss of mitochondrial quality control. Targeting mitochondrial retrograde signaling may therefore be promising in the treatment or prevention of metabolic disorders.

DOI: https://doi.org/10.1126/science.adf2034
Med Oncol. 2025 Feb 01. 42(3): 60

Integrative pan-cancer genomic analysis highlights mitochondrial protein p32 as a potential therapeutic target in Myc-driven tumorigenesis.

Qiufen Bi, Jun Nie, Qiang Wu, Liang Sun, Shuang Zhu, Jin Bai, Yong Liu, Fang Huang, Keli Chai.

  Tumor metabolic reprogramming, particularly involving mitochondrial metabolism, is a hallmark of malignancy. The mitochondrial protein p32 (C1QBP) has emerged as a critical regulator in various cancers, frequently associated with poor patient prognosis. However, the role of p32 across different cancer types remains largely unexplored. Our bioinformatics analysis demonstrates that p32 is significantly overexpressed in several malignancies and is closely involved in multiple oncogenic pathways related to tumor progression and metabolic reprogramming. Moreover, p32 expression positively correlates with genomic heterogeneity and drug sensitivity. We identified a strong association between p32 and c-Myc in both normal and cancerous tissues. We confirmed that p32 is a direct transcriptional target of c-Myc, which upregulates p32 by binding to its promoter. Functional experiments established that p32 is crucial for MYC-driven tumorigenesis, with its knockdown or knockout inhibiting tumor proliferation and extending survival. Targeting p32 may inhibit MYC-driven tumorigenesis, highlighting its potential as a therapeutic target in MYC-driven cancers.

Keywords:  Bioinformatics; Mitochondrial metabolism; Pan-cancer analysis; Tumorigenesis; c-Myc; p32

DOI:  https://doi.org/10.1007/s12032-025-02604-9
Oncogene. 2025 Jan 31.

CREB1-BCL2 drives mitochondrial resilience in RAS GAP-dependent breast cancer chemoresistance.

Ki-Fong Man, Omeed Darweesh, Jinghui Hong, Alexandra Thompson, Charlotte O'Connor, Chiara Bonaldo, Mark N Melkonyan, Mo Sun, Rajnikant Patel, Leif W Ellisen, Tim Robinson, Dong Song, Siang-Boon Koh.

Triple-negative breast cancer (TNBC) is an aggressive and heterogenous breast cancer subtype. RASAL2 is a RAS GTPase-activating protein (GAP) that has been associated with platinum resistance in TNBC, but the underlying mechanism is unknown. Here, we show that RASAL2 is enriched following neoadjuvant chemotherapy in TNBC patients. This enrichment is specific to the tumour compartment compared to adjacent normal tissues, suggesting that RASAL2 upregulation is tumour-selective. Analyses based on 2D/3D cultures and patient-derived xenograft models reveal that RASAL2 confers cross-resistance to common DNA-damaging chemotherapies other than platinum. Mechanistically, we found that apoptotic signalling is significantly downregulated upon RASAL2 expression. This feature is characterised by substantial alterations in the expression of anti-versus pro-apoptotic factors, pointing to heterogeneous mechanisms. In particular, RASAL2 upregulates BCL2 via activation of the oncogenic transcription co-factor YAP. CREB1, a YAP-interacting protein, was identified as the common transcription factor that binds to the promoter regions of RASAL2 and BCL2, driving their collective expression. A subset of RASAL2 colocalises with BCL2 subcellularly. Both proteins decorate mitochondria, where the high levels of mitochondrial RASAL2-induced BCL2 expression render the organelles refractory to apoptosis. Accordingly, mitochondrial outer membrane permeabilisation assay using live mitochondria from RASAL2-high/chemoresistant tumour cells demonstrated attenuated release of death signal, cytochrome c, when exposed to pro-apoptotic factors BAX and tBID. Similarly, these cells were more resilient towards chemotherapy-induced mitochondrial depolarisation. Together, this work reveals a previously undocumented molecular link between RAS GAP and apoptosis regulation, providing a new mechanistic framework for targeting a subset of chemorefractory tumours.

DOI: https://doi.org/10.1038/s41388-025-03284-5
Cancer Discov. 2025 Feb 06.

High-purity CTC RNA sequencing identifies prostate cancer lineage phenotypes prognostic for clinical outcomes.

Marina N Sharifi, Jamie M Sperger, Amy K Taylor, Katharine E Tippins, Shannon R Reese, Viridiana Carreno, Katherine R Kaufmann, Alex H Chang, Luke A Nunamaker, Charlotte Linebarger, Leilani Mora-Rodriguez, Jennifer L Schehr, Hannah M Krause, Kyle T Helzer, Matthew L Bootsma, Grace C Blitzer, John M Floberg, Christos E Kyriakopoulos, Hamid Emamekhoo, Elisabeth I Heath, Meghan Wells, Scott T Tagawa, Martin Sjöström, Atish D Choudhury, Menggang Yu, Andrew J Armstrong, Dana E Rathkopf, Himisha Beltran, Peter S Nelson, Felix Y Feng, Scott M Dehm, David Kosoff, Xiao X Wei, Rana R McKay, Shuang G Zhao, Joshua M Lang.

The development of treatment resistance remains universal for patients with metastatic prostate cancer, driven by AR alterations and lineage state transitions. Identifying the evolution of lineage transitions in treatment resistance has been limited by the challenges of collecting serial tissue biopsies on treatment, which can be overcome using blood-based liquid biopsies. Utilizing a novel circulating tumor cell (CTC) isolation approach, we collected 273 CTC samples from 117 patients with metastatic prostate cancer for RNA sequencing. 146 samples from 70 patients had tumor purity comparable to tissue biopsies. We identified four CTC transcriptional phenotypes, mirroring lineage states identified in tissue. Patients with a luminal-B-like CTC phenotype defined by persistent AR signaling and high proliferation, as well as those with a neuroendocrine CTC phenotype, had significantly shorter survival than patients with luminal-A-like and low proliferation phenotypes. In a prospective substudy, pre-treatment CTC luminal-B-like phenotype was associated with early progression on 177Lu-PSMA-617.

DOI: https://doi.org/10.1158/2159-8290.CD-24-1509
bioRxiv. 2025 Jan 24. pii: 2025.01.23.633049. [Epub ahead of print]

Oxidative Phosphorylation (OXPHOS) Promotes the Formation and Growth of Melanoma Lung and Brain Metastases.

Renato A Guerrieri, Grant M Fischer, David A Kircher, Aron Y Joon, Jacob R Cortez, Allie H Grossman, Courtney W Hudgens, Debora A Ledesma, Rossana Lazcano, Christian Yb Onana, Barbara G Knighton, Swaminathan Kumar, Qianghua Hu, Y N Vashisht Gopal, Jennifer L McQuade, Wanleng Deng, Lauren E Haydu, Jeffrey E Gershenwald, Alexander J Lazar, Michael T Tetzlaff, Sheri L Holmen, Michael A Davies.

Melanoma mortality is driven by the formation and growth of distant metastases. Here, we interrogated the role of tumor oxidative phosphorylation (OXPHOS) in the formation of distant metastases in melanoma. OXPHOS was the most upregulated metabolic pathway in primary tumors that formed distant metastases in the RCAS-TVA mouse model of spontaneous lung and brain metastases, and in melanoma patients that developed brain or other distant metastases. Knockout of PGC1α in melanocytes in the RCAS-TVA melanoma mouse model had no impact on primary tumor formation, but markedly reduced the incidence of lung and brain metastases. Genetic knockout of a component of electron transport chain complex I, NDUFS4, in B16-F10 and D4M-UV2 murine melanoma cell lines did not impact tumor incidence following subcutaneous, intravenous, or intracranial injection, but decreased tumor burden specifically in the lungs and brain. Together, these data demonstrate that OXPHOS is critical for the formation of metastases in melanoma.
STRUCTURED ABSTRACT: Purpose: Melanoma mortality is driven by the formation and growth of distant metastases. However, the process and pathogenesis of melanoma metastasis remain poorly understood. Here, we interrogate the role of tumor oxidative phosphorylation (OXPHOS) in the formation of distant metastases in melanoma.Experimental Design: This study includes (1) new RNA-seq analysis of primary melanomas from patients characterized for distant metastasis events; (2) RNA-seq analysis and functional testing of genetic OXPHOS inhibition (PGC1α KO) the RCAS-TVA model, which is the only existing immunocompetent murine model of autochthonous lung and brain metastasis formation from primary melanoma tumors; and (3) functional experiments of genetic OXPHOS inhibition (NDUFS4 KO) in the B16-F10 and D4M-UV2 murine melanoma cell lines, including evaluation of subcutaneous, lung, and brain metastatic site dependencies.Results: OXPHOS was the most upregulated metabolic pathway in primary tumors that formed distant metastases in the RCAS-TVA mouse model of spontaneous lung and brain metastases, and in melanoma patients that developed brain or other distant metastases. Knockout of PGC1a in melanocytes in the RCAS-TVA melanoma mouse model had no impact on primary tumor formation, but markedly reduced the incidence of lung and brain metastases. Genetic knockout of a component of electron transport chain complex I, NDUFS4, in B16-F10 and D4M-UV2 murine melanoma cell lines did not impact tumor incidence following subcutaneous, intravenous, or intracranial injection, but decreased tumor burden specifically in the lungs and brain.Conclusions: Together, these data demonstrate that OXPHOS is critical for the formation of metastases in melanoma.
TRANSLATIONAL RELEVANCE: Melanoma is the most aggressive form of skin cancer. One hallmark of this disease is a high risk of distant metastasis formation. The process and pathogenesis of metastasis in this disease remain poorly understood and there is controversy regarding the role of oxidative phosphorylation (OXPHOS) in melanoma metastasis. This study incorporates RNAseq analysis of primary melanoma tumors from patients characterized for distant metastasis events, RNAseq analysis of the only existing immunocompetent murine model of autochthonous lung and brain metastasis formation from primary melanoma tumors, and functional testing in multiple syngeneic models of melanoma at different tissue sites. This integrated analysis consistently demonstrates that melanoma OXPHOS promotes distant metastasis to the lungs and brain, two of the most common and clinically relevant sites of melanoma metastasis. This improved understanding of tumor OXPHOS may represent novel vulnerabilities for therapeutics development and surveillance/preventative strategies for melanoma metastasis.

DOI: https://doi.org/10.1101/2025.01.23.633049
Cancer Lett. 2025 Feb 03. pii: S0304-3835(25)00091-6. [Epub ahead of print] 217527

Intranuclear TCA and mitochondrial overload: the nascent sprout of tumors metabolism.

Weixi Yuan, Guozhong Lu, Yin Zhao, Xiang He, Senyi Liao, Zhe Wang, Xiaoyong Lei, Zhizhong Xie, Xiaoyan Yang, Shengsong Tang, Guotao Tang, Xiangping Deng.

  Abnormal glucose metabolism in tumors is a well-known form of metabolic reprogramming in tumor cells, the most representative of which, the Warburg effect, has been widely studied and discussed since its discovery. However, contradictions in a large number of studies and suboptimal efficacy of drugs targeting glycolysis have prompted us to further deepen our understanding of glucose metabolism in tumors. Here, we review recent studies on mitochondrial overload, nuclear localization of metabolizing enzymes, and intranuclear TCA (nTCA) in the context of the anomalies produced by inhibition of the Warburg effect. We provide plausible explanations for many of the contradictory points in the existing studies, including the causes of the Warburg effect. Furthermore, we provide a detailed prospective discussion of these studies in the context of these new findings, providing new ideas for the use of nTCA and mitochondrial overload in tumor therapy.

Keywords:  Acquired drug resistance in tumors; Metabolism in the nucleus; Mitochondrial overload; Nuclear TCA cycle; Nuclear localization of metabolic enzymes; Tumor heterogeneity; Tumor immune escape; Tumor metabolism; Warburg effect

DOI:  https://doi.org/10.1016/j.canlet.2025.217527
Sci Rep. 2025 Feb 04. 15(1): 4298

CRIP1 inhibits cutaneous melanoma progression through TFAM-mediated mitochondrial biogenesis.

Jianqiang Wu, Lixia Chen, Peijun Wen.

  Metastasis is the leading cause of death in patients with cutaneous melanoma. CRIP1 (cysteine-rich protein 1) has been reported to be associated with malignant progression of several cancers. However, the biological function and underlying mechanisms of CRIP1 in melanoma progression are largely unknown. Bioinformatic prediction of CRIP1 expression in melanoma and its association with clinical parameters and prognosis of patients. Real-time quantitative polymerase chain reaction (RT-qPCR) and Western blots (WB) were used to detect stable overexpression and knockdown of CRIP1 in melanoma cells. The function of CRIP1 in cutaneous melanoma cells was determined by in vitro functional assays. WB, immunofluorescence, OCR detection, mitochondrial DNA assay, and cytosolic ATP assay were used to determine the relationship between CRIP1 and mitochondrial biogenesis, relationship between TFAM. The expression level of CRIP1 in melanoma tissues is lower than that in normal tissues and suggests a poor prognosis for melanoma patients. Functionally, CRIP1 inhibits the proliferation, migration, and invasion of melanoma cells in vitro. Mechanistic studies revealed that CRIP1 inhibited mitochondrial biogenesis in melanoma cells, which included suppression of relative mitochondrial content, mitochondrial DNA copy number, ATP production, respiratory capacity, and expression levels of oxidative phosphorylation-related proteins. Further studies revealed that CRIP1 inhibits mitochondrial biogenesis and malignant progression in melanoma cells by suppressing the protein levels of TFAM. Our results suggest that CRIP1 inhibits the proliferation and invasive ability of cutaneous melanoma cells by suppressing TFAM-mediated mitochondrial biogenesis. Therefore, CRIP1 may be a potential therapeutic target for melanoma.

Keywords:  CRIP1; Melanoma; Mitochondrial biogenesis; TFAM

DOI:  https://doi.org/10.1038/s41598-025-88373-x