bims-mibica 2025-03-16 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2025–03–16
seventeen papers selected by
Kelsey Fisher-Wellman, Wake Forest University

Succinate dehydrogenase activity supports de novo purine synthesis.
Mitochondrial priming and response to BH3 mimetics in "one-two punch" senogenic-senolytic strategies.
A dual-purification system to isolate mitochondrial subpopulations.
Engineering mtDNA deletions by reconstituting end joining in human mitochondria.
VDAC2 and Bak scarcity in liver mitochondria enables targeting hepatocarcinoma while sparing hepatocytes.
Pathway Coessentiality Mapping Reveals Complex II is Required for de novo Purine Biosynthesis in Acute Myeloid Leukemia.
SLC25A35 enhances fatty acid oxidation and mitochondrial biogenesis to promote the carcinogenesis and progression of hepatocellular carcinoma by upregulating PGC-1α.
TIMM23 overexpression drives NSCLC cell growth and survival by enhancing mitochondrial function.
Arylamine N-acetyltransferase 1 expression predicts glucose dependence and mitochondrial bioenergetics in cancer cells.
WBP1 regulates mitochondrial function and ferroptosis to modulate chemoresistance in colorectal cancer.
Targeting TRAP1-dependent metabolic reprogramming to overcome doxorubicin resistance in quiescent breast cancer.
Measurement of Mitochondrial Membrane Potential In Vivo using a Genetically Encoded Voltage Indicator.
The E3 ubiquitin ligase RNF126 facilitates quality control of unimported mitochondrial membrane proteins.
Glycogen drives tumour initiation and progression in lung adenocarcinoma.
The mitochondrial protease ClpP is a promising target for multiple myeloma treatment.
Sphingolipid metabolism drives mitochondria remodeling during aging and oxidative stress.
Branched-chain amino acid catabolism promotes ovarian cancer cell proliferation via phosphorylation of mTOR.

bioRxiv. 2025 Mar 01. pii: 2025.02.26.640389. [Epub ahead of print]

Succinate dehydrogenase activity supports de novo purine synthesis.

Mushtaq A Nengroo, Austin T Klein, Heather S Carr, Olivia Vidal-Cruchez, Umakant Sahu, Daniel J McGrail, Nidhi Sahni, Peng Gao, John M Asara, Hardik Shah, Marc L Mendillo, Issam Ben-Sahra.

The de novo purine synthesis pathway is fundamental for nucleic acid production and cellular energetics, yet the role of mitochondrial metabolism in modulating this process remains underexplored. In many cancers, metabolic reprogramming supports rapid proliferation and survival, but the specific contributions of the tricarboxylic acid (TCA) cycle enzymes to nucleotide biosynthesis are not fully understood. Here, we demonstrate that the TCA cycle enzyme succinate dehydrogenase (SDH) is essential for maintaining optimal de novo purine synthesis in normal and cancer cells. Genetic or pharmacological inhibition of SDH markedly attenuates purine synthesis, leading to a significant reduction in cell proliferation. Mechanistically, SDH inhibition causes an accumulation of succinate, which directly impairs the purine biosynthetic pathway. In response, cancer cells compensate by upregulating the purine salvage pathway, a metabolic adaptation that represents a potential therapeutic vulnerability. Notably, co-inhibition of SDH and the purine salvage pathway induces pronounced antiproliferative and antitumoral effects in preclinical models. These findings not only reveal a signaling role for mitochondrial succinate in regulating nucleotide metabolism but also provide a promising therapeutic strategy for targeting metabolic dependencies in cancer.

DOI: https://doi.org/10.1101/2025.02.26.640389
Cell Death Discov. 2025 Mar 07. 11(1): 91

Mitochondrial priming and response to BH3 mimetics in "one-two punch" senogenic-senolytic strategies.

Júlia López, Àngela Llop-Hernández, Sara Verdura, Eila Serrano-Hervás, Eva Martinez-Balibrea, Joaquim Bosch-Barrera, Eduard Teixidor, Eugeni López-Bonet, Begoña Martin-Castillo, Josep Sardanyés, Tomás Alarcón, Ruth Lupu, Elisabet Cuyàs, Javier A Menendez.

A one-two punch sequential regimen of senescence-inducing agents followed by senolytic drugs has emerged as a novel therapeutic strategy in cancer. Unfortunately, cancer cells undergoing therapy-induced senescence (TIS) vary widely in their sensitivity to senotherapeutics, and companion diagnostics to predict the response of TIS cancer cells to a specific senolytic drug are lacking. Here, we hypothesized that the ability of the BH3 profiling assay to functionally measure the mitochondrial priming state-the proximity to the apoptotic threshold-and the dependencies on pro-survival BCL-2 family proteins can be exploited to inform the sensitivity of TIS cancer cells to BH3-mimetics. Replicative, mitotic, oxidative, and genotoxic forms of TIS were induced in p16-null/p53-proficient, BAX-deficient, and BRCA1-mutant cancer cells using mechanistically distinct TIS-inducing cancer therapeutics, including palbociclib, alisertib, doxorubicin, bleomycin, and olaparib. When the overall state of mitochondrial priming and competence was determined using activator peptides, the expected increase in overall mitochondrial priming was an exception rather than a generalizable feature across TIS phenotypes. A higher level of overall priming paralleled a higher sensitivity of competent TIS cancer cells to BCL-2/BCL-xL- and BCL-xL-targeted inhibitors when comparing TIS phenotypes among themselves. Unexpectedly, however, TIS cancer cells remained equally or even less overally primed than their proliferative counterparts. When sensitizing peptides were used to map dependencies on anti-apoptotic BCL-2 family proteins, competent TIS cancer cells appeared to share a dependency on BCL-xL. Furthermore, regardless of senescence-inducing therapeutic, stable/transient senescence acquisition, or genetic context, all TIS phenotypes shared a variable but significant senolytic response to the BCL-xL-selective BH3 mimetic A1331852. These findings may help to rethink the traditional assumption of the primed apoptotic landscape of TIS cancer cells. BCL-xL is a conserved anti-apoptotic effector of the TIS BCL2/BH3 interactome that can be exploited to maximize the efficacy of "one-two punch" senogenic-senolytic strategies.

DOI: https://doi.org/10.1038/s41420-025-02379-y
J Cell Sci. 2025 Mar 13. pii: jcs.263693. [Epub ahead of print]

A dual-purification system to isolate mitochondrial subpopulations.

Corey N Cunningham, Jonathan G Van Vranken, Jakeline Larios, Katarina Heyden, Steven P Gygi, Jared Rutter.

  Mitochondria perform diverse functions, such as producing ATP through oxidative phosphorylation, synthesizing macromolecule precursors, maintaining redox balance, and many others. Given this diversity of functions, we and others have hypothesized that cells maintain specialized subpopulations of mitochondria. To begin addressing this hypothesis, we developed a new dual-purification system to isolate subpopulations of mitochondria for chemical and biochemical analyses. We used APEX2 proximity labeling such that mitochondria were biotinylated based on proximity to another organelle. All mitochondria were isolated by an elutable MitoTag-based affinity precipitation system. Biotinylated mitochondria were then purified using immobilized avidin. We used this system to compare the proteomes of endosome- and lipid droplet-associated mitochondria in U-2 OS cells, which demonstrated that these subpopulations were indistinguishable from one another but were distinct from the global mitochondria proteome. Our results suggest that this purification system could aid in describing subpopulations that contribute to intracellular mitochondrial heterogeneity, and that this heterogeneity might be more substantial than previously imagined.

Keywords:  Biochemistry; Mitochondria; Proximity Labeling; Purification

DOI:  https://doi.org/10.1242/jcs.263693
Cell. 2025 Mar 05. pii: S0092-8674(25)00194-1. [Epub ahead of print]

Engineering mtDNA deletions by reconstituting end joining in human mitochondria.

Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B Thompson, Dana Pe'er, Agnel Sfeir.

  Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.

Keywords:  DOGMA-seq; end joining; mitochondrial pathologies; mtDNA; mtDNA deletion

DOI:  https://doi.org/10.1016/j.cell.2025.02.009
Nat Commun. 2025 Mar 11. 16(1): 2416

VDAC2 and Bak scarcity in liver mitochondria enables targeting hepatocarcinoma while sparing hepatocytes.

Shamim Naghdi, Piyush Mishra, Soumya Sinha Roy, David Weaver, Ludivine Walter, Erika Davies, Anil Noronha Antony, Xuena Lin, Gisela Moehren, Mark A Feitelson, Christopher A Reed, Tullia Lindsten, Craig B Thompson, Hien T Dang, Jan B Hoek, Erik S Knudsen, György Hajnóczky.

Differences between normal tissues and invading tumors that allow tumor targeting while saving normal tissue are much sought after. Here we show that scarcity of VDAC2, and the consequent lack of Bak recruitment to mitochondria, renders hepatocyte mitochondria resistant to permeabilization by truncated Bid (tBid), a Bcl-2 Homology 3 (BH3)-only, Bcl-2 family protein. Increased VDAC2 and Bak is found in most human liver cancers and mitochondria from tumors and hepatic cancer cell lines exhibit VDAC2- and Bak-dependent tBid sensitivity. Exploring potential therapeutic targeting, we find that combinations of activators of the tBid pathway with inhibitors of the Bcl-2 family proteins that suppress Bak activation enhance VDAC2-dependent death of hepatocarcinoma cells with little effect on normal hepatocytes. Furthermore, in vivo, combination of S63845, a selective Mcl-1 inhibitor, with tumor-nectrosis factor-related, apoptosis-induncing ligand (TRAIL) peptide reduces tumor growth, but only in tumors expressing VDAC2. Thus, we describe mitochondrial molecular fingerprint that discriminates liver from hepatocarcinoma and allows sparing normal tissue while targeting tumors.

DOI: https://doi.org/10.1038/s41467-025-56898-4
bioRxiv. 2025 Mar 02. pii: 2025.02.26.640463. [Epub ahead of print]

Pathway Coessentiality Mapping Reveals Complex II is Required for de novo Purine Biosynthesis in Acute Myeloid Leukemia.

Amy E Stewart, Derek K Zachman, Pol Castellano-Escuder, Lois M Kelly, Ben Zolyomi, Michael D I Aiduk, Christopher D Delaney, Ian C Lock, Claudie Bosc, John Bradley, Shane T Killarney, Olga R Ilkayeva, Christopher B Newgard, Navdeep S Chandel, Alexandre Puissant, Kris C Wood, Matthew D Hirschey.

Understanding how cellular pathways interact is crucial for treating complex diseases like cancer, yet our ability to map these connections systematically remains limited. Individual gene-gene interaction studies have provided insights 1,2 , but they miss the emergent properties of pathways working together. To address this challenge, we developed a multi-gene approach to pathway mapping and applied it to CRISPR data from the Cancer Dependency Map 3 . Our analysis of the electron transport chain revealed certain blood cancers, including acute myeloid leukemia (AML), depend on an unexpected link between Complex II and purine metabolism. Through stable isotope metabolomic tracing, we found that Complex II directly supports de novo purine biosynthesis and exogenous purines rescue AML from Complex II inhibition. The mechanism involves a metabolic circuit where glutamine provides nitrogen to build the purine ring, producing glutamate that Complex II must oxidize to sustain purine synthesis. This connection translated to a metabolic vulnerability whereby increasing intracellular glutamate levels suppresses purine production and sensitizes AML to Complex II inhibition. In mouse models, targeting Complex II triggered rapid disease regression and extended survival in aggressive AML. The clinical relevance of this pathway emerged in human studies, where higher Complex II gene expression correlates with both resistance to mitochondria-targeted therapies and worse survival outcomes specifically in AML patients. These findings establish Complex II as a central regulator of de novo purine biosynthesis and identify it as a promising therapeutic target in AML.

DOI: https://doi.org/10.1101/2025.02.26.640463
Cell Commun Signal. 2025 Mar 10. 23(1): 130

SLC25A35 enhances fatty acid oxidation and mitochondrial biogenesis to promote the carcinogenesis and progression of hepatocellular carcinoma by upregulating PGC-1α.

Heng-Chao Yu, Lu Bai, Liang Jin, Yu-Jia Zhang, Zi-Han Xi, De-Sheng Wang.

  Mitochondria dysfunction has been closely linked to a wide spectrum of human cancers, whereas the molecular basis has yet to be fully understood. SLC25A35 belongs to the SLC25 family of mitochondrial carrier proteins. However, the role of SLC25A35 in mitochondrial metabolism reprogramming, development and progression in human cancers remains unclear. Here, we found that SLC25A35 markedly reprogramed mitochondrial metabolism, characterized by increased oxygen consumption rate and ATP production and decreased ROS level, via enhancing fatty acid oxidation (FAO). Meanwhile, SLC25A35 also enhanced mitochondrial biogenesis characterized by increased mitochondrial mass and DNA content. Mechanistic studies revealed that SLC25A35 facilitated FAO and mitochondrial biogenesis through upregulating peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) via increasing acetyl-CoA-mediated acetylation of PGC-1α. Clinically, SLC25A35 was highly expressed in HCC and correlated with adverse patients' survival. Functionally, SLC25A35 promoted the proliferation and metastasis of HCC cells both in vitro and in vivo, as well as the carcinogenesis in a DEN-induced HCC mice model. Moreover, we found that SLC25A35 upregulation is caused, at least in part, by decreased miR-663a in HCC cells. Together, our results suggest a crucial oncogenic role of SLC25A35 in HCC by reprogramming mitochondrial metabolism and suggest SLC25A35 as a potential therapeutic target for the treatment of HCC.

Keywords:  Fatty acid oxidation; HCC; Metastasis; Mitochondrial biogenesis; Proliferation; SLC25A35

DOI:  https://doi.org/10.1186/s12964-025-02109-y
Cell Death Dis. 2025 Mar 13. 16(1): 174

TIMM23 overexpression drives NSCLC cell growth and survival by enhancing mitochondrial function.

Jianhua Zha, Jiaxin Li, Hui Yin, Mingjing Shen, Yingchen Xia.

Mitochondrial hyperfunction is implicated in promoting non-small cell lung cancer (NSCLC) cell growth. TIMM23 (translocase of inner mitochondrial membrane 23) is a core component of the mitochondrial import machinery, facilitating the translocation of proteins across the inner mitochondrial membrane into the matrix. Its expression and potential functions in NSCLC were tested. Comprehensive bioinformatic analysis revealed a strong correlation between TIMM23 overexpression and adverse clinical outcomes in NSCLC patients. Single-cell RNA sequencing data further corroborated these findings, demonstrating elevated TIMM23 expression within the cancer cells of NSCLC mass. Subsequent experimental validation confirmed significantly increased TIMM23 mRNA and protein levels in locally-treated NSCLC tissues compared to matched normal lung tissues. Moreover, TIMM23 expression was consistently elevated across multiple primary/established NSCLC cells. Silencing or ablation of TIMM23 via shRNA or CRISPR/Cas9 in NSCLC cells resulted in impaired mitochondrial function, characterized by reduced complex I activity, ATP depletion, mitochondrial membrane potential dissipation, oxidative stress, and lipid peroxidation. These mitochondrial perturbations coincided with attenuated cell viability, proliferation, and migratory capacity, and concomitant induction of apoptosis. Conversely, ectopic overexpression of TIMM23 significantly enhanced mitochondrial complex I activity and ATP production, promoting NSCLC cell proliferation and motility. In vivo, intratumoral delivery of a TIMM23 shRNA-expressing adeno-associated virus significantly suppressed the growth of subcutaneous NSCLC xenografts in nude mice. Subsequent analysis of tumor tissues revealed depleted TIMM23 expression, ATP reduction, oxidative damage, proliferative arrest, and apoptotic induction. Collectively, these findings establish TIMM23 as a critical pro-tumorigenic factor in NSCLC, highlighting its potential as a prognostic biomarker and therapeutic target.

DOI: https://doi.org/10.1038/s41419-025-07505-3
Biochim Biophys Acta Mol Cell Res. 2025 Mar 05. pii: S0167-4889(25)00034-5. [Epub ahead of print] 119929

Arylamine N-acetyltransferase 1 expression predicts glucose dependence and mitochondrial bioenergetics in cancer cells.

Chandra Choudhury, Neville J Butcher, Rodney F Minchin.

  To investigate the effects of varying NAT1 activity in different cell-lines, mitochondrial oxidative phosphorylation, aerobic glycolysis and mitochondrial fuel usage was quantified in a panel of human cell-lines. As NAT1 activity increased, mitochondrial reserve respiratory capacity increased while aerobic glycolysis decreased. In addition, phosphorylation of PDH-E1α in these cells limited their ability to use glucose as a primary fuel source. Those cells with high NAT1 activity exhibited a quiescent metabolic phenotype and proliferated more slowly. This might explain, in part, why some cancer patients with low NAT1 expression in their tumour tissue show poorer survival outcomes compared to those with high NAT1 expression. The current study demonstrated that NAT1 enzymatic activity is important for metabolism in cancer cell-lines and increasing NAT1 activity may better equip cells to survive under stressed conditions by increasing reserve respiratory capacity.

Keywords:  Acetyl-coenzyme A; Aerobic glycolysis; Arylamine N-acetyltransferase; Fuel usage; Mitochondrial respiration; Pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.bbamcr.2025.119929
Mol Med. 2025 Mar 12. 31(1): 93

WBP1 regulates mitochondrial function and ferroptosis to modulate chemoresistance in colorectal cancer.

Yang Wang, Dachuan Qi, Guijie Ge, Ning Cao, Xiangdong Liu, Na Zhu, Feng Li, Xiang Huang, Kui Yu, Jinzhou Zheng, Daoheng Wang, Wenyan Yao, Lili Chen, Ziyang Dong.

  Chemoresistance continues to pose a significant challenge in managing colorectal cancer (CRC), resulting in unfavorable outcomes for patients. Recent findings indicate that ferroptosis, an innovative type of regulated cell death, might influence chemoresistance. In this research, we explored how WW domain-binding protein 1 (WBP1) affects mitochondrial function, cell growth, ferroptosis, and chemoresistance in CRC cells. By employing both genetic and pharmacological methods, we found that WBP1 is essential for maintaining mitochondrial respiration in CRC cells. WBP1 depletion impaired mitochondrial function, leading to reduced cell proliferation and increased ferroptosis. Exogenous mitochondria from wild-type cells restored mitochondrial function, cell proliferation, and suppressed ferroptosis in WBP1-deficient cells, indicating that mitochondrial function acts downstream of WBP1. Importantly, we demonstrated that targeting WBP1 or its mediated mitochondrial function sensitized chemoresistant CRC cells to 5-fluorouracil and oxaliplatin by inducing ferroptosis. Furthermore, we analyzed transcriptome data from CRC patients, which indicated that increased WBP1 expression correlated with poor outcomes for patients receiving chemotherapy, thus highlighting the clinical significance of our observations. Collectively, our results pinpoint WBP1 as a significant modulator of mitochondrial function and ferroptosis in CRC cells and imply that targeting WBP1 may represent a viable approach to tackling chemoresistance. These insights offer a deeper understanding of the molecular pathways underlying CRC chemoresistance and may guide the development of new treatment options.

Keywords:  Chemoresistance; Colorectal cancer; Ferroptosis; Mitochondrial function

DOI:  https://doi.org/10.1186/s10020-025-01151-3
Drug Resist Updat. 2025 Mar 03. pii: S1368-7646(25)00026-3. [Epub ahead of print]81 101226

Targeting TRAP1-dependent metabolic reprogramming to overcome doxorubicin resistance in quiescent breast cancer.

Muhammad Zubair Saleem, Ruyi Huang, Yingying Huang, Xin Guo, Yang Liu, Miao Gao, Yinjuan Fan, Zhe-Sheng Chen, Zun-Fu Ke, Shengnan Ye, Jianhua Xu.

   AIMS: TRAP1 is involved in metabolic reprogramming and promotes drug resistance. We aimed to explore whether a novel HSP90 inhibitor, C210, overcomes doxorubicin (DOX) resistance of quiescent breast cancer cells by targeting TRAP1.
METHODS: Breast cancer cells were induced to quiescence by hypoxia and low glucose. The relationship of cell metabolism with HSP90 and TRAP1 was investigated by Western blotting, ECAR, OCR, mitochondrial complex activity, and proteomic analysis. The targets of C210 and their functions were analyzed by SPR and immunoprecipitation. The antitumor effect in vivo was investigated with mouse tumor model.
RESULTS: In hypoxia and glucose deprivation, breast cancer cells exhibited elevated TRAP1 and an OXPHOS-enhanced quiescent phenotype. These cells were highly resistant to DOX but more sensitive to C210. C210 disrupted TRAP1's interaction with OXPHOS-associated client proteins, prompting proteasome-dependent degradation of these proteins, thereby reducing OCR, mitochondrial ATP production and resulting in selective elimination of the quiescent cancer cells by inducing mitochondrial apoptosis which could be reversed by exogenous ATP. Moreover, C210 targeted glycolytic, amino acid, and β-oxidation-associated proteome. C210 demonstrated promising in vivo anticancer efficacy which was particularly related to OXPHOS inhibition.
CONCLUSIONS: C210 eliminates DOX-resistant quiescent breast cancer cells by targeting TRAP1-dependent bioenergetics.

Keywords:  Apoptosis; Drug resistance; HSP90; Oxidative phosphorylation; Quiescence; TRAP1

DOI:  https://doi.org/10.1016/j.drup.2025.101226
J Vis Exp. 2025 Feb 21.

Measurement of Mitochondrial Membrane Potential In Vivo using a Genetically Encoded Voltage Indicator.

Run-Zhou Yang, Dian-Dian Wang, Sen-Miao Li, Pei-Pei Liu, Jian-Sheng Kang.

Mitochondrial membrane potential (MMP, ΔΨm) is critical for mitochondrial functions, including ATP synthesis, ion transport, reactive oxygen species (ROS) generation, and the import of proteins encoded by the nucleus. Existing methods for measuring ΔΨm typically use lipophilic cation dyes, such as Rhodamine 800 and tetramethylrhodamine methyl ester (TMRM), but these are limited by low specificity and are not well-suited for in vivo applications. To address these limitations, we have developed a novel protocol utilizing genetically encoded voltage indicators (GEVIs). Genetically encoded voltage indicators (GEVIs), which generate fluorescent signals in response to membrane potential changes, have demonstrated significant potential for monitoring plasma membrane and neuronal potentials. However, their application to mitochondrial membranes remains unexplored. Here, we developed protein-based mitochondrial-targeted GEVIs capable of detecting ΔΨm fluctuations in cells and the motor cortex of living animals. The mitochondrial potential indicator (MPI)offers a non-invasive approach to study ΔΨm dynamics in real-time, providing a method to investigate mitochondrial function under both normal and pathological conditions.

DOI: https://doi.org/10.3791/67911
J Biol Chem. 2025 Mar 12. pii: S0021-9258(25)00252-2. [Epub ahead of print] 108403

The E3 ubiquitin ligase RNF126 facilitates quality control of unimported mitochondrial membrane proteins.

Di Liu, Xin-Yu Huo, Xiaoli Zhang, Zai-Rong Zhang.

  Pathological stress can lead to failure in the translocation of mitochondrial proteins, resulting in accumulation of unimported proteins within the cytosol and upregulation of proteasome for their quality control. Malfunction or delay in protein clearance causes dysregulation of mitochondrial protein homeostasis, cellular toxicity, and diseases. Ubiquilins (UBQLNs) are known to serve as chaperone which associates with unimported mitochondrial membrane protein precursors, and facilitates their proteasomal degradation. However, how UBQLN-engaged proteins are ubiquitinated and efficiently targeted to the proteasome are poorly understood. Here, using mitochondrial membrane protein ATP5G1 as a model substrate, we report that E3 ubiquitin ligase RNF126 interacts with substrate-engaged UBQLN1, thereby promoting ubiquitination and degradation of unimported proteins during mitochondrial stress. We find that UBQLN1's ubiquitin-associated domain (UBA) recruits RNF126 when its middle domain binds to unimported protein substrate. Recombinant RNF126 forms ternary complex with UBQLN1 and pATP5G1 in vitro and catalyzes ubiquitination of UBQLN1-bound ATP5G1. Without RNF126, proteasomal degradation of ATP5G1 was compromised. These results explain how RNF126 and ubiquilins interplay to ensure specific quality control of unimported mitochondrial membrane proteins under pathophysiological conditions.

Keywords:  ATP synthase F(0) complex subunit C1; RNF126; Ubiquilin; cytosolic quality control; mitochondrial membrane protein degradation

DOI:  https://doi.org/10.1016/j.jbc.2025.108403
Nat Metab. 2025 Mar 11.

Glycogen drives tumour initiation and progression in lung adenocarcinoma.

Harrison A Clarke, Tara R Hawkinson, Cameron J Shedlock, Terrymar Medina, Roberto A Ribas, Lei Wu, Zizhen Liu, Xin Ma, Yi Xia, Yu Huang, Xing He, Josephine E Chang, Lyndsay E A Young, Jelena A Juras, Michael D Buoncristiani, Alexis N James, Anna Rushin, Matthew E Merritt, Annette Mestas, Jessica F Lamb, Elena C Manauis, Grant L Austin, Li Chen, Pankaj K Singh, Jiang Bian, Craig W Vander Kooi, B Mark Evers, Christine F Brainson, Derek B Allison, Matthew S Gentry, Ramon C Sun.

Lung adenocarcinoma (LUAD) is an aggressive cancer defined by oncogenic drivers and metabolic reprogramming. Here we leverage next-generation spatial screens to identify glycogen as a critical and previously underexplored oncogenic metabolite. High-throughput spatial analysis of human LUAD samples revealed that glycogen accumulation correlates with increased tumour grade and poor survival. Furthermore, we assessed the effect of increasing glycogen levels on LUAD via dietary intervention or via a genetic model. Approaches that increased glycogen levels provided compelling evidence that elevated glycogen substantially accelerates tumour progression, driving the formation of higher-grade tumours, while the genetic ablation of glycogen synthase effectively suppressed tumour growth. To further establish the connection between glycogen and cellular metabolism, we developed a multiplexed spatial technique to simultaneously assess glycogen and cellular metabolites, uncovering a direct relationship between glycogen levels and elevated central carbon metabolites essential for tumour growth. Our findings support the conclusion that glycogen accumulation drives LUAD cancer progression and provide a framework for integrating spatial metabolomics with translational models to uncover metabolic drivers of cancer.

DOI: https://doi.org/10.1038/s42255-025-01243-8
Biochem Pharmacol. 2025 Mar 05. pii: S0006-2952(25)00117-0. [Epub ahead of print] 116855

The mitochondrial protease ClpP is a promising target for multiple myeloma treatment.

Xiang Liu, Jinlong Gu, Song Liu, Jingcao Huang, Linfeng Li, Fangfang Wang, Siyao He, Ziyue Mi, Yue Zhang, Jingjing Wen, Qianwen Gao, Haonan Yang, Yu Feng, Hongmei Luo, Xinyu Zhai, Li Zhang, Yuhuan Zheng, Youfu Luo, Ting Niu.

  Drug resistance and relapse are the major obstacles in multiple myeloma (MM) treatment, driving the search for novel therapeutics. The chemoactivation of mitochondrial caseinolytic protease P (ClpP) has shown to have anticancer effects on many tumors, but has seldom been elucidated in MM. Here we found that the CLPP expression was elevated in MM patients, and further increased in relapsed cases. After synthesizing and screening a panel of ClpP agonists, we identified a compound, 7b, as the most potent anti-MM agent in vitro. 7b activated ClpP protease activity, selectively degrading mitochondrial proteins, many of which are involved in oxidative phosphorylation (OXPHOS). As result, 7b treated MM had metabolic dysfunction, the mitochondrial membrane potential (MMP) collapse, reduced OXPHOS levels, and increased mitochondrial reactive oxygen species (ROS), leading to mitophagy-mediated MM cell death. Notably, 7b also showed efficacy against drug-resistant MM cell lines, including bortezomib- and lenalidomide-resistant cells. In vivo, 7b also exhibited remarkable anti-MM activity with tolerable side effects. In conclusion, targeting ClpP represents a promising therapeutic strategy for MM, with 7b serving as a potent anti-MM agent, especially for relapsed and refractory MM.

Keywords:  ClpP; Mitochondria; Multiple myeloma; Oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.bcp.2025.116855
bioRxiv. 2025 Feb 27. pii: 2025.02.26.640157. [Epub ahead of print]

Sphingolipid metabolism drives mitochondria remodeling during aging and oxidative stress.

Adam C Ebert, Nathaniel L Hepowit, Thyandra A Martinez, Henrik Vollmer, Hayley L Singkhek, Kyrie D Frazier, Sophia A Kantejeva, Maulik R Patel, Jason A MacGurn.

One of the hallmarks of aging is a decline in the function of mitochondria, which is often accompanied by altered morphology and dynamics. In some cases, these changes may reflect macromolecular damage to mitochondria that occurs with aging and stress, while in other cases they may be part of a programmed, adaptive response. In this study, we report that mitochondria undergo dramatic morphological changes in chronologically aged yeast cells. These changes are characterized by a large, rounded morphology, decreased co-localization of outer membrane and matrix markers, and decreased mitochondrial membrane potential. Notably, these transitions are prevented by pharmacological or genetic interventions that perturb sphingolipid biosynthesis, indicating that sphingolipids are required for these mitochondrial transitions in aging cells. Consistent with these findings, we observe that overexpression of inositol phospholipid phospholipase (Isc1) prevents these alterations to mitochondria morphology in aging cells. We also report that mitochondria exhibit similar sphingolipid-dependent morphological transitions following acute exposure to oxidative stress. These findings suggest that sphingolipid metabolism contributes to mitochondrial remodeling in aging cells and during oxidative stress, perhaps as a result of damaged sphingolipids that localize to mitochondrial membranes. These findings underscore the complex relationship between mitochondria function and sphingolipid metabolism, particularly in the context of aging and stress.

DOI: https://doi.org/10.1101/2025.02.26.640157
Cancer Res Commun. 2025 Mar 11.

Branched-chain amino acid catabolism promotes ovarian cancer cell proliferation via phosphorylation of mTOR.

Hannah J Lusk, Monica A Haughan, Tova M Bergsten, Joanna E Burdette, Laura M Sanchez.

Ovarian cancer is the sixth leading cause of cancer-related mortality among individuals with ovaries, and high-grade serous ovarian cancer (HGSOC) is the most common and lethal subtype. Characterized by a distinct and aggressive metastatic pattern, HGSOC can originate in the fallopian tube with the transformation of fallopian tube epithelial (FTE) cells, which metastasize to the ovary and subsequently to the omentum and peritoneal cavity. The omentum is a privileged metastatic site, and the metabolic exchange underlying omental metastasis could provide enzyme or receptor targets to block spread. In this study, we adapted a mass spectrometry imaging (MSI) protocol to investigate spatial location of 3D cocultures of tumorigenic FTE cells when grown in proximity to murine omental explants as a model of early metastatic colonization. Our analysis revealed several altered metabolites in tumorigenic FTE/omentum cocultures, namely changes in branched-chain amino acids (BCAA), including valine. We quantified the heightened consumption of valine, other BCAAs, and other amino acid-derived metabolites in omental cocultures using LC-MS assays. Our analysis revealed that metabolite concentrations when monitored with MSI from cell culture media in living culture systems have notable considerations for how MSI data may produce signatures that induce ionization suppression. Supplementation with valine enhanced proliferation and mTOR signaling in tumorigenic FTE cells, suggesting the potential of BCAA's as a nutrient utilized by tumor cells during omental colonization and a possible target for metastasis.

DOI: https://doi.org/10.1158/2767-9764.CRC-24-0532