bims-midysc 2025-03-02 papers

bims-midysc

Biomed News

on Mitochondria dysfunction in cancer

Issue of 2025–03–02
eleven papers selected by
Papachristodoulou Lab

A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.
Development of a cell-penetrating peptide-based nanocomplex for long-term delivery of intact mitochondrial DNA into epithelial cells.
Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.
SREBF1-based metabolic reprogramming in prostate cancer promotes tumor ferroptosis resistance.
Protocol for real-time measurement of mitochondrial bioenergetics in 3D-cultured brain tumor stem cells using the Resipher system.
Fatty acid synthase (FASN) inhibition cooperates with BH3 mimetic drugs to overcome resistance to mitochondrial apoptosis in pancreatic cancer.
The Landscape of Prostate Tumour Methylation.
TOMM20 as a driver of cancer aggressiveness via oxidative phosphorylation, maintenance of a reduced state, and resistance to apoptosis.
Thermal proteome profiling and proteome analysis using high-definition mass spectrometry demonstrate modulation of cholesterol biosynthesis by next-generation galeterone analog VNPP433-3β in castration-resistant prostate cancer.
ER-mitochondria contact sites: a refuge for mitochondrial mRNAs under ER stress.
Lineage plasticity of the integrated stress response is a hallmark of cancer evolution.

Res Sq. 2025 Feb 14. pii: rs.3.rs-5961609. [Epub ahead of print]

A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.

Martin Picard, Anna Monzel, Jack Devine, Darshana Kapri, Jose Enriquez, Caroline Trumpff.

Mitochondria are a diverse family of organelles that specialize to accomplish complimentary functions 1-3. All mitochondria share general features, but not all mitochondria are created equal 4.Here we develop a quantitative pipeline to define the degree of molecular specialization among different mitochondrial phenotypes - or mitotypes. By distilling hundreds of validated mitochondrial genes/proteins into 149 biologically interpretable MitoPathway scores (MitoCarta 3.0 5) the simple mitotyping pipeline allows investigators to quantify and interpret mitochondrial diversity and plasticity from transcriptomics or proteomics data across a variety of natural and experimental contexts. We show that mouse and human multi-organ mitotypes segregate along two main axes of mitochondrial specialization, contrasting anabolic (liver) and catabolic (brain) tissues. In cultured primary human fibroblasts exhibiting robust time-dependent and treatment-induced metabolic plasticity 6-8, we demonstrate how the mitotype of a given cell type recalibrates i) over time in parallel with hallmarks of aging, and ii) in response to genetic, pharmacological, and metabolic perturbations. Investigators can now use MitotypeExplorer.org and the associated code to visualize, quantify and interpret the multivariate space of mitochondrial biology.

DOI: https://doi.org/10.21203/rs.3.rs-5961609/v1
Mol Ther Nucleic Acids. 2025 Mar 11. 36(1): 102449

Development of a cell-penetrating peptide-based nanocomplex for long-term delivery of intact mitochondrial DNA into epithelial cells.

Kyrie Wilson, Charles Holjencin, Hwaran Lee, Balasubramaniam Annamalai, Masaaki Ishii, Jeremy L Gilbert, Andrew Jakymiw, Bärbel Rohrer.

  Gene therapy approaches for mitochondrial DNA (mtDNA)-associated damage/diseases have thus far been limited, and despite advancements in single gene therapy for mtDNA mutations and progress in mitochondrial transplantation, no method exists for restoring the entire mtDNA molecule in a clinically translatable manner. Here, we present for the first time a strategy to deliver an exogenous, fully intact, and healthy mtDNA template into cells to correct endogenous mtDNA mutations and deletions, with the potential to be developed into an efficient pan-therapy for inherited and/or acquired mtDNA disorders. More specifically, the novel therapeutic nanoparticle complex used in our study was generated by combining a cell-penetrating peptide (CPP) with purified mtDNA, in conjunction with a mitochondrial targeting reagent. The generated nanoparticle complexes were found to be taken up by cells and localized to mitochondria, with exogenous mtDNA retention/maintenance, along with mitochondrial RNA and protein production, observed in mitochondria-depleted ARPE-19 cells at least 4 weeks following a single treatment. These data demonstrate the feasibility of restoring mtDNA in cells via a CPP carrier, with the therapeutic potential to correct mtDNA damage independent of the number of gene mutations found within the mtDNA.

Keywords:  MT: Delivery Strategies; age-related diseases; cell-penetrating peptide; mitochondria; mitochondrial DNA; mitochondrial transplantation; mtDNA; mtDNA gene therapy; mtDNA mutations; nucleic acid delivery

DOI:  https://doi.org/10.1016/j.omtn.2025.102449
Cell Rep Methods. 2025 Feb 24. pii: S2667-2375(25)00025-6. [Epub ahead of print]5(2): 100989

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.

Yi Jiang, Haoyu Wang, Kevin M Boergens, Norman Rzepka, Fangfang Wang, Yunfeng Hua.

  Recent technical advances in volume electron microscopy (vEM) and artificial-intelligence-assisted image processing have facilitated high-throughput quantifications of cellular structures, such as mitochondria, that are ubiquitous and morphologically diversified. A still often-overlooked computational challenge is to assign a cell identity to numerous mitochondrial instances, for which both mitochondrial and cell membrane contouring used to be required. Here, we present a vEM reconstruction procedure (called mito-SegEM) that utilizes virtual-path-based annotation to assign automatically segmented mitochondrial instances at the cellular scale, therefore bypassing the requirement of membrane contouring. The embedded toolset in webKnossos (an open-source online annotation platform) is optimized for fast annotation, visualization, and proofreading of cellular organelle networks. We demonstrate the broad applications of mito-SegEM on volumetric datasets from various tissues, including the brain, intestine, and testis, to achieve an accurate and efficient reconstruction of mitochondria in a use-dependent fashion.

Keywords:  CP: Cell biology; CP: Imaging; cell biology; image processing; mitochondrion; software; volume electron microscopy

DOI:  https://doi.org/10.1016/j.crmeth.2025.100989
Cell Death Discov. 2025 Feb 23. 11(1): 75

SREBF1-based metabolic reprogramming in prostate cancer promotes tumor ferroptosis resistance.

Guojiang Wei, Ying Huang, Wenya Li, Yuxin Xie, Deyi Zhang, Yuanjie Niu, Yang Zhao.

Metabolic reprogramming in prostate cancer has been widely recognized as a promoter of tumor progression and treatment resistance. This study investigated its association with ferroptosis resistance in prostate cancer and explored its therapeutic potential. In this study, we identified differences in the epithelial characteristics between normal prostate tissue and tissues of various types of prostate cancer using single-cell sequencing. Through transcription factor regulatory network analysis, we focused on the candidate transcription factor, SREBF1. We identified the differences in SREBF1 transcriptional activity and its association with ferroptosis, and further verified this association using hdWGCNA. We constructed a risk score based on SREBF1 target genes associated with the biochemical recurrence of prostate cancer by combining bulk RNA analysis. Finally, we verified the effects of the SREBPs inhibitor Betulin on the treatment of prostate cancer and its chemosensitization effect. We observed characteristic differences in fatty acid and cholesterol metabolism between normal prostate tissue and prostate cancer tissue, identifying high transcriptional activity of SREBF1 in prostate cancer tissue. This indicates that SREBF1 is crucial for the metabolic reprogramming of prostate cancer, and that its mediated metabolic changes promoted ferroptosis resistance in prostate cancer in multiple ways. SREBF1 target genes are associated with biochemical recurrence of prostate cancer. Finally, our experiments verified that SREBF1 inhibitors can significantly promote an increase in ROS, the decrease in GSH, and the decrease in mitochondrial membrane potential in prostate cancer cells and confirmed their chemosensitization effect in vivo. Our findings highlighted a close association between SREBF1 and ferroptosis resistance in prostate cancer. SREBF1 significantly influences metabolic reprogramming in prostate cancer cells, leading to ferroptosis resistance. Importantly, our results demonstrated that SREBF1 inhibitors can significantly enhance the therapeutic effect and chemosensitization of prostate cancer, suggesting a promising therapeutic potential for the treatment of prostate cancer.

DOI: https://doi.org/10.1038/s41420-025-02354-7
STAR Protoc. 2025 Feb 24. pii: S2666-1667(25)00057-7. [Epub ahead of print]6(1): 103651

Protocol for real-time measurement of mitochondrial bioenergetics in 3D-cultured brain tumor stem cells using the Resipher system.

Cloé Tessier, Maxime Toujas, Antonio C Pagano Zottola, Andreas Bikfalvi, Thomas Mathivet, Thomas Daubon, Lucie Brisson, Audrey Burban, Ahmad Sharanek.

  Aberrant mitochondrial function can lead to severe human diseases, including neurodegenerative diseases and cancer. Here, we describe a cell-based protocol for measuring different mitochondrial respiratory parameters using the high-resolution real-time Resipher system. We optimized this protocol on brain tumor stem cells cultured in three-dimensional spheroids. We provide essential optimization steps for cell seeding density, mitochondrial respiration modulator concentrations, running the assay, and data analysis. For complete details on the use and execution of this protocol, please refer to Burban et al.1.

Keywords:  Cancer; Cell-based Assays; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2025.103651
Neoplasia. 2025 Feb 24. pii: S1476-5586(25)00022-3. [Epub ahead of print]62 101143

Fatty acid synthase (FASN) inhibition cooperates with BH3 mimetic drugs to overcome resistance to mitochondrial apoptosis in pancreatic cancer.

Travis Vander Steen, Ingrid Espinoza, Cristina Duran, Guillem Casadevall, Eila Serrano-Hervás, Elisabet Cuyàs, Sara Verdura, George Kemble, Scott H Kaufmann, Robert McWilliams, Sílvia Osuna, Daniel D Billadeau, Javier A Menendez, Ruth Lupu.

  Resistance to mitochondrial apoptosis is a major driver of chemoresistance in pancreatic ductal adenocarcinoma (PDAC). However, pharmacological manipulation of the mitochondrial apoptosis threshold in PDAC cells remains an unmet therapeutic goal. We hypothesized that fatty acid synthase inhibitors (FASNis), a family of targeted metabolic therapeutics recently entering the clinic, could lower the apoptotic threshold in chemoresistant PDAC cells and be synergistic with BH3 mimetics that neutralize anti-apoptotic proteins. Computational studies with TVB-3166 and TVB-3664, two analogues of the clinical-grade FASNi TVB-2640 (denifanstat), confirmed their uncompetitive behavior towards NADPH when bound to the FASN ketoacyl reductase domain. The extent of NADPH accumulation, a consequence of FASN inhibition, paralleled the sensitivity of PDAC cells to the apoptotic effects of TVB FASNis in conventional PDAC cell lines that naturally express varying levels of FASN. FASN inhibition dramatically increased the sensitivity of "FASN-high" expressing PDAC cells to the BCL2/BCL-XL/BCL-W inhibitor ABT-263/navitoclax and the BCL2-selective inhibitor ABT-199/venetoclax, both in vitro and in in vivo xenografted tumors. The ability of TVB FASNis to shift the balance of pro- and anti-apoptotic proteins and thereby push PDAC cells closer to the apoptotic threshold was also observed in cell lines developed from patient-derived xenografts (PDXs) representative of the classical (pancreatic) transcriptomic subtype of PDAC. Experiments in PDAC PDXs in vivo confirmed the synergistic antitumor activity of TVB-3664 with navitoclax and venetoclax, independent of the nature of the replication stress signature of patient-derived PDAC cells. The discovery that targeted inhibition of FASN is a metabolic perturbation that sensitizes PDAC cells to BH3 mimetics warrants further investigation to overcome resistance to mitochondrial apoptosis in PDAC patients.

Keywords:  BH3 mimetics; Fatty acid synthase; Gemcitabine; Pancreatic cancer

DOI:  https://doi.org/10.1016/j.neo.2025.101143
bioRxiv. 2025 Feb 15. pii: 2025.02.07.637178. [Epub ahead of print]

The Landscape of Prostate Tumour Methylation.

Jaron Arbet, Takafumi N Yamaguchi, Yu-Jia Shiah, Rupert Hugh-White, Adriana Wiggins, Jieun Oh, Tsumugi Gebo, Adrien Foucal, Robert Lesurf, Chol-Hee Jung, Rachel M A Dang, Raag Agrawal, Julie Livingstone, Adriana Salcedo, Cindy Q Yao, Shadrielle Melijah G Espiritu, Kathleen E Houlahan, Fouad Yousif, Lawrence E Heisler, Michael Fraser, Amar Kishan, Alejandro Berlin, Melvin Lk Chua, Theodorus van der Kwast, Christopher M Hovens, Robert G Bristow, Paul C Boutros.

Prostate cancer is characterized by profound heterogeneity in its clinical trajectory. While genomic heterogeneity has been well-characterized, epigenomic heterogeneity remains less understood. To fill this gap, we compiled 2,149 multi-ancestric prostate methylomes spanning normal tissue through localized disease of varying grades to poly-metastatic disease, most with multi-omic DNA and/or RNA characterization. We identify four subtypes that varied by stage, grade and mutational subtype. We identify extensive interplay between DNA ploidy and DNA methylation, with transcriptional consequences that vary across driver-genes. Each major prostate cancer driver gene mutation triggers a specific epigenetic dysregulation, and we define a set of 14 reusable models that accurately predict clinico-molecular features of a prostate cancer from DNA methylation data. Specific epigenetic features predict disease aggression, including metastasis, with epigenomic and genomic features synergizing to optimize predictions. These results define a complex interplay between tumour genetics and epigenetics that converges to modify gene-expression programs, and subsequent clinical presentation.

DOI: https://doi.org/10.1101/2025.02.07.637178
Mol Oncol. 2025 Feb 25.

TOMM20 as a driver of cancer aggressiveness via oxidative phosphorylation, maintenance of a reduced state, and resistance to apoptosis.

Ranakul Islam, Megan E Roche, Zhao Lin, Diana Whitaker-Menezes, Victor Diaz-Barros, Eurico Serrano, Maria Paula Martinez Cantarin, Nancy J Philp, Atrayee Basu Mallick, Ubaldo Martinez-Outschoorn.

  Chondrosarcomas are common bone sarcomas frequently resistant to radiation and chemotherapy, with high recurrence rates, development of metastatic disease, and death. Fibrosarcomas are soft tissue sarcomas associated with poor outcomes. Translocase of outer mitochondrial membrane receptor 20 (TOMM20) is a mitochondrial receptor protein associated with cancer aggressiveness in many cancer subtypes, but the mechanisms remain poorly understood. Here, we studied the effects of TOMM20 overexpression and downregulation on the redox state, mitochondrial oxidative phosphorylation (OXPHOS), and tumor growth using fibrosarcoma and chondrosarcoma models. TOMM20 overexpression increased OXPHOS, NADH, and NADPH with reduced cellular reactive oxygen species (ROS). TOMM20 induced resistance to apoptosis, including with BCL-2 and OXPHOS complex IV inhibitors, but with increased sensitivity to an OXPHOS complex I inhibitor. Also, TOMM20 induced cell growth and migration in vitro and promoted tumor growth in vivo. Conversely, knocking down TOMM20 using CRISPR-Cas9 reduced cancer aggressiveness in vivo in both chondrosarcoma and fibrosarcoma mouse models. In conclusion, TOMM20 is a driver of cancer aggressiveness by OXPHOS, apoptosis resistance, and the maintenance of a reduced state.

Keywords:  OXPHOS; ROS; TOMM; apoptosis; mitochondria; redox

DOI:  https://doi.org/10.1002/1878-0261.70002
Mol Oncol. 2025 Feb 26.

Thermal proteome profiling and proteome analysis using high-definition mass spectrometry demonstrate modulation of cholesterol biosynthesis by next-generation galeterone analog VNPP433-3β in castration-resistant prostate cancer.

Retheesh S Thankan, Elizabeth Thomas, Mehari M Weldemariam, Puranik Purushottamachar, Weiliang Huang, Maureen A Kane, Yuji Zhang, Nicholas Ambulos, Bi-Dar Wang, David Weber, Vincent C O Njar.

  Cholesterol (CHOL) homeostasis is significantly modulated in prostate cancer (PCa) suggesting an active role in PCa development and progression. Several studies indicate a strong correlation between elevated CHOL levels and increased PCa risk and severity. Inhibition of CHOL biosynthesis at different steps, including lanosterol synthase (LSS), has shown significant efficacy against both hormone-dependent and castration-resistant PCa. Earlier, we reported proteasomal degradation of androgen receptor (AR)/AR-Vs and Mnk1/2 as the primary mechanisms of action of VNPP433-3β in inhibiting PCa cell proliferation and tumor growth. Through thermal proteome profiling, comparative proteomics and cellular thermal shift assay, we identified VNPP433-3β's ancillary effect of lowering CHOL by binding to LSS and lanosterol 14-alpha demethylase, potentially inhibiting CHOL biosynthesis in PCa cells and tumors. Additionally, in conjunction with our previously reported transcriptome analysis, proteomics reveals that VNPP433-3β modulated upstream regulators and pathways critical for PCa stem cell maintenance and recurrence. The inhibition of CHOL biosynthesis by VNPP433-3β reinforces its multifaceted effects in PCa across all stages, highlighting its potential as a single-agent therapy. Achieving reduced CHOL levels aligns with better treatment outcomes, further substantiating VNPP433-3β's therapeutic potential.

Keywords:  CYP51A1; cholesterol; lanosterol synthase; next‐generation galeterone analog; prostate cancer; thermal proteome profiling

DOI:  https://doi.org/10.1002/1878-0261.70009
Trends Cell Biol. 2025 Feb 25. pii: S0962-8924(25)00036-4. [Epub ahead of print]

ER-mitochondria contact sites: a refuge for mitochondrial mRNAs under ER stress.

Philippe Pihán, Lisa M Ellerby, Claudio Hetz.

  Tight mitochondria-endoplasmic reticulum (ER) contacts (MERCS) play essential roles in cellular homeostasis. Brar et al. reveal a novel mechanism where mitochondrial mRNAs escape global translational repression at novel context-specific MERCS during ER stress, uncovering spatially regulated translation as a critical adaptive strategy to cope with cellular stress.

Keywords:  ATAD3A; PERK; endoplasmic reticulum stress; mitochondria–ER contact sites (MERCS); spatial translation regulation

DOI:  https://doi.org/10.1016/j.tcb.2025.02.002
bioRxiv. 2025 Feb 13. pii: 2025.02.10.637516. [Epub ahead of print]

Lineage plasticity of the integrated stress response is a hallmark of cancer evolution.

Shiqi Diao, Jia Yi Zou, Shuo Wang, Nour Ghaddar, Jason E Chan, Hyungdong Kim, Nicolas Poulain, Constantinos Koumenis, Maria Hatzoglou, Peter Walter, Nahum Sonenberg, John Le Quesne, Tuomas Tammela, Antonis E Koromilas.

The link between the "stress phenotype"-a well-established hallmark of cancer-and its role in tumor progression and intratumor heterogeneity remains poorly defined. The integrated stress response (ISR) is a key adaptive pathway that enables tumor survival under oncogenic stress. While ISR has been implicated in promoting tumor growth, its precise role in driving tumor evolution and heterogeneity has not been elucidated. In this study, using a genetically engineered mouse models, we demonstrate that ISR activation-indicated by elevated levels of phosphorylated eIF2 (p-eIF2) and ATF4-is essential for the emergence of dedifferentiated, therapy-resistant cell states. ISR, through the coordinated actions of ATF4 and MYC, facilitates the development of tumor cell populations characterized by high plasticity, stemness, and an epithelial-mesenchymal transition (EMT)-prone phenotype. This process is driven by ISR-mediated expression of genes that maintain mitochondrial integrity and function, critical for sustaining tumor progression. Importantly, genetic, or pharmacological inhibition of the p-eIF2-ATF4 signaling axis leads to mitochondrial dysfunction and significantly impairs tumor growth in mouse models of lung adenocarcinoma (LUAD). Moreover, ISR-driven dedifferentiation is associated with poor prognosis and therapy resistance in advanced human LUAD, underscoring ISR inhibition as a promising therapeutic strategy to disrupt tumor evolution and counteract disease progression.

DOI: https://doi.org/10.1101/2025.02.10.637516