bims-nenemi 2025-01-19 papers

bioRxiv. 2024 Dec 30. pii: 2024.12.30.630791. [Epub ahead of print]

Rewriting nuclear epigenetic scripts in mitochondrial diseases as a strategy for heteroplasmy control.

María J Pérez, Rocío B Colombo, Sebastián M Real, María T Branham, Sergio R Laurito, Carlos T Moraes, Lía Mayorga.

Mitochondrial diseases, caused by mutations in either nuclear or mitochondrial DNA (mtDNA), currently have limited treatment options. For mtDNA mutations, reducing mutant-to-wild-type mtDNA ratio (heteroplasmy shift) is a promising therapeutic option, though current approaches face significant challenges. Previous research has shown that severe mitochondrial dysfunction triggers an adaptive nuclear epigenetic response, characterized by changes in DNA methylation, which does not occur or is less important when mitochondrial impairment is subtle. Building on this, we hypothesized that targeting nuclear DNA methylation could selectively compromise cells with high levels of mutant mtDNA, favor ones with lower mutant load and thereby reduce overall heteroplasmy. Using cybrid models harboring two disease-causing mtDNA mutations-m.13513G>A and m.8344A>G-at varying heteroplasmy levels, we discovered that both the mutation type and load distinctly shape the nuclear DNA methylome. We found this methylation pattern to be critical for the survival of high-heteroplasmy cells but not for the low-heteroplasmy ones. Consequently, by disrupting this epigenetic programming with FDA approved DNA methylation inhibitors we managed to selectively impact high-heteroplasmy cybrids and reduce heteroplasmy. These findings were validated in both cultured cells and an in vivo xenograft model. Our study reveals a previously unrecognized role for nuclear DNA methylation in regulating cell survival in the context of mitochondrial heteroplasmy. This insight not only advances our understanding of mitochondrial-nuclear interactions but also introduces epigenetic modulation as a possible therapeutic avenue for mitochondrial diseases.

DOI: https://doi.org/10.1101/2024.12.30.630791

Theranostics. 2025 ;15(4): 1304-1319

Acylglycerol kinase inhibits macrophage anti-tumor activity via limiting mtDNA release and cGAS-STING-type I IFN response.

Qiuyang Du, Na Ning, Xiujuan Zhao, Feifan Liu, Si Zhang, Yuting Xia, Fei Li, Shijie Yuan, Xiaorong Xie, Mengdi Zhu, Zehan Huang, Zhaohui Tang, Jing Wang, Ran He, Xiang-Ping Yang.

Background: Tumor associated macrophages (TAMs) are critical components in regulating the immune statuses of the tumor microenvironments. Although TAM has been intensively studied, it is unclear how mitochondrial proteins such as AGK regulate the TAMs' function. Methods: We investigated the AGK function in TAMs using macrophage-specific Agk deficient mice with B16 and LLC syngeneic tumor models. Flow cytometry was used to evaluate the stemness and activation of CD8+ T cells. The enhanced release of mtDNA into the cytosol in the Agk-deficient BMDMs was measured by RT-PCR and immunofluorescence; the cGAS-STING-type I IFN pathway was evaluated by immunoblotting. Mitochondria functions were evaluated by electron microscope and seahorse equipment. Results: We have noted an increased expression of AGK in TAMs of multiple tumor types, which was negatively correlates with the tumor tissue immune scores. In the B16 and LLC tumor models, macrophage Agk-deficient mice have reduced tumor growth and enhanced populations of CD8+ Tpex. AGK-deficient macrophages have increased mitochondrial damage and mtDNA release into the cytosol, which leads to enhanced cGAS-STING-type I IFN activation. Blockade of the type I IFN signaling pathway with anti-IFNAR reversed the phenotype in Agk-deficient mice. Conclusions: Our findings define a critical role of AGK in maintaining the macrophage mitochondrial homeostasis that is associated with mtDNA release and following cGAS-STING activation and type I IFN pathway. Targeting AGK in TAMs may represent a novel strategy to enhance anti-tumoral activity.

Keywords: Acylglycerol kinase; Mitochondrial ROS; TAMs; cGAS-STING-type I IFN signaling pathway; mitochondrial DNA

DOI: https://doi.org/10.7150/thno.101298

Sci Transl Med. 2025 Jan 15. 17(781): eadn8699

Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease.

TRR241 IBDome Consortium

Dysregulation at the intestinal epithelial barrier is a driver of inflammatory bowel disease (IBD). However, the molecular mechanisms of barrier failure are not well understood. Here, we demonstrate dysregulated mitochondrial fusion in intestinal epithelial cells (IECs) of patients with IBD and show that impaired fusion is sufficient to drive chronic intestinal inflammation. We found reduced expression of mitochondrial fusion-related genes, such as the dynamin-related guanosine triphosphatase (GTPase) optic atrophy 1 (OPA1), and fragmented mitochondrial networks in crypt IECs of patients with IBD. Mice with Opa1 deficiency in the gut epithelium (Opa1i∆IEC) spontaneously developed chronic intestinal inflammation with mucosal ulcerations and immune cell infiltration. Intestinal inflammation in Opa1i∆IEC mice was driven by microbial translocation and associated with epithelial progenitor cell death and gut barrier dysfunction. Opa1-deficient epithelial cells and human organoids exposed to a pharmacological OPA1 inhibitor showed disruption of the mitochondrial network with mitochondrial fragmentation and changes in mitochondrial size, ultrastructure, and function, resembling changes observed in patient samples. Pharmacological inhibition of the GTPase dynamin-1-like protein in organoids derived from Opa1i∆IEC mice partially reverted this phenotype. Together, our data demonstrate a role for epithelial OPA1 in regulating intestinal immune homeostasis and epithelial barrier function. Our data provide a mechanistic explanation for the observed mitochondrial dysfunction in IBD and identify mitochondrial fusion as a potential therapeutic target in this disease.

DOI: https://doi.org/10.1126/scitranslmed.adn8699

iScience. 2025 Jan 17. 28(1): 111544

ZFAND6 promotes TRAF2-dependent mitophagy to restrain cGAS-STING signaling.

Kashif Shaikh, Melissa Bowman, Sarah M McCormick, Linlin Gao, Jiawen Zhang, Jesse White, John Tawil, Arun Kapoor, Ravit Arav-Boger, Christopher C Norbury, Edward W Harhaj.

ZFAND6 is a zinc finger protein that interacts with TNF receptor-associated factor 2 (TRAF2) and polyubiquitin chains and has been linked to tumor necrosis factor (TNF) signaling. Here, we report a previously undescribed function of ZFAND6 in maintaining mitochondrial homeostasis by promoting mitophagy. Deletion of ZFAND6 in bone marrow-derived macrophages (BMDMs) upregulates reactive oxygen species (ROS) and the accumulation of damaged mitochondria due to impaired mitophagy. Consequently, mitochondrial DNA (mtDNA) is released into the cytoplasm, triggering the spontaneous expression of interferon-stimulated genes (ISGs) in a stimulator of interferon genes (STING) dependent manner, which leads to enhanced viral resistance. Mechanistically, ZFAND6 bridges a TRAF2-cIAP1 interaction and mediates the recruitment of TRAF2 to damaged mitochondria, which is required for the initiation of ubiquitin-dependent mitophagy. Our results suggest that ZFAND6 promotes the interactions of TRAF2 and cIAP1 and the clearance of damaged mitochondria by mitophagy to maintain mitochondrial homeostasis.

Keywords: Cell biology; Omics; Transcriptomics

DOI: https://doi.org/10.1016/j.isci.2024.111544

bioRxiv. 2025 Jan 02. pii: 2024.12.26.630414. [Epub ahead of print]

Quantitative analyses of single mitochondrial components reveal an early role of small-mitochondrial-networks in priming neoplasticity.

Mayank Saini, Swati Agarwala, Biratal Wagle, Brian Spurlock, Bharti Golchha, Danitra Parker, Kasturi Mitra.

Quantitative understanding of mitochondrial heterogeneity is necessary for elucidating the precise role of these multifaceted organelles in tumor cell development. We demonstrate an early mechanistic role of mitochondria in initiating neoplasticity by performing quantitative analyses of structure-function of single mitochondrial components coupled with single cell transcriptomics. We demonstrate that the large Hyperfused-Mitochondrial-Networks (HMNs) of keratinocytes promptly get converted to the heterogenous Small-Mitochondrial-Networks (SMNs) as the stem cell enriching dose of the model carcinogen, TCDD, depolarizes mitochondria. This happens by physical reorganization of the HMN nodes and edges, which enriches redox tuned SMNs with distinct network complexity. This leads to establishment of transcriptomic interaction between the upregulated redox relevant mtDNA genes and the lineage specific stemness gene, KRT15, prior to cell cycle exit. The SMN enrichment and related transcriptomic connections are sustained in the neoplastic cell population. Consistently, carcinogenic dose incapable of causing pronounced neoplastic stem cell enrichment fails to establish specific enrichment of SMNs and its linked mtDNA-KRT15(stemness) transcriptomic interaction prior to cell cycle exit. The mtDNA-KRT15 modulation is confirmed in cSCC tumors, while highlighting patient heterogeneity. Therefore, we propose that early enrichment of redox-tuned SMNs primes neoplastic transformation by establishing mtDNA-stemness transcriptomic interaction prior to cell cycle exit towards specifying quiescent neoplastic stem cells. Our data implies that redox-tuned SMNs, created by mitochondrial fission, would be sustained by tuning the balance of mitochondrial fission-fusion during neoplastic transformation. The proposed early role of mitochondria in cancer etiology is potentially relevant for designing precision strategies for cancer prevention and therapy.
Significance Statement: The challenges of understanding the complex role of the multifaceted and heterogenous cellular organelles, mitochondria, can be potentially overcome with their quantitative analyses. We use a combinatorial approach of quantitative analyses of single-mitochondrial-components and scRNA-seq to elucidate a mechanism of mitochondrial priming of cancer initiation by a model carcinogen. We propose that conversion of large Hyperfused-Mitochondrial-Networks (HMNs) to Small-Mitochondrial-Networks (SMNs) primes non-transformed keratinocytes towards their neoplastic transformation. Mechanistically, the SMNs, enriched by modulation of the physical nodes and edges of mitochondrial networks, tunes mitochondrial redox balance to establish transcriptomic interactions towards specifying a state of stemness. Further probing of our fundamental findings in the light of cancer heterogeneity may facilitate refinement of the various proposed mitochondria based targeted cancer therapies.

DOI: https://doi.org/10.1101/2024.12.26.630414

Nat Aging. 2025 Jan 10.

Gut microbial-derived phenylacetylglutamine accelerates host cellular senescence.

Gut microbiota plays a crucial role in the host health in the aging process. However, the mechanisms for how gut microbiota triggers cellular senescence and the consequent impact on human aging remain enigmatic. Here we show that phenylacetylglutamine (PAGln), a metabolite linked to gut microbiota, drives host cellular senescence. Our findings indicate that the gut microbiota alters with age, which leads to increased production of phenylacetic acid (PAA) and its downstream metabolite PAGln in older individuals. The PAGln-induced senescent phenotype was verified in both cellular models and mouse models. Further experiments revealed that PAGln induces mitochondrial dysfunction and DNA damage via adrenoreceptor (ADR)-AMP-activated protein kinase (AMPK) signaling. Blockade of ADRs as well as senolytics therapy impede PAGln-induced cellular senescence in vivo, implying potential anti-aging therapies. This combined evidence reveals that PAGln, a naturally occurring metabolite of human gut microbiota, mechanistically accelerates host cellular senescence.

DOI: https://doi.org/10.1038/s43587-024-00795-w