bims-mibica Biomed News
on Mitochondrial bioenergetics in cancer
Issue of 2024–05–12
eightteen papers selected by
Kelsey Fisher-Wellman, East Carolina University
  1. Reprogrammed mitochondria: a central hub of cancer cell metabolism.
  2. Multiomics analysis identifies oxidative phosphorylation as a cancer vulnerability arising from myristoylation inhibition.
  3. MTHFD2-mediated redox homeostasis promotes gastric cancer progression under hypoxic conditions.
  4. A mitochondrial surveillance mechanism activated by SRSF2 mutations in hematologic malignancies.
  5. Improved CAR-T cell activity associated with increased mitochondrial function primed by galactose.
  6. An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.
  7. Identification of a family of species-selective complex I inhibitors as potential anthelmintics.
  8. Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease.
  9. Time-dependent proteomics and drug response in expanding cancer cells.
  10. Targetable leukaemia dependency on noncanonical PI3Kγ signalling.
  11. Blockage of BCL-XL overcomes venetoclax resistance across BCL2-positive lymphoid malignancies irrespective of BIM status.
  12. Effect of the mitochondrial membrane potential on the absorbance of the reduced form of cytochrome c oxidase.
  13. A novel protein CYTB-187AA encoded by the mitochondrial gene CYTB modulates mammalian early development.
  14. The intrinsic substrate specificity of the human tyrosine kinome.
  15. Human CD4+ memory phenotype T cells use mitochondrial metabolism to generate sensitive IFN-γ responses.
  16. A systematic mutational framework for studying oxidative phosphorylation-related proteins.
  17. The Warburg Effect Reinterpreted 100 yr on: A First-Principles Stoichiometric Analysis and Interpretation from the Perspective of ATP Metabolism in Cancer Cells.
  18. mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics.
  1. Biochem Soc Trans. 2024 May 08. pii: BST20231090. [Epub ahead of print]
    Reprogrammed mitochondria: a central hub of cancer cell metabolism.
    Fabio Ciccarone, Maria Rosa Ciriolo.
      Mitochondria represent the metabolic hub of normal cells and play this role also in cancer but with different functional purposes. While cells in differentiated tissues have the prerogative of maintaining basal metabolism and support the biosynthesis of specialized products, cancer cells have to rewire the metabolic constraints imposed by the differentiation process. They need to balance the bioenergetic supply with the anabolic requirements that entail the intense proliferation rate, including nucleotide and membrane lipid biosynthesis. For this aim, mitochondrial metabolism is reprogrammed following the activation of specific oncogenic pathways or due to specific mutations of mitochondrial proteins. The main process leading to mitochondrial metabolic rewiring is the alteration of the tricarboxylic acid cycle favoring the appropriate orchestration of anaplerotic and cataplerotic reactions. According to the tumor type or the microenvironmental conditions, mitochondria may decouple glucose catabolism from mitochondrial oxidation in favor of glutaminolysis or disable oxidative phosphorylation for avoiding harmful production of free radicals. These and other metabolic settings can be also determined by the neo-production of oncometabolites that are not specific for the tissue of origin or the accumulation of metabolic intermediates able to boost pro-proliferative metabolism also impacting epigenetic/transcriptional programs. The full characterization of tumor-specific mitochondrial signatures may provide the identification of new biomarkers and therapeutic opportunities based on metabolic approaches.
    Keywords:  TCA cycle; metabolic disorders; mitochondrial dysfunction
    DOI:  https://doi.org/10.1042/BST20231090
  2. J Transl Med. 2024 May 07. 22(1): 431
    Multiomics analysis identifies oxidative phosphorylation as a cancer vulnerability arising from myristoylation inhibition.
    Erwan Beauchamp, Jay M Gamma, Christopher R Cromwell, Eman W Moussa, Rony Pain, Morris A Kostiuk, Claudia Acevedo-Morantes, Aishwarya Iyer, Megan Yap, Krista M Vincent, Lynne M Postovit, Olivier Julien, Basil P Hubbard, John R Mackey, Luc G Berthiaume.
       BACKGROUND: In humans, two ubiquitously expressed N-myristoyltransferases, NMT1 and NMT2, catalyze myristate transfer to proteins to facilitate membrane targeting and signaling. We investigated the expression of NMTs in numerous cancers and found that NMT2 levels are dysregulated by epigenetic suppression, particularly so in hematologic malignancies. This suggests that pharmacological inhibition of the remaining NMT1 could allow for the selective killing of these cells, sparing normal cells with both NMTs.
    METHODS AND RESULTS: Transcriptomic analysis of 1200 NMT inhibitor (NMTI)-treated cancer cell lines revealed that NMTI sensitivity relates not only to NMT2 loss or NMT1 dependency, but also correlates with a myristoylation inhibition sensitivity signature comprising 54 genes (MISS-54) enriched in hematologic cancers as well as testis, brain, lung, ovary, and colon cancers. Because non-myristoylated proteins are degraded by a glycine-specific N-degron, differential proteomics revealed the major impact of abrogating NMT1 genetically using CRISPR/Cas9 in cancer cells was surprisingly to reduce mitochondrial respiratory complex I proteins rather than cell signaling proteins, some of which were also reduced, albeit to a lesser extent. Cancer cell treatments with the first-in-class NMTI PCLX-001 (zelenirstat), which is undergoing human phase 1/2a trials in advanced lymphoma and solid tumors, recapitulated these effects. The most downregulated myristoylated mitochondrial protein was NDUFAF4, a complex I assembly factor. Knockout of NDUFAF4 or in vitro cell treatment with zelenirstat resulted in loss of complex I, oxidative phosphorylation and respiration, which impacted metabolomes.
    CONCLUSIONS: Targeting of both, oxidative phosphorylation and cell signaling partly explains the lethal effects of zelenirstat in select cancer types. While the prognostic value of the sensitivity score MISS-54 remains to be validated in patients, our findings continue to warrant the clinical development of zelenirstat as cancer treatment.
    Keywords:  Cancer; Complex I; N-myristoylation; N-myristoyltransferase; NDUFAF4; NMT inhibitor (NMTI); Oxidative phosphorylation; PCLX-001 (zelenirstat); Respiration
    DOI:  https://doi.org/10.1186/s12967-024-05150-6
  3. Redox Rep. 2024 Dec;29(1): 2345455
    MTHFD2-mediated redox homeostasis promotes gastric cancer progression under hypoxic conditions.
    Hai-Yu Mo, Ruo-Bing Wang, Meng-Yao Ma, Yi Zhang, Xin-Yu Li, Wang-Rong Wen, Yi Han, Tian Tian.
       OBJECTIVES: Cancer cells undergo metabolic reprogramming to adapt to high oxidative stress, but little is known about how metabolic remodeling enables gastric cancer cells to survive stress associated with aberrant reactive oxygen species (ROS) production. Here, we aimed to identify the key metabolic enzymes that protect gastric cancer (GC) cells from oxidative stress.
    METHODS: ROS level was detected by DCFH-DA probes. Multiple cell biological studies were performed to identify the underlying mechanisms. Furthermore, cell-based xenograft and patient-derived xenograft (PDX) model were performed to evaluate the role of MTHFD2 in vivo.
    RESULTS: We found that overexpression of MTHFD2, but not MTHFD1, is associated with reduced overall and disease-free survival in gastric cancer. In addition, MTHFD2 knockdown reduces the cellular NADPH/NADP+ ratio, colony formation and mitochondrial function, increases cellular ROS and cleaved PARP levels and induces in cell death under hypoxia, a hallmark of solid cancers and a common inducer of oxidative stress. Moreover, genetic or pharmacological inhibition of MTHFD2 reduces tumor burden in both tumor cell lines and patient-derived xenograft-based models.
    DISCUSSION: our study highlights the crucial role of MTHFD2 in redox regulation and tumor progression, demonstrating the therapeutic potential of targeting MTHFD2.
    Keywords:  Gastric cancer; NADPH; methylene tetrahydrofolate dehydrogenase 2 (MTHFD2); reactive oxygen species (ROS); redox metabolism
    DOI:  https://doi.org/10.1080/13510002.2024.2345455
  4. J Clin Invest. 2024 May 07. pii: e175619. [Epub ahead of print]
    A mitochondrial surveillance mechanism activated by SRSF2 mutations in hematologic malignancies.
    Xiaolei Liu, Sudhish A Devadiga, Robert F Stanley, Ryan M Morrow, Kevin A Janssen, Mathieu Quesnel-Vallières, Oz Pomp, Adam A Moverley, Chenchen Li, Nicolas Skuli, Martin P Carroll, Jian Huang, Douglas C Wallace, Kristen W Lynch, Omar Abdel-Wahab, Peter S Klein.
      Splicing factor mutations are common in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), but how they alter cellular functions is unclear. We show that the pathogenic SRSF2P95H/+ mutation disrupts the splicing of mitochondrial mRNAs, impairs mitochondrial complex I function, and robustly increases mitophagy. We also identified a mitochondrial surveillance mechanism by which mitochondrial dysfunction modifies splicing of the mitophagy activator PINK1 to remove a poison intron, increasing the stability and abundance of PINK1 mRNA and protein. SRSF2P95H-induced mitochondrial dysfunction increased PINK1 expression through this mechanism, which is essential for survival of SRSF2P95H/+ cells. Inhibition of splicing with a glycogen synthase kinase 3 inhibitor promoted retention of the poison intron, impairing mitophagy and activating apoptosis in SRSF2P95H/+ cells. These data reveal a homeostatic mechanism for sensing mitochondrial stress through PINK1 splicing and identify increased mitophagy as a disease marker and a therapeutic vulnerability in SRSF2P95H mutant MDS and AML.
    Keywords:  Autophagy; Hematology; Leukemias; Mitochondria; Oncology
    DOI:  https://doi.org/10.1172/JCI175619
  5. Leukemia. 2024 May 07.
    Improved CAR-T cell activity associated with increased mitochondrial function primed by galactose.
    Golda Gross, Suha Alkadieri, Amilia Meir, Orit Itzhaki, Yarden Aharoni-Tevet, Shahar Ben Yosef, Angi Zenab, Liat Shbiro, Amos Toren, Tal Yardeni, Elad Jacoby.
      CD19 CAR-T cells have led to durable remissions in patients with refractory B-cell malignancies; nevertheless, most patients eventually relapse in the long term. Many interventions aimed at improving current products have been reported, with a subset of them focusing on a direct or indirect link to the metabolic state of the CAR-T cells. We assessed clinical products from an ongoing clinical trial utilizing CD19-28z CAR-T cells from patients with acute lymphoblastic leukemia. CAR-T clinical products leading to a complete response had significantly higher mitochondrial function (by oxygen consumption rate) irrespective of mitochondrial content. Next, we replaced the carbon source of the media from glucose to galactose to impact cellular metabolism. Galactose-containing media increased mitochondrial activity in CAR-T cells, and improved in in-vitro efficacy, without any consistent phenotypic change in memory profile. Finally, CAR-T cells produced in galactose-based glucose-free media resulted in increased mitochondrial activity. Using an in-vivo model of Nalm6 injected mice, galactose-primed CAR-T cells significantly improved leukemia-free survival compared to standard glucose-cultured CAR-T cells. Our results prove the significance of mitochondrial metabolism on CAR-T cell efficacy and suggest a translational pathway to improve clinical products.
    DOI:  https://doi.org/10.1038/s41375-024-02257-z
  6. Nat Commun. 2024 May 07. 15(1): 3793
    An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.
    Stephen M Coscia, Andrew S Moore, Cameron P Thompson, Christian F Tirrito, E Michael Ostap, Erika L F Holzbaur.
      Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.
    DOI:  https://doi.org/10.1038/s41467-024-48189-1
  7. Nat Commun. 2024 May 08. 15(1): 3367
    Identification of a family of species-selective complex I inhibitors as potential anthelmintics.
    Taylor Davie, Xènia Serrat, Lea Imhof, Jamie Snider, Igor Štagljar, Jennifer Keiser, Hiroyuki Hirano, Nobumoto Watanabe, Hiroyuki Osada, Andrew G Fraser.
      Soil-transmitted helminths (STHs) are major pathogens infecting over a billion people. There are few classes of anthelmintics and there is an urgent need for new drugs. Many STHs use an unusual form of anaerobic metabolism to survive the hypoxic conditions of the host gut. This requires rhodoquinone (RQ), a quinone electron carrier. RQ is not made or used by vertebrate hosts making it an excellent therapeutic target. Here we screen 480 structural families of natural products to find compounds that kill Caenorhabditis elegans specifically when they require RQ-dependent metabolism. We identify several classes of compounds including a family of species-selective inhibitors of mitochondrial respiratory complex I. These identified complex I inhibitors have a benzimidazole core and we determine key structural requirements for activity by screening 1,280 related compounds. Finally, we show several of these compounds kill adult STHs. We suggest these species-selective complex I inhibitors are potential anthelmintics.
    DOI:  https://doi.org/10.1038/s41467-024-47331-3
  8. Nat Metab. 2024 May 08.
    Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease.
    Andrew Y Sung, Rachel M Guerra, Laura H Steenberge, Charlotte L Alston, Kei Murayama, Yasushi Okazaki, Masaru Shimura, Holger Prokisch, Daniele Ghezzi, Alessandra Torraco, Rosalba Carrozzo, Agnès Rötig, Robert W Taylor, James L Keck, David J Pagliarini.
      Isolated complex I (CI) deficiencies are a major cause of primary mitochondrial disease. A substantial proportion of CI deficiencies are believed to arise from defects in CI assembly factors (CIAFs) that are not part of the CI holoenzyme. The biochemistry of these CIAFs is poorly defined, making their role in CI assembly unclear, and confounding interpretation of potential disease-causing genetic variants. To address these challenges, we devised a deep mutational scanning approach to systematically assess the function of thousands of NDUFAF6 genetic variants. Guided by these data, biochemical analyses and cross-linking mass spectrometry, we discovered that the CIAF NDUFAF6 facilitates incorporation of NDUFS8 into CI and reveal that NDUFS8 overexpression rectifies NDUFAF6 deficiency. Our data further provide experimental support of pathogenicity for seven novel NDUFAF6 variants associated with human pathology and introduce functional evidence for over 5,000 additional variants. Overall, our work defines the molecular function of NDUFAF6 and provides a clinical resource for aiding diagnosis of NDUFAF6-related diseases.
    DOI:  https://doi.org/10.1038/s42255-024-01039-2
  9. Pharmacol Res. 2024 May 08. pii: S1043-6618(24)00152-X. [Epub ahead of print] 107208
    Time-dependent proteomics and drug response in expanding cancer cells.
    Yuting Pan, Ying Xuan, Piliang Hao, Xianzhi Chen, Rong Yan, Chengqian Zhang, Xisong Ke, Yi Qu, Xue Zhang.
      Cancer cell line is commonly used for discovery and development of anti-cancer drugs. It is generally considered that drug response remains constant for a certain cell line due to the identity of genetics thus protein patterns. Here, we demonstrated that cancer cells continued dividing even after reaching confluence, in that the proteomics was changed continuously and dramatically with strong relevance to cell division, cell adhesion and cell metabolism, indicating time-dependent intrinsically reprogramming of cells during expansion. Of note, the inhibition effect of most anti-cancer drugs was strikingly attenuated in culture cells along with cell expansion, with the strongest change at the third day when cells were still expanding. Profiling of an FDA-approved drug library revealed that attenuation of response with cell expansion is common for most drugs, an exception was TAK165 that was a selective inhibitor of mitochondrial respiratory chain complex I. Finally, we screened a panel of natural products and identified four pentacyclic triterpenes as selective inhibitors of cancer cells under prolonged growth. Taken together, our findings underscore that caution should be taken in evaluation of anti-cancer drugs using culture cells, and provide agents selectively targeting overgrowth cancer cells.
    Keywords:  Anti-cancer agents; Cell expansion; Cell metabolism; Drug tolerance; Pentacyclic triterpenoids; Time-dependent proteomics
    DOI:  https://doi.org/10.1016/j.phrs.2024.107208
  10. Nature. 2024 May 08.
    Targetable leukaemia dependency on noncanonical PI3Kγ signalling.
    Qingyu Luo, Evangeline G Raulston, Miguel A Prado, Xiaowei Wu, Kira Gritsman, Karley S Whalen, Kezhi Yan, Christopher A G Booth, Ran Xu, Peter van Galen, John G Doench, Shai Shimony, Henry W Long, Donna S Neuberg, Joao A Paulo, Andrew A Lane.
      Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1-4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukaemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid and dendritic lineages. This dependency is characterized by innate inflammatory signalling and activation of phosphoinositide 3-kinase regulatory subunit 5 (PIK3R5), which encodes a regulatory subunit of PI3Kγ5 and stabilizes the active enzymatic complex. We identify p21 (RAC1)-activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency and find that dephosphorylation of PAK1 by PI3Kγ inhibition impairs mitochondrial oxidative phosphorylation. Treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukaemias with activated PIK3R5. In addition, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukaemia xenografts with low baseline PIK3R5 expression, as residual leukaemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Together, our study reveals a targetable dependency on PI3Kγ-PAK1 signalling that is amenable to near-term evaluation in patients with acute leukaemia.
    DOI:  https://doi.org/10.1038/s41586-024-07410-3
  11. Blood Adv. 2024 May 07. pii: bloodadvances.2024012906. [Epub ahead of print]
    Blockage of BCL-XL overcomes venetoclax resistance across BCL2-positive lymphoid malignancies irrespective of BIM status.
    Alexandra Dolnikova, Dmitry Kazantsev, Magdalena Klanova, Eva Pokorna, Dana Sovilj, Cristina Daniela Kelemen, Liliana Tuskova, Eva Hoferkova, Marek Mraz, Karel Helman, Nikola Curik, Katerina Machova Polakova, Ladislav Anděra, Marek Trněný, Pavel Klener.
      Venetoclax, a BCL2 inhibitor, has a promising single-agent activity in mantle cell lymphoma (MCL), acute lymphoblastic leukemia (ALL), and large B-cell lymphomas (LBCL), but remissions were generally short, which calls for rational drug combinations. Using a panel of 21 lymphoma and leukemia cell lines and 28 primary samples we demonstrated strong synergy between venetoclax and A1155463, a BCL-XL inhibitor. Immunoprecipitation experiments, and studies on clones with knockout of expression, or transgenic expression of BCL-XL confirmed its key role in mediating inherent and acquired venetoclax resistance. Of note, the venetoclax and A1155463 combination was synthetically lethal even in the cell lines with lack of expression of the pro-apoptotic BCL2L11/BIM, and in the derived clones with genetic knockout of BCL2L11/BIM. This is clinically important because BCL2L11/BIM deletion, downregulation, or sequestration results in venetoclax resistance. Immunoprecipitation experiments further suggested that the pro-apoptotic effector BAX belongs to principal mediators of the venetoclax and A1155463 mode of action in the BIM-deficient cells. Lastly, the efficacy of the new pro-apoptotic combination was confirmed in vivo on a panel of 9 PDX models including MCL (n = 3), B-ALL (n = 2), T-ALL (n = 1), and DLBCL (n = 3). Because continuous inhibition of BCL-XL causes thrombocytopenia, we proposed and tested an interrupted 4 days ON / 3 days OFF treatment regimen, which retained the desired anti-tumor synergy with manageable platelet toxicity. The proposed VEN and A1155463 combination represents an innovative chemotherapy-free regimen with significant preclinical activity across diverse BCL2-positive hematologic malignancies irrespective of the BCL1L11/BIM status.
    DOI:  https://doi.org/10.1182/bloodadvances.2024012906
  12. Biochim Biophys Acta Bioenerg. 2024 May 07. pii: S0005-2728(24)00018-5. [Epub ahead of print]1865(3): 149048
    Effect of the mitochondrial membrane potential on the absorbance of the reduced form of cytochrome c oxidase.
    Raul Covian, Lanelle O Edwards, Robert S Balaban.
      The effect of mitochondrial membrane potential (ΔΨm) on the absorbance of the reduced cytochrome c oxidase (COX) was evaluated in isolated rabbit heart mitochondria using integrating sphere optical spectroscopy. Maximal reduction of the mitochondrial cytochromes was achieved by either blowing nitrogen to remove oxygen, or by adding cyanide. Gradual depolarization of ΔΨm by adding increasing concentrations of uncoupler resulted in an increase of up to 50 % in the absorbance of cytochrome aa3 under nitrogen saturation, and of 25 % with cyanide. Cytochrome aa3 absorbance increases were also observed in the presence of cyanide with apyrase (20 %) or oligomycin (12 %). The bL heme absorbance also decreased as expected from ΔΨm depolarization. A ~ 1 nm red shift in the peak wavelength of cytochrome aa3 was observed under anoxic conditions as ΔΨm was depolarized. Importantly, cytochrome c and c1 absorbances remained constant at levels corresponding to full reduction under all experimental manipulations of ΔΨm, especially with cyanide. These data suggest that ΔΨm-dependent changes in the absorbance of reduced COX were due to a variable extinction coefficient of heme a and/or a3 as a function of ΔΨm. A similar increase in the reduced cytochrome aa3 absorbance without changes in cytochrome c and c1 was observed in the perfused rabbit heart when decreasing ΔΨm with uncoupler. Our results imply that COX absorbance in its fully reduced state does not simply reflect the oxygen tension but also the ΔΨm. This may prove useful in monitoring ΔΨm under anoxic or ischemic conditions in intact tissue.
    Keywords:  Cytochrome c oxidase; Heart; Membrane potential; Mitochondria; Respiration; Spectroscopy; electron transfer
    DOI:  https://doi.org/10.1016/j.bbabio.2024.149048
  13. Cell Metab. 2024 Apr 29. pii: S1550-4131(24)00132-3. [Epub ahead of print]
    A novel protein CYTB-187AA encoded by the mitochondrial gene CYTB modulates mammalian early development.
    Zhijuan Hu, Liang Yang, Maolei Zhang, Haite Tang, Yile Huang, Yujie Su, Yingzhe Ding, Chong Li, Mengfei Wang, Yunhao Zhou, Qing Zhang, Liman Guo, Yue Wu, Qianqian Wang, Ning Liu, Haoran Kang, Yi Wu, Deyang Yao, Yukun Li, Zifeng Ruan, Hao Wang, Feixiang Bao, Guopan Liu, Junwei Wang, Yaofeng Wang, Wuming Wang, Gang Lu, Dajiang Qin, Duanqing Pei, Wai-Yee Chan, Xingguo Liu.
      The mitochondrial genome transcribes 13 mRNAs coding for well-known proteins essential for oxidative phosphorylation. We demonstrate here that cytochrome b (CYTB), the only mitochondrial-DNA-encoded transcript among complex III, also encodes an unrecognized 187-amino-acid-long protein, CYTB-187AA, using the standard genetic code of cytosolic ribosomes rather than the mitochondrial genetic code. After validating the existence of this mtDNA-encoded protein arising from cytosolic translation (mPACT) using mass spectrometry and antibodies, we show that CYTB-187AA is mainly localized in the mitochondrial matrix and promotes the pluripotent state in primed-to-naive transition by interacting with solute carrier family 25 member 3 (SLC25A3) to modulate ATP production. We further generated a transgenic knockin mouse model of CYTB-187AA silencing and found that reduction of CYTB-187AA impairs females' fertility by decreasing the number of ovarian follicles. For the first time, we uncovered the novel mPACT pattern of a mitochondrial mRNA and demonstrated the physiological function of this 14th protein encoded by mtDNA.
    Keywords:  early development; mitochondria; mitochondrial DNA; ovarian follicles; pluripotency; primed-to-naive transition; ribosomes; translation
    DOI:  https://doi.org/10.1016/j.cmet.2024.04.012
  14. Nature. 2024 May 08.
    The intrinsic substrate specificity of the human tyrosine kinome.
    Tomer M Yaron-Barir, Brian A Joughin, Emily M Huntsman, Alexander Kerelsky, Daniel M Cizin, Benjamin M Cohen, Amit Regev, Junho Song, Neil Vasan, Ting-Yu Lin, Jose M Orozco, Christina Schoenherr, Cari Sagum, Mark T Bedford, R Max Wynn, Shih-Chia Tso, David T Chuang, Lei Li, Shawn S-C Li, Pau Creixell, Konstantin Krismer, Mina Takegami, Harin Lee, Bin Zhang, Jingyi Lu, Ian Cossentino, Sean D Landry, Mohamed Uduman, John Blenis, Olivier Elemento, Margaret C Frame, Peter V Hornbeck, Lewis C Cantley, Benjamin E Turk, Michael B Yaffe, Jared L Johnson.
      Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.
    DOI:  https://doi.org/10.1038/s41586-024-07407-y
  15. iScience. 2024 May 17. 27(5): 109775
    Human CD4+ memory phenotype T cells use mitochondrial metabolism to generate sensitive IFN-γ responses.
    Nikhila S Bharadwaj, Nicholas A Zumwalde, Arvinder Kapur, Manish Patankar, Jenny E Gumperz.
      The transition of naive T lymphocytes into antigenically activated effector cells is associated with a metabolic shift from oxidative phosphorylation to aerobic glycolysis. This shift facilitates production of the key anti-tumor cytokine interferon (IFN)-γ; however, an associated loss of mitochondrial efficiency in effector T cells ultimately limits anti-tumor immunity. Memory phenotype (MP) T cells are a newly recognized subset that arises through homeostatic activation signals following hematopoietic transplantation. We show here that human CD4+ MP cell differentiation is associated with increased glycolytic and oxidative metabolic activity, but MP cells retain less compromised mitochondria compared to effector CD4+ T cells, and their IFN-γ response is less dependent on glucose and more reliant on glutamine. MP cells also produced IFN-γ more efficiently in response to weak T cell receptor (TCR) agonism than effectors and mediated stronger responses to transformed B cells. MP cells may thus be particularly well suited to carry out sustained immunosurveillance against neoplastic cells.
    Keywords:  cell biology; immunity
    DOI:  https://doi.org/10.1016/j.isci.2024.109775
  16. Nat Metab. 2024 May 08.
    A systematic mutational framework for studying oxidative phosphorylation-related proteins.
      
    DOI:  https://doi.org/10.1038/s42255-024-01042-7
  17. Function (Oxf). 2024 ;5(3): zqae008
    The Warburg Effect Reinterpreted 100 yr on: A First-Principles Stoichiometric Analysis and Interpretation from the Perspective of ATP Metabolism in Cancer Cells.
    Sunil Nath, Rudi Balling.
      The Warburg Effect is a longstanding enigma in cancer biology. Despite the passage of 100 yr since its discovery, and the accumulation of a vast body of research on the subject, no convincing biochemical explanation has been given for the original observations of aerobic glycolysis in cancer cell metabolism. Here, we have worked out a first-principles quantitative analysis of the problem from the principles of stoichiometry and available electron balance. The results have been interpreted using Nath's unified theory of energy coupling and adenosine triphosphate (ATP) synthesis, and the original data of Warburg and colleagues have been analyzed from this new perspective. Use of the biomass yield based on ATP per unit substrate consumed, [Formula: see text], or the Nath-Warburg number, NaWa has been shown to excellently model the original data on the Warburg Effect with very small standard deviation values, and without employing additional fitted or adjustable parameters. Based on the results of the quantitative analysis, a novel conservative mechanism of synthesis, utilization, and recycling of ATP and other key metabolites (eg, lactate) is proposed. The mechanism offers fresh insights into metabolic symbiosis and coupling within and/or among proliferating cells. The fundamental understanding gained using our approach should help in catalyzing the development of more efficient metabolism-targeting anticancer drugs.
    Keywords:  Nath’s two-ion theory of energy coupling and torsional mechanism of ATP synthesis; Nath’s unified theory of ATP synthesis/hydrolysis; Warburg-Nath ratio; Nath-Warburg number, NaWa; metabolic regulation based on ATP demand and supply; aerobic glycolysis and the Warburg Effect; biomass yield coefficients based on ATP; cancer, malignancy, and heterogeneity; lactate and lactic acid; mathematical model; metabolic coupling and symbiosis; oxidative phosphorylation (OXPHOS) and F0F1-ATP synthase; stoichiometry and available electron balance
    DOI:  https://doi.org/10.1093/function/zqae008
  18. Nucleic Acids Res. 2024 May 06. pii: gkae296. [Epub ahead of print]
    mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics.
    Hansi Weissensteiner, Lukas Forer, Florian Kronenberg, Sebastian Schönherr.
      Over the past decade, mtDNA-Server established itself as one of the most widely used variant calling web-services for human mitochondrial genomes. The service accepts sequencing data in BAM format and returns an annotated variant analysis report for both homoplasmic and heteroplasmic variants. In this work we present mtDNA-Server 2, which includes several new features highly requested by the community. Most importantly, it includes (a) the integration of a novel variant calling mode that accurately call insertions, deletions and single nucleotide variants at once, (b) the integration of additional quality control and input validation modules, (c) a method to estimate the required coverage to minimize false positives and (d) an interactive analytics dashboard. Furthermore, we migrated the complete analysis workflow to the Nextflow workflow manager for improved parallelization, reproducibility and local execution. Recognizing the importance of insertions and deletions as well as offering novel quality control, validation and reporting features, mtDNA-Server 2 provides researchers and clinicians a new state-of-the-art analysis platform for interpreting mitochondrial genomes. mtDNA-Server 2 is available via mitoverse, our analysis platform that offers a centralized place for mtDNA analysis in the cloud. The web-service, source code and its documentation are freely accessible at https://mitoverse.i-med.ac.at.
    DOI:  https://doi.org/10.1093/nar/gkae296
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