bims-camemi 2023-10-01 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023–10–01
forty-six papers selected by
Christian Frezza, Universität zu Köln

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.
Mitochondrial proteome research: the road ahead.
Microenvironmental stiffness induces metabolic reprogramming in glioblastoma.
The Mitochondrial Calcium Uniporter (MCU): Molecular Identity and Role in Human Diseases.
All-optical spatiotemporal mapping of ROS dynamics across mitochondrial microdomains in situ.
TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis.
mTORC1 Regulates the Metabolic Switch of Postnatal Cardiomyocytes During Regeneration.
Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer.
Aspartic Acid in Health and Disease.
Filippo Giancotti (1958-2023).
Orai inhibition modulates pulmonary ILC2 metabolism and alleviates airway hyperreactivity in murine and humanized models.
Iron drives anabolic metabolism through active histone demethylation and mTORC1.
Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction.
ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control.
Acidic Methanol Treatment Facilitates Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging of Energy Metabolism.
Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation.
Pyruvate Kinase Activity Regulates Cystine Starvation Induced Ferroptosis through Malic Enzyme 1 in Pancreatic Cancer Cells.
UDP-glucose dehydrogenase (UGDH) in clinical oncology and cancer biology.
Alpha-Ketoglutarate Regulates Tnfrsf12a/Fn14 Expression via Histone Modification and Prevents Cancer-Induced Cachexia.
Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors.
Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex.
Proteome census upon nutrient stress reveals Golgiphagy membrane receptors.
Early fate decision for mitochondrially encoded proteins by a molecular triage.
Adenylosuccinate lyase deficiency affects neurobehavior via perturbations to tyramine signaling in Caenorhabditis elegans.
Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors.
Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages.
Loss of p53 and mutational heterogeneity drives immune resistance in an autochthonous mouse lung cancer model with high tumor mutational burden.
Impact of Opioids on Cellular Metabolism: Implications for Metabolic Pathways Involved in Cancer.
Metabolic hallmarks for purine nucleotide biosynthesis in small-cell lung carcinoma.
Developmental priming of cancer susceptibility.
Pitfalls of Mitochondrial Redox Signaling Research.
Acod1 Expression in Cancer Cells Promotes Immune Evasion through the Generation of Inhibitory Peptides.
BCAT1 regulates glioblastoma cell plasticity and contributes to immunosuppression.
Emerging principles of primary cilia dynamics in controlling tissue organization and function.
Lysosomal cyst(e)ine storage potentiates tolerance to oxidative stress in cancer cells.
Towards solving the mystery of peroxisomal matrix protein import.
Exploring the pan-cancer landscape of posttranscriptional regulation.
Mechanical stiffness promotes skin fibrosis through Piezo1-mediated arginine and proline metabolism.
Endothelial Notch1 signaling in white adipose tissue promotes cancer cachexia.
Tracking cell-type-specific temporal dynamics in human and mouse brains.
Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities.
Choline metabolism underpins macrophage IL-4 polarization and RELMα up-regulation in helminth infection.
The Methylcitrate Cycle and Its Crosstalk with the Glyoxylate Cycle and Tricarboxylic Acid Cycle in Pathogenic Fungi.
Immune evasion on the nanoscale: Small Extracellular Vesicles in Pancreatic Ductal Adenocarcinoma immunity.
Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme.
Convergent TP53 loss and evolvability in cancer.

Nat Cell Biol. 2023 Sep 28.

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.

Nicholas J Kramer, Gyan Prakash, R Stefan Isaac, Karine Choquet, Iliana Soto, Boryana Petrova, Hope E Merens, Naama Kanarek, L Stirling Churchman.

Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

DOI: https://doi.org/10.1038/s41556-023-01244-3
Nat Rev Mol Cell Biol. 2023 Sep 29.

Mitochondrial proteome research: the road ahead.

Zakery N Baker, Patrick Forny, David J Pagliarini.

Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.

DOI: https://doi.org/10.1038/s41580-023-00650-7
Cell Rep. 2023 Sep 26. pii: S2211-1247(23)01187-7. [Epub ahead of print]42(10): 113175

Microenvironmental stiffness induces metabolic reprogramming in glioblastoma.

Alireza Sohrabi, Austin E Y T Lefebvre, Mollie J Harrison, Michael C Condro, Talia M Sanazzaro, Gevick Safarians, Itay Solomon, Soniya Bastola, Shadi Kordbacheh, Nadia Toh, Harley I Kornblum, Michelle A Digman, Stephanie K Seidlits.

  The mechanical properties of solid tumors influence tumor cell phenotype and the ability to invade surrounding tissues. Using bioengineered scaffolds to provide a matrix microenvironment for patient-derived glioblastoma (GBM) spheroids, this study demonstrates that a soft, brain-like matrix induces GBM cells to shift to a glycolysis-weighted metabolic state, which supports invasive behavior. We first show that orthotopic murine GBM tumors are stiffer than peritumoral brain tissues, but tumor stiffness is heterogeneous where tumor edges are softer than the tumor core. We then developed 3D scaffolds with μ-compressive moduli resembling either stiffer tumor core or softer peritumoral brain tissue. We demonstrate that the softer matrix microenvironment induces a shift in GBM cell metabolism toward glycolysis, which manifests in lower proliferation rate and increased migration activities. Finally, we show that these mechanical cues are transduced from the matrix via CD44 and integrin receptors to induce metabolic and phenotypic changes in cancer cells.

Keywords:  CP: Cancer; CP: Metabolism; extracellular matrix; tissue mechanics

DOI:  https://doi.org/10.1016/j.celrep.2023.113175
Biomolecules. 2023 Aug 25. pii: 1304. [Epub ahead of print]13(9):

The Mitochondrial Calcium Uniporter (MCU): Molecular Identity and Role in Human Diseases.

Donato D'Angelo, Rosario Rizzuto.

  Calcium (Ca2+) ions act as a second messenger, regulating several cell functions. Mitochondria are critical organelles for the regulation of intracellular Ca2+. Mitochondrial calcium (mtCa2+) uptake is ensured by the presence in the inner mitochondrial membrane (IMM) of the mitochondrial calcium uniporter (MCU) complex, a macromolecular structure composed of pore-forming and regulatory subunits. MtCa2+ uptake plays a crucial role in the regulation of oxidative metabolism and cell death. A lot of evidence demonstrates that the dysregulation of mtCa2+ homeostasis can have serious pathological outcomes. In this review, we briefly discuss the molecular structure and the function of the MCU complex and then we focus our attention on human diseases in which a dysfunction in mtCa2+ has been shown.

Keywords:  MCU; cancer; cardiovascular diseases; metabolic diseases; mitochondrial Ca2+ signaling; neurodegenerative disorders; skeletal muscle diseases

DOI:  https://doi.org/10.3390/biom13091304
Nat Commun. 2023 Sep 27. 14(1): 6036

All-optical spatiotemporal mapping of ROS dynamics across mitochondrial microdomains in situ.

Shon A Koren, Nada Ahmed Selim, Lizbeth De la Rosa, Jacob Horn, M Arsalan Farooqi, Alicia Y Wei, Annika Müller-Eigner, Jacen Emerson, Gail V W Johnson, Andrew P Wojtovich.

Hydrogen peroxide (H2O2) functions as a second messenger to signal metabolic distress through highly compartmentalized production in mitochondria. The dynamics of reactive oxygen species (ROS) generation and diffusion between mitochondrial compartments and into the cytosol govern oxidative stress responses and pathology, though these processes remain poorly understood. Here, we couple the H2O2 biosensor, HyPer7, with optogenetic stimulation of the ROS-generating protein KillerRed targeted into multiple mitochondrial microdomains. Single mitochondrial photogeneration of H2O2 demonstrates the spatiotemporal dynamics of ROS diffusion and transient hyperfusion of mitochondria due to ROS. This transient hyperfusion phenotype required mitochondrial fusion but not fission machinery. Measurement of microdomain-specific H2O2 diffusion kinetics reveals directionally selective diffusion through mitochondrial microdomains. All-optical generation and detection of physiologically-relevant concentrations of H2O2 between mitochondrial compartments provide a map of mitochondrial H2O2 diffusion dynamics in situ as a framework to understand the role of ROS in health and disease.

DOI: https://doi.org/10.1038/s41467-023-41682-z
Nat Commun. 2023 Sep 29. 14(1): 6099

TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis.

Donghua Hu, Min Tan, Dongliang Lu, Brian Kleiboeker, Xuejing Liu, Hongsuk Park, Alexxai V Kravitz, Kooresh I Shoghi, Yu-Hua Tseng, Babak Razani, Akihiro Ikeda, Irfan J Lodhi.

Mitochondrial morphology, which is controlled by mitochondrial fission and fusion, is an important regulator of the thermogenic capacity of brown adipocytes. Adipose-specific peroxisome deficiency impairs thermogenesis by inhibiting cold-induced mitochondrial fission due to decreased mitochondrial membrane content of the peroxisome-derived lipids called plasmalogens. Here, we identify TMEM135 as a critical mediator of the peroxisomal regulation of mitochondrial fission and thermogenesis. Adipose-specific TMEM135 knockout in mice blocks mitochondrial fission, impairs thermogenesis, and increases diet-induced obesity and insulin resistance. Conversely, TMEM135 overexpression promotes mitochondrial division, counteracts obesity and insulin resistance, and rescues thermogenesis in peroxisome-deficient mice. Mechanistically, thermogenic stimuli promote association between peroxisomes and mitochondria and plasmalogen-dependent localization of TMEM135 in mitochondria, where it mediates PKA-dependent phosphorylation and mitochondrial retention of the fission factor Drp1. Together, these results reveal a previously unrecognized inter-organelle communication regulating mitochondrial fission and energy homeostasis and identify TMEM135 as a potential target for therapeutic activation of BAT.

DOI: https://doi.org/10.1038/s41467-023-41849-8
bioRxiv. 2023 Sep 13. pii: 2023.09.12.557400. [Epub ahead of print]

mTORC1 Regulates the Metabolic Switch of Postnatal Cardiomyocytes During Regeneration.

Wyatt G Paltzer, Timothy J Aballo, Jiyoung Bae, Katharine A Hubert, Dakota J Nuttall, Cassidy Perry, Kayla N Wanless, Raya Nahlawi, Ying Ge, Ahmed I Mahmoud.

The metabolic switch from glycolysis to fatty acid oxidation in postnatal cardiomyocytes contributes to the loss of the cardiac regenerative potential of the mammalian heart. However, the mechanisms that regulate this metabolic switch remain unclear. The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) is a central signaling hub that regulates cellular metabolism and protein synthesis, yet its role during mammalian heart regeneration and postnatal metabolic maturation is undefined. Here, we use immunoblotting, rapamycin treatment, myocardial infarction, and global proteomics to define the role of mTORC1 in postnatal heart development and regeneration. Our results demonstrate that the activity of mTORC1 is dynamically regulated between the regenerating and the non-regenerating hearts. Acute inhibition of mTORC1 by rapamycin or everolimus reduces cardiomyocyte proliferation and inhibits neonatal heart regeneration following injury. Our quantitative proteomic analysis demonstrates that transient inhibition of mTORC1 during neonatal heart injury did not reduce protein synthesis, but rather shifts the cardiac proteome of the neonatal injured heart from glycolysis towards fatty acid oxidation. This indicates that mTORC1 inhibition following injury accelerates the postnatal metabolic switch, which promotes metabolic maturation and impedes cardiomyocyte proliferation and heart regeneration. Taken together, our results define an important role for mTORC1 in regulating postnatal cardiac metabolism and may represent a novel target to modulate cardiac metabolism and promote heart regeneration.

DOI: https://doi.org/10.1101/2023.09.12.557400
Genes Dev. 2023 Sep 29.

Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer.

Jincheng Han, Jiaqian Xu, Yonghong Liu, Shaoheng Liang, Kyle A LaBella, Deepavali Chakravarti, Denise J Spring, Yan Xia, Ronald A DePinho.

  Activating KRAS mutations (KRAS*) in pancreatic ductal adenocarcinoma (PDAC) drive anabolic metabolism and support tumor maintenance. KRAS* inhibitors show initial antitumor activity followed by recurrence due to cancer cell-intrinsic and immune-mediated paracrine mechanisms. Here, we explored the potential role of cancer-associated fibroblasts (CAFs) in enabling KRAS* bypass and identified CAF-derived NRG1 activation of cancer cell ERBB2 and ERBB3 receptor tyrosine kinases as a mechanism by which KRAS*-independent growth is supported. Genetic extinction or pharmacological inhibition of KRAS* resulted in up-regulation of ERBB2 and ERBB3 expression in human and murine models, which prompted cancer cell utilization of CAF-derived NRG1 as a survival factor. Genetic depletion or pharmacological inhibition of ERBB2/3 or NRG1 abolished KRAS* bypass and synergized with KRASG12D inhibitors in combination treatments in mouse and human PDAC models. Thus, we found that CAFs can contribute to KRAS* inhibitor therapy resistance via paracrine mechanisms, providing an actionable therapeutic strategy to improve the effectiveness of KRAS* inhibitors in PDAC patients.

Keywords:  ERBB3; NRG1; cancer-associated fibroblasts; oncogenic KRAS bypass; pancreas cancer; receptor tyrosine kinase; tumor microenvironment

DOI:  https://doi.org/10.1101/gad.351037.123
Nutrients. 2023 Sep 17. pii: 4023. [Epub ahead of print]15(18):

Aspartic Acid in Health and Disease.

Milan Holeček.

  Aspartic acid exists in L- and D-isoforms (L-Asp and D-Asp). Most L-Asp is synthesized by mitochondrial aspartate aminotransferase from oxaloacetate and glutamate acquired by glutamine deamidation, particularly in the liver and tumor cells, and transamination of branched-chain amino acids (BCAAs), particularly in muscles. The main source of D-Asp is the racemization of L-Asp. L-Asp transported via aspartate-glutamate carrier to the cytosol is used in protein and nucleotide synthesis, gluconeogenesis, urea, and purine-nucleotide cycles, and neurotransmission and via the malate-aspartate shuttle maintains NADH delivery to mitochondria and redox balance. L-Asp released from neurons connects with the glutamate-glutamine cycle and ensures glycolysis and ammonia detoxification in astrocytes. D-Asp has a role in brain development and hypothalamus regulation. The hereditary disorders in L-Asp metabolism include citrullinemia, asparagine synthetase deficiency, Canavan disease, and dicarboxylic aminoaciduria. L-Asp plays a role in the pathogenesis of psychiatric and neurologic disorders and alterations in BCAA levels in diabetes and hyperammonemia. Further research is needed to examine the targeting of L-Asp metabolism as a strategy to fight cancer, the use of L-Asp as a dietary supplement, and the risks of increased L-Asp consumption. The role of D-Asp in the brain warrants studies on its therapeutic potential in psychiatric and neurologic disorders.

Keywords:  aspartame; aspartate and cell-to-cell interactions; branched-chain amino acids; gluconeogenesis; glutamate–glutamine cycle; malate–aspartate shuttle; neurotransmission; oxaloacetate; purine-nucleotide cycle; urea cycle

DOI:  https://doi.org/10.3390/nu15184023
Nat Cancer. 2023 Sep 28.

Filippo Giancotti (1958-2023).

Ronald DePinho, Joan Massagué, Gulam Manji, Anil K Rustgi, Benjamin Izar.

DOI: https://doi.org/10.1038/s43018-023-00639-3
Nat Commun. 2023 Sep 26. 14(1): 5989

Orai inhibition modulates pulmonary ILC2 metabolism and alleviates airway hyperreactivity in murine and humanized models.

Emily Howard, Benjamin P Hurrell, Doumet Georges Helou, Pedram Shafiei-Jahani, Spyridon Hasiakos, Jacob Painter, Sonal Srikanth, Yousang Gwack, Omid Akbari.

Ca2+ entry via Ca2+ release-activated Ca2+ (CRAC) channels is a predominant mechanism of intracellular Ca2+ elevation in immune cells. Here we show the immunoregulatory role of CRAC channel components Orai1 and Orai2 in Group 2 innate lymphoid cells (ILC2s), that play crucial roles in the induction of type 2 inflammation. We find that blocking or genetic ablation of Orai1 and Orai2 downregulates ILC2 effector function and cytokine production, consequently ameliorating the development of ILC2-mediated airway inflammation in multiple murine models. Mechanistically, ILC2 metabolic and mitochondrial homeostasis are inhibited and lead to the upregulation of reactive oxygen species production. We confirm our findings in human ILC2s, as blocking Orai1 and Orai2 prevents the development of airway hyperreactivity in humanized mice. Our findings have a broad impact on the basic understanding of Ca2+ signaling in ILC2 biology, providing potential insights into the development of therapies for the treatment of allergic and atopic inflammatory diseases.

DOI: https://doi.org/10.1038/s41467-023-41065-4
Nat Cell Biol. 2023 Sep 25.

Iron drives anabolic metabolism through active histone demethylation and mTORC1.

Jason S Shapiro, Hsiang-Chun Chang, Yuki Tatekoshi, Zibo Zhao, Zohra Sattar Waxali, Bong Jin Hong, Haimei Chen, Justin A Geier, Elizabeth T Bartom, Adam De Jesus, Farnaz K Nejad, Amir Mahmoodzadeh, Tatsuya Sato, Lucia Ramos-Alonso, Antonia Maria Romero, Maria Teresa Martinez-Pastor, Shang-Chuan Jiang, Shiv K Sah-Teli, Liming Li, David Bentrem, Gary Lopaschuk, Issam Ben-Sahra, Thomas V O'Halloran, Ali Shilatifard, Sergi Puig, Joy Bergelson, Peppi Koivunen, Hossein Ardehali.

All eukaryotic cells require a minimal iron threshold to sustain anabolic metabolism. However, the mechanisms by which cells sense iron to regulate anabolic processes are unclear. Here we report a previously undescribed eukaryotic pathway for iron sensing in which molecular iron is required to sustain active histone demethylation and maintain the expression of critical components of the pro-anabolic mTORC1 pathway. Specifically, we identify the iron-binding histone-demethylase KDM3B as an intrinsic iron sensor that regulates mTORC1 activity by demethylating H3K9me2 at enhancers of a high-affinity leucine transporter, LAT3, and RPTOR. By directly suppressing leucine availability and RAPTOR levels, iron deficiency supersedes other nutrient inputs into mTORC1. This process occurs in vivo and is not an indirect effect by canonical iron-utilizing pathways. Because ancestral eukaryotes share homologues of KDMs and mTORC1 core components, this pathway probably pre-dated the emergence of the other kingdom-specific nutrient sensors for mTORC1.

DOI: https://doi.org/10.1038/s41556-023-01225-6
Cell Rep. 2023 Sep 27. pii: S2211-1247(23)01188-9. [Epub ahead of print]42(10): 113176

Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction.

Utsarga Adhikary, Joao A Paulo, Marina Godes, Shrabasti Roychoudhury, Michelle S Prew, Yael Ben-Nun, Ellen W Yu, Amit Budhraja, Joseph T Opferman, Dipanjan Chowdhury, Steven P Gygi, Loren D Walensky.

  MCL-1 is a high-priority target due to its dominant role in the pathogenesis and chemoresistance of cancer, yet clinical trials of MCL-1 inhibitors are revealing toxic side effects. MCL-1 biology is complex, extending beyond apoptotic regulation and confounded by its multiple isoforms, its domains of unresolved structure and function, and challenges in distinguishing noncanonical activities from the apoptotic response. We find that, in the presence or absence of an intact mitochondrial apoptotic pathway, genetic deletion or pharmacologic targeting of MCL-1 induces DNA damage and retards cell proliferation. Indeed, the cancer cell susceptibility profile of MCL-1 inhibitors better matches that of anti-proliferative than pro-apoptotic drugs, expanding their potential therapeutic applications, including synergistic combinations, but heightening therapeutic window concerns. Proteomic profiling provides a resource for mechanistic dissection and reveals the minichromosome maintenance DNA helicase as an interacting nuclear protein complex that links MCL-1 to the regulation of DNA integrity and cell-cycle progression.

Keywords:  BCL-2 family; CP: Cancer; CP: Molecular biology; DNA damage; MCL-1; apoptosis; cancer; cell cycle; cell proliferation; chemotherapy; minichrosome maintenance complex; proteomics

DOI:  https://doi.org/10.1016/j.celrep.2023.113176
Cell Rep. 2023 Sep 23. pii: S2211-1247(23)01175-0. [Epub ahead of print]42(10): 113163

ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control.

Yimeng Gao, Joshua T Zimmer, Radovan Vasic, Chengyang Liu, Rana Gbyli, Shu-Jian Zheng, Amisha Patel, Wei Liu, Zhihong Qi, Yaping Li, Raman Nelakanti, Yuanbin Song, Giulia Biancon, Andrew Z Xiao, Sarah Slavoff, Richard G Kibbey, Richard A Flavell, Matthew D Simon, Toma Tebaldi, Hua-Bing Li, Stephanie Halene.

  N6-methyladenosine (m6A) RNA modification controls numerous cellular processes. To what extent these post-transcriptional regulatory mechanisms play a role in hematopoiesis has not been fully elucidated. We here show that the m6A demethylase alkB homolog 5 (ALKBH5) controls mitochondrial ATP production and modulates hematopoietic stem and progenitor cell (HSPC) fitness in an m6A-dependent manner. Loss of ALKBH5 results in increased RNA methylation and instability of oxoglutarate-dehydrogenase (Ogdh) messenger RNA and reduction of OGDH protein levels. Limited OGDH availability slows the tricarboxylic acid (TCA) cycle with accumulation of α-ketoglutarate (α-KG) and conversion of α-KG into L-2-hydroxyglutarate (L-2-HG). L-2-HG inhibits energy production in both murine and human hematopoietic cells in vitro. Impaired mitochondrial energy production confers competitive disadvantage to HSPCs and limits clonogenicity of Mll-AF9-induced leukemia. Our study uncovers a mechanism whereby the RNA m6A demethylase ALKBH5 regulates the stability of metabolic enzyme transcripts, thereby controlling energy metabolism in hematopoiesis and leukemia.

Keywords:  ALKBH5; ATP production; CP: Molecular biology; CP: Stem cell research; OXPHOS; RNA stability; energy metabolism; hematopoietic stem and progenitor cells; leukemia; m(6)A modification; oxidative phosphorylation; stress hematopoiesis

DOI:  https://doi.org/10.1016/j.celrep.2023.113163
Anal Chem. 2023 Sep 27.

Acidic Methanol Treatment Facilitates Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging of Energy Metabolism.

Wenyun Lu, Noel R Park, Tara TeSlaa, Connor S R Jankowski, Laith Samarah, Melanie McReynolds, Xi Xing, Jessica Schembri, Morgan T Woolf, Joshua D Rabinowitz, Shawn M Davidson.

Detection of small molecule metabolites (SMM), particularly those involved in energy metabolism using MALDI-mass spectrometry imaging (MSI), is challenging due to factors including ion suppression from other analytes present (e.g., proteins and lipids). One potential solution to enhance SMM detection is to remove analytes that cause ion suppression from tissue sections before matrix deposition through solvent washes. Here, we systematically investigated solvent treatment conditions to improve SMM signal and preserve metabolite localization. Washing with acidic methanol significantly enhances the detection of phosphate-containing metabolites involved in energy metabolism. The improved detection is due to removing lipids and highly polar metabolites that cause ion suppression and denaturing proteins that release bound phosphate-containing metabolites. Stable isotope infusions of [13C6]nicotinamide coupled to MALDI-MSI ("Iso-imaging") in the kidney reveal patterns that indicate blood vessels, medulla, outer stripe, and cortex. We also observed different ATP:ADP raw signals across mouse kidney regions, consistent with regional differences in glucose metabolism favoring either gluconeogenesis or glycolysis. In mouse muscle, Iso-imaging using [13C6]glucose shows high glycolytic flux from infused circulating glucose in type 1 and 2a fibers (soleus) and relatively lower glycolytic flux in type 2b fiber type (gastrocnemius). Thus, improved detection of phosphate-containing metabolites due to acidic methanol treatment combined with isotope tracing provides an improved way to probe energy metabolism with spatial resolution in vivo.

DOI: https://doi.org/10.1021/acs.analchem.3c01875
bioRxiv. 2023 Sep 13. pii: 2023.09.13.557496. [Epub ahead of print]

Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation.

Ayaka Sugiura, Katherine L Beier, Channing Chi, Darren R Heintzman, Xiang Ye, Melissa M Wolf, Andrew R Patterson, Jacqueline-Yvonne Cephus, Hanna S Hong, Costas A Lyssiotis, Dawn C Newcomb, Jeffrey C Rathmell.

Amino acid (AA) uptake is essential for T cell metabolism and function, but how tissue sites and inflammation affect CD4 + T cell subset requirements for specific AA remains uncertain. Here we tested CD4 + T cell AA demands with in vitro and multiple in vivo CRISPR screens and identify subset- and tissue-specific dependencies on the AA transporter SLC38A1 (SNAT1). While dispensable for T cell persistence and expansion over time in vitro and in vivo lung inflammation, SLC38A1 was critical for Th1 but not Th17 cell-driven Experimental Autoimmune Encephalomyelitis (EAE) and contributed to Th1 cell-driven inflammatory bowel disease. SLC38A1 deficiency reduced mTORC1 signaling and glycolytic activity in Th1 cells, in part by reducing intracellular glutamine and disrupting hexosamine biosynthesis and redox regulation. Similarly, pharmacological inhibition of SLC38 transporters delayed EAE but did not affect lung inflammation. Subset- and tissue-specific dependencies of CD4 + T cells on AA transporters may guide selective immunotherapies.
HIGHLIGHTS: T cells dynamically regulate glutamine amino acid transporters when activatedSLC38A1 supports Th1 cell mTORC1 and proliferation by redox and hexosamine pathwaysTargeting SLC38A1 does not affect lung inflammation but delays IBD and EAENutrient transporter needs of T cell subsets vary based on disease and tissue site.

DOI: https://doi.org/10.1101/2023.09.13.557496
bioRxiv. 2023 Sep 17. pii: 2023.09.15.557984. [Epub ahead of print]

Pyruvate Kinase Activity Regulates Cystine Starvation Induced Ferroptosis through Malic Enzyme 1 in Pancreatic Cancer Cells.

Elliot Ensink, Tessa Jordan, Hyllana C D Medeiros, Galloway Thurston, Anmol Pardal, Lei Yu, Sophia Y Lunt.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with high mortality and limited efficacious therapeutic options. PDAC cells undergo metabolic alterations to survive within a nutrient-depleted tumor microenvironment. One critical metabolic shift in PDAC cells occurs through altered isoform expression of the glycolytic enzyme, pyruvate kinase (PK). Pancreatic cancer cells preferentially upregulate pyruvate kinase muscle isoform 2 isoform (PKM2). PKM2 expression reprograms many metabolic pathways, but little is known about its impact on cystine metabolism. Cystine metabolism is critical for supporting survival through its role in defense against ferroptosis, a non-apoptotic iron-dependent form of cell death characterized by unchecked lipid peroxidation. To improve our understanding of the role of PKM2 in cystine metabolism and ferroptosis in PDAC, we generated PKM2 knockout (KO) human PDAC cells. Fascinatingly, PKM2KO cells demonstrate a remarkable resistance to cystine starvation mediated ferroptosis. This resistance to ferroptosis is caused by decreased PK activity, rather than an isoform-specific effect. We further utilized stable isotope tracing to evaluate the impact of glucose and glutamine reprogramming in PKM2KO cells. PKM2KO cells depend on glutamine metabolism to support antioxidant defenses against lipid peroxidation, primarily by increased glutamine flux through the malate aspartate shuttle and utilization of ME1 to produce NADPH. Ferroptosis can be synergistically induced by the combination of PKM2 activation and inhibition of the cystine/glutamate antiporter in vitro . Proof-of-concept in vivo experiments demonstrate the efficacy of this mechanism as a novel treatment strategy for PDAC.
Highlights: PKM2KO in pancreatic ductal adenocarcinoma (PDAC) cells produces enhanced defense against cystine starvation induced ferroptosis.Pharmacologic activation of pyruvate kinase (PK) activity promotes ferroptosis under cystine starvation, while inhibition promotes ferroptosis survival in PDAC cells.Decrease in PK activity reprograms glutamine metabolism to increase use of malic enzyme 1 and promote survival under cystine starvation in PDAC cells. Cystine starvation and activation of pyruvate kinase synergistically decreases progression of pancreatic cancer in vivo .

DOI: https://doi.org/10.1101/2023.09.15.557984
Oncotarget. 2023 Sep 28. 14 843-857

UDP-glucose dehydrogenase (UGDH) in clinical oncology and cancer biology.

Meghan J Price, Annee D Nguyen, Jovita K Byemerwa, Jasmine Flowers, César D Baëta, C Rory Goodwin.

  UDP-glucose-6-dehydrogenase (UGDH) is a cytosolic, hexameric enzyme that converts UDP-glucose to UDP-glucuronic acid (UDP-GlcUA), a key reaction in hormone and xenobiotic metabolism and in the production of extracellular matrix precursors. In this review, we classify UGDH as a molecular indicator of tumor progression in multiple cancer types, describe its involvement in key canonical cancer signaling pathways, and identify methods to inhibit UGDH, its substrates, and its downstream products. As such, we position UGDH as an enzyme to be exploited as a potential prognostication marker in oncology and a therapeutic target in cancer biology.

Keywords:  UDP-6 glucose dehydrogenase; UGDH; cancer; cancer biology; oncology

DOI:  https://doi.org/10.18632/oncotarget.28514
Genes (Basel). 2023 Sep 19. pii: 1818. [Epub ahead of print]14(9):

Alpha-Ketoglutarate Regulates Tnfrsf12a/Fn14 Expression via Histone Modification and Prevents Cancer-Induced Cachexia.

Bryan I Ruiz, Xazmin H Lowman, Ying Yang, Qi Fan, Tianhong Wang, Hongmei Wu, Eric A Hanse, Mei Kong.

  Previous studies have shown that inhibition of TNF family member FN14 (gene: TNFRSF12A) in colon tumors decreases inflammatory cytokine expression and mitigates cancer-induced cachexia. However, the molecular mechanisms underlying the regulation of FN14 expression remain unclear. Tumor microenvironments are often devoid of nutrients and oxygen, yet how the cachexic response relates to the tumor microenvironment and, importantly, nutrient stress is unknown. Here, we looked at the connections between metabolic stress and FN14 expression. We found that TNFRSF12A expression was transcriptionally induced during glutamine deprivation in cancer cell lines. We also show that the downstream glutaminolysis metabolite, alpha-ketoglutarate (aKG), is sufficient to rescue glutamine-deprivation-promoted TNFRSF12A induction. As aKG is a co-factor for histone de-methylase, we looked at histone methylation and found that histone H3K4me3 at the Tnfrsf12a promoter is increased under glutamine-deprived conditions and rescued via DM-aKG supplementation. Finally, expression of Tnfrsf12a and cachexia-induced weight loss can be inhibited in vivo by DM-aKG in a mouse cancer cachexia model. These findings highlight a connection between metabolic stress and cancer cachexia development.

Keywords:  FN14; TNFRSF12A; alpha-ketoglutarate; cachexia; cancer; colon cancer; histone

DOI:  https://doi.org/10.3390/genes14091818
Nat Genet. 2023 Sep 27.

Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors.

James L Reading, Deborah R Caswell, Charles Swanton.

DOI: https://doi.org/10.1038/s41588-023-01492-x
Enzymes. 2023 ;pii: S1874-6047(23)00006-9. [Epub ahead of print]53 33-68

Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex.

Imad Soukar, Anjalie Amarasinghe, Lori A Pile.

  Post-translational modifications of histone proteins control the expression of genes. Metabolites from central and one-carbon metabolism act as donor moieties to modify histones and regulate gene expression. Thus, histone modification and gene regulation are connected to the metabolite status of the cell. Histone modifiers, such as the SIN3 complex, regulate genes involved in proliferation and metabolism. The SIN3 complex contains a histone deacetylase and a histone demethylase, which regulate the chromatin landscape and gene expression. In this chapter, we review the cross-talk between metabolic pathways that produce donor moieties, and epigenetic complexes regulating proliferation and metabolic genes. This cross-talk between gene regulation and metabolism is tightly controlled, and disruption of this cross-talk leads to metabolic diseases. We discuss promising therapeutics that directly regulate histone modifiers, and can affect the metabolic status of the cell, alleviating some metabolic diseases.

Keywords:  Diabetes; Epigenetics; Histone deacetylase; Histone demethylase; Metabolism; SIN3; Therapeutics; Transcription

DOI:  https://doi.org/10.1016/bs.enz.2023.06.001
Nature. 2023 Sep 27.

Proteome census upon nutrient stress reveals Golgiphagy membrane receptors.

Kelsey L Hickey, Sharan Swarup, Ian R Smith, Julia C Paoli, Enya Miguel Whelan, Joao A Paulo, J Wade Harper.

During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome1,2. While machinery responsible for initiation of macroautophagy is well characterized3,4, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a spatial proteome census of autophagic cargo during nutrient stress in mammalian cells. We find that macroautophagy has selectivity for recycling membrane-bound organelles (principally Golgi and ER). Through autophagic cargo prioritization, we identify a complex of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF3 and YIPF4 interact with ATG8s via LIR motifs and are mobilized into autophagosomes that traffic to lysosomes in a process that requires the canonical autophagic machinery. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of a specific cohort of Golgi membrane proteins during nutrient stress. Moreover, YIPF3/4 play an analogous role in Golgi remodeling during programmed conversion of stem cells to the neuronal lineage in vitro. Collectively, this study reveals prioritization of membrane protein cargo during nutrient stress-dependent proteome remodeling and identifies an unanticipated Golgi remodeling pathway requiring membrane-embedded receptors.

DOI: https://doi.org/10.1038/s41586-023-06657-6
Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00696-2. [Epub ahead of print]

Early fate decision for mitochondrially encoded proteins by a molecular triage.

Andreas Kohler, Andreas Carlström, Hendrik Nolte, Verena Kohler, Sung-Jun Jung, Sagar Sridhara, Takashi Tatsuta, Jens Berndtsson, Thomas Langer, Martin Ott.

  Folding of newly synthesized proteins poses challenges for a functional proteome. Dedicated protein quality control (PQC) systems either promote the folding of nascent polypeptides at ribosomes or, if this fails, ensure their degradation. Although well studied for cytosolic protein biogenesis, it is not understood how these processes work for mitochondrially encoded proteins, key subunits of the oxidative phosphorylation (OXPHOS) system. Here, we identify dedicated hubs in proximity to mitoribosomal tunnel exits coordinating mitochondrial protein biogenesis and quality control. Conserved prohibitin (PHB)/m-AAA protease supercomplexes and the availability of assembly chaperones determine the fate of newly synthesized proteins by molecular triaging. The localization of these competing activities in the vicinity of the mitoribosomal tunnel exit allows for a prompt decision on whether newly synthesized proteins are fed into OXPHOS assembly or are degraded.

Keywords:  assembly factors; complex assembly; m-AAA protease; mitochondria; mitoribosome; prohibitin; protein biogenesis; protein quality control; respiratory chain; translation

DOI:  https://doi.org/10.1016/j.molcel.2023.09.001
PLoS Genet. 2023 Sep 29. 19(9): e1010974

Adenylosuccinate lyase deficiency affects neurobehavior via perturbations to tyramine signaling in Caenorhabditis elegans.

Corinna A Moro, Sabrina A Sony, Latisha P Franklin, Shirley Dong, Mia M Peifer, Kathryn E Wittig, Wendy Hanna-Rose.

Adenylosuccinate lyase deficiency is an ultrarare congenital metabolic disorder associated with muscle weakness and neurobehavioral dysfunction. Adenylosuccinate lyase is required for de novo purine biosynthesis, acting twice in the pathway at non-sequential steps. Genetic models can contribute to our understanding of the etiology of disease phenotypes and pave the way for development of therapeutic treatments. Here, we establish the first model to specifically study neurobehavioral aspects of adenylosuccinate lyase deficiency. We show that reduction of adsl-1 function in C. elegans is associated with a novel learning phenotype in a gustatory plasticity assay. The animals maintain capacity for gustatory plasticity, evidenced by a change in their behavior in response to cue pairing. However, their behavioral output is distinct from that of control animals. We link substrate accumulation that occurs upon adsl-1 deficiency to an unexpected perturbation in tyrosine metabolism and show that a lack of tyramine mediates the behavioral changes through action on the metabotropic TYRA-2 tyramine receptor. Our studies reveal a potential for wider metabolic perturbations, beyond biosynthesis of purines, to impact behavior under conditions of adenylosuccinate lyase deficiency.

DOI: https://doi.org/10.1371/journal.pgen.1010974
Sci Adv. 2023 Sep 29. 9(39): eadd9668

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors.

Samantha E Hoffman, Todd W Dowrey, Carlos Villacorta Martin, Kevin Bi, Breanna Titchen, Shreya Johri, Laura DelloStritto, Miraj Patel, Colin Mackichan, Stephanie Inga, Judy Chen, Grace Grimaldi, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Jason Yeung, Asaf Rotem, Ewa Sicinska, Erin Shannon, Thomas Clancy, Jiping Wang, Sarah Denning, Lauren Brais, Naomi R Besson, Kathleen L Pfaff, Ying Huang, Katrina Z Kao, Scott Rodig, Jason L Hornick, Sebastien Vigneau, Jihye Park, Matthew H Kulke, Jennifer Chan, Eliezer M Van Allen, George J Murphy.

Neuroendocrine tumors (NETs) are rare cancers that most often arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic (GEP)-NET growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we investigated the single-cell transcriptomes of tumor and immune cells from patients with gastroenteropancreatic NETs. Malignant GEP-NET cells expressed genes and regulons associated with normal, gastrointestinal endocrine cell differentiation, and fate determination stages. Tumor and lymphoid compartments sparsely expressed immunosuppressive targets commonly investigated in clinical trials, such as the programmed cell death protein-1/programmed death ligand-1 axis. However, infiltrating myeloid cell types within both primary and metastatic GEP-NETs were enriched for genes encoding other immune checkpoints, including VSIR (VISTA), HAVCR2 (TIM3), LGALS9 (Gal-9), and SIGLEC10. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.

DOI: https://doi.org/10.1126/sciadv.add9668
Sci Adv. 2023 Sep 29. 9(39): eadh4119

Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages.

Shivraj M Yabaji, Oleksii S Rukhlenko, Sujoy Chatterjee, Bidisha Bhattacharya, Emily Wood, Marina Kasaikina, Boris N Kholodenko, Alexander A Gimelbrant, Igor Kramnik.

Understanding cell state transitions and purposefully controlling them to improve therapies is a longstanding challenge in biological research and medicine. Here, we identify a transcriptional signature that distinguishes activated macrophages from the tuberculosis (TB) susceptible and resistant mice. We then apply the cSTAR (cell state transition assessment and regulation) approach to data from screening-by-RNA sequencing to identify chemical perturbations that shift the transcriptional state of tumor necrosis factor (TNF)-activated TB-susceptible macrophages toward that of TB-resistant cells, i.e., prevents their aberrant activation without suppressing beneficial TNF responses. Last, we demonstrate that the compounds identified with this approach enhance the resistance of the TB-susceptible mouse macrophages to virulent Mycobacterium tuberculosis.

DOI: https://doi.org/10.1126/sciadv.adh4119
Cancer Cell. 2023 Sep 26. pii: S1535-6108(23)00322-7. [Epub ahead of print]

Loss of p53 and mutational heterogeneity drives immune resistance in an autochthonous mouse lung cancer model with high tumor mutational burden.

Mingrui Zhu, Jiwoong Kim, Qing Deng, Biagio Ricciuti, Joao V Alessi, Buse Eglenen-Polat, Matthew E Bender, Hai-Cheng Huang, Ryan R Kowash, Ileana Cuevas, Zachary T Bennett, Jinming Gao, John D Minna, Diego H Castrillon, Mark M Awad, Lin Xu, Esra A Akbay.

  The role of tumor mutational burden (TMB) in shaping tumor immunity is a key question that has not been addressable using genetically engineered mouse models (GEMMs) of lung cancer. To induce TMB in lung GEMMs, we expressed an ultra-mutator variant of DNA polymerase-E (POLE)P286R in lung epithelial cells. Introduction of PoleP286R allele into KrasG12D and KrasG12D; p53L/L (KP) models significantly increase their TMB. Immunogenicity and sensitivity to immune checkpoint blockade (ICB) induced by Pole is partially dependent on p53. Corroborating these observations, survival of NSCLC patients whose tumors have TP53truncating mutations is shorter than those with TP53WT with immunotherapy. Immune resistance is in part through reduced antigen presentation and in part due to mutational heterogeneity. Total STING protein levels are elevated in Pole mutated KP tumors creating a vulnerability. A stable polyvalent STING agonist or p53 induction increases sensitivity to immunotherapy offering therapeutic options in these polyclonal tumors.

Keywords:  GEMM; Immunotherapy; Kras; TMB; TP53; antigen presentation; clonality; heterogeneity; mice; patient survival

DOI:  https://doi.org/10.1016/j.ccell.2023.09.006
Pharmaceutics. 2023 Aug 29. pii: 2225. [Epub ahead of print]15(9):

Impact of Opioids on Cellular Metabolism: Implications for Metabolic Pathways Involved in Cancer.

Doorsa Tarazi, Jason T Maynes.

  Opioid utilization for pain management is prevalent among cancer patients. There is significant evidence describing the many effects of opioids on cancer development. Despite the pivotal role of metabolic reprogramming in facilitating cancer growth and metastasis, the specific impact of opioids on crucial oncogenic metabolic pathways remains inadequately investigated. This review provides an understanding of the current research on opioid-mediated changes to cellular metabolic pathways crucial for oncogenesis, including glycolysis, the tricarboxylic acid cycle, glutaminolysis, and oxidative phosphorylation (OXPHOS). The existing literature suggests that opioids affect energy production pathways via increasing intracellular glucose levels, increasing the production of lactic acid, and reducing ATP levels through impediment of OXPHOS. Opioids modulate pathways involved in redox balance which may allow cancer cells to overcome ROS-mediated apoptotic signaling. The majority of studies have been conducted in healthy tissue with a predominant focus on neuronal cells. To comprehensively understand the impact of opioids on metabolic pathways critical to cancer progression, research must extend beyond healthy tissue and encompass patient-derived cancer tissue, allowing for a better understanding in the context of the metabolic reprogramming already undergone by cancer cells. The current literature is limited by a lack of direct experimentation exploring opioid-induced changes to cancer metabolism as they relate to tumor growth and patient outcome.

Keywords:  TCA; cancer; glycolysis; metabolic pathway; metabolomics; morphine; opioid; tumor

DOI:  https://doi.org/10.3390/pharmaceutics15092225
Mol Cancer Res. 2023 Sep 29.

Metabolic hallmarks for purine nucleotide biosynthesis in small-cell lung carcinoma.

Sho Tabata, Shigeki Umemura, Miyu Narita, Hibiki Udagawa, Takamasa Ishikawa, Masahiro Tsuboi, Koichi Goto, Genichiro Ishii, Katsuya Tsuchihara, Atsushi Ochiai, Susumu S Kobayashi, Tomoyoshi Soga, Hideki Makinoshima.

Small-cell lung cancer (SCLC) has a poor prognosis, emphasizing the necessity for developing new therapies. The de novo synthesis pathway of purine nucleotides, which is involved in the malignant growth of SCLC, has emerged as a novel therapeutic target. Purine nucleotides are supplied by two pathways: de novo and salvage. However, the role of the salvage pathway in SCLC and the differences in utilization and crosstalk between the two pathways remain largely unclear. Here, we found that deletion of the HPRT1 gene, which codes for the rate-limiting enzyme of the purine salvage pathway, significantly suppressed tumor growth in vivo in several SCLC cells. We also demonstrated that HPRT1 expression confers resistance to lemetrexol (LMX), an inhibitor of the purine de novo pathway. Interestingly, HPRT1-knockout had less effect on SCLC SBC-5 cells, which are more sensitive to LMX than other SCLC cell lines, suggesting that a preference for either the purine de novo or salvage pathway occurs in SCLC. Furthermore, metabolome analysis of HPRT1-knockout cells revealed increased intermediates in the pentose phosphate pathway and elevated metabolic flux in the purine de novo pathway, indicating compensated metabolism between the de novo and salvage pathways in purine nucleotide biosynthesis. These results suggest that HPRT1 has therapeutic implications in SCLC and provide fundamental insights into the regulation of purine nucleotide biosynthesis. Implications: SCLC tumors preferentially utilize either the de novo or salvage pathway in purine nucleotide biosynthesis, and HPRT1 has therapeutic implications in SCLC.

DOI: https://doi.org/10.1158/1541-7786.MCR-23-0386
bioRxiv. 2023 Sep 15. pii: 2023.09.12.557446. [Epub ahead of print]

Developmental priming of cancer susceptibility.

PERMUTE

DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity ( Trim28 +/D9 ) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.

DOI: https://doi.org/10.1101/2023.09.12.557446
Antioxidants (Basel). 2023 Aug 31. pii: 1696. [Epub ahead of print]12(9):

Pitfalls of Mitochondrial Redox Signaling Research.

Petr Ježek.

  Redox signaling from mitochondria (mt) to the cytosol and plasma membrane (PM) has been scarcely reported, such as in the case of hypoxic cell adaptation or (2-oxo-) 2-keto-isocaproate (KIC) β-like-oxidation stimulating insulin secretion in pancreatic β-cells. Mutual redox state influence between mitochondrial major compartments, the matrix and the intracristal space, and the cytosol is therefore derived theoretically in this article to predict possible conditions, when mt-to-cytosol and mt-to-PM signals may occur, as well as conditions in which the cytosolic redox signaling is not overwhelmed by the mitochondrial antioxidant capacity. Possible peroxiredoxin 3 participation in mt-to-cytosol redox signaling is discussed, as well as another specific case, whereby mitochondrial superoxide release is diminished, whereas the matrix MnSOD is activated. As a result, the enhanced conversion to H2O2 allows H2O2 diffusion into the cytosol, where it could be a predominant component of the H2O2 release. In both of these ways, mt-to-cytosol and mt-to-PM signals may be realized. Finally, the use of redox-sensitive probes is discussed, which disturb redox equilibria, and hence add a surplus redox-buffering to the compartment, where they are localized. Specifically, when attempts to quantify net H2O2 fluxes are to be made, this should be taken into account.

Keywords:  H2O2 release into intracristal space; MnSOD; cytosolic H2O2 release; matrix H2O2 release; peroxiredoxins; redox buffers; redox signaling from mitochondria; redox-sensitive probes

DOI:  https://doi.org/10.3390/antiox12091696
bioRxiv. 2023 Sep 17. pii: 2023.09.14.557799. [Epub ahead of print]

Acod1 Expression in Cancer Cells Promotes Immune Evasion through the Generation of Inhibitory Peptides.

James H Schofield, Joseph Longo, Ryan D Sheldon, Emma Albano, Mark A Hawk, Sean Murphy, Loan Duong, Sharif Rahmy, Xin Lu, Russell G Jones, Zachary T Schafer.

Targeting PD-1 is an important component of many immune checkpoint blockade (ICB) therapeutic approaches. However, ICB is not an efficacious strategy in a variety of cancer types, in part due to immunosuppressive metabolites in the tumor microenvironment (TME). Here, we find that αPD-1-resistant cancer cells produce abundant itaconate (ITA) due to enhanced levels of aconitate decarboxylase (Acod1). Acod1 has an important role in the resistance to αPD-1, as decreasing Acod1 levels in αPD-1 resistant cancer cells can sensitize tumors to αPD-1 therapy. Mechanistically, cancer cells with high Acod1 inhibit the proliferation of naïve CD8 + T cells through the secretion of inhibitory factors. Surprisingly, inhibition of CD8 + T cell proliferation is not dependent on secretion of ITA, but is instead a consequence of the release of small inhibitory peptides. Our study suggests that strategies to counter the activity of Acod1 in cancer cells may sensitize tumors to ICB therapy.

DOI: https://doi.org/10.1101/2023.09.14.557799
Neuro Oncol. 2023 Sep 28. pii: noad190. [Epub ahead of print]

BCAT1 regulates glioblastoma cell plasticity and contributes to immunosuppression.

Pavle Boskovic, Nathalie Wilke, Ka-Hou Man, Peter Lichter, Liliana Francois, Bernhard Radlwimmer.

  Glioblastoma is the most common malignant brain tumor in adults. Cellular plasticity and the poorly differentiated features result in a fast relapse of the tumors following treatment. Moreover, the immunosuppressive microenvironment proved to be a major obstacle to immunotherapeutic approaches. Branched-chain amino acid transaminase 1 (BCAT1) is a metabolic enzyme that converts branched-chain amino acids into branched-chain keto acids, depleting cellular α-ketoglutarate and producing glutamate. BCAT1 was shown to drive the growth of glioblastoma and other cancers; however, its oncogenic mechanism remains poorly understood. Here, we show that BCAT1 is crucial for maintaining the poorly differentiated state of glioblastoma cells and that its low expression correlates with a more differentiated glioblastoma phenotype. Furthermore, orthotopic tumor injection into immunocompetent mice demonstrated that the brain microenvironment is sufficient to induce differentiation of Bcat1-KO tumors in vivo. We link the transition to a differentiated cell state to the increased activity of TET demethylases and the hypomethylation and activation of neuronal differentiation genes. In addition, the knockout of Bcat1 attenuated immunosuppression, allowing for an extensive infiltration of CD8 + cytotoxic T-cells and complete abrogation of tumor growth. Further analysis in immunodeficient mice revealed that both tumor cell differentiation and immunomodulation following BCAT1-KO contribute to the long-term suppression of tumor growth. In summary, our study unveils BCAT1's pivotal role in promoting glioblastoma growth by inhibiting tumor cell differentiation and sustaining an immunosuppressive milieu. These findings offer a novel therapeutic avenue for targeting glioblastoma through the inhibition of BCAT1.

Keywords:  BCAT1; differentiation; immunosuppression; neurooncology

DOI:  https://doi.org/10.1093/neuonc/noad190
EMBO J. 2023 Sep 25. e113891

Emerging principles of primary cilia dynamics in controlling tissue organization and function.

Jay Gopalakrishnan, Kerstin Feistel, Benjamin M Friedrich, Anne Grapin-Botton, Nathalie Jurisch-Yaksi, Elvira Mass, David U Mick, Roman-Ulrich Müller, Helen May-Simera, Bernhard Schermer, Miriam Schmidts, Peter Walentek, Dagmar Wachten.

  Primary cilia project from the surface of most vertebrate cells and are key in sensing extracellular signals and locally transducing this information into a cellular response. Recent findings show that primary cilia are not merely static organelles with a distinct lipid and protein composition. Instead, the function of primary cilia relies on the dynamic composition of molecules within the cilium, the context-dependent sensing and processing of extracellular stimuli, and cycles of assembly and disassembly in a cell- and tissue-specific manner. Thereby, primary cilia dynamically integrate different cellular inputs and control cell fate and function during tissue development. Here, we review the recently emerging concept of primary cilia dynamics in tissue development, organization, remodeling, and function.

Keywords:  cilia dynamics; ciliary signaling; cilium disassembly; primary cilia; tissue organization

DOI:  https://doi.org/10.15252/embj.2023113891
Mol Cell. 2023 Sep 20. pii: S1097-2765(23)00695-0. [Epub ahead of print]

Lysosomal cyst(e)ine storage potentiates tolerance to oxidative stress in cancer cells.

Lixin He, Jinxin Chen, Pinwei Deng, Shumei Huang, Pian Liu, Chanjuan Wang, Xinjian Huang, Yue Li, Boyu Chen, Dongni Shi, Yunyun Xiao, Xiangfu Chen, Ying Ouyang, Libing Song, Chuyong Lin.

  Cyst(e)ine is a key precursor for the synthesis of glutathione (GSH), which protects cancer cells from oxidative stress. Cyst(e)ine is stored in lysosomes, but its role in redox regulation is unclear. Here, we show that breast cancer cells upregulate major facilitator superfamily domain containing 12 (MFSD12) to increase lysosomal cyst(e)ine storage, which is released by cystinosin (CTNS) to maintain GSH levels and buffer oxidative stress. We find that mTORC1 regulates MFSD12 by directly phosphorylating residue T254, while mTORC1 inhibition enhances lysosome acidification that activates CTNS. This switch modulates lysosomal cyst(e)ine levels in response to oxidative stress, fine-tuning redox homeostasis to enhance cell fitness. MFSD12-T254A mutant inhibits MFSD12 function and suppresses tumor progression. Moreover, MFSD12 overexpression correlates with poor neoadjuvant chemotherapy response and prognosis in breast cancer patients. Our findings reveal the critical role of lysosomal cyst(e)ine storage in adaptive redox homeostasis and suggest that MFSD12 is a potential therapeutic target.

Keywords:  CTNS; GSH; MFSD12; breast cancer; chemotherapy; cyst(e)ine; lysosome; mTORC1; oxidative stress; redox homeostasis

DOI:  https://doi.org/10.1016/j.molcel.2023.08.032
Trends Cell Biol. 2023 Sep 22. pii: S0962-8924(23)00169-1. [Epub ahead of print]

Towards solving the mystery of peroxisomal matrix protein import.

Michael L Skowyra, Peiqiang Feng, Tom A Rapoport.

  Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.

Keywords:  PEX13; PEX5; peroxisomal matrix protein import; peroxisome; phase separation; protein translocation

DOI:  https://doi.org/10.1016/j.tcb.2023.08.005
Cell Rep. 2023 Sep 22. pii: S2211-1247(23)01184-1. [Epub ahead of print]42(10): 113172

Exploring the pan-cancer landscape of posttranscriptional regulation.

Umesh Ghoshdastider, Ataman Sendoel.

  Understanding the mechanisms underlying cancer gene expression is critical for precision oncology. Posttranscriptional regulation is a key determinant of protein abundance and cancer cell behavior. However, to what extent posttranscriptional regulatory mechanisms impact protein levels and cancer progression is an ongoing question. Here, we exploit cancer proteogenomics data to systematically compare mRNA-protein correlations across 14 different human cancer types. We identify two clusters of genes with particularly low mRNA-protein correlations across all cancer types, shed light on the role of posttranscriptional regulation of cancer driver genes and drug targets, and unveil a cohort of 55 mutations that alter systems-wide posttranscriptional regulation. Surprisingly, we find that decreased levels of posttranscriptional control in patients correlate with shorter overall survival across multiple cancer types, prompting further mechanistic studies into how posttranscriptional regulation affects patient outcomes. Our findings underscore the importance of a comprehensive understanding of the posttranscriptional regulatory landscape for predicting cancer progression.

Keywords:  CP: Cancer; CP: Genomics; proteogenomics; translational regulation

DOI:  https://doi.org/10.1016/j.celrep.2023.113172
Cell Death Discov. 2023 Sep 26. 9(1): 354

Mechanical stiffness promotes skin fibrosis through Piezo1-mediated arginine and proline metabolism.

Jiahao He, Bin Fang, Shengzhou Shan, Qingfeng Li.

The increased mechanics of fibrotic skin tissue continuously regulate fibroblast functions such as survival and differentiation. Although all these processes consume metabolites, it is unclear whether and how cells adapt their metabolic activity to increased matrix stiffness. Here, we show that transferring mouse dermal fibroblasts from soft to stiff substrates causes an up-regulation of arginine and proline metabolism. Increased matrix stiffness stimulates the expression and activity of key metabolic enzymes, leading to the synthesis of L-proline, a major source of collagen. In addition, the novel mechanosensitive channel Piezo1 was identified as a key regulator of arginine and proline metabolism in fibroblasts under increased stiffness. Consistently, targeting Piezo1 to dermal fibroblasts in vivo effectively reduces fibrosis and arginine-proline metabolism in mouse skin. Therefore, mechanical stiffness is a critical environmental cue for fibroblast metabolism and skin fibrosis progression.

DOI: https://doi.org/10.1038/s41420-023-01656-y
Nat Cancer. 2023 Sep 25.

Endothelial Notch1 signaling in white adipose tissue promotes cancer cachexia.

Jacqueline Taylor, Leonie Uhl, Iris Moll, Sana Safatul Hasan, Lena Wiedmann, Jakob Morgenstern, Benedetto Daniele Giaimo, Tobias Friedrich, Elisenda Alsina-Sanchis, Francesca De Angelis Rigotti, Ronja Mülfarth, Sarah Kaltenbach, Darius Schenk, Felix Nickel, Thomas Fleming, David Sprinzak, Carolin Mogler, Thomas Korff, Adrian T Billeter, Beat P Müller-Stich, Mauricio Berriel Diaz, Tilman Borggrefe, Stephan Herzig, Maria Rohm, Juan Rodriguez-Vita, Andreas Fischer.

Cachexia is a major cause of morbidity and mortality in individuals with cancer and is characterized by weight loss due to adipose and muscle tissue wasting. Hallmarks of white adipose tissue (WAT) remodeling, which often precedes weight loss, are impaired lipid storage, inflammation and eventually fibrosis. Tissue wasting occurs in response to tumor-secreted factors. Considering that the continuous endothelium in WAT is the first line of contact with circulating factors, we postulated whether the endothelium itself may orchestrate tissue remodeling. Here, we show using human and mouse cancer models that during precachexia, tumors overactivate Notch1 signaling in distant WAT endothelium. Sustained endothelial Notch1 signaling induces a WAT wasting phenotype in male mice through excessive retinoic acid production. Pharmacological blockade of retinoic acid signaling was sufficient to inhibit WAT wasting in a mouse cancer cachexia model. This demonstrates that cancer manipulates the endothelium at distant sites to mediate WAT wasting by altering angiocrine signals.

DOI: https://doi.org/10.1038/s43018-023-00622-y
Cell. 2023 Sep 28. pii: S0092-8674(23)00976-5. [Epub ahead of print]186(20): 4345-4364.e24

Tracking cell-type-specific temporal dynamics in human and mouse brains.

Ziyu Lu, Melissa Zhang, Jasper Lee, Andras Sziraki, Sonya Anderson, Zehao Zhang, Zihan Xu, Weirong Jiang, Shaoyu Ge, Peter T Nelson, Wei Zhou, Junyue Cao.

  Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.

Keywords:  aging; cell-type-specific; neurogenesis; oligodendrogenesis; single-cell epigenome; single-cell transcriptome; temporal dynamics

DOI:  https://doi.org/10.1016/j.cell.2023.08.042
Nat Genet. 2023 Sep 25.

Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities.

Liang Chang, Nancy Y Jung, Adel Atari, Diego J Rodriguez, Devishi Kesar, Tian-Yu Song, Matthew G Rees, Melissa Ronan, Ruitong Li, Paloma Ruiz, Saireudee Chaturantabut, Takahiro Ito, Laurens M van Tienen, Yuen-Yi Tseng, Jennifer A Roth, William R Sellers.

The paradigm of cancer-targeted therapies has focused largely on inhibition of critical pathways in cancer. Conversely, conditional activation of signaling pathways as a new source of selective cancer vulnerabilities has not been deeply characterized. In this study, we sought to systematically identify context-specific gene-activation-induced lethalities in cancer. To this end, we developed a method for gain-of-function genetic perturbations simultaneously across ~500 barcoded cancer cell lines. Using this approach, we queried the pan-cancer vulnerability landscape upon activating ten key pathway nodes, revealing selective activation dependencies of MAPK and PI3K pathways associated with specific biomarkers. Notably, we discovered new pathway hyperactivation dependencies in subsets of APC-mutant colorectal cancers where further activation of the WNT pathway by APC knockdown or direct β-catenin overexpression led to robust antitumor effects in xenograft and patient-derived organoid models. Together, this study reveals a new class of conditional gene-activation dependencies in cancer.

DOI: https://doi.org/10.1038/s41588-023-01515-7
PLoS Pathog. 2023 Sep 25. 19(9): e1011658

Choline metabolism underpins macrophage IL-4 polarization and RELMα up-regulation in helminth infection.

Peyman Ghorbani, Sang Yong Kim, Tyler K T Smith, Lucía Minarrieta, Victoria Robert-Gostlin, Marisa K Kilgour, Maja Ilijevska, Irina Alecu, Shayne A Snider, Kaitlyn D Margison, Julia R C Nunes, Daniel Woo, Ciara Pember, Conor O'Dwyer, Julie Ouellette, Pavel Kotchetkov, Julie St-Pierre, Steffany A L Bennett, Baptiste Lacoste, Alexandre Blais, Meera G Nair, Morgan D Fullerton.

Type 2 cytokines like IL-4 are hallmarks of helminth infection and activate macrophages to limit immunopathology and mediate helminth clearance. In addition to cytokines, nutrients and metabolites critically influence macrophage polarization. Choline is an essential nutrient known to support normal macrophage responses to lipopolysaccharide; however, its function in macrophages polarized by type 2 cytokines is unknown. Using murine IL-4-polarized macrophages, targeted lipidomics revealed significantly elevated levels of phosphatidylcholine, with select changes to other choline-containing lipid species. These changes were supported by the coordinated upregulation of choline transport compared to naïve macrophages. Pharmacological inhibition of choline metabolism significantly suppressed several mitochondrial transcripts and dramatically inhibited select IL-4-responsive transcripts, most notably, Retnla. We further confirmed that blocking choline metabolism diminished IL-4-induced RELMα (encoded by Retnla) protein content and secretion and caused a dramatic reprogramming toward glycolytic metabolism. To better understand the physiological implications of these observations, naïve or mice infected with the intestinal helminth Heligmosomoides polygyrus were treated with the choline kinase α inhibitor, RSM-932A, to limit choline metabolism in vivo. Pharmacological inhibition of choline metabolism lowered RELMα expression across cell-types and tissues and led to the disappearance of peritoneal macrophages and B-1 lymphocytes and an influx of infiltrating monocytes. The impaired macrophage activation was associated with some loss in optimal immunity to H. polygyrus, with increased egg burden. Together, these data demonstrate that choline metabolism is required for macrophage RELMα induction, metabolic programming, and peritoneal immune homeostasis, which could have important implications in the context of other models of infection or cancer immunity.

DOI: https://doi.org/10.1371/journal.ppat.1011658
Molecules. 2023 Sep 17. pii: 6667. [Epub ahead of print]28(18):

The Methylcitrate Cycle and Its Crosstalk with the Glyoxylate Cycle and Tricarboxylic Acid Cycle in Pathogenic Fungi.

Zhicheng Huang, Qing Wang, Irshad Ali Khan, Yan Li, Jing Wang, Jiaoyu Wang, Xiaohong Liu, Fucheng Lin, Jianping Lu.

  In fungi, the methylcitrate cycle converts cytotoxic propionyl-coenzyme A (CoA) to pyruvate, which enters gluconeogenesis. The glyoxylate cycle converts acetyl-CoA to succinate, which enters gluconeogenesis. The tricarboxylic acid cycle is a central carbon metabolic pathway that connects the methylcitrate cycle, the glyoxylate cycle, and other metabolisms for lipids, carbohydrates, and amino acids. Fungal citrate synthase and 2-methylcitrate synthase as well as isocitrate lyase and 2-methylisocitrate lyase, each evolved from a common ancestral protein. Impairment of the methylcitrate cycle leads to the accumulation of toxic intermediates such as propionyl-CoA, 2-methylcitrate, and 2-methylisocitrate in fungal cells, which in turn inhibits the activity of many enzymes such as dehydrogenases and remodels cellular carbon metabolic processes. The methylcitrate cycle and the glyoxylate cycle synergistically regulate carbon source utilization as well as fungal growth, development, and pathogenic process in pathogenic fungi.

Keywords:  2-methylcitrate synthase; 2-methylisocitrate lyase; acetyl-CoA; citrate synthase; growth; isocitrate lyase; propionyl-CoA; virulence

DOI:  https://doi.org/10.3390/molecules28186667
Semin Cancer Biol. 2023 Sep 23. pii: S1044-579X(23)00126-8. [Epub ahead of print]

Immune evasion on the nanoscale: Small Extracellular Vesicles in Pancreatic Ductal Adenocarcinoma immunity.

Jordan Fyfe, Danielle Dye, Norbaini Binti Abdol Razak, Pat Metharom, Marco Falasca.

  Pancreatic ductal adenocarcinoma (PDAC) is a type of cancer alarmingly expanding in our modern societies that is still proving to be very challenging to counteract. This disease constitutes a quintessential example of the multiple interactions existing between the tumour and its surrounding microenvironment. In particular, PDAC is characterized by a very immunosuppressive environment that favours cancer growth and makes this cancer type very resistant to immunotherapy. The primary tumour releases many factors that influence both the microenvironment and the immune landscape. Extracellular vesicles (EVs), recently identified as indispensable entities ensuring cell-to-cell communication in both physiological and pathological processes, seem to play a pivotal function in ensuring the delivery of these factors to the tumour-surrounding tissues. In this review, we summarize the present understanding on the crosstalk among tumour cells and the cellular immune microenvironment emphasizing the pro-malignant role played by extracellular vesicles. We also discuss how a greater knowledge of the roles of EVs in tumour immune escape could be translated into clinical applications.

Keywords:  Biomarker; Cell signalling; Extracellular Vesicle; Immune; Pancreatic cancer

DOI:  https://doi.org/10.1016/j.semcancer.2023.09.004
Nat Chem Biol. 2023 Sep 28.

Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme.

Mark Dulchavsky, Rishav Mitra, Kevin Wu, Joshua Li, Karli Boer, Xiaomeng Liu, Zhiyao Zhang, Cristian Vasquez, Christopher T Clark, Kaitrin Funckes, Kokila Shankar, Selene Bonnet-Zahedi, Mohammad Siddiq, Yadira Sepulveda, Raymond T Suhandynata, Jeremiah D Momper, Antonio N Calabrese, Olivier George, Frederick Stull, James C A Bardwell.

The flavoenzyme nicotine oxidoreductase (NicA2) is a promising injectable treatment to aid in the cessation of smoking, a behavior responsible for one in ten deaths worldwide. NicA2 acts by degrading nicotine in the bloodstream before it reaches the brain. Clinical use of NicA2 is limited by its poor catalytic activity in the absence of its natural electron acceptor CycN. Without CycN, NicA2 is instead oxidized slowly by dioxygen (O2), necessitating unfeasibly large doses in a therapeutic setting. Here, we report a genetic selection strategy that directly links CycN-independent activity of NicA2 to growth of Pseudomonas putida S16. This selection enabled us to evolve NicA2 variants with substantial improvement in their rate of oxidation by O2. The encoded mutations cluster around a putative O2 tunnel, increasing flexibility and accessibility to O2 in this region. These mutations further confer desirable clinical properties. A variant form of NicA2 is tenfold more effective than the wild type at degrading nicotine in the bloodstream of rats.

DOI: https://doi.org/10.1038/s41589-023-01426-y
BMC Ecol Evol. 2023 Sep 25. 23(1): 54

Convergent TP53 loss and evolvability in cancer.

Marcela Braga Mansur, Mel Greaves.

  Cancer cell populations evolve by a stepwise process involving natural selection of the fittest variants within a tissue ecosystem context and as modified by therapy. Genomic scrutiny of patient samples reveals an extraordinary diversity of mutational profiles both between patients with similar cancers and within the cancer cell population of individual patients. Does this signify highly divergent evolutionary trajectories or are there repetitive and predictable patterns?Major evolutionary innovations or adaptations in different species are frequently repeated, or convergent, reflecting both common selective pressures and constraints on optimal solutions. We argue this is true of evolving cancer cells, especially with respect to the TP53 gene. Functional loss variants in TP53 are the most common genetic change in cancer. We discuss the likely microenvironmental selective pressures involved and the profound impact this has on cell fitness, evolvability and probability of subsequent drug resistance.

Keywords:  TP53; cancer; convergence; drug resistance; hypoxia; stem cells

DOI:  https://doi.org/10.1186/s12862-023-02146-6