bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024–12–01
38 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. NFE2L2 and SLC25A39 drive cuproptosis resistance through GSH metabolism.
  2. Metabolomics and 13C labelled glucose tracing to identify carbon incorporation into aberrant cell membrane glycans in cancer.
  3. Glucose limitation protects cancer cells from apoptosis induced by pyrimidine restriction and replication inhibition.
  4. Association of epigenetic landscapes with heterogeneity and plasticity in pancreatic cancer.
  5. Inceptor binds to and directs insulin towards lysosomal degradation in β cells.
  6. Mechano-dependent sorbitol accumulation supports biomolecular condensate.
  7. Plasma membrane remodeling determines adipocyte expansion and mechanical adaptability.
  8. CARMIL1-AA selectively inhibits macropinocytosis while sparing autophagy.
  9. High-density sampling reveals volume growth in human tumours.
  10. Inhibition of lung tumorigenesis by transient reprogramming in cancer cells.
  11. Photoacoustic polydopamine-indocyanine green (PDA-ICG) nanoprobe for detection of senescent cells.
  12. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs.
  13. Cancers adapt to their mutational load by buffering protein misfolding stress.
  14. Selective metabolic regulations by p53 mutant variants in pancreatic cancer.
  15. An Activity-Based Sensing Approach to Multiplex Mapping of Labile Copper Pools by Stimulated Raman Scattering.
  16. Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets.
  17. A panoramic view of cell population dynamics in mammalian aging.
  18. PTPN23-dependent ESCRT machinery functions as a cell death checkpoint.
  19. C/EBPβ-dependent autophagy inhibition hinders NK cell function in cancer.
  20. ACSL4 and polyunsaturated lipids support metastatic extravasation and colonization.
  21. Local Stress in Cylindrically Curved Lipid Membrane: Insights into Local Versus Global Lateral Fluidity Models.
  22. Age-related decline in CD8+ tissue resident memory T cells compromises antitumor immunity.
  23. Lipid composition differentiates ferroptosis sensitivity between in vitro and in vivo systems.
  24. Cancer cells impair monocyte-mediated T cell stimulation to evade immunity.
  25. CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.
  26. Stiffening symphony of aging: Biophysical changes in senescent osteocytes.
  27. Unraveling membrane protein localization and interactions in nanodiscs.
  28. Steatosarcopenia: A New Terminology for Clinical Conditions Related to Body Composition Classification.
  29. Plasmalogens in Innate Immune Cells: From Arachidonate Signaling to Ferroptosis.
  30. Protein-free domains in native and ferroptosis-driven oxidized cell membranes: a molecular dynamics study of biophysical properties and doxorubicin uptake.
  31. HSP90 buffers deleterious genetic variations in BRCA1.
  32. Lipid droplet protein Perilipin 2 is critical for the regulation of insulin secretion through beta cell lipophagy and glucagon expression in pancreatic islets.
  33. Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer.
  34. Proteolethargy is a pathogenic mechanism in chronic disease.
  35. A mortality timer based on nucleolar size triggers nucleolar integrity loss and catastrophic genomic instability.
  36. Small-Molecule Probe for Imaging Oxidative Stress-Induced Carbonylation in Live Cells.
  37. Inactivity-mediated molecular adaptations: Insights from a preclinical model of physical activity reduction.
  38. Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics.
  1. Sci Rep. 2024 Nov 28. 14(1): 29579
    NFE2L2 and SLC25A39 drive cuproptosis resistance through GSH metabolism.
    Jiao Liu, Hu Tang, Fangquan Chen, Changfeng Li, Yangchun Xie, Rui Kang, Daolin Tang.
      Cuproptosis is a recently discovered form of regulated cell death triggered by mitochondrial copper accumulation and proteotoxic stress. Here, we provide the first evidence that glutathione (GSH), a major non-protein thiol in cells, acts as a cuproptosis inhibitor in pancreatic ductal adenocarcinoma (PDAC) cells. Mechanistically, GSH inhibits cuproptosis by chelating copper, contrasting its role in blocking ferroptosis by inhibiting lipid peroxidation. The classical cuproptosis inducer, ES-Cu (elesclomol plus copper), increases the protein stability of the transcription factor NFE2L2 (also known as NRF2), leading to the upregulation of gene expression of glutamate-cysteine ligase modifier subunit (GCLM) and glutamate-cysteine ligase catalytic subunit (GCLC). GCLM and GCLC are rate-limiting enzymes in GSH synthesis, and increased GSH is transported into mitochondria via the solute carrier family 25 member 39 (SLC25A39) transporter. Consequently, genetic inhibition of the NFE2L2-GSH-SLC25A39 pathway enhances cuproptosis-mediated tumor suppression in cell culture and in mouse tumor models. These findings not only reveal distinct mechanisms of GSH in inhibiting cuproptosis and ferroptosis, but also suggest a potential combination strategy to suppress PDAC tumor growth.
    Keywords:  Copper; Cuproptosis; Elesclomol; Glutathione; NFE2L2; SLC25A39
    DOI:  https://doi.org/10.1038/s41598-024-81317-x
  2. Commun Biol. 2024 Nov 26. 7(1): 1576
    Metabolomics and 13C labelled glucose tracing to identify carbon incorporation into aberrant cell membrane glycans in cancer.
    Alfredo Reyes-Oliveras, Abigail E Ellis, Ryan D Sheldon, Brian Haab.
      Cell membrane glycans contribute to immune recognition, signaling, and cellular adhesion and migration, and altered membrane glycosylation is a feature of cancer cells that contributes to cancer progression. The uptake and metabolism of glucose and other nutrients essential for glycan synthesis could underlie altered membrane glycosylation, but the relationship between shifts in nutrient metabolism and the effects on glycans have not been directly examined. We developed a method that combines stable isotope tracing with metabolomics to enable direct observations of glucose allocation to nucleotide sugars and cell-membrane glycans. We compared the glucose allocation to membrane glycans of two pancreatic cancer cell lines that are genetically identical but have differing energy requirements. The 8988-S cells had higher glucose allocation to membrane glycans and intracellular pathways relating to glycan synthesis, but the 8988-T cells had higher glucose uptake and commitment of glucose to non-glycosylation pathways. The cell lines differed in the requirements of glucose for energy production, resulting in differences in glucose bioavailability for glycan synthesis. The workflow demonstrated here enables studies on the effects of metabolic shifts on the commitment of nutrients to cell-membrane glycans. The results suggest that cell-membrane glycans are remodeled through shifts in glucose commitment to non-glycosylation pathways.
    DOI:  https://doi.org/10.1038/s42003-024-07277-0
  3. Nat Metab. 2024 Nov 26.
    Glucose limitation protects cancer cells from apoptosis induced by pyrimidine restriction and replication inhibition.
    Minwoo Nam, Wenxin Xia, Abdul Hannan Mir, Alexandra Jerrett, Jessica B Spinelli, Tony T Huang, Richard Possemato.
      Cancer cells often experience nutrient-limiting conditions because of their robust proliferation and inadequate tumour vasculature, which results in metabolic adaptation to sustain proliferation. Most cancer cells rapidly consume glucose, which is severely reduced in the nutrient-scarce tumour microenvironment. In CRISPR-based genetic screens to identify metabolic pathways influenced by glucose restriction, we find that tumour-relevant glucose concentrations (low glucose) protect cancer cells from inhibition of de novo pyrimidine biosynthesis, a pathway that is frequently targeted by chemotherapy. We identify two mechanisms to explain this result, which is observed broadly across cancer types. First, low glucose limits uridine-5-diphosphate-glucose synthesis, preserving pyrimidine nucleotide availability and thereby prolonging the time to replication fork stalling. Second, low glucose directly modulates apoptosis downstream of replication fork stalling by suppressing BAK activation and subsequent cytochrome c release, key events that activate caspase-9-dependent mitochondrial apoptosis. These results indicate that the low glucose levels frequently observed in tumours may limit the efficacy of specific chemotherapeutic agents, highlighting the importance of considering the effects of the tumour nutrient environment on cancer therapy.
    DOI:  https://doi.org/10.1038/s42255-024-01166-w
  4. Crit Rev Oncol Hematol. 2024 Nov 22. pii: S1040-8428(24)00316-0. [Epub ahead of print]206 104573
    Association of epigenetic landscapes with heterogeneity and plasticity in pancreatic cancer.
    Paul Manoukian, Leo C Kuhnen, Hanneke W M van Laarhoven, Maarten F Bijlsma.
      Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Due to a lack of clear symptoms, patients often present with advanced disease, with limited clinical intervention options. The high mortality rate of PDAC is, however, also a result of several other factors that include a high degree of heterogeneity and treatment resistant cellular phenotypes. Molecular subtypes of PDAC have been identified that are thought to represent cellular phenotypes at the tissue level. The epigenetic landscape is an important factor that dictates these subtypes. Permissive epigenetic landscapes serve as drivers of molecular heterogeneity and cellular plasticity in developing crypts as well as metaplastic lesions. Drawing parallels with other cancers, we hypothesize that epigenetic permissiveness is a potential driver of cellular plasticity in PDAC. In this review will explore the epigenetic alterations that underlie PDAC cell states and relate them to cellular plasticity from other contexts. In doing so, we aim to highlight epigenomic drivers of PDAC heterogeneity and plasticity and, with that, offer some insight to guide pre-clinical research.
    Keywords:  Cell state; Epigenetics; Heterogeneity; Hybrid chromatin states; Pancreatic ductal adenocarcinoma; Plasticity
    DOI:  https://doi.org/10.1016/j.critrevonc.2024.104573
  5. Nat Metab. 2024 Nov 25.
    Inceptor binds to and directs insulin towards lysosomal degradation in β cells.
    Johanna Siehler, Sara Bilekova, Prisca Chapouton, Alessandro Dema, Pascal Albanese, Sem Tamara, Chirag Jain, Michael Sterr, Stephen J Enos, Chunguang Chen, Chetna Malhotra, Adrian Villalba, Leopold Schomann, Sreya Bhattacharya, Jin Feng, Melis Akgün Canan, Federico Ribaudo, Ansarullah, Ingo Burtscher, Christin Ahlbrecht, Oliver Plettenburg, Thomas Kurth, Raphael Scharfmann, Stephan Speier, Richard A Scheltema, Heiko Lickert.
      Blunted first-phase insulin secretion and insulin deficiency are indicators of β cell dysfunction and diabetes manifestation. Therefore, insights into molecular mechanisms that regulate insulin homeostasis might provide entry sites to replenish insulin content and restore β cell function. Here, we identify the insulin inhibitory receptor (inceptor; encoded by the gene IIR/ELAPOR1) as an insulin-binding receptor that regulates insulin stores by lysosomal degradation. Using human induced pluripotent stem cell (SC)-derived islets, we show that IIR knockout (KO) results in enhanced SC β cell differentiation and survival. Strikingly, extended in vitro culture of IIR KO SC β cells leads to greatly increased insulin content and glucose-stimulated insulin secretion (GSIS). We find that inceptor localizes to clathrin-coated vesicles close to the plasma membrane and in the trans-Golgi network as well as in secretory granules, where it acts as a sorting receptor to direct proinsulin and insulin towards lysosomal degradation. Targeting inceptor using a monoclonal antibody increases proinsulin and insulin content and improves SC β cell GSIS. Altogether, our findings reveal the basic mechanisms of β cell insulin turnover and identify inceptor as an insulin degradation receptor.
    DOI:  https://doi.org/10.1038/s42255-024-01164-y
  6. Cell. 2024 Nov 16. pii: S0092-8674(24)01271-6. [Epub ahead of print]
    Mechano-dependent sorbitol accumulation supports biomolecular condensate.
    Stephanie Torrino, William M Oldham, Andrés R Tejedor, Ignacio S Burgos, Lara Nasr, Nesrine Rachedi, Kéren Fraissard, Caroline Chauvet, Chaima Sbai, Brendan P O'Hara, Sophie Abélanet, Frederic Brau, Cyril Favard, Stephan Clavel, Rosana Collepardo-Guevara, Jorge R Espinosa, Issam Ben-Sahra, Thomas Bertero.
      Condensed droplets of protein regulate many cellular functions, yet the physiological conditions regulating their formation remain largely unexplored. Increasing our understanding of these mechanisms is paramount, as failure to control condensate formation and dynamics can lead to many diseases. Here, we provide evidence that matrix stiffening promotes biomolecular condensation in vivo. We demonstrate that the extracellular matrix links mechanical cues with the control of glucose metabolism to sorbitol. In turn, sorbitol acts as a natural crowding agent to promote biomolecular condensation. Using in silico simulations and in vitro assays, we establish that variations in the physiological range of sorbitol concentrations, but not glucose concentrations, are sufficient to regulate biomolecular condensates. Accordingly, pharmacological and genetic manipulation of intracellular sorbitol concentration modulates biomolecular condensates in breast cancer-a mechano-dependent disease. We propose that sorbitol is a mechanosensitive metabolite enabling protein condensation to control mechano-regulated cellular functions.
    Keywords:  LLPS; biomolecular condensate; breast cancer; cell metabolism; glucose metabolism; mechanobiology; phase transition; sorbitol
    DOI:  https://doi.org/10.1016/j.cell.2024.10.048
  7. Nat Commun. 2024 Nov 28. 15(1): 10102
    Plasma membrane remodeling determines adipocyte expansion and mechanical adaptability.
    María C M Aboy-Pardal, Marta C Guadamillas, Carlos R Guerrero, Mauro Català-Montoro, Mónica Toledano-Donado, Sara Terrés-Domínguez, Dácil M Pavón, Víctor Jiménez-Jiménez, Daniel Jimenez-Carretero, Moreno Zamai, Cintia Folgueira, Ana Cerezo, Fidel-Nicolás Lolo, Rubén Nogueiras, Guadalupe Sabio, Miguel Sánchez-Álvarez, Asier Echarri, Ricardo Garcia, Miguel A Del Pozo.
      Adipocytes expand massively to accommodate excess energy stores and protect the organism from lipotoxicity. Adipose tissue expandability is at the center of disorders such as obesity and lipodystrophy; however, little is known about the relevance of adipocyte biomechanics on the etiology of these conditions. Here, we show in male mice in vivo that the adipocyte plasma membrane undergoes caveolar domain reorganization upon lipid droplet expansion. As the lipid droplet grows, caveolae disassemble to release their membrane reservoir and increase cell surface area, and transfer specific caveolar components to the LD surface. Adipose tissue null for caveolae is stiffer, shows compromised deformability, and is prone to rupture under mechanical compression. Mechanistically, phosphoacceptor Cav1 Tyr14 is required for caveolae disassembly: adipocytes bearing a Tyr14Phe mutation at this residue are stiffer and smaller, leading to decreased adiposity in vivo; exhibit deficient transfer of Cav1 and EHD2 to the LD surface, and show distinct Cav1 molecular dynamics and tension adaptation. These results indicate that Cav1 phosphoregulation modulates caveolar dynamics as a relevant component of the homeostatic mechanoadaptation of the differentiated adipocyte.
    DOI:  https://doi.org/10.1038/s41467-024-54224-y
  8. Mol Biol Cell. 2024 Nov 27. mbcE24090434
    CARMIL1-AA selectively inhibits macropinocytosis while sparing autophagy.
    Rebecca M Lim, Alexa Lu, Brennan M Chuang, Cecily Anaraki, Brandon Chu, Christopher J Halbrook, Aimee L Edinger.
      Macropinocytosis is reported to fuel tumor growth and drug resistance by allowing cancer cells to scavenge extracellular macromolecules. However, accurately defining the role of macropinocytosis in cancer depends on our ability to selectively block this process. 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) is widely used to inhibit macropinocytosis but affects multiple Na+/H+ exchangers (NHE) that regulate cytoplasmic and organellar pH. Consistent with this, we report that EIPA slows proliferation to a greater extent than can be accounted for by macropinocytosis inhibition and triggers conjugation of ATG8 to single membranes (CASM). Knocking down only NHE1 would not avoid macropinocytosis-independent effects on pH. Moreover, contrary to published reports, NHE1 loss did not block macropinocytosis in multiple cell lines. Knocking down CARMIL1 with CRISPR-Cas9 editing limited macropinocytosis, but only by 50%. In contrast, expressing the CARMIL1-AA mutant inhibits macropinocytosis induced by a wide range of macropinocytic stimuli to a similar extent as EIPA. CARMIL1-AA expression did not inhibit proliferation, highlighting the shortcomings of EIPA as a macropinocytosis inhibitor. Importantly, autophagy, another actin dependent, nutrient-producing process, was not affected by CARMIL1-AA expression. In sum, constitutive or inducible CARMIL1-AA expression reduced macropinocytosis without affecting proliferation, RAC activation, or autophagy, other processes that drive tumor initiation and progression. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E24-09-0434
  9. Elife. 2024 Nov 26. pii: RP95338. [Epub ahead of print]13
    High-density sampling reveals volume growth in human tumours.
    Arman Angaji, Michel Owusu, Christoph Velling, Nicola Dick, Donate Weghorn, Johannes Berg.
      In growing cell populations such as tumours, mutations can serve as markers that allow tracking the past evolution from current samples. The genomic analyses of bulk samples and samples from multiple regions have shed light on the evolutionary forces acting on tumours. However, little is known empirically on the spatio-temporal dynamics of tumour evolution. Here, we leverage published data from resected hepatocellular carcinomas, each with several hundred samples taken in two and three dimensions. Using spatial metrics of evolution, we find that tumour cells grow predominantly uniformly within the tumour volume instead of at the surface. We determine how mutations and cells are dispersed throughout the tumour and how cell death contributes to the overall tumour growth. Our methods shed light on the early evolution of tumours in vivo and can be applied to high-resolution data in the emerging field of spatial biology.
    Keywords:  cancer biology; evolutionary biology; human; multi-region tumour samples; spatial genomics; tumour samples
    DOI:  https://doi.org/10.7554/eLife.95338
  10. Cell Death Dis. 2024 Nov 25. 15(11): 857
    Inhibition of lung tumorigenesis by transient reprogramming in cancer cells.
    Pablo Pedrosa, Zhenguang Zhang, Victor Nuñez-Quintela, David Macias, Jianfeng Ge, Mary Denholm, Anna Dyas, Valentin Estevez-Souto, Patricia Lado-Fernandez, Patricia Gonzalez, Maria Gomez, Jose Ezequiel Martin, Sabela Da Silva-Alvarez, Manuel Collado, Daniel Muñoz-Espín.
      Oncogenic transformation and Oct4, Sox2, Klf4 and c-Myc (OSKM)-mediated induction of pluripotency are two independent and incompatible cellular fates. While continuous expression of OSKM can convert normal somatic cells into teratogenic pluripotent cells, it remains speculative what is the impact of transient OSKM expression in cancer cells. Here, we find that OSKM expression limits the growth of transformed lung cells by inducing apoptosis and senescence. We identify Oct4 and Klf4 as the main individual reprogramming factors responsible for this effect. Mechanistically, the induction of cell cycle inhibitor p21 downstream of the reprogramming factors acts as mediator of cell death and senescence. Using a variety of in vivo systems, including allografts, orthotopic transplantation and KRAS-driven lung cancer mouse models, we demonstrate that transient reprogramming by OSKM expression in cancer cells impairs tumor growth and reduces tumor burden. Altogether, our results show that the induction of transient reprogramming in cancer cells is antitumorigenic opening novel potential therapeutic avenues in oncology.
    DOI:  https://doi.org/10.1038/s41419-024-07207-2
  11. Sci Rep. 2024 Nov 27. 14(1): 29506
    Photoacoustic polydopamine-indocyanine green (PDA-ICG) nanoprobe for detection of senescent cells.
    Muhamad Hartono, Andrew G Baker, Thomas R Else, Alexander S Evtushenko, Sarah E Bohndiek, Daniel Muñoz-Espín, Ljiljana Fruk.
      Cellular senescence is considered an important tumour suppression mechanism in response to damage and oncogenic stress in early lesions. However, when senescent cells are not immune-cleared and persist in the tumour microenvironment, they can drive a variety of tumour-promoting activities, including cancer initiation, progression, and metastasis. Additionally, there is compelling evidence demonstrating a direct connection between chemo(radio)therapy-induced senescence and the development of drug resistance and cancer recurrence. Therefore, detection of senescent cells in tissues holds great promise for predicting cancer occurrence earlier, assessing tumour progression, aiding patient stratification and prognosis, and informing about the efficacy of potential senotherapies. However, effective detection of senescent cells is limited by lack of biomarkers and readout strategies suitable for in vivo clinical imaging. To this end, a nanoprobe composed of biocompatible polydopamine (PDA) nanoparticle doped with FDA-approved indocyanine green (ICG) dye, namely PDA-ICG, was designed as a contrast agent for senescence detection using photoacoustic imaging (PAI). In an in vitro model of chemotherapy-induced senescence, PDA-ICG nanoprobe showed an elevated uptake in senescent cells relative to cancer cells. In addition to its improved photostability, 2.5-fold enhancement in photoacoustic signal relative to ICG was observed. Collectively, the results indicate that the PDA-ICG nanoprobe has the potential to be used as a contrast agent for senescence detection of chemotherapy-induced senescence using PAI.
    Keywords:  Cancer; Detection; ICG; Photoacoustic; Polydopamine; Senescence
    DOI:  https://doi.org/10.1038/s41598-024-79667-7
  12. Nat Methods. 2024 Nov 28.
    A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs.
    Caroline Brown, Snehasish Ghosh, Rachel McAllister, Mukesh Kumar, Gerard Walker, Eric Sun, Talat Aman, Aniruddha Panda, Shailesh Kumar, Wenxue Li, Jeff Coleman, Yansheng Liu, James E Rothman, Moitrayee Bhattacharyya, Kallol Gupta.
      The native membrane environment profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergents to disrupt and remove this vital membrane context, impeding our ability to decipher the local molecular context and its effect. Here we develop a membrane proteome-wide platform that enables rapid spatially resolved extraction of target MPs directly from cellular membranes into native nanodiscs that maintain the local membrane context, using a library of membrane-active polymers. We accompany this with an open-access database that quantifies the polymer-specific extraction efficiency for 2,065 unique mammalian MPs and provides the most optimized extraction condition for each. To validate, we demonstrate how this resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, we show how the database can be extended to capture overexpressed multiprotein complexes by taking two synaptic vesicle MPs. We expect these publicly available resources to empower researchers across disciplines to efficiently capture membrane 'nano-scoops' containing a target MP and interface with structural, functional and bioanalytical approaches.
    DOI:  https://doi.org/10.1038/s41592-024-02517-x
  13. Elife. 2024 Nov 25. pii: RP87301. [Epub ahead of print]12
    Cancers adapt to their mutational load by buffering protein misfolding stress.
    Susanne Tilk, Judith Frydman, Christina Curtis, Dmitri A Petrov.
      In asexual populations that don't undergo recombination, such as cancer, deleterious mutations are expected to accrue readily due to genome-wide linkage between mutations. Despite this mutational load of often thousands of deleterious mutations, many tumors thrive. How tumors survive the damaging consequences of this mutational load is not well understood. Here, we investigate the functional consequences of mutational load in 10,295 human tumors by quantifying their phenotypic response through changes in gene expression. Using a generalized linear mixed model (GLMM), we find that high mutational load tumors up-regulate proteostasis machinery related to the mitigation and prevention of protein misfolding. We replicate these expression responses in cancer cell lines and show that the viability in high mutational load cancer cells is strongly dependent on complexes that degrade and refold proteins. This indicates that the upregulation of proteostasis machinery is causally important for high mutational burden tumors and uncovers new therapeutic vulnerabilities.
    Keywords:  cancer; cancer biology; evolutionary biology; human; mutational load; proteostasis; somatic evolution
    DOI:  https://doi.org/10.7554/eLife.87301
  14. J Exp Clin Cancer Res. 2024 Nov 26. 43(1): 310
    Selective metabolic regulations by p53 mutant variants in pancreatic cancer.
    Sabrina Caporali, Alessio Butera, Alessia Ruzza, Carlotta Zampieri, Marina Bantula', Sandra Scharsich, Anna-Katerina Ückert, Ivana Celardo, Ian U Kouzel, Luigi Leanza, Andreas Gruber, Joan Montero, Angelo D'Alessandro, Thomas Brunner, Marcel Leist, Ivano Amelio.
       BACKGROUND: Approximately half of all human cancers harbour mutations in the p53 gene, leading to the generation of neomorphic p53 mutant proteins. These mutants can exert gain-of-function (GOF) effects, potentially promoting tumour progression. However, the clinical significance of p53 GOF mutations, as well as the selectivity of individual variants, remains controversial and unclear.
    METHODS: To elucidate the metabolic regulations and molecular underpinnings associated with the specific p53R270H and p53R172H mutant variants (the mouse equivalents of human p53R273H and p53R175H, respectively), we employed a comprehensive approach. This included integrating global metabolomic analysis with epigenomic and transcriptomic profiling in mouse pancreatic cancer cells. Additionally, we assessed metabolic parameters such as oxygen consumption rate and conducted analyses of proliferation and cell-cell competition to validate the biological impact of metabolic changes on pancreatic ductal adenocarcinoma (PDAC) phenotype. Our findings were further corroborated through analysis of clinical datasets from human cancer cohorts.
    RESULTS: Our investigation revealed that the p53R270H variant, but not p53R172H, sustains mitochondrial function and energy production while also influencing cellular antioxidant capacity. Conversely, p53R172H, while not affecting mitochondrial metabolism, attenuates the activation of pro-tumorigenic metabolic pathways such as the urea cycle. Thus, the two variants selectively control different metabolic pathways in pancreatic cancer cells. Mechanistically, p53R270H induces alterations in the expression of genes associated with oxidative stress and reduction in mitochondrial respiration. In contrast, p53R172H specifically impacts the expression levels of enzymes involved in the urea metabolism. However, our analysis of cell proliferation and cell competition suggested that the expression of either p53R270H or p53R172H does not influence confer any selective advantage to this cellular model in vitro. Furthermore, assessment of mitochondrial priming indicated that the p53R270H-driven mitochondrial effect does not alter cytochrome c release or the apoptotic propensity of pancreatic cancer cells.
    CONCLUSIONS: Our study elucidates the mutant-specific impact of p53R270H and p53R172H on metabolism of PDAC cancer cells, highlighting the need to shift from viewing p53 mutant variants as a homogeneous group of entities to a systematic assessment of each specific p53 mutant protein. Moreover, our finding underscores the importance of further exploring the significance of p53 mutant proteins using models that more accurately reflect tumor ecology.
    Keywords:  Anti-oxidant capacity; Cancer Metabolism; Gain-of-function; Tumour suppressor
    DOI:  https://doi.org/10.1186/s13046-024-03232-3
  15. J Am Chem Soc. 2024 Nov 25.
    An Activity-Based Sensing Approach to Multiplex Mapping of Labile Copper Pools by Stimulated Raman Scattering.
    Yishu Jiang, Elsy El Khoury, Aidan T Pezacki, Naixin Qian, Miku Oi, Laura Torrente, Sophia G Miller, Martina Ralle, Gina M DeNicola, Wei Min, Christopher J Chang.
      Molecular imaging with analyte-responsive probes offers a powerful chemical approach to studying biological processes. Many reagents for bioimaging employ a fluorescence readout, but the relatively broad emission bands of this modality and the need to alter the chemical structure of the fluorophore for different signal colors can potentially limit multiplex imaging. Here, we report a generalizable approach to multiplex analyte imaging by leveraging the comparably narrow spectral signatures of stimulated Raman scattering (SRS) in activity-based sensing (ABS) mode. We illustrate this concept with two copper Raman probes (CRPs), CRP2181 and CRP2153.2, that react selectively with loosely bound Cu(I/II) and Cu(II) ions, respectively, termed the labile copper pool, through copper-directed acyl imidazole (CDAI) chemistry. These reagents label proximal proteins in a copper-dependent manner using a dye scaffold bearing a 13C≡N or 13C≡15N isotopic SRS tag with nearly identical physiochemical properties in terms of shape and size. SRS imaging with the CRP reagents enables duplex monitoring of changes in intracellular labile Cu(I) and Cu(II) pools upon exogenous copper supplementation or copper depletion or genetic perturbations to copper transport proteins. Moreover, CRP imaging reveals reciprocal increases in labile Cu(II) pools upon decreases in activity of the antioxidant response nuclear factor-erythroid 2-related factor 2 (NRF2) in cellular models of lung adenocarcinoma. By showcasing the use of narrow-bandwidth ABS probes for multiplex imaging of copper pools in different oxidation states and identifying alterations in labile metal nutrient pools in cancer, this work establishes a foundation for broader SRS applications in analyte-responsive imaging in biological systems.
    DOI:  https://doi.org/10.1021/jacs.4c06296
  16. Nat Commun. 2024 Nov 25. 15(1): 10204
    Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets.
    Martin P Schwalm, Johannes Dopfer, Adarsh Kumar, Francesco A Greco, Nicolas Bauer, Frank Löhr, Jan Heering, Sara Cano-Franco, Severin Lechner, Thomas Hanke, Ivana Jaser, Viktoria Morasch, Christopher Lenz, Daren Fearon, Peter G Marples, Charles W E Tomlinson, Lorene Brunello, Krishna Saxena, Nathan B P Adams, Frank von Delft, Susanne Müller, Alexandra Stolz, Ewgenij Proschak, Bernhard Kuster, Stefan Knapp, Vladimir V Rogov.
      Recent successes in developing small molecule degraders that act through the ubiquitin system have spurred efforts to extend this technology to other mechanisms, including the autophagosomal-lysosomal pathway. Therefore, reports of autophagosome tethering compounds (ATTECs) have received considerable attention from the drug development community. ATTECs are based on the recruitment of targets to LC3/GABARAP, a family of ubiquitin-like proteins that presumably bind to the autophagosome membrane and tether cargo-loaded autophagy receptors into the autophagosome. In this work, we rigorously tested the target engagement of the reported ATTECs to validate the existing LC3/GABARAP ligands. Surprisingly, we were unable to detect interaction with their designated target LC3 using a diversity of biophysical methods. Intrigued by the idea of developing ATTECs, we evaluated the ligandability of LC3/GABARAP by in silico docking and large-scale crystallographic fragment screening. Data based on approximately 1000 crystal structures revealed that most fragments bound to the HP2 but not to the HP1 pocket within the LIR docking site, suggesting a favorable ligandability of HP2. Through this study, we identified diverse validated LC3/GABARAP ligands and fragments as starting points for chemical probe and ATTEC development.
    DOI:  https://doi.org/10.1038/s41467-024-54409-5
  17. Science. 2024 Nov 28. eadn3949
    A panoramic view of cell population dynamics in mammalian aging.
    Zehao Zhang, Chloe Schaefer, Weirong Jiang, Ziyu Lu, Jasper Lee, Andras Sziraki, Abdulraouf Abdulraouf, Brittney Wick, Maximilian Haeussler, Zhuoyan Li, Gesmira Molla, Rahul Satija, Wei Zhou, Junyue Cao.
      To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, sexes, and genotypes. This comprehensive dataset reveals more than 3,000 unique cellular states and over 200 aging-associated cell populations. Our panoramic analysis uncovered organ-, lineage-, and sex-specific shifts of cellular dynamics during lifespan progression. Moreover, we identify both systematic and organ-specific alterations in immune cell populations associated with aging. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte dependent. Our "cell-omics" strategy enhances comprehension of cellular aging and lays the groundwork for exploring the complex cellular regulatory networks in aging and aging-associated diseases.
    DOI:  https://doi.org/10.1126/science.adn3949
  18. Nat Commun. 2024 Nov 28. 15(1): 10364
    PTPN23-dependent ESCRT machinery functions as a cell death checkpoint.
    Dongyan Song, Yuxin Cen, Zhe Qian, Xiaoli S Wu, Keith Rivera, Tse-Luen Wee, Osama E Demerdash, Kenneth Chang, Darryl Pappin, Christopher R Vakoc, Nicholas K Tonks.
      Cell death plasticity is crucial for modulating tissue homeostasis and immune responses, but our understanding of the molecular components that regulate cell death pathways to determine cell fate remains limited. Here, a CRISPR screen of acute myeloid leukemia cells identifies protein tyrosine phosphatase non-receptor type 23 (PTPN23) as essential for survival. Loss of PTPN23 activates nuclear factor-kappa B, apoptotic, necroptotic, and pyroptotic pathways by causing the accumulation of death receptors and toll-like receptors (TLRs) in endosomes. These effects are recapitulated by depletion of PTPN23 co-dependent genes in the endosomal sorting complex required for transport (ESCRT) pathway. Through proximity-dependent biotin labeling, we show that NAK-associated protein 1 interacts with PTPN23 to facilitate endosomal sorting of tumor necrosis factor receptor 1 (TNFR1), sensitizing cells to TNF-α-induced cytotoxicity. Our findings reveal PTPN23-dependent ESCRT machinery as a cell death checkpoint that regulates the spatiotemporal distribution of death receptors and TLRs to restrain multiple cell death pathways.
    DOI:  https://doi.org/10.1038/s41467-024-54749-2
  19. Nat Commun. 2024 Nov 28. 15(1): 10343
    C/EBPβ-dependent autophagy inhibition hinders NK cell function in cancer.
    Federica Portale, Roberta Carriero, Marta Iovino, Paolo Kunderfranco, Marta Pandini, Giulia Marelli, Nicolò Morina, Massimo Lazzeri, Paolo Casale, Piergiuseppe Colombo, Gabriele De Simone, Chiara Camisaschi, Enrico Lugli, Gianluca Basso, Javier Cibella, Sergio Marchini, Matteo Bordi, Greta Meregalli, Anna Garbin, Monica Dambra, Elena Magrini, Wiebke Rackwitz, Francesco Cecconi, Alessandro Corbelli, Fabio Fiordaliso, Jiri Eitler, Torsten Tonn, Diletta Di Mitri.
      NK cells are endowed with tumor killing ability, nevertheless most cancers impair NK cell functionality, and cell-based therapies have limited efficacy in solid tumors. How cancers render NK cell dysfunctional is unclear, and overcoming resistance is an important immune-therapeutic aim. Here, we identify autophagy as a central regulator of NK cell anti-tumor function. Analysis of differentially expressed genes in tumor-infiltrating versus non-tumor NK cells from our previously published scRNA-seq data of advanced human prostate cancer shows deregulation of the autophagic pathway in tumor-infiltrating NK cells. We confirm this by flow cytometry in patients and in diverse cancer models in mice. We further demonstrate that exposure of NK cells to cancer deregulates the autophagic process, decreases mitochondrial polarization and impairs effector functions. Mechanistically, CCAAT enhancer binding protein beta (C/EBPβ), downstream of CXCL12-CXCR4 interaction, acts as regulator of NK cell metabolism. Accordingly, inhibition of CXCR4 and C/EBPβ restores NK cell fitness. Finally, genetic and pharmacological activation of autophagy improves NK cell effector and cytotoxic functions, which enables tumour control by NK and CAR-NK cells. In conclusion, our study identifies autophagy as an intracellular checkpoint in NK cells and introduces autophagy regulation as an approach to strengthen NK-cell-based immunotherapies.
    DOI:  https://doi.org/10.1038/s41467-024-54355-2
  20. Cell. 2024 Nov 19. pii: S0092-8674(24)01270-4. [Epub ahead of print]
    ACSL4 and polyunsaturated lipids support metastatic extravasation and colonization.
    Yuqi Wang, Mangze Hu, Jian Cao, Fengxiang Wang, Jingrong Regina Han, Tianshu William Wu, Luxiao Li, Jinshi Yu, Yujing Fan, Guanglei Xie, Heyuan Lian, Yueying Cao, Nathchar Naowarojna, Xi Wang, Yilong Zou.
      Metastatic dissemination to distant organs demands that cancer cells possess high morphological and metabolic adaptability. However, contributions of the cellular lipidome to metastasis remain elusive. Here, we uncover a correlation between metastasis potential and ferroptosis susceptibility in multiple cancers. Metastases-derived cancer cells exhibited higher ferroptosis sensitivity and polyunsaturated fatty acyl (PUFA)-lipid contents than primary-tumor-derived cells from ovarian cancer patients. Metabolism-focused CRISPR screens in a mouse model for ovarian cancer distant metastasis established via two rounds of in vivo selection revealed the PUFA-lipid biosynthesis enzyme acyl-coenzyme A (CoA) synthetase long-chain family member 4 (ACSL4) as a pro-hematogenous metastasis factor. ACSL4 promotes metastatic extravasation by enhancing membrane fluidity and cellular invasiveness. While promoting metastasis, the high PUFA-lipid state creates dependencies on abhydrolase-domain-containing 6, acylglycerol lipase (ABHD6), enoyl-CoA delta isomerase 1 (ECI1), and enoyl-CoA hydratase 1 (ECH1)-rate-limiting enzymes preparing unsaturated fatty acids (UFAs) for β-oxidation. ACSL4/ECH1 co-inhibition achieved potent suppression of metastasis. Our work establishes the dual functions of PUFA-lipids in tumor progression and metastasis that may be exploitable for therapeutic development.
    Keywords:  ACSL4; ECH1; cancer metastasis; extravasation; ferroptosis susceptibility; in vivo CRISPR screens; lipid metabolism; metastatic colonization; ovarian cancer; polyunsaturated lipids
    DOI:  https://doi.org/10.1016/j.cell.2024.10.047
  21. Biomolecules. 2024 Nov 19. pii: 1471. [Epub ahead of print]14(11):
    Local Stress in Cylindrically Curved Lipid Membrane: Insights into Local Versus Global Lateral Fluidity Models.
    Konstantin V Pinigin.
      Lipid membranes, which are fundamental to cellular function, undergo various mechanical deformations. Accurate modeling of these processes necessitates a thorough understanding of membrane elasticity. The lateral shear modulus, a critical parameter describing membrane resistance to lateral stresses, remains elusive due to the membrane's fluid nature. Two contrasting hypotheses, local fluidity and global fluidity, have been proposed. While the former suggests a zero local lateral shear modulus anywhere within lipid monolayers, the latter posits that only the integral of this modulus over the monolayer thickness vanishes. These differing models lead to distinct estimations of other elastic moduli and affect the modeling of biological processes, such as membrane fusion/fission and membrane-mediated interactions. Notably, they predict distinct local stress distributions in cylindrically curved membranes. The local fluidity model proposes isotropic local lateral stress, whereas the global fluidity model predicts anisotropy due to anisotropic local lateral stretching of lipid monolayers. Using molecular dynamics simulations, this study directly investigates these models by analyzing local stress in a cylindrically curved membrane. The results conclusively demonstrate the existence of static local lateral shear stress and anisotropy in local lateral stress within the monolayers of the cylindrical membrane, strongly supporting the global fluidity model. These findings have significant implications for the calculation of surface elastic moduli and offer novel insights into the fundamental principles governing lipid membrane elasticity.
    Keywords:  biological membranes; elasticity of lipid membranes; lipid bilayers; lipid membranes; lipid monolayers; membrane biophysics; molecular dynamics of lipid membranes
    DOI:  https://doi.org/10.3390/biom14111471
  22. Nat Aging. 2024 Nov 26.
    Age-related decline in CD8+ tissue resident memory T cells compromises antitumor immunity.
    Siyu Pei, Xiuyu Deng, Ruirui Yang, Hui Wang, Jian-Hong Shi, Xueqing Wang, Jia Huang, Yu Tian, Rongjing Wang, Sulin Zhang, Hui Hou, Jing Xu, Qingcheng Zhu, Huan Huang, Jialing Ye, Cong-Yi Wang, Wei Lu, Qingquan Luo, Zhi-Yu Ni, Mingyue Zheng, Yichuan Xiao.
      Aging compromises antitumor immunity, but the underlying mechanisms remain elusive. Here, we report that aging impairs the generation of CD8+ tissue resident memory T (TRM) cells in nonlymphoid tissues in mice, thus compromising the antitumor activity of aged CD8+ T cells, which we also observed in human lung adenocarcinoma. We further identified that the apoptosis regulator BFAR was highly enriched in aged CD8+ T cells, in which BFAR suppressed cytokine-induced JAK2 signaling by activating JAK2 deubiquitination, thereby limiting downstream STAT1-mediated TRM reprogramming. Targeting BFAR either through Bfar knockout or treatment with our developed BFAR inhibitor, iBFAR2, rescued the antitumor activity of aged CD8+ T cells by restoring TRM generation in the tumor microenvironment, thus efficiently inhibiting tumor growth in aged CD8+ T cell transfer and anti-programmed cell death protein 1 (PD-1)-resistant mouse tumor models. Together, our findings establish BFAR-induced TRM restriction as a key mechanism causing aged CD8+ T cell dysfunction and highlight the translational potential of iBFAR2 in restoring antitumor activity in aged individuals or patients resistant to anti-PD-1 therapy.
    DOI:  https://doi.org/10.1038/s43587-024-00746-5
  23. bioRxiv. 2024 Nov 15. pii: 2024.11.14.622381. [Epub ahead of print]
    Lipid composition differentiates ferroptosis sensitivity between in vitro and in vivo systems.
    Vivian S Park, Lauren E Pope, Justin Ingram, Grace A Alchemy, Julie Purkal, Eli Y Andino-Frydman, Sha Jin, Sanjana Singh, Anlu Chen, Priya Narayanan, Sarah Kongpachith, Darren C Phillips, Scott J Dixon, Relja Popovic.
      Ferroptosis is a regulated non-apoptotic cell death process characterized by iron-dependent lipid peroxidation. This process has recently emerged as a promising approach for cancer therapy. Peroxidation of polyunsaturated fatty acid-containing phospholipids (PUFA-PLs) is necessary for the execution of ferroptosis. Ferroptosis is normally suppressed by glutathione peroxidase 4 (GPX4), which reduces lipid hydroperoxides to lipid alcohols. Some evidence indicates that GPX4 may be a useful target for drug development, yet factors that govern GPX4 inhibitor sensitivity in vivo are poorly understood. We find that pharmacological and genetic loss of GPX4 function was sufficient to induce ferroptosis in multiple adherent ("2D") cancer cell cultures. However, reducing GPX4 protein levels did not affect tumor xenograft growth when these cells were implanted in mice. Furthermore, sensitivity to GPX4 inhibition was markedly reduced when cells were cultured as spheroids ("3D"). Mechanistically, growth in 3D versus 2D conditions reduced the abundance of PUFA-PLs. 3D culture conditions upregulated the monounsaturated fatty acid (MUFA) biosynthetic gene stearoyl-CoA desaturase (SCD). SCD-derived MUFAs appear to protect against ferroptosis in 3D conditions by displacing PUFAs from phospholipids. Various structurally related long chain MUFAs can inhibit ferroptosis through this PUFA-displacement mechanism. These findings suggest that growth-condition-dependent lipidome remodeling is an important mechanism governing GPX4 inhibitor effects. This resistance mechanism may specifically limit GPX4 inhibitor effectiveness in vivo .
    DOI:  https://doi.org/10.1101/2024.11.14.622381
  24. Nature. 2024 Nov 27.
    Cancer cells impair monocyte-mediated T cell stimulation to evade immunity.
    Anais Elewaut, Guillem Estivill, Felix Bayerl, Leticia Castillon, Maria Novatchkova, Elisabeth Pottendorfer, Lisa Hoffmann-Haas, Martin Schönlein, Trung Viet Nguyen, Martin Lauss, Francesco Andreatta, Milica Vulin, Izabela Krecioch, Jonas Bayerl, Anna-Marie Pedde, Naomi Fabre, Felix Holstein, Shona M Cronin, Sarah Rieser, Denarda Dangaj Laniti, David Barras, George Coukos, Camelia Quek, Xinyu Bai, Miquel Muñoz I Ordoño, Thomas Wiesner, Johannes Zuber, Göran Jönsson, Jan P Böttcher, Sakari Vanharanta, Anna C Obenauf.
      The tumour microenvironment is programmed by cancer cells and substantially influences anti-tumour immune responses1,2. Within the tumour microenvironment, CD8+ T cells undergo full effector differentiation and acquire cytotoxic anti-tumour functions in specialized niches3-7. Although interactions with type 1 conventional dendritic cells have been implicated in this process3-5,8-10, the underlying cellular players and molecular mechanisms remain incompletely understood. Here we show that inflammatory monocytes can adopt a pivotal role in intratumoral T cell stimulation. These cells express Cxcl9, Cxcl10 and Il15, but in contrast to type 1 conventional dendritic cells, which cross-present antigens, inflammatory monocytes obtain and present peptide-major histocompatibility complex class I complexes from tumour cells through 'cross-dressing'. Hyperactivation of MAPK signalling in cancer cells hampers this process by coordinately blunting the production of type I interferon (IFN-I) cytokines and inducing the secretion of prostaglandin E2 (PGE2), which impairs the inflammatory monocyte state and intratumoral T cell stimulation. Enhancing IFN-I cytokine production and blocking PGE2 secretion restores this process and re-sensitizes tumours to T cell-mediated immunity. Together, our work uncovers a central role of inflammatory monocytes in intratumoral T cell stimulation, elucidates how oncogenic signalling disrupts T cell responses through counter-regulation of PGE2 and IFN-I, and proposes rational combination therapies to enhance immunotherapies.
    DOI:  https://doi.org/10.1038/s41586-024-08257-4
  25. Nucleic Acids Res. 2024 Nov 28. pii: gkae1142. [Epub ahead of print]
    CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.
    CZI Cell Science Program
      Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data. Despite the promise of these and emerging analytical tools for analyzing large amounts of data, the sheer number of datasets, data models and accessibility remains a challenge. Here, we present CZ CELLxGENE Discover (cellxgene.cziscience.com), a data platform that provides curated and interoperable single-cell data. Available via a free-to-use online data portal, CZ CELLxGENE hosts a growing corpus of community-contributed data of over 93 million unique cells. Curated, standardized and associated with consistent cell-level metadata, this collection of single-cell transcriptomic data is the largest of its kind and growing rapidly via community contributions. A suite of tools and features enables accessibility and reusability of the data via both computational and visual interfaces to allow researchers to explore individual datasets, perform cross-corpus analysis, and run meta-analyses of tens of millions of cells across studies and tissues at the resolution of single cells.
    DOI:  https://doi.org/10.1093/nar/gkae1142
  26. Aging Cell. 2024 Nov 24. e14421
    Stiffening symphony of aging: Biophysical changes in senescent osteocytes.
    Maryam Tilton, Megan Weivoda, Maria Astudillo Potes, Anne Gingery, Alan Y Liu, Tamara Tchkonia, Lichun Lu, James L Kirkland.
      Senescent osteocytes are key contributors to age-related bone loss and fragility; however, the impact of mechanobiological changes in these cells remains poorly understood. This study provides a novel analysis of these changes in primary osteocytes following irradiation-induced senescence. By integrating subcellular mechanical measurements with gene expression analyses, we identified significant, time-dependent alterations in the mechanical properties of senescent bone cells. Increases in classical markers such as SA-β-Gal activity and p16Ink4a expression levels confirmed the senescence status post-irradiation. Our key findings include a time-dependent increase in cytoskeletal Young's modulus and altered viscoelastic properties of the plasma membrane, affecting the contractility of primary osteocytes. Additionally, we observed a significant increase in Sclerostin (Sost) expression 21 days post-irradiation. These biophysical changes may impair osteocyte mechanosensation and mechanotransduction, contributing to bone fragility. This is the first study to time-map senescence-associated mechanical changes in the osteocyte cytoskeleton. Our findings highlight the potential of biophysical markers as indicators of cellular senescence, providing more specificity than traditional, variable biomolecular markers. We believe these results may support biomechanical stimulation as a potential therapeutic strategy to rejuvenate aging osteocytes and enhance bone health.
    Keywords:  cellular senescence; cytoskeleton mechanics; osteocyte mechanobiology; sub cellular structure
    DOI:  https://doi.org/10.1111/acel.14421
  27. FEBS Lett. 2024 Nov 28.
    Unraveling membrane protein localization and interactions in nanodiscs.
    Young Hoon Koh, So-Jung Kim, Soung-Hun Roh.
      Nanodiscs, consisting of a lipid bilayer surrounded by membrane scaffold proteins (MSPs), are extensively used to study membrane proteins (MPs) because they provide a stable lipid environment. However, the precise mechanism governing MP behavior within the nanodisc remains elusive. Here, we examined the cryo-EM structures of various MPs reconstituted in nanodiscs from EMPIAR. By analyzing the heterogeneity and interactions in the nanodiscs, we discovered that MPs display a distinct spatial preference toward the edges of the nanodisc shells. Furthermore, MPs can establish direct, amphipathic interactions with the MSPs, causing a reduction in local protein dynamics. These interactions may rearrange MSP-MSP interactions into MP-MSP interactions. Collectively, we provide structural insights into how nanodiscs contribute to MP structural behavior and dynamics. Impact statement Nanodiscs are used to study membrane proteins (MPs), but the mechanisms governing the behavior of MPs within nanodiscs remain elusive. Here, we provide structural insights into how nanodiscs contribute to the behavior of MPs, which will aid the interpretation of cryo-EM studies performed using nanodiscs.
    Keywords:  cryo‐EM; membrane proteins; membrane scaffold proteins; nanodisc
    DOI:  https://doi.org/10.1002/1873-3468.15059
  28. Life (Basel). 2024 Oct 28. pii: 1383. [Epub ahead of print]14(11):
    Steatosarcopenia: A New Terminology for Clinical Conditions Related to Body Composition Classification.
    SBRAG (Steatosarcopenia & Sarcopenia Brazilian Study Group)
      Body composition analysis focuses on measuring skeletal muscle mass and total body fat. The loss of muscle function and mass is related to clinical conditions such as frailty, increased risk of falls, and prolonged hospitalizations. Despite the relevance of the definition of sarcopenic obesity, there is still a gap in the monitoring of patients who have the combination of sarcopenia and myosteatosis, regardless of the presence of obesity. Therefore, we propose a new nomenclature, steatosarcopenia, a condition characterized by the loss of mass or skeletal muscle strength and performance associated with the excessive deposition of ectopic reserve fat in muscle tissue, in the same individual, not necessarily related to excess fat total body mass. A greater understanding of this condition may assist in developing strategies for preventing and treating metabolic diseases.
    Keywords:  muscle mass; myosteatosis intermuscular; myosteatosis intramyocellular; sarcopenia; sarcopenic obesity
    DOI:  https://doi.org/10.3390/life14111383
  29. Biomolecules. 2024 Nov 18. pii: 1461. [Epub ahead of print]14(11):
    Plasmalogens in Innate Immune Cells: From Arachidonate Signaling to Ferroptosis.
    Jesús Balsinde, María A Balboa.
      Polyunsaturated fatty acids such as arachidonic acid are indispensable components of innate immune signaling. Plasmalogens are glycerophospholipids with a vinyl ether bond in the sn-1 position of the glycerol backbone instead of the more common sn-1 ester bond present in "classical" glycerophospholipids. This kind of phospholipid is particularly rich in polyunsaturated fatty acids, especially arachidonic acid. In addition to or independently of the role of plasmalogens as major providers of free arachidonic acid for eicosanoid synthesis, plasmalogens also perform a varied number of functions. Membrane plasmalogen levels may determine parameters of the plasma membrane, such as fluidity and the formation of microdomains that are necessary for efficient signal transduction leading to optimal phagocytosis by macrophages. Also, plasmalogens may be instrumental for the execution of ferroptosis. This is a nonapoptotic form of cell death that is associated with oxidative stress. This review discusses recent data suggesting that, beyond their involvement in the cellular metabolism of arachidonic acid, the cells maintain stable pools of plasmalogens rich in polyunsaturated fatty acids for executing specific responses.
    Keywords:  arachidonic acid; ferroptosis; inflammation; innate immunity; plasmalogens; polyunsaturated fatty acids
    DOI:  https://doi.org/10.3390/biom14111461
  30. Front Mol Biosci. 2024 ;11 1494257
    Protein-free domains in native and ferroptosis-driven oxidized cell membranes: a molecular dynamics study of biophysical properties and doxorubicin uptake.
    Yaser Shabanpour, Behnam Hajipour-Verdom, Parviz Abdolmaleki, Mozhgan Alipour.
      Ferroptosis is a regulated form of cell death characterized by iron-dependent lipid peroxidation of polyunsaturated fatty acids (PUFAs). Despite its significance, the precise molecular mechanisms underlying ferroptosis remain elusive, particularly concerning their impact on membrane properties. This study aimed to investigate the biophysical changes in plasma membranes due to lipid peroxidation during ferroptosis and their impact on the uptake of doxorubicin (DOX), a potent anticancer agent linked to ferroptosis. Using all-atom molecular dynamics simulations, we compared native red blood cell membranes (protein-free domains) with a ferroptosis model, in which PUFAs were replaced with hydroperoxide derivatives. Our findings reveal that the ferroptotic membrane exhibits decreased thickness and increased lipid area while maintaining overall integrity. The hydroperoxide groups localized in the disordered tail regions, enhancing tail mobility and facilitating hydrogen bonding. Lipid lateral diffusion was significantly altered, both layers of the ferroptotic membrane exhibited slower diffusion rates compared to the native membrane. Furthermore, lipid oxidation affected diffusion activation energies. Importantly, we found that DOX could penetrate the oxidized ferroptosis membrane with a lower free-energy barrier (∆GPB) of approximately 38 kJ.mol-1. Consequently, DOX's permeability was approximately seven orders of magnitude higher than that of the native membrane. In summary, lipid peroxidation during ferroptosis induces extensive structural and dynamic changes, influencing membrane behavior and potentially offering insights that could inform future therapeutic strategies.
    Keywords:  ferroptosis; hydroperoxide derivatives; molecular dynamics simulation; oxidized membrane; realistic membrane
    DOI:  https://doi.org/10.3389/fmolb.2024.1494257
  31. bioRxiv. 2024 Nov 17. pii: 2024.11.15.623783. [Epub ahead of print]
    HSP90 buffers deleterious genetic variations in BRCA1.
    Brant Gracia, Patricia Montes, Min Huang, Junjie Chen, Georgios Ioannis Karras.
      Protein-folding chaperone HSP90 buffers genetic variation in diverse organisms, but the clinical significance of HSP90 buffering in disease remains unclear. Here, we show that HSP90 buffers mutations in the BRCT domain of BRCA1. HSP90-buffered BRCA1 mutations encode protein variants that retain interactions with partner proteins and rely on HSP90 for protein stability and function in cell survival. Moreover, HSP90-buffered BRCA1 variants confer PARP inhibitor resistance in cancer cell lines. Low-level HSP90 inhibition alleviates this resistance, revealing a cryptic and mutant-specific HSP90-contingent synthetic lethality. Hence, by stabilizing metastable variants across the entirety of the BRCT domain, HSP90 reduces the clinical severity of BRCA1 mutations allowing them to accumulate in populations. We estimate that HSP90 buffers 11% to 28% of known human BRCA1- BRCT missense mutations. Our work extends the clinical significance of HSP90 buffering to a prevalent class of variations in BRCA1 , pioneering its importance in cancer predisposition and therapy resistance.
    DOI:  https://doi.org/10.1101/2024.11.15.623783
  32. bioRxiv. 2024 Nov 18. pii: 2024.11.17.624030. [Epub ahead of print]
    Lipid droplet protein Perilipin 2 is critical for the regulation of insulin secretion through beta cell lipophagy and glucagon expression in pancreatic islets.
    Siming Liu, Israel Wipf, Aditya Joglekar, Aidan Freshly, Corinne E Bovee, Lucy Kim, Syreine L Richtsmeier, Spencer Peachee, Shayla Kopriva, Anamika Vikram, Dalal El Ladiki, Fatma Ilerisoy, Beyza Ilerisoy, Gianna Sagona, Claudia Jun, Michelle Giedt, Tina L Tootle, James Ankrum, Yumi Imai.
      Knockdown (KD) of lipid droplet (LD) protein perilipin 2 (PLIN2) in beta cells impairs glucose-stimulated insulin secretion (GSIS) and mitochondrial function. Here, we addressed a pathway responsible for compromised mitochondrial integrity in PLIN2 KD beta cells. In PLIN2 KD human islets, mitochondria were fragmented in beta cells but not in alpha cells. Glucagon but not insulin level was elevated. While the formation of early LDs followed by fluorescent fatty acids (FA) analog Bodipy C12 (C12) was preserved, C12 accumulated in mitochondria over time in PLIN2 KD INS-1 cells. A lysosomal acid lipase inhibitor Lali2 prevented C12 transfer to mitochondria, mitochondrial fragmentation, and the impairment of GSIS. Direct interactions between LD-lysosome and lysosome-mitochondria were increased in PLIN2 KD INS-1 cells. Thus, FA released from LDs by microlipophagy cause mitochondrial changes and impair GSIS in PLIN2 KD beta cells. Interestingly, glucolipotoxic condition (GLT) caused C12 accumulation and mitochondrial fragmentation similar to PLIN2 KD in beta cells. Moreover, Lali2 reversed mitochondrial fragmentation and improved GSIS in human islets under GLT. In summary, PLIN2 regulates microlipophagy to prevent excess FA flux to mitochondria in beta cells. This pathway also contributes to GSIS impairment when LD pool expands under nutrient load in beta cells.
    DOI:  https://doi.org/10.1101/2024.11.17.624030
  33. Nat Aging. 2024 Nov 25.
    Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer.
    Brittany L Angarola, Siddhartha Sharma, Neerja Katiyar, Hyeon Gu Kang, Djamel Nehar-Belaid, SungHee Park, Rachel Gott, Giray N Eryilmaz, Mark A LaBarge, Karolina Palucka, Jeffrey H Chuang, Ron Korstanje, Duygu Ucar, Olga Anczukόw.
      Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. In this study, we investigated how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single-cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory and cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveals co-localization of aged immune and epithelial cells in situ. Lastly, we found transcriptional signatures of aging mammary cells in human breast tumors, suggesting possible links between aging and cancer. Together, these data uncover that epithelial, immune and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment and neoplasia risk.
    DOI:  https://doi.org/10.1038/s43587-024-00751-8
  34. Cell. 2024 Nov 25. pii: S0092-8674(24)01274-1. [Epub ahead of print]
    Proteolethargy is a pathogenic mechanism in chronic disease.
    Alessandra Dall'Agnese, Ming M Zheng, Shannon Moreno, Jesse M Platt, An T Hoang, Deepti Kannan, Giuseppe Dall'Agnese, Kalon J Overholt, Ido Sagi, Nancy M Hannett, Hailey Erb, Olivia Corradin, Arup K Chakraborty, Tong Ihn Lee, Richard A Young.
      The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here, we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia, and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.
    Keywords:  chronic disease; cysteine; protein mobility; proteolethargy; reactive oxygen species; signaling
    DOI:  https://doi.org/10.1016/j.cell.2024.10.051
  35. Nat Aging. 2024 Nov 25.
    A mortality timer based on nucleolar size triggers nucleolar integrity loss and catastrophic genomic instability.
    J Ignacio Gutierrez, Jessica K Tyler.
      Genome instability is a hallmark of aging, with the highly repetitive ribosomal DNA (rDNA) within the nucleolus being particularly prone to genome instability. Nucleolar enlargement accompanies aging in organisms ranging from yeast to mammals, and treatment with many antiaging interventions results in small nucleoli. Here, we report that an engineered system to reduce nucleolar size robustly extends budding yeast replicative lifespan in a manner independent of protein synthesis rate or rDNA silencing. Instead, when nucleoli expand beyond a size threshold, their biophysical properties change, allowing entry of proteins normally excluded from the nucleolus, including the homologous recombinational repair protein Rad52. This triggers rDNA instability due to aberrant recombination, catastrophic genome instability and imminent death. These results establish that nucleolar expansion is sufficient to drive aging. Moreover, nucleolar expansion beyond a specific size threshold is a mortality timer, as the accompanying disruption of the nucleolar condensate boundary results in catastrophic genome instability that ends replicative lifespan.
    DOI:  https://doi.org/10.1038/s43587-024-00754-5
  36. Bio Protoc. 2024 Nov 20. 14(22): e5112
    Small-Molecule Probe for Imaging Oxidative Stress-Induced Carbonylation in Live Cells.
    Ozlem Dilek, Dilek Telci, Hazel Erkan-Candag.
      Protein carbonylation has been known as the major form of irreversible protein modifications and is also widely used as an indicator of oxidative stress in the biological environment. In the presence of oxidative stress, biological systems tend to produce large amounts of carbonyl moieties; these carbonyl groups do not have particular UV-Vis and fluorescence spectroscopic characteristics that we can differentiate, observe, and detect. Thus, their detection and quantification can only be performed using specific chemical probes. Commercially available fluorescent probes to detect specific carbonylation in biological systems have been used, but their chemical portfolio is still very limited. This protocol outlines the methods and procedures employed to synthesize a probe, (E,Z)-2-(2-(2-hydroxybenzylidene)hydrazonyl)-5-nitrophenol (2Hzin5NP), and assess its impact on carbonylation in human cells. The synthesis involves several steps, including the preparation of its hydrazone compounds mimicking cell carbonyls, 2-Hydrazinyl 5-nitrophenol, (E,Z)-2-(2-ethylidenehydrazonyl)-5-nitrophenol, and the final product (E,Z)-2-(2-(2-hydroxybenzylidene)hydrazonyl)-5-nitrophenol. The evaluation of fluorescence quantum yield and subsequent cell culture experiments are detailed for the investigation of 2Hzin5NP effects on cell proliferation and carbonylation. Key features • This protocol builds upon probe development using click chemistry method by Dilek et al. [1], and its biolabeling application in renal cancer cell lines. • The non-fluorescent probe has a fast reaction with carbonyl moieties at neutral pH to form a stable fluorescent product leading to a spectroscopic alteration. • Microscopic and fluorometric analyses can distinguish the exogenous and endogenous ROS-induced carbonylation profile in human dermal fibroblasts along with renal cell carcinoma. • Carbonylation level that differs in response to exogenous and endogenous stress in healthy and cancer cells can be detected by the newly synthesized fluorescent probe.
    Keywords:  Bioorthogonal chemistry; Cancer cells; Click chemistry; Diagnostics; Fluorescence imaging; Fluorescent probes
    DOI:  https://doi.org/10.21769/BioProtoc.5112
  37. Physiol Rep. 2024 Dec;12(23): e70140
    Inactivity-mediated molecular adaptations: Insights from a preclinical model of physical activity reduction.
    Alice Meyer, Nicole Kim, Melissa Nguyen, Monica Misch, Kevin Marmo, Jacob Dowd, Christian Will, Milica Janosevic, Erin J Stephenson.
      Insufficient physical activity is associated with increased relative risk of cardiometabolic disease and is an independent risk factor for mortality. Experimentally reducing physical activity rapidly induces insulin resistance, impairs glucose handling, and drives metabolic inflexibility. These adaptations manifest during the early stages of physical inactivity, even when energy balance is maintained, suggesting that inactivity-mediated metabolic reprogramming is an early event that precedes changes in body composition. To identify mechanisms that promote metabolic adaptations associated with physical inactivity, we developed a mouse model of physical activity reduction that permits the study of inactivity in animals prior to the onset of overt changes in body composition. Adult mice were randomized into three groups: an inactive control group (standard rodent housing), an active control group (treadmill running 5 d/week for 6-weeks), and an activity reduction group (treadmill running for 4-weeks, followed by 2-weeks of inactivity). Transcriptional profiling of gastrocnemius muscle identified seven transcripts uniquely altered by physical activity reduction compared to the inactive and active control groups. Most identified transcripts had reported functions linked to bioenergetic adaptation. Future studies will provide deeper characterization of the function(s) of each the identified transcripts while also determining how inactivity affects transcriptional regulation in other tissues.
    Keywords:  physical activity reduction; physical inactivity; skeletal muscle metabolism; skeletal muscle transcriptome
    DOI:  https://doi.org/10.14814/phy2.70140
  38. NPJ Aging. 2024 Nov 26. 10(1): 57
    Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics.
    Abhijeet Venkataraman, Ivan Kordic, JiaXun Li, Nicholas Zhang, Nivik Sanjay Bharadwaj, Zhou Fang, Sandip Das, Ahmet F Coskun.
      Aging has profound effects on the body, most notably an increase in the prevalence of several diseases. An important aging hallmark is the presence of senescent cells that no longer multiply nor die off properly. Another characteristic is an altered immune system that fails to properly self-surveil. In this multi-player aging process, cellular senescence induces a change in the secretory phenotype, known as senescence-associated secretory phenotype (SASP), of many cells with the intention of recruiting immune cells to accelerate the clearance of these damaged senescent cells. However, the SASP phenotype results in inducing secondary senescence of nearby cells, resulting in those cells becoming senescent, and improper immune activation resulting in a state of chronic inflammation, called inflammaging, in many diseases. Senescence in immune cells, termed immunosenescence, results in further dysregulation of the immune system. An interdisciplinary approach is needed to physiologically assess aging changes of the immune system at the cellular and tissue level. Thus, the intersection of biomaterials, microfluidics, and spatial omics has great potential to collectively model aging and immunosenescence. Each of these approaches mimics unique aspects of the body undergoes as a part of aging. This perspective highlights the key aspects of how biomaterials provide non-cellular cues to cell aging, microfluidics recapitulate flow-induced and multi-cellular dynamics, and spatial omics analyses dissect the coordination of several biomarkers of senescence as a function of cell interactions in distinct tissue environments. An overview of how senescence and immune dysregulation play a role in organ aging, cancer, wound healing, Alzheimer's, and osteoporosis is included. To illuminate the societal impact of aging, an increasing trend in anti-senescence and anti-aging interventions, including pharmacological interventions, medical procedures, and lifestyle changes is discussed, including further context of senescence.
    DOI:  https://doi.org/10.1038/s41514-024-00178-w
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