bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022‒05‒22
43 papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. PHGDH heterogeneity potentiates cancer cell dissemination and metastasis.
  2. Purine nucleotide depletion prompts cell migration by stimulating the serine synthesis pathway.
  3. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer.
  4. Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence.
  5. Suppression of nuclear GSK3 signaling promotes serine/one-carbon metabolism and confers metabolic vulnerability in lung cancer cells.
  6. Reflected stemness as a potential driver of the tumour microenvironment.
  7. A CRISPR view on autophagy.
  8. Cytoskeleton grows p62 condensates for autophagy.
  9. Phase Separation in Regulation of Autophagy.
  10. Different hotspot p53 mutants exert distinct phenotypes and predict outcome of colorectal cancer patients.
  11. Intracellular lipid surveillance by small G protein geranylgeranylation.
  12. Visual barcodes for clonal-multiplexing of live microscopy-based assays.
  13. KRAS mutant-driven SUMOylation controls extracellular vesicle transmission to trigger lymphangiogenesis in pancreatic cancer.
  14. Metabolic diversity drives cancer cell invasion.
  15. Actomyosin contractility requirements and reciprocal cell-tissue mechanics for cancer cell invasion through collagen-based channels.
  16. Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors.
  17. Telomere length and epigenetic clocks as markers of cellular aging: a comparative study.
  18. Individualized discovery of rare cancer drivers in global network context.
  19. Emerging mechanisms of telomerase reactivation in cancer.
  20. Biophysical physiology of phosphoinositide rapid dynamics and regulation in living cells.
  21. Ambra1 deficiency impairs mitophagy in skeletal muscle.
  22. Balance of osmotic pressures determines the nuclear-to-cytoplasmic volume ratio of the cell.
  23. Technological and computational advances driving high-throughput oncology.
  24. Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells.
  25. Neoadjuvant chemotherapy with or without radiotherapy versus upfront surgery for resectable pancreatic adenocarcinoma: a meta-analysis of randomized clinical trials.
  26. Pyruvate kinase M1 suppresses development and progression of prostate adenocarcinoma.
  27. Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion.
  28. Mitochondrial complex complexification.
  29. Proton-gated anion transport governs macropinosome shrinkage.
  30. Effect of reversible osmotic stress on live cell plasma membranes, probed via Laurdan general polarization measurements.
  31. Lymph node colonization and metastasis.
  32. Visualizing Scar Development Using SCAD Assay - An Ex-situ Skin Scarring Assay.
  33. Osmotic stress activates RIPK3/MLKL-mediated necroptosis by increasing cytosolic pH through a plasma membrane Na+/H+ exchanger.
  34. Calorie restriction and calorie dilution have different impacts on body fat, metabolism, behavior, and hypothalamic gene expression.
  35. Deep Visual Proteomics defines single-cell identity and heterogeneity.
  36. Diet-responsive transcriptional regulation of insulin in a single neuron controls systemic metabolism.
  37. Interleukin 6/gp130 axis promotes neural invasion in pancreatic cancer.
  38. Mitochondrial calcium uniporter stabilization preserves energetic homeostasis during Complex I impairment.
  39. Transcriptional control of energy metabolism by nuclear receptors.
  40. Plasticity Enables Cooperation among Heterogeneous Cancer Cell Populations to Support Metastatic Fitness.
  41. Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model.
  42. Epithelial cells adapt to curvature induction via transient active osmotic swelling.
  43. Dynamic human liver proteome atlas reveals functional insights into disease pathways.
  1. Nature. 2022 May 18.
    PHGDH heterogeneity potentiates cancer cell dissemination and metastasis.
    Matteo Rossi, Patricia Altea-Manzano, Margherita Demicco, Ginevra Doglioni, Laura Bornes, Marina Fukano, Anke Vandekeere, Alejandro M Cuadros, Juan Fernández-García, Carla Riera-Domingo, Cristina Jauset, Mélanie Planque, H Furkan Alkan, David Nittner, Dongmei Zuo, Lindsay A Broadfield, Sweta Parik, Antonino Alejandro Pane, Francesca Rizzollo, Gianmarco Rinaldi, Tao Zhang, Shao Thing Teoh, Arin B Aurora, Panagiotis Karras, Ines Vermeire, Dorien Broekaert, Joke Van Elsen, Maximilian M L Knott, Martin F Orth, Sofie Demeyer, Guy Eelen, Lacey E Dobrolecki, Ayse Bassez, Thomas Van Brussel, Karl Sotlar, Michael T Lewis, Harald Bartsch, Manfred Wuhrer, Peter van Veelen, Peter Carmeliet, Jan Cools, Sean J Morrison, Jean-Christophe Marine, Diether Lambrechts, Massimiliano Mazzone, Gregory J Hannon, Sophia Y Lunt, Thomas G P Grünewald, Morag Park, Jacco van Rheenen, Sarah-Maria Fendt.
      Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs1. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process2,3. Metabolic heterogeneity has also been observed4, yet its role in cancer progression is less explored. Here we find that the loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumours of patients with breast cancer is associated with decreased metastasis-free survival time. In mice, circulating tumour cells and early metastatic lesions are enriched with Phgdhlow cancer cells, and silencing Phgdh in primary tumours increases metastasis formation. Mechanistically, Phgdh interacts with the glycolytic enzyme phosphofructokinase, and the loss of this interaction activates the hexosamine-sialic acid pathway, which provides precursors for protein glycosylation. As a consequence, aberrant protein glycosylation occurs, including increased sialylation of integrin αvβ3, which potentiates cell migration and invasion. Inhibition of sialylation counteracts the metastatic ability of Phgdhlow cancer cells. In conclusion, although the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumours could be considered a sign of tumour aggressiveness.
    DOI:  https://doi.org/10.1038/s41586-022-04758-2
  2. Nat Commun. 2022 May 16. 13(1): 2698
    Purine nucleotide depletion prompts cell migration by stimulating the serine synthesis pathway.
    Mona Hoseini Soflaee, Rushendhiran Kesavan, Umakant Sahu, Alpaslan Tasdogan, Elodie Villa, Zied Djabari, Feng Cai, Diem H Tran, Hieu S Vu, Eunus S Ali, Halie Rion, Brendan P O'Hara, Sherwin Kelekar, James Hughes Hallett, Misty Martin, Thomas P Mathews, Peng Gao, John M Asara, Brendan D Manning, Issam Ben-Sahra, Gerta Hoxhaj.
      Purine nucleotides are necessary for various biological processes related to cell proliferation. Despite their importance in DNA and RNA synthesis, cellular signaling, and energy-dependent reactions, the impact of changes in cellular purine levels on cell physiology remains poorly understood. Here, we find that purine depletion stimulates cell migration, despite effective reduction in cell proliferation. Blocking purine synthesis triggers a shunt of glycolytic carbon into the serine synthesis pathway, which is required for the induction of cell migration upon purine depletion. The stimulation of cell migration upon a reduction in intracellular purines required one-carbon metabolism downstream of de novo serine synthesis. Decreased purine abundance and the subsequent increase in serine synthesis triggers an epithelial-mesenchymal transition (EMT) and, in cancer models, promotes metastatic colonization. Thus, reducing the available pool of intracellular purines re-routes metabolic flux from glycolysis into de novo serine synthesis, a metabolic change that stimulates a program of cell migration.
    DOI:  https://doi.org/10.1038/s41467-022-30362-z
  3. Nature. 2022 May 19.
    Neoantigen quality predicts immunoediting in survivors of pancreatic cancer.
    Marta Łuksza, Zachary M Sethna, Luis A Rojas, Jayon Lihm, Barbara Bravi, Yuval Elhanati, Kevin Soares, Masataka Amisaki, Anton Dobrin, David Hoyos, Pablo Guasp, Abderezak Zebboudj, Rebecca Yu, Adrienne Kaya Chandra, Theresa Waters, Zagaa Odgerel, Joanne Leung, Rajya Kappagantula, Alvin Makohon-Moore, Amber Johns, Anthony Gill, Mathieu Gigoux, Jedd Wolchok, Taha Merghoub, Michel Sadelain, Erin Patterson, Remi Monasson, Thierry Mora, Aleksandra M Walczak, Simona Cocco, Christine Iacobuzio-Donahue, Benjamin D Greenbaum, Vinod P Balachandran.
      Cancer immunoediting1 is a hallmark of cancer2 that predicts that lymphocytes kill more immunogenic cancer cells to cause less immunogenic clones to dominate a population. Although proven in mice1,3, whether immunoediting occurs naturally in human cancers remains unclear. Here, to address this, we investigate how 70 human pancreatic cancers evolved over 10 years. We find that, despite having more time to accumulate mutations, rare long-term survivors of pancreatic cancer who have stronger T cell activity in primary tumours develop genetically less heterogeneous recurrent tumours with fewer immunogenic mutations (neoantigens). To quantify whether immunoediting underlies these observations, we infer that a neoantigen is immunogenic (high-quality) by two features-'non-selfness'  based on neoantigen similarity to known antigens4,5, and 'selfness'  based on the antigenic distance required for a neoantigen to differentially bind to the MHC or activate a T cell compared with its wild-type peptide. Using these features, we estimate cancer clone fitness as the aggregate cost of T cells recognizing high-quality neoantigens offset by gains from oncogenic mutations. With this model, we predict the clonal evolution of tumours to reveal that long-term survivors of pancreatic cancer develop recurrent tumours with fewer high-quality neoantigens. Thus, we submit evidence that that the human immune system naturally edits neoantigens. Furthermore, we present a model to predict how immune pressure induces cancer cell populations to evolve over time. More broadly, our results argue that the immune system fundamentally surveils host genetic changes to suppress cancer.
    DOI:  https://doi.org/10.1038/s41586-022-04735-9
  4. Aging (Albany NY). 2022 May 16. 14(undefined):
    Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence.
    Ryan Wallis, Deborah Milligan, Bethany Hughes, Hannah Mizen, José Alberto López-Domínguez, Ugochim Eduputa, Eleanor J Tyler, Manuel Serrano, Cleo L Bishop.
      Senescence occurs in response to a number of damaging stimuli to limit oncogenic transformation and cancer development. As no single, universal senescence marker has been discovered, the confident classification of senescence induction requires the parallel assessment of a series of hallmarks. Therefore, there is a growing need for "first-pass" tools of senescence identification to streamline experimental workflows and complement conventional markers. Here, we utilise a high content, multidimensional phenotypic profiling-based approach, to assess the morphological profiles of senescent cells induced via a range of stimuli. In the context of senescence, we refer to these as senescence-associated morphological profiles (SAMPs), as they facilitate distinction between senescent and proliferating cells. The complexity of the profiles generated also allows exploration of the heterogeneity both between models of senescence and within an individual senescence model, providing a level of insight at the single cell level. Furthermore, we also demonstrate that these models are applicable to the assessment of senescence in vivo, which remains a key challenge for the field. Therefore, we believe SAMPs has the potential to serve as a useful addition in the repertoire of senescence researchers, either as a first-pass tool or as part of the established senescence hallmarks.
    Keywords:  high content profiling of senescence hallmarks; morphology; senescence; senescence-associated morphological profiles (SAMPs)
    DOI:  https://doi.org/10.18632/aging.204072
  5. Sci Adv. 2022 May 20. 8(20): eabm8786
    Suppression of nuclear GSK3 signaling promotes serine/one-carbon metabolism and confers metabolic vulnerability in lung cancer cells.
    Long He, Jennifer Endress, Sungyun Cho, Zhongchi Li, Yuxiang Zheng, John M Asara, John Blenis.
      Serine/one-carbon metabolism provides critical resources for nucleotide biosynthesis and epigenetic maintenance and is thus necessary in cancer cell growth, although the detailed regulatory mechanisms remain unclear. We uncover a critical role of glycogen synthase kinase 3 (GSK3) in regulating the expression of serine/one-carbon metabolic enzymes. Nuclear enrichment of GSK3 significantly suppresses genes that mediate de novo serine synthesis, including PHGDH, PSAT1, PSPH, and one-carbon metabolism, including SHMT2 and MTHFD2. FRAT1 promotes nuclear exclusion of GSK3, enhances serine/one-carbon metabolism, and, as a result, confers cell vulnerability to inhibitors that target this metabolic process such as SHIN1, a specific SHMT1/2 inhibitor. Furthermore, pharmacological or genetic suppression of GSK3 promotes serine/one-carbon metabolism and exhibits a significant synergistic effect in combination with SHIN1 in suppressing cancer cell proliferation in cultured cells and in vivo. Our observations indicate that inhibition of nuclear GSK3 signaling creates a vulnerability, which results in enhanced efficacy of serine/one-carbon metabolism inhibitors for the treatment of cancer.
    DOI:  https://doi.org/10.1126/sciadv.abm8786
  6. Trends Cell Biol. 2022 May 16. pii: S0962-8924(22)00108-8. [Epub ahead of print]
    Reflected stemness as a potential driver of the tumour microenvironment.
    Felipe S Rodrigues, Francesca D Ciccarelli, Ilaria Malanchi.
      A fundamental requirement for cancer initiation is the activation of developmental programmes by mutant cells. Oncogenic signals often confer an undifferentiated, stem cell-like phenotype that supports the long-term proliferative potential of cancer cells. Although cancer is a genetically driven disease, mutations in cancer-driver genes alone are insufficient for tumour formation, and the proliferation of cells harbouring oncogenic mutations depends on their microenvironment. In this Opinion article we discuss how the reprogrammed status of cancer cells not only represents the essence of their tumorigenicity but triggers 'reflected stemness' in their surrounding normal counterparts. We propose that this reciprocal interaction underpins the establishment of the tumour microenvironment (TME).
    Keywords:  cancer drivers; metastasis; stem cells; tissue regeneration; tumour microenvironment
    DOI:  https://doi.org/10.1016/j.tcb.2022.04.007
  7. Trends Cell Biol. 2022 May 14. pii: S0962-8924(22)00107-6. [Epub ahead of print]
    A CRISPR view on autophagy.
    Jin Rui Liang, Jacob E Corn.
      Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
    Keywords:  CRISPR; autophagy; functional genomics; genome-wide screens; organellophagy
    DOI:  https://doi.org/10.1016/j.tcb.2022.04.006
  8. Cell Res. 2022 May 19.
    Cytoskeleton grows p62 condensates for autophagy.
    Nobuo N Noda.
      
    DOI:  https://doi.org/10.1038/s41422-022-00671-5
  9. Front Cell Dev Biol. 2022 ;10 910640
    Phase Separation in Regulation of Autophagy.
    Yi Lu, Chunmei Chang.
      
    Keywords:  autophagosome formation; autophagy; autophagy substrate; cargo receptor; phase separation; selective autophagy
    DOI:  https://doi.org/10.3389/fcell.2022.910640
  10. Nat Commun. 2022 May 19. 13(1): 2800
    Different hotspot p53 mutants exert distinct phenotypes and predict outcome of colorectal cancer patients.
    Ori Hassin, Nishanth Belugali Nataraj, Michal Shreberk-Shaked, Yael Aylon, Rona Yaeger, Giulia Fontemaggi, Saptaparna Mukherjee, Martino Maddalena, Adi Avioz, Ortal Iancu, Giuseppe Mallel, Anat Gershoni, Inna Grosheva, Ester Feldmesser, Shifra Ben-Dor, Ofra Golani, Ayal Hendel, Giovanni Blandino, David Kelsen, Yosef Yarden, Moshe Oren.
      The TP53 gene is mutated in approximately 60% of all colorectal cancer (CRC) cases. Over 20% of all TP53-mutated CRC tumors carry missense mutations at position R175 or R273. Here we report that CRC tumors harboring R273 mutations are more prone to progress to metastatic disease, with decreased survival, than those with R175 mutations. We identify a distinct transcriptional signature orchestrated by p53R273H, implicating activation of oncogenic signaling pathways and predicting worse outcome. These features are shared also with the hotspot mutants p53R248Q and p53R248W. p53R273H selectively promotes rapid CRC cell spreading, migration, invasion and metastasis. The transcriptional output of p53R273H is associated with preferential binding to regulatory elements of R273 signature genes. Thus, different TP53 missense mutations contribute differently to cancer progression. Elucidation of the differential impact of distinct TP53 mutations on disease features may make TP53 mutational information more actionable, holding potential for better precision-based medicine.
    DOI:  https://doi.org/10.1038/s41467-022-30481-7
  11. Nature. 2022 May 18.
    Intracellular lipid surveillance by small G protein geranylgeranylation.
    Abigail Watterson, Lexus Tatge, Naureen Wajahat, Sonja L B Arneaud, Rene Solano Fonseca, Shaghayegh T Beheshti, Patrick Metang, Melina Mihelakis, Kielen R Zuurbier, Chase D Corley, Ishmael Dehghan, Jeffrey G McDonald, Peter M Douglas.
      Imbalances in lipid homeostasis can have deleterious effects on health1,2. Yet how cells sense metabolic demand due to lipid depletion and respond by increasing nutrient absorption remains unclear. Here we describe a mechanism for intracellular lipid surveillance in Caenorhabditis elegans that involves transcriptional inactivation of the nuclear hormone receptor NHR-49 through its cytosolic sequestration to endocytic vesicles via geranylgeranyl conjugation to the small G protein RAB-11.1. Defective de novo isoprenoid synthesis caused by lipid depletion limits RAB-11.1 geranylgeranylation, which promotes nuclear translocation of NHR-49 and activation of rab-11.2 transcription to enhance transporter residency at the plasma membrane. Thus, we identify a critical lipid sensed by the cell, its conjugated G protein, and the nuclear receptor whose dynamic interactions enable cells to sense metabolic demand due to lipid depletion and respond by increasing nutrient absorption and lipid metabolism.
    DOI:  https://doi.org/10.1038/s41586-022-04729-7
  12. Nat Commun. 2022 May 18. 13(1): 2725
    Visual barcodes for clonal-multiplexing of live microscopy-based assays.
    Tom Kaufman, Erez Nitzan, Nir Firestein, Miriam Bracha Ginzberg, Seshu Iyengar, Nish Patel, Rotem Ben-Hamo, Ziv Porat, Jaryd Hunter, Andreas Hilfinger, Varda Rotter, Ran Kafri, Ravid Straussman.
      While multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop visual barcodes that discriminate the clonal identity of single cells by different fluorescent proteins that are targeted to specific subcellular locations. We demonstrate that deconvolution of these barcodes is highly accurate and robust to many cellular perturbations. We then use visual barcodes to generate 'Signalome' cell-lines by mixing 12 clones of different live reporters into a single population, allowing simultaneous monitoring of the activity in 12 branches of signaling, at clonal resolution, over time. Using the 'Signalome' we identify two distinct clusters of signaling pathways that balance growth and proliferation, emphasizing the importance of growth homeostasis as a central organizing principle in cancer signaling. The ability to multiplex samples in live imaging applications, both in vitro and in vivo may allow better high-content characterization of complex biological systems.
    DOI:  https://doi.org/10.1038/s41467-022-30008-0
  13. J Clin Invest. 2022 May 17. pii: e157644. [Epub ahead of print]
    KRAS mutant-driven SUMOylation controls extracellular vesicle transmission to trigger lymphangiogenesis in pancreatic cancer.
    Yuming Luo, Zhihua Li, Yao Kong, Wang He, Hanhao Zheng, Mingjie An, Yan Lin, Dingwen Zhang, Jiabin Yang, Yue Zhao, Changhao Chen, Rufu Chen.
      Lymph node (LN) metastasis occurs frequently in pancreatic ductal adenocarcinoma (PDAC) and predicts poor prognosis for patients. The KRASG12D mutation confers an aggressive PDAC phenotype that is susceptible to lymphatic dissemination. However, the regulatory mechanism underlying KRASG12D mutation-driven LN metastasis in PDAC remains unclear. Herein, we identified that PDAC with KRASG12D mutation (KRASG12D PDAC) sustained extracellular vesicle (EV)-mediated transmission of hnRNPA1 in a SUMOylation-dependent manner and promoted lymphangiogenesis and LN metastasis in vitro and in vivo. Mechanistically, hnRNPA1 bound with SUMO2 at the lysine 113 residue via KRASG12D-induced hyperactivation of SUMOylation, which enabled its interaction with TSG101 to enhance hnRNPA1 packaging and transmission via EVs. Subsequently, SUMOylation induced EV-packaged hnRNPA1 anchoring to the adenylate and uridylate-rich elements of PROX1 in lymphatic endothelial cells, thus stabilizing PROX1 mRNA. Importantly, impeding SUMOylation of EV-packaged hnRNPA1 dramatically inhibited LN metastasis of KRASG12D PDAC in a genetically engineered KrasG12D/+; Trp53R172H/+; Pdx-1-Cre (KPC) mice model. Our findings highlight the mechanism by which KRAS mutant-driven SUMOylation triggers EV-packaged hnRNPA1 transmission to promote lymphangiogenesis and LN metastasis, shedding light on the potential application of hnRNPA1 as a therapeutic target in patients with KRASG12D PDAC.
    Keywords:  Cancer; Lymph; Molecular biology; Oncology
    DOI:  https://doi.org/10.1172/JCI157644
  14. Nature. 2022 May 18.
    Metabolic diversity drives cancer cell invasion.
    Sanjeethan C Baksh, Lydia W S Finley.
      
    Keywords:  Cancer; Medical research; Metabolism
    DOI:  https://doi.org/10.1038/d41586-022-01301-1
  15. Eur Phys J E Soft Matter. 2022 May 16. 45(5): 48
    Actomyosin contractility requirements and reciprocal cell-tissue mechanics for cancer cell invasion through collagen-based channels.
    Lianne Beunk, Gert-Jan Bakker, Diede van Ens, Jeroen Bugter, Floris Gal, Martin Svoren, Peter Friedl, Katarina Wolf.
      The interstitial tumor microenvironment is composed of heterogeneously organized collagen-rich porous networks as well as channel-like structures and interfaces which provide both barriers and guidance for invading cells. Tumor cells invading 3D random porous collagen networks depend upon actomyosin contractility to deform and translocate the nucleus, whereas Rho/Rho-associated kinase-dependent contractility is largely dispensable for migration in stiff capillary-like confining microtracks. To investigate whether this dichotomy of actomyosin contractility dependence also applies to physiological, deformable linear collagen environments, we developed nearly barrier-free collagen-scaffold microtracks of varying cross section using two-photon laser ablation. Both very narrow and wide tracks supported single-cell migration by either outward pushing of collagen up to four times when tracks were narrow, or cell pulling on collagen walls down to 50% of the original diameter by traction forces of up to 40 nN when tracks were wide, resulting in track widths optimized to single-cell diameter. Targeting actomyosin contractility by synthetic inhibitors increased cell elongation and nuclear shape change in narrow tracks and abolished cell-mediated deformation of both wide and narrow tracks. Accordingly, migration speeds in all channel widths reduced, with migration rates of around 45-65% of the original speed persisting. Together, the data suggest that cells engage actomyosin contraction to reciprocally adjust both own morphology and linear track width to optimal size for effective cellular locomotion.
    DOI:  https://doi.org/10.1140/epje/s10189-022-00182-6
  16. Elife. 2022 May 16. pii: e75526. [Epub ahead of print]11
    Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors.
    Gökçe Senger, Stefano Santaguida, Martin H Schaefer.
      Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole-chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic and proteomic data from hundreds of TCGA/CPTAC tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observe that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-translational control and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.
    Keywords:  cancer biology; computational biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.75526
  17. Geroscience. 2022 May 18.
    Telomere length and epigenetic clocks as markers of cellular aging: a comparative study.
    Emily E Pearce, Rotana Alsaggaf, Shilpa Katta, Casey Dagnall, Geraldine Aubert, Belynda D Hicks, Stephen R Spellman, Sharon A Savage, Steve Horvath, Shahinaz M Gadalla.
      Telomere length (TL) and DNA methylation-based epigenetic clocks are markers of biological age, but the relationship between the two is not fully understood. Here, we used multivariable regression models to evaluate the relationships between leukocyte TL (LTL; measured by qPCR [n = 635] or flow FISH [n = 144]) and five epigenetic clocks (Hannum, DNAmAge pan-tissue, PhenoAge, SkinBlood, or GrimAge clocks), or their epigenetic age acceleration measures in healthy adults (age 19-61 years). LTL showed statistically significant negative correlations with all clocks (qPCR: r =  - 0.26 to - 0.32; flow FISH: r =  - 0.34 to - 0.49; p < 0.001 for all). Yet, models adjusted for age, sex, and race revealed significant associations between three of five clocks (PhenoAge, GrimAge, and Hannum clocks) and LTL by flow FISH (p < 0.01 for all) or qPCR (p < 0.001 for all). Significant associations between age acceleration measures for the same three clocks and qPCR or flow FISH TL were also found (p < 0.01 for all). Additionally, LTL (by qPCR or flow FISH) showed significant associations with extrinsic epigenetic age acceleration (EEAA: p < 0.0001 for both), but not intrinsic epigenetic age acceleration (IEAA; p > 0.05 for both). In conclusion, the relationships between LTL and epigenetic clocks were limited to clocks reflecting phenotypic age. The observed association between LTL and EEAA reflects the ability of both measures to detect immunosenescence. The observed modest correlations between LTL and epigenetic clocks highlight a possible benefit from incorporating both measures in understanding disease etiology and prognosis.
    Keywords:  Epigenetic clocks; Methylation age; Telomere length
    DOI:  https://doi.org/10.1007/s11357-022-00586-4
  18. Elife. 2022 May 20. pii: e74010. [Epub ahead of print]11
    Individualized discovery of rare cancer drivers in global network context.
    Iurii Petrov, Andrey Alexeyenko.
      Late advances in genome sequencing expanded the space of known cancer driver genes several-fold. However, most of this surge was based on computational analysis of somatic mutation frequencies and/or their impact on the protein function. On the contrary, experimental research necessarily accounted for functional context of mutations interacting with other genes and conferring cancer phenotypes. Eventually, just such results become 'hard currency' of cancer biology. The new method, NEAdriver employs knowledge accumulated thus far in the form of global interaction network and functionally annotated pathways in order to recover known and predict novel driver genes. The driver discovery was individualized by accounting for mutations' co-occurrence in each tumour genome - as an alternative to summarizing information over the whole cancer patient cohorts. For each somatic genome change, probabilistic estimates from two lanes of network analysis were combined into joint likelihoods of being a driver. Thus, ability to detect previously unnoticed candidate driver events emerged from combining individual genomic context with network perspective. The procedure was applied to ten largest cancer cohorts followed by evaluating error rates against previous cancer gene sets. The discovered driver combinations were shown to be informative on cancer outcome. This revealed driver genes with individually sparse mutation patterns that would not be detectable by other computational methods and related to cancer biology domains poorly covered by previous analyses. In particular, recurrent mutations of collagen, laminin, and integrin genes were observed in the adenocarcinoma and glioblastoma cancers. Considering constellation patterns of candidate drivers in individual cancer genomes opens a novel avenue for personalized cancer medicine.
    Keywords:  cancer biology; computational biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.74010
  19. Trends Cancer. 2022 May 11. pii: S2405-8033(22)00071-1. [Epub ahead of print]
    Emerging mechanisms of telomerase reactivation in cancer.
    Shalu Sharma, Shantanu Chowdhury.
      Mutations in the promoter of human telomerase reverse transcriptase (hTERT) result in hyperactivation of hTERT. Notably, all mutations are G>A transitions, frequently found in a wide range of cancer types, and causally associated with cancer progression. Initially, the mutations were understood to reactivate hTERT by generating novel E26 transformation-specific (ETS) binding sites. Recent work reveals the role of DNA secondary structure G-quadruplexes, telomere binding factor(s), and chromatin looping in hTERT regulation. Here, we discuss these emerging findings in relation to the clinically significant promoter mutations to provide a broader understanding of the context-dependent outcomes that result in hTERT activation in normal and pathogenic conditions.
    Keywords:  ETS; G-quadruplex; GABPA/B; TRF2; cancer; chromosome looping; epigenetics; glioblastoma; hTERT; melanoma; telomerase; telomere; telomere looping
    DOI:  https://doi.org/10.1016/j.trecan.2022.03.005
  20. J Gen Physiol. 2022 Jun 06. pii: e202113074. [Epub ahead of print]154(6):
    Biophysical physiology of phosphoinositide rapid dynamics and regulation in living cells.
    Jill B Jensen, Bjoern H Falkenburger, Eamonn J Dickson, Lizbeth de la Cruz, Gucan Dai, Jongyun Myeong, Seung-Ryoung Jung, Martin Kruse, Oscar Vivas, Byung-Chang Suh, Bertil Hille.
      Phosphoinositide membrane lipids are ubiquitous low-abundance signaling molecules. They direct many physiological processes that involve ion channels, membrane identification, fusion of membrane vesicles, and vesicular endocytosis. Pools of these lipids are continually broken down and refilled in living cells, and the rates of some of these reactions are strongly accelerated by physiological stimuli. Recent biophysical experiments described here measure and model the kinetics and regulation of these lipid signals in intact cells. Rapid on-line monitoring of phosphoinositide metabolism is made possible by optical tools and electrophysiology. The experiments reviewed here reveal that as for other cellular second messengers, the dynamic turnover and lifetimes of membrane phosphoinositides are measured in seconds, controlling and timing rapid physiological responses, and the signaling is under strong metabolic regulation. The underlying mechanisms of this metabolic regulation remain questions for the future.
    DOI:  https://doi.org/10.1085/jgp.202113074
  21. J Cachexia Sarcopenia Muscle. 2022 May 20.
    Ambra1 deficiency impairs mitophagy in skeletal muscle.
    Lisa Gambarotto, Samuele Metti, Martina Chrisam, Cristina Cerqua, Patrizia Sabatelli, Andrea Armani, Carlo Zanon, Marianna Spizzotin, Silvia Castagnaro, Flavie Strappazzon, Paolo Grumati, Matilde Cescon, Paola Braghetta, Eva Trevisson, Francesco Cecconi, Paolo Bonaldo.
      BACKGROUND: Maintaining healthy mitochondria is mandatory for muscle viability and function. An essential surveillance mechanism targeting defective and harmful mitochondria to degradation is the selective form of autophagy called mitophagy. Ambra1 is a multifaceted protein with well-known autophagic and mitophagic functions. However, the study of its role in adult tissues has been extremely limited due to the embryonic lethality caused by full-body Ambra1 deficiency.METHODS: To establish the role of Ambra1 as a positive regulator of mitophagy, we exploited in vivo overexpression of a mitochondria-targeted form of Ambra1 in skeletal muscle. To dissect the consequence of Ambra1 inactivation in skeletal muscle, we generated muscle-specific Ambra1 knockout (Ambra1fl/fl :Mlc1f-Cre) mice. Mitochondria-enriched fractions were obtained from muscles of fed and starved animals to investigate the dynamics of the mitophagic flux.
    RESULTS: Our data show that Ambra1 has a critical role in the mitophagic flux of adult murine skeletal muscle and that its genetic inactivation leads to mitochondria alterations and myofibre remodelling. Ambra1 overexpression in wild-type muscles is sufficient to enhance mitochondria clearance through the autophagy-lysosome system. Consistently with this, Ambra1-deficient muscles display an abnormal accumulation of the mitochondrial marker TOMM20 by +76% (n = 6-7; P < 0.05), a higher presence of myofibres with swollen mitochondria by +173% (n = 4; P < 0.05), and an alteration in the maintenance of the mitochondrial membrane potential and a 34% reduction in the mitochondrial respiratory complex I activity (n = 4; P < 0.05). Lack of Ambra1 in skeletal muscle leads to impaired mitophagic flux, without affecting the bulk autophagic process. This is due to a significantly decreased recruitment of DRP1 (n = 6-7 mice; P < 0.01) and Parkin (n = 6-7 mice; P < 0.05) to the mitochondrial compartment, when compared with controls. Ambra1-deficient muscles also show a marked dysregulation of the endolysosome compartment, as the incidence of myofibres with lysosomal accumulation is 20 times higher than wild-type muscles (n = 4; P < 0.05). Histologically, Ambra1-deficient muscles of both 3- and 6-month-old animals display a significant decrease of myofibre cross-sectional area and a 52% reduction in oxidative fibres (n = 6-7; P < 0.05), thus highlighting a role for Ambra1 in the proper structure and activity of skeletal muscle.
    CONCLUSIONS: Our study indicates that Ambra1 is critical for skeletal muscle mitophagy and for the proper maintenance of functional mitochondria.
    Keywords:  Ambra1; Mitochondria; Mitophagy; Skeletal muscle
    DOI:  https://doi.org/10.1002/jcsm.13010
  22. Proc Natl Acad Sci U S A. 2022 May 24. 119(21): e2118301119
    Balance of osmotic pressures determines the nuclear-to-cytoplasmic volume ratio of the cell.
    Dan Deviri, Samuel A Safran.
      SignificanceFor over a century, it has been known that the ratio of the nuclear and cytoplasm volumes (NC ratio), rather than the separate volumes, is constant among cells of many types of organisms. Changes of the NC ratio are associated with cancerous transformations, suggesting that the ratio has physiological importance. Notably, the dominant regulatory mechanism of the NC ratio has not been identified. Here, we use physical estimates of the forces implicated in nuclear volume determination and show that they are dominated by the osmotic pressure of actively transported proteins. Inspired by this, we formulate a minimal model for the cytoplasmic and nuclear volumes that predicts the NC ratio and the factors that modulate it, in agreement with published experiments.
    Keywords:  biological physics; mechanobiology; nuclear volume
    DOI:  https://doi.org/10.1073/pnas.2118301119
  23. Trends Cell Biol. 2022 May 13. pii: S0962-8924(22)00109-X. [Epub ahead of print]
    Technological and computational advances driving high-throughput oncology.
    Leonie Kolmar, Alexis Autour, Xiaoli Ma, Blandine Vergier, Federica Eduati, Christoph A Merten.
      Engineering and computational advances have opened many new avenues in cancer research, particularly when being exploited in interdisciplinary approaches. For example, the combination of microfluidics, novel sequencing technologies, and computational analyses has been crucial to enable single-cell assays, giving a detailed picture of tumor heterogeneity for the very first time. In a similar way, these 'tech' disciplines have been elementary for generating large data sets in multidimensional cancer 'omics' approaches, cell-cell interaction screens, 3D tumor models, and tissue level analyses. In this review we summarize the most important technology and computational developments that have been or will be instrumental for transitioning classical cancer research to a large data-driven, high-throughput, high-content discipline across all biological scales.
    Keywords:  computational tools; microfluidics; personalized oncology; sequencing; single-cell multi-omics
    DOI:  https://doi.org/10.1016/j.tcb.2022.04.008
  24. Gut. 2022 May 13. pii: gutjnl-2021-325811. [Epub ahead of print]
    Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells.
    Gabriele Alfarano, Matteo Audano, Pierluigi Di Chiaro, Chiara Balestrieri, Marta Milan, Sara Polletti, Paola Spaggiari, Alessandro Zerbi, Giuseppe Riccardo Diaferia, Nico Mitro, Gioacchino Natoli.
      OBJECTIVE: Pancreatic ductal adenocarcinomas (PDACs) include heterogeneous mixtures of low-grade cells forming pseudoglandular structures and compact nests of high-grade cells organised in non-glandular patterns. We previously reported that low-grade PDAC cells display high expression of interferon regulatory factor 1 (IRF1), a pivotal transcription factor of the interferon (IFN) system, suggesting grade-specific, cell-intrinsic activation of IFN responses. Here, we set out to determine the molecular bases and the functional impact of the activation of IFN-regulated responses in human PDACs.DESIGN: We first confirmed the correlation between glandular differentiation and molecular subtypes of PDAC on the one hand, and the expression of IRF1 and IFN-stimulated genes on the other. We next used unbiased omics approaches to systematically analyse basal and IFN-regulated responses in low-grade and high-grade PDAC cells, as well as the impact of IRF1 on gene expression programmes and metabolic profiles of PDAC cells.
    RESULTS: High-level expression of IRF1 in low-grade PDAC cells was controlled by endodermal lineage-determining transcription factors. IRF1-regulated gene expression equipped low-grade PDAC cells with distinctive properties related to antigen presentation and processing as well as responsiveness to IFN stimulation. Notably, IRF1 also controlled the characteristic metabolic profile of low-grade PDAC cells, suppressing both mitochondrial respiration and fatty acid synthesis, which may in part explain its growth-inhibiting activity.
    CONCLUSION: IRF1 links endodermal differentiation to the expression of genes controlling antigen presentation and processing as well as to the specification of the metabolic profile characteristic of classical PDAC cells.
    Keywords:  energy metabolism; gene expression; interferon; pancreatic cancer
    DOI:  https://doi.org/10.1136/gutjnl-2021-325811
  25. ESMO Open. 2022 May 14. pii: S2059-7029(22)00105-3. [Epub ahead of print]7(3): 100485
    Neoadjuvant chemotherapy with or without radiotherapy versus upfront surgery for resectable pancreatic adenocarcinoma: a meta-analysis of randomized clinical trials.
    I Ghanem, D Lora, N Herradón, G de Velasco, A Carretero-González, M Á Jiménez-Varas, P Vázquez de Parga, J Feliu.
      BACKGROUND: The role of neoadjuvant chemotherapy (NC) in resectable pancreatic cancer (RPC) has yet to be defined. This review aims to analyze the benefit of NC in RPC compared with upfront surgery (US) in terms of overall survival (OS) and disease-free survival (DFS).PATIENTS AND METHODS: PubMed, CENTRAL (The Cochrane Library), and Embase were systematically reviewed until 3 November 2021. Abstract proceedings and virtual meeting presentations from the American Society of Clinical Oncology and the European Society of Medical Oncology conferences, reference articles of published clinical trials, and review articles were considered. Only randomized clinical trials (RCTs) comparing NC administration with or without radiotherapy previous with surgery (experimental arm) versus US followed by adjuvant chemotherapy with or without radiotherapy (control arm) for RPC were included.
    RESULTS: A total of 1135 studies were screened. Of these, 1117 studies were primarily excluded. Of the remaining 18 studies, 5 were excluded because of no adequate trial design for this work and 7 others had no available results. Finally, 6 trials with 469 patients with pancreatic cancer randomized to NC (n = 212) or US (n = 257) were selected. Compared with US, NC significantly improved OS [hazard ratio (HR) 0.75; 95% confidence interval (CI) 0.58-0.98; P = 0.033] and DFS (HR 0.73; 95% CI 0.59-0.89; P = 0.002). While the NC approach was not significantly associated with lower resection rate [relative risk (RR) 0.92; 95% CI 0.84-1.01; P = 0.069], the R0 resection rate was significantly higher for NC than for US (RR 1.31; 95% CI 1.13-1.52; P = 0.0004).
    CONCLUSION: This is the first meta-analysis of RCTs showing that NC improves OS for RPC compared with US followed by adjuvant therapy. Ongoing RCTs should confirm these findings with FOLFIRINOX to generalize the indication of NC.
    Keywords:  meta-analysis; neoadjuvant; randomized clinical trials; resectable pancreatic cancer; upfront surgery
    DOI:  https://doi.org/10.1016/j.esmoop.2022.100485
  26. Cancer Res. 2022 May 18. pii: canres.CAN-21-2352-E.2021. [Epub ahead of print]
    Pyruvate kinase M1 suppresses development and progression of prostate adenocarcinoma.
    Shawn M Davdison, Daniel R Schmidt, Julia E Heyman, James P O'Brien, Amy C Liu, William J Israelsen, Talya L Dayton, Raghav Sehgal, Roderick T Bronson, Elizaveta Freinkman, Howard H Mak, Giuseppe Nicolo Fanelli, Scott Malstrom, Gary Bellinger, Arkaitz Carracedo, Pier Paolo Pandolfi, Kevin D Courtney, Abhishek Jha, Ronald A DePinho, James W Horner, Craig J Thomas, Lewis C Cantley, Massimo Loda, Matthew G Vander Heiden.
      Altered metabolisms helps sustain cancer cell proliferation and survival. Most cancers, including prostate cancers, express the M2 splice isoform of pyruvate kinase (Pkm2), which can support anabolic metabolism to support cell proliferation. However, Pkm2 expression is dispensable for the formation and growth of many cancers in vivo. Expression of pyruvate kinase isoform M1 (Pkm1) is restricted to relatively few tissues and has been reported to promote growth of select tumors, but the role of Pkm1 in cancer has been less studied than Pkm2. To test how differential expression of pyruvate kinase isoforms affects cancer initiation and progression, we generated mice harboring a conditional allele of Pkm1, and crossed these mice or those with a Pkm2 conditional allele with a Pten loss-driven prostate cancer model. Pkm1 loss led to increased Pkm2 expression and accelerated prostate cancer development, while Pkm2 deletion of led to increased Pkm1 expression and suppressed tumor progression. Metabolic profiling revealed altered nucleotide levels in tumors with high Pkm1 expression, and failure of these tumors to progress was associated with DNA replication stress and senescence. Consistent with these data, a small molecule pyruvate kinase activator that mimics a high activity Pkm1-like state suppressed progression of established prostate tumors. Analysis of human specimens showed PKM2 expression is retained in most human prostate cancers. Overall, this study uncovers a role for pyruvate kinase isoforms in prostate cancer initiation and progression, and argues that pharmacological pyruvate kinase activation may be beneficial for treating prostate cancer.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2352
  27. J Immunother Cancer. 2022 May;pii: e004337. [Epub ahead of print]10(5):
    Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion.
    Byong-Sop Song, Ji Sun Moon, Jingwen Tian, Ho Yeop Lee, Byeong Chang Sim, Seok-Hwan Kim, Seul Gi Kang, Jung Tae Kim, Ha Thi Nga, Rui Benfeitas, Yeongmin Kim, Sanghee Park, Robert R Wolfe, Hyuk Soo Eun, Minho Shong, Sunjae Lee, Il-Young Kim, Hyon-Seung Yi.
      BACKGROUND: Mitochondria are involved in cancer energy metabolism, although the mechanisms underlying the involvement of mitoribosomal dysfunction in hepatocellular carcinoma (HCC) remain poorly understood. Here, we investigated the effects of mitoribosomal impairment-mediated alterations on the immunometabolic characteristics of liver cancer.METHODS: We used a mouse model of HCC, liver tissues from patients with HCC, and datasets from The Cancer Genome Atlas (TCGA) to elucidate the relationship between mitoribosomal proteins (MRPs) and HCC. In a mouse model, we selectively disrupted expression of the mitochondrial ribosomal protein CR6-interacting factor 1 (CRIF1) in hepatocytes to determine the impact of hepatocyte-specific impairment of mitoribosomal function on liver cancer progression. The metabolism and immunophenotype of liver cancer was assessed by glucose flux assays and flow cytometry, respectively.
    RESULTS: Single-cell RNA-seq analysis of tumor tissue and TCGA HCC transcriptome analysis identified mitochondrial defects associated with high-MRP expression and poor survival outcomes. In the mouse model, hepatocyte-specific disruption of the mitochondrial ribosomal protein CRIF1 revealed the impact of mitoribosomal dysfunction on liver cancer progression. Crif1 deficiency promoted programmed cell death protein 1 expression by immune cells in the hepatic tumor microenvironment. A [U-13C6]-glucose tracer demonstrated enhanced glucose entry into the tricarboxylic acid cycle and lactate production in mice with mitoribosomal defects during cancer progression. Mice with hepatic mitoribosomal defects also exhibited enhanced progression of liver cancer accompanied by highly exhausted tumor-infiltrating T cells. Crif1 deficiency induced an environment unfavorable to T cells, leading to exhaustion of T cells via elevation of reactive oxygen species and lactate production.
    CONCLUSIONS: Hepatic mitoribosomal defects promote glucose partitioning toward glycolytic flux and lactate synthesis, leading to T cell exhaustion and cancer progression. Overall, the results suggest a distinct role for mitoribosomes in regulating the immunometabolic microenvironment during HCC progression.
    Keywords:  gene expression profiling; inflammation; liver neoplasms; lymphocytes, tumor-infiltrating
    DOI:  https://doi.org/10.1136/jitc-2021-004337
  28. Science. 2022 May 20. 376(6595): 794-795
    Mitochondrial complex complexification.
    Martijn A Huynen, Dei M Elurbe.
      Variation in complex composition provides clues about the function of individual subunits.
    DOI:  https://doi.org/10.1126/science.abq0368
  29. Nat Cell Biol. 2022 May 19.
    Proton-gated anion transport governs macropinosome shrinkage.
    Mariia Zeziulia, Sandy Blin, Franziska W Schmitt, Martin Lehmann, Thomas J Jentsch.
      Intracellular organelles change their size during trafficking and maturation. This requires the transport of ions and water across their membranes. Macropinocytosis, a ubiquitous form of endocytosis of particular importance for immune and cancer cells, generates large vacuoles that can be followed optically. Shrinkage of macrophage macropinosomes depends on TPC-mediated Na+ efflux and Cl- exit through unknown channels. Relieving osmotic pressure facilitates vesicle budding, positioning osmotic shrinkage upstream of vesicular sorting and trafficking. Here we identify the missing macrophage Cl- channel as the proton-activated Cl- channel ASOR/TMEM206. ASOR activation requires Na+-mediated depolarization and luminal acidification by redundant transporters including H+-ATPases and CLC 2Cl-/H+ exchangers. As corroborated by mathematical modelling, feedback loops requiring the steep voltage and pH dependencies of ASOR and CLCs render vacuole resolution resilient towards transporter copy numbers. TMEM206 disruption increased albumin-dependent survival of cancer cells. Our work suggests a function for the voltage and pH dependence of ASOR and CLCs, provides a comprehensive model for ion-transport-dependent vacuole maturation and reveals biological roles of ASOR.
    DOI:  https://doi.org/10.1038/s41556-022-00912-0
  30. Biophys J. 2022 May 19. pii: S0006-3495(22)00409-X. [Epub ahead of print]
    Effect of reversible osmotic stress on live cell plasma membranes, probed via Laurdan general polarization measurements.
    Elmer Zapata-Mercado, Evgenia V Azarova, Kalina Hristova.
      Here we seek to gain insight into changes in the plasma membrane of live cells upon the application of osmotic stress using Laurdan, a fluorescent probe that reports on membrane organization, hydration, and dynamics. It is known that the application of osmotic stress to lipid vesicles causes a decrease in Laurdan's generalized polarization (GP), which has been interpreted as an indication of membrane stretching. In cells, we see the opposite effects, as GP increases when the osmolarity of the solution is decreased. This increase in GP is associated with the presence of caveolae, which are known to disassemble and flatten in response to osmotic stress.
    DOI:  https://doi.org/10.1016/j.bpj.2022.05.016
  31. Sci Signal. 2022 May 17. 15(734): eadc9985
    Lymph node colonization and metastasis.
    Amy E Baek.
      Lymph nodes open an immune-tolerant pathway for metastasis.
    DOI:  https://doi.org/10.1126/scisignal.adc9985
  32. J Vis Exp. 2022 Apr 28.
    Visualizing Scar Development Using SCAD Assay - An Ex-situ Skin Scarring Assay.
    Pushkar Ramesh, Haifeng Ye, Bikram Dasgupta, Hans-Günther Machens, Yuval Rinkevich.
      The mammalian global response to sealing deep tissue wounds is through scar formation and tissue contraction, mediated by specialized fascia fibroblasts. Despite the clinical significance of scar formation and impaired wound healing, our understanding of fascia fibroblast dynamics in wound healing is cursory due to the lack of relevant assays that enable direct visualization of fibroblast choreography and dynamics in complex environments such as in skin wounds. This paper presents a protocol to generate ex- situ skin scars using SCAD or "SCar-like tissue in A Dish" that emulate the complex environment of skin wounds. In this assay, 2 mm full-thickness skin is excised and cultured upside down in media for 5 days, during which scars and skin contractures develop uniformly. This methodology, coupled with fibroblast-lineage specific transgenic mouse models, enables visualization of individual fibroblast lineages across the entire wound repair process. Overall, this protocol aids researchers in understanding fundamental processes and mechanisms of wound repair, directly exploring the effects of modulators on wound healing outcomes.
    DOI:  https://doi.org/10.3791/63808
  33. Sci Signal. 2022 May 17. 15(734): eabn5881
    Osmotic stress activates RIPK3/MLKL-mediated necroptosis by increasing cytosolic pH through a plasma membrane Na+/H+ exchanger.
    Wenbin Zhang, Weiliang Fan, Jia Guo, Xiaodong Wang.
      Necroptosis is a form of cell death triggered by stimuli such as the tumor necrosis factor family of cytokines, which induce necrotic cell death through the RIPK1-RIPK3-MLKL pathway. We report here that necroptosis is also activated by extracellular osmotic stresses. Unlike the previously identified inducers of necroptosis, osmotic stress stimulated necroptosis through the direct activation of the kinase activity of RIPK3 by an increase in cytosolic pH mediated by the Na+/H+ exchanger SLC9A1. Knockout, knockdown, or chemical inhibition of SLC9A1 blocked necroptosis induced by osmotic stresses. Moreover, setting intracellular pH at above-physiological values directly activated RIPK3 and necroptosis. The activation of RIPK3 by osmotic stresses did not require its RHIM domain, the protein-interacting domain required for the activation of RIPK3 when cells respond to other previously identified necroptotic stimuli. These results thus delineate a pathway that activates necroptosis in response to osmotic stresses.
    DOI:  https://doi.org/10.1126/scisignal.abn5881
  34. Cell Rep. 2022 May 17. pii: S2211-1247(22)00608-8. [Epub ahead of print]39(7): 110835
    Calorie restriction and calorie dilution have different impacts on body fat, metabolism, behavior, and hypothalamic gene expression.
    Xue Liu, Zengguang Jin, Stephanie Summers, Davina Derous, Min Li, Baoguo Li, Li Li, John R Speakman.
      Caloric restriction is a robust intervention to increase lifespan. Giving less food (calorie restriction [CR]) or allowing free access to a diluted diet with indigestible components (calorie dilution [CD]) are two methods to impose restriction. CD does not generate the same lifespan effect as CR. We compare responses of C57BL/6 mice with equivalent levels of CR and CD. The two groups have different responses in fat loss, circulating hormones, and metabolic rate. CR mice are hungrier, as assessed by behavioral assays. Although gene expression of Npy, Agrp, and Pomc do not differ between CR and CD groups, CR mice had a distinctive hypothalamic gene-expression profile with many genes related to starvation upregulated relative to CD. While both result in lower calorie intake, CR and CD are not equivalent procedures. Increased hunger under CR supports the hypothesis that hunger signaling is a key process mediating the benefits of CR.
    Keywords:  CP: Metabolism; behavior; body fat; caloric restriction; diluted diet; energy expenditure; hunger; hypothalamus; lifespan; metabolic effects; physical activity
    DOI:  https://doi.org/10.1016/j.celrep.2022.110835
  35. Nat Biotechnol. 2022 May 19.
    Deep Visual Proteomics defines single-cell identity and heterogeneity.
    Andreas Mund, Fabian Coscia, András Kriston, Réka Hollandi, Ferenc Kovács, Andreas-David Brunner, Ede Migh, Lisa Schweizer, Alberto Santos, Michael Bzorek, Soraya Naimy, Lise Mette Rahbek-Gjerdrum, Beatrice Dyring-Andersen, Jutta Bulkescher, Claudia Lukas, Mark Adam Eckert, Ernst Lengyel, Christian Gnann, Emma Lundberg, Peter Horvath, Matthias Mann.
      Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples.
    DOI:  https://doi.org/10.1038/s41587-022-01302-5
  36. PLoS Biol. 2022 May 20. 20(5): e3001655
    Diet-responsive transcriptional regulation of insulin in a single neuron controls systemic metabolism.
    Ava Handley, Qiuli Wu, Tessa Sherry, Rebecca Cornell, Roger Pocock.
      Metabolic homeostasis is coordinated through a robust network of signaling pathways acting across all tissues. A key part of this network is insulin-like signaling, which is fundamental for surviving glucose stress. Here, we show that Caenorhabditis elegans fed excess dietary glucose reduce insulin-1 (INS-1) expression specifically in the BAG glutamatergic sensory neurons. We demonstrate that INS-1 expression in the BAG neurons is directly controlled by the transcription factor ETS-5, which is also down-regulated by glucose. We further find that INS-1 acts exclusively from the BAG neurons, and not other INS-1-expressing neurons, to systemically inhibit fat storage via the insulin-like receptor DAF-2. Together, these findings reveal an intertissue regulatory pathway where regulation of insulin expression in a specific neuron controls systemic metabolism in response to excess dietary glucose.
    DOI:  https://doi.org/10.1371/journal.pbio.3001655
  37. Cancer Med. 2022 May 16.
    Interleukin 6/gp130 axis promotes neural invasion in pancreatic cancer.
    Hidetaka Suzuki, Shuichi Mitsunaga, Masafumi Ikeda, Takao Aoyama, Kazumi Yoshizawa, Masayuki Yamaguchi, Masami Suzuki, Minoru Narita, Toshikatsu Kawasaki, Atsushi Ochiai.
      BACKGROUND: Nerve invasion (N-inv) is an important prognostic factor in pancreatic ductal adenocarcinoma (PDAC). Elucidation of circulating N-inv stimulators could provide deeper insights and novel perspectives for PDAC therapy. The interleukin (IL)-6/gp130 axis was evaluated in this study as a candidate N-inv stimulator.METHODS: A human pancreatic cancer (PC) cell, Capan-1, was confirmed to have the stimulant activity of IL-6/gp130 axis through the evaluation of mRNA, cell surface protein and intracellular protein levels and chemotaxis and wound healing assay. The upregulation of IL-6/gp130 axis was evaluated using tumor-derived IL-6 level and intratumoral pSTAT3 expression in N-inv of murine sciatic nerves by intraneural injection of Capan-1 cell (N-inv model) and using resected pancreatic cancer tissue and clinical data from 46 PDAC patients.
    RESULTS: mRNA and protein expressions of IL-6 and IL-6 receptor were found in whole cell lysate and condition medium from PC cell. Cell surface protein expression of gp130 were clearly detected on PC cell. IL-6 promoted migration and chemotaxis of PC cell. Serum IL-6 and tumoral IL-6 mRNA levels in N-inv model mice were significantly higher than those in subcutaneous tumor mice (p = 0.004 and p = 0.002, respectively). Silencing of IL-6 and gp130 on PC cell and administration of an anti-IL-6 receptor antibody, tocilizumab, suppressed N-inv, compared to each control (p = 0.070, p = 0.118 and p = 0.122, respectively). In PDAC patients, the high-N-inv group showed poor prognosis (p =0.059) and elevated serum levels of IL-6 and C-reactive protein, synthesis of which is promoted by IL-6, compared to those in the low-N-inv group (p = 0.006 and p = 0.075, respectively). Tumoral gp130 expression at N-inv was higher than that in the primary pancreatic tumor (p = 0.026).
    CONCLUSION: Biological activity of IL-6/gp130 axis promoted N-inv in murine model and was upregulated in PDAC patients with severe N-inv. This study is the first evidence that the IL-6/gp130 axis offers a potential therapeutic target in PDAC with N-inv.
    Keywords:  mouse models; pancreatic cancer; pancreatic ductal adenocarcinoma; translational research
    DOI:  https://doi.org/10.1002/cam4.4823
  38. Nat Commun. 2022 May 19. 13(1): 2769
    Mitochondrial calcium uniporter stabilization preserves energetic homeostasis during Complex I impairment.
    Enrique Balderas, David R Eberhardt, Sandra Lee, John M Pleinis, Salah Sommakia, Anthony M Balynas, Xue Yin, Mitchell C Parker, Colin T Maguire, Scott Cho, Marta W Szulik, Anna Bakhtina, Ryan D Bia, Marisa W Friederich, Timothy M Locke, Johan L K Van Hove, Stavros G Drakos, Yasemin Sancak, Martin Tristani-Firouzi, Sarah Franklin, Aylin R Rodan, Dipayan Chaudhuri.
      Calcium entering mitochondria potently stimulates ATP synthesis. Increases in calcium preserve energy synthesis in cardiomyopathies caused by mitochondrial dysfunction, and occur due to enhanced activity of the mitochondrial calcium uniporter channel. The signaling mechanism that mediates this compensatory increase remains unknown. Here, we find that increases in the uniporter are due to impairment in Complex I of the electron transport chain. In normal physiology, Complex I promotes uniporter degradation via an interaction with the uniporter pore-forming subunit, a process we term Complex I-induced protein turnover. When Complex I dysfunction ensues, contact with the uniporter is inhibited, preventing degradation, and leading to a build-up in functional channels. Preventing uniporter activity leads to early demise in Complex I-deficient animals. Conversely, enhancing uniporter stability rescues survival and function in Complex I deficiency. Taken together, our data identify a fundamental pathway producing compensatory increases in calcium influx during Complex I impairment.
    DOI:  https://doi.org/10.1038/s41467-022-30236-4
  39. Nat Rev Mol Cell Biol. 2022 May 16.
    Transcriptional control of energy metabolism by nuclear receptors.
    Charlotte Scholtes, Vincent Giguère.
      Transcriptional regulation of catabolic pathways is a central mechanism by which cells respond to physiological cues to generate the energy required for anabolic pathways, transport of molecules and mechanical work. Nuclear receptors are members of a superfamily of transcription factors that transduce hormonal, nutrient, metabolite and redox signals into specific metabolic gene programmes, and thus hold a major status as regulators of cellular energy generation. Nuclear receptors also regulate the expression of genes involved in cellular processes that are implicated in energy production, including mitochondrial biogenesis and autophagy. Recent advances in genome-wide approaches have considerably expanded the repertoire of both nuclear receptors and metabolic genes under their direct transcriptional control. To fine-tune the expression of their target genes, nuclear receptors must act cooperatively with other transcription factors and coregulator proteins, integrate signals from key metabolic sensory systems such as the AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR) complexes and synchronize their activities with the biological clock. Therefore, nuclear receptors must function as more than molecular switches for small lipophilic ligands - as initially ascribed - but rather must be capable of orchestrating a large ensemble of input signals. Therefore, a primary role for several nuclear receptors is to serve as the focal point of transcriptional hubs in energy metabolism: their molecular task is to receive and transduce multiple systemic and intracellular metabolic signals to maintain energy homeostasis from individual cells to the whole organism.
    DOI:  https://doi.org/10.1038/s41580-022-00486-7
  40. Cancer Res. 2022 May 16. 82(10): 1870-1871
    Plasticity Enables Cooperation among Heterogeneous Cancer Cell Populations to Support Metastatic Fitness.
    Valerie S LeBleu.
      The invasive progression of cancer known as metastasis remains strongly associated with morbidity and lethality. New meaningful therapeutic interventions could be derived from a better understanding of the underlying processes driving cancer cell seeding and proliferation at secondary sites. Emerging findings regarding the heterogeneity of cancer cells observed in metastases have led us to revisit concepts surrounding metastatic fitness. Novel model systems to study the markers of cancer stem cell plasticity and their evolution during metastatic growth have uncovered that dynamic and heterogeneous cancer cell populations are observed during metastatic disease progression. Heinz and colleagues studied the heterogeneity of colorectal carcinomas, where primary tumors evolve alongside an epithelium well characterized for its self-renewing stem cell population. Their work revealed a functional dynamic interplay in the organization of the metastatic lesions as they transition from stagnating to expanding nodules, wherein the heterogeneous mixture of cancer cell stem cells with more differentiated cancer cells is essential for metastatic outgrowth. Their work supports that dynamic YAP signaling enables the growth-permissive heterogeneous composition of the metastatic nodule, in contrast with growth-restricted homogeneous compositions. See related article by Heinz et al., p. 1953.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0819
  41. Nat Commun. 2022 May 19. 13(1): 2813
    Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model.
    Ludmila A Kasatkina, Chenshuo Ma, Mikhail E Matlashov, Tri Vu, Mucong Li, Andrii A Kaberniuk, Junjie Yao, Vladislav V Verkhusha.
      Optogenetic manipulation and optical imaging in the near-infrared range allow non-invasive light-control and readout of cellular and organismal processes in deep tissues in vivo. Here, we exploit the advantages of Rhodopseudomonas palustris BphP1 bacterial phytochrome, which incorporates biliverdin chromophore and reversibly photoswitches between the ground (740-800 nm) and activated (620-680 nm) states, to generate a loxP-BphP1 transgenic mouse model. The mouse enables Cre-dependent temporal and spatial targeting of BphP1 expression in vivo. We validate the optogenetic performance of endogenous BphP1, which in the activated state binds its engineered protein partner QPAS1, to trigger gene transcription in primary cells and living mice. We demonstrate photoacoustic tomography of BphP1 expression in different organs, developing embryos, virus-infected tissues and regenerating livers, with the centimeter penetration depth. The transgenic mouse model provides opportunities for both near-infrared optogenetics and photoacoustic imaging in vivo and serves as a source of primary cells and tissues with genomically encoded BphP1.
    DOI:  https://doi.org/10.1038/s41467-022-30547-6
  42. Dev Cell. 2022 May 09. pii: S1534-5807(22)00285-4. [Epub ahead of print]
    Epithelial cells adapt to curvature induction via transient active osmotic swelling.
    Caterina Tomba, Valeriy Luchnikov, Luca Barberi, Carles Blanch-Mercader, Aurélien Roux.
      Generation of tissue curvature is essential to morphogenesis. However, how cells adapt to changing curvature is still unknown because tools to dynamically control curvature in vitro are lacking. Here, we developed self-rolling substrates to study how flat epithelial cell monolayers adapt to a rapid anisotropic change of curvature. We show that the primary response is an active and transient osmotic swelling of cells. This cell volume increase is not observed on inducible wrinkled substrates, where concave and convex regions alternate each other over short distances; and this finding identifies swelling as a collective response to changes of curvature with a persistent sign over large distances. It is triggered by a drop in membrane tension and actin depolymerization, which is perceived by cells as a hypertonic shock. Osmotic swelling restores tension while actin reorganizes, probably to comply with curvature. Thus, epithelia are unique materials that transiently and actively swell while adapting to large curvature induction.
    Keywords:  cell volume; curvature; epithelial mechanics; mTORC2; membrane tension
    DOI:  https://doi.org/10.1016/j.devcel.2022.04.017
  43. Mol Syst Biol. 2022 May;18(5): e10947
    Dynamic human liver proteome atlas reveals functional insights into disease pathways.
    Lili Niu, Philipp E Geyer, Rajat Gupta, Alberto Santos, Florian Meier, Sophia Doll, Nicolai J Wewer Albrechtsen, Sabine Klein, Cristina Ortiz, Frank E Uschner, Robert Schierwagen, Jonel Trebicka, Matthias Mann.
      Deeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence-unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time course of primary cell cultures, and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serve as spectral library to characterize a human cohort of non-alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of hepatic stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web-based dashboard application for the interactive exploration of our resource (www.liverproteome.org).
    Keywords:  MS-based proteomics; clinical proteomics; liver disease; liver fibrosis; tissue proteome atlas
    DOI:  https://doi.org/10.15252/msb.202210947
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