bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023–07–30
twenty-one papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Travelling under pressure - hypoxia and shear stress in the metastatic journey.
  2. Heparanase 2 (Hpa2)- a new player essential for pancreatic acinar cell differentiation.
  3. Parallel CRISPR-Cas9 screens identify mechanisms of PLIN2 and lipid droplet regulation.
  4. Sphingolipid metabolism and complement signaling in cancer progression.
  5. Surface-induced phase separation of reconstituted nascent integrin clusters on lipid membranes.
  6. The circulation stage of the metastatic cascade: A mathematical description and its clinical implications.
  7. Evolutionarily divergent mTOR remodels translatome for tissue regeneration.
  8. Modeling epigenetic lesions that cause gliomas.
  9. Cancers make their own luck: theories of cancer origins.
  10. MR Elastography of the Pancreas: Bowel Preparation and Repeatability Assessment in Pancreatic Cancer Patients and Healthy Controls.
  11. A proximity labeling strategy enables proteomic analysis of inter-organelle membrane contacts.
  12. Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface.
  13. Lipid Sorting and Organelle Identity.
  14. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler.
  15. Fluctuations of formin binding in the generation of membrane patterns.
  16. Plasma proteome of growing tumors.
  17. Red Blood Cell Metabolism In Vivo and In Vitro.
  18. Ultrafast distant wound response is essential for whole-body regeneration.
  19. Visualizing Loss of Plasma Membrane Lipid Asymmetry Using Annexin V Staining.
  20. Conformable ultrasound breast patch for deep tissue scanning and imaging.
  21. DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning.
  1. Clin Exp Metastasis. 2023 Jul 25.
    Travelling under pressure - hypoxia and shear stress in the metastatic journey.
    Ece Su Ildiz, Ana Gvozdenovic, Werner J Kovacs, Nicola Aceto.
      Cancer cell invasion, intravasation and survival in the bloodstream are early steps of the metastatic process, pivotal to enabling the spread of cancer to distant tissues. Circulating tumor cells (CTCs) represent a highly selected subpopulation of cancer cells that tamed these critical steps, and a better understanding of their biology and driving molecular principles may facilitate the development of novel tools to prevent metastasis. Here, we describe key research advances in this field, aiming at describing early metastasis-related processes such as collective invasion, shedding, and survival of CTCs in the bloodstream, paying particular attention to microenvironmental factors like hypoxia and mechanical stress, considered as important influencers of the metastatic journey.
    Keywords:  Circulating tumor cell (CTC); Hypoxia; Hypoxia-inducible factors; Metastasis; Shear stress
    DOI:  https://doi.org/10.1007/s10585-023-10224-8
  2. Cell Death Dis. 2023 07 25. 14(7): 465
    Heparanase 2 (Hpa2)- a new player essential for pancreatic acinar cell differentiation.
    Yasmin Kayal, Uri Barash, Inna Naroditsky, Neta Ilan, Israel Vlodavsky.
      Heparanase 2 (Hpa2, HPSE2) is a close homolog of heparanase. Hpa2, however, lacks intrinsic heparan sulfate (HS)-degrading activity, the hallmark of heparanase enzymatic activity. Mutations of HPSE2 were identified in patients diagnosed with urofacial syndrome (UFS), a rare genetic disorder that exhibits abnormal facial expression and bladder voiding dysfunction, leading to renal damage and eventually renal failure. In order to reveal the role of HPSE2 in tissue homeostasis, we established a conditional Hpa2-KO mouse. Interestingly, the lack of Hpa2 was associated with a marked decrease in the expression of key pancreatic transcription factors such as PTF1, GATA6, and Mist1. This was associated with a two-fold decrease in pancreas weight, increased pancreatic inflammation, and profound morphological alterations of the pancreas. These include massive accumulation of fat cells, possibly a result of acinar-to-adipocyte transdifferentiation (AAT), as well as acinar-to-ductal metaplasia (ADM), both considered to be pro-tumorigenic. Furthermore, exposing Hpa2-KO but not wild-type mice to a carcinogen (AOM) and pancreatic inflammation (cerulein) resulted in the formation of pancreatic intraepithelial neoplasia (PanIN), lesions that are considered to be precursors of invasive ductal adenocarcinoma of the pancreas (PDAC). These results strongly support the notion that Hpa2 functions as a tumor suppressor. Moreover, Hpa2 is shown here for the first time to play a critical role in the exocrine aspect of the pancreas.
    DOI:  https://doi.org/10.1038/s41419-023-05990-y
  3. Dev Cell. 2023 Jul 18. pii: S1534-5807(23)00331-3. [Epub ahead of print]
    Parallel CRISPR-Cas9 screens identify mechanisms of PLIN2 and lipid droplet regulation.
    Melissa A Roberts, Kirandeep K Deol, Alyssa J Mathiowetz, Mike Lange, Dara E Leto, Julian Stevenson, Sayed Hadi Hashemi, David W Morgens, Emilee Easter, Kartoosh Heydari, Mike A Nalls, Michael C Bassik, Martin Kampmann, Ron R Kopito, Faraz Faghri, James A Olzmann.
      Despite the key roles of perilipin-2 (PLIN2) in governing lipid droplet (LD) metabolism, the mechanisms that regulate PLIN2 levels remain incompletely understood. Here, we leverage a set of genome-edited human PLIN2 reporter cell lines in a series of CRISPR-Cas9 loss-of-function screens, identifying genetic modifiers that influence PLIN2 expression and post-translational stability under different metabolic conditions and in different cell types. These regulators include canonical genes that control lipid metabolism as well as genes involved in ubiquitination, transcription, and mitochondrial function. We further demonstrate a role for the E3 ligase MARCH6 in regulating triacylglycerol biosynthesis, thereby influencing LD abundance and PLIN2 stability. Finally, our CRISPR screens and several published screens provide the foundation for CRISPRlipid (http://crisprlipid.org), an online data commons for lipid-related functional genomics data. Our study identifies mechanisms of PLIN2 and LD regulation and provides an extensive resource for the exploration of LD biology and lipid metabolism.
    Keywords:  CRISPR; ERAD; MARCH6; PLIN2; endoplasmic reticulum; genetic screen; lipid droplet; metabolism; perilipin; resource
    DOI:  https://doi.org/10.1016/j.devcel.2023.07.001
  4. Trends Cancer. 2023 Jul 26. pii: S2405-8033(23)00125-5. [Epub ahead of print]
    Sphingolipid metabolism and complement signaling in cancer progression.
    Alhaji H Janneh, Carl Atkinson, Stephen Tomlinson, Besim Ogretmen.
      Cancer treatment options are limited due to therapeutic resistance; thus, understanding the tumor microenvironment (TME) is crucial. Sphingolipid metabolism and complement activation products have essential roles in promoting tumor survival. Emerging evidence shows that sphingolipid signaling can regulate intracellular complement activation to induce inflammasome-mediated metastasis, offering a promising strategy for cancer therapy.
    Keywords:  S1P receptor signaling; complement signaling; sphingolipid metabolism; sphingosine 1-phosphate (S1P)
    DOI:  https://doi.org/10.1016/j.trecan.2023.07.001
  5. Proc Natl Acad Sci U S A. 2023 08;120(31): e2301881120
    Surface-induced phase separation of reconstituted nascent integrin clusters on lipid membranes.
    Chiao-Peng Hsu, Jonas Aretz, Arsenii Hordeichyk, Reinhard Fässler, Andreas R Bausch.
      Integrin adhesion complexes are essential membrane-associated cellular compartments for metazoan life. The formation of initial integrin adhesion complexes is a dynamic process involving focal adhesion proteins assembled at the integrin cytoplasmic tails and the inner leaflet of the plasma membrane. The weak multivalent protein interactions within the complex and with the plasma membrane suggest that liquid-liquid phase separation could play a role in the nascent adhesion assembly. Here, we report that solid-supported lipid membranes supplemented with phosphoinositides induce the phase separation of minimal integrin adhesion condensates composed of integrin β1 tails, kindlin, talin, paxillin, and FAK at physiological ionic strengths and protein concentrations. We show that the presence of phosphoinositides is key to enriching kindlin and talin on the lipid membrane, which is necessary to further induce the phase separation of paxillin and FAK at the membrane. Our data demonstrate that lipid membrane surfaces set the local solvent conditions for steering the membrane-localized phase separation even in a regime where no condensate formation of proteins occurs in bulk solution.
    Keywords:  integrin; membrane; phase separation; surface
    DOI:  https://doi.org/10.1073/pnas.2301881120
  6. J Theor Biol. 2023 Jul 20. pii: S0022-5193(23)00179-0. [Epub ahead of print] 111582
    The circulation stage of the metastatic cascade: A mathematical description and its clinical implications.
    Leonid Hanin.
      Metastatic cascade is a multi-stage process that starts with separation of a cancer cell from the primary tumor and ends with the emergence of a detectable metastasis. In the process the initiator cancer cell enters the circulatory system (intravasates), flows with the blood, and exits the circulation (extravasates) into an organ or tissue. The time period between intravasation and extravasation constitutes the circulation stage of the metastatic cascade. This stage is unique in that it lends itself naturally to various non-invasive observations and measurements in an individual cancer patient. This creates an opportunity for gaining insight into metastasis, its mathematical modeling, and designing diagnostic/prognostic tools and new cancer therapies. Although mechanisms of intravasation, survival and extravasation of circulating tumor cells (CTCs) are very complex and largely unknown, mathematical modeling of the circulation stage of the metastatic cascade is facilitated by two inter-related factors: a relative simplicity of the circulatory network and the cyclic nature of blood flow. The article presents a single-subject stochastic model of CTC dynamics that leads to simple formulas, applicable to any homogeneous CTC population, for organ-specific extravasation probabilities, the distribution and expected value of the number, X, of circulation cycles completed by a CTC prior to extravasation, and the average circulation time. In particular, we found that the distribution of random variable X is geometric G(x), where parameter x is measurable, at least in principle, in an individual subject. We also discuss implications of our results for cancer research and treatment.
    Keywords:  Circulating tumor cell; Circulation time; Extravasation probability; Geometric distribution; Half-life; Intravasation
    DOI:  https://doi.org/10.1016/j.jtbi.2023.111582
  7. Nature. 2023 Jul 26.
    Evolutionarily divergent mTOR remodels translatome for tissue regeneration.
    Olena Zhulyn, Hannah D Rosenblatt, Leila Shokat, Shizhong Dai, Duygu Kuzuoglu-Öztürk, Zijian Zhang, Davide Ruggero, Kevan M Shokat, Maria Barna.
      An outstanding mystery in biology is why some species, such as the axolotl, can regenerate tissues whereas mammals cannot1. Here, we demonstrate that rapid activation of protein synthesis is a unique feature of the injury response critical for limb regeneration in the axolotl (Ambystoma mexicanum). By applying polysome sequencing, we identify hundreds of transcripts, including antioxidants and ribosome components that are selectively activated at the level of translation from pre-existing messenger RNAs in response to injury. By contrast, protein synthesis is not activated in response to non-regenerative digit amputation in the mouse. We identify the mTORC1 pathway as a key upstream signal that mediates tissue regeneration and translational control in the axolotl. We discover unique expansions in mTOR protein sequence among urodele amphibians. By engineering an axolotl mTOR (axmTOR) in human cells, we show that these changes create a hypersensitive kinase that allows axolotls to maintain this pathway in a highly labile state primed for rapid activation. This change renders axolotl mTOR more sensitive to nutrient sensing, and inhibition of amino acid transport is sufficient to inhibit tissue regeneration. Together, these findings highlight the unanticipated impact of the translatome on orchestrating the early steps of wound healing in a highly regenerative species and provide a missing link in our understanding of vertebrate regenerative potential.
    DOI:  https://doi.org/10.1038/s41586-023-06365-1
  8. Cell. 2023 Jul 20. pii: S0092-8674(23)00729-8. [Epub ahead of print]
    Modeling epigenetic lesions that cause gliomas.
    Gilbert J Rahme, Nauman M Javed, Kaitlyn L Puorro, Shouhui Xin, Volker Hovestadt, Sarah E Johnstone, Bradley E Bernstein.
      Epigenetic lesions that disrupt regulatory elements represent potential cancer drivers. However, we lack experimental models for validating their tumorigenic impact. Here, we model aberrations arising in isocitrate dehydrogenase-mutant gliomas, which exhibit DNA hypermethylation. We focus on a CTCF insulator near the PDGFRA oncogene that is recurrently disrupted by methylation in these tumors. We demonstrate that disruption of the syntenic insulator in mouse oligodendrocyte progenitor cells (OPCs) allows an OPC-specific enhancer to contact and induce Pdgfra, thereby increasing proliferation. We show that a second lesion, methylation-dependent silencing of the Cdkn2a tumor suppressor, cooperates with insulator loss in OPCs. Coordinate inactivation of the Pdgfra insulator and Cdkn2a drives gliomagenesis in vivo. Despite locus synteny, the insulator is CpG-rich only in humans, a feature that may confer human glioma risk but complicates mouse modeling. Our study demonstrates the capacity of recurrent epigenetic lesions to drive OPC proliferation in vitro and gliomagenesis in vivo.
    Keywords:  CDKN2A; DNA methylation; IDH mutation; PDGFRA; cell of origin; chromatin; genome topology; glioma; nuclear architecture; oligodendrocyte progenitor cells
    DOI:  https://doi.org/10.1016/j.cell.2023.06.022
  9. Nat Rev Cancer. 2023 Jul 24.
    Cancers make their own luck: theories of cancer origins.
    Amir Jassim, Eric P Rahrmann, Ben D Simons, Richard J Gilbertson.
      Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
    DOI:  https://doi.org/10.1038/s41568-023-00602-5
  10. J Magn Reson Imaging. 2023 Jul 24.
    MR Elastography of the Pancreas: Bowel Preparation and Repeatability Assessment in Pancreatic Cancer Patients and Healthy Controls.
    Nienke P M Wassenaar, Anne-Sophie van Schelt, Eric M Schrauben, Marnix P M Kop, C Yung Nio, Johanna W Wilmink, Marc G H Besselink, Hanneke W M van Laarhoven, Jaap Stoker, Aart J Nederveen, Jurgen H Runge.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) stromal viscoelasticity can be measured using MR elastography (MRE). Bowel preparation regimens could affect MRE quality and knowledge on repeatability is crucial for clinical implementation.
    PURPOSE: To assess effects of four bowel preparation regimens on MRE quality and to evaluate repeatability and differentiate patients from healthy controls.
    STUDY TYPE: Prospective.
    POPULATION: 15 controls (41 ± 16 years; 47% female), 16 PDAC patients (one excluded, 66 ± 12 years; 40% female) with 15 age-/sex-matched controls (65 ± 11 years; 40% female). Final sample size was 25 controls and 15 PDAC.
    FIELD STRENGTH/SEQUENCE: 3-T, spin-echo echo-planar-imaging, turbo spin-echo, and fast field echo gradient-echo.
    ASSESSMENT: Four different regimens were used: fasting; scopolaminebutyl; drinking 0.5 L water; combination of 0.5 L water and scopolaminebutyl. MRE signal-to-noise ratio (SNR) was compared between all regimens. MRE repeatability (test-retest) and differences in shear wave speed (SWS) and phase angle (ϕ) were assessed in PDAC and controls. Regions-of-interest were defined for tumor, nontumorous (n = 8) tissue in PDAC, and whole pancreas in controls. Two radiologists delineated tumors twice for evaluation of intraobserver and interobserver variability.
    STATISTICAL TESTS: Repeated measures analysis of variance, coefficients of variation (CoVs), Bland-Altman analysis, (un)paired t-test, Mann-Whitney U-test, and Wilcoxon signed-rank test. P-value<0.05 was considered statistically significant.
    RESULTS: Preparation regimens did not significantly influence MRE-SNR. Therefore, the least burdensome preparation (fasting only) was continued. CoVs for tumor SWS were: intrasession (12.8%) and intersession (21.7%), and intraobserver (7.9%) and interobserver (10.3%) comparisons. For controls, CoVs were intrasession (4.6%) and intersession (6.4%). Average SWS for tumor, nontumor, and healthy tissue were: 1.74 ± 0.58, 1.38 ± 0.27, and 1.18 ± 0.16 m/sec (ϕ: 1.02 ± 0.17, 0.91 ± 0.07, and 0.85 ± 0.08 rad), respectively. Significant differences were found between all groups, except for ϕ between healthy-nontumor (P = 0.094).
    DATA CONCLUSION: The proposed bowel preparation regimens may not influence MRE quality. MRE may be able to differentiate between healthy tissue-tumor and tumor-nontumor.
    LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY STAGE: 2.
    Keywords:  magnetic resonance elastography; observer variation; pancreas; pancreatic ductal carcinoma; reproducibility of results; tumor microenvironment
    DOI:  https://doi.org/10.1002/jmri.28918
  11. iScience. 2023 Jul 21. 26(7): 107159
    A proximity labeling strategy enables proteomic analysis of inter-organelle membrane contacts.
    Maoge Zhou, Bingjie Kong, Xiang Zhang, Ke Xiao, Jing Lu, Weixing Li, Min Li, Zonghong Li, Wei Ji, Junjie Hou, Tao Xu.
      Inter-organelle membrane contacts are highly dynamic and act as central hubs for many biological processes, but the protein compositions remain largely unknown due to the lack of efficient tools. Here, we developed BiFCPL to analyze the contact proteome in living cells by a bimolecular fluorescence complementation (BiFC)-based proximity labeling (PL) strategy. BiFCPL was applied to study mitochondria-endoplasmic reticulum contacts (MERCs) and mitochondria-lipid droplet (LD) contacts. We identified 403 highly confident MERC proteins, including many transiently resident proteins and potential tethers. Moreover, we demonstrated that mitochondria-LD contacts are sensitive to nutrient status. A comparative proteomic analysis revealed that 60 proteins are up- or downregulated at contact sites under metabolic challenge. We verified that SQLE, an enzyme for cholesterol synthesis, accumulates at mitochondria-LD contact sites probably to utilize local ATP for cholesterol synthesis. This work provides an efficient method to identify key proteins at inter-organelle membrane contacts in living cells.
    Keywords:  Biophysics; Membranes; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2023.107159
  12. Proc Natl Acad Sci U S A. 2023 08;120(31): e2300475120
    Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface.
    Qingqing Liu, Benjamin Fong, Seungmin Yoo, Jay R Unruh, Fengli Guo, Zulin Yu, Jingjing Chen, Kausik Si, Rong Li, Chuankai Zhou.
      Eukaryotes organize cellular contents into membrane-bound organelles and membrane-less condensates, for example, protein aggregates. An unsolved question is why the ubiquitously distributed proteins throughout the cytosol give rise to spatially localized protein aggregates on the organellar surface, like mitochondria. We report that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in budding yeast and human cells. This is because misfolded cytosolic proteins do not autonomously aggregate in vivo; instead, they are recruited to the condensation sites initiated by Tom70's substrates (nascent mitochondrial proteins) on the organellar membrane using multivalent hydrophobic interactions. Knocking out Tom70 partially impairs, while overexpressing Tom70 increases the formation and association between cytosolic protein aggregates and mitochondria. In addition, ectopic targeting Tom70 and its substrates to the vacuole surface is able to redirect the localized aggregation from mitochondria to the vacuolar surface. Although other redundant mechanisms may exist, this nascent mitochondrial proteins-based initiation of protein aggregation likely explains the localized condensation of otherwise ubiquitously distributed molecules on the mitochondria. Disrupting the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
    Keywords:  condensate; mitochondria; protein aggregation
    DOI:  https://doi.org/10.1073/pnas.2300475120
  13. Cold Spring Harb Perspect Biol. 2023 Jul 24. pii: a041397. [Epub ahead of print]
    Lipid Sorting and Organelle Identity.
    Yeongho Kim, Christopher G Burd.
      The sorting and trafficking of lipids between organelles gives rise to a dichotomy of bulk membrane properties between organelles of the secretory and endolysosome networks, giving rise to two "membrane territories" based on differences in lipid-packing density, net membrane charge, and bilayer leaflet asymmetries. The cellular organelle membrane dichotomy emerges from ER-to-PM anterograde membrane trafficking and the synthesis of sphingolipids and cholesterol flux at the trans-Golgi network, which constitutes the interface between the two membrane territories. Organelle homeostasis is maintained by vesicle-mediated retrieval of bulk membrane from the distal organelles of each territory to the endoplasmic reticulum or plasma membrane and by soluble lipid transfer proteins that traffic particular lipids. The concept of cellular membrane territories emphasizes the contrasting features of organelle membranes of the secretory and endolysosome networks and the essential roles of lipid-sorting pathways that maintain organelle function.
    DOI:  https://doi.org/10.1101/cshperspect.a041397
  14. Cell Genom. 2023 Jul 12. 3(7): 100346
    Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler.
    Samantha Laber, Sophie Strobel, Josep M Mercader, Hesam Dashti, Felipe R C Dos Santos, Phil Kubitz, Maya Jackson, Alina Ainbinder, Julius Honecker, Saaket Agrawal, Garrett Garborcauskas, David R Stirling, Aaron Leong, Katherine Figueroa, Nasa Sinnott-Armstrong, Maria Kost-Alimova, Giacomo Deodato, Alycen Harney, Gregory P Way, Alham Saadat, Sierra Harken, Saskia Reibe-Pal, Hannah Ebert, Yixin Zhang, Virtu Calabuig-Navarro, Elizabeth McGonagle, Adam Stefek, Josée Dupuis, Beth A Cimini, Hans Hauner, Miriam S Udler, Anne E Carpenter, Jose C Florez, Cecilia Lindgren, Suzanne B R Jacobs, Melina Claussnitzer.
      A primary obstacle in translating genetic associations with disease into therapeutic strategies is elucidating the cellular programs affected by genetic risk variants and effector genes. Here, we introduce LipocyteProfiler, a cardiometabolic-disease-oriented high-content image-based profiling tool that enables evaluation of thousands of morphological and cellular profiles that can be systematically linked to genes and genetic variants relevant to cardiometabolic disease. We show that LipocyteProfiler allows surveillance of diverse cellular programs by generating rich context- and process-specific cellular profiles across hepatocyte and adipocyte cell-state transitions. We use LipocyteProfiler to identify known and novel cellular mechanisms altered by polygenic risk of metabolic disease, including insulin resistance, fat distribution, and the polygenic contribution to lipodystrophy. LipocyteProfiler paves the way for large-scale forward and reverse deep phenotypic profiling in lipocytes and provides a framework for the unbiased identification of causal relationships between genetic variants and cellular programs relevant to human disease.
    Keywords:  cardio-metabolic disease-oriented image-based profiling; high-dimensional mapping of cellular phenotypes; variant-to-function studies
    DOI:  https://doi.org/10.1016/j.xgen.2023.100346
  15. Biophys J. 2023 Jul 24. pii: S0006-3495(23)00465-4. [Epub ahead of print]
    Fluctuations of formin binding in the generation of membrane patterns.
    Mary Ecke, Jana Prassler, Günther Gerisch.
      Circular actin waves that propagate on the substrate-attached membrane of Dictyostelium cells separate two distinct membrane domains from each other: an inner territory rich in phosphatidyl-(3,4,5) trisphosphate (PIP3), and an external area decorated with the PIP3-degrading 3-phosphatase PTEN. During wave propagation, the inner territory increases on the expense of the external area. Beyond a size limit, the inner territory becomes unstable, breaking into an inner and an external domain. The sharp boundary between these domains is demarcated by the insertion of an actin wave. During the conversion of inner territory to external area, the state of the membrane fluctuates, as visualized by dynamic landscapes of Formin B binding. Here we analyze the Formin B fluctuations in relation to three markers of the membrane state: activated Ras, PIP3, and PTEN.
    Keywords:  PTEN; Ras; actin waves; formin; phosphatidylinositides
    DOI:  https://doi.org/10.1016/j.bpj.2023.07.014
  16. Sci Rep. 2023 Jul 27. 13(1): 12195
    Plasma proteome of growing tumors.
    Shashi Gupta, Matthew J Westacott, Deborah G Ayers, Sophie J Weiss, Penn Whitley, Christopher Mueller, Daniel C Weaver, Daniel J Schneider, Anis Karimpour-Fard, Lawrence E Hunter, Daniel W Drolet, Nebojsa Janjic.
      Early detection of cancer is vital for the best chance of successful treatment, but half of all cancers are diagnosed at an advanced stage. A simple and reliable blood screening test applied routinely would therefore address a major unmet medical need. To gain insight into the value of protein biomarkers in early detection and stratification of cancer we determined the time course of changes in the plasma proteome of mice carrying transplanted human lung, breast, colon, or ovarian tumors. For protein measurements we used an aptamer-based assay which simultaneously measures ~ 5000 proteins. Along with tumor lineage-specific biomarkers, we also found 15 markers shared among all cancer types that included the energy metabolism enzymes glyceraldehyde-3-phosphate dehydrogenase, glucose-6-phophate isomerase and dihydrolipoyl dehydrogenase as well as several important biomarkers for maintaining protein, lipid, nucleotide, or carbohydrate balance such as tryptophanyl t-RNA synthetase and nucleoside diphosphate kinase. Using significantly altered proteins in the tumor bearing mice, we developed models to stratify tumor types and to estimate the minimum detectable tumor volume. Finally, we identified significantly enriched common and unique biological pathways among the eight tumor cell lines tested.
    DOI:  https://doi.org/10.1038/s41598-023-38079-9
  17. Metabolites. 2023 Jun 27. pii: 793. [Epub ahead of print]13(7):
    Red Blood Cell Metabolism In Vivo and In Vitro.
    Angelo D'Alessandro, Alkmini T Anastasiadi, Vassilis L Tzounakas, Travis Nemkov, Julie A Reisz, Anastsios G Kriebardis, James C Zimring, Steven L Spitalnik, Michael P Busch.
      Red blood cells (RBC) are the most abundant cell in the human body, with a central role in oxygen transport and its delivery to tissues. However, omics technologies recently revealed the unanticipated complexity of the RBC proteome and metabolome, paving the way for a reinterpretation of the mechanisms by which RBC metabolism regulates systems biology beyond oxygen transport. The new data and analytical tools also informed the dissection of the changes that RBCs undergo during refrigerated storage under blood bank conditions, a logistic necessity that makes >100 million units available for life-saving transfusions every year worldwide. In this narrative review, we summarize the last decade of advances in the field of RBC metabolism in vivo and in the blood bank in vitro, a narrative largely influenced by the authors' own journeys in this field. We hope that this review will stimulate further research in this interesting and medically important area or, at least, serve as a testament to our fascination with this simple, yet complex, cell.
    Keywords:  erythrocyte; hematology; hemolysis; iron; mitochondria; red blood cell; spleen; storage lesion; transfusion medicine
    DOI:  https://doi.org/10.3390/metabo13070793
  18. Cell. 2023 Jul 16. pii: S0092-8674(23)00695-5. [Epub ahead of print]
    Ultrafast distant wound response is essential for whole-body regeneration.
    Yuhang Fan, Chew Chai, Pengyang Li, Xinzhi Zou, James E Ferrell, Bo Wang.
      Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.
    Keywords:  ERK pathway; muscle; planarian; regeneration; signal propagation; systemic wound responses; trigger waves
    DOI:  https://doi.org/10.1016/j.cell.2023.06.019
  19. Bio Protoc. 2023 Jul 20. 13(14): e4754
    Visualizing Loss of Plasma Membrane Lipid Asymmetry Using Annexin V Staining.
    Julia F Baum, Huriye D Uzun, Thomas Günther Pomorski.
      Loss of plasma membrane lipid asymmetry contributes to many cellular functions and responses, including apoptosis, blood coagulation, and cell fusion. In this protocol, we describe the use of fluorescently labeled annexin V to detect loss of lipid asymmetry in the plasma membrane of adherent living cells by fluorescence microscopy. The approach provides a simple, sensitive, and reproducible method to detect changes in lipid asymmetry but is limited by low sample throughput. The protocol can also be adapted to other fluorescently labeled lipid-binding proteins or peptide probes. To validate the lipid binding properties of such probes, we additionally describe here the preparation and use of giant unilamellar vesicles as simple model membrane systems that have a size comparable to cells. Key features Monitoring loss of lipid asymmetry in the plasma membrane via confocal microscopy. Protocol can be applied to any type of cell that is adherent in culture, including primary cells. Assay can be adapted to other fluorescently labeled lipid-binding proteins or peptide probes. Giant unilamellar vesicles serve as a tool to validate the lipid binding properties of such probes. Graphical overview Imaging the binding of fluorescent annexin V to adherent mammalian cells and giant vesicles by confocal microscopy. Annexin V labeling is a useful method for detecting a loss of plasma membrane lipid asymmetry in cells (top image, red); DAPI can be used to identify nuclei (top image, blue). Giant vesicles are used as a tool to validate the lipid binding properties of annexin V to anionic lipids (lower image, red).
    Keywords:  Confocal microscopy; Giant vesicle; Lipid asymmetry; Lipid-binding protein; Mammalian cells; Plasma membrane
    DOI:  https://doi.org/10.21769/BioProtoc.4754
  20. Sci Adv. 2023 Jul 28. 9(30): eadh5325
    Conformable ultrasound breast patch for deep tissue scanning and imaging.
    Wenya Du, Lin Zhang, Emma Suh, Dabin Lin, Colin Marcus, Lara Ozkan, Avani Ahuja, Sara Fernandez, Ikra Iftekhar Shuvo, David Sadat, Weiguo Liu, Fei Li, Anantha P Chandrakasan, Tolga Ozmen, Canan Dagdeviren.
      Ultrasound is widely used for tissue imaging such as breast cancer diagnosis; however, fundamental challenges limit its integration with wearable technologies, namely, imaging over large-area curvilinear organs. We introduced a wearable, conformable ultrasound breast patch (cUSBr-Patch) that enables standardized and reproducible image acquisition over the entire breast with less reliance on operator training and applied transducer compression. A nature-inspired honeycomb-shaped patch combined with a phased array is guided by an easy-to-operate tracker that provides for large-area, deep scanning, and multiangle breast imaging capability. The in vitro studies and clinical trials reveal that the array using a piezoelectric crystal [Yb/Bi-Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3] (Yb/Bi-PIN-PMN-PT) exhibits a sufficient contrast resolution (~3 dB) and axial/lateral resolutions of 0.25/1.0 mm at 30 mm depth, allowing the observation of small cysts (~0.3 cm) in the breast. This research develops a first-of-its-kind ultrasound technology for breast tissue scanning and imaging that offers a noninvasive method for tracking real-time dynamic changes of soft tissue.
    DOI:  https://doi.org/10.1126/sciadv.adh5325
  21. Nat Methods. 2023 Jul 27.
    DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning.
    Alon Saguy, Onit Alalouf, Nadav Opatovski, Soohyen Jang, Mike Heilemann, Yoav Shechtman.
      Single-molecule localization microscopy (SMLM) has revolutionized biological imaging, improving the spatial resolution of traditional microscopes by an order of magnitude. However, SMLM techniques require long acquisition times, typically a few minutes, to yield a single super-resolved image, because they depend on accumulation of many localizations over thousands of recorded frames. Hence, the capability of SMLM to observe dynamics at high temporal resolution has always been limited. In this work, we present DBlink, a deep-learning-based method for super spatiotemporal resolution reconstruction from SMLM data. The input to DBlink is a recorded video of SMLM data and the output is a super spatiotemporal resolution video reconstruction. We use a convolutional neural network combined with a bidirectional long short-term memory network architecture, designed for capturing long-term dependencies between different input frames. We demonstrate DBlink performance on simulated filaments and mitochondria-like structures, on experimental SMLM data under controlled motion conditions and on live-cell dynamic SMLM. DBlink's spatiotemporal interpolation constitutes an important advance in super-resolution imaging of dynamic processes in live cells.
    DOI:  https://doi.org/10.1038/s41592-023-01966-0
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