bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020‒11‒15
38 papers selected by
Kıvanç Görgülü
Technical University of Munich


  1. Elife. 2020 11 10. pii: e62420. [Epub ahead of print]9
    Drijvers JM, Sharpe AH, Haigis MC.
      Average age and obesity prevalence are increasing globally. Both aging and obesity are characterized by profound systemic metabolic and immunologic changes and are cancer risk factors. The mechanisms linking age and body weight to cancer are incompletely understood, but recent studies have provided evidence that the anti-tumor immune response is reduced in both conditions, while responsiveness to immune checkpoint blockade, a form of cancer immunotherapy, is paradoxically intact. Dietary restriction, which promotes health and lifespan, may enhance cancer immunity. These findings illustrate that the systemic context can impact anti-tumor immunity and immunotherapy responsiveness. Here, we review the current knowledge of how age and systemic metabolic state affect the anti-tumor immune response, with an emphasis on CD8+ T cells, which are key players in anti-tumor immunity. A better understanding of the underlying mechanisms may lead to novel therapies enhancing anti-tumor immunity in the context of aging or metabolic dysfunction.
    Keywords:  aging; cancer biology; cancer metabolism; immunity; immunology; inflammation; metabolism; obesity
    DOI:  https://doi.org/10.7554/eLife.62420
  2. Nat Rev Mol Cell Biol. 2020 Nov 13.
    Romani P, Valcarcel-Jimenez L, Frezza C, Dupont S.
      Mechanical forces shape cells and tissues during development and adult homeostasis. In addition, they also signal to cells via mechanotransduction pathways to control cell proliferation, differentiation and death. These processes require metabolism of nutrients for both energy generation and biosynthesis of macromolecules. However, how cellular mechanics and metabolism are connected is still poorly understood. Here, we discuss recent evidence indicating how the mechanical cues exerted by the extracellular matrix (ECM), cell-ECM and cell-cell adhesion complexes influence metabolic pathways. Moreover, we explore the energy and metabolic requirements associated with cell mechanics and ECM remodelling, implicating a reciprocal crosstalk between cell mechanics and metabolism.
    DOI:  https://doi.org/10.1038/s41580-020-00306-w
  3. Autophagy. 2020 Nov 08.
    Li J, Chen X, Kang R, Zeh H, Klionsky DJ, Tang D.
      Oncogenic KRAS mutation-driven pancreatic ductal adenocarcinoma is currently the fourth-leading cause of cancer-related deaths in the United States. Macroautophagy (hereafter "autophagy") is one of the lysosome-dependent degradation systems that can remove abnormal proteins, damaged organelles, or invading pathogens by activating dynamic membrane structures (e.g., phagophores, autophagosomes, and autolysosomes). Impaired autophagy (including excessive activation and defects) is a pathological feature of human diseases, including pancreatic cancer. However, dysfunctional autophagy has many types and plays a complex role in pancreatic tumor biology, depending on various factors, such as tumor stage, microenvironment, immunometabolic state, and death signals. As a modulator connecting various cellular events, pharmacological targeting of nonselective autophagy may lead to both good and bad therapeutic effects. In contrast, targeting selective autophagy could reduce potential side effects of the drugs used. In this review, we describe the advances and challenges of autophagy in the development and therapy of pancreatic cancer.
    Keywords:  PDAC; disease; lysosome; macroautophagy; pancreatic ductal adenocarcinoma; tumor
    DOI:  https://doi.org/10.1080/15548627.2020.1847462
  4. Cell Metab. 2020 Nov 06. pii: S1550-4131(20)30535-0. [Epub ahead of print]
    Zhang Y, Xu Y, Lu W, Ghergurovich JM, Guo L, Blair IA, Rabinowitz JD, Yang X.
      The emergence of cancer from diverse normal tissues has long been rationalized to represent a common set of fundamental processes. However, these processes are not fully defined. Here, we show that forced expression of glucose-6-phosphate dehydrogenase (G6PD) affords immortalized mouse and human cells anchorage-independent growth in vitro and tumorigenicity in animals. Mechanistically, G6PD augments the NADPH pool by stimulating NAD+ kinase-mediated NADP+ biosynthesis in addition to converting NADP+ to NADPH, bolstering antioxidant defense. G6PD also increases nucleotide precursor levels through the production of ribose and NADPH, promoting cell proliferation. Supplementation of antioxidants or nucleosides suffices to convert immortalized mouse and human cells into a tumorigenic state, and supplementation of both is required when their overlapping metabolic consequences are minimized. These results suggest that normal cells have a limited capacity for redox balance and nucleotide synthesis, and overcoming this limit might represent a key aspect of oncogenic transformation.
    Keywords:  G6PD; NAD kinase; NADPH; antioxidants; cancer metabolism; nucleosides; nucleotide synthesis; oncogenic transformation; pentose phosphate pathway; redox regulation
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.002
  5. Cancer Res. 2020 Nov 10. pii: canres.0256.2020. [Epub ahead of print]
    Geng Y, Fan J, Chen L, Zhang C, Qu C, Qian L, Chen K, Meng Z, Chen Z, Wang P.
      Notch activation has been detected in pancreatic ductal adenocarcinoma (PDAC). However, its role in PDAC metastasis remains unknown. In this study, we identify a Notch-dependent feedback circuit between pancreatic cancer cells and macrophages which contributes to PDAC metastasis. In this circuit, miR-124 regulated Notch signaling in cancer cells by directly targeting the Notch ligand Jagged 1 (JAG1). Auto-amplified Notch signaling promoted the recruitment and activation of macrophages to a tumor-supporting M2-like phenotype via downstream interleukin (IL)-8, CCL2, IL-1α, and uPA paracrine signaling. In turn, activated macrophage-derived IL-6 activated the oncogenic transcription factor STAT3 that directly repressed miR-124 genes via a conserved STAT3-binding site in their promoters, thereby promoting cancer cell EMT and invasion. Disrupting this circuit suppressed liver metastasis in mouse models. Thus, our study suggests that manipulation of this Notch-dependent circuit has a therapeutic potential for the treatment of PDAC metastasis.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-0256
  6. Aging Cell. 2020 Nov 09. e13270
    Kowald A, Passos JF, Kirkwood TBL.
      The idea that senescent cells are causally involved in aging has gained strong support from findings that the removal of such cells alleviates many age-related diseases and extends the life span of mice. While efforts proceed to make therapeutic use of such discoveries, it is important to ask what evolutionary forces might have been behind the emergence of cellular senescence, in order better to understand the biology that we might seek to alter. Cellular senescence is often regarded as an anti-cancer mechanism, since it limits the division potential of cells. However, many studies have shown that senescent cells often also have carcinogenic properties. This is difficult to reconcile with the simple idea of an anti-cancer mechanism. Furthermore, other studies have shown that cellular senescence is involved in wound healing and tissue repair. Here, we bring these findings and ideas together and discuss the possibility that these functions might be the main reason for the evolution of cellular senescence. Furthermore, we discuss the idea that senescent cells might accumulate with age because the immune system had to strike a balance between false negatives (overlooking some senescent cells) and false positives (destroying healthy body cells).
    Keywords:  aging; anti-aging; cellular senescence; evolution; senolytics
    DOI:  https://doi.org/10.1111/acel.13270
  7. Mol Cell. 2020 Oct 29. pii: S1097-2765(20)30725-5. [Epub ahead of print]
    Chen S, Liu S, Wang J, Wu Q, Wang A, Guan H, Zhang Q, Zhang D, Wang X, Song H, Qin J, Zou J, Jiang Z, Ouyang S, Feng XH, Liang T, Xu P.
      Mitochondrial morphology shifts rapidly to manage cellular metabolism, organelle integrity, and cell fate. It remains unknown whether innate nucleic acid sensing, the central and general mechanisms of monitoring both microbial invasion and cellular damage, can reprogram and govern mitochondrial dynamics and function. Here, we unexpectedly observed that upon activation of RIG-I-like receptor (RLR)-MAVS signaling, TBK1 directly phosphorylated DRP1/DNM1L, which disabled DRP1, preventing its high-order oligomerization and mitochondrial fragmentation function. The TBK1-DRP1 axis was essential for assembly of large MAVS aggregates and healthy antiviral immunity and underlay nutrient-triggered mitochondrial dynamics and cell fate determination. Knockin (KI) strategies mimicking TBK1-DRP1 signaling produced dominant-negative phenotypes reminiscent of human DRP1 inborn mutations, while interrupting the TBK1-DRP1 connection compromised antiviral responses. Thus, our findings establish an unrecognized function of innate immunity governing both morphology and physiology of a major organelle, identify a lacking loop during innate RNA sensing, and report an elegant mechanism of shaping mitochondrial dynamics.
    Keywords:  DRP1; RLR-MAVS; TBK1; antiviral immunity; cell fate determination; innate immunity; mitochondrial dynamics; mitochondrion; nucleic acid sensing; phosphorylation
    DOI:  https://doi.org/10.1016/j.molcel.2020.10.018
  8. EMBO Rep. 2020 Nov 13. e50615
    Hernandez-Monge J, Martínez-Sánchez M, Rousset-Roman A, Medina-Medina I, Olivares-Illana V.
      The retinoblastoma tumour suppressor protein (RB) regulates a number of diverse cellular functions including differentiation, angiogenesis, chromatin remodelling, senescence and apoptosis. The best-characterised function of RB is cell cycle regulation, and it has been considered a phosphoprotein regulated by cyclin-dependent kinases. In its hypophosphorylated form, RB binds the transcription factor E2F1, arresting the cell cycle in the G1 phase. Here, we show that MDM2 controls the cell cycle through synthesis and degradation of RB protein in a cell cycle condition-dependent fashion. MDM2 induces G1 cell cycle arrest by enhancing the translation of the RB mRNA under genotoxic stress. Translation requires direct interaction between the RB mRNA and the MDM2 protein that accompanies the RB mRNA to the polysomes. However, MDM2 ubiquitinates and degrades RB protein at the G2/M phase under genotoxic stress. The ATM phosphomimetic mutant MDM2(S395D) corroborates that the effect on the RB levels is dependent on the DNA damage. These results provide the basis of a dual regulatory mechanism by which MDM2 controls cell cycle progression during DNA damage.
    Keywords:  MDM2; RB; RB mRNA; cell cycle; protein translation
    DOI:  https://doi.org/10.15252/embr.202050615
  9. Visc Med. 2020 Oct;36(5): 373-380
    Ciecielski KJ, Berninger A, Algül H.
      Background: Pancreatic ductal adenocarcinoma (PDAC), with a mortality rate of 94% and a 5-year-survival rate of only 8%, is one of the deadliest cancer entities worldwide, and early diagnostic methods as well as effective therapies are urgently needed.Summary: This review summarizes current clinical procedure and recent developments of oncological therapy in the palliative setting of metastatic PDAC. It further gives examples of successful, as well as failed, targeted therapy approaches and finally discusses promising ongoing research into the decade-old question of the "undruggability" of KRAS.
    Key Messages: Bench-driven concepts change the clinical landscape from "one size fits all" towards precision medicine. With growing insight into the molecular mechanisms of pancreatic cancer the era of targeted therapy in PDAC is gaining a new momentum.
    Keywords:  KRAS; Pancreatic adenocarcinoma; SHP2; Targeted therapy
    DOI:  https://doi.org/10.1159/000509232
  10. Nat Chem Biol. 2020 Nov 09.
    Kobayashi H, Hatakeyama H, Nishimura H, Yokota M, Suzuki S, Tomabechi Y, Shirouzu M, Osada H, Mimaki M, Goto YI, Yoshida M.
      Mitochondrial DNA (mtDNA) mutations are the major cause of mitochondrial diseases. Cells harboring disease-related mtDNA mutations exhibit various phenotypic abnormalities, such as reduced respiration and elevated lactic acid production. Induced pluripotent stem cell (iPSC) lines derived from patients with mitochondrial disease, with high proportions of mutated mtDNA, exhibit defects in maturation into neurons or cardiomyocytes. In this study, we have discovered a small-molecule compound, which we name tryptolinamide (TLAM), that activates mitochondrial respiration in cybrids generated from patient-derived mitochondria and fibroblasts from patient-derived iPSCs. We found that TLAM inhibits phosphofructokinase-1 (PFK1), which in turn activates AMPK-mediated fatty-acid oxidation to promote oxidative phosphorylation, and redirects carbon flow from glycolysis toward the pentose phosphate pathway to reinforce anti-oxidative potential. Finally, we found that TLAM rescued the defect in neuronal differentiation of iPSCs carrying a high ratio of mutant mtDNA, suggesting that PFK1 represents a potential therapeutic target for mitochondrial diseases.
    DOI:  https://doi.org/10.1038/s41589-020-00676-4
  11. Cancer Res. 2020 Nov 09. pii: canres.2569.2020. [Epub ahead of print]
    Liu Y, Zhang T, Zhang H, Li J, Zhou N, Fiskesund R, Chen J, Lv J, Ma J, Zhang H, Tang K, Cheng F, Zhou Y, Zhang XH, Wang N, Huang B.
      Biomechanics is a fundamental feature of a cell. However, the manner by which actomysin tension affects tumor immune evasion remains unclear. Here we show that although cytotoxic T lymphocytes (CTL) can effectively destroy stiff differentiated tumor cells, they fail to kill soft tumor-repopulating cells (TRC). TRC softness prevented membrane pore formation caused by CTL-released perforin. Perforin interacting with nonmuscle myosin heavy chain 9 transmitted forces to less F-actins in soft TRC, thus generating an inadequate contractile force for perforin pore formation. Stiffening TRC allowed perforin the ability to drill through the membrane, leading to CTL-mediated killing of TRC. Importantly, overcoming mechanical softness in human TRC also enhanced TRC cell death caused by human CTL, potentiating a mechanics-based immunotherapeutic strategy. These findings reveal a mechanics-mediated tumor immune evasion, thus potentially providing an alternative approach for tumor immunotherapy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2569
  12. Dev Cell. 2020 Nov 09. pii: S1534-5807(20)30761-9. [Epub ahead of print]55(3): 259-271
    Marescal O, Cheeseman IM.
      Quiescence is a state of reversible proliferative arrest in which cells are not actively dividing and yet retain the capacity to reenter the cell cycle upon receiving an appropriate stimulus. Quiescent cells are remarkably diverse-they reside in different locations throughout the body, serve distinct roles, and are activated by a variety of signals. Despite this diversity, all quiescent cells must be able to persist in a nondividing state without compromising their proliferative potential, which requires changes to core cellular programs. How drastically different cell types are able to implement extensive changes to their gene-expression programs, metabolism, and cellular structures to induce a common cellular state is a fascinating question in cell and developmental biology. In this review, we explore the diversity of quiescent cells and highlight the unifying characteristics that define the quiescent state.
    Keywords:  aging; cancer; cell cycle; gene expression; proliferation; quiescence; senescence; signaling; stem cell; terminal differentiation
    DOI:  https://doi.org/10.1016/j.devcel.2020.09.029
  13. Elife. 2020 Nov 13. pii: e63603. [Epub ahead of print]9
    Fomicheva M, Macara IG.
      Epithelial cells possess intrinsic mechanisms to maintain an appropriate cell density for normal tissue morphogenesis and homeostasis. Defects in such mechanisms likely contribute to hyperplasia and cancer initiation. To identify genes that regulate the density-dependent proliferation of murine mammary epithelial cells, we developed a fluorescence-activated cell sorting assay based on FUCCI, which marks different stages of the cell cycle with distinct fluorophores. Using this powerful assay, we performed a genome-wide CRISPR/Cas9 knockout screen, selecting for cells that proliferate normally at low density but continue to divide at high density. Unexpectedly, one top hit was Traf3, a negative regulator of NF-κB signaling that has never previously been linked to density-dependent proliferation. We demonstrate that loss of Traf3 specifically activates non-canonical NF-κB signaling. This in turn triggers an innate immune response and drives cell division independently of known density-dependent proliferation mechanisms, including YAP/TAZ signaling and cyclin kinase inhibitors, by blocking entry into quiescence.
    Keywords:  cell biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.63603
  14. Nat Commun. 2020 11 09. 11(1): 5661
    Lee SM, Lee SH, Jung Y, Lee Y, Yoon JH, Choi JY, Hwang CY, Son YH, Park SS, Hwang GS, Lee KP, Kwon KS.
      Sarcopenia is characterized by decreased skeletal muscle mass and function with age. Aged muscles have altered lipid compositions; however, the role and regulation of lipids are unknown. Here we report that FABP3 is upregulated in aged skeletal muscles, disrupting homeostasis via lipid remodeling. Lipidomic analyses reveal that FABP3 overexpression in young muscles alters the membrane lipid composition to that of aged muscle by decreasing polyunsaturated phospholipid acyl chains, while increasing sphingomyelin and lysophosphatidylcholine. FABP3-dependent membrane lipid remodeling causes ER stress via the PERK-eIF2α pathway and inhibits protein synthesis, limiting muscle recovery after immobilization. FABP3 knockdown induces a young-like lipid composition in aged muscles, reduces ER stress, and improves protein synthesis and muscle recovery. Further, FABP3 reduces membrane fluidity and knockdown increases fluidity in vitro, potentially causing ER stress. Therefore, FABP3 drives membrane lipid composition-mediated ER stress to regulate muscle homeostasis during aging and is a valuable target for sarcopenia.
    DOI:  https://doi.org/10.1038/s41467-020-19501-6
  15. J Clin Invest. 2020 Nov 09. pii: 141828. [Epub ahead of print]
    Cifarelli V, Beeman SC, Smith GI, Yoshino J, Morozov D, Beals JW, Kayser BD, Watrous JD, Jain M, Patterson BW, Klein S.
      BACKGROUNDData from studies conducted in rodent models have shown that decreased adipose tissue (AT) oxygenation is involved in the pathogenesis of obesity-induced insulin resistance. Here, we evaluated the potential influence of AT oxygenation on AT biology and insulin sensitivity in people.METHODSWe evaluated subcutaneous AT oxygen partial pressure (pO2); liver and whole-body insulin sensitivity; AT expression of genes and pathways involved in inflammation, fibrosis, and branched-chain amino acid (BCAA) catabolism; systemic markers of inflammation; and plasma BCAA concentrations, in 3 groups of participants that were rigorously stratified by adiposity and insulin sensitivity: metabolically healthy lean (MHL; n = 11), metabolically healthy obese (MHO; n = 15), and metabolically unhealthy obese (MUO; n = 20).RESULTSAT pO2 progressively declined from the MHL to the MHO to the MUO group, and was positively associated with hepatic and whole-body insulin sensitivity. AT pO2 was positively associated with the expression of genes involved in BCAA catabolism, in conjunction with an inverse relationship between AT pO2 and plasma BCAA concentrations. AT pO2 was negatively associated with AT gene expression of markers of inflammation and fibrosis. Plasma PAI-1 increased from the MHL to the MHO to the MUO group and was negatively correlated with AT pO2, whereas the plasma concentrations of other cytokines and chemokines were not different among the MHL and MUO groups.CONCLUSIONThese results support the notion that reduced AT oxygenation in individuals with obesity contributes to insulin resistance by increasing plasma PAI-1 concentrations and decreasing AT BCAA catabolism and thereby increasing plasma BCAA concentrations.TRIAL REGISTRATIONClinicalTrials.gov NCT02706262.FUNDINGThis study was supported by NIH grants K01DK109119, T32HL130357, K01DK116917, R01ES027595, P42ES010337, DK56341 (Nutrition Obesity Research Center), DK20579 (Diabetes Research Center), DK052574 (Digestive Disease Research Center), and UL1TR002345 (Clinical and Translational Science Award); NIH Shared Instrumentation Grants S10RR0227552, S10OD020025, and S10OD026929; and the Foundation for Barnes-Jewish Hospital.
    Keywords:  Adipose tissue; Glucose metabolism; Metabolism; Obesity
    DOI:  https://doi.org/10.1172/JCI141828
  16. Cancer Res. 2020 Nov 15. 80(22): 4886-4887
    Man J, Pajic M, Joshua AM.
      In this issue of Cancer Research, Rozeveld and colleagues present intriguing evidence of the importance of lipid droplets and hormone-sensitive lipase (HSL) in regulating the aggressive nature of pancreatic cancer. Initially demonstrating a dependency of preloaded lipids on an invasive phenotype, the authors then establish that oncogenic KRAS mutation downregulates HSL, thereby facilitating lipid storage during steady state. Thereafter, a phenotypic switch to oxidative metabolism with lipid utilization to fuel invasion and metastasis occurs. Experimentally, blocking the KRAS-HSL axis results in fewer lipid droplets, as well as metabolic reprogramming of the invasive cell phenotype, effectively reducing invasive capacity of KRAS-mutant pancreatic cancer. Of note, HSL overexpression in tumor cells also inhibited invasion, due to depletion of lipid droplets and the stored lipids, which are essential during invasion. Collectively, these novel findings highlight the importance of energy metabolism and its dynamic regulation in the evolution of the metastatic capacity of pancreatic cancer.See related article by Rozeveld et al., p. 4932.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-3082
  17. Autophagy. 2020 Nov 08.
    Bensalem J, Hattersley KJ, Hein LK, Tong Teong X, Carosi JM, Hassiotis S, Grose RH, Fourrier C, Heilbronn LK, Sargeant TJ.
      Autophagic flux is a critical cellular process that is vastly under-appreciated in terms of its importance to human health. Preclinical studies have demonstrated that reductions in autophagic flux cause cancer and exacerbate chronic diseases, including heart disease and the pathological hallmarks of dementia. Autophagic flux can be increased by targeting nutrition-related biochemical signaling. To date, translation of this knowledge has been hampered because there has been no way to directly measure autophagic flux in humans. In this study we detail a method whereby human macroautophagic/autophagic flux can be directly measured from human blood samples. We show that whole blood samples can be treated with the lysosomal inhibitor chloroquine, and peripheral blood mononuclear cells isolated from these samples could be used to measure autophagic machinery protein LC3B-II. Blocking of autophagic flux in cells while still in whole blood represents an important advance because it preserves genetic, nutritional, and signaling parameters inherent to the individual. We show this method was reproducible and defined LC3B-II as the best protein to measure autophagic flux in these cells. Finally, we show that this method is relevant to assess intra-individual variation induced by an intervention by manipulating nutrition signaling with an ex vivo treatment of whole blood that comprised leucine and insulin. Significantly, this method will enable the identification of factors that alter autophagic flux in humans, and better aid their translation in the clinic. With further research, it could also be used as a novel biomarker for risk of age-related chronic disease.
    Keywords:  Autophagy; LC3B; PBMC; biomarker; blood; chloroquine; human; lysosome
    DOI:  https://doi.org/10.1080/15548627.2020.1846302
  18. Cancer Lett. 2020 Nov 10. pii: S0304-3835(20)30571-1. [Epub ahead of print]
    Praharaj PP, Panigrahi DP, Bhol CS, Patra S, Mishra SR, Mahapatra KK, Behera BP, Singh A, Patil S, Bhutia SK.
      Cancer stem cells (CSCs) are distinct subpopulations of cancer cells with stem cell-like abilities and are more resilient to chemotherapy, causing tumor relapse. Mitophagy, a selective form of autophagy, removes damaged unwanted mitochondria from cells through a lysosome-based degradation pathway to maintain cellular homeostasis. CSCs use mitophagy as a chief survival response mechanism for their growth, propagation, and tumorigenic ability. Mitochondrial biogenesis is a crucial cellular event replacing damaged mitochondria through the coordinated regulation of several transcription factors to achieve the bioenergetic demands of the cell. Because of the high mitochondrial content in CSCs, mitochondrial biogenesis is an interesting target to address the resistance mechanisms of anti-CSC therapy. However, to what extent both mitophagy and mitochondrial biogenesis are vital in promoting stemness, metabolic reprogramming, and drug resistance in CSCs has yet to be established. Therefore, in this review, we focus on understanding the interesting aspects of mitochondrial rewiring that involve mitophagy and mitochondrial biogenesis in CSCs. We also discuss their coordinated regulation in the elimination of CSCs, with respect to stemness and differentiation of the CSC phenotype, and the different aspects of tumorigenesis such as cancer initiation, progression, resistance, and tumor relapse. Finally, we address several other unanswered questions relating to targeted anti-CSC cancer therapy, which improves patient survival.
    Keywords:  Anti-CSC cancer Therapy; Cancer stem cell; Metabolic reprograming; Mitochondrial biogenesis; Mitophagy
    DOI:  https://doi.org/10.1016/j.canlet.2020.10.036
  19. Trends Cancer. 2020 Nov 06. pii: S2405-8033(20)30281-8. [Epub ahead of print]
    Walker SA, Pham A, Nizzero S, Kim M, Riter B, Bletz J, Judge S, Phillips B, Noble D, Murray D, Wetzel E, Samson S, McMahon M, Flink C, Couch J, Tomlin C, Swanson K, Anderson ARA, Odde D, Shen H, Hughes S, Zahir N, Enderling H, Wolfram J.
      Physical sciences are often overlooked in the field of cancer research. The Physical Sciences in Oncology Initiative was launched to integrate physics, mathematics, chemistry, and engineering with cancer research and clinical oncology through education, outreach, and collaboration. Here, we provide a framework for education and outreach in emerging transdisciplinary fields.
    Keywords:  cancer awareness; developing field; science education and outreach; scientific network
    DOI:  https://doi.org/10.1016/j.trecan.2020.10.007
  20. Clin Cancer Res. 2020 Nov 13. pii: clincanres.2667.2020. [Epub ahead of print]
    Semaan A, Bernard V, Lee JJ, Wong JW, Huang J, Swartzlander DB, Stephens BM, Monberg ME, Weston B, Bhutani MS, Chang K, Scheet P, Maitra A, Jakubek YA, Guerrero PA.
      PURPOSE: Most patients with pancreatic ductal adenocarcinoma (PDAC) present with surgically unresectable cancer. As a result, endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is the most common biospecimen source available for diagnosis in treatment-naïve patients. Unfortunately, these limited samples are often not considered adequate for genomic analysis, precluding the opportunity for enrollment on precision medicine trials.EXPERIMENTAL DESIGN: Applying an EpCAM-enrichment strategy, we show the feasibility of using real-world EUS-FNAs for in depth, molecular-barcoded, whole-exome sequencing (WES) and somatic copy number alteration (SCNA) analysis in 23 PDAC patients.
    RESULTS: Potentially actionable mutations were identified in >20% of patients. Further, an increased mutational burden and higher aneuploidy in WES data were associated with an adverse prognosis. To identify predictive biomarkers for first line chemotherapy, we developed an SCNA based complexity score (CS) that was associated with response to platinum-based regimens in this cohort.
    CONCLUSIONS: Collectively, these results emphasize the feasibility of real-world cytology samples for in depth genomic characterization of PDAC and show the prognostic potential of SCNA for PDAC diagnosis.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-2667
  21. Science. 2020 Nov 13. 370(6518): 853-856
    Lamper AM, Fleming RH, Ladd KM, Lee ASY.
      Shutoff of global protein synthesis is a conserved response to cellular stresses. This general phenomenon is accompanied by the induction of distinct gene programs tailored to each stress. Although the mechanisms driving repression of general protein synthesis are well characterized, how cells reprogram the translation machinery for selective gene expression remains poorly understood. Here, we found that the noncanonical 5' cap-binding protein eIF3d was activated in response to metabolic stress in human cells. Activation required reduced CK2-mediated phosphorylation near the eIF3d cap-binding pocket. eIF3d controls a gene program enriched in factors important for glucose homeostasis, including members of the mammalian target of rapamycin (mTOR) pathway. eIF3d-directed translation adaptation was essential for cell survival during chronic glucose deprivation. Thus, this mechanism of translation reprogramming regulates the cellular response to metabolic stress.
    DOI:  https://doi.org/10.1126/science.abb0993
  22. Pathologica. 2020 Sep;112(3): 210-226
    Luchini C, Grillo F, Fassan M, Vanoli A, Capelli P, Paolino G, Ingravallo G, Renzulli G, Doglioni C, D'Amuri A, Mattiolo P, Pecori S, Parente P, Florena AM, Zamboni G, Scarpa A.
      Pancreatic malignant exocrine tumors represent the most important cause of cancer-related death for pancreatic neoplasms. The most common tumor type in this category is represented by pancreatic ductal adenocarcinoma (PDAC), an ill defined, stroma-rich, scirrhous neoplasm with glandular differentiation. Here we present the relevant characteristics of the most important PDAC variants, namely adenosquamous carcinoma, colloid carcinoma, undifferentiated carcinoma, undifferentiated carcinoma with osteoclast-like giant cells, signet ring carcinoma, medullary carcinoma and hepatoid carcinoma. The other categories of malignant exocrine tumors, characterized by fleshy, stroma-poor, circumscribed neoplasms, include acinar cell carcinoma (pure and mixed), pancreatoblastoma, and solid pseudopapillary neoplasms. The most important macroscopic, histologic, immunohistochemical and molecular hallmarks of all these tumors, highlighting their key diagnostic/pathological features are presented. Lastly, standardized indications regarding gross sampling and how to compile a formal pathology report for pancreatic malignant exocrine tumors will be provided.
    Keywords:  PDAC; acinar; pancreatic cancer; pancreatic ductal adenocarcinoma; solid pseudopapillary
    DOI:  https://doi.org/10.32074/1591-951X-167
  23. Autophagy. 2020 Nov 13. 1-17
    Siva Sankar D, Dengjel J.
      Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms. Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
    Keywords:  Autophagy; affinity purification; mass spectrometry; protein-protein interactions; proximity labeling; quantitative proteomics
    DOI:  https://doi.org/10.1080/15548627.2020.1847461
  24. Mol Med Rep. 2020 Dec;22(6): 4967-4980
    Yang W, Huang J, Wu H, Wang Y, Du Z, Ling Y, Wang W, Wu Q, Gao W.
      Muscle atrophy is a severe clinical problem involving the loss of muscle mass and strength that frequently accompanies the development of numerous types of cancer, including pancreatic, lung and gastric cancers. Cancer cachexia is a multifactorial syndrome characterized by a continuous decline in skeletal muscle mass that cannot be reversed by conventional nutritional therapy. The pathophysiological characteristic of cancer cachexia is a negative protein and energy balance caused by a combination of factors, including reduced food intake and metabolic abnormalities. Numerous necessary cellular processes are disrupted by the presence of abnormal metabolites, which mediate several intracellular signaling pathways and result in the net loss of cytoplasm and organelles in atrophic skeletal muscle during various states of cancer cachexia. Currently, the clinical morbidity and mortality rates of patients with cancer cachexia are high. Once a patient enters the cachexia phase, the consequences are difficult to reverse and the treatment methods for cancer cachexia are very limited. The present review aimed to summarize the recent discoveries regarding the pathogenesis of cancer cachexia‑induced muscle atrophy and provided novel ideas for the comprehensive treatment to improve the prognosis of affected patients.
    DOI:  https://doi.org/10.3892/mmr.2020.11608
  25. Cancer Cell. 2020 Nov 09. pii: S1535-6108(20)30550-X. [Epub ahead of print]38(5): 624-625
    Passaro A, Stenzinger A, Peters S.
      A recent study in The Lancet Oncology reports that high tumor mutational burden (TMB) is associated with response to anti-PD-1 pembrolizumab, leading to the second FDA approval of a tissue-agnostic predictive biomarker for immunotherapy in solid tumors. This is a step forward in realizing the full potential of cancer immunotherapy.
    DOI:  https://doi.org/10.1016/j.ccell.2020.10.019
  26. Sci Adv. 2020 Nov;pii: eabc8492. [Epub ahead of print]6(46):
    Vaziri A, Khabiri M, Genaw BT, May CE, Freddolino PL, Dus M.
      Diets rich in sugar, salt, and fat alter taste perception and food preference, contributing to obesity and metabolic disorders, but the molecular mechanisms through which this occurs are unknown. Here, we show that in response to a high sugar diet, the epigenetic regulator Polycomb Repressive Complex 2.1 (PRC2.1) persistently reprograms the sensory neurons of Drosophila melanogaster flies to reduce sweet sensation and promote obesity. In animals fed high sugar, the binding of PRC2.1 to the chromatin of the sweet gustatory neurons is redistributed to repress a developmental transcriptional network that modulates the responsiveness of these cells to sweet stimuli, reducing sweet sensation. Half of these transcriptional changes persist despite returning the animals to a control diet, causing a permanent decrease in sweet taste. Our results uncover a new epigenetic mechanism that, in response to the dietary environment, regulates neural plasticity and feeding behavior to promote obesity.
    DOI:  https://doi.org/10.1126/sciadv.abc8492
  27. Transl Cancer Res. 2020 Sep;9(9): 5760-5771
    Ligibel JA, Schmitz KH, Berger NA.
      Sarcopenia, defined as loss of muscle mass, strength and physical performance, is a hallmark of aging and is invariably associated with perturbation of amino acid metabolism, increased muscle protein catabolism relative to anabolism, and loss of muscle fibers. Sarcopenia may be associated with general loss of body mass, or it may also occur along with obesity [sarcopenic obesity (SO)]. Although sarcopenia is associated with multiple comorbidities in older adults, its effects may even be more severe in patients with malignant disease where it has been shown to contribute to poor surgical outcomes, increased chemotherapy toxicity associated with both cytotoxic and targeted agents, as well as adversely impacting survival. While development of sarcopenia is a common age-related phenomenon, the associated catabolic processes appear to be promoted by physical inactivity, inadequate nutrition, and systemic low-grade inflammation, as well as intrinsic muscle and molecular changes, including mitochondrial dysfunction and impaired muscle stem cell regenerative capacity. Increased physical activity and adequate protein intake can reduce incidence and severity of sarcopenia in cancer patients, but many older cancer patients do not meet physical activity and nutrition recommendations, and cancer treatment can make it more difficult to make favorable lifestyle changes. Sarcopenia is discussed in terms of its adverse clinical consequences in older subjects and particularly, in older patients with cancer. Contributions of lifestyle, molecular, and cellular factors are likewise reviewed with suggestions for interventions to improve sarcopenia and its comorbid sequalae.
    Keywords:  Sarcopenia; aging; cancer; muscle mass; obesity; sarcopenic obesity (SO)
    DOI:  https://doi.org/10.21037/tcr-2019-eaoc-05
  28. Nature. 2020 Nov 11.
    Lu XY, Shi XJ, Hu A, Wang JQ, Ding Y, Jiang W, Sun M, Zhao X, Luo J, Qi W, Song BL.
      Cholesterol is an essential lipid and its synthesis is nutritionally and energetically costly1,2. In mammals, cholesterol biosynthesis increases after feeding and is inhibited under fasting conditions3. However, the regulatory mechanisms of cholesterol biosynthesis at the fasting-feeding transition remain poorly understood. Here we show that the deubiquitylase ubiquitin-specific peptidase 20 (USP20) stabilizes HMG-CoA reductase (HMGCR), the rate-limiting enzyme in the cholesterol biosynthetic pathway, in the feeding state. The post-prandial increase in insulin and glucose concentration stimulates mTORC1 to phosphorylate USP20 at S132 and S134; USP20 is recruited to the HMGCR complex and antagonizes its degradation. The feeding-induced stabilization of HMGCR is abolished in mice with liver-specific Usp20 deletion and in USP20(S132A/S134A) knock-in mice. Genetic deletion or pharmacological inhibition of USP20 markedly decreases diet-induced body weight gain, reduces lipid levels in the serum and liver, improves insulin sensitivity and increases energy expenditure. These metabolic changes are reversed by expression of the constitutively stable HMGCR(K248R). This study reveals an unexpected regulatory axis from mTORC1 to HMGCR via USP20 phosphorylation and suggests that inhibitors of USP20 could be used to lower cholesterol levels to treat metabolic diseases including hyperlipidaemia, liver steatosis, obesity and diabetes.
    DOI:  https://doi.org/10.1038/s41586-020-2928-y
  29. Front Physiol. 2020 ;11 567796
    Corkey BE, Deeney JT.
      Key tissues are dysfunctional in obesity, diabetes, cardiovascular disease, fatty liver and other metabolic diseases. Focus has centered on individual organs as though each was isolated. Attention has been paid to insulin resistance as the key relevant pathosis, particularly insulin receptor signaling. However, many tissues play important roles in synergistically regulating metabolic homeostasis and should be considered part of a network. Our approach identifies redox as an acute regulator of the greater metabolic network. Redox reactions involve the transfer of electrons between two molecules and in this work refer to commonly shared molecules, reflective of energy state, that can readily lose electrons to increase or gain electrons to decrease the oxidation state of molecules including NAD(P), NAD(P)H, and thiols. Metabolism alters such redox molecules to impact metabolic function in many tissues, thus, responding to anabolic and catabolic stimuli appropriately and synergistically. It is also important to consider environmental factors that have arisen or increased in recent decades as putative modifiers of redox and reactive oxygen species (ROS) and thus metabolic state. ROS are highly reactive, controlled by the thiol redox state and influence the function of thousands of proteins. Lactate (L) and pyruvate (P) in cells are present in a ratio of about 10 reflective of the cytosolic NADH to NAD ratio. Equilibrium is maintained in cells because lactate dehydrogenase is highly expressed and near equilibrium. The major source of circulating lactate and pyruvate is muscle, although other tissues also contribute. Acetoacetate (A) is produced primarily by liver mitochondria where β-hydroxybutyrate dehydrogenase is highly expressed, and maintains a ratio of β-hydroxybutyrate (β) to A of about 2, reflective of the mitochondrial NADH to NAD ratio. All four metabolites as well as the thiols, cysteine and glutathione, are transported into and out of cells, due to high expression of relevant transporters. Our model supports regulation of all collaborating metabolic organs through changes in circulating redox metabolites, regardless of whether change was initiated exogenously or by a single organ. Validation of these predictions suggests novel ways to understand function by monitoring and impacting redox state.
    Keywords:  ROS; adipocytes; energy metabolism; hepatocytes; metabolic regulation; network; redox; β-cells
    DOI:  https://doi.org/10.3389/fphys.2020.567796
  30. Nat Rev Genet. 2020 Nov 09.
    Armingol E, Officer A, Harismendy O, Lewis NE.
      Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
    DOI:  https://doi.org/10.1038/s41576-020-00292-x
  31. Int J Mol Sci. 2020 Nov 10. pii: E8416. [Epub ahead of print]21(22):
    da Rocha AL, Pinto AP, Morais GP, Marafon BB, Rovina RL, Veras ASC, Teixeira GR, Pauli JR, de Moura LP, Cintra DE, Ropelle ER, Rivas DA, da Silva ASR.
      The protective effects of chronic moderate exercise-mediated autophagy include the prevention and treatment of several diseases and the extension of lifespan. In addition, physical exercise may impair cellular structures, requiring the action of the autophagy mechanism for clearance and renovation of damaged cellular components. For the first time, we investigated the adaptations on basal autophagy flux in vivo in mice's liver, heart, and skeletal muscle tissues submitted to four different chronic exercise models: endurance, resistance, concurrent, and overtraining. Measuring the autophagy flux in vivo is crucial to access the functionality of the autophagy pathway since changes in this pathway can occur in more than five steps. Moreover, the responses of metabolic, performance, and functional parameters, as well as genes and proteins related to the autophagy pathway, were addressed. In summary, the regular exercise models exhibited normal/enhanced adaptations with reduced autophagy-related proteins in all tissues. On the other hand, the overtrained group presented higher expression of Sqstm1 and Bnip3 with negative morphological and physical performance adaptations for the liver and heart, respectively. The groups showed different adaptions in autophagy flux in skeletal muscle, suggesting the activation or inhibition of basal autophagy may not always be related to improvement or impairment of performance.
    Keywords:  autophagy; colchicine; concurrent training; endurance training; exercise; overtraining; resistance training
    DOI:  https://doi.org/10.3390/ijms21228416
  32. Sci Adv. 2020 Nov;pii: eabb2454. [Epub ahead of print]6(46):
    Bonet-Ponce L, Beilina A, Williamson CD, Lindberg E, Kluss JH, Saez-Atienzar S, Landeck N, Kumaran R, Mamais A, Bleck CKE, Li Y, Cookson MR.
      Genetic variation around the LRRK2 gene affects risk of both familial and sporadic Parkinson's disease (PD). However, the biological functions of LRRK2 remain incompletely understood. Here, we report that LRRK2 is recruited to lysosomes after exposure of cells to the lysosome membrane-rupturing agent LLOME. Using an unbiased proteomic screen, we identified the motor adaptor protein JIP4 as an LRRK2 partner at the lysosomal membrane. LRRK2 can recruit JIP4 to lysosomes in a kinase-dependent manner via the phosphorylation of RAB35 and RAB10. Using super-resolution live-cell imaging microscopy and FIB-SEM, we demonstrate that JIP4 promotes the formation of LAMP1-negative tubules that release membranous content from lysosomes. Thus, we describe a new process orchestrated by LRRK2, which we name LYTL (LYsosomal Tubulation/sorting driven by LRRK2), by which lysosomal tubulation is used to release vesicles from lysosomes. Given the central role of the lysosome in PD, LYTL is likely to be disease relevant.
    DOI:  https://doi.org/10.1126/sciadv.abb2454
  33. Sci Adv. 2020 Nov;pii: eabc1087. [Epub ahead of print]6(46):
    Kamino K, Keegstra JM, Long J, Emonet T, Shimizu TS.
      In the face of uncertainty, cell populations tend to diversify to enhance survival and growth. Previous studies established that cells can optimize such bet hedging upon environmental change by modulating gene expression to adapt both the average and diversity of phenotypes. Here, we demonstrate that cells can tune phenotypic diversity also using posttranslational modifications. In the chemotaxis network of Escherichia coli, we find, for both major chemoreceptors Tar and Tsr, that cell-to-cell variation in response sensitivity is dynamically modulated depending on the presence or absence of their cognate chemoeffector ligands in the environment. Combining experiments with mathematical modeling, we show that this diversity tuning requires only the environment-dependent covalent modification of chemoreceptors and a standing cell-to-cell variation in their allosteric coupling. Thus, when environmental cues are unavailable, phenotypic diversity enhances the population's readiness for many signals. However, once a signal is perceived, the population focuses on tracking that signal.
    DOI:  https://doi.org/10.1126/sciadv.abc1087
  34. J Phys Chem Lett. 2020 Nov 10. 9938-9945
    Lu H, Martí J.
      RAS proteins work as GDP-GTP binary switches and regulate cytoplasmic signaling networks that are able to control several cellular processes, playing an essential role in signal transduction pathways involved in cell growth, differentiation, and survival, so that overacting RAS signaling can lead to cancer. One of the hardest challenges to face is the design of mutation-selective therapeutic strategies. In this work, a G12D-mutated farnesylated GTP-bound Kirsten RAt sarcoma (KRAS) protein has been simulated at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane. A specific long-lasting salt bridge connection between farnesyl and the hypervariable region of the protein has been identified as the main mechanism responsible for the binding of oncogenic farnesylated KRAS-4B to the cell membrane. Free-energy landscapes allowed us to characterize local and global minima of KRAS-4B binding to the cell membrane, revealing the main pathways between anchored and released states.
    DOI:  https://doi.org/10.1021/acs.jpclett.0c02809
  35. Autophagy. 2020 Nov 10.
    Cedric B, Armen S.
      Cell migration is a highly dynamic and energy-intensive process that ensures the correct targeting of cells during embryonic and postnatal development. In recent work, we highlighted the importance of macroautophagy/autophagy in regulating the dynamics of cell migration under baseline conditions and in response to a diverse set of molecular factors. Genetic suppression of autophagy-related genes induced longer stationary phases in migrating cells and cell stalling at the beginning of the migratory stream. We also showed that autophagy is required for recycling of the focal adhesion molecule PXN (paxillin), and is induced by energy levels of cells via AMPK activation. This recent study revealed the importance of autophagy in the maintenance of cell migration, and showed that the dynamic interplay between autophagy and energy levels is required to sustain neuronal migration and to cope with diverse micro-environmental factors.
    Keywords:  AMPK; ATP/ADP; Atg12; Atg5; autophagy; cell migration; paxillin; time-lapse imaging
    DOI:  https://doi.org/10.1080/15548627.2020.1848120
  36. Cell Death Dis. 2020 Nov 11. 11(11): 966
    Tan JH, Cao RC, Zhou L, Zhou ZT, Chen HJ, Xu J, Chen XM, Jin YC, Lin JY, Qi ZC, Zeng JL, Li SJ, Luo M, Hu GD, Jin J, Zhang GW.
      Treatment of acute pancreatitis (AP) and chronic pancreatitis (CP) remains problematic due to a lack of knowledge about disease-specific regulatory targets and mechanisms. The purpose of this study was to screen proteins related to endoplasmic reticulum (ER) stress and apoptosis pathways that may play a role in pancreatitis. Human pancreatic tissues including AP, CP, and healthy volunteers were collected during surgery. Humanized PRSS1 (protease serine 1) transgenic (PRSS1Tg) mice were constructed and treated with caerulein to mimic the development of human AP and CP. Potential regulatory proteins in pancreatitis were identified by proteomic screen using pancreatic tissues of PRSS1Tg AP mice. Adenoviral shRNA-mediated knockdown of identified proteins, followed by functional assays was performed to validate their roles. Functional analyses included transmission electron microscopy for ultrastructural analysis; qRT-PCR, western blotting, co-immunoprecipitation, immunohistochemistry, and immunofluorescence for assessment of gene or protein expression, and TUNEL assays for assessment of acinar cell apoptosis. Humanized PRSS1Tg mice could mimic the development of human pancreatic inflammatory diseases. EMC6 and APAF1 were identified as potential regulatory molecules in AP and CP models by proteomic analysis. Both EMC6 and APAF1 regulated apoptosis and inflammatory injury in pancreatic inflammatory diseases. Moreover, APAF1 was regulated by EMC6, induced apoptosis to injure acinar cells and promoted inflammation. In the progression of pancreatitis, EMC6 was activated and then upregulated APAF1 to induce acinar cell apoptosis and inflammatory injury. These findings suggest that EMC6 may be a new therapeutic target for the treatment of pancreatic inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41419-020-03177-3
  37. Metabolites. 2020 Nov 06. pii: E447. [Epub ahead of print]10(11):
    Wang Y, Wondisford FE, Song C, Zhang T, Su X.
      Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates' labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
    Keywords:  MFA assumptions; metabolic flux analysis; non-steady-state versus steady-state; tracer selection
    DOI:  https://doi.org/10.3390/metabo10110447
  38. Bioelectromagnetics. 2020 Nov 12.
    Zablotskii V, Polyakova T, Dejneka A.
      To explore cellular responses to high magnetic fields (HMF), we present a model of the interactions of cells with a homogeneous HMF that accounts for the magnetic force exerted on paramagnetic/diamagnetic species. There are various chemical species inside a living cell, many of which may have large concentration gradients. Thus, when an HMF is applied to a cell, the concentration-gradient magnetic forces act on paramagnetic or diamagnetic species and can either assist or oppose large particle movement through the cytoplasm. We demonstrate possibilities for changing the machinery in living cells with HMFs and predict two new mechanisms for modulating cellular functions with HMFs via (i) changes in the membrane potential and (ii) magnetically assisted intracellular diffusiophoresis of large proteins. By deriving a generalized form for the Nernst equation, we find that an HMF can change the membrane potential of the cell and thus have a significant impact on the properties and biological functionality of cells. The elaborated model provides a universal framework encompassing current studies on controlling cell functions by high static magnetic fields. Bioelectromagnetics. © 2020 Bioelectromagnetics Society.
    Keywords:  cell responses to magnetic fields; diffusiophoresis; ion diffusion; magnetogenetics; membrane potential
    DOI:  https://doi.org/10.1002/bem.22309