bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒01‒03
eighty-four papers selected by
Kıvanç Görgülü
Technical University of Munich


  1. Cancer Res. 2020 Dec 22. pii: canres.3219.2019. [Epub ahead of print]
    Sin TK, Zhang G, Zhang Z, Zhu JZ, Zuo Y, Frost JA, Li M, Li YP.
      Cancer-associated cachexia, characterized by muscle wasting, is a lethal metabolic syndrome without defined etiology or established treatment. We previously found that p300 mediates cancer-induced muscle wasting by activating C/EBPbeta, which then upregulates key catabolic genes. However, the signaling mechanism that activates p300 in response to cancer is unknown. Here we show that upon cancer-induced activation of Toll-like receptor 4 (TLR4) in skeletal muscle, p38beta MAPK phosphorylates Ser-12 on p300 to stimulate C/EBPbeta acetylation, which is necessary and sufficient to cause muscle wasting. Thus, p38beta MAPK is a central mediator and therapeutic target of cancer-induced muscle wasting. In addition, nilotinib, an FDA-approved kinase inhibitor that preferentially binds p38beta MAPK, inhibited p300 activation 20-fold more potently than the p38alpha/beta MAPK inhibitor SB202190 and abrogated cancer cell-induced muscle protein loss in C2C12 myotubes without suppressing p38beta MAPK-dependent myogenesis. Systemic administration of nilotinib at a low dose (0.5 mg/kg/day, IP) in tumor-bearing mice not only alleviated muscle wasting but also prolonged survival. Therefore, nilotinib appears to be a promising treatment for human cancer cachexia due to its selective inhibition of p38beta MAPK.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-3219
  2. Nat Rev Mol Cell Biol. 2020 Dec 22.
    Covarrubias AJ, Perrone R, Grozio A, Verdin E.
      Nicotinamide adenine dinucleotide (NAD+) is a coenzyme for redox reactions, making it central to energy metabolism. NAD+ is also an essential cofactor for non-redox NAD+-dependent enzymes, including sirtuins, CD38 and poly(ADP-ribose) polymerases. NAD+ can directly and indirectly influence many key cellular functions, including metabolic pathways, DNA repair, chromatin remodelling, cellular senescence and immune cell function. These cellular processes and functions are critical for maintaining tissue and metabolic homeostasis and for healthy ageing. Remarkably, ageing is accompanied by a gradual decline in tissue and cellular NAD+ levels in multiple model organisms, including rodents and humans. This decline in NAD+ levels is linked causally to numerous ageing-associated diseases, including cognitive decline, cancer, metabolic disease, sarcopenia and frailty. Many of these ageing-associated diseases can be slowed down and even reversed by restoring NAD+ levels. Therefore, targeting NAD+ metabolism has emerged as a potential therapeutic approach to ameliorate ageing-related disease, and extend the human healthspan and lifespan. However, much remains to be learnt about how NAD+ influences human health and ageing biology. This includes a deeper understanding of the molecular mechanisms that regulate NAD+ levels, how to effectively restore NAD+ levels during ageing, whether doing so is safe and whether NAD+ repletion will have beneficial effects in ageing humans.
    DOI:  https://doi.org/10.1038/s41580-020-00313-x
  3. Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30654-9. [Epub ahead of print]
    Chen Y, Pu Q, Ma Y, Zhang H, Ye T, Zhao C, Huang X, Ren Y, Qiao L, Liu HM, Esmon CT, Ding BS, Cao Z.
      Regenerative capacity is frequently impaired in aged organs. Stress to aged organs often causes scar formation (fibrosis) at the expense of regeneration. It remains to be defined how hematopoietic and vascular cells contribute to aging-induced regeneration to fibrotic transition. Here, we find that aging aberrantly reprograms the crosstalk between hematopoietic and vascular cells to impede the regenerative capacity and enhance fibrosis. In aged lung, liver, and kidney, induction of Neuropilin-1/hypoxia-inducible-factor 2α (HIF2α) suppresses anti-thrombotic and anti-inflammatory endothelial protein C receptor (EPCR) pathway, leading to formation of pro-fibrotic platelet-macrophage rosette. Activated platelets via supplying interleukin 1α synergize with endothelial-produced angiocrine chemokine to recruit fibrogenic TIMP1high macrophages. In mouse models, genetic targeting of endothelial Neuropilin-1-HIF2α, platelet interleukin 1α, or macrophage TIMP1 normalized the pro-fibrotic hematopoietic-vascular niche and restored the regenerative capacity of old organs. Targeting of aberrant endothelial node molecules might help propel "regeneration without scarring" in the repair of multiple organs.
    Keywords:  aging; endothelial cell; endothelial protein C receptor; hypoxia-inducible factor 2 alpha; interleukin-1alpha; liver fibrosis; lung fibrosis; macrophage; neuropilin1; platelet; vascular niche
    DOI:  https://doi.org/10.1016/j.cmet.2020.11.019
  4. Mol Cell. 2020 Dec 22. pii: S1097-2765(20)30904-7. [Epub ahead of print]
    Luengo A, Li Z, Gui DY, Sullivan LB, Zagorulya M, Do BT, Ferreira R, Naamati A, Ali A, Lewis CA, Thomas CJ, Spranger S, Matheson NJ, Vander Heiden MG.
      Aerobic glycolysis, or preferential fermentation of glucose-derived pyruvate to lactate despite available oxygen, is associated with proliferation across many organisms and conditions. To better understand that association, we examined the metabolic consequence of activating the pyruvate dehydrogenase complex (PDH) to increase pyruvate oxidation at the expense of fermentation. We find that increasing PDH activity impairs cell proliferation by reducing the NAD+/NADH ratio. This change in NAD+/NADH is caused by increased mitochondrial membrane potential that impairs mitochondrial electron transport and NAD+ regeneration. Uncoupling respiration from ATP synthesis or increasing ATP hydrolysis restores NAD+/NADH homeostasis and proliferation even when glucose oxidation is increased. These data suggest that when demand for NAD+ to support oxidation reactions exceeds the rate of ATP turnover in cells, NAD+ regeneration by mitochondrial respiration becomes constrained, promoting fermentation, despite available oxygen. This argues that cells engage in aerobic glycolysis when the demand for NAD+ is in excess of the demand for ATP.
    Keywords:  Aerobic Glycolysis; Cell Metabolism; Fermentation; NAD+; PDK; Warburg Effect
    DOI:  https://doi.org/10.1016/j.molcel.2020.12.012
  5. Cancer Discov. 2020 Dec 18. pii: CD-20-1065. [Epub ahead of print]
    Fresquet V, Garcia-Barchino MJ, Larrayoz MJ, Celay J, Vicente C, Fernandez-Galilea M, Larrayoz MJ, Calasanz MJ, Panizo C, Junza A, Han J, Prior C, Fortes P, Pio R, Oyarzabal J, Martínez-Baztán Á, Paiva B, Moreno-Aliaga MJ, Odero MD, Agirre X, Yanes O, Prósper F, Martinez-Climent JA.
      During millions of years, endogenous retroelements have remained transcriptionally silent within mammalian genomes by epigenetic mechanisms. Modern anti-cancer therapies targeting the epigenetic machinery awaken retroelement expression, inducing anti-viral responses that eliminate tumors through mechanisms not completely understood. Here we find that massive binding of epigenetically-activated retroelements by RIG-I and MDA5 viral sensors promotes ATP hydrolysis and depletes intracellular energy, driving tumor killing independently of immune signaling. Energy depletion boosts compensatory ATP production by switching glycolysis to mitochondrial oxidative phosphorylation, thereby reversing the Warburg effect. However, hyperfunctional succinate dehydrogenase in mitochondrial electron transport chain generates excessive oxidative stress that unleashes RIP1-mediated necroptosis. To maintain ATP generation, hyperactive mitochondrial membrane blocks intrinsic apoptosis by increasing BCL2 dependency. Accordingly, drugs targeting BCL2-family proteins and epigenetic inhibitors yield synergistic responses in multiple cancer types. Thus, epigenetic therapy kills cancer cells by rewiring mitochondrial metabolism upon retroelement activation, which primes mitochondria to apoptosis by BH3-mimetics.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1065
  6. Aging Cell. 2020 Dec 30. e13294
    Chen XK, Yi ZN, Wong GT, Hasan KMM, Kwan JS, Ma AC, Chang RC.
      Cellular senescence, a state of irreversible growth arrest triggered by various stressors, engages in a category of pathological processes, whereby senescent cells accumulate in mitotic tissues. Senolytics as novel medicine against aging and various diseases through the elimination of senescent cells has emerged rapidly in recent years. Exercise is a potent anti-aging and anti-chronic disease medicine, which has shown the capacity to lower the markers of cellular senescence over the past decade. However, whether exercise is a senolytic medicine for aging and various diseases remains unclear. Here, we have conducted a systematic review of the published literature studying the senolytic effects of exercise or physical activity on senescent cells under various states in both human and animal models. Exercise can reduce the markers of senescent cells in healthy humans, while it lowered the markers of senescent cells in obese but not healthy animals. The discrepancy between human and animal studies may be due to the relatively small volume of research and the variations in markers of senescent cells, types of cells/tissues, and health conditions. These findings suggest that exercise has senolytic properties under certain conditions, which warrant further investigations.
    Keywords:  cellular senescence; exercise; senescent cells; senolytic medicine; senolytics
    DOI:  https://doi.org/10.1111/acel.13294
  7. Cancer Discov. 2020 Dec 28. pii: CD-20-0387. [Epub ahead of print]
    Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF.
      Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS-STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune stimulatory metabolite whose breakdown products include the immune suppressor, adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wildtype ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part, through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti-PD1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune suppressive pathway.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0387
  8. Life Sci Alliance. 2021 Mar;pii: e202000952. [Epub ahead of print]4(3):
    Chan CS, Sun Y, Ke H, Zhao Y, Belete M, Zhang C, Feng Z, Levine AJ, Hu W.
      p53 is the most frequently mutated gene in human cancers. Li-Fraumeni syndrome patients inheriting heterozygous p53 mutations often have a much-increased risk to develop cancer(s) at early ages. Recent studies suggest that some individuals inherited p53 mutations do not have the early onset or high frequency of cancers. These observations suggest that other genetic, environmental, immunological, epigenetic, or stochastic factors modify the penetrance of the cancerous mutant Tp53 phenotype. To test this possibility, this study explored dominant genetic modifiers of Tp53 mutations in heterozygous mice with different genetic backgrounds. Both genetic and stochastic effects upon tumor formation were observed in these mice. The genetic background of mice carrying Tp53 mutations has a strong influence upon the tissue type of the tumor produced and the number of tumors formed in a single mouse. The onset age of a tumor is correlated with the tissue type of that tumor, although identical tumor tissue types can occur at very different ages. These observations help to explain the great diversity of cancers in different Li-Fraumeni patients over lifetimes.
    DOI:  https://doi.org/10.26508/lsa.202000952
  9. Cancer Res. 2020 Dec 15. pii: canres.2275.2020. [Epub ahead of print]
    Kumarasamy V, Vail P, Nambiar R, Witkiewicz AK, Knudsen ES.
      Intrinsic or acquired resistance to clinically approved CDK4/6 inhibitors has emerged as a major obstacle that hinders their utility beyond ER+ breast cancer. In this study, CDK4/6-dependent and -resistant models were employed to identify functional determinants of response to pharmacological CDK4/6 inhibitors. In all models tested, the activation of RB and inhibition of CDK2 activity emerged as determinants of sensitivity. While depleting CDK4 and 6 was sufficient to limit proliferation in specific resistance settings, RB loss rendered cells completely independent of these kinases. The main downstream target in this context was the activation status of CDK2, which was suppressed with CDK4/6 inhibition in an RB-dependent fashion. Protein levels of p27 were associated with plasticity/rigidity of the cell cycle and correlated with sensitivity to CDK4/6 inhibition. Exogenous overexpression and pharmacological induction of p27 via inhibition of SKP2 and targeting the MEK/ERK pathway enhanced the cytostatic effect of CDK4/6 inhibitors. Mice bearing ER+ xenografts displayed a durable ani-tumor response to palbociclib; however, over the course of treatment, few cells retained RB phosphorylation, which is associated with limited p27 protein levels as determined by multi-spectral imaging. Similarly, combination treatment of palbociclib with a MEK inhibitor in pancreatic cancer PDX models upregulated p27 and further enhanced the in vivo tumor response to palbociclib. Collectively, these results suggest that the cell cycle plasticity that enables tumor models to evade palbociclib-mediated activation of RB could be targeted using a clinically applicable CDK2 inhibitor.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2275
  10. Front Cell Dev Biol. 2020 ;8 603292
    Mohammadalipour A, Dumbali SP, Wenzel PL.
      Mesenchymal stromal cell (MSC) metabolism plays a crucial role in the surrounding microenvironment in both normal physiology and pathological conditions. While MSCs predominantly utilize glycolysis in their native hypoxic niche within the bone marrow, new evidence reveals the importance of upregulation in mitochondrial activity in MSC function and differentiation. Mitochondria and mitochondrial regulators such as sirtuins play key roles in MSC homeostasis and differentiation into mature lineages of the bone and hematopoietic niche, including osteoblasts and adipocytes. The metabolic state of MSCs represents a fine balance between the intrinsic needs of the cellular state and constraints imposed by extrinsic conditions. In the context of injury and inflammation, MSCs respond to reactive oxygen species (ROS) and damage-associated molecular patterns (DAMPs), such as damaged mitochondria and mitochondrial products, by donation of their mitochondria to injured cells. Through intercellular mitochondria trafficking, modulation of ROS, and modification of nutrient utilization, endogenous MSCs and MSC therapies are believed to exert protective effects by regulation of cellular metabolism in injured tissues. Similarly, these same mechanisms can be hijacked in malignancy whereby transfer of mitochondria and/or mitochondrial DNA (mtDNA) to cancer cells increases mitochondrial content and enhances oxidative phosphorylation (OXPHOS) to favor proliferation and invasion. The role of MSCs in tumor initiation, growth, and resistance to treatment is debated, but their ability to modify cancer cell metabolism and the metabolic environment suggests that MSCs are centrally poised to alter malignancy. In this review, we describe emerging evidence for adaptations in MSC bioenergetics that orchestrate developmental fate decisions and contribute to cancer progression. We discuss evidence and potential strategies for therapeutic targeting of MSC mitochondria in regenerative medicine and tissue repair. Lastly, we highlight recent progress in understanding the contribution of MSCs to metabolic reprogramming of malignancies and how these alterations can promote immunosuppression and chemoresistance. Better understanding the role of metabolic reprogramming by MSCs in tissue repair and cancer progression promises to broaden treatment options in regenerative medicine and clinical oncology.
    Keywords:  MSC differentiation; cancer metabolism; hematological malignancy; mesenchymal stromal cells (MSCs); metabolic reprogramming; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial transfer
    DOI:  https://doi.org/10.3389/fcell.2020.603292
  11. Science. 2021 Jan 01. pii: eabb6896. [Epub ahead of print]371(6524):
    You K, Wang L, Chou CH, Liu K, Nakata T, Jaiswal A, Yao J, Lefkovith A, Omar A, Perrigoue JG, Towne JE, Regev A, Graham DB, Xavier RJ.
      Tissue homeostasis is perturbed in a diversity of inflammatory pathologies. These changes can elicit endoplasmic reticulum (ER) stress, protein misfolding, and cell death. ER stress triggers the unfolded protein response (UPR), which can promote recovery of ER proteostasis and cell survival or trigger programmed cell death. Here, we leveraged single-cell RNA sequencing to define dynamic transcriptional states associated with the adaptive versus terminal UPR in the mouse intestinal epithelium. We integrated these transcriptional programs with genome-scale CRISPR screening to dissect the UPR pathway functionally. We identified QRICH1 as a key effector of the PERK-eIF2α axis of the UPR. QRICH1 controlled a transcriptional program associated with translation and secretory networks that were specifically up-regulated in inflammatory pathologies. Thus, QRICH1 dictates cell fate in response to pathological ER stress.
    DOI:  https://doi.org/10.1126/science.abb6896
  12. Cell Metab. 2020 Dec 08. pii: S1550-4131(20)30655-0. [Epub ahead of print]
    Zhang GF, Jensen MV, Gray SM, El K, Wang Y, Lu D, Becker TC, Campbell JE, Newgard CB.
      Metabolic fuels regulate insulin secretion by generating second messengers that drive insulin granule exocytosis, but the biochemical pathways involved are incompletely understood. Here we demonstrate that stimulation of rat insulinoma cells or primary rat islets with glucose or glutamine + 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (Gln + BCH) induces reductive, "counter-clockwise" tricarboxylic acid (TCA) cycle flux of glutamine to citrate. Molecular or pharmacologic suppression of isocitrate dehydrogenase-2 (IDH2), which catalyzes reductive carboxylation of 2-ketoglutarate to isocitrate, results in impairment of glucose- and Gln + BCH-stimulated reductive TCA cycle flux, lowering of NADPH levels, and inhibition of insulin secretion. Pharmacologic suppression of IDH2 also inhibits insulin secretion in living mice. Reductive TCA cycle flux has been proposed as a mechanism for generation of biomass in cancer cells. Here we demonstrate that reductive TCA cycle flux also produces stimulus-secretion coupling factors that regulate insulin secretion, including in non-dividing cells.
    Keywords:  NADPH; anaplerosis; insulin secretion; isocitrate dehydrogenase-2; metabolic flux; pancreatic islet β cells; reductive TCA cycle; stable isotopes
    DOI:  https://doi.org/10.1016/j.cmet.2020.11.020
  13. Nature. 2020 Dec 23.
    Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z.
      Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis1,2. NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36)3-7. However, the molecular basis that underlies this mechanism is largely unknown. Here we solve the cryo-electron microscopy structures of NSD2 and NSD3 bound to mononucleosomes. We find that binding of NSD2 and NSD3 to mononucleosomes causes DNA near the linker region to unwrap, which facilitates insertion of the catalytic core between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between NSD2 or NSD3 and the nucleosome precisely defines the position of the enzyme on the nucleosome, explaining the specificity of methylation to H3K36. Intermolecular contacts between NSD proteins and nucleosomes are altered by several recurrent cancer-associated mutations in NSD2 and NSD3. NSDs that contain these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes the proliferation of cancer cells and the growth of xenograft tumours. Together, our research provides molecular insights into the nucleosome-based recognition and histone-modification mechanisms of NSD2 and NSD3, which could lead to strategies for therapeutic targeting of proteins of the NSD family.
    DOI:  https://doi.org/10.1038/s41586-020-03069-8
  14. Cancer Res. 2020 Dec 29. pii: canres.1377.2020. [Epub ahead of print]
    Gheghiani L, Wang L, Zhang Y, Moore XTR, Zhang J, Smith SC, Tian Y, Wang L, Turner K, Jackson-Cook CK, Mukhopadhyay ND, Fu Z.
      Polo-like kinase 1 (PLK1) is an essential cell cycle regulator that is frequently overexpressed in various human cancers. To determine whether Plk1 overexpression drives tumorigenesis, we established transgenic mouse lines that ubiquitously express increased levels of Plk1. High Plk1 levels were a driving force for different types of spontaneous tumors. Increased Plk1 levels resulted in multiple defects in mitosis and cytokinesis, supernumerary centrosomes, and compromised cell cycle checkpoints, allowing accumulation of chromosomal instability (CIN) which resulted in aneuploidy and tumor formation. Clinically, higher expression of PLK1 positively associated with an increase in genome-wide copy number alterations in multiple human cancers. This study provides in vivo evidence that aberrant expression of PLK1 triggers CIN and tumorigenesis and highlights potential therapeutic opportunities for CIN-positive cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1377
  15. Science. 2020 Dec 31. pii: eaay3446. [Epub ahead of print]
    Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F.
      Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how in situ genome sequencing can directly connect sequence and structure across length scales from single base pairs to whole organisms.
    DOI:  https://doi.org/10.1126/science.aay3446
  16. J Cachexia Sarcopenia Muscle. 2020 Dec 31.
    Prado CM, Anker SD, Coats AJS, Laviano A, von Haehling S.
      
    Keywords:  Cachexia; Muscle; Muscle loss; Nutrition; Nutrition intervention; Sarcopenia; Supplements
    DOI:  https://doi.org/10.1002/jcsm.12673
  17. EMBO Rep. 2020 Dec 29. e50967
    Yang G, Yuan Y, Yuan H, Wang J, Yun H, Geng Y, Zhao M, Li L, Weng Y, Liu Z, Feng J, Bu Y, Liu L, Wang B, Zhang X.
      Lysine succinylation (Ksucc) is an evolutionarily conserved and widespread post-translational modification. Histone acetyltransferase 1 (HAT1) is a type B histone acetyltransferase, regulating the acetylation of both histone and non-histone proteins. However, the role of HAT1 in succinylation modulation remains unclear. Here, we employ a quantitative proteomics approach to study succinylation in HepG2 cancer cells and find that HAT1 modulates lysine succinylation on various proteins including histones and non-histones. HAT1 succinylates histone H3 on K122, contributing to epigenetic regulation and gene expression in cancer cells. Moreover, HAT1 catalyzes the succinylation of PGAM1 on K99, resulting in its increased enzymatic activity and the stimulation of glycolytic flux in cancer cells. Clinically, HAT1 is significantly elevated in liver cancer, pancreatic cancer, and cholangiocarcinoma tissues. Functionally, HAT1 succinyltransferase activity and the succinylation of PGAM1 by HAT1 play critical roles in promoting tumor progression in vitro and in vivo. Thus, we conclude that HAT1 is a succinyltransferase for histones and non-histones in tumorigenesis.
    Keywords:  HAT1; epigenetic regulation; glycolysis; succinylation; tumorigenesis
    DOI:  https://doi.org/10.15252/embr.202050967
  18. STAR Protoc. 2021 Mar 19. 2(1): 100220
    Phifer CJ, Bergdorf KN, Bechard ME, Vilgelm A, Baregamian N, McDonald OG, Lee E, Weiss VL.
      Patient-derived tumor organoid cultures are an essential and innovative methodology for translational research. However, current techniques to establish these cultures are cumbersome, expensive, and often require irreplaceable clinical tissue from surgery or core biopsies. Fine-needle aspiration (FNA) provides a minimally invasive biopsy technique commonly performed in clinical settings. Here, we provide a protocol for FNA. We have found that FNA provides a cost-effective, rapid, and streamlined method for tissue acquisition for cancer organoid culture. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020) and Vilgelm et al. (2020).
    Keywords:  cancer; cell culture; cell isolation; organoids
    DOI:  https://doi.org/10.1016/j.xpro.2020.100220
  19. Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30660-4. [Epub ahead of print]
    Jeong S, Savino AM, Chirayil R, Barin E, Cheng Y, Park SM, Schurer A, Mullarky E, Cantley LC, Kharas MG, Keshari KR.
      A significant increase in dietary fructose consumption has been implicated as a potential driver of cancer. Metabolic adaptation of cancer cells to utilize fructose confers advantages for their malignant growth, but compelling therapeutic targets have not been identified. Here, we show that fructose metabolism of leukemic cells can be inhibited by targeting the de novo serine synthesis pathway (SSP). Leukemic cells, unlike their normal counterparts, become significantly dependent on the SSP in fructose-rich conditions as compared to glucose-rich conditions. This metabolic program is mediated by the ratio of redox cofactors, NAD+/NADH, and the increased SSP flux is beneficial for generating alpha-ketoglutarate from glutamine, which allows leukemic cells to proliferate even in the absence of glucose. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, dramatically reduces leukemia engraftment in mice in the presence of high fructose, confirming the essential role of the SSP in the metabolic plasticity of leukemic cells.
    Keywords:  in vivo isotope tracing; metabolic flux; redox; serine synthesis pathway
    DOI:  https://doi.org/10.1016/j.cmet.2020.12.005
  20. Mol Metab. 2020 Dec 21. pii: S2212-8778(20)30221-0. [Epub ahead of print] 101147
    Ruiz-Ojeda FJ, Wang J, Bäcker T, Krueger M, Zamani S, Rosowski S, Gruber T, Onogi Y, Feuchtinger A, Schulz TJ, Fässler R, Müller TD, García-Cáceres C, Meier M, Blüher M, Ussar S.
      OBJECTIVE: Reorganization of the extracellular matrix is a prerequisite for healthy adipose tissue expansion, whereas fibrosis is a key feature of adipose dysfunction and inflammation. However, very little is known about the direct effects of impaired cell-matrix interaction in adipocyte function and insulin sensitivity. The objective of this study was to determine whether integrin activity can regulate insulin sensitivity in adipocytes and thereby systemic metabolism.METHODS: We characterized integrin activity in adipose tissue and its consequences on whole body metabolism using adipose selective deletion of β1 integrin (Itgb1adipo-cre) and Kindlin-2 (Kind2adipo-cre) in mice.
    RESULTS: We demonstrate that integrin signaling regulates white adipocyte insulin action and systemic metabolism. Consequently, loss of adipose integrin activity, similar to loss of adipose insulin receptors, results in a lipodystrophy-like phenotype and systemic insulin resistance. However, brown adipose tissue of Kind2adipo-cre and Itgb1adipo-cre mice is chronically hyperactivated, and has increased substrate delivery, reduced endothelial basement membrane thickness, and increased endothelial vesicular transport.
    CONCLUSION: Thus, we establish integrin-extracellular matrix interactions as key regulators of white and brown adipose tissue function and whole body metabolism.
    Keywords:  Integrins; Kindlin-2; adipose tissue; brown fat; insulin receptor; insulin resistance; lipodystrophy; obesity
    DOI:  https://doi.org/10.1016/j.molmet.2020.101147
  21. Biochim Biophys Acta Mol Cell Res. 2020 Dec 28. pii: S0167-4889(20)30302-5. [Epub ahead of print] 118944
    Paunovic V, Kosic M, Misirkic-Marjanovic M, Trajkovic V, Harhaji-Trajkovic L.
      To sustain their proliferative and metastatic capacity, tumor cells increase the activity of energy-producing pathways and lysosomal compartment, resorting to autophagolysosomal degradation when nutrients are scarce. Consequently, large fragile lysosomes and enhanced energy metabolism may serve as targets for anticancer therapy. A simultaneous induction of energy stress (by caloric restriction, serum deprivation, and inhibition of glycolysis, oxidative phosphorylation, Krebs cycle, or amino acid/fatty acid metabolism) and lysosomal stress (by lysosomotropic detergents, vacuolar ATPase inhibitors, or cationic amphiphilic drugs) is an efficient anti-cancer strategy demonstrated in a number of studies. However, the mechanisms of lysosomal/energy stress co-amplification, apart from the protective autophagy inhibition, are poorly understood. We here summarize the established and suggest potential mechanisms and candidates for anticancer therapy based on the dual targeting of lysosomes and energy metabolism.
    Keywords:  anticancer therapy; autophagy; energy metabolism; lysosomal membrane permeabilization; lysosomal stress
    DOI:  https://doi.org/10.1016/j.bbamcr.2020.118944
  22. STAR Protoc. 2020 Dec 18. 1(3): 100144
    Lee H, Engin F.
      Pancreatic islets consist of several cell types, including alpha, beta, delta, epsilon, and PP cells. Due to cellular heterogeneity, it is challenging to interpret whole-islet transcriptome data. Single-cell transcriptomics offers a powerful method for investigating gene expression at the single-cell level and identifying cellular heterogeneity and subpopulations. Here, we describe a protocol for mouse pancreatic islet isolation, culturing, and dissociation into a single-cell suspension. This protocol yields highly viable cells for successful library preparation and single-cell RNA sequencing. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020).
    DOI:  https://doi.org/10.1016/j.xpro.2020.100144
  23. Proc Natl Acad Sci U S A. 2021 Jan 05. pii: e2017603118. [Epub ahead of print]118(1):
    Chen C, Mahar R, Merritt ME, Denlinger DL, Hahn DA.
      Metabolic suppression is a hallmark of animal dormancy that promotes overall energy savings. Some diapausing insects and some mammalian hibernators have regular cyclic patterns of substantial metabolic depression alternating with periodic arousal where metabolic rates increase dramatically. Previous studies, largely in mammalian hibernators, have shown that periodic arousal is driven by an increase in aerobic mitochondrial metabolism and that many molecules related to energy metabolism fluctuate predictably across periodic arousal cycles. However, it is still not clear how these rapid metabolic shifts are regulated. We first found that diapausing flesh fly pupae primarily use anaerobic glycolysis during metabolic depression but engage in aerobic respiration through the tricarboxylic acid cycle during periodic arousal. Diapausing pupae also clear anaerobic by-products and regenerate many metabolic intermediates depleted in metabolic depression during arousal, consistent with patterns in mammalian hibernators. We found that decreased levels of reactive oxygen species (ROS) induced metabolic arousal and elevated ROS extended the duration of metabolic depression. Our data suggest ROS regulates the timing of metabolic arousal by changing the activity of two critical metabolic enzymes, pyruvate dehydrogenase and carnitine palmitoyltransferase I by modulating the levels of hypoxia inducible transcription factor (HIF) and phosphorylation of adenosine 5'-monophosphate-activated protein kinase (AMPK). Our study shows that ROS signaling regulates periodic arousal in our insect diapasue system, suggesting the possible importance ROS for regulating other types of of metabolic cycles in dormancy as well.
    Keywords:  ROS; diapause; hibernation; hypoxia signaling; periodic arousal
    DOI:  https://doi.org/10.1073/pnas.2017603118
  24. J Cell Sci. 2020 Dec 29. pii: jcs249136. [Epub ahead of print]133(24):
    Cremer T, Neefjes J, Berlin I.
      Calcium is the third most abundant metal on earth, and the fundaments of its homeostasis date back to pre-eukaryotic life forms. In higher organisms, Ca2+ serves as a cofactor for a wide array of (enzymatic) interactions in diverse cellular contexts and constitutes the most important signaling entity in excitable cells. To enable responsive behavior, cytosolic Ca2+ concentrations are kept low through sequestration into organellar stores, particularly the endoplasmic reticulum (ER), but also mitochondria and lysosomes. Specific triggers are then used to instigate a local release of Ca2+ on demand. Here, communication between organelles comes into play, which is accomplished through intimate yet dynamic contacts, termed membrane contact sites (MCSs). The field of MCS biology in relation to cellular Ca2+ homeostasis has exploded in recent years. Taking advantage of this new wealth of knowledge, in this Review, we invite the reader on a journey of Ca2+ flux through the ER and its associated MCSs. New mechanistic insights and technological advances inform the narrative on Ca2+ acquisition and mobilization at these sites of communication between organelles, and guide the discussion of their consequences for cellular physiology.
    Keywords:  Calcium; ER; Endosome; Membrane contact sites; Mitochondria
    DOI:  https://doi.org/10.1242/jcs.249136
  25. Elife. 2020 Dec 24. pii: e58461. [Epub ahead of print]9
    Aharon-Hefetz N, Frumkin I, Mayshar Y, Dahan O, Pilpel Y, Rak R.
      Different subsets of the tRNA pool in human are expressed in different cellular conditions. The 'proliferation-tRNAs' are induced upon normal and cancerous cell division, while the 'differentiation tRNAs' are active in non-dividing, differentiated cells. Here we examine the essentiality of the various tRNAs upon cellular growth and arrest. We established a CRISPR-based editing procedure with sgRNAs that each target a tRNA family. We measured tRNA essentiality for cellular growth and found that most proliferation tRNAs are essential compared to differentiation tRNAs in rapidly growing cell lines. Yet in more slowly dividing lines, the differentiation tRNAs were more essential. In addition, we measured the essentiality of each tRNA family upon response to cell cycle arresting signals. Here we detected a more complex behavior with both proliferation-tRNAs and differentiation-tRNAs showing various levels of essentiality. These results provide the so-far most comprehensive functional characterization of human tRNAs with intricate roles in various cellular states.
    Keywords:  cell biology; genetics; genomics; human
    DOI:  https://doi.org/10.7554/eLife.58461
  26. Aging Cell. 2020 Dec 23. e13283
    Lazo S, Noren Hooten N, Green J, Eitan E, Mode NA, Liu QR, Zonderman AB, Ezike N, Mattson MP, Ghosh P, Evans MK.
      The mitochondrial free radical theory of aging suggests that accumulating oxidative damage to mitochondria and mitochondrial DNA (mtDNA) plays a central role in aging. Circulating cell-free mtDNA (ccf-mtDNA) isolated from blood may be a biomarker of disease. Extracellular vesicles (EVs) are small (30-400 nm), lipid-bound vesicles capable of shuttling proteins, nucleic acids, and lipids as part of intercellular communication systems. Here, we report that a portion of ccf-mtDNA in plasma is encapsulated in EVs. To address whether EV mtDNA levels change with human age, we analyzed mtDNA in EVs from individuals aged 30-64 years cross-sectionally and longitudinally. EV mtDNA levels decreased with age. Furthermore, the maximal mitochondrial respiration of cultured cells was differentially affected by EVs from old and young donors. Our results suggest that plasma mtDNA is present in EVs, that the level of EV-derived mtDNA is associated with age, and that EVs affect mitochondrial energetics in an EV age-dependent manner.
    Keywords:  aging; biomarker; circulating cell-free mitochondrial DNA; exosomes; extracellular vesicles; intercellular communication; microvesicles; mitochondrial DNA
    DOI:  https://doi.org/10.1111/acel.13283
  27. Elife. 2020 Dec 30. pii: e64919. [Epub ahead of print]9
    Krautz R, Khalili D, Theopold U.
      Postmitotic tissues are incapable of replacing damaged cells through proliferation, but need to rely on buffering mechanisms to prevent tissue disintegration. By constitutively activating the Ras/MAPK-pathway via RasV12-overexpression in the postmitotic salivary glands of Drosophila larvae, we overrode the glands adaptability to growth signals and induced hypertrophy. The accompanied loss of tissue integrity, recognition by cellular immunity and cell death are all buffered by blocking stress signalling through a genuine tissue-autonomous immune response. This novel, spatio-temporally tightly regulated mechanism relies on the inhibition of a feedback-loop in the JNK-pathway by the immune effector and antimicrobial peptide Drosomycin. While this interaction might allow growing salivary glands to cope with temporary stress, continuous Drosomycin expression in RasV12-glands favors unrestricted hypertrophy. These findings indicate the necessity to refine therapeutic approaches that stimulate immune responses by acknowledging their possible, detrimental effects in damaged or stressed tissues.
    Keywords:  D. melanogaster; cancer biology; immunology; inflammation
    DOI:  https://doi.org/10.7554/eLife.64919
  28. Cell. 2020 Dec 23. pii: S0092-8674(20)31622-6. [Epub ahead of print]183(7): 1742-1756
    Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD.
      It is unclear how disease mutations impact intrinsically disordered protein regions (IDRs), which lack a stable folded structure. These mutations, while prevalent in disease, are frequently neglected or annotated as variants of unknown significance. Biomolecular phase separation, a physical process often mediated by IDRs, has increasingly appreciated roles in cellular organization and regulation. We find that autism spectrum disorder (ASD)- and cancer-associated proteins are enriched for predicted phase separation propensities, suggesting that IDR mutations disrupt phase separation in key cellular processes. More generally, we hypothesize that combinations of small-effect IDR mutations perturb phase separation, potentially contributing to "missing heritability" in complex disease susceptibility.
    Keywords:  Phase separation; autism spectrum disorder; biomolecular condensates; cancer; intrinsic disorder; intrinsically disordered protein regions; neurodevelopment
    DOI:  https://doi.org/10.1016/j.cell.2020.11.050
  29. Mol Ther. 2020 Dec 24. pii: S1525-0016(20)30687-0. [Epub ahead of print]
    Thomas D, Sagar S, Liu X, Lee HR, Grunkemeyer JA, Grandgenett PM, Caffrey T, O'Connell KA, Swanson B, Marcos-Silva L, Steentoft C, Wandall HH, Maurer HC, Peng XL, Yeh JJ, Qiu F, Yu F, Madiyalakan R, Olive KP, Mandel U, Clausen H, Hollingsworth MA, Radhakrishnan P.
      Aberrant expression of CA125/MUC16 is associated with pancreatic ductal adenocarcinoma (PDAC) progression and metastasis. However, knowledge of the contribution of MUC16 to pancreatic tumorigenesis is limited. Here, we show that MUC16 expression is associated with disease progression, basal-like and squamous tumor subtypes, increased tumor metastasis, and short-term survival of PDAC patients. MUC16 enhanced tumor malignancy through the activation of AKT and GSK3β oncogenic signaling pathways. Activation of these oncogenic signaling pathways resulted in part from increased interactions between MUC16 and EGF-type receptors, which were enhanced for aberrant glycoforms of MUC16. Treatment of PDAC cells with mAb AR9.6 significantly reduced MUC16 induced oncogenic signaling. mAb AR9.6 binds to a unique conformational epitope on MUC16, which is influenced by O-glycosylation. Additionally, treatment of PDAC tumor-bearing mice with either mAb AR9.6 alone or in combination with gemcitabine significantly reduced tumor growth and metastasis. We conclude that the aberrant expression of MUC16 enhances PDAC progression to an aggressive phenotype by modulating oncogenic signaling through ErbB receptors. Anti-MUC16 mAb AR9.6 blocks oncogenic activities and tumor growth and could be a novel immunotherapeutic agent against MUC16 mediated PDAC tumor malignancy.
    Keywords:  COSMC; MUC16; Pancreatic Ductal Adenocarcinoma; Sialyl-Tn; Tn; mAb AR9.6
    DOI:  https://doi.org/10.1016/j.ymthe.2020.12.029
  30. Cancer Res. 2020 Dec 21. pii: canres.2818.2020. [Epub ahead of print]
    Fei F, Sun S, Li Q, Pei Z, Wang L, Zhang R, Luo F, Yu M, Wang X.
      The role and significance of liver-derived cytokines in cancer-associated cachexia syndrome (CACS) remain elusive. Here we report that combinatorial counterbalances of the leptin and Igf1 signaling pathways in hepatocellular carcinoma (HCC) models significantly relieves cachexia. Double transgenic zebrafish models of HCC that stably displayed focal lesions, anorexia, and wasting of adipose and muscle tissues were first generated. Knockout of lepr or mc4r from these zebrafish partially restored appetite and exerted moderate or no effect on tissue wasting. However, genetic replenishment of Igf1 in a lepr mutant background effectively relieved the cachexia-like phenotype without affecting tumor growth. Similarly, administration of napabucasin, a Stat3/Socs3 inhibitor, on the zebrafish HCC model, mammalian cell lines with exogenous IGF1, and two mouse xenograft models restored insulin sensitivity and rescued the wasting of non-tumoros tissues. Together these results describe the synergistic impact of leptin and Igf1 normalization in treating certain HCC-associated cachexia as a practical strategy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2818
  31. J Biol Chem. 2020 Dec 30. pii: jbc.RA120.015188. [Epub ahead of print]
    Volonte D, Sedorovitz M, Cespedes VE, Beecher ML, Galbiati F.
      Oncogenic K-Ras (K-RasG12V) promotes senescence in normal cells but fuels transformation of cancer cells after the senescence barrier is bypassed. The mechanisms regulating this pleiotropic function of K-Ras remain to be fully established and bear high pathological significance. We find that K-RasG12V activates the angiotensinogen (AGT) gene promoter and promotes AGT protein expression in a Kruppel Like Factor 6 (KLF6)-dependent manner in normal cells. We show that AGT is then converted to angiotensin II (Ang II) in a cell-autonomous manner by cellular proteases. We show that blockade of the Ang II receptor type 1 (AT1-R) in normal cells inhibits oncogene-induced senescence (OIS). We provide evidence that the oncogenic K-Ras-induced synthesis of Ang II and AT1-R activation promote senescence through caveolin-1-dependent and NOX2-mediated oxidative stress. Interestingly, we find that expression of AGT remains elevated in lung cancer cells but in a KLF6-independent and High Mobility Group AT-Hook 1 (HMGA1)-dependent manner. We show that Ang II-mediated activation of the AT1-R promotes cell proliferation and anchorage-independent growth of lung cancer cells through a STAT3-dependent pathway. Finally, we find that expression of AGT is elevated in lung tumors of K-RasLA2-G12D mice, a mouse model of lung cancer, and human lung cancer. Treatment with the AT1-R antagonist losartan inhibits lung tumor formation in K-RasLA2-G12D mice. Together, our data provide evidence of the existence of a novel cell-autonomous and pleiotropic Ang II-dependent signaling pathway through which oncogenic K-Ras promotes OIS in normal cells while fueling transformation in cancer cells.
    Keywords:  Ras protein; angiotensin II; caveolin; cellular senescence; oncogene
    DOI:  https://doi.org/10.1074/jbc.RA120.015188
  32. JCI Insight. 2020 Dec 22. pii: 145307. [Epub ahead of print]
    Stabile LP, Kumar V, Gaither-Davis A, Huang EH, Vendetti FP, Devadassan P, Dacic S, Bao R, Steinman RA, Burns TF, Bakkenist CJ.
      Human lung adenocarcinoma (LUAD) in current or former smokers exhibits a high tumor mutational burden (TMB) and distinct mutational signatures. Syngeneic mouse models of clinically relevant smoking-related LUAD are lacking. We established and characterized a tobacco-associated transplantable murine LUAD cell line, designated FVBW-17, from a LUAD induced by the tobacco carcinogen 4-(methylnitrosoamino)-1-(3-pyridyl)-1-butanone (NNK) in the FVB/N mouse strain. Whole exome sequencing of FVBW-17 cells identified tobacco-associated KrasG12D and Trp53 mutations and a similar mutation profile to that of classic alkylating agents with a TMB >500. FVBW-17 cells transplanted subcutaneously, via tail vein and orthotopically generated tumors in FVB/N mice that were histologically similar to human LUAD. FVBW-17 tumors expressed PD-L1, were infiltrated with CD8+ T cells, and responsive to anti-PD-L1 therapy. FVBW-17 cells were also engineered to express green fluorescent protein and luciferase to facilitate the detection and quantification of tumor growth. Distant metastases to lung, spleen, liver, and kidney were observed from subcutaneously transplanted tumors. This novel cell line is a robust representation of human smoking-related LUAD biology and provides a much needed pre-clinical model in which to test promising new agents and combinations including immune-based therapies.
    Keywords:  Lung cancer; Mouse models; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.145307
  33. J Cell Physiol. 2020 Dec 23.
    Jung YY, Ko JH, Um JY, Chinnathambi A, Alharbi SA, Sethi G, Ahn KS.
      Hypercholesterolemia has been found to be closely linked with a significant increase in both cancer incidence and mortality. However, the exact correlation between serum cholesterol levels and cancer has not been completely deciphered. Here we analyzed the effect of low-density lipoprotein (LDL) cholesterol on prostate and pancreatic cancer cells. We noted that LDL induced a substantial STAT3 activation and JAK1, JAK2, Src activation in diverse prostate and pancreatic tumor cells. Moreover, LDL promoted cancer cell proliferation, migration, and invasion as well as upregulated the expression of diverse oncogenic gene products. However, deletion of LDL-activated STAT3 in LNCaP and PANC-1 cells and reduced LDL-induced cell viability. Simvastatin (SV) treatment also alleviated LDL-induced cell viability and migration ability in both the prostate and pancreatic tumor cells. These results demonstrate that LDL-induced STAT3 activation may exert a profound effect on the proliferation and survival of tumor cells.
    Keywords:  STAT3; invasion; low-density lipoprotein cholesterol; pancreatic cancer; prostate cancer
    DOI:  https://doi.org/10.1002/jcp.30229
  34. Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30662-8. [Epub ahead of print]
    Kang YP, Mockabee-Macias A, Jiang C, Falzone A, Prieto-Farigua N, Stone E, Harris IS, DeNicola GM.
      Cysteine is required for maintaining cellular redox homeostasis in both normal and transformed cells. Deprivation of cysteine induces the iron-dependent form of cell death known as ferroptosis; however, the metabolic consequences of cysteine starvation beyond impairment of glutathione synthesis are poorly characterized. Here, we find that cystine starvation of non-small-cell lung cancer cell lines induces an unexpected accumulation of γ-glutamyl-peptides, which are produced due to a non-canonical activity of glutamate-cysteine ligase catalytic subunit (GCLC). This activity is enriched in cell lines with high levels of NRF2, a key transcriptional regulator of GCLC, but is also inducible in healthy murine tissues following cysteine limitation. γ-glutamyl-peptide synthesis limits the accumulation of glutamate, thereby protecting against ferroptosis. These results indicate that GCLC has a glutathione-independent, non-canonical role in the protection against ferroptosis by maintaining glutamate homeostasis under cystine starvation.
    Keywords:  GCLC; NRF2; cysteine; cystine; ferroptosis; glutamate; γ-glutamyl
    DOI:  https://doi.org/10.1016/j.cmet.2020.12.007
  35. Proc Natl Acad Sci U S A. 2021 Jan 12. pii: e2014013118. [Epub ahead of print]118(2):
    Rothman DL, Stearns SC, Shulman RG.
      A key issue in both molecular and evolutionary biology has been to define the roles of genes and phenotypes in the adaptation of organisms to environmental changes. The dominant view has been that an organism's metabolic adaptations are driven by gene expression and that gene mutations, independent of the starting phenotype, are responsible for the evolution of new metabolic phenotypes. We propose an alternate hypothesis, in which the phenotype and genotype together determine metabolic adaptation both in the lifetime of the organism and in the evolutionary selection of adaptive metabolic traits. We tested this hypothesis by flux-balance and metabolic-control analysis of the relative roles of the starting phenotype and gene expression in regulating the metabolic adaptations during the Crabtree effect in yeast, when they are switched from a low- to high-glucose environment. Critical for successful short-term adaptation was the ability of the glycogen/trehalose shunt to balance the glycolytic pathway. The role of later gene expression of new isoforms of glycolytic enzymes, rather than flux control, was to provide additional homeostatic mechanisms allowing an increase in the amount and efficiency of adenosine triphosphate and product formation while maintaining glycolytic balance. We further showed that homeostatic mechanisms, by allowing increased phenotypic plasticity, could have played an important role in guiding the evolution of the Crabtree effect. Although our findings are specific to Crabtree yeast, they are likely to be broadly found because of the well-recognized similarities in glucose metabolism across kingdoms and phyla from yeast to humans.
    Keywords:  Crabtree effect; adaptation; glucose metabolism; glycogen shunt; homeostasis
    DOI:  https://doi.org/10.1073/pnas.2014013118
  36. Science. 2021 Jan 01. 371(6524): 52-57
    Shivaraju M, Chitta UK, Grange RMH, Jain IH, Capen D, Liao L, Xu J, Ichinose F, Zapol WM, Mootha VK, Rajagopal J.
      Neuroendocrine (NE) cells are epithelial cells that possess many of the characteristics of neurons, including the presence of secretory vesicles and the ability to sense environmental stimuli. The normal physiologic functions of solitary airway NE cells remain a mystery. We show that mouse and human airway basal stem cells sense hypoxia. Hypoxia triggers the direct differentiation of these stem cells into solitary NE cells. Ablation of these solitary NE cells during hypoxia results in increased epithelial injury, whereas the administration of the NE cell peptide CGRP rescues this excess damage. Thus, we identify stem cells that directly sense hypoxia and respond by differentiating into solitary NE cells that secrete a protective peptide that mitigates hypoxic injury.
    DOI:  https://doi.org/10.1126/science.aba0629
  37. Cell Rep. 2020 Dec 29. pii: S2211-1247(20)31555-2. [Epub ahead of print]33(13): 108566
    Li CM, Shapiro H, Tsiobikas C, Selfors LM, Chen H, Rosenbluth J, Moore K, Gupta KP, Gray GK, Oren Y, Steinbaugh MJ, Guerriero JL, Pinello L, Regev A, Brugge JS.
      Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a detailed transcriptomic atlas of young and aged murine mammary tissues. By analyzing epithelial, stromal, and immune cells, we identify age-dependent alterations in cell proportions and gene expression, providing evidence that suggests alveolar maturation and physiological decline. The analysis also uncovers potential pro-tumorigenic mechanisms coupled to the age-associated loss of tumor suppressor function and change in microenvironment. In addition, we identify a rare, age-dependent luminal population co-expressing hormone-sensing and secretory-alveolar lineage markers, as well as two macrophage populations expressing distinct gene signatures, underscoring the complex heterogeneity of the mammary epithelia and stroma. Collectively, this rich single-cell atlas reveals the effects of aging on mammary physiology and can serve as a useful resource for understanding aging-associated cancer risk.
    Keywords:  aging; endothelial cells; fibroblasts; luminal and myoepithelial cells; macrophages; mammary epithelia and stroma; single-cell RNA-seq
    DOI:  https://doi.org/10.1016/j.celrep.2020.108566
  38. EMBO J. 2020 Dec 28. e105120
    Morleo M, Brillante S, Formisano U, Ferrante L, Carbone F, Iaconis D, Palma A, Buonomo V, Maione AS, Grumati P, Settembre C, Franco B.
      Autophagy is a lysosome-dependent degradation pathway essential to maintain cellular homeostasis. Therefore, either defective or excessive autophagy may be detrimental for cells and tissues. The past decade was characterized by significant advances in molecular dissection of stimulatory autophagy inputs; however, our understanding of the mechanisms that restrain autophagy is far from complete. Here, we describe a negative feedback mechanism that limits autophagosome biogenesis based on the selective autophagy-mediated degradation of ATG13, a component of the ULK1 autophagy initiation complex. We demonstrate that the centrosomal protein OFD1 acts as bona fide autophagy receptor for ATG13 via direct interaction with the Atg8/LC3/GABARAP family of proteins. We also show that patients with Oral-Facial-Digital type I syndrome, caused by mutations in the OFD1 gene, display excessive autophagy and that genetic inhibition of autophagy in a mouse model of the disease, significantly ameliorates polycystic kidney, a clinical manifestation of the disorder. Collectively, our data report the discovery of an autophagy self-regulated mechanism and implicate dysregulated autophagy in the pathogenesis of renal cystic disease in mammals.
    Keywords:  OFD1; autophagy receptor; polycystic kidney; selective autophagy
    DOI:  https://doi.org/10.15252/embj.2020105120
  39. STAR Protoc. 2020 Dec 18. 1(3): 100191
    Takahashi K, Kubota SI, Ehata S, Ueda HR, Miyazono K.
      Tissue-clearing technologies have developed rapidly in the past decade, especially for use in neuroscience research. We previously reported that CUBIC, which is one tissue-clearing method, is useful for applications in cancer research. CUBIC cancer analysis can be used to detect cancer metastasis with single-cell resolution at whole mouse body/organ level. This approach can also analyze the tumor characteristics with high-quality 3D images. Here, we describe a detailed CUBIC cancer protocol from tissue clearing, capturing 3D images and post-immunohistochemistry. For complete details on the use and execution of this protocol, please refer to Kubota et al. (2017).
    Keywords:  Cancer; Microscopy; Model Organisms
    DOI:  https://doi.org/10.1016/j.xpro.2020.100191
  40. STAR Protoc. 2020 Dec 18. 1(3): 100167
    Shen Y, Schmidt T, Diz-Muñoz A.
      Tumors have complex microenvironments that provide not only biochemical but also mechanical cues to the cells within. In particular, tumor stiffness has been shown to regulate tumor growth, invasion, and metastasis. Understanding how the mechanical microenvironment controls cell behavior could be key to unraveling new therapeutic approaches. Here, we describe a protocol to prepare primary and metastatic human colorectal cancer samples and measure tumor stiffness at the tissue level using an atomic force microscope in spectroscopy mode. For complete details on the use and execution of this protocol, please refer to Shen et al. (2020).
    Keywords:  Atomic Force Microscopy (AFM); Biophysics; Cancer
    DOI:  https://doi.org/10.1016/j.xpro.2020.100167
  41. Trends Cell Biol. 2020 Dec 26. pii: S0962-8924(20)30244-0. [Epub ahead of print]
    Davidson PM, Cadot B.
      Actin plays roles in many important cellular processes, including cell motility, organelle movement, and cell signaling. The discovery of transmembrane actin-binding proteins at the outer nuclear membrane (ONM) raises the exciting possibility that actin can play a role in direct force transmission to the nucleus and the genome at its interior. Actin-dependent nucleus displacement was first described a decade ago. We are now gaining a more detailed understanding of its mechanisms, as well as new roles for actin during mitosis and meiosis, for gene expression, and in the cell's response to mechanical stimuli. Here we review these recent developments, the actin-binding proteins involved, the tissue specificity of these mechanisms, and methods developed to reconstitute and study this interaction in vitro.
    Keywords:  Nesprin; actin; mechanotransduction; mitosis; myosin; nucleus
    DOI:  https://doi.org/10.1016/j.tcb.2020.11.009
  42. Aging (Albany NY). 2020 12 27.
    Lennicke C, Dos Santos E, Cochemé HM.
      
    Keywords:  Drosophila; aging; diabetes; metabolic disease; obesity; purine catabolism; sugar diet; uric acid
    DOI:  https://doi.org/10.18632/aging.104223
  43. Cancer Invest. 2020 Dec 22. 1-7
    Colloca GA, Venturino A, Guarneri D.
      BACKGROUND: Systemic inflammation response (SIR)-related variables are controversial as predictive variables.METHODS: Patients with metastatic pancreatic adenocarcinoma (mPDAC) receiving chemotherapy were identified, three SIR-related variables and the relationships between each of them with overall survival (OS) were analysed.
    RESULTS: Of 129 patients receiving chemotherapy, 97 had metastases. A significant relationship between SIR and OS has been documented. Each of the SIR-related variables retained its independent prognostic role after multivariate analysis, whereas tri-linear peripheric blood-cell score (TRIS) appeared as the most reliable predictive parameter.
    CONCLUSIONS: Among patients with mPDAC receiving chemotherapy, SIR is prognostic and could predict the effectiveness of chemotherapy.
    Keywords:  Metastatic pancreatic cancer; derived neutrophil-to-lymphocyte ratio; systemic inflammation response; trilinear peripheric blood cell score
    DOI:  https://doi.org/10.1080/07357907.2020.1863419
  44. STAR Protoc. 2020 Dec 18. 1(3): 100212
    Bergdorf K, Phifer C, Bharti V, Westover D, Bauer J, Vilgelm A, Lee E, Weiss V.
      Generation of fine-needle aspiration (FNA)-derived cancer organoids has allowed us to develop a number of downstream applications. In this protocol, we start with organoids cultured in a semi-solid format. We dissociate organoids into single cells and then plate in a 384-well format for high-throughput drug screening. While this method must be fine-tuned for each individual organoid culture, it offers a format well suited for rapidly screening medium-sized drug/compound libraries (500-5,000 molecules) and generating dose-response curves to measure relative efficacy. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020) and Vilgelm et al. (2020).
    Keywords:  Cancer; Cell culture; Cell-based Assays; High Throughput Screening; Organoids
    DOI:  https://doi.org/10.1016/j.xpro.2020.100212
  45. J Clin Invest. 2020 Dec 22. pii: 143301. [Epub ahead of print]
    Saleh M, Sharma K, Kalsi RS, Fusco JC, Sehrawat A, Saloman JL, Guo P, Zhang T, Mohamed N, Wang Y, Prasadan K, Gittes G.
      Chronic pancreatitis affects over 250,000 people in the US and millions worldwide. It is associated with chronic debilitating pain, pancreatic exocrine failure, high-risk of pancreatic cancer, and usually progresses to diabetes. Treatment options are limited and ineffective. We developed a new potential therapy, wherein a pancreatic ductal infusion of 1-2% acetic acid in mice and non-human primates resulted in a non-regenerative, near-complete ablation of the exocrine pancreas, with complete preservation of the islets. Pancreatic ductal infusion of acetic acid in a mouse model of chronic pancreatitis led to resolution of chronic inflammation and pancreatitis-associated pain. Furthermore, acetic acid-treated animals showed improved glucose tolerance and insulin secretion. The loss of exocrine tissue in this procedure would not typically require further management in patients with chronic pancreatitis because they usually have pancreatic exocrine failure requiring dietary enzyme supplements. Thus, this procedure, which should be readily translatable to humans through an endoscopic retrograde cholangiopancreatography (ERCP), may offer a potential innovative non-surgical therapy for chronic pancreatitis that relieves pain and prevents the progression of pancreatic diabetes.
    Keywords:  Diabetes; Endocrinology; Gastroenterology
    DOI:  https://doi.org/10.1172/JCI143301
  46. Curr Treat Options Oncol. 2021 Jan 02. 22(1): 8
    Lee KG, Roy V, Laszlo M, Atkins KM, Lin KJ, Tomassian S, Hendifar AE.
      OPINION STATEMENT: Despite extensive research that has identified new risk factors, genetic mutations, and therapeutic options, pancreatic ductal adenocarcinoma continues to be a leading cause of cancer related death. Patients with pancreatic cancer, along with their clinicians, must balance realistic hope alongside a life-threatening diagnosis. As the search for treatments to reduce the morbidity and mortality continues, symptom management and quality of life remain the focus of our efforts. In addition to side effects of cancer-directed therapy, patients are at risk for malnutrition, pain, and fatigue. These factors are often overlooked in practice, so a multidisciplinary team is critical in optimizing the care of patients.
    Keywords:  Ascites; Depression; Multidisciplinary approach; Pancreatic cancer; Portal hypertension; Symptom management; Weight loss
    DOI:  https://doi.org/10.1007/s11864-020-00801-4
  47. Sci Adv. 2020 Dec;pii: eabd0263. [Epub ahead of print]6(51):
    Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P.
      Chaperones are essential for assisting protein folding and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone-client binding, but our understanding of how additional interactions enable client specificity is sparse. Here, we decipher what determines binding of two chaperones (TIM8·13 and TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1 and Tim23, which has an additional disordered hydrophilic domain. Combining NMR, SAXS, and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity versus specificity.
    DOI:  https://doi.org/10.1126/sciadv.abd0263
  48. STAR Protoc. 2020 Dec 18. 1(3): 100192
    Driehuis E, Gracanin A, Vries RGJ, Clevers H, Boj SF.
      Establishment of patient-derived adult stem cell-based pancreatic (tumor) organoids was first described in 2015. Since then, multiple laboratories have demonstrated the robustness of this method. We recently described the generation of a pancreatic cancer biobank containing 30 well-characterized tumor organoid models. Here, we describe the applied methods in detail. Use of tumor-selective media prevents contamination with normal cells. Generated organoids can be cryopreserved and can serve as a living biobank of pancreatic cancer for biomarker identification and drug screening. For complete information on the generation and use of this protocol, please refer to Driehuis et al. (2019).
    Keywords:  Cancer; Organoids; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2020.100192
  49. J Exp Clin Cancer Res. 2020 Dec 24. 39(1): 289
    Pfitzinger PL, Fangmann L, Wang K, Demir E, Gürlevik E, Fleischmann-Mundt B, Brooks J, D'Haese JG, Teller S, Hecker A, Jesinghaus M, Jäger C, Ren L, Istvanffy R, Kühnel F, Friess H, Ceyhan GO, Demir IE.
      BACKGROUND: Nerve-cancer interactions are increasingly recognized to be of paramount importance for the emergence and progression of pancreatic cancer (PCa). Here, we investigated the role of indirect cholinergic activation on PCa progression through inhibition of acetylcholinesterase (AChE) via clinically available AChE-inhibitors, i.e. physostigmine and pyridostigmine.METHODS: We applied immunohistochemistry, immunoblotting, MTT-viability, invasion, flow-cytometric-cell-cycle-assays, phospho-kinase arrays, multiplex ELISA and xenografted mice to assess the impact of AChE inhibition on PCa cell growth and invasiveness, and tumor-associated inflammation. Survival analyses were performed in a novel genetically-induced, surgically-resectable mouse model of PCa under adjuvant treatment with gemcitabine+/-physostigmine/pyridostigmine (n = 30 mice). Human PCa specimens (n = 39) were analyzed for the impact of cancer AChE expression on tumor stage and survival.
    RESULTS: We discovered a strong expression of AChE in cancer cells of human PCa specimens. Inhibition of this cancer-cell-intrinsic AChE via pyridostigmine and physostigmine, or administration of acetylcholine (ACh), diminished PCa cell viability and invasion in vitro and in vivo via suppression of pERK signaling, and reduced tumor-associated macrophage (TAM) infiltration and serum pro-inflammatory cytokine levels. In the novel genetically-induced, surgically-resectable PCa mouse model, adjuvant co-therapy with AChE blockers had no impact on survival. Accordingly, survival of resected PCa patients did not differ based on tumor AChE expression levels. Patients with higher-stage PCa also exhibited loss of the ACh-synthesizing enzyme, choline-acetyltransferase (ChAT), in their nerves.
    CONCLUSION: For future clinical trials of PCa, direct cholinergic stimulation of the muscarinic signaling, rather than indirect activation via AChE blockade, may be a more effective strategy.
    Keywords:  Acetylcholinesterase; Cholinergic; Electroporation; Pancreatic cancer; Parasympathomimetics
    DOI:  https://doi.org/10.1186/s13046-020-01796-4
  50. Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30656-2. [Epub ahead of print]
    Fischer AW, Jaeckstein MY, Gottschling K, Heine M, Sass F, Mangels N, Schlein C, Worthmann A, Bruns OT, Yuan Y, Zhu H, Chen O, Ittrich H, Nilsson SK, Stefanicka P, Ukropec J, Balaz M, Dong H, Sun W, Reimer R, Scheja L, Heeren J.
      In response to cold exposure, thermogenic adipocytes internalize large amounts of fatty acids after lipoprotein lipase-mediated hydrolysis of triglyceride-rich lipoproteins (TRL) in the capillary lumen of brown adipose tissue (BAT) and white adipose tissue (WAT). Here, we show that in cold-exposed mice, vascular endothelial cells in adipose tissues endocytose substantial amounts of entire TRL particles. These lipoproteins subsequently follow the endosomal-lysosomal pathway, where they undergo lysosomal acid lipase (LAL)-mediated processing. Endothelial cell-specific LAL deficiency results in impaired thermogenic capacity as a consequence of reduced recruitment of brown and brite/beige adipocytes. Mechanistically, TRL processing by LAL induces proliferation of endothelial cells and adipocyte precursors via beta-oxidation-dependent production of reactive oxygen species, which in turn stimulates hypoxia-inducible factor-1α-dependent proliferative responses. In conclusion, this study demonstrates a physiological role for TRL particle uptake into BAT and WAT and establishes endothelial lipoprotein processing as an important determinant of adipose tissue remodeling during thermogenic adaptation.
    Keywords:  angiogenesis; beige adipocytes; brown adipose tissue; endothelial cells; hypoxia-inducible factor 1α; lipoproteins; lysosomal acid lipase; thermogenesis; triglycerides; white adipose tissue
    DOI:  https://doi.org/10.1016/j.cmet.2020.12.001
  51. Cancer Res. 2020 Dec 28. pii: canres.2121.2020. [Epub ahead of print]
    Dai M, Boudreault J, Wang N, Poulet S, Daliah G, Yan G, Moamer A, Burgos SA, Sabri S, Ali S, Lebrun JJ.
      Although the cyclin-dependent kinases CDK4 and CDK6 play fundamental roles in cancer, the specific pathways and downstream targets by which they exert their tumorigenic effects remain elusive. In this study, we uncover distinct and novel functions for these kinases in regulating tumor formation and metastatic colonization in various solid tumors, including those of the breast, prostate, and pancreas. Combining in vivo CRISPR-based CDK4 and CDK6 gene editing with pharmacological inhibition approaches in orthotopic transplantation and patient-derived xenograft preclinical models, we defined clear functions for CDK4 and CDK6 in facilitating tumor growth and progression in metastatic cancers. Transcriptomic profiling of CDK4/6 CRISPR knockouts in breast cancer revealed these two kinases to regulate cancer progression through distinct mechanisms. CDK4 regulated pro-metastatic inflammatory cytokine signaling whereas CDK6 mainly controlled DNA replication and repair processes. Inhibition of CDK6 but not CDK4 resulted in defective DNA repair and increased DNA damage. Multiple CDK6 DNA replication/repair genes were not only associated with cancer subtype, grades, and poor clinical outcomes, but also facilitated primary tumor growth and metastasis in vivo. CRISPR-based genomic deletion of CDK6 efficiently blocked tumor formation and progression in pre-established cell- and patient-derived xenograft preclinical models of breast cancer, providing a potential novel targeted therapy for these deadly tumors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2121
  52. Elife. 2020 Dec 28. pii: e57243. [Epub ahead of print]9
    Barrett RL, Puré E.
      Fibroblasts play an essential role in organogenesis and the integrity of tissue architecture and function. Growth in most solid tumors is dependent upon remodeling 'stroma', composed of cancer-associated fibroblasts (CAFs) and extracellular matrix (ECM), which plays a critical role in tumor initiation, progression, metastasis, and therapeutic resistance. Recent studies have clearly established that the potent immunosuppressive activity of stroma is a major mechanism by which stroma can promote tumor progression and confer resistance to immune-based therapies. Herein, we review recent advances in identifying the stroma-dependent mechanisms that regulate cancer-associated inflammation and antitumor immunity, in particular, the interactions between fibroblasts and immune cells. We also review the potential mechanisms by which stroma can confer resistance to immune-based therapies for solid tumors and current advancements in stroma-targeted therapies.
    Keywords:  T-cell; cancer; cancer biology; fibroblast; immunotherapy; macrophages; tumor immunity
    DOI:  https://doi.org/10.7554/eLife.57243
  53. Pancreas. 2021 Jan 01. 50(1): 83-88
    Ueno M, Morinaga S, Hashimoto Y, Umemoto K, Sasahira N, Saiura A, Seyama Y, Honda G, Ioka T, Takahashi H, Miyamoto A, Nakamori S, Unno M, Takadate T, Mizuno N, Shimizu Y, Ueno H, Sugiyama M, Fukutomi A, Shimizu S, Okusaka T, Furuse J.
      OBJECTIVE: The combination of gemcitabine plus nab-paclitaxel (GnP) has not been studied in Japanese patients with resectable pancreatic cancer (PC). This study aimed to assess the tolerability of adjuvant GnP in Japanese patients with resected PC.METHODS: This was a Phase I, open-label, multicenter, single-arm study of patients with resected PC in Japan. Patients received 125 mg/m2 of nab-paclitaxel and 1000 mg/m2 of gemcitabine on days 1, 8, and 15 of a 28-day cycle for a total of 6 cycles. The primary end point was tolerability, defined as the absence of specific grade 3 or higher treatment-related adverse events by the end of cycle 2. Secondary end points included safety, disease-free survival, and overall survival.
    RESULTS: Forty-one patients were enrolled between June 2016 and February 2017 (median age, 68 years; 51% male; stage II, 95%). Gemcitabine plus nab-paclitaxel met the tolerability criteria in 39 of the 40 patients included in the tolerability analysis set (97.5%). The most common treatment-related adverse events were leukopenia, neutropenia, alopecia, and peripheral sensory neuropathy. After a follow-up of 30.1 months, median disease-free survival was 17.0 months and median overall survival was not reached.
    CONCLUSIONS: These results show that adjuvant GnP is tolerable in Japanese patients with resected PC.Clinical Trial Registration No.: JapicCTI-163179.
    DOI:  https://doi.org/10.1097/MPA.0000000000001702
  54. Biology (Basel). 2020 Dec 19. pii: E481. [Epub ahead of print]9(12):
    Cairns G, Thumiah-Mootoo M, Burelle Y, Khacho M.
      The fundamental importance of functional mitochondria in the survival of most eukaryotic cells, through regulation of bioenergetics, cell death, calcium dynamics and reactive oxygen species (ROS) generation, is undisputed. However, with new avenues of research in stem cell biology these organelles have now emerged as signaling entities, actively involved in many aspects of stem cell functions, including self-renewal, commitment and differentiation. With this recent knowledge, it becomes evident that regulatory pathways that would ensure the maintenance of mitochondria with state-specific characteristics and the selective removal of organelles with sub-optimal functions must play a pivotal role in stem cells. As such, mitophagy, as an essential mitochondrial quality control mechanism, is beginning to gain appreciation within the stem cell field. Here we review and discuss recent advances in our knowledge pertaining to the roles of mitophagy in stem cell functions and the potential contributions of this specific quality control process on to the progression of aging and diseases.
    Keywords:  metabolism; mitochondria; mitochondrial quality control; mitophagy; self-renewal; stem cells
    DOI:  https://doi.org/10.3390/biology9120481
  55. PLoS Comput Biol. 2020 Dec;16(12): e1008469
    Lin S, Ali I, Wilson G.
      The distribution of scholarly content today happens in the context of an immense deluge of information found on the internet. As a result, researchers face serious challenges when archiving and finding information that relates to their work. Library science principles provide a framework for navigating information ecosystems in order to help researchers improve findability of their professional output. Here, we describe the information ecosystem which consists of users, context, and content, all 3 of which must be addressed to make information findable and usable. We provide a set of tips that can help researchers evaluate who their users are, how to archive their research outputs to encourage findability, and how to leverage structural elements of software to make it easier to find information within and beyond their publications. As scholars evaluate their research communication strategies, they can use these steps to improve how their research is discovered and reused.
    DOI:  https://doi.org/10.1371/journal.pcbi.1008469
  56. J Clin Med. 2020 Dec 21. pii: E4128. [Epub ahead of print]9(12):
    Espiau-Romera P, Courtois S, Parejo-Alonso B, Sancho P.
      Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is an extremely lethal disease due to late diagnosis, aggressiveness and lack of effective therapies. Considering its intrinsic heterogeneity, patient stratification models based on transcriptomic and genomic signatures, with partially overlapping subgroups, have been established. Besides molecular alterations, PDAC tumours show a strong desmoplastic response, resulting in profound metabolic reprogramming involving increased glucose and amino acid consumption, as well as lipid scavenging and biosynthesis. Interestingly, recent works have also revealed the existence of metabolic subtypes with differential prognosis within PDAC, which correlated to defined molecular subclasses in patients: lipogenic subtype correlated with a classical/progenitor signature, while glycolytic tumours associated with the highly aggressive basal/squamous profile. Bioinformatic analyses have demonstrated that the representative genes of each metabolic subtype are up-regulated in PDAC samples and predict patient survival. This suggests a relationship between the genetic signature, metabolic profile, and aggressiveness of the tumour. Considering all this, defining metabolic subtypes represents a clear opportunity for patient stratification considering tumour functional behaviour independently of their mutational background.
    Keywords:  PDAC; classification; glycolysis; lipid metabolism; pancreatic cancer; stratification
    DOI:  https://doi.org/10.3390/jcm9124128
  57. Nature. 2020 Dec 23.
    Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW.
      Focal chromosomal amplification contributes to the initiation of cancer by mediating overexpression of oncogenes1-3, and to the development of cancer therapy resistance by increasing the expression of genes whose action diminishes the efficacy of anti-cancer drugs. Here we used whole-genome sequencing of clonal cell isolates that developed chemotherapeutic resistance to show that chromothripsis is a major driver of circular extrachromosomal DNA (ecDNA) amplification (also known as double minutes) through mechanisms that depend on poly(ADP-ribose) polymerases (PARP) and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). Longitudinal analyses revealed that a further increase in drug tolerance is achieved by structural evolution of ecDNAs through additional rounds of chromothripsis. In situ Hi-C sequencing showed that ecDNAs preferentially tether near chromosome ends, where they re-integrate when DNA damage is present. Intrachromosomal amplifications that formed initially under low-level drug selection underwent continuing breakage-fusion-bridge cycles, generating amplicons more than 100 megabases in length that became trapped within interphase bridges and then shattered, thereby producing micronuclei whose encapsulated ecDNAs are substrates for chromothripsis. We identified similar genome rearrangement profiles linked to localized gene amplification in human cancers with acquired drug resistance or oncogene amplifications. We propose that chromothripsis is a primary mechanism that accelerates genomic DNA rearrangement and amplification into ecDNA and enables rapid acquisition of tolerance to altered growth conditions.
    DOI:  https://doi.org/10.1038/s41586-020-03064-z
  58. Proc Natl Acad Sci U S A. 2021 Jan 12. pii: e2024058118. [Epub ahead of print]118(2):
    Goodman JM.
      
    DOI:  https://doi.org/10.1073/pnas.2024058118
  59. J Cell Sci. 2020 Dec 24. pii: jcs.253401. [Epub ahead of print]
    Daneri-Becerra C, Valeiras B, Gallo LI, Lagadari M, Galigniana MD.
      Cyclophilin A (CyPA) is an abundant and ubiquitously expressed protein belonging to the immunophilin family that has intrinsic peptidyl-prolyl-(cis/trans)-isomerase enzymatic activity. CyPA mediates immunosuppressive action of the cyclic undecapeptide cyclosporine A and is also involved in multiple cellular processes such as protein folding, intracellular trafficking, signal transduction, and transcriptional regulation. CyPA is abundantly expressed in cancer cells, and due to its chaperone nature, its expression is induced upon the onset of stress. In this study, it is demonstrated that a significant pool of this immunophilin is primarily an intramitochondrial factor that migrates to the nucleus when cells are stimulated with stressors. CyPA shows antiapoptotic action per se and the capability of forming ternary complexes with cytochrome c and the small acidic cochaperone p23, the latter interaction being independent of the usual association of p23 with the heat-shock protein of 90-kDa, Hsp90. These CyPA•p23 complexes enhance the antiapoptotic response of the cell, suggesting that both proteins form a functional unit whose high level of expression plays a significant role in cell survival.
    Keywords:  Apoptosis; Cyclophilin A; Immunophilin; Mitochondria; Trafficking; p23
    DOI:  https://doi.org/10.1242/jcs.253401
  60. Biology (Basel). 2020 Dec 18. pii: E479. [Epub ahead of print]9(12):
    Moro L.
      Mitochondria are highly dynamic and regulated organelles implicated in a variety of important functions in the cell, including energy production, fatty acid metabolism, iron homeostasis, programmed cell death, and cell signaling. Changes in mitochondrial metabolism, signaling and dynamics are hallmarks of cancer. Understanding whether these modifications are associated with alterations of the mitochondrial proteome is particularly relevant from a translational point of view because it may contribute to better understanding the molecular bases of cancer development and progression and may provide new potential prognostic and diagnostic biomarkers as well as novel molecular targets for anti-cancer treatment. Making an inventory of the mitochondrial proteins has been particularly challenging given that there is no unique consensus targeting sequence that directs protein import into mitochondria, some proteins are present at very low levels, while other proteins are expressed only in some cell types, in a particular developmental stage or under specific stress conditions. This review aims at providing the state-of-the-art on methodologies used to characterize the mitochondrial proteome in tumors and highlighting the biological relevance of changes in expression and delocalization of proteins in and out the mitochondria in cancer biology.
    Keywords:  cancer; immunofluorescence; interactome; mass spectrometry; mitochondria; mitochondrial proteome
    DOI:  https://doi.org/10.3390/biology9120479
  61. Cancer Res. 2020 Dec 22. pii: canres.2488.2020. [Epub ahead of print]
    Lenz LS, Faccioni JL, Bracco PA, Santos JAF, Pereira LC, Buss JH, Tamborindeguy MT, Torgo D, Monteiro T, Mantovani GB, Santo CN, Marcolin JC, Dalsin E, Vigo A, Callegari-Jacques SM, Silva AO, Onzi GR, Begnini KR, Lenz G.
      Several phenotypes that impact the capacity of cancer cells to survive and proliferate are dynamic. Here we used the number of cells in colonies as an assessment of fitness and devised a novel method called Dynamic Fitness Analysis (DynaFit) to measure the dynamics in fitness over the course of colony formation. DynaFit is based on the variance in growth rate of a population of founder cells compared with the variance in growth rate of colonies with different sizes. DynaFit revealed that cell fitness in cancer cell lines, primary cancer cells, and fibroblasts under unhindered growth conditions is dynamic. Key cellular mechanisms such as ERK signaling and cell cycle synchronization differed significantly among cells in colonies after 2 to 4 generations and became indistinguishable from randomly sampled cells regarding these features. In the presence of cytotoxic agents, colonies reduced their variance in growth rate when compared to their founder cell, indicating a dynamic nature in the capacity to survive and proliferate in the presence of a drug. This finding was supported by measurable differences in DNA damage and induction of senescence among cells of colonies. The presence of epigenetic modulators during the formation of colonies stabilized their fitness for at least 4 generations. Collectively, these results support the understanding that cancer cell fitness is dynamic and its modulation is a fundamental aspect to be considered in comprehending cancer cell biology and its response to therapeutic interventions.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2488
  62. EMBO Mol Med. 2020 Dec 28. e13158
    Soria LR, Gurung S, De Sabbata G, Perocheau DP, De Angelis A, Bruno G, Polishchuk E, Paris D, Cuomo P, Motta A, Orford M, Khalil Y, Eaton S, Mills PB, Waddington SN, Settembre C, Muro AF, Baruteau J, Brunetti-Pierri N.
      Urea cycle disorders (UCD) are inherited defects in clearance of waste nitrogen with high morbidity and mortality. Novel and more effective therapies for UCD are needed. Studies in mice with constitutive activation of autophagy unravelled Beclin-1 as druggable candidate for therapy of hyperammonemia. Next, we investigated efficacy of cell-penetrating autophagy-inducing Tat-Beclin-1 (TB-1) peptide for therapy of the two most common UCD, namely ornithine transcarbamylase (OTC) and argininosuccinate lyase (ASL) deficiencies. TB-1 reduced urinary orotic acid and improved survival under protein-rich diet in spf-ash mice, a model of OTC deficiency (proximal UCD). In AslNeo/Neo mice, a model of ASL deficiency (distal UCD), TB-1 increased ureagenesis, reduced argininosuccinate, and improved survival. Moreover, it alleviated hepatocellular injury and decreased both cytoplasmic and nuclear glycogen accumulation in AslNeo/Neo mice. In conclusion, Beclin-1-dependent activation of autophagy improved biochemical and clinical phenotypes of proximal and distal defects of the urea cycle.
    Keywords:  OTC deficiency; Tat-Beclin-1 peptide; argininosuccinic aciduria; autophagy; urea cycle disorders
    DOI:  https://doi.org/10.15252/emmm.202013158
  63. Front Med. 2021 Jan 02.
    Lv L, Lei Q.
      Cancer development is a complicated process controlled by the interplay of multiple signaling pathways and restrained by oxygen and nutrient accessibility in the tumor microenvironment. High plasticity in using diverse nutrients to adapt to metabolic stress is one of the hallmarks of cancer cells. To respond to nutrient stress and to meet the requirements for rapid cell proliferation, cancer cells reprogram metabolic pathways to take up more glucose and coordinate the production of energy and intermediates for biosynthesis. Such actions involve gene expression and activity regulation by the moonlighting function of oncoproteins and metabolic enzymes. The signal - moonlighting protein - metabolism axis facilitates the adaptation of tumor cells under varying environment conditions and can be therapeutically targeted for cancer treatment.
    Keywords:  epigenetics; moonlighting function; tumor metabolism
    DOI:  https://doi.org/10.1007/s11684-020-0818-1
  64. Bioinformatics. 2020 Dec 30. 36(Supplement_2): i911-i918
    Liu Q, Hu Z, Jiang R, Zhou M.
      MOTIVATION: Accurate prediction of cancer drug response (CDR) is challenging due to the uncertainty of drug efficacy and heterogeneity of cancer patients. Strong evidences have implicated the high dependence of CDR on tumor genomic and transcriptomic profiles of individual patients. Precise identification of CDR is crucial in both guiding anti-cancer drug design and understanding cancer biology.RESULTS: In this study, we present DeepCDR which integrates multi-omics profiles of cancer cells and explores intrinsic chemical structures of drugs for predicting CDR. Specifically, DeepCDR is a hybrid graph convolutional network consisting of a uniform graph convolutional network and multiple subnetworks. Unlike prior studies modeling hand-crafted features of drugs, DeepCDR automatically learns the latent representation of topological structures among atoms and bonds of drugs. Extensive experiments showed that DeepCDR outperformed state-of-the-art methods in both classification and regression settings under various data settings. We also evaluated the contribution of different types of omics profiles for assessing drug response. Furthermore, we provided an exploratory strategy for identifying potential cancer-associated genes concerning specific cancer types. Our results highlighted the predictive power of DeepCDR and its potential translational value in guiding disease-specific drug design.
    AVAILABILITY AND IMPLEMENTATION: DeepCDR is freely available at https://github.com/kimmo1019/DeepCDR.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa822
  65. Cell Rep. 2020 Dec 22. pii: S2211-1247(20)31524-2. [Epub ahead of print]33(12): 108535
    Leung C, Murad KBA, Tan ALT, Yada S, Sagiraju S, Bode PK, Barker N.
      Regeneration of adult skeletal muscle is driven largely by resident satellite cells, a stem cell population increasingly considered to display a high degree of molecular heterogeneity. In this study, we find that Lgr5, a receptor for Rspo and a potent mediator of Wnt/β-catenin signaling, marks a subset of activated satellite cells that contribute to muscle regeneration. Lgr5 is found to be rapidly upregulated in purified myogenic progenitors following acute cardiotoxin-induced injury. In vivo lineage tracing using our Lgr5-2ACreERT2R26tdTomatoLSL reporter mouse model shows that Lgr5+ cells can reconstitute damaged muscle fibers following muscle injury, as well as replenish the quiescent satellite cell pool. Moreover, conditional mutation in Lgr52ACreERT2;KrasG12D;Trp53flox/flox mice drives undifferentiated pleomorphic sarcoma formation in adult mice, thereby substantiating Lgr5+ cells as a cell of origin of sarcomas. Our findings provide the groundwork for developing Rspo/Wnt-signaling-based therapeutics to potentially enhance regenerative outcomes of skeletal muscles in degenerative muscle diseases.
    Keywords:  Lgr5; lineage tracing; muscle injury; muscle progenitors; muscle regeneration; sarcoma; satellite stem cells
    DOI:  https://doi.org/10.1016/j.celrep.2020.108535
  66. Front Pharmacol. 2020 ;11 590344
    Lim J, Murthy A.
      Autophagy is a catabolic process that targets its cargo for lysosomal degradation. In addition to its function in maintaining tissue homeostasis, autophagy is recognized to play a context-dependent role in cancer. Autophagy may inhibit tumor initiation under specific contexts; however, a growing body of evidence supports a pro-tumorigenic role of this pathway in established disease. In this setting, autophagy drives treatment resistance, metabolic changes, and immunosuppression both in a tumor-intrinsic and extrinsic manner. This observation has prompted renewed interest in targeting autophagy for cancer therapy. Novel genetic models have proven especially insightful, revealing unique and overlapping roles of individual autophagy-related genes in tumor progression. Despite identification of pharmacologically actionable nodes in the pathway, fundamental challenges still exist for successful therapeutic inhibition of autophagy. Here we summarize the current understanding of autophagy as a driver of resistance against targeted and immuno-therapies and highlight knowledge gaps that, if addressed, may provide meaningful advances in the treatment of cancer.
    Keywords:  agy; autoph; cancer; immunology; immunotherapy; oncology
    DOI:  https://doi.org/10.3389/fphar.2020.590344
  67. Pancreas. 2021 Jan 01. 50(1): 37-46
    Sonohara F, Yamada S, Kurimoto K, Inokawa Y, Takami H, Hayashi M, Shimizu D, Hattori N, Kanda M, Tanaka C, Nakayama G, Koike M, Fujii T, Kodera Y.
      OBJECTIVES: In this study, we retrospectively assessed the feasibility and prognostic efficacy of perioperative chemo(radio)therapy for pancreatic cancer (PC) patients according to age.METHODS: A total of 556 consecutive patients who underwent curative-intent pancreatectomy for PC between 2000 and 2018 were enrolled.
    RESULTS: Of the 556 patients who underwent resection, 95 (17%) were elderly (age, ≥75 years). Postoperative complications did not significantly differ between the 2 age groups, and postoperative prognoses were also similar (recurrence-free survival [RFS], P = 0.68; overall survival [OS], P = 0.28). In this cohort, 103 patients (19%) underwent preoperative chemo(radio)therapy, and 417 (77%) underwent postoperative chemotherapy. Perioperative therapy was found to be significantly beneficial for younger patients (preoperative therapy: RFS, P = 0.006; OS, P < 0.001; postoperative therapy: RFS, P < 0.001; OS, P < 0.001). Conversely, no significant survival benefit of perioperative therapy was found for the elderly (preoperative therapy: RFS, P = 0.28; OS, P = 0.44; postoperative therapy: RFS, P = 0.77; OS, P = 0.08).
    CONCLUSIONS: This study demonstrated that, although perioperative therapy is feasible for selected elderly patients with PC, this approach might not be as beneficial as it is for younger PC patients.
    DOI:  https://doi.org/10.1097/MPA.0000000000001712
  68. J Exp Med. 2021 Feb 01. pii: e20201217. [Epub ahead of print]218(2):
    Wang A, Ding L, Wu Z, Ding R, Teng XL, Wang F, Hu Z, Chen L, Yu X, Zou Q.
      Autophagy programs the metabolic and functional fitness of regulatory T (T reg) cells to establish immune tolerance, yet the mechanisms governing autophagy initiation in T reg cells remain unclear. Here, we show that the E3 ubiquitin ligase ZFP91 facilitates autophagy activation to sustain T reg cell metabolic programming and functional integrity. T reg cell-specific deletion of Zfp91 caused T reg cell dysfunction and exacerbated colonic inflammation and inflammation-driven colon carcinogenesis. TCR-triggered autophagy induction largely relied on T reg cell-derived ZFP91 to restrict hyperglycolysis, which is required for the maintenance of T reg cell homeostasis. Mechanistically, ZFP91 rapidly translocated from the nucleus to the cytoplasm in response to TCR stimulation and then mediated BECN1 ubiquitination to promote BECN1-PIK3C3 complex formation. Therefore, our results highlight a ZFP91-dependent mechanism promoting TCR-initiated autophagosome maturation to maintain T reg cell homeostasis and function.
    DOI:  https://doi.org/10.1084/jem.20201217
  69. Trends Mol Med. 2020 Dec 28. pii: S1471-4914(20)30315-4. [Epub ahead of print]
    Weskamp K, Olwin BB, Parker R.
      Skeletal muscle formation is a complex process that requires tight spatiotemporal control of key myogenic factors. Emerging evidence suggests that RNA processing is crucial for the regulation of these factors, and that multiple post-transcriptional regulatory pathways work dependently and independently of one another to enable precise control of transcripts throughout muscle development and repair. Moreover, disruption of these pathways is implicated in neuromuscular disease, and the recent development of RNA-mediated therapies shows enormous promise in the treatment of these disorders. We discuss the overlapping post-transcriptional regulatory pathways that mediate muscle development, how these pathways are disrupted in neuromuscular disorders, and advances in RNA-mediated therapies that present a novel approach to the treatment of these diseases.
    Keywords:  RNA; myogenesis; myopathy; neuromuscular disease; post-transcriptional regulation; skeletal muscle
    DOI:  https://doi.org/10.1016/j.molmed.2020.12.002
  70. Cancers (Basel). 2020 Dec 24. pii: E36. [Epub ahead of print]13(1):
    Kimura N, Yamada S, Takami H, Murotani K, Yoshioka I, Shibuya K, Sonohara F, Hoshino Y, Hirano K, Watanabe T, Baba H, Mori K, Miwa T, Kanda M, Hayashi M, Matsui K, Okumura T, Kodera Y, Fujii T.
      Background: The objective of this study was to investigate the optimal neoadjuvant therapy (NAT) for borderline resectable pancreatic cancer invading the portal vein (BR-PV) or abutting major arteries (BR-A). Methods: We retrospectively analyzed 88 patients with BR-PV and 111 patients with BR-A. Results: In BR-PV patients who underwent upfront surgery (n = 46)/NAT (n = 42), survival was significantly better in the NAT group (3-year overall survival (OS): 5.8%/35.5%, p = 0.004). In BR-A patients who underwent upfront surgery (n = 48)/NAT (n = 63), survival was also significantly better in the NAT group (3-year OS:15.5%/41.7%, p < 0.001). The prognosis tended to be better in patients who received newer chemotherapeutic regimens, such as FOLFIRINOX and gemcitabine with nab-paclitaxel. In 36 BR-PV patients who underwent surgery after NAT, univariate analysis revealed that normalization of tumor marker (TM) levels (p = 0.028) and preoperative high prognostic nutritional index (PNI) (p = 0.022) were significantly associated with a favorable prognosis. In 39 BR-A patients who underwent surgery after NAT, multivariate analysis revealed that preoperative PNI > 42.5 was an independent prognostic factor (HR: 0.15, p = 0.014). Conclusions: NAT using newer chemotherapy is essential for improving the prognosis of BR pancreatic cancer. These findings suggest that prognosis may be prolonged by maintaining good nutritional status during preoperative treatment.
    Keywords:  borderline resectable; chemoradiotherapy; neoadjuvant treatment; pancreatic cancer; prognostic nutritional index
    DOI:  https://doi.org/10.3390/cancers13010036
  71. Cell Syst. 2020 Dec 21. pii: S2405-4712(20)30464-6. [Epub ahead of print]
    Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C.
      Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides informative data resources for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in a complex multidimensional space and mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of cell dynamics with a machine-learning framework, implemented in TensorFlow. We tested the modeling framework on a perturbation-response dataset of a melanoma cell line after drug treatments. The models can be efficiently trained to describe cellular behavior accurately. Even though completely data driven and independent of prior knowledge, the resulting de novo network models recapitulate some known interactions. The approach is readily applicable to various kinetic models of cell biology. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
    Keywords:  cancer; cell dynamics; combinatorial therapy; dynamical systems; interpretability; machine learning; network pharmacology; perturbation biology; systems biology
    DOI:  https://doi.org/10.1016/j.cels.2020.11.013
  72. Semin Cancer Biol. 2020 Dec 26. pii: S1044-579X(20)30277-7. [Epub ahead of print]
    Moiseeva O, Guillon J, Ferbeyre G.
      Senescence is a tumor suppressor response that prevents the proliferation of mutated cells and alert the immune system for their elimination. However, this program is not perfect and with time additional genetic and epigenetic changes can impair tumor suppression and promote cancer progression both in cell autonomous and non-cell autonomous manners. A polyploid barrier is implemented in senescent cells to further prevent cell expansion but polyploid cells can generate highly malignant tumor cells via de-polyploidization. The nuclear lamina can act as an additional fail safe to prevent cancer in these cells and drugs able to stabilize the nuclear lamina may help to treat cancers by preventing senescence escape.
    Keywords:  Nuclear lamina; PML; Polyploidy; Progerin; Therapy induced senescence (TIS)
    DOI:  https://doi.org/10.1016/j.semcancer.2020.12.017
  73. FEBS Open Bio. 2021 Jan 01.
    Ye Y, Chen Z, Shen Y, Qin Y, Wang H.
      Abnormal lipid metabolism is closely related to the malignant biological behavior of tumor cells. Such abnormal lipid metabolism provides energy for rapid proliferation, and certain genes related to lipid metabolism encode important components of tumor signaling pathways. In this study, we analyzed pancreatic cancer datasets from The Cancer Genome Atlas (TCGA) and searched for prognostic genes related to lipid metabolism in the Molecular Signature Database. A risk score model was built and verified using the GSE57495 dataset and International Cancer Genome Consortium (ICGC) dataset. Four molecular subtypes and 4,249 differentially expressed genes were identified. The differentially expressed genes obtained by Weighted Gene Co-expression Network Construction (WGCNA) analysis were intersected with 4249 differentially expressed genes to obtain a total of 1340 differentially expressed genes. The final prognosis model included CA8, CEP55, GNB3 and SGSM2, and these had a significant effect on overall survival (OS). The area under the curve (AUC) at 1 years, 3 years and 5 years was 0.72, 0.79 and 0.87, respectively. These same results were obtained using the validation cohort. Survival analysis data showed that the model could stratify the prognosis of patients with different clinical characteristics and the model has clinical independence. Functional analysis indicated that the model is associated with multiple cancer-related pathways. Compared with published models, our model has a higher C-index and greater risk value. In summary, this 4-gene signature is an independent risk factor of pancreatic cancer survival, and may be an effective prognostic indicator.
    Keywords:  4-gene signature; TCGA; WGCNA; pancreatic cancer; prognosis
    DOI:  https://doi.org/10.1002/2211-5463.13074
  74. Cancer Res. 2020 Dec 21. pii: canres.0668.2020. [Epub ahead of print]
    Lee S, Amgad M, Mobadersany P, McCormick M, Pollack BP, Elfandy H, Hussein H, Gutman DA, Cooper LA.
      Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer, but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists. In this paper, we describe HistomicsML2, a software tool for learn-by-example training of machine learning classifiers for histologic patterns in whole-slide images. This tool improves training efficiency and classifier performance by guiding users to the most informative training examples for labeling and can be used to develop classifiers for prospective application or as a rapid annotation tool that is adaptable to different cancer types. HistomicsML2 runs as a containerized server application that provides web-based user interfaces for classifier training, validation, exporting inference results, and collaborative review and can be deployed on GPU servers or cloud platforms. We demonstrate the utility of this tool by using it to classify tumor-infiltrating lymphocytes in breast carcinoma and cutaneous melanoma.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-0668
  75. Gastroenterology. 2020 Dec 29. pii: S0016-5085(20)35597-9. [Epub ahead of print]
    Kaur S, Jain M, Batra SK.
      
    Keywords:  IPMN; MUC5AC; and extracellular vesicles; cystic lesions; pancreatic cancer
    DOI:  https://doi.org/10.1053/j.gastro.2020.12.039
  76. Mol Omics. 2020 Dec 23.
    Tao L, Zhong L, Li Y, Li D, Xiu D, Zhou J.
      Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis largely owing to its inefficient diagnosis, rapid progress, and tenacious drug resistance. Here, we aimed to analyze the expressive patterns of proteins and phosphorylation in PDAC tissue samples and compare them to normal pancreatic tissue to investigate the underlying mechanisms and to reveal potential protein targets for diagnosis and drug development. Liquid chromatography coupled to mass spectrometry (LC-MS) based proteomics and phosphoproteomics analyses were performed using 20 pairs of patient-derived PDAC tissue and normal pancreatic tissue samples. Protein identification and quantification were conducted using MaxQuant software. Bioinformatics analysis was used to retrieve PDAC-relevant pathways and gene ontology (GO) terms. 4985 proteins and 3643 phosphoproteins were identified with high confidence; of these, 322 proteins and 235 phosphoproteins were dysregulated in PDAC. Several pathways, including several extracellular matrix-related pathways, were found to be strongly associated with PDAC. Further, the expression levels of filamin A (FLNA), integrin alpha-V (ITGAV), thymidine phosphorylase (TYMP), medium-chain specific acyl-CoA dehydrogenase, mitochondrial (ACADM), short-chain specific acyl-CoA dehydrogenase, mitochondrial (ACADS), and acetyl-CoA acetyltransferase, mitochondrial (ACAT1) were examined through western blot and immunohistochemistry analysis, and the results confirmed the validity of the proteomics analysis results. These findings provide comprehensive insight into the dysregulated regulative networks in PDAC tissue samples at the protein and phosphorylation levels, and they provide clues for further pathological studies and drug-target development.
    DOI:  https://doi.org/10.1039/d0mo00125b
  77. FEBS J. 2021 Jan 02.
    Koch PA, Dornan GL, Hessenberger M, Haucke V.
      The phosphoinositide 3-kinase (PI3K) family of lipid-modifying enzymes plays vital roles in cell signalling and membrane trafficking through the production of 3-phosphorylated phosphoinositides. Numerous studies have analyzed the structure and function of class I and class III PI3Ks. In contrast, we know comparably little about the structure and physiological functions of the class II enzymes. Only recent studies have begun to unravel their roles in development, endocytic and endolysosomal membrane dynamics, signal transduction, and cell migration, while the mechanisms that control their localization and enzymatic activity remain largely unknown. Here we summarize our current knowledge of the class II PI3Ks and outline open questions related to their structure, enzymatic activity, and their physiological and pathophysiological functions.
    Keywords:  Phosphatidylinositol 3-kinase; cancer; cell migration; endocytosis; myopathy; nutrient signaling; vesicle traffic
    DOI:  https://doi.org/10.1111/febs.15692
  78. J Cell Physiol. 2020 Dec 24.
    Liu YR, Cheng YQ, Wang SB, Su YR, Liu Y, Li CY, Jin L, Wan Q, Sang X, Wang ZC.
      Senescent cells can secrete a plethora of cytokines which induce senescent phenotype of neighboring cells and was called senescence-associated secretory phenotype. Previously, it was believed that cancer was caused by the infinite division and uncontrolled proliferation of cells. Based on this, anticancer treatments were all aimed at killing cancer cells. Cancer is now considered an age-related disease. Cancer cells are not exogenous, but one of the worst results of injuries which initially induce cell senescence. Therefore, reversing cell senescence can fundamentally prevent and treat cancer. Though current anticancer treatments induce the cancer cells apoptosis, they induce senescence of normal cells at the same time, thus promoting the occurrence and development of cancer and forming a vicious circle. Extracellular vesicles (EVs) are nano-sized vesicles which partially mirror their parent cells. In the tumor microenvironment, EVs of senescent cells can change the expression profile of cancer cells, contributing to their resistance to chemotherapy. There is growing evidence indicates that stem cell EVs exert effective antiaging and anticancer actions by transferring functional microRNAs and proteins. This review will summarize the therapeutic role of stem cell EVs in reversing aging and cancer, which suggests the broad clinical application perspective.
    Keywords:  cancer; cell senescence; extracellular vesicles (EVs); miRNA; stem cell
    DOI:  https://doi.org/10.1002/jcp.30212
  79. Science. 2021 Jan 01. pii: eabb0738. [Epub ahead of print]371(6524):
    Sancar A, Van Gelder RN.
      The circadian clock coordinates daily rhythmicity of biochemical, physiologic, and behavioral functions in humans. Gene expression, cell division, and DNA repair are modulated by the clock, which gives rise to the hypothesis that clock dysfunction may predispose individuals to cancer. Although the results of many epidemiologic and animal studies are consistent with there being a role for the clock in the genesis and progression of tumors, available data are insufficient to conclude that clock disruption is generally carcinogenic. Similarly, studies have suggested a circadian time-dependent efficacy of chemotherapy, but clinical trials of chronochemotherapy have not demonstrated improved outcomes compared with conventional regimens. Future hypothesis-driven and discovery-oriented research should focus on specific interactions between clock components and carcinogenic mechanisms to realize the full clinical potential of the relationship between clocks and cancer.
    DOI:  https://doi.org/10.1126/science.abb0738
  80. Nature. 2020 Dec 23.
    Gao X, Zhang D, Xu C, Li H, Caron KM, Frenette PS.
      Haematopoietic stem cells (HSCs) reside in specialized microenvironments in the bone marrow-often referred to as 'niches'-that represent complex regulatory milieux influenced by multiple cellular constituents, including nerves1,2. Although sympathetic nerves are known to regulate the HSC niche3-6, the contribution of nociceptive neurons in the bone marrow remains unclear. Here we show that nociceptive nerves are required for enforced HSC mobilization and that they collaborate with sympathetic nerves to maintain HSCs in the bone marrow. Nociceptor neurons drive granulocyte colony-stimulating factor (G-CSF)-induced HSC mobilization via the secretion of calcitonin gene-related peptide (CGRP). Unlike sympathetic nerves, which regulate HSCs indirectly via the niche3,4,6, CGRP acts directly on HSCs via receptor activity modifying protein 1 (RAMP1) and the calcitonin receptor-like receptor (CALCRL) to promote egress by activating the Gαs/adenylyl cyclase/cAMP pathway. The ingestion of food containing capsaicin-a natural component of chili peppers that can trigger the activation of nociceptive neurons-significantly enhanced HSC mobilization in mice. Targeting the nociceptive nervous system could therefore represent a strategy to improve the yield of HSCs for stem cell-based therapeutic agents.
    DOI:  https://doi.org/10.1038/s41586-020-03057-y
  81. J Cell Mol Med. 2020 Dec 30.
    Wu N, Xu XF, Xin JQ, Fan JW, Wei YY, Peng QX, Duan LF, Wang W, Zhang H.
      The activation of pancreatic stellate cells (PSCs) plays a critical role in the progression of pancreatic fibrosis. Nuclear factor-kappa B (NF-κB) is associated with chronic pancreatitis (CP). Previous evidence indicated that NF-κB in acinar cells played a double-edged role upon pancreatic injury, whereas NF-κB in inflammatory cells promoted the progression of CP. However, the effects of NF-κB in PSCs have not been studied. In the present study, using two CP models and RNAi strategy of p65 in cultured PSCs, we found that the macrophage infiltration and MCP-1 expression were increased, and the NF-κBp65 protein level was elevated. NF-κBp65 was co-expressed with PSCs. In vitro, TGF-β1 induced overexpression of the TGF-β receptor 1, phosphorylated TGF-β1-activated kinase 1 (p-TAK1) and NF-κB in the PSCs. Moreover, the concentration of MCP-1 in the supernatant of activated PSCs was elevated. The migration of BMDMs was promoted by the supernatant of activated PSCs. Further knockdown of NF-κBp65 in PSCs resulted in a decline of BMDM migration, accompanied by a lower production of MCP-1. These findings indicate that TGF-β1 can induce the activation of NF-κB pathway in PSCs by regulating p-TAK1, and the NF-κB pathway in PSCs may be a target of chronic inflammation and fibrosis.
    Keywords:  chronic pancreatitis; fibrosis; inflammatory; nuclear factor-kappa B; pancreatic stellate cells
    DOI:  https://doi.org/10.1111/jcmm.16213
  82. Clin Cancer Res. 2020 Dec 22. pii: clincanres.3281.2020. [Epub ahead of print]
    Hackeng WM, Dreijerink KMA, de Leng WWJ, Morsink FH, Valk GD, Vriens MR, Offerhaus GJA, Geisenberger C, Brosens LAA.
      PURPOSE: The primary origin of neuroendocrine tumor metastases can be difficult to determine by histopathology alone, but is critical for therapeutic decision making. DNA methylation-based profiling is now routinely used in the diagnostic workup of brain tumors. This has been enabled by the availability of cost-efficient array-based platforms. We have extended these efforts to augment histopathological diagnosis in neuroendocrine tumors.EXPERIMENTAL DESIGN AND RESULTS: We compiled data of 69 small-intestinal, pulmonary, and pancreatic neuroendocrine tumors. These data were used to build a ridge regression calibrated random forest classification algorithm (NEN-ID) that predicts the origin of tumor samples with high accuracy (> 95%). The model was validated during 3x3 nested cross validation and tested in a local and external cohort (n = 198 cases). In addition, we show that our diagnostic approach is robust across a range of possible confounding experimental parameters such as tumor purity and array quality. A software infrastructure and online user interface was built to make the model available to the scientific community.
    CONCLUSIONS: This DNA methylation-based prediction model can be used in the workup for patients with neuroendocrine tumors of unknown primary. To facilitate validation and clinical implementation, we provide a user-friendly, publicly available web-based version of NEN-ID.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-3281