bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020‒12‒06
sixty-four papers selected by
Kıvanç Görgülü
Technical University of Munich


  1. Cell Metab. 2020 Dec 01. pii: S1550-4131(20)30598-2. [Epub ahead of print]32(6): 981-995.e7
    Corrado M, Edwards-Hicks J, Villa M, Flachsmann LJ, Sanin DE, Jacobs M, Baixauli F, Stanczak M, Anderson E, Azuma M, Quintana A, Curtis JD, Clapes T, Grzes KM, Kabat AM, Kyle R, Patterson AE, Geltink RK, Amulic B, Steward CG, Strathdee D, Trompouki E, O'Sullivan D, Pearce EJ, Pearce EL.
      Mitochondria constantly adapt to the metabolic needs of a cell. This mitochondrial plasticity is critical to T cells, which modulate metabolism depending on antigen-driven signals and environment. We show here that de novo synthesis of the mitochondrial membrane-specific lipid cardiolipin maintains CD8+ T cell function. T cells deficient for the cardiolipin-synthesizing enzyme PTPMT1 had reduced cardiolipin and responded poorly to antigen because basal cardiolipin levels were required for activation. However, neither de novo cardiolipin synthesis, nor its Tafazzin-dependent remodeling, was needed for T cell activation. In contrast, PTPMT1-dependent cardiolipin synthesis was vital when mitochondrial fitness was required, most notably during memory T cell differentiation or nutrient stress. We also found CD8+ T cell defects in a small cohort of patients with Barth syndrome, where TAFAZZIN is mutated, and in a Tafazzin-deficient mouse model. Thus, the dynamic regulation of a single mitochondrial lipid is crucial for CD8+ T cell immunity.
    Keywords:  Barth Syndrome; CD8 T cells; PTPMT1; Tafazzin; cardiolipin; immune memory; immunometabolism; mitochodria
    DOI:  https://doi.org/10.1016/j.cmet.2020.11.003
  2. Nat Rev Genet. 2020 Nov 30.
    Persi E, Wolf YI, Horn D, Ruppin E, Demichelis F, Gatenby RA, Gillies RJ, Koonin EV.
      Intratumour heterogeneity and phenotypic plasticity, sustained by a range of somatic aberrations, as well as epigenetic and metabolic adaptations, are the principal mechanisms that enable cancers to resist treatment and survive under environmental stress. A comprehensive picture of the interplay between different somatic aberrations, from point mutations to whole-genome duplications, in tumour initiation and progression is lacking. We posit that different genomic aberrations generally exhibit a temporal order, shaped by a balance between the levels of mutations and selective pressures. Repeat instability emerges first, followed by larger aberrations, with compensatory effects leading to robust tumour fitness maintained throughout the tumour progression. A better understanding of the interplay between genetic aberrations, the microenvironment, and epigenetic and metabolic cellular states is essential for early detection and prevention of cancer as well as development of efficient therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41576-020-00299-4
  3. Cell Rep. 2020 Dec 01. pii: S2211-1247(20)31435-2. [Epub ahead of print]33(9): 108446
    Wood NE, Kositangool P, Hariri H, Marchand AJ, Henne WM.
      Isogenic cells manifest distinct cellular fates for a single stress; however, the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergoes distinct fates, becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, senescence occurs even in the absence of lipid droplets. Importantly, we identify the nutrient-sensing kinase Rim15 as a key biomarker predicting cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contains determinants influencing post-stress fate and demonstrate that specific nutrient signaling, stress response, trafficking, and inter-organelle biomarkers are early indicators for long-term fate outcomes.
    Keywords:  Bayesian analysis; LD; NVJ; cell cycle; cellular decision making; lipid droplet; nucleus-vacuole junction; quantitative imaging; quiescence; senescence; statistical evidence
    DOI:  https://doi.org/10.1016/j.celrep.2020.108446
  4. Nat Mater. 2020 Nov 30.
    Maller O, Drain AP, Barrett AS, Borgquist S, Ruffell B, Zakharevich I, Pham TT, Gruosso T, Kuasne H, Lakins JN, Acerbi I, Barnes JM, Nemkov T, Chauhan A, Gruenberg J, Nasir A, Bjarnadottir O, Werb Z, Kabos P, Chen YY, Hwang ES, Park M, Coussens LM, Nelson AC, Hansen KC, Weaver VM.
      Stromal stiffening accompanies malignancy, compromises treatment and promotes tumour aggression. Clarifying the molecular nature and the factors that regulate stromal stiffening in tumours should identify biomarkers to stratify patients for therapy and interventions to improve outcome. We profiled lysyl hydroxylase-mediated and lysyl oxidase-mediated collagen crosslinks and quantified the greatest abundance of total and complex collagen crosslinks in aggressive human breast cancer subtypes with the stiffest stroma. These tissues harbour the highest number of tumour-associated macrophages, whose therapeutic ablation in experimental models reduced metastasis, and decreased collagen crosslinks and stromal stiffening. Epithelial-targeted expression of the crosslinking enzyme, lysyl oxidase, had no impact on collagen crosslinking in PyMT mammary tumours, whereas stromal cell targeting did. Stromal cells in microdissected human tumours expressed the highest level of collagen crosslinking enzymes. Immunohistochemical analysis of biopsies from a cohort of patients with breast cancer revealed that stromal expression of lysyl hydroxylase 2, an enzyme that induces hydroxylysine aldehyde-derived collagen crosslinks and stromal stiffening, correlated significantly with disease specific mortality. The findings link tissue inflammation, stromal cell-mediated collagen crosslinking and stiffening to tumour aggression and identify lysyl hydroxylase 2 as a stromal biomarker.
    DOI:  https://doi.org/10.1038/s41563-020-00849-5
  5. Genes Dev. 2020 Dec 01. 34(23-24): 1577-1598
    Shen M, Kang Y.
      Metastasis is the ultimate "survival of the fittest" test for cancer cells, as only a small fraction of disseminated tumor cells can overcome the numerous hurdles they encounter during the transition from the site of origin to a distinctly different distant organ in the face of immune and therapeutic attacks and various other stresses. During cancer progression, tumor cells develop a variety of mechanisms to cope with the stresses they encounter, and acquire the ability to form metastases. Restraining these stress-releasing pathways could serve as potentially effective strategies to prevent or reduce metastasis and improve the survival of cancer patients. Here, we provide an overview of the tumor-intrinsic, microenvironment- and treatment-induced stresses that tumor cells encounter in the metastatic cascade and the molecular pathways they develop to relieve these stresses. We also summarize the preclinical and clinical studies that evaluate the potential therapeutic benefit of targeting these stress-relieving pathways.
    Keywords:  cancer therapeutics; metastasis; stress; tumor microenvironment
    DOI:  https://doi.org/10.1101/gad.343251.120
  6. Sci Adv. 2020 Dec;pii: eabc4517. [Epub ahead of print]6(49):
    Hsieh A, Pitarresi JR, Lerner J, Donahue G, Hsiehchen D, Rustgi AK, Zaret K.
      Here, we selectively target pancreatic ductal adenocarcinoma (PDAC) cells harboring a hemizygous gene essential for cell growth. MYB binding protein 1A (MYBBP1A), encoding a chromatin-bound protein, is hemizygous in most of the PDAC due to a chromosome 17p deletion that also spans TP53 We find that hemizygous MYBBP1A loss in isogenic PDAC cells promotes tumorigenesis but, paradoxically, homozygous MYBBP1A loss is associated with impaired cell growth and decreased tumorigenesis. Poly-adenosine 5'-diphosphate-ribose polymerase 1 (PARP1) interacts with MYBBP1A and displaces it from chromatin. Small molecules, such as olaparib, that trap PARP1 to chromatin are able to evict the minimal pool of chromatin-bound MYBBP1A protein in MYBBP1A hemizygous cells and impair cell growth, greater than its impact on wild-type cells. Our findings reveal how a cell essential gene with one allele lost in cancer cells can be preferentially susceptible to a specific molecular therapy, when compared to wild-type cells.
    DOI:  https://doi.org/10.1126/sciadv.abc4517
  7. Cancer Immunol Res. 2020 Dec 04. pii: canimm.0384.2020. [Epub ahead of print]
    Drijvers JM, Gillis JE, Muijlwijk T, Nguyen TH, Gaudiano EF, Harris IS, LaFleur MW, Ringel AE, Yao CH, Kurmi K, Juneja VR, Trombley JD, Haigis M, Sharpe AH.
      Metabolic constraints in the tumor microenvironment constitute a barrier to effective anti-tumor immunity and similarities in the metabolic properties of T cells and cancer cells impede the specific therapeutic targeting of metabolism in either population. To identify distinct metabolic vulnerabilities of CD8+ T cells and cancer cells, we developed a high-throughput in vitro pharmacologic screening platform and used it to measure the cell type-specific sensitivities of activated CD8+ T cells and B16 melanoma cells to a wide array of metabolic perturbations during antigen-specific killing of cancer cells by CD8+ T cells. We illustrated the applicability of this screening platform by showing that CD8+ T cells were more sensitive to ferroptosis than B16 and MC38 cancer cells. Overexpression of ferroptosis suppressor protein 1 (FSP1) or cytosolic GPX4 yielded ferroptosis-resistant CD8+ T cells without compromising their function, while genetic deletion of the ferroptosis sensitivity-promoting enzyme acyl-CoA synthetase long-chain family member 4 (ACSL4) protected CD8+ T cells from ferroptosis, but impaired anti-tumor CD8+ T cell responses. Our screen also revealed high T cell-specific vulnerabilities for compounds targeting NAD+ metabolism or autophagy and ER stress pathways. We focused the current screening effort on metabolic agents. However, this in vitro screening platform may also be valuable for rapid testing of other types of compounds to identify regulators of anti-tumor CD8+ T-cell function and potential therapeutic targets.
    DOI:  https://doi.org/10.1158/2326-6066.CIR-20-0384
  8. Cancer Lett. 2020 Nov 29. pii: S0304-3835(20)30625-X. [Epub ahead of print]
    Lu W, Li X, Luo Y.
      The endocrine FGF21 was discovered as a novel metabolic regulator in 2005 with new functions bifurcating from the canonic heparin-binding FGFs that directly promote cell proliferation and growth independent of a co-receptor. Early studies have demonstrated that FGF21 is a stress sensor in the liver and possibly, several other endocrine and metabolic tissues. Hepatic FGF21 signals via endocrine routes to quench episodes of metabolic derangements, promoting metabolic homeostasis. The convergence of mouse and human studies shows that FGF21 promotes lipid catabolism, including lipolysis, fatty acid oxidation, mitochondrial oxidative activity, and thermogenic energy dissipation, rather than directly regulating insulin and appetite. The white and brown adipose tissues and, to some extent, the hypothalamus, all of which host a transmembrane receptor binary complex of FGFR1 and co-receptor KLB, are considered the essential tissue and molecular targets of hepatic or pharmacological FGF21. On the other hand, a growing body of work has revealed that pancreatic acinar cells form a constitutive high-production site for FGF21, which then acts in an autocrine or paracrine mode. Beyond regulation of macronutrient metabolism and physiological energy expenditure, FGF21 appears to function in forestalling the development of fatty pancreas, steato-pancreatitis, fatty liver, and steato-hepatitis, thereby preventing the development of advanced pathologies such as pancreatic ductal adenocarcinoma or hepatocellular carcinoma. This review is intended to provide updates on these new discoveries that illuminate the protective roles of FGF21-FGFR1-KLB signal pathway in metabolic anomalies-associated severe tissue damage and malignancy, and to inform potential new preventive or therapeutic strategies for obesity-inflicted cancer patients via reducing metabolic risks and inflammation.
    Keywords:  Hepatocellular carcinoma; Inflammation; Obesity; Oncogenic KRAS; Pancreatic cancer
    DOI:  https://doi.org/10.1016/j.canlet.2020.11.026
  9. Metabolomics. 2020 Nov 29. 16(12): 125
    Roci I, Watrous JD, Lagerborg KA, Jain M, Nilsson R.
      INTRODUCTION: Choline is an essential human nutrient that is particular important for proliferating cells, and altered choline metabolism has been associated with cancer transformation. Yet, the various metabolic fates of choline in proliferating cells have not been investigated systematically.OBJECTIVES: This study aims to map the metabolic products of choline in normal and cancerous proliferating cells.
    METHODS: We performed 13C-choline tracing followed by liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis of metabolic products in normal and in vitro-transformed (tumor-forming) epithelial cells, and also in tumor-derived cancer cell lines. Selected metabolites were quantified by internal standards.
    RESULTS: Untargeted analysis revealed 121 LCMS peaks that were 13C-labeled from choline, including various phospholipid species, but also previously unknown products such as monomethyl- and dimethyl-ethanolamines. Interestingly, we observed formation of betaine from choline specifically in tumor-derived cells. Expression of choline dehydrogenase (CHDH), which catalyzes the first step of betaine synthesis, correlated with betaine synthesis across the cell lines studied. RNAi silencing of CHDH did not affect cell proliferation, although we observed an increased fraction of G2M phase cells with some RNAi sequences, suggesting that CHDH and its product betaine may play a role in cell cycle progression. Betaine cell concentration was around 10 µM, arguing against an osmotic function, and was not used as a methyl donor. The function of betaine in these tumor-derived cells is presently unknown.
    CONCLUSION: This study identifies novel metabolites of choline in cancer and normal cell lines, and reveals altered choline metabolism in cancer cells.
    Keywords:  13C3 choline; Betaine; CHDH; Isotope tracing; Methylation
    DOI:  https://doi.org/10.1007/s11306-020-01749-0
  10. Int J Mol Sci. 2020 Nov 28. pii: E9075. [Epub ahead of print]21(23):
    Ayuso JM, Rehman S, Farooqui M, Virumbrales-Muñoz M, Setaluri V, Skala MC, Beebe DJ.
      Tumor-specific metabolic adaptations offer an interesting therapeutic opportunity to selectively destroy cancer cells. However, solid tumors also present gradients of nutrients and waste products across the tumor mass, forcing tumor cells to adapt their metabolism depending on nutrient availability in the surrounding microenvironment. Thus, solid tumors display a heterogenous metabolic phenotype across the tumor mass, which complicates the design of effective therapies that target all the tumor populations present. In this work, we used a microfluidic device to study tumor metabolic vulnerability to several metabolic inhibitors. The microdevice included a central chamber to culture tumor cells in a three-dimensional (3D) matrix, and a lumen in one of the chamber flanks. This design created an asymmetric nutrient distribution across the central chamber, generating gradients of cell viability. The results revealed that tumor cells located in a nutrient-enriched environment showed low to no sensitivity to metabolic inhibitors targeting glycolysis, fatty acid oxidation, or oxidative phosphorylation. Conversely, when cell density inside of the model was increased, compromising nutrient supply, the addition of these metabolic inhibitors disrupted cellular redox balance and led to tumor cell death.
    Keywords:  microfluidics; redox ratio; tumor metabolism; tumor-on-a-chip
    DOI:  https://doi.org/10.3390/ijms21239075
  11. Curr Protoc Pharmacol. 2020 Dec;91(1): e80
    Markov SD, Gonzalez D, Mehla K.
      Cancer-associated cachexia is defined by loss of weight and muscle mass, and by the potential loss of adipose tissue accompanied by insulin resistance and increased resting energy expenditure. Cachexia is most prevalent in pancreatic cancer, the third leading cause of cancer-related deaths. While various factors interact to induce cachexia, the precise mechanisms underlying this clinical condition are not fully understood. Clinically relevant animal models of cachexia are needed given the lack of standard diagnostic methods or treatments for this condition. Described in this article are in vitro and in vivo models used to study the role of macrophages in the induction of cachexia in pancreatic cancer. Included are procedures for isolating and culturing bone marrow-derived macrophages, harvesting tumor- and macrophage-derived conditioned medium, and studying the effect of conditioned medium on C2C12 myotubes. Also described are procedures involving the use of an orthotopic model of pancreatic cancer, including a method for examining skeletal muscle atrophy in this model. © 2020 Wiley Periodicals LLC. Basic Protocol 1: In vitro model of pancreatic tumor-induced cachexia using C2C12 cell lines (myotube model) Support Protocol 1: Molecular evaluation of cachectic markers in C2C12 myotubes using real-time PCR and immunoblotting Basic Protocol 2: In vivo model to study cachectic phenotype in pancreatic tumor-bearing mice Support Protocol 2: Evaluation of cachectic markers in the skeletal muscle of tumor-bearing mice.
    Keywords:  MyHC; cachexia; myotube atrophy; pancreatic cancer; skeletal muscle
    DOI:  https://doi.org/10.1002/cpph.80
  12. Nat Metab. 2020 Nov 30.
    Kim J, Lee HM, Cai F, Ko B, Yang C, Lieu EL, Muhammad N, Rhyne S, Li K, Haloul M, Gu W, Faubert B, Kaushik AK, Cai L, Kasiri S, Marriam U, Nham K, Girard L, Wang H, Sun X, Kim J, Minna JD, Unsal-Kacmaz K, DeBerardinis RJ.
      In non-small-cell lung cancer (NSCLC), concurrent mutations in the oncogene KRAS and the tumour suppressor STK11 (also known as LKB1) encoding the kinase LKB1 result in aggressive tumours prone to metastasis but with liabilities arising from reprogrammed metabolism. We previously demonstrated perturbed nitrogen metabolism and addiction to an unconventional pathway of pyrimidine synthesis in KRAS/LKB1 co-mutant cancer cells. To gain broader insight into metabolic reprogramming in NSCLC, we analysed tumour metabolomes in a series of genetically engineered mouse models with oncogenic KRAS combined with mutations in LKB1 or p53. Metabolomics and gene expression profiling pointed towards activation of the hexosamine biosynthesis pathway (HBP), another nitrogen-related metabolic pathway, in both mouse and human KRAS/LKB1 co-mutant tumours. KRAS/LKB1 co-mutant cells contain high levels of HBP metabolites, higher flux through the HBP pathway and elevated dependence on the HBP enzyme glutamine-fructose-6-phosphate transaminase [isomerizing] 2 (GFPT2). GFPT2 inhibition selectively reduced KRAS/LKB1 co-mutant tumour cell growth in culture, xenografts and genetically modified mice. Our results define a new metabolic vulnerability in KRAS/LKB1 co-mutant tumours and provide a rationale for targeting GFPT2 in this aggressive NSCLC subtype.
    DOI:  https://doi.org/10.1038/s42255-020-00316-0
  13. Mol Cell. 2020 Nov 23. pii: S1097-2765(20)30786-3. [Epub ahead of print]
    Najafov A, Luu HS, Mookhtiar AK, Mifflin L, Xia HG, Amin PP, Ordureau A, Wang H, Yuan J.
      The mechanisms of cellular energy sensing and AMPK-mediated mTORC1 inhibition are not fully delineated. Here, we discover that RIPK1 promotes mTORC1 inhibition during energetic stress. RIPK1 is involved in mediating the interaction between AMPK and TSC2 and facilitate TSC2 phosphorylation at Ser1387. RIPK1 loss results in a high basal mTORC1 activity that drives defective lysosomes in cells and mice, leading to accumulation of RIPK3 and CASP8 and sensitization to cell death. RIPK1-deficient cells are unable to cope with energetic stress and are vulnerable to low glucose levels and metformin. Inhibition of mTORC1 rescues the lysosomal defects and vulnerability to energetic stress and prolongs the survival of RIPK1-deficient neonatal mice. Thus, RIPK1 plays an important role in the cellular response to low energy levels and mediates AMPK-mTORC1 signaling. These findings shed light on the regulation of mTORC1 during energetic stress and unveil a point of crosstalk between pro-survival and pro-death pathways.
    Keywords:  AMPK; CASP8; MLKL; RIPK1; RIPK3; TSC2; lysosome; mTORC1; neonatal lethality
    DOI:  https://doi.org/10.1016/j.molcel.2020.11.008
  14. Blood. 2020 Dec 03. pii: blood.2020005710. [Epub ahead of print]
    Feinauer MJ, Schneider SW, Berghoff AS, Robador JR, Tehranian C, Karreman MA, Venkataramani V, Solecki G, Grosch JK, Gunkel K, Kovalchuk B, Mayer FT, Fischer M, O Breckwoldt M, Brune M, Schwab Y, Wick W, Bauer AT, Winkler F.
      Clinically relevant brain metastases (BM) frequently form in cancer patients, with limited options for effective treatment. Circulating cancer cells must first permanently arrest in brain microvessels to colonize the brain, but the critical factors are not well understood. Here, in vivo multiphoton laser-scanning microscopy (MPLSM) of the entire brain metastatic cascade allowed unprecedented insights into how blood clot formation and von Willebrand factor (VWF) deposition determine the arrest of circulating cancer cells and subsequent brain colonization in mice. Clot formation in brain microvessels occurred frequently (>95%) and specifically at intravascularly arrested cancer cells, allowing their long-time arrest. An extensive clot embedded approximately 20% of brain-arrested cancer cells, and those were more likely to successfully extravasate and form a macrometastasis. Mechanistically, tissue factor-mediated thrombin generation by cancer cells accounted for local activation of plasmatic coagulation in the brain. Thrombin inhibition by treatment with low-molecular weight heparin or dabigatran and an anti-VWF antibody prevented clot formation, cancer cell arrest, extravasation, and brain macrometastasis formation. In contrast, tumor cells were not able to directly activate platelets, and antiplatelet treatments did reduce platelet dispositions at intravascular cancer cells but did not reduce overall BM formation. In conclusion, our data shows that plasmatic coagulation is activated early by intravascular tumor cells in the brain, with subsequent clot formation, discovering a novel and specific mechanism that is crucial for brain colonization. Direct or indirect thrombin and VWF inhibitors emerge as promising drug candidates for BM prevention trials.
    DOI:  https://doi.org/10.1182/blood.2020005710
  15. Nature. 2020 Dec;588(7836): 124-129
    Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann EM, Karg MM, Schultz MB, Kane AE, Davidsohn N, Korobkina E, Chwalek K, Rajman LA, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander MS, Ksander BR, He Z, Sinclair DA.
      Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity1-3. Changes to DNA methylation patterns over time form the basis of ageing clocks4, but whether older individuals retain the information needed to restore these patterns-and, if so, whether this could improve tissue function-is not known. Over time, the central nervous system (CNS) loses function and regenerative capacity5-7. Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2. These data indicate that mammalian tissues retain a record of youthful epigenetic information-encoded in part by DNA methylation-that can be accessed to improve tissue function and promote regeneration in vivo.
    DOI:  https://doi.org/10.1038/s41586-020-2975-4
  16. Ageing Res Rev. 2020 Nov 25. pii: S1568-1637(20)30366-4. [Epub ahead of print] 101231
    Elyahu Y, Monsonego A.
      Aging is generally characterized as a gradual increase in tissue damage, which is associated with senescence and chronic systemic inflammation and is evident in a variety of age-related diseases. The extent to which such tissue damage is a result of a gradual decline in immune regulation, which consequently compromises the capacity of the body to repair damages, has not been fully explored. Whereas CD4 T lymphocytes play a critical role in the orchestration of immunity, thymus involution initiates gradual changes in the CD4 T-cell landscape, which may significantly compromise tissue repair. In this review, we describe the lifespan accumulation of specific dysregulated CD4 T-cell subsets and their coevolution with systemic inflammation in the process of declined immunity and tissue repair capacity with age. Then, we discuss the process of thymus involution-which appears to be most pronounced around puberty-as a possible driver of the aging T-cell landscape. Finally, we identify individualized T cell-based early diagnostic biomarkers and therapeutic strategies for age-related diseases.
    Keywords:  Aging; Chronic systemic inflammation; Dysregulated CD4 T cells; Immune-mediated repair; Thymus
    DOI:  https://doi.org/10.1016/j.arr.2020.101231
  17. EMBO Rep. 2020 Dec 04. e49634
    Veliova M, Ferreira CM, Benador IY, Jones AE, Mahdaviani K, Brownstein AJ, Desousa BR, Acín-Pérez R, Petcherski A, Assali EA, Stiles L, Divakaruni AS, Prentki M, Corkey BE, Liesa M, Oliveira MF, Shirihai OS.
      Combined fatty acid esterification and lipolysis, termed lipid cycling, is an ATP-consuming process that contributes to energy expenditure. Therefore, interventions that stimulate energy expenditure through lipid cycling are of great interest. Here we find that pharmacological and genetic inhibition of the mitochondrial pyruvate carrier (MPC) in brown adipocytes activates lipid cycling and energy expenditure, even in the absence of adrenergic stimulation. We show that the resulting increase in ATP demand elevates mitochondrial respiration coupled to ATP synthesis and fueled by lipid oxidation. We identify that glutamine consumption and the Malate-Aspartate Shuttle are required for the increase in Energy Expenditure induced by MPC inhibition in Brown Adipocytes (MAShEEBA). We thus demonstrate that energy expenditure through enhanced lipid cycling can be activated in brown adipocytes by decreasing mitochondrial pyruvate availability. We present a new mechanism to increase energy expenditure and fat oxidation in brown adipocytes, which does not require adrenergic stimulation of mitochondrial uncoupling.
    Keywords:  futile cycle; malate aspartate shuttle; metabolism; mitochondrial pyruvate carrier; thermogenesis
    DOI:  https://doi.org/10.15252/embr.201949634
  18. Nucleic Acids Res. 2020 Dec 02. pii: gkaa1103. [Epub ahead of print]
    Gerashchenko MV, Peterfi Z, Yim SH, Gladyshev VN.
      There has been a surge of interest towards targeting protein synthesis to treat diseases and extend lifespan. Despite the progress, few options are available to assess translation in live animals, as their complexity limits the repertoire of experimental tools to monitor and manipulate processes within organs and individual cells. It this study, we developed a labeling-free method for measuring organ- and cell-type-specific translation elongation rates in vivo. It is based on time-resolved delivery of translation initiation and elongation inhibitors in live animals followed by ribosome profiling. It also reports translation initiation sites in an organ-specific manner. Using this method, we found that the elongation rates differ more than 50% among mouse organs and determined them to be 6.8, 5.0 and 4.3 amino acids per second for liver, kidney, and skeletal muscle, respectively. We further found that the elongation rate is reduced by 20% between young adulthood and mid-life. Thus, translation, a major metabolic process in cells, is tightly regulated at the level of elongation of nascent polypeptide chains.
    DOI:  https://doi.org/10.1093/nar/gkaa1103
  19. Br J Cancer. 2020 Dec 02.
    Edwards SC, Hoevenaar WHM, Coffelt SB.
      Major advances in cancer immunotherapy have dramatically expanded the potential to manipulate immune cells in cancer patients with metastatic disease to counteract cancer spread and extend patient lifespan. One of the most successful types of immunotherapy is the immune checkpoint inhibitors, such as anti-CTLA-4 and anti-PD-1, that keep anti-tumour T cells active. However, not every patient with metastatic disease benefits from this class of drugs and patients often develop resistance to these therapies over time. Tremendous research effort is now underway to uncover new immunotherapeutic targets that can be used in patients who are refractory to anti-CTLA-4 or anti-PD-1 treatment. Here, we discuss results from experimental model systems demonstrating that modulating the immune response can negatively affect metastasis formation. We focus on molecules that boost anti-tumour immune cells and opportunities to block immunosuppression, as well as cell-based therapies with enhanced tumour recognition properties for solid tumours. We also present a list of challenges in treating metastatic disease with immunotherapy that must be considered in order to move laboratory observations into clinical practice and maximise patient benefit.
    DOI:  https://doi.org/10.1038/s41416-020-01160-5
  20. Br J Cancer. 2020 Dec 01.
    Perea Paizal J, Au SH, Bakal C.
      During metastasis, tumour cells navigating the vascular circulatory system-circulating tumour cells (CTCs)-encounter capillary beds, where they start the process of extravasation. Biomechanical constriction forces exerted by the microcirculation compromise the survival of tumour cells within capillaries, but a proportion of CTCs manage to successfully extravasate and colonise distant sites. Despite the profound importance of this step in the progression of metastatic cancers, the factors about this deadly minority of cells remain elusive. Growing evidence suggests that mechanical forces exerted by the capillaries might induce adaptive mechanisms in CTCs, enhancing their survival and metastatic potency. Advances in microfluidics have enabled a better understanding of the cell-survival capabilities adopted in capillary-mimicking constrictions. In this review, we will highlight adaptations developed by CTCs to endure mechanical constraints in the microvasculature and outline how these mechanical forces might trigger dynamic changes towards a more invasive phenotype. A better understanding of the dynamic mechanisms adopted by CTCs within the microcirculation that ultimately lead to metastasis could open up novel therapeutic avenues.
    DOI:  https://doi.org/10.1038/s41416-020-01176-x
  21. Cancer Immunol Res. 2020 Dec;8(12): 1465-1469
    Fritsch EF, Burkhardt UE, Hacohen N, Wu CJ.
      Personal neoantigen-based cancer vaccines are designed to target antigens arising from tumor-specific mutations within individual cancers and present a tremendous opportunity to capitalize on their favorable and intrinsic properties of escape from central tolerance and exquisite tumor specificity. With the endpoint of creating an optimal T-cell army to attack a tumor, neoantigen-based vaccines have demonstrated the ability to coax naïve T-cell recruits against epitopes that do not induce spontaneous immunity to raise long-lasting T-cell responses against multiple tumor-specific epitopes and subsequently to extend the breadth of responses, as immunity begets immunity via epitope spreading. Importantly, on both preclinical and clinical fronts, the association of T-cell responses to neoantigens and favorable outcomes has been demonstrated time and time again. We recognize, however, that the path forward remains long and winding and requires the field to address several key challenges, particularly overcoming evolved tumor escape mechanisms and optimizing vaccine-induced immunity. Some challenges stem from gaps in science that enable in silico prediction of antigen presentation and recognition by T-cell receptors, whereas others stem from the logistical obstacles and cost of personalization. Nevertheless, with perseverance and innovative solutions, we have little doubt that the ability of neoantigen vaccination to induce potent cancer-specific T cells will fundamentally succeed in enabling greater effectiveness of a broad array of immunotherapies. We provide our perspective on the progress and the remaining challenges to realizing the opportunity of personal neoantigen cancer vaccines.
    DOI:  https://doi.org/10.1158/2326-6066.CIR-20-0526
  22. EMBO Rep. 2020 Dec 03. e51869
    Barz S, Kriegenburg F, Henning A, Bhattacharya A, Mancilla H, Sánchez-Martín P, Kraft C.
      Autophagy mediates the degradation of cytoplasmic material. Upon autophagy induction, autophagosomes form a sealed membrane around the cargo and fuse with the lytic compartment to release the cargo for degradation. In order to avoid premature fusion of immature autophagosomal membranes with the lytic compartment, this process needs to be tightly regulated. Several factors mediating autophagosome-vacuole fusion have recently been identified. In budding yeast, autophagosome-vacuole fusion requires the R-SNARE Ykt6 on the autophagosome, together with the three Q-SNAREs Vam3, Vam7, and Vti1 on the vacuole. However, how these SNAREs are regulated during the fusion process is poorly understood. In this study, we investigate the regulation of Ykt6. We found that Ykt6 is directly phosphorylated by Atg1 kinase, which keeps this SNARE in an inactive state. Ykt6 phosphorylation prevents SNARE bundling by disrupting its interaction with the vacuolar SNAREs Vam3 and Vti1, thereby preventing premature autophagosome-vacuole fusion. These findings shed new light on the regulation of autophagosome-vacuole fusion and reveal a further step in autophagy controlled by the Atg1 kinase.
    Keywords:  Atg1; SNARE; Ykt6; autophagosome; autophagy
    DOI:  https://doi.org/10.15252/embr.202051869
  23. Aging (Albany NY). 2020 Nov 29.
    Robinson O, Lau CE.
      
    Keywords:  biological age; biomarkers; epigenetic; metabolic; metabolomics
    DOI:  https://doi.org/10.18632/aging.104216
  24. Biomedicines. 2020 Nov 22. pii: E526. [Epub ahead of print]8(11):
    Schirrmacher V.
      Mitochondria are of great relevance to health, and their dysregulation is associated with major chronic diseases. Research on mitochondria-156 brand new publications from 2019 and 2020-have contributed to this review. Mitochondria have been fundamental for the evolution of complex organisms. As important and semi-autonomous organelles in cells, they can adapt their function to the needs of the respective organ. They can program their function to energy supply (e.g., to keep heart muscle cells going, life-long) or to metabolism (e.g., to support hepatocytes and liver function). The capacity of mitochondria to re-program between different options is important for all cell types that are capable of changing between a resting state and cell proliferation, such as stem cells and immune cells. Major chronic diseases are characterized by mitochondrial dysregulation. This will be exemplified by cardiovascular diseases, metabolic syndrome, neurodegenerative diseases, immune system disorders, and cancer. New strategies for intervention in chronic diseases will be presented. The tumor microenvironment can be considered a battlefield between cancer and immune defense, competing for energy supply and metabolism. Cancer cachexia is considered as a final stage of cancer progression. Nevertheless, the review will present an example of complete remission of cachexia via immune cell transfer. These findings should encourage studies along the lines of mitochondria, energy supply, and metabolism.
    Keywords:  OXPHOS; TCA; cachexia; cancer; chronic diseases; cyanobacteria; glycosylation; hydrogen; oxygen; redox enzymes; tumor microenvironment
    DOI:  https://doi.org/10.3390/biomedicines8110526
  25. J Cell Sci. 2020 Dec 04. pii: jcs.250191. [Epub ahead of print]
    Kanda Y, Satoh R, Takasaki T, Tomimoto N, Tsuchiya K, Tsai CA, Tanaka T, Kyomoto S, Hamada K, Fujiwara T, Sugiura R.
      The PKC signaling is a highly conserved signaling module, which plays a central role in a myriad of physiological processes, ranging from cell proliferation to cell death via various signaling pathways, including MAPK. Stress granules (SGs) are non-membranous cytoplasmic foci that aggregate in cells exposed to environmental stresses. Here we explored the role of SGs in PKC/MAPK signaling activation in fission yeast. High heat-stress (HHS) induced Pmk1 MAPK activation and Pck2/PKC translocation from the cell tips into poly(A)-binding protein (Pabp)-positive SGs. Pck2 dispersal from the cell tips required Pck2 kinase activity and the constitutively active Pck2 promotes its translocation to SGs. Importantly, Pmk1 deletion impaired Pck2 recruitment into SGs, indicating that MAPK activation stimulates Pck2 SG translocation. Consistently, HHS-induced SGs delayed Pck2 relocalization at the cell tips, thereby blocking subsequent Pmk1 reactivation after recovery from HHS. HHS partitioned Pck2 into the Pabp-positive SG-containing fraction, which resulted in the reduced Pck2 abundance and kinase activity in the soluble fraction. Collectively, MAPK-dependent Pck2 SG recruitment serves as a feedback mechanism to intercept PKC/MAPK activation induced by HHS, which might underlie PKC-related diseases.
    Keywords:  Heat stress; MAPK signaling; PKC; Phase separation; Spatiotemporal regulation; Stress granules
    DOI:  https://doi.org/10.1242/jcs.250191
  26. Biochem Biophys Res Commun. 2020 Oct 22. pii: S0006-291X(20)31950-1. [Epub ahead of print]
    Kuang F, Liu J, Li C, Kang R, Tang D.
      Ferroptosis is a type of non-apoptotic regulated cell death that involves excessive iron accumulation and subsequent lipid peroxidation. Although the antioxidant mechanisms of ferroptosis have been extensively studied recently, little is known about the interactions between the different organelles that control ferroptosis. Here, we show that the translocation of lysosomal cysteine protease cathepsin B (CTSB) into the nucleus is an important molecular event that mediates organelle-specific initiation of ferroptosis in human pancreatic cancer cells. Iron-dependent lysosomal membrane permeability triggers the release of CTSB from the lysosome to nucleus during ferroptosis. Mechanistically, nuclear CTSB accumulation causes DNA damage and subsequent activation of the stimulator of interferon response CGAMP interactor 1 (STING1/STING)-dependent DNA sensor pathway, which ultimately leads to autophagy-dependent ferroptosis. Consequently, the genetic inhibition of CTSB-dependent STING1 activation by RNAi prevents ferroptosis in cell culture and animal models. These new findings not only enhance our understanding of the mechanism by which organelles specifically trigger ferroptosis, but also may provide a potential way to enhance the anticancer activity of ferroptosis therapy.
    Keywords:  Autophagy; Cathepsin B; DNA damage; Ferroptosis; Lysosome; STING1
    DOI:  https://doi.org/10.1016/j.bbrc.2020.10.035
  27. Nat Commun. 2020 Dec 04. 11(1): 6216
    Pajovic S, Siddaway R, Bridge T, Sheth J, Rakopoulos P, Kim B, Ryall S, Agnihotri S, Phillips L, Yu M, Li C, Milos S, Patel P, Srikanthan D, Huang A, Hawkins C.
      Histone H3 lysine 27 (H3K27M) mutations represent the canonical oncohistone, occurring frequently in midline gliomas but also identified in haematopoietic malignancies and carcinomas. H3K27M functions, at least in part, through widespread changes in H3K27 trimethylation but its role in tumour initiation remains obscure. To address this, we created a transgenic mouse expressing H3.3K27M in diverse progenitor cell populations. H3.3K27M expression drives tumorigenesis in multiple tissues, which is further enhanced by Trp53 deletion. We find that H3.3K27M epigenetically activates a transcriptome, enriched for PRC2 and SOX10 targets, that overrides developmental and tissue specificity and is conserved between H3.3K27M-mutant mouse and human tumours. A key feature of the H3K27M transcriptome is activation of a RAS/MYC axis, which we find can be targeted therapeutically in isogenic and primary DIPG cell lines with H3.3K27M mutations, providing an explanation for the common co-occurrence of alterations in these pathways in human H3.3K27M-driven cancer. Taken together, these results show how H3.3K27M-driven transcriptome remodelling promotes tumorigenesis and will be critical for targeting cancers with these mutations.
    DOI:  https://doi.org/10.1038/s41467-020-19972-7
  28. Nat Commun. 2020 Dec 04. 11(1): 6215
    Meng H, Gonzales NM, Lonard DM, Putluri N, Zhu B, Dacso CC, York B, O'Malley BW.
      A distinct 12-hour clock exists in addition to the 24-hour circadian clock to coordinate metabolic and stress rhythms. Here, we show that liver-specific ablation of X-box binding protein 1 (XBP1) disrupts the hepatic 12-hour clock and promotes spontaneous non-alcoholic fatty liver disease (NAFLD). We show that hepatic XBP1 predominantly regulates the 12-hour rhythmicity of gene transcription in the mouse liver and demonstrate that perturbation of the 12-hour clock, but not the core circadian clock, is associated with the onset and progression of this NAFLD phenotype. Mechanistically, we provide evidence that the spliced form of XBP1 (XBP1s) binds to the hepatic 12-hour cistrome to directly regulate the 12-hour clock, with a periodicity paralleling the harmonic activation of the 12-hour oscillatory transcription of many rate-limiting metabolic genes known to have perturbations in human metabolic disease. Functionally, we show that Xbp1 ablation significantly reduces cellular membrane fluidity and impairs lipid homeostasis via rate-limiting metabolic processes in fatty acid monounsaturated and phospholipid remodeling pathways. These findings reveal that genetic disruption of the hepatic 12-hour clock links to the onset and progression of NAFLD development via transcriptional regulator XBP1, and demonstrate a role for XBP1 and the 12-hour clock in the modulation of phospholipid composition and the maintenance of lipid homeostasis.
    DOI:  https://doi.org/10.1038/s41467-020-20028-z
  29. Cancer Res. 2020 Dec 04. pii: canres.1346.2020. [Epub ahead of print]
    Oravecz-Wilson K, Rossi C, Zajac C, Sun Y, Li L, Decoville T, Fujiwara H, Kim S, Peltier D, Reddy P.
      Autophagy is a vital cellular process whose role in T immune cells is poorly understood, specifically, in its regulation of allo-immunity. Stimulation of wild type T cells in vitro and in vivo with allo-antigens enhances autophagy. To assess the relevance of autophagy to T cell allo-immunity, we generated T cell specific ATG5 knock-out mice. Deficiency of ATG5 dependent autophagy reduced T cell proliferation, increased apoptosis following in vitro and in vivo allo-stimulation. The absence of ATG5 in allo-stimulated T cells enhanced their ability to release effector cytokines and cytotoxic functions, uncoupling their proliferation and effector functions. Absence of autophagy reduced intracellular degradation of cytotoxic enzymes such as granzyme B, thus enhancing the cytotoxicity of T cells. In several in vivo models of allo-HSCT, ATG5-dependent dissociation of T cell functions contributed to significant reduction in graft-versus-host disease (GVHD) but retained sufficient graft versus tumor (GVT) response. Our findings demonstrate that ATG5 dependent autophagy uncouples T cell proliferation from its effector functions and offers a potential new strategy to enhance outcomes after allo-HSCT.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1346
  30. Transl Oncol. 2020 Nov 25. pii: S1936-5233(20)30457-5. [Epub ahead of print]14(1): 100965
    Iovanna J.
      A major obstacle for the effective treatment of pancreatic ductal adenocarcinoma (PDAC) is its molecular heterogeneity, reflected by the diverse clinical outcomes and responses to therapies that occur. The tumors of patients with PDAC must therefore be closely examined and classified before treatment initiation in order to predict the natural evolution of the disease and the response to therapy. To stratify patients, it is absolutely necessary to identify biological markers that are highly specific and reproducible, and easily measurable by inexpensive sensitive techniques. Several promising strategies to find biomarkers are already available or under development, such as the use of liquid biopsies to detect circulating tumor cells, circulating free DNA, methylated DNA, circulating RNA, and exosomes and extracellular vesicles, as well as immunological markers and molecular markers. Such biomarkers are capable of classifying patients with PDAC and predicting their therapeutic sensitivity. Interestingly, developing chemograms using primary cell lines or organoids and analyzing the resulting high-throughput data via artificial intelligence would be highly beneficial to patients. How can exploiting these biomarkers benefit patients with resectable, borderline resectable, locally advanced, and metastatic PDAC? In fact, the utility of these biomarkers depends on the patient's clinical situation. At the early stages of the disease, the clinician's priority lies in rapid diagnosis, so that the patient receives surgery without delay; at advanced disease stages, where therapeutic possibilities are severely limited, the priority is to determine the PDAC tumor subtype so as to estimate the clinical outcome and select a suitable effective treatment.
    Keywords:  Biomarkers; Immunotherapy; Pancreatic cancer; Patients stratification; Personalized medicine
    DOI:  https://doi.org/10.1016/j.tranon.2020.100965
  31. Proc Natl Acad Sci U S A. 2020 Nov 30. pii: 202018138. [Epub ahead of print]
    Sabath N, Levy-Adam F, Younis A, Rozales K, Meller A, Hadar S, Soueid-Baumgarten S, Shalgi R.
      Proteostasis collapse, the diminished ability to maintain protein homeostasis, has been established as a hallmark of nematode aging. However, whether proteostasis collapse occurs in humans has remained unclear. Here, we demonstrate that proteostasis decline is intrinsic to human senescence. Using transcriptome-wide characterization of gene expression, splicing, and translation, we found a significant deterioration in the transcriptional activation of the heat shock response in stressed senescent cells. Furthermore, phosphorylated HSF1 nuclear localization and distribution were impaired in senescence. Interestingly, alternative splicing regulation was also dampened. Surprisingly, we found a decoupling between different unfolded protein response (UPR) branches in stressed senescent cells. While young cells initiated UPR-related translational and transcriptional regulatory responses, senescent cells showed enhanced translational regulation and endoplasmic reticulum (ER) stress sensing; however, they were unable to trigger UPR-related transcriptional responses. This was accompanied by diminished ATF6 nuclear localization in stressed senescent cells. Finally, we found that proteasome function was impaired following heat stress in senescent cells, and did not recover upon return to normal temperature. Together, our data unraveled a deterioration in the ability to mount dynamic stress transcriptional programs upon human senescence with broad implications on proteostasis control and connected proteostasis decline to human aging.
    Keywords:  UPR; chaperones; heat shock response; protein homeostasis; senescence
    DOI:  https://doi.org/10.1073/pnas.2018138117
  32. Elife. 2020 Dec 01. pii: e61235. [Epub ahead of print]9
    Schmutz I, Mensenkamp AR, Takai KK, Haadsma M, Spruijt L, de Voer RM, Choo SS, Lorbeer FK, van Grinsven EJ, Hockemeyer D, Jongmans MC, de Lange T.
      Telomere shortening is a presumed tumor suppressor pathway that imposes a proliferative barrier (the Hayflick limit) during tumorigenesis. This model predicts that excessively long somatic telomeres predispose to cancer. Here, we describe cancer-prone families with two unique TINF2 mutations that truncate TIN2, a shelterin subunit that controls telomere length. Patient lymphocyte telomeres were unusually long. We show that the truncated TIN2 proteins do not localize to telomeres, suggesting that the mutations create loss-of-function alleles. Heterozygous knock-in of the mutations or deletion of one copy of TINF2 resulted in excessive telomere elongation in clonal lines, indicating that TINF2 is haploinsufficient for telomere length control. In contrast, telomere protection and genome stability were maintained in all heterozygous clones. The data establish that the TINF2 truncations predispose to a tumor syndrome. We conclude that TINF2 acts as a haploinsufficient tumor suppressor that limits telomere length to ensure a timely Hayflick limit.
    Keywords:  TIN2; cancer biology; cancer predisposition; human; telomere length
    DOI:  https://doi.org/10.7554/eLife.61235
  33. Nat Commun. 2020 12 01. 11(1): 6145
    Girardi E, Agrimi G, Goldmann U, Fiume G, Lindinger S, Sedlyarov V, Srndic I, Gürtl B, Agerer B, Kartnig F, Scarcia P, Noia MAD, Liñeiro E, Rebsamen M, Wiedmer T, Bergthaler A, Palmieri L, Superti-Furga G.
      About a thousand genes in the human genome encode for membrane transporters. Among these, several solute carrier proteins (SLCs), representing the largest group of transporters, are still orphan and lack functional characterization. We reasoned that assessing genetic interactions among SLCs may be an efficient way to obtain functional information allowing their deorphanization. Here we describe a network of strong genetic interactions indicating a contribution to mitochondrial respiration and redox metabolism for SLC25A51/MCART1, an uncharacterized member of the SLC25 family of transporters. Through a combination of metabolomics, genomics and genetics approaches, we demonstrate a role for SLC25A51 as enabler of mitochondrial import of NAD, showcasing the potential of genetic interaction-driven functional gene deorphanization.
    DOI:  https://doi.org/10.1038/s41467-020-19871-x
  34. J Cachexia Sarcopenia Muscle. 2020 Nov 30.
    Palus S, Springer J.
      
    Keywords:  Biomarker; Cancer cachexia; Lipids; Sphingolipids
    DOI:  https://doi.org/10.1002/jcsm.12641
  35. J Clin Invest. 2020 Dec 01. pii: 136655. [Epub ahead of print]
    Kahn BM, Lucas A, Alur R, Wengyn MD, Schwartz GW, Li J, Sun K, Maurer HC, Olive KP, Faryabi RB, Stanger B.
      Tumors depend on a blood supply to deliver oxygen and nutrients, making tumor vasculature an attractive anti-cancer target. However, only a fraction of cancer patients benefits from angiogenesis inhibitors. Whether anti-angiogenic therapy would be more effective if targeted to individuals with specific tumor characteristics is unknown. To better characterize the tumor vascular environment both within and between cancer types, we developed a standardized metric - the Endothelial Index (EI) - to estimate vascular density in over 10,000 human tumors, corresponding to 31 solid tumor types, from transcriptome data. We then used this index to compare hyper- and hypo-vascular tumors, enabling the classification of human tumors into six vascular microenvironment signatures (VMSs) based on the expression of a panel of 24 vascular hub genes. EI and VMS correlated with known tumor vascular features and were independently associated with prognosis in certain cancer types. Retrospective testing of clinical trial data identified VMS2 classification as a powerful biomarker for response to bevacizumab. Our studies thus provide an unbiased picture of human tumor vasculature which may enable more precise deployment of anti-angiogenesis therapy.
    Keywords:  Angiogenesis; Cancer; Oncology; endothelial cells
    DOI:  https://doi.org/10.1172/JCI136655
  36. Cell Calcium. 2020 Nov 22. pii: S0143-4160(20)30164-0. [Epub ahead of print]93 102322
    Feno S, Rizzuto R, Raffaello A, Vecellio Reane D.
      The role of mitochondria in regulating cellular Ca2+ homeostasis is crucial for the understanding of different cellular functions in physiological and pathological conditions. Nevertheless, the study of this aspect was severely limited by the lack of the molecular identity of the proteins responsible for mitochondrial Ca2+ uptake. In 2011, the discovery of the gene encoding for the Mitochondrial Calcium Uniporter (MCU), the selective channel responsible for mitochondrial Ca2+ uptake, gave rise to an explosion of studies aimed to characterize the composition, the regulation of the channel and its pathophysiological roles. Here, we summarize the recent discoveries on the molecular structure and composition of the MCU complex by providing new insights into the mechanisms that regulate MCU channel activity.
    Keywords:  Calcium homeostasis; Mitochondria; Mitochondrial Calcium Uniporter
    DOI:  https://doi.org/10.1016/j.ceca.2020.102322
  37. Semin Immunol. 2020 Nov 30. pii: S1044-5323(20)30051-8. [Epub ahead of print] 101435
    Han J, Khatwani N, Searles TG, Turk MJ, Angeles CV.
      Long-lived memory CD8+ T cells play important roles in tumor immunity. Studies over the past two decades have identified four subsets of memory CD8+ T cells - central, effector, stem-like, and tissue resident memory - that either circulate through blood, lymphoid and peripheral organs, or reside in tissues where cancers develop. In this article, we will review studies from both pre-clinical mouse models and human patients to summarize the phenotype, distribution and unique features of each memory subset, and highlight specific roles of each subset in anti-tumor immunity. Moreover, we will discuss how stem-cell like and resident memory CD8+ T cell subsets relate to exhausted tumor-infiltrating lymphocytes (TIL) populations. These studies reveal how memory CD8+ T cell subsets together orchestrate durable immunity to cancer.
    Keywords:  Central memory (T(CM)); Effector memory (T(EM)); Exhaustion; Resident memory (T(RM)); Stem cell memory (T(SCM)); Tumor immunity
    DOI:  https://doi.org/10.1016/j.smim.2020.101435
  38. Bioinformatics. 2020 Dec 04. pii: btaa965. [Epub ahead of print]
    Chervoneva I, Peck AR, Yi M, Freydin B, Rui H.
      MOTIVATION: Quantitative Immunofluorescence (QIF) is often used for immunohistochemistry (IHC) quantification of proteins that serve as cancer biomarkers. Advanced image analysis systems for pathology allow capturing expression levels in each individual cell or subcellular compartment. However, only the Mean Signal Intensity (MSI) within the cancer tissue region of interest is usually considered as biomarker completely ignoring the issue of tumor heterogeneity.RESULTS: We propose using IHC image-derived information on the spatial distribution of cellular signal intensity (CSI) of protein expression within the cancer cell population to quantify both mean expression level and tumor heterogeneity of CSI levels. We view CSI levels as marks in a marked point process of cancer cells in the tissue and define spatial indices based on conditional mean and conditional variance of the marked point process. The proposed methodology provides objective metrics of cell-to-cell heterogeneity in protein expressions that allow discriminating between different patterns of heterogeneity. The prognostic utility of new spatial indices is investigated and compared to the standard MSI biomarkers using the protein expressions in tissue microarrays (TMAs) incorporating tumor tissues from1000+ breast cancer patients.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa965
  39. Sci Transl Med. 2020 Dec 02. pii: eaaz2253. [Epub ahead of print]12(572):
    Armstrong JPK, Keane TJ, Roques AC, Patrick PS, Mooney CM, Kuan WL, Pisupati V, Oreffo ROC, Stuckey DJ, Watt FM, Forbes SJ, Barker RA, Stevens MM.
      The past few decades have produced a large number of proof-of-concept studies in regenerative medicine. However, the route to clinical adoption is fraught with technical and translational obstacles that frequently consign promising academic solutions to the so-called "valley of death." Here, we present a proposed blueprint for translational regenerative medicine. We offer principles to help guide the selection of cells and materials, present key in vivo imaging modalities, and argue that the host immune response should be considered throughout design and development. Last, we suggest a pathway to navigate the often complex regulatory and manufacturing landscape of translational regenerative medicine.
    DOI:  https://doi.org/10.1126/scitranslmed.aaz2253
  40. EMBO J. 2020 Dec 04. e106123
    Lv J, Liu Y, Cheng F, Li J, Zhou Y, Zhang T, Zhou N, Li C, Wang Z, Ma L, Liu M, Zhu Q, Liu X, Tang K, Ma J, Zhang H, Xie J, Fang Y, Zhang H, Wang N, Liu Y, Huang B.
      Identifying and sorting highly tumorigenic and metastatic tumor cells from a heterogeneous cell population is a daunting challenge. Here, we show that microfluidic devices can be used to sort marker-based heterogeneous cancer stem cells (CSC) into mechanically stiff and soft subpopulations. The isolated soft tumor cells (< 400 Pa) but not the stiff ones (> 700 Pa) can form a tumor in immunocompetent mice with 100 cells per inoculation. Notably, only the soft, but not the stiff cells, isolated from CD133+ , ALDH+ , or side population CSCs, are able to form a tumor with only 100 cells in NOD-SCID or immunocompetent mice. The Wnt signaling protein BCL9L is upregulated in soft tumor cells and regulates their stemness and tumorigenicity. Clinically, BCL9L expression is correlated with a worse prognosis. Our findings suggest that the intrinsic softness is a unique marker of highly tumorigenic and metastatic tumor cells.
    Keywords:  BCL9L; metastasis; microfluidic sorting; soft tumor cells; stemness
    DOI:  https://doi.org/10.15252/embj.2020106123
  41. Cell Metab. 2020 Dec 01. pii: S1550-4131(20)30602-1. [Epub ahead of print]32(6): 1063-1075.e7
    Argüello RJ, Combes AJ, Char R, Gigan JP, Baaziz AI, Bousiquot E, Camosseto V, Samad B, Tsui J, Yan P, Boissonneau S, Figarella-Branger D, Gatti E, Tabouret E, Krummel MF, Pierre P.
      Energetic metabolism reprogramming is critical for cancer and immune responses. Current methods to functionally profile the global metabolic capacities and dependencies of cells are performed in bulk. We designed a simple method for complex metabolic profiling called SCENITH, for single-cell energetic metabolism by profiling translation inhibition. SCENITH allows for the study of metabolic responses in multiple cell types in parallel by flow cytometry. SCENITH is designed to perform metabolic studies ex vivo, particularly for rare cells in whole blood samples, avoiding metabolic biases introduced by culture media. We analyzed myeloid cells in solid tumors from patients and identified variable metabolic profiles, in ways that are not linked to their lineage or their activation phenotype. SCENITH's ability to reveal global metabolic functions and determine complex and linked immune-phenotypes in rare cell subpopulations will contribute to the information needed for evaluating therapeutic responses or patient stratification.
    Keywords:  cell culture media and metabolism; functional assay metabolism single cells; metabolic function by flow cytometry; metabolic gene signatures; metabolic profiling of blood samples; metabolism analysis in samples from patients; protein synthesis and metabolism; translation and metabolism; tumor immunometabolism
    DOI:  https://doi.org/10.1016/j.cmet.2020.11.007
  42. Elife. 2020 Dec 02. pii: e61487. [Epub ahead of print]9
    Blanden AR, Yu X, Blayney AJ, Demas C, Ha JH, Liu Y, Withers T, Carpizo DR, Loh SN.
      Missense mutations in the p53 DNA binding domain (DBD) contribute to half of new cancer cases annually. Here we present a thermodynamic model that quantifies and links the major pathways by which mutations inactivate p53. We find that DBD possesses two unusual properties-one of the highest zinc affinities of any eukaryotic protein and extreme instability in the absence of zinc-which are predicted to poise p53 on the cusp of folding/unfolding in the cell, with a major determinant being available zinc concentration. We analyze the 20 most common tumorigenic p53 mutations and find that 80% impair zinc affinity, thermodynamic stability, or both. Biophysical, cell-based, and murine xenograft experiments demonstrate that a synthetic zinc metallochaperone rescues not only mutations that decrease zinc affinity, but also mutations that destabilize DBD without impairing zinc binding. The results suggest that zinc metallochaperones have the capability to treat 120,500 patients annually in the U.S.
    Keywords:  cancer biology; molecular biophysics; mouse; structural biology
    DOI:  https://doi.org/10.7554/eLife.61487
  43. Elife. 2020 Nov 30. pii: e56830. [Epub ahead of print]9
    Saclier N, Chardon P, Malard F, Konecny-Dupré L, Eme D, Bellec A, Breton V, Duret L, Lefebure T, Douady CJ.
      All organisms on Earth are exposed to low doses of natural radioactivity but some habitats are more radioactive than others. Yet, documenting the influence of natural radioactivity on the evolution of biodiversity is challenging. Here, we addressed whether organisms living in naturally more radioactive habitats accumulate more mutations across generations using 14 species of waterlice living in subterranean habitats with contrasted levels of radioactivity. We found that the mitochondrial and nuclear mutation rates across a waterlouse species' genome increased on average by 60 and 30%, respectively, when radioactivity increased by a factor of three. We also found a positive correlation between the level of radioactivity and the probability of G to T (and complementary C to A) mutations, a hallmark of oxidative stress. We conclude that even low doses of natural bedrock radioactivity influence the mutation rate possibly through the accumulation of oxidative damage, in particular in the mitochondrial genome.
    Keywords:  evolutionary biology; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.56830
  44. Clin Cancer Res. 2020 Dec 04. pii: clincanres.2974.2020. [Epub ahead of print]
    Zheng L, Ding D, Edil BH, Judkin C, Durham JN, Thomas DL, Bever KM, Mo G, Solt S, Hoare J, Bhattacharya R, Zhu Q, Osipov A, Onners BL, Purtell K, Cai H, Parkinson RM, Hacker-Prietz A, Herman J, Le DT, Azad NS, De Jesus-Acosta A, Blair AB, Kim VM, Soares KC, Manos L, Cameron JL, Makary MA, Weiss MJ, Schulick RD, He J, Wolfgang CL, Thompson ED, Anders RA, Sugar EA, Jaffee EM, Laheru DA.
      PURPOSE: Immunotherapy is currently ineffective for nearly all pancreatic ductal adenocarcinomas(PDAC), largely due to its tumor microenvironment(TME) that lacks antigen experienced T effector cells(Teffs). Vaccine-based immunotherapies are known to activate antigen-specific Teffs in the peripheral blood. To evaluate the effect of vaccine therapy on the PDAC TME, we designed a neoadjuvant and adjuvant clinical trial of an irradiated, granulocyte-macrophage colony-stimulating factor(GM-CSF)-secreting, allogeneic PDAC vaccine(GVAX).EXPERIMENTAL DESIGN: Eighty-seven eligible patients with resectable PDAC were randomly assigned(1:1:1) to receive GVAX alone or in combination with two forms of low-dose cyclophosphamide(Cy). Resected tumors following neoadjuvant immunotherapy were assessed for the formation of tertiary lymphoid aggregates(TLA) in response to treatment. The clinical endpoints are disease-free survival(DFS) and overall survival(OS).
    RESULTS: The neoadjuvant treatment with GVAX either alone or with two forms of low dose Cy is safe and feasible without adversely increasing the surgical complication rate. Patients in Arm A who received neoadjuvant and adjuvant GVAX alone had a trend toward longer median OS(35.0 months) than that(24.8 months) in the historical controls who received adjuvant GVAX alone. However, Arm C, who received low dose oral Cy in addition to GVAX, had a significantly shorter DFS than Arm A. When comparing patients with OS>24 months to those with OS<15 months, longer OS was found to be associated with higher density of intratumoral TLA.
    CONCLUSIONS: It is safe and feasible to use a neoadjuvant immunotherapy approach for PDACs to evaluate early biologic responses. In-depth analysis of TLAs is warranted in future neoadjuvant immunotherapy clinical trials.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-2974
  45. Sci Signal. 2020 Dec 01. pii: eaaz1236. [Epub ahead of print]13(660):
    Kokaji T, Hatano A, Ito Y, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka KI, Egami R, Terakawa A, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Ikeda K, Arita M, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S.
      Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in healthy and obese states, we constructed and analyzed transomics glucose-responsive metabolic networks with layers for metabolites, expression data for metabolic enzyme genes, transcription factors, and insulin signaling proteins from the livers of healthy and obese mice. We integrated multiomics time course data from wild-type and leptin-deficient obese (ob/ob) mice after orally administered glucose. In wild-type mice, metabolic reactions were rapidly regulated within 10 min of oral glucose administration by glucose-responsive metabolites, which functioned as allosteric regulators and substrates of metabolic enzymes, and by Akt-induced changes in the expression of glucose-responsive genes encoding metabolic enzymes. In ob/ob mice, the majority of rapid regulation by glucose-responsive metabolites was absent. Instead, glucose administration produced slow changes in the expression of carbohydrate, lipid, and amino acid metabolic enzyme-encoding genes to alter metabolic reactions on a time scale of hours. Few regulatory events occurred in both healthy and obese mice. Thus, our transomics network analysis revealed that regulation of glucose-responsive liver metabolism is mediated through different mechanisms in healthy and obese states. Rapid changes in allosteric regulators and substrates and in gene expression dominate the healthy state, whereas slow changes in gene expression dominate the obese state.
    DOI:  https://doi.org/10.1126/scisignal.aaz1236
  46. Mol Biol Cell. 2020 Dec 02. mbcE19080436
    Eisenberg S, Haimov E, Walpole GFW, Plumb J, Kozlov MM, Grinstein S.
      Anionic phospholipids can confer a net negative charge to biological membranes. This surface charge generates an electrical field that serves to recruit extrinsic cationic proteins, can alter the disposition of transmembrane proteins and causes the local accumulation of soluble counterions, altering the local pH and the concentration of physiologically important ions like calcium. Because the phospholipid composition of the different organellar membranes varies, their surface charge is similarly expected to diverge. Yet, despite the important functional implications, remarkably little is known about the electrostatic properties of the individual organellar membranes. We therefore designed and implemented approaches to estimate the surface charge of the cytosolic membrane of various organelles in situ in intact cells. Our data indicate that the inner leaflet of the plasma membrane is most negative, with a surface potential of approximately -35 mV, followed by the Golgi complex > lysosomes > mitochondria ≈ peroxisomes > the endoplasmic reticulum, in decreasing order.
    DOI:  https://doi.org/10.1091/mbc.E19-08-0436
  47. Front Physiol. 2020 ;11 541040
    Glancy B, Kim Y, Katti P, Willingham TB.
      Mitochondria are key determinants of cellular health. However, the functional role of mitochondria varies from cell to cell depending on the relative demands for energy distribution, metabolite biosynthesis, and/or signaling. In order to support the specific needs of different cell types, mitochondrial functional capacity can be optimized in part by modulating mitochondrial structure across several different spatial scales. Here we discuss the functional implications of altering mitochondrial structure with an emphasis on the physiological trade-offs associated with different mitochondrial configurations. Within a mitochondrion, increasing the amount of cristae in the inner membrane improves capacity for energy conversion and free radical-mediated signaling but may come at the expense of matrix space where enzymes critical for metabolite biosynthesis and signaling reside. Electrically isolating individual cristae could provide a protective mechanism to limit the spread of dysfunction within a mitochondrion but may also slow the response time to an increase in cellular energy demand. For individual mitochondria, those with relatively greater surface areas can facilitate interactions with the cytosol or other organelles but may be more costly to remove through mitophagy due to the need for larger phagophore membranes. At the network scale, a large, stable mitochondrial reticulum can provide a structural pathway for energy distribution and communication across long distances yet also enable rapid spreading of localized dysfunction. Highly dynamic mitochondrial networks allow for frequent content mixing and communication but require constant cellular remodeling to accommodate the movement of mitochondria. The formation of contact sites between mitochondria and several other organelles provides a mechanism for specialized communication and direct content transfer between organelles. However, increasing the number of contact sites between mitochondria and any given organelle reduces the mitochondrial surface area available for contact sites with other organelles as well as for metabolite exchange with cytosol. Though the precise mechanisms guiding the coordinated multi-scale mitochondrial configurations observed in different cell types have yet to be elucidated, it is clear that mitochondrial structure is tailored at every level to optimize mitochondrial function to meet specific cellular demands.
    Keywords:  cristae; energetics; mitochondria; mitochondrial dynamics; mitochondrial networks; organelle interaction
    DOI:  https://doi.org/10.3389/fphys.2020.541040
  48. Nat Cancer. 2020 Apr;1(4): 394-409
    Gong K, Guo G, Panchani N, Bender ME, Gerber DE, Minna JD, Fattah F, Gao B, Peyton M, Kernstine K, Mukherjee B, Burma S, Chiang CM, Zhang S, Sathe AA, Xing C, Dao KH, Zhao D, Akbay EA, Habib AA.
      EGFR inhibition is an effective treatment in the minority of non-small cell lung cancer (NSCLC) cases harboring EGFR-activating mutations, but not in EGFR wild type (EGFRwt) tumors. Here, we demonstrate that EGFR inhibition triggers an antiviral defense pathway in NSCLC. Inhibiting mutant EGFR triggers Type I IFN-I upregulation via a RIG-I-TBK1-IRF3 pathway. The ubiquitin ligase TRIM32 associates with TBK1 upon EGFR inhibition, and is required for K63-linked ubiquitination and TBK1 activation. Inhibiting EGFRwt upregulates interferons via an NF-κB-dependent pathway. Inhibition of IFN signaling enhances EGFR-TKI sensitivity in EGFR mutant NSCLC and renders EGFRwt/KRAS mutant NSCLC sensitive to EGFR inhibition in xenograft and immunocompetent mouse models. Furthermore, NSCLC tumors with decreased IFN-I expression are more responsive to EGFR TKI treatment. We propose that IFN-I signaling is a major determinant of EGFR-TKI sensitivity in NSCLC and that a combination of EGFR TKI plus IFN-neutralizing antibody could be useful in most NSCLC patients.
    DOI:  https://doi.org/10.1038/s43018-020-0048-0
  49. Oncogene. 2020 Dec 01.
    Lin WH, Chang YW, Hong MX, Hsu TC, Lee KC, Lin C, Lee JL.
      Epithelial-mesenchymal transition (EMT)/mesenchymal-epithelial transition (MET) processes are proposed to be a driving force of cancer metastasis. By studying metastasis in bone marrow-derived mesenchymal stem cell (BM-MSC)-driven lung cancer models, microarray time-series data analysis by systems biology approaches revealed BM-MSC-induced signaling triggers early dissemination of CD133+/CD83+ cancer stem cells (CSCs) from primary sites shortly after STAT3 activation but promotes proliferation towards secondary sites. The switch from migration to proliferation was regulated by BM-MSC-secreted LIF and activated LIFR/p-ERK/pS727-STAT3 signaling to promote early disseminated cancer cells MET and premetastatic niche formation. Then, tumor-tropic BM-MSCs circulated to primary sites and triggered CD151+/CD38+ cells acquiring EMT-associated CSC properties through IL6R/pY705-STAT3 signaling to promote tumor initiation and were also attracted by and migrated towards the premetastatic niche. In summary, STAT3 phosphorylation at tyrosine 705 and serine 727 differentially regulates the EMT-MET switch within the distinct molecular subtypes of CSCs to complete the metastatic process.
    DOI:  https://doi.org/10.1038/s41388-020-01566-8
  50. Cancer Discov. 2020 Dec 04.
      In mice and nonhuman primates, a GDF-15 antibody blocked platinum-based chemotherapy side effects.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2020-175
  51. Cancer Res. 2020 Dec 01. 80(23): 5164-5165
    Horikawa I.
      Aging and death of cells (cellular senescence and apoptosis, respectively), triggered by or associated with cellular stress and DNA damage, impair organ function and homeostasis, leading to organismal aging and death. On the other hand, defects in physiologic regulations of cellular aging and death (escape from cellular senescence and failed apoptosis of severely damaged cells) contribute to uncontrolled cell division and genetic instability in cancer. In an oversimplified scenario, p53, an inducer of cellular senescence and apoptosis, may thus unfavorably contribute to aging and favorably suppress tumorigenesis. However, physiologic mechanisms should exist and therapeutic approaches may be developed to balance between aging and tumor suppression, for example, by differentially regulating cellular senescence, apoptosis, and other p53-mediated biological processes, such as DNA repair, autophagy, and energy metabolism. Possible mechanisms for such differential regulation of different subsets of p53 target genes may involve posttranslational modifications (e.g., phosphorylation and acetylation) and DNA binding cooperativity of p53. In this issue of Cancer Research, Timofeev and colleagues show that a previously uncharacterized phosphorylation in the p53 core DNA-binding domain regulates the DNA binding cooperativity and transcriptional activity of p53. Their mice deficient for this p53 phosphorylation were resistant to spontaneous and induced tumorigenesis, while they had shortened lifespan, but did not show progeria-like phenotypes. Prompted by this study, research on p53, aging, and cancer will explore balancing and differentiating different p53 activities toward a challenging goal of achieving longevity with no cancer.See related article by Timofeev et al., p. 5231.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-3080
  52. FEBS Lett. 2020 Nov 28.
    Krämer L, Groh C, Herrmann JM.
      Most mitochondrial proteins are synthesized in the cytosol and subsequently translocated as unfolded polypeptides into mitochondria. Cytosolic chaperones maintain precursor proteins in an import-competent state. This post-translational import reaction is under surveillance of the cytosolic ubiquitin-proteasome system, which carries out several distinguishable activities. On the one hand, the proteasome degrades non-productive protein precursors from the cytosol and nucleus, import intermediates that are stuck in mitochondrial translocases, and misfolded or damaged proteins from the outer membrane and the intermembrane space. These surveillance activities of the proteasome are essential for mitochondrial functionality, as well as cellular fitness and survival. On the other hand, the proteasome competes with mitochondria for non-imported cytosolic precursor proteins, which can compromise mitochondrial biogenesis. In order to balance the positive and negative effects of the cytosolic protein quality control system on mitochondria, mitochondrial import efficiency directly regulates the capacity of the proteasome via transcription factor Rpn4 in yeast and nuclear respiratory factor (Nrf) 1 and 2 in animal cells. In this review, we provide a thorough overview of how the proteasome regulates mitochondrial biogenesis.
    Keywords:  Aging; Mitochondria; Mitochondria-Associated Degradation; Mitoprotein-Induced Stress Response; Proteasome; Protein Quality Control; Protein degradation; Rpn4; Ubiquitin
    DOI:  https://doi.org/10.1002/1873-3468.14010
  53. Cell Signal. 2020 Nov 28. pii: S0898-6568(20)30327-2. [Epub ahead of print]78 109850
    Lee SC, Lin KH, Balogh A, Norman DD, Bavaria M, Kuo B, Yue J, Balázs L, Benyó Z, Tigyi G.
      The TP53 gene has been widely studied for its roles in cell cycle control, maintaining genome stability, activating repair mechanisms upon DNA damage, and initiating apoptosis should repair mechanisms fail. Thus, it is not surprising that mutations of p53 are the most common genetic alterations found in human cancer. Emerging evidence indicates that dysregulation of lipid metabolism by p53 can have a profound impact not only on cancer cells but also cells of the tumor microenvironment (TME). In particular, intermediates of the sphingolipid and lysophospholipid pathways regulate many cellular responses common to p53 such as cell survival, migration, DNA damage repair and apoptosis. The majority of these cellular events become dysregulated in cancer as well as cell senescence. In this review, we will provide an account on the seminal contributions of Prof. Lina Obeid, who deciphered the crosstalk between p53 and the sphingolipid pathway particularly in modulating DNA damage repair and apoptosis in non-transformed as well as transformed cells. We will also provide insights on the integrative role of p53 with the lysophosphatidic acid (LPA) signaling pathway in cancer progression and TME regulation.
    DOI:  https://doi.org/10.1016/j.cellsig.2020.109850
  54. F1000Res. 2020 ;9 732
    Ren AH, Prassas I, Soosaipillai A, Jarvi S, Gallinger S, Kulasingam V, Diamandis EP.
      Background: To account for cancer heterogeneity, we previously introduced the concept of "personalized" tumor markers, which are biomarkers that are informative in subsets of patients or even a single patient. Recent developments in various multiplex protein technologies create excitement for the discovery of markers of tumor burden in individual patients, but the reliability of the technologies remains to be tested for this purpose. Here, we sought to explore the potential of a novel proteomics platform, which utilizes a multiplexed antibody microarray, to detect changes in serum protein concentration that may correlate to tumor burden in pancreatic cancer. Methods: We applied the Quantibody® Human Kiloplex Array to simultaneously measure 1,000 proteins in sera obtained pre- and post-surgically from five pancreatic cancer patients. We expected that proteins which decreased post-surgery may correlate to tumor burden. Sera from two healthy individuals, split into two aliquots each, were used as controls. To validate the multiplexed results, we used single-target ELISA assays to measure the proteins with the largest serum concentration changes after surgery in sera collected pre- and post-surgically from the previous five patients and 10 additional patients. Results: The multiplexed array revealed nine proteins with more than two-fold post-surgical decrease in at least two of five patients. However, validation using single ELISAs showed that only two proteins tested displayed more than two-fold post-surgical decrease in one of the five original patients. In the independent cohort, six of the proteins tested showed at least a two-fold decrease post-surgery in at least one patient. Conclusions: Our study found that the Quantibody® Human Kiloplex Array results could not be reliably replicated with individual ELISA assays and most hits would likely represent false positives if applied to biomarker discovery. These findings suggest that data from novel, high-throughput proteomic platforms need stringent validation to avoid false discoveries.
    Keywords:  ELISA; immunoassay; multiplex; pancreatic cancer; protein technologies; proteomics
    DOI:  https://doi.org/10.12688/f1000research.24654.1
  55. Nucleic Acids Res. 2020 Dec 03. pii: gkaa1104. [Epub ahead of print]
    Huang HY, Li J, Tang Y, Huang YX, Chen YG, Xie YY, Zhou ZY, Chen XY, Ding SY, Luo MF, Jin CN, Zhao LS, Xu JT, Zhou Y, Lin YC, Hong HC, Zuo HL, Hu SY, Xu PY, Li X, Huang HD.
      DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.0) is an integrated and web-based resource focusing on the aberrant methylomes of human diseases, specifically cancer. This paper presents an updated implementation of MethHC 2.0 by incorporating additional DNA methylomes and transcriptomes from several public repositories, including 33 human cancers, over 50 118 microarray and RNA sequencing data from TCGA and GEO, and accumulating up to 3586 manually curated data from >7000 collected published literature with experimental evidence. MethHC 2.0 has also been equipped with enhanced data annotation functionality and a user-friendly web interface for data presentation, search, and visualization. Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation profiles, available for research such as biomarker panel design, cancer comparison, diagnosis, prognosis, therapy study and identifying potential epigenetic biomarkers. MethHC 2.0 is now available at http://awi.cuhk.edu.cn/∼MethHC.
    DOI:  https://doi.org/10.1093/nar/gkaa1104
  56. FEBS Open Bio. 2020 Dec 04.
    Kobayashi M, Yasukawa H, Arikawa T, Deguchi Y, Mizushima N, Sakurai M, Onishi S, Tagawa R, Sudo Y, Okita N, Higashi K, Higami Y.
      Adipocytes, which comprise the majority of white adipose tissue (WAT), are involved in obesity-related pathology via various mechanisms, including disturbed lysosomal enzymatic activity and accumulation of oxidative stress. Sequestosome 1 (SQSTM1/p62) is an autophagy marker that participates in antioxidative responses via the activation of nuclear factor erythroid-derived 2-like 2 (NRF2). Trehalose is a non-reducing disaccharide reported to suppress adipocyte hypertrophy in obese mice and improve glucose tolerance in humans. We recently revealed that trehalose increases SQSTM1 levels and enhances antioxidative capacity in hepatocytes. Here, to further evaluate the mechanism behind the beneficial effects of trehalose on metabolism, we examined SQSTM1 levels, autophagy, and oxidative stress in trehalose-treated adipocytes. We initially confirmed that trehalose increases SQSTM1 transcription and protein levels without affecting autophagy in adipocytes. Trehalose also elevated transcription of several lysosomal genes and the activity of cathepsin L, a lysosomal enzyme, independently of the transcription factor EB. In agreement with our data from hepatocytes, trehalose induced the nuclear translocation of NRF2 and the transcription of its downstream antioxidative genes, resulting in reduced cellular reactive oxygen species levels. Moreover, some cellular trehalose was detected in trehalose-treated adipocytes, implying that extracellular trehalose is taken into cells. These observations reveal the mechanism behind the beneficial effects of trehalose on metabolism and suggest its potential for preventing or treating obesity-related pathology.
    Keywords:  Adipocyte; Lysosome; Oxidative Stress; SQSTM1; Trehalose
    DOI:  https://doi.org/10.1002/2211-5463.13055
  57. PLoS Genet. 2020 Dec 04. 16(12): e1009255
    Lipatova Z, Gyurkovska V, Zhao SF, Segev N.
      Thirty percent of all cellular proteins are inserted into the endoplasmic reticulum (ER), which spans throughout the cytoplasm. Two well-established stress-induced pathways ensure quality control (QC) at the ER: ER-phagy and ER-associated degradation (ERAD), which shuttle cargo for degradation to the lysosome and proteasome, respectively. In contrast, not much is known about constitutive ER-phagy. We have previously reported that excess of integral-membrane proteins is delivered from the ER to the lysosome via autophagy during normal growth of yeast cells. Whereas endogenously expressed ER resident proteins serve as cargos at a basal level, this level can be induced by overexpression of membrane proteins that are not ER residents. Here, we characterize this pathway as constitutive ER-phagy. Constitutive and stress-induced ER-phagy share the basic macro-autophagy machinery including the conserved Atgs and Ypt1 GTPase. However, induction of stress-induced autophagy is not needed for constitutive ER-phagy to occur. Moreover, the selective receptors needed for starvation-induced ER-phagy, Atg39 and Atg40, are not required for constitutive ER-phagy and neither these receptors nor their cargos are delivered through it to the vacuole. As for ERAD, while constitutive ER-phagy recognizes cargo different from that recognized by ERAD, these two ER-QC pathways can partially substitute for each other. Because accumulation of membrane proteins is associated with disease, and constitutive ER-phagy players are conserved from yeast to mammalian cells, this process could be critical for human health.
    DOI:  https://doi.org/10.1371/journal.pgen.1009255
  58. Nat Commun. 2020 11 30. 11(1): 6118
    Clements KE, Schleicher EM, Thakar T, Hale A, Dhoonmoon A, Tolman NJ, Sharma A, Liang X, Imamura Kawasawa Y, Nicolae CM, Wang HG, De S, Moldovan GL.
      Inhibitors of poly-ADP-ribose polymerase 1 (PARPi) are highly effective in killing cells deficient in homologous recombination (HR); thus, PARPi have been clinically utilized to successfully treat BRCA2-mutant tumors. However, positive response to PARPi is not universal, even among patients with HR-deficiency. Here, we present the results of genome-wide CRISPR knockout and activation screens which reveal genetic determinants of PARPi response in wildtype or BRCA2-knockout cells. Strikingly, we report that depletion of the ubiquitin ligase HUWE1, or the histone acetyltransferase KAT5, top hits from our screens, robustly reverses the PARPi sensitivity caused by BRCA2-deficiency. We identify distinct mechanisms of resistance, in which HUWE1 loss increases RAD51 levels to partially restore HR, whereas KAT5 depletion rewires double strand break repair by promoting 53BP1 binding to double-strand breaks. Our work provides a comprehensive set of putative biomarkers that advance understanding of PARPi response, and identifies novel pathways of PARPi resistance in BRCA2-deficient cells.
    DOI:  https://doi.org/10.1038/s41467-020-19961-w
  59. Cells. 2020 Nov 24. pii: E2536. [Epub ahead of print]9(12):
    Aquila G, Re Cecconi AD, Brault JJ, Corli O, Piccirillo R.
      Cancer cachexia (CC) is a debilitating multifactorial syndrome, involving progressive deterioration and functional impairment of skeletal muscles. It affects about 80% of patients with advanced cancer and causes premature death. No causal therapy is available against CC. In the last few decades, our understanding of the mechanisms contributing to muscle wasting during cancer has markedly increased. Both inflammation and oxidative stress (OS) alter anabolic and catabolic signaling pathways mostly culminating with muscle depletion. Several preclinical studies have emphasized the beneficial roles of several classes of nutraceuticals and modes of physical exercise, but their efficacy in CC patients remains scant. The route of nutraceutical administration is critical to increase its bioavailability and achieve the desired anti-cachexia effects. Accumulating evidence suggests that a single therapy may not be enough, and a bimodal intervention (nutraceuticals plus exercise) may be a more effective treatment for CC. This review focuses on the current state of the field on the role of inflammation and OS in the pathogenesis of muscle atrophy during CC, and how nutraceuticals and physical activity may act synergistically to limit muscle wasting and dysfunction.
    Keywords:  bimodal approach; cancer cachexia; exercise; lifestyle interventions; muscle atrophy; muscle wasting; myokine; nutraceutical; nutrition
    DOI:  https://doi.org/10.3390/cells9122536
  60. Genes (Basel). 2020 Nov 24. pii: E1391. [Epub ahead of print]11(12):
    Hlavac V, Mohelnikova-Duchonova B, Lovecek M, Ehrmann J, Brynychova V, Kolarova K, Soucek P.
      Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation frequencies or mutational loads accounting separately for drivers, druggable, or clinically actionable genes, did not significantly associate with patients' survival. LRP1B was markedly mutated in primaries of patients who generalized (71%) compared to those developing solitary pulmonary metastases (0%). FLG2 was mutated exclusively in primary tumors compared to paired metastases. In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine.
    Keywords:  adenocarcinoma; metastases; next-generation sequencing; pancreas; pulmonary; survival
    DOI:  https://doi.org/10.3390/genes11121391
  61. Lancet Diabetes Endocrinol. 2020 Nov 26. pii: S2213-8587(20)30365-X. [Epub ahead of print]
    Cheng F, Carroll L, Joglekar MV, Januszewski AS, Wong KK, Hardikar AA, Jenkins AJ, Ma RCW.
      Telomeres are regions of repetitive nucleotide sequences at the ends of chromosomes. Telomere length is a marker of DNA damage, which is often considered a biomarker for biological ageing, and has also been linked with cardiovascular disease, diabetes, and cancer. Emerging studies have highlighted the role of genetic and environmental factors, and explored the effect of modulating telomere length. We provide an overview of studies to date on diabetes and telomere length, and compare different methods and assays for evaluating telomere length and telomerase activity. We highlight the limitations of current studies and areas that warrant further research to unravel the link between diabetes and telomere length. The value of adding telomere length to clinical risk factors to improve risk prediction of diabetes and related complications also merits further investigation.
    DOI:  https://doi.org/10.1016/S2213-8587(20)30365-X
  62. Cold Spring Harb Protoc. 2020 Dec 01. 2020(12): pdb.prot099630
    Rodig SJ.
      Increasing use is being made of cell smears for cell-staining studies. Suspension cells can be attached to slides by drying, and cell smears can also be prepared from biopsy samples, such as needle aspirates, tissue scrapings, or freshly dissected tissues. In these procedures, a thin layer of cells is deposited on a dry slide by physical methods. The most important factor in obtaining good staining patterns is that the smear be only a single cell thick. Tissue smears do not preserve tissue architecture, but are useful for identifying pathological changes and infectious organisms in tissue samples. Cell smears are easily prepared and can be fixed readily by any of the methods used for attached cells.
    DOI:  https://doi.org/10.1101/pdb.prot099630
  63. Mol Cell Proteomics. 2020 Nov 30. pii: mcp.R120.002190. [Epub ahead of print]
    Ross AB, Langer JD, Jovanovic M.
      In all cells, proteins are continuously synthesized and degraded in order to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation in order to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable-isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
    Keywords:  Mass Spectrometry; Protein Degradation*; Protein Synthesis*; Protein Turnover*; Protein-Protein Interactions*; Quantification; SILAC
    DOI:  https://doi.org/10.1074/mcp.R120.002190
  64. Pancreatology. 2020 Nov 24. pii: S1424-3903(20)30844-9. [Epub ahead of print]
    Aslam M, Jagtap N, Karyampudi A, Talukdar R, Reddy DN.
      Endocrine insufficiency is a common and frequent complication of chronic pancreatitis. Identifying the role of pancreatic damage in the development of diabetes is important for early identification and appropriate management.METHODS: All consecutive CP patients between January 2019 and May 2020 were retrospectively studied. Relevant statistical tests were performed. A two sided p value < 0.05 was considered statistically significant.
    RESULTS: Total 587 chronic pancreatitis patients were included of which 118 (20.1%) patients developed diabetes with duration of 12 (IQR 4-48) months. Older age (OR 1.079; 95% CI 1.045-1.113; p < 0.001), presence of pancreatic parenchymal (OR 2.284; 95% CI 1.036-5.038; p = 0.041) and ductal (OR 2.351; 95% CI 1.062-5.207; p = 0.035) calcifications, exocrine insufficiency (OR 6.287; 95% CI 2.258-17.504; p < 0.001), and pancreatic duct stricture (OR 3.358; 95% CI 1.138-9.912; p = 0.028) were independently associated with development of diabetes mellitus in chronic pancreatitis patients. On cox-regression analysis, smoking (HR 2.370; 95% CI 1.290-4.354; p = 0.005) and pancreatic ductal calcification (HR 2.033; 95% CI 1.286-3.212; p = 0.002) were independently associated with earlier onset of diabetes mellitus in patients with chronic pancreatitis.
    CONCLUSION: Pancreatic calcification, pancreatic duct stricture and pancreatic exocrine insufficiency are associated with development of diabetes mellitus in chronic pancreatitis indicating disease progression. Smoking is the modifiable risk factors associated with early onset of diabetes mellitus in CP patients.
    Keywords:  Chronic pancreatitis; Diabetes mellitus; Pancreatic calcification; Pancreatic duct stricture; Pancreatic exocrine insufficiency; Smoking
    DOI:  https://doi.org/10.1016/j.pan.2020.11.011