bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒03‒21
sixty-two papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Cancer cells escape autophagy inhibition via NRF2-induced macropinocytosis.
  2. Mesenchymal stem cell-derived extracellular vesicles reduce senescence and extend health span in mouse models of aging.
  3. Pancreatic cancer cachexia: three dimensions of a complex syndrome.
  4. Mitophagy in Pancreatic Cancer.
  5. Diet-related interventions for cancer-associated cachexia.
  6. Mutagenesis screen uncovers lifespan extension through integrated stress response inhibition without reduced mRNA translation.
  7. Harnessing metabolic dependencies in pancreatic cancers.
  8. Exploiting Tumor Neoantigens to Target Cancer Evolution: Current Challenges and Promising Therapeutic Approaches.
  9. Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome.
  10. Peroxisomal-derived ether phospholipids link nucleotides to respirasome assembly.
  11. AMPK-dependent phosphorylation is required for transcriptional activation of TFEB and TFE3.
  12. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis.
  13. A nuclear-based quality control pathway for non-imported mitochondrial proteins.
  14. Ribosome states signal RNA quality control.
  15. Mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming via p53 activation and reducing acetyl-CoA production.
  16. Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time.
  17. Measurement of Metabolites from Migrating Cells.
  18. Identification of bacteria-derived HLA-bound peptides in melanoma.
  19. Pancreatic cancer induces muscle wasting by promoting the release of pancreatic adenocarcinoma upregulated factor.
  20. MYOF Reduces Lysosome Membrane Stress to Promote Pancreatic Cancer.
  21. Differential roles of GDF15 and FGF21 in systemic metabolic adaptation to the mitochondrial integrated stress response.
  22. Advanced cancer is also a heart failure syndrome: a hypothesis.
  23. The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism.
  24. The lysosomal membrane protein Sidt2 is a vital regulator of mitochondrial quality control in skeletal muscle.
  25. Lysosomes and Cancer Progression: A Malignant Liaison.
  26. α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation.
  27. Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.
  28. Landmarks of human embryonic development inscribed in somatic mutations.
  29. Clinical impact of pre-surgery circulating tumor DNA after total neoadjuvant treatment in locally advanced rectal cancer: a biomarker study from the GEMCAD1402 Trial.
  30. Exploiting bone niches: progression of disseminated tumor cells to metastasis.
  31. Simple, Affordable, and Modular Patterning of Cells using DNA.
  32. γδ T cells regulate the intestinal response to nutrient sensing.
  33. TCF7 is not essential for glucose homeostasis in mice.
  34. Genetic and non-genetic clonal diversity in cancer evolution.
  35. Germline sequence analysis of RABL3 in a large series of pancreatic ductal adenocarcinoma patients reveals no evidence of deleterious variants.
  36. NAD+ supplementation prevents STING-induced senescence in ataxia telangiectasia by improving mitophagy.
  37. Protein arginine methylation: from enigmatic functions to therapeutic targeting.
  38. The decrease of intraflagellar transport impairs sensory perception and metabolism in ageing.
  39. A Guide To… The Regulation Of Selective Autophagy Receptors.
  40. Cancer metastasis as a non-healing wound.
  41. The Chicken Egg Chorioallantoic Membrane (CAM) Model as an In Vivo Method for the Investigation of the Invasion and Metastasis Cascade of Malignant Tumor Cells.
  42. Lipid metabolism in adaptation to extreme nutritional challenges.
  43. Metabolic plasticity allows cancer cells to thrive under nutrient starvation.
  44. Obesity results in adipose tissue T cell exhaustion.
  45. An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer.
  46. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies.
  47. De novo formation of early endosomes during Rab5 to Rab7 transition.
  48. Proteomics in aging research: A roadmap to clinical, translational research.
  49. Choline restores respiration in Psd1-deficient yeast by replenishing mitochondrial phosphatidylethanolamine.
  50. Metabolic implications of non-Electrogenic ATP/ADP exchange in Cancer cells: A mechanistic basis for the Warburg effect.
  51. Utility of mismatch repair protein expression screening via an endoscopic ultrasound assessment of treatment-naive pancreas ductal adenocarcinoma.
  52. VCP/p97 modulates PtdIns3P production and autophagy initiation.
  53. Preoperative assessment of the resectability of pancreatic ductal adenocarcinoma on CT according to the NCCN Guidelines focusing on SMA/SMV branch invasion.
  54. ATP Redux.
  55. Aging: All roads lead to mitochondria.
  56. Abel Prize celebrates union of mathematics and computer science.
  57. Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.
  58. Leveraging microenvironmental synthetic lethalities to treat cancer.
  59. Engineered models of tumor metastasis with immune cell contributions.
  60. Patient-Derived Xenografts from Solid Tumors (PDX) for Models of Metastasis.
  61. Reduced nicotinamide mononucleotide is a new and potent NAD+ precursor in mammalian cells and mice.
  62. Nuclear genome-wide associations with mitochondrial heteroplasmy.
  1. Cancer Cell. 2021 Mar 10. pii: S1535-6108(21)00118-5. [Epub ahead of print]
    Cancer cells escape autophagy inhibition via NRF2-induced macropinocytosis.
    Hua Su, Fei Yang, Rao Fu, Xin Li, Randall French, Evangeline Mose, Xiaohong Pu, Brittney Trinh, Avi Kumar, Junlai Liu, Laura Antonucci, Jelena Todoric, Yuan Liu, Yinling Hu, Maria T Diaz-Meco, Jorge Moscat, Christian M Metallo, Andrew M Lowy, Beicheng Sun, Michael Karin.
      Many cancers, including pancreatic ductal adenocarcinoma (PDAC), depend on autophagy-mediated scavenging and recycling of intracellular macromolecules, suggesting that autophagy blockade should cause tumor starvation and regression. However, until now autophagy-inhibiting monotherapies have not demonstrated potent anti-cancer activity. We now show that autophagy blockade prompts established PDAC to upregulate and utilize an alternative nutrient procurement pathway: macropinocytosis (MP) that allows tumor cells to extract nutrients from extracellular sources and use them for energy generation. The autophagy to MP switch, which may be evolutionarily conserved and not cancer cell restricted, depends on activation of transcription factor NRF2 by the autophagy adaptor p62/SQSTM1. NRF2 activation by oncogenic mutations, hypoxia, and oxidative stress also results in MP upregulation. Inhibition of MP in autophagy-compromised PDAC elicits dramatic metabolic decline and regression of transplanted and autochthonous tumors, suggesting the therapeutic promise of combining autophagy and MP inhibitors in the clinic.
    Keywords:  NRF2; RAS-driven cancer; autophagy; macropinocytosis; p62/SQSTM1
    DOI:  https://doi.org/10.1016/j.ccell.2021.02.016
  2. Aging Cell. 2021 Mar 16. e13337
    Mesenchymal stem cell-derived extracellular vesicles reduce senescence and extend health span in mouse models of aging.
    Akaitz Dorronsoro, Fernando E Santiago, Diego Grassi, Tianpeng Zhang, Ruenn Chai Lai, Sara J McGowan, Luise Angelini, Mitra Lavasani, Lana Corbo, Aiping Lu, Robert W Brooks, Marta Garcia-Contreras, Donna B Stolz, Antonio Amelio, Siddaraju V Boregowda, Mohammad Fallahi, Adrian Reich, Camillo Ricordi, Donald G Phinney, Johnny Huard, Sai Kiang Lim, Laura J Niedernhofer, Paul D Robbins.
      Aging drives progressive loss of the ability of tissues to recover from stress, partly through loss of somatic stem cell function and increased senescent burden. We demonstrate that bone marrow-derived mesenchymal stem cells (BM-MSCs) rapidly senescence and become dysfunctional in culture. Injection of BM-MSCs from young mice prolonged life span and health span, and conditioned media (CM) from young BM-MSCs rescued the function of aged stem cells and senescent fibroblasts. Extracellular vesicles (EVs) from young BM-MSC CM extended life span of Ercc1-/- mice similarly to injection of young BM-MSCs. Finally, treatment with EVs from MSCs generated from human ES cells reduced senescence in culture and in vivo, and improved health span. Thus, MSC EVs represent an effective and safe approach for conferring the therapeutic effects of adult stem cells, avoiding the risks of tumor development and donor cell rejection. These results demonstrate that MSC-derived EVs are highly effective senotherapeutics, slowing the progression of aging, and diseases driven by cellular senescence.
    Keywords:  aging; extracellular vesicles; mesenchymal stem cells; senescence; stem cells
    DOI:  https://doi.org/10.1111/acel.13337
  3. Br J Cancer. 2021 Mar 19.
    Pancreatic cancer cachexia: three dimensions of a complex syndrome.
    Maximilian Kordes, Lars Larsson, Lars Engstrand, J-Matthias Löhr.
      Cancer cachexia is a multifactorial syndrome that is characterised by a loss of skeletal muscle mass, is commonly associated with adipose tissue wasting and malaise, and responds poorly to therapeutic interventions. Although cachexia can affect patients who are severely ill with various malignant or non-malignant conditions, it is particularly common among patients with pancreatic cancer. Pancreatic cancer often leads to the development of cachexia through a combination of distinct factors, which, together, explain its high prevalence and clinical importance in this disease: systemic factors, including metabolic changes and pathogenic signals related to the tumour biology of pancreatic adenocarcinoma; factors resulting from the disruption of the digestive and endocrine functions of the pancreas; and factors related to the close anatomical and functional connection of the pancreas with the gut. In this review, we conceptualise the various insights into the mechanisms underlying pancreatic cancer cachexia according to these three dimensions to expose its particular complexity and the challenges that face clinicians in trying to devise therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41416-021-01301-4
  4. Front Oncol. 2021 ;11 616079
    Mitophagy in Pancreatic Cancer.
    Yangchun Xie, Jiao Liu, Rui Kang, Daolin Tang.
      Pancreatic ductal adenocarcinoma (PDAC), one of the most aggressive solid malignancies, is characterized by the presence of oncogenic KRAS mutations, poor response to current therapies, prone to metastasis, and a low 5-year overall survival rate. Macroautophagy (herein referred to as autophagy) is a lysosome-dependent degradation system that forms a series of dynamic membrane structures to engulf, degrade, and recycle various cargoes, such as unused proteins, damaged organelles, and invading pathogens. Autophagy is usually upregulated in established cancers, but it plays a dual role in the regulation of the initiation and progression of PDAC. As a type of selective autophagy, mitophagy is a mitochondrial quality control mechanism that uses ubiquitin-dependent (e.g., the PINK1-PRKN pathway) and -independent (e.g., BNIP3L/NIX, FUNDC1, and BNIP3) pathways to regulate mitochondrial turnover and participate in the modulation of metabolism and cell death. Genetically engineered mouse models indicate that the loss of PINK1 or PRKN promotes, whereas the depletion of BNIP3L inhibits oncogenic KRAS-driven pancreatic tumorigenesis. Mitophagy also play a dual role in the regulation of the anticancer activity of certain cytotoxic agents (e.g., rocaglamide A, dichloroacetate, fisetin, and P. suffruticosa extracts) in PDAC cells or xenograft models. In this min-review, we summarize the latest advances in understanding the complex role of mitophagy in the occurrence and treatment of PDAC.
    Keywords:  PDAC - pancreatic ductal adenocarcinoma; autophagy; mitophagy; therapy; tumorigenesis
    DOI:  https://doi.org/10.3389/fonc.2021.616079
  5. J Cancer Res Clin Oncol. 2021 Mar 15.
    Diet-related interventions for cancer-associated cachexia.
    Alan J Kim, David S Hong, Goldy C George.
      PURPOSE: Cancer-associated cachexia is a common condition in patients with advanced cancer, and is associated with extreme and involuntary weight loss and irreversible muscle wasting. Despite its high morbidity and mortality, there is no known treatment to reverse its effects. Thus, there is increasing interest in whether diet and exercise can assist in the minimization of cancer-associated cachexia.METHODS: We reviewed the literature on the impact of dietary patterns, dietary components, and exercise on the progress and severity of cancer cachexia.
    RESULTS: Although most studies have produced inconclusive or controversial findings, some promising studies using animal models and early human clinical trials suggest that dietary and physical therapy interventions may alleviate cancer-associated cachexia. Moreover, many studies suggest that controlling diet and exercise nevertheless improved the quality of life (QoL) for cancer patients with cachexia.
    CONCLUSION: Ongoing studies will continue to examine whether different forms of multimodal therapy-combinations of cancer treatment, dietary regimens, anti-inflammatory therapy, and physical therapy-are effective methods to improve outcomes in advanced cancer patients with cachexia. Moreover, future studies should examine the effects of such interventions on long-term QoL and establish nutritional guidelines for the management of cancer-associated cachexia.
    Keywords:  Cachexia; Cancer; Diet; Exercise; Multimodal
    DOI:  https://doi.org/10.1007/s00432-021-03592-9
  6. Nat Commun. 2021 03 15. 12(1): 1678
    Mutagenesis screen uncovers lifespan extension through integrated stress response inhibition without reduced mRNA translation.
    Maxime J Derisbourg, Laura E Wester, Ruth Baddi, Martin S Denzel.
      Protein homeostasis is modulated by stress response pathways and its deficiency is a hallmark of aging. The integrated stress response (ISR) is a conserved stress-signaling pathway that tunes mRNA translation via phosphorylation of the translation initiation factor eIF2. ISR activation and translation initiation are finely balanced by eIF2 kinases and by the eIF2 guanine nucleotide exchange factor eIF2B. However, the role of the ISR during aging remains poorly understood. Using a genomic mutagenesis screen for longevity in Caenorhabditis elegans, we define a role of eIF2 modulation in aging. By inhibiting the ISR, dominant mutations in eIF2B enhance protein homeostasis and increase lifespan. Consistently, full ISR inhibition using phosphorylation-defective eIF2α or pharmacological ISR inhibition prolong lifespan. Lifespan extension through impeding the ISR occurs without a reduction in overall protein synthesis. Instead, we observe changes in the translational efficiency of a subset of mRNAs, of which the putative kinase kin-35 is required for lifespan extension. Evidently, lifespan is limited by the ISR and its inhibition may provide an intervention in aging.
    DOI:  https://doi.org/10.1038/s41467-021-21743-x
  7. Nat Rev Gastroenterol Hepatol. 2021 Mar 19.
    Harnessing metabolic dependencies in pancreatic cancers.
    Joel Encarnación-Rosado, Alec C Kimmelman.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with a 5-year survival rate of <10%. The tumour microenvironment (TME) of PDAC is characterized by excessive fibrosis and deposition of extracellular matrix, termed desmoplasia. This unique TME leads to high interstitial pressure, vascular collapse and low nutrient and oxygen diffusion. Together, these factors contribute to the unique biology and therapeutic resistance of this deadly tumour. To thrive in this hostile environment, PDAC cells adapt by using non-canonical metabolic pathways and rely on metabolic scavenging pathways such as autophagy and macropinocytosis. Here, we review the metabolic pathways that PDAC use to support their growth in the setting of an austere TME. Understanding how PDAC tumours rewire their metabolism and use scavenging pathways under environmental stressors might enable the identification of novel therapeutic approaches.
    DOI:  https://doi.org/10.1038/s41575-021-00431-7
  8. Cancer Discov. 2021 Mar 15.
    Exploiting Tumor Neoantigens to Target Cancer Evolution: Current Challenges and Promising Therapeutic Approaches.
    Ravi G Gupta, Fenge Li, Jason Roszik, Gregory Lizée.
      Immunotherapeutic manipulation of the antitumor immune response offers an attractive strategy to target genomic instability in cancer. A subset of tumor-specific somatic mutations can be translated into immunogenic and HLA-bound epitopes called neoantigens, which can induce the activation of helper and cytotoxic T lymphocytes. However, cancer immunoediting and immunosuppressive mechanisms often allow tumors to evade immune recognition. Recent evidence also suggests that the tumor neoantigen landscape extends beyond epitopes originating from nonsynonymous single-nucleotide variants in the coding exome. Here we review emerging approaches for identifying, prioritizing, and immunologically targeting personalized neoantigens using polyvalent cancer vaccines and T-cell receptor gene therapy. SIGNIFICANCE: Several major challenges currently impede the clinical efficacy of neoantigen-directed immunotherapy, such as the relative infrequency of immunogenic neoantigens, suboptimal potency and priming of de novo tumor-specific T cells, and tumor cell-intrinsic and -extrinsic mechanisms of immune evasion. A deeper understanding of these biological barriers could help facilitate the development of effective and durable immunotherapy for any type of cancer, including immunologically "cold" tumors that are otherwise therapeutically resistant.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1575
  9. Cancer Discov. 2021 Mar 16. pii: candisc.0841.2020. [Epub ahead of print]
    Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome.
    Shannon M Liudahl, Courtney B Betts, Shamilene Sivagnanam, Vicente Morales-Oyarvide, Annacarolina da Silva, Chen Yuan, Samuel Hwang, Alison Grossblatt-Wait, Kenna R Leis, William Larson, Meghan B Lavoie, Padraic Robinson, Andressa Dias Costa, Sara A Vayrynen, Thomas E Clancy, Douglas A Rubinson, Jason Link, Dove Keith, Wesley Horton, Margaret A Tempero, Robert H Vonderheide, Elizabeth M Jaffee, Brett Sheppard, Jeremy Goecks, Rosalie C Sears, Byung S Park, Motomi Mori, Jonathan A Nowak, Brian M Wolpin, Lisa M Coussens.
      Immunotherapies targeting aspects of T cell functionality are efficacious in many solid tumors, but pancreatic ductal adenocarcinoma (PDAC) remains refractory to these treatments. Deeper understanding of the PDAC immune ecosystem is needed to identify additional therapeutic targets and predictive biomarkers for therapeutic response and resistance monitoring. To address these needs, we quantitatively evaluated leukocyte contexture in 135 human PDACs at single-cell resolution by profiling density and spatial distribution of myeloid and lymphoid cells within histopathologically-defined regions of surgical resections from treatment-naïve and presurgically (neoadjuvant)-treated patients and biopsies from metastatic PDAC. Resultant data establishes an immune atlas of PDAC heterogeneity, identifies leukocyte features correlating with clinical outcomes, and through an in silico study, provides guidance for use of PDAC tissue microarrays to optimally measure intratumoral immune heterogeneity. Atlas data has direct applicability as a reference for evaluating immune responses to investigational neoadjuvant PDAC therapeutics where pre-therapy baseline specimens are not available.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0841
  10. Nat Chem Biol. 2021 Mar 15.
    Peroxisomal-derived ether phospholipids link nucleotides to respirasome assembly.
    Christopher F Bennett, Katherine E O'Malley, Elizabeth A Perry, Eduardo Balsa, Pedro Latorre-Muro, Christopher L Riley, Chi Luo, Mark Jedrychowski, Steven P Gygi, Pere Puigserver.
      The protein complexes of the mitochondrial electron transport chain exist in isolation and in higher order assemblies termed supercomplexes (SCs) or respirasomes (SC I+III2+IV). The association of complexes I, III and IV into the respirasome is regulated by unknown mechanisms. Here, we designed a nanoluciferase complementation reporter for complex III and IV proximity to determine in vivo respirasome levels. In a chemical screen, we found that inhibitors of the de novo pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH) potently increased respirasome assembly and activity. By-passing DHODH inhibition via uridine supplementation decreases SC assembly by altering mitochondrial phospholipid composition, specifically elevated peroxisomal-derived ether phospholipids. Cell growth rates upon DHODH inhibition depend on ether lipid synthesis and SC assembly. These data reveal that nucleotide pools signal to peroxisomes to modulate synthesis and transport of ether phospholipids to mitochondria for SC assembly, which are necessary for optimal cell growth in conditions of nucleotide limitation.
    DOI:  https://doi.org/10.1038/s41589-021-00772-z
  11. Autophagy. 2021 Mar 18. 1-19
    AMPK-dependent phosphorylation is required for transcriptional activation of TFEB and TFE3.
    Mathieu Paquette, Leeanna El-Houjeiri, Linda C Zirden, Pietri Puustinen, Paola Blanchette, Hyeonju Jeong, Kurt Dejgaard, Peter M Siegel, Arnim Pause.
      Increased macroautophagy/autophagy and lysosomal activity promote tumor growth, survival and chemo-resistance. During acute starvation, autophagy is rapidly engaged by AMPK (AMP-activated protein kinase) activation and MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) inhibition to maintain energy homeostasis and cell survival. TFEB (transcription factor E3) and TFE3 (transcription factor binding to IGHM enhancer 3) are master transcriptional regulators of autophagy and lysosomal activity and their cytoplasm/nuclear shuttling is controlled by MTORC1-dependent multisite phosphorylation. However, it is not known whether and how the transcriptional activity of TFEB or TFE3 is regulated. We show that AMPK mediates phosphorylation of TFEB and TFE3 on three serine residues, leading to TFEB and TFE3 transcriptional activity upon nutrient starvation, FLCN (folliculin) depletion and pharmacological manipulation of MTORC1 or AMPK. Collectively, we show that MTORC1 specifically controls TFEB and TFE3 cytosolic retention, whereas AMPK is essential for TFEB and TFE3 transcriptional activity. This dual and opposing regulation of TFEB and TFE3 by MTORC1 and AMPK is reminiscent of the regulation of another critical regulator of autophagy, ULK1 (unc-51 like autophagy activating kinase 1). Surprisingly, we show that chemoresistance is mediated by AMPK-dependent activation of TFEB, which is abolished by pharmacological inhibition of AMPK or mutation of serine 466, 467 and 469 to alanine residues within TFEB. Altogether, we show that AMPK is a key regulator of TFEB and TFE3 transcriptional activity, and we validate AMPK as a promising target in cancer therapy to evade chemotherapeutic resistance.AbbreviationsACACA: acetyl-CoA carboxylase alpha; ACTB: actin beta; AICAR: 5-aminoimidazole-4-carboxamide ribonucleotide; AMPK: AMP-activated protein kinase; AMPKi: AMPK inhibitor, SBI-0206965; CA: constitutively active; CARM1: coactivator-associated arginine methyltransferase 1; CFP: cyan fluorescent protein; CLEAR: coordinated lysosomal expression and regulation; DKO: double knock-out; DMEM: Dulbecco's modified Eagle's medium; DMSO: dimethyl sulfoxide; DQ-BSA: self-quenched BODIPY® dye conjugates of bovine serum albumin; EBSS: Earle's balanced salt solution; FLCN: folliculin; GFP: green fluorescent protein; GST: glutathione S-transferases; HD: Huntington disease; HTT: huntingtin; KO: knock-out; LAMP1: lysosomal associated membrane protein 1; MEF: mouse embryonic fibroblasts; MITF: melanocyte inducing transcription factor; MTORC1: MTOR complex 1; PolyQ: polyglutamine; RPS6: ribosomal protein S6; RT-qPCR: reverse transcription quantitative polymerase chain reaction; TCL: total cell lysates; TFE3: transcription factor binding to IGHM enhancer 3; TFEB: transcription factor EB; TKO: triple knock-out; ULK1: unc-51 like autophagy activating kinase 1.
    Keywords:  AMP-activated protein kinase; autophagy; drug resistance; lysosomal biogenesis; mechanistic target of rapamycin kinase; phosphorylation; transcription factor E3; transcription factor EB
    DOI:  https://doi.org/10.1080/15548627.2021.1898748
  12. Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00187-X. [Epub ahead of print]34(11): 108873
    Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis.
    Irene Anastasia, Nicolò Ilacqua, Andrea Raimondi, Philippe Lemieux, Rana Ghandehari-Alavijeh, Guilhem Faure, Sergei L Mekhedov, Kevin J Williams, Federico Caicci, Giorgio Valle, Marta Giacomello, Ariel D Quiroga, Richard Lehner, Michael J Miksis, Katalin Toth, Thomas Q de Aguiar Vallim, Eugene V Koonin, Luca Scorrano, Luca Pellegrini.
      Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by sheets of curved rough endoplasmic reticulum closely wrapped around the mitochondria (wrappER). To elucidate the in vivo function of this contact, mouse liver fractions enriched in wrappER-associated mitochondria are analyzed by transcriptomics, proteomics, and lipidomics. The biochemical signature of the wrappER points to a role in the biogenesis of very-low-density lipoproteins (VLDL). Altering wrappER-mitochondria contacts curtails VLDL secretion and increases hepatic fatty acids, lipid droplets, and neutral lipid content. Conversely, acute liver-specific ablation of Mttp, the most upstream regulator of VLDL biogenesis, recapitulates this hepatic dyslipidemia phenotype and promotes remodeling of the wrappER-mitochondria contact. The discovery that liver wrappER-mitochondria contacts participate in VLDL biology suggests an involvement of inter-organelle contacts in systemic lipid homeostasis.
    Keywords:  MAM; MUP; Rrbp1; VLDL; endoplasmic reticulum; inter-organelle contact; lipoprotein; liver metabolism; mitochondria; wrappER
    DOI:  https://doi.org/10.1016/j.celrep.2021.108873
  13. Elife. 2021 Mar 18. pii: e61230. [Epub ahead of print]10
    A nuclear-based quality control pathway for non-imported mitochondrial proteins.
    Viplendra Ps Shakya, William A Barbeau, Tianyao Xiao, Christina S Knutson, Max H Schuler, Adam L Hughes.
      Mitochondrial import deficiency causes cellular toxicity due to the accumulation of non-imported mitochondrial precursor proteins, termed mitoprotein-induced stress. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we cataloged the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment in S. cerevisiae. We found that a number of non-imported mitochondrial proteins localize to the nucleus, where they are subjected to proteasome-dependent degradation through a process we term nuclear-associated mitoprotein degradation (mitoNUC). Recognition and destruction of mitochondrial precursors by the mitoNUC pathway requires the presence of an N-terminal mitochondrial targeting sequence (MTS) and is mediated by combined action of the E3 ubiquitin ligases San1, Ubr1, and Doa10. Impaired breakdown of precursors leads to alternative sequestration in nuclear-associated foci. These results identify the nucleus as an important destination for the disposal of non-imported mitochondrial precursors.
    Keywords:  S. cerevisiae; cell biology
    DOI:  https://doi.org/10.7554/eLife.61230
  14. Mol Cell. 2021 Mar 04. pii: S1097-2765(21)00132-5. [Epub ahead of print]
    Ribosome states signal RNA quality control.
    Karole N D'Orazio, Rachel Green.
      Eukaryotic cells integrate multiple quality control (QC) responses during protein synthesis in the cytoplasm. These QC responses are signaled by slow or stalled elongating ribosomes. Depending on the nature of the delay, the signal may lead to translational repression, messenger RNA decay, ribosome rescue, and/or nascent protein degradation. Here, we discuss how the structure and composition of an elongating ribosome in a troubled state determine the downstream quality control pathway(s) that ensue. We highlight the intersecting pathways involved in RNA decay and the crosstalk that occurs between RNA decay and ribosome rescue.
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.022
  15. Cell Death Differ. 2021 Mar 15.
    Mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming via p53 activation and reducing acetyl-CoA production.
    Kunlun Yin, Jordan Lee, Zhaoli Liu, Hyeoncheol Kim, David R Martin, Dandan Wu, Meilian Liu, Xiang Xue.
      Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the US. Understanding the mechanisms of CRC progression is essential to improve treatment. Mitochondria is the powerhouse for healthy cells. However, in tumor cells, less energy is produced by the mitochondria and metabolic reprogramming is an early hallmark of cancer. The metabolic differences between normal and cancer cells are being interrogated to uncover new therapeutic approaches. Mitochondria targeting PTEN-induced kinase 1 (PINK1) is a key regulator of mitophagy, the selective elimination of damaged mitochondria by autophagy. Defective mitophagy is increasingly associated with various diseases including CRC. However, a significant gap exists in our understanding of how PINK1-dependent mitophagy participates in the metabolic regulation of CRC. By mining Oncomine, we found that PINK1 expression was downregulated in human CRC tissues compared to normal colons. Moreover, disruption of PINK1 increased colon tumorigenesis in two colitis-associated CRC mouse models, suggesting that PINK1 functions as a tumor suppressor in CRC. PINK1 overexpression in murine colon tumor cells promoted mitophagy, decreased glycolysis and increased mitochondrial respiration potentially via activation of p53 signaling pathways. In contrast, PINK1 deletion decreased apoptosis, increased glycolysis, and reduced mitochondrial respiration and p53 signaling. Interestingly, PINK1 overexpression in vivo increased apoptotic cell death and suppressed colon tumor xenograft growth. Metabolomic analysis revealed that acetyl-CoA was significantly reduced in tumors with PINK1 overexpression, which was partly due to activation of the HIF-1α-pyruvate dehydrogenase (PDH) kinase 1 (PDHK1)-PDHE1α axis. Strikingly, treating mice with acetate increased acetyl-CoA levels and rescued PINK1-suppressed tumor growth. Importantly, PINK1 disruption simultaneously increased xenografted tumor growth and acetyl-CoA production. In conclusion, mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming and reducing acetyl-CoA production.
    DOI:  https://doi.org/10.1038/s41418-021-00760-9
  16. Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00168-6. [Epub ahead of print]34(11): 108854
    Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time.
    Alain R Bonny, Karl Kochanowski, Maren Diether, Hana El-Samad.
      A near-constant feature of stress responses is a downregulation or arrest of the cell cycle, resulting in transient growth slowdown. To investigate the role of growth slowdown in the hyperosmotic shock response of S. cerevisiae, we perturbed the G1/S checkpoint protein Sic1 to enable osmo-stress response activation with diminished growth slowdown. We document that in this mutant, adaptation to stress is accelerated rather than delayed. This accelerated recovery of the mutant proceeds by liquidation of internal glycogen stores, which are then shunted into the osmo-shock response. Therefore, osmo-adaptation in wild-type cells is delayed because growth slowdown prevents full accessibility to cellular glycogen stores. However, faster adaptation comes at the cost of acute sensitivity to subsequent osmo-stresses. We suggest that stress-induced growth slowdown acts as an arbiter to regulate the resources devoted to osmo-shock, balancing short-term adaptation with long-term robustness.
    Keywords:  adaptation; metabolism; osmotic shock; stress response
    DOI:  https://doi.org/10.1016/j.celrep.2021.108854
  17. Methods Mol Biol. 2021 ;2294 143-150
    Measurement of Metabolites from Migrating Cells.
    Demond Williams, Barbara Fingleton.
      Metastasis is a multistep process that involves responses to extrinsic and intrinsic signals at every step. It is thus only truly appreciated in the context of a whole organism. Nevertheless, in vitro studies can be used to facilitate understanding of the possible factors contributing to any phenotype that is associated with metastatic competence. The use of migration assays-where monolayers of cells migrate to cover gaps or "wounds"-has been described for decades to identify signaling pathways that regulate motile competence and to screen for ways of interfering with this ability. Here we depict the combination of such an assay with assessment of indicators of carbon metabolism using commercially available assays. This enables identification of changes in cellular metabolism associated with actively migrating cells.
    Keywords:  Glucose consumption; Lactate production; Metastasis; Migration; Scratch assay
    DOI:  https://doi.org/10.1007/978-1-0716-1350-4_10
  18. Nature. 2021 Mar 17.
    Identification of bacteria-derived HLA-bound peptides in melanoma.
    Shelly Kalaora, Adi Nagler, Deborah Nejman, Michal Alon, Chaya Barbolin, Eilon Barnea, Steven L C Ketelaars, Kuoyuan Cheng, Kevin Vervier, Noam Shental, Yuval Bussi, Ron Rotkopf, Ronen Levy, Gil Benedek, Sophie Trabish, Tali Dadosh, Smadar Levin-Zaidman, Leore T Geller, Kun Wang, Polina Greenberg, Gal Yagel, Aviyah Peri, Garold Fuks, Neerupma Bhardwaj, Alexandre Reuben, Leandro Hermida, Sarah B Johnson, Jessica R Galloway-Peña, William C Shropshire, Chantale Bernatchez, Cara Haymaker, Reetakshi Arora, Lior Roitman, Raya Eilam, Adina Weinberger, Maya Lotan-Pompan, Michal Lotem, Arie Admon, Yishai Levin, Trevor D Lawley, David J Adams, Mitchell P Levesque, Michal J Besser, Jacob Schachter, Ofra Golani, Eran Segal, Naama Geva-Zatorsky, Eytan Ruppin, Pia Kvistborg, Scott N Peterson, Jennifer A Wargo, Ravid Straussman, Yardena Samuels.
      A variety of species of bacteria are known to colonize human tumours1-11, proliferate within them and modulate immune function, which ultimately affects the survival of patients with cancer and their responses to treatment12-14. However, it is not known whether antigens derived from intracellular bacteria are presented by the human leukocyte antigen class I and II (HLA-I and HLA-II, respectively) molecules of tumour cells, or whether such antigens elicit a tumour-infiltrating T cell immune response. Here we used 16S rRNA gene sequencing and HLA peptidomics to identify a peptide repertoire derived from intracellular bacteria that was presented on HLA-I and HLA-II molecules in melanoma tumours. Our analysis of 17 melanoma metastases (derived from 9 patients) revealed 248 and 35 unique HLA-I and HLA-II peptides, respectively, that were derived from 41 species of bacteria. We identified recurrent bacterial peptides in tumours from different patients, as well as in different tumours from the same patient. Our study reveals that peptides derived from intracellular bacteria can be presented by tumour cells and elicit immune reactivity, and thus provides insight into a mechanism by which bacteria influence activation of the immune system and responses to therapy.
    DOI:  https://doi.org/10.1038/s41586-021-03368-8
  19. Exp Mol Med. 2021 Mar 17.
    Pancreatic cancer induces muscle wasting by promoting the release of pancreatic adenocarcinoma upregulated factor.
    Wonbeak Yoo, Hyunji Choi, Young Hoon Son, Jaemin Lee, Seongyea Jo, Dana Jung, Yeon Jeong Kim, Sang Seok Koh, Yong Ryoul Yang, Eun-Soo Kwon, Kwang-Pyo Lee, Kyung Hee Noh, Kyung Won Kim, Yousun Ko, Eunsung Jun, Song Cheol Kim, Seokho Kim.
      Cancer cachexia is a highly debilitating condition characterized by weight loss and muscle wasting that contributes significantly to the morbidity and mortality of pancreatic cancer. The factors that induce cachexia in pancreatic cancer are largely unknown. We previously showed that pancreatic adenocarcinoma upregulated factor (PAUF) secreted by pancreatic cancer cells is responsible for tumor growth and metastasis. Here, we analyzed the relation between pancreatic cancer-derived PAUF and cancer cachexia in mice and its clinical significance. Body weight loss and muscle weight loss were significantly higher in mice with Panc-1/PAUF tumors than in those with Panc-1/Mock tumors. Direct administration of rPAUF to muscle recapitulated tumor-induced atrophy, and a PAUF-neutralizing antibody abrogated tumor-induced muscle wasting in Panc-1/PAUF tumor-bearing mice. C2C12 myotubes treated with rPAUF exhibited rapid inactivation of Akt-Foxo3a signaling, resulting in Atrogin1/MAFbx upregulation, myosin heavy chain loss, and muscle atrophy. The neutrophil-to-lymphocyte ratio and body weight loss were significantly higher in pancreatic cancer patients with high PAUF expression than in those with low PAUF expression. Analysis of different pancreatic cancer datasets showed that PAUF expression was significantly higher in the pancreatic cancer group than in the nontumor group. Analysis of The Cancer Genome Atlas data found associations between high PAUF expression or a high DNA copy number and poor overall survival. Our data identified tumor-secreted circulating PAUF as a key factor of cachexia, causing muscle wasting in mice. Neutralizing PAUF may be a useful therapeutic strategy for the treatment of pancreatic cancer-induced cachexia.
    DOI:  https://doi.org/10.1038/s12276-021-00582-2
  20. Cancer Discov. 2021 Mar 19.
    MYOF Reduces Lysosome Membrane Stress to Promote Pancreatic Cancer.
      The membrane repair factor MYOF prevented lysosome membrane damage in pancreatic cancer cells.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2021-041
  21. iScience. 2021 Mar 19. 24(3): 102181
    Differential roles of GDF15 and FGF21 in systemic metabolic adaptation to the mitochondrial integrated stress response.
    Seul Gi Kang, Min Jeong Choi, Saet-Byel Jung, Hyo Kyun Chung, Joon Young Chang, Jung Tae Kim, Yea Eun Kang, Ju Hee Lee, Hyun Jung Hong, Sang Mi Jun, Hyun-Joo Ro, Jae Myoung Suh, Hail Kim, Johan Auwerx, Hyon-Seung Yi, Minho Shong.
      Perturbation of mitochondrial proteostasis provokes cell autonomous and cell non-autonomous responses that contribute to homeostatic adaptation. Here, we demonstrate distinct metabolic effects of hepatic metabokines as cell non-autonomous factors in mice with mitochondrial OxPhos dysfunction. Liver-specific mitochondrial stress induced by a loss-of-function mutation in Crif1 (LKO) leads to aberrant oxidative phosphorylation and promotes the mitochondrial unfolded protein response. LKO mice are highly insulin sensitive and resistant to diet-induced obesity. The hepatocytes of LKO mice secrete large quantities of metabokines, including GDF15 and FGF21, which confer metabolic benefits. We evaluated the metabolic phenotypes of LKO mice with global deficiency of GDF15 or FGF21 and show that GDF15 regulates body and fat mass and prevents diet-induced hepatic steatosis, whereas FGF21 upregulates insulin sensitivity, energy expenditure, and thermogenesis in white adipose tissue. This study reveals that the mitochondrial integrated stress response (ISRmt) in liver mediates metabolic adaptation through hepatic metabokines.
    Keywords:  Cell Biology; Physiology; Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2021.102181
  22. J Cachexia Sarcopenia Muscle. 2021 Mar 18.
    Advanced cancer is also a heart failure syndrome: a hypothesis.
    Markus S Anker, Ana Pardo Sanz, José L Zamorano, Mandeep R Mehra, Javed Butler, Hanno Riess, Andrew J S Coats, Stefan D Anker.
      We present the hypothesis that advanced stage cancer is also a heart failure syndrome. It can develop independently of or in addition to cardiotoxic effects of anti-cancer therapies. This includes an increased risk of ventricular arrhythmias. We suggest the pathophysiologic link for these developments includes generalized muscle wasting (i.e. sarcopenia) due to tissue homeostasis changes leading to cardiac wasting associated cardiomyopathy. Cardiac wasting with thinning of the ventricular wall increases ventricular wall stress, even in the absence of ventricular dilatation. In addition, arrhythmias may be facilitated by cellular wasting processes affecting structure and function of electrical cells and conduction pathways. We submit that in some patients with advanced cancer (but not terminal cancer), heart failure therapy or defibrillators may be relevant treatment options. The key points in selecting patients for such therapies may be the predicted life expectancy, quality of life at intervention time, symptomatic burden, and consequences for further anti-cancer therapies. The cause of death in advanced cancer is difficult to ascertain and consensus on event definitions in cancer is not established yet. Clinical investigations on this are called for. Broader ethical considerations must be taken into account when aiming to target cardiovascular problems in cancer patients. We suggest that focused attention to evaluating cardiac wasting and arrhythmias in cancer will herald a further evolution in the rapidly expanding field of cardio-oncology.
    Keywords:  Arrhythmia; Cancer; Cardiac wasting associated cardiomyopathy; Heart failure
    DOI:  https://doi.org/10.1002/jcsm.12694
  23. Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00183-2. [Epub ahead of print]34(11): 108869
    The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism.
    Michelle Grace Acoba, Ebru S Selen Alpergin, Santosh Renuse, Lucía Fernández-Del-Río, Ya-Wen Lu, Oleh Khalimonchuk, Catherine F Clarke, Akhilesh Pandey, Michael J Wolfgang, Steven M Claypool.
      Mitochondrial carriers (MCs) mediate the passage of small molecules across the inner mitochondrial membrane (IMM), enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterize SFXN1, a member of the non-canonical, sideroflexin family. We find that SFXN1, an integral IMM protein with an uneven number of transmembrane domains, is a TIM22 complex substrate. SFXN1 deficiency leads to mitochondrial respiratory chain impairments, most detrimental to complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. The CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and α-ketoglutarate metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.
    Keywords:  Complex III; OXPHOS; SFXN1; TIM22 complex; amino acid; heme; mitochondria; mitochondrial carrier; serine; sideroflexin
    DOI:  https://doi.org/10.1016/j.celrep.2021.108869
  24. FASEB J. 2021 Apr;35(4): e21223
    The lysosomal membrane protein Sidt2 is a vital regulator of mitochondrial quality control in skeletal muscle.
    Lizhuo Wang, Cui Yu, Wenjun Pei, Mengya Geng, Yao Zhang, Zihui Li, Feiteng Liang, Fengbiao Tan, Hui Du, Jialin Gao.
      The role of Sidt2 in the process of glucose and lipid metabolism has been recently reported. However, whether Sidt2 is involved in the metabolic regulation in skeletal muscle remains unknown. In this study, for the first time, using skeletal muscle-selective Sidt2 knockout mice, we found that Sidt2 was vital for the quality control of mitochondria in mouse skeletal muscle. These mice showed significantly reduced muscle tolerance and structurally abnormal mitochondria. Deletion of the Sidt2 gene resulted in decreased expression of mitochondrial fusion protein 2 (Mfn2) and Dynamin-related protein 1 (Drp1), as well as peroxisome proliferator-activated receptor γ coactivator-1 (PGC1-α). In addition, the clearance of damaged mitochondria in skeletal muscle was inhibited upon Sidt2 deletion, which was caused by blockade of autophagy flow. Mechanistically, the fusion of autophagosomes and lysosomes was compromised in Sidt2 knockout skeletal muscle cells. In summary, the deletion of the Sidt2 gene not only interfered with the quality control of mitochondria, but also inhibited the clearance of mitochondria and caused the accumulation of a large number of damaged mitochondria, ultimately leading to the abnormal structure and function of skeletal muscle.
    Keywords:  Sidt2; autophagy; mitochondria; myopathy; quality control
    DOI:  https://doi.org/10.1096/fj.202000424R
  25. Front Cell Dev Biol. 2021 ;9 642494
    Lysosomes and Cancer Progression: A Malignant Liaison.
    Eda R Machado, Ida Annunziata, Diantha van de Vlekkert, Gerard C Grosveld, Alessandra d'Azzo.
      During primary tumorigenesis isolated cancer cells may undergo genetic or epigenetic changes that render them responsive to additional intrinsic or extrinsic cues, so that they enter a transitional state and eventually acquire an aggressive, metastatic phenotype. Among these changes is the alteration of the cell metabolic/catabolic machinery that creates the most permissive conditions for invasion, dissemination, and survival. The lysosomal system has emerged as a crucial player in this malignant transformation, making this system a potential therapeutic target in cancer. By virtue of their ubiquitous distribution in mammalian cells, their multifaced activities that control catabolic and anabolic processes, and their interplay with other organelles and the plasma membrane (PM), lysosomes function as platforms for inter- and intracellular communication. This is due to their capacity to adapt and sense nutrient availability, to spatially segregate specific functions depending on their position, to fuse with other compartments and with the PM, and to engage in membrane contact sites (MCS) with other organelles. Here we review the latest advances in our understanding of the role of the lysosomal system in cancer progression. We focus on how changes in lysosomal nutrient sensing, as well as lysosomal positioning, exocytosis, and fusion perturb the communication between tumor cells themselves and between tumor cells and their microenvironment. Finally, we describe the potential impact of MCS between lysosomes and other organelles in propelling cancer growth and spread.
    Keywords:  cancer progression; lysosomal exocytosis; lysosomal membrane contact sites; lysosome movement; lysosome positioning
    DOI:  https://doi.org/10.3389/fcell.2021.642494
  26. Nat Commun. 2021 03 17. 12(1): 1703
    α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation.
    Mariana Pavel, So Jung Park, Rebecca A Frake, Sung Min Son, Marco M Manni, Carla F Bento, Maurizio Renna, Thomas Ricketts, Fiona M Menzies, Radu Tanasa, David C Rubinsztein.
      The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Recent literature suggests that autophagy compromise may cause opposite effects in different contexts by either activating or inhibiting YAP/TAZ co-transcriptional regulators of the Hippo pathway via unrelated mechanisms. Here, we confirm that autophagy perturbation in different cell types can cause opposite responses in growth-promoting oncogenic YAP/TAZ transcriptional signalling. These apparently contradictory responses can be resolved by a feedback loop where autophagy negatively regulates the levels of α-catenins, LC3-interacting proteins that inhibit YAP/TAZ, which, in turn, positively regulate autophagy. High basal levels of α-catenins enable autophagy induction to positively regulate YAP/TAZ, while low α-catenins cause YAP/TAZ activation upon autophagy inhibition. These data reveal how feedback loops enable post-transcriptional determination of cell identity and how levels of a single intermediary protein can dictate the direction of response to external or internal perturbations.
    DOI:  https://doi.org/10.1038/s41467-021-21882-1
  27. J Proteome Res. 2021 Mar 15.
    Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.
    Ann Morgell, Julie A Reisz, Zeeshan Ateeb, Haleh Davanian, Susanne E Reinsbach, Asif Halimi, Rogier Gaiser, Roberto Valente, Urban Arnelo, Marco Del Chiaro, Margaret Sällberg Chen, Angelo D'Alessandro.
      Pancreatic cancer is the seventh leading cause of cancer-related death worldwide, with a 5 year survival rate as low as 9%. One factor complicating the management of pancreatic cancer is the lack of reliable tools for early diagnosis. While up to 50% of the adult population has been shown to develop precancerous pancreatic cysts, limited and insufficient approaches are currently available to determine whether a cyst is going to progress into pancreatic cancer. Recently, we used metabolomics approaches to identify candidate markers of disease progression in patients diagnosed with intraductal papillary mucinous neoplasms (IPMNs) undergoing pancreatic resection. Here, we enrolled an independent cohort to verify the candidate markers from our previous study with orthogonal quantitative methods in plasma and cyst fluid from serous cystic neoplasm and IPMN (either low- or high-grade dysplasia or pancreatic ductal adenocarcinoma). We thus validated these markers with absolute quantitative methods through the auxilium of stable isotope-labeled internal standards in a new independent cohort. Finally, we identified novel markers of IPMN status and disease progression-including amino acids, carboxylic acids, conjugated bile acids, free and carnitine-conjugated fatty acids, purine oxidation products, and trimethylamine-oxide. We show that the levels of these metabolites of potential bacterial origin correlated with the degree of bacterial enrichment in the cyst, as determined by 16S RNA. Overall, our findings are interesting per se, owing to the validation of previous markers and identification of novel small molecule signatures of IPMN and disease progression. In addition, our findings further fuel the provoking debate as to whether bacterial infections may represent an etiological contributor to the development and severity of the disease in pancreatic cancer, in like fashion to other cancers (e.g., Helicobacter pylori and gastric cancer).
    Keywords:  IPMN; cyst; metabolomics; microbiome
    DOI:  https://doi.org/10.1021/acs.jproteome.1c00018
  28. Science. 2021 Mar 19. 371(6535): 1249-1253
    Landmarks of human embryonic development inscribed in somatic mutations.
    Sara Bizzotto, Yanmei Dou, Javier Ganz, Ryan N Doan, Minseok Kwon, Craig L Bohrson, Sonia N Kim, Taejeong Bae, Alexej Abyzov, , Peter J Park, Christopher A Walsh.
      Although cell lineage information is fundamental to understanding organismal development, very little direct information is available for humans. We performed high-depth (250×) whole-genome sequencing of multiple tissues from three individuals to identify hundreds of somatic single-nucleotide variants (sSNVs). Using these variants as "endogenous barcodes" in single cells, we reconstructed early embryonic cell divisions. Targeted sequencing of clonal sSNVs in different organs (about 25,000×) and in more than 1000 cortical single cells, as well as single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin sequencing of ~100,000 cortical single cells, demonstrated asymmetric contributions of early progenitors to extraembryonic tissues, distinct germ layers, and organs. Our data suggest onset of gastrulation at an effective progenitor pool of about 170 cells and about 50 to 100 founders for the forebrain. Thus, mosaic mutations provide a permanent record of human embryonic development at very high resolution.
    DOI:  https://doi.org/10.1126/science.abe1544
  29. Clin Cancer Res. 2021 Mar 16. pii: clincanres.4769.2020. [Epub ahead of print]
    Clinical impact of pre-surgery circulating tumor DNA after total neoadjuvant treatment in locally advanced rectal cancer: a biomarker study from the GEMCAD1402 Trial.
    Joana Vidal, David Casadevall, Beatriz Bellosillo, Carles Pericay, Rocio Garcia-Carbonero, Ferran Losa, Laura Layos, Vicente Alonso, Jaume Capdevila, Javier Gallego-Plazas, Ruth Vera, Antonieta Salud, Marta MArtín Richard, Miguel Nogué, Elena Cillan, Joan Maurel, Iris Faull, Victoria M Raymond, Carlos Fernández-Martos, Clara Montagut.
      PURPOSE: Total neoadjuvant treatment (TNT) is a valid strategy for patients with high-risk locally advanced rectal cancer (LARC). Biomarkers of response to TNT are an unmet clinical need. We aimed to determine the value of circulating tumor (ct)DNA to predict tumor response, recurrence and survival in patients with LARC treated with TNT.EXPERIMENTAL DESIGN: The GEMCAD 1402 is a phase II randomized, multicentric clinical trial that randomized 180 patients with LARC to mFOLFOX6 +/- Aflibercept followed by chemoradiation and surgery. Plasma samples were collected at baseline and after TNT within 48h before surgery (pre-surgery). An ultrasensitive assay that integrates genomic and epigenomic cancer signatures was used to assess ctDNA status. ctDNA results were correlated with variables of local tumor response in the surgery sample, local / systemic recurrence and survival.
    RESULTS: 144 paired plasma samples from 72 patients were included. ctDNA was detectable in 83% of patients at baseline and in 15% following TNT (pre-surgery). No association was found between ctDNA status and pathological response. . Detectable pre-surgery ctDNA was significantly associated with systemic recurrence, shorter disease-free survival (HR 4 p=0.033) and shorter overall survival (HR 23 p<0.0001).
    CONCLUSION: In patients with LARC treated with TNT, pre-surgery ctDNA detects minimal metastatic disease (MMD) identifying patients at high risk of distant recurrence and death. This study sets the basis for prospective clinical trials that use liquid biopsy to personalize the therapeutic approach following TNT.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-4769
  30. J Clin Invest. 2021 Mar 15. pii: 143764. [Epub ahead of print]131(6):
    Exploiting bone niches: progression of disseminated tumor cells to metastasis.
    Aaron M Muscarella, Sergio Aguirre, Xiaoxin Hao, Sarah M Waldvogel, Xiang H-F Zhang.
      Many solid cancers metastasize to the bone and bone marrow (BM). This process may occur even before the diagnosis of primary tumors, as evidenced by the discovery of disseminated tumor cells (DTCs) in patients without occult malignancies. The cellular fates and metastatic progression of DTCs are determined by complicated interactions between cancer cells and BM niches. Not surprisingly, these niches also play important roles in normal biology, including homeostasis and turnover of skeletal and hematopoiesis systems. In this Review, we summarize recent findings on functions of BM niches in bone metastasis (BoMet), particularly during the early stage of colonization. In light of the rich knowledge of hematopoiesis and osteogenesis, we highlight how DTCs may progress into overt BoMet by taking advantage of niche cells and their activities in tissue turnover, especially those related to immunomodulation and bone repair.
    DOI:  https://doi.org/10.1172/JCI143764
  31. J Vis Exp. 2021 Feb 24.
    Simple, Affordable, and Modular Patterning of Cells using DNA.
    Katelyn A Cabral, David M Patterson, Olivia J Scheideler, Russell Cole, Adam R Abate, David V Schaffer, Lydia L Sohn, Zev J Gartner.
      The relative positioning of cells is a key feature of the microenvironment that organizes cell-cell interactions. To study the interactions between cells of the same or different type, micropatterning techniques have proved useful. DNA Programmed Assembly of Cells (DPAC) is a micropatterning technique that targets the adhesion of cells to a substrate or other cells using DNA hybridization. The most basic operations in DPAC begin with decorating cell membranes with lipid-modified oligonucleotides, then flowing them over a substrate that has been patterned with complementary DNA sequences. Cells adhere selectively to the substrate only where they find a complementary DNA sequence. Non-adherent cells are washed away, revealing a pattern of adherent cells. Additional operations include further rounds of cell-substrate or cell-cell adhesion, as well as transferring the patterns formed by DPAC to an embedding hydrogel for long-term culture. Previously, methods for patterning oligonucleotides on surfaces and decorating cells with DNA sequences required specialized equipment and custom DNA synthesis, respectively. We report an updated version of the protocol, utilizing an inexpensive benchtop photolithography setup and commercially available cholesterol modified oligonucleotides (CMOs) deployed using a modular format. CMO-labeled cells adhere with high efficiency to DNA-patterned substrates. This approach can be used to pattern multiple cell types at once with high precision and to create arrays of microtissues embedded within an extracellular matrix. Advantages of this method include its high resolution, ability to embed cells into a three-dimensional microenvironment without disrupting the micropattern, and flexibility in patterning any cell type.
    DOI:  https://doi.org/10.3791/61937
  32. Science. 2021 Mar 19. pii: eaba8310. [Epub ahead of print]371(6535):
    γδ T cells regulate the intestinal response to nutrient sensing.
    Zuri A Sullivan, William Khoury-Hanold, Jaechul Lim, Chris Smillie, Moshe Biton, Bernardo S Reis, Rachel K Zwick, Scott D Pope, Kavita Israni-Winger, Roham Parsa, Naomi H Philip, Saleh Rashed, Noah Palm, Andrew Wang, Daniel Mucida, Aviv Regev, Ruslan Medzhitov.
      The intestine is a site of direct encounter with the external environment and must consequently balance barrier defense with nutrient uptake. To investigate how nutrient uptake is regulated in the small intestine, we tested the effect of diets with different macronutrient compositions on epithelial gene expression. We found that enzymes and transporters required for carbohydrate digestion and absorption were regulated by carbohydrate availability. The "on-demand" induction of this machinery required γδ T cells, which regulated this program through the suppression of interleukin-22 production by type 3 innate lymphoid cells. Nutrient availability altered the tissue localization and transcriptome of γδ T cells. Additionally, transcriptional responses to diet involved cellular remodeling of the epithelial compartment. Thus, this work identifies a role for γδ T cells in nutrient sensing.
    DOI:  https://doi.org/10.1126/science.aba8310
  33. Mol Metab. 2021 Mar 16. pii: S2212-8778(21)00053-3. [Epub ahead of print] 101213
    TCF7 is not essential for glucose homeostasis in mice.
    Kiran Deep Kaur, Chi Kin Wong, Laurie L Baggio, Jacqueline L Beaudry, Shai Fuchs, Brandon L Panaro, Dianne Matthews, Xiemin Cao, Daniel J Drucker.
      OBJECTIVE: Glucose-dependent insulinotropic polypeptide (GIP) and Glucagon-like peptide-1(GLP-1) are incretin hormones that exert overlapping yet distinct actions on islet β-cells. We recently observed that GIP, but not GLP-1, upregulated islet expression of Transcription Factor 7 (TCF7), a gene expressed in immune cells and associated with the risk of developing type 1 diabetes. TCF7 has also been associated with control of glucose homeostasis in the liver. Here we studied the relative metabolic importance of TCF7 expression in hepatocytes vs. islet β-cells in mice.METHODS: Tcf7 expression was selectively inactivated in adult mouse hepatocytes using adenoviral Cre expression and targeted in β-cells using two different lines of insulin promoter-Cre mice. Glucose homeostasis, plasma insulin and triglyceride responses, islet histology, hepatic and islet gene expression and body weight gain were evaluated in mice fed regular chow or high fat diets. Tcf7 expression within pancreatic islets and immune cells was evaluated using published single cell RNA-seq (scRNA-seq) data, and in islet RNA from immunodeficient Rag2-/-Il2rg-/- mice.
    RESULTS: Reduction of hepatocyte Tcf7 expression did not impair glucose homeostasis, lipid tolerance or hepatic gene expression profiles linked to control of metabolic or immune pathways. Similarly, oral and intraperitoneal glucose tolerance, plasma insulin responses, islet histology, body weight gain, and insulin tolerance were not different in mice with targeted recombination of Tcf7 in insulin-positive β-cells. Surprisingly, islet Tcf7 mRNA transcripts were not reduced in total islet RNA containing endocrine and associated non-endocrine cell types from Tcf7βcell-/- mice, despite Cre-mediated recombination of islet genomic DNA. Furthermore, glucose tolerance was normal in whole body Tcf7-/- mice. Analysis of scRNA-seq datasets localized pancreatic Tcf7 expression to islet progenitors during development, and immune cells, but not within differentiated islet β-cells or endocrine lineages within mature islets. Moreover, the expression of Tcf7 was extremely low in islet RNA from Rag2-/-Il2rg-/- mice and consistent with expression within immune cells, Tcf7 was highly correlated with levels of Cd3g mRNA transcripts in RNA from wild type mouse islets.
    CONCLUSION: These findings demonstrate that Tcf7 expression is not a critical determinant of glucose homeostasis in mice. Moreover, detection of Tcf7 expression within islet mRNA is attributable to expression of Tcf7 RNA in islet-associated immune cells, and not islet β-cells.
    Keywords:  Islets; glucose; immune cells; knockout mice; liver; transcription factors
    DOI:  https://doi.org/10.1016/j.molmet.2021.101213
  34. Nat Rev Cancer. 2021 Mar 16.
    Genetic and non-genetic clonal diversity in cancer evolution.
    James R M Black, Nicholas McGranahan.
      The observation and analysis of intra-tumour heterogeneity (ITH), particularly in genomic studies, has advanced our understanding of the evolutionary forces that shape cancer growth and development. However, only a subset of the variation observed in a single tumour will have an impact on cancer evolution, highlighting the need to distinguish between functional and non-functional ITH. Emerging studies highlight a role for the cancer epigenome, transcriptome and immune microenvironment in functional ITH. Here, we consider the importance of both genetic and non-genetic ITH and their role in tumour evolution, and present the rationale for a broad research focus beyond the cancer genome. Systems-biology analytical approaches will be necessary to outline the scale and importance of functional ITH. By allowing a deeper understanding of tumour evolution this will, in time, encourage development of novel therapies and improve outcomes for patients.
    DOI:  https://doi.org/10.1038/s41568-021-00336-2
  35. Genes Chromosomes Cancer. 2021 Mar 16.
    Germline sequence analysis of RABL3 in a large series of pancreatic ductal adenocarcinoma patients reveals no evidence of deleterious variants.
    Nicholas J Roberts, Robert C Grant, Steven Gallinger, Alison P Klein, .
      Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a 5-year survival rate of less than 10%. Individuals with a pathogenic germline variant in a pancreatic cancer susceptibility gene are at an increased risk of developing pancreatic cancer. Understanding the inherited genetic basis of pancreatic tumor development provides a unique opportunity to improve patient care and outcomes. For example, relatives of a patients with PDAC who have a pathogenic germline variant in a pancreatic cancer susceptibility gene are eligible for disease surveillance where cancers may be detected early, and 5-year survival greatly improved. Furthermore, for some patients with PDAC and a pathogenic germline variant in a pancreatic cancer susceptibility gene, their tumors may be susceptible to specific anti-cancer therapies. Recently, RABL3 was identified as a pancreatic cancer susceptibility gene. To validate these findings and inform clinical translation, we determined the prevalence of deleterious RABL3 variants in a large cohort of 1037 patients with PDAC that had undergone either whole genome or whole exome germline sequencing. We identified two synonymous variants and four missense variants classified as variants of unknown significance. We found no pathogenic RABL3 variants, indicating that the maximum prevalence of such variants in patients with PDAC is less than 0.36% (minor allele frequency 0, 97.5% one-sided confidence interval: 0-0.0036). This finding has important implications for germline genetic testing of patients with PDAC. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/gcc.22947
  36. Aging Cell. 2021 Mar 18. e13329
    NAD+ supplementation prevents STING-induced senescence in ataxia telangiectasia by improving mitophagy.
    Beimeng Yang, Xiuli Dan, Yujun Hou, Jong-Hyuk Lee, Noah Wechter, Sudarshan Krishnamurthy, Risako Kimura, Mansi Babbar, Tyler Demarest, Ross McDevitt, Shiliang Zhang, Yongqing Zhang, Mark P Mattson, Deborah L Croteau, Vilhelm A Bohr.
      Senescence phenotypes and mitochondrial dysfunction are implicated in aging and in premature aging diseases, including ataxia telangiectasia (A-T). Loss of mitochondrial function can drive age-related decline in the brain, but little is known about whether improving mitochondrial homeostasis alleviates senescence phenotypes. We demonstrate here that mitochondrial dysfunction and cellular senescence with a senescence-associated secretory phenotype (SASP) occur in A-T patient fibroblasts, and in ATM-deficient cells and mice. Senescence is mediated by stimulator of interferon genes (STING) and involves ectopic cytoplasmic DNA. We further show that boosting intracellular NAD+ levels with nicotinamide riboside (NR) prevents senescence and SASP by promoting mitophagy in a PINK1-dependent manner. NR treatment also prevents neurodegeneration, suppresses senescence and neuroinflammation, and improves motor function in Atm-/- mice. Our findings suggest a central role for mitochondrial dysfunction-induced senescence in A-T pathogenesis, and that enhancing mitophagy as a potential therapeutic intervention.
    Keywords:  Ataxia Telangiectasia; Nicotinamide riboside; SASP; mitophagy; senescence
    DOI:  https://doi.org/10.1111/acel.13329
  37. Nat Rev Drug Discov. 2021 Mar 19.
    Protein arginine methylation: from enigmatic functions to therapeutic targeting.
    Qin Wu, Matthieu Schapira, Cheryl H Arrowsmith, Dalia Barsyte-Lovejoy.
      Protein arginine methyltransferases (PRMTs) are emerging as attractive therapeutic targets. PRMTs regulate transcription, splicing, RNA biology, the DNA damage response and cell metabolism; these fundamental processes are altered in many diseases. Mechanistically understanding how these enzymes fuel and sustain cancer cells, especially in specific metabolic contexts or in the presence of certain mutations, has provided the rationale for targeting them in oncology. Ongoing inhibitor development, facilitated by structural biology, has generated tool compounds for the majority of PRMTs and enabled clinical programmes for the most advanced oncology targets, PRMT1 and PRMT5. In-depth mechanistic investigations using genetic and chemical tools continue to delineate the roles of PRMTs in regulating immune cells and cancer cells, and cardiovascular and neuronal function, and determine which pathways involving PRMTs could be synergistically targeted in combination therapies for cancer. This research is enhancing our knowledge of the complex functions of arginine methylation, will guide future clinical development and could identify new clinical indications.
    DOI:  https://doi.org/10.1038/s41573-021-00159-8
  38. Nat Commun. 2021 Mar 19. 12(1): 1789
    The decrease of intraflagellar transport impairs sensory perception and metabolism in ageing.
    Yincong Zhang, Xiaona Zhang, Yumin Dai, Mengjiao Song, Yifei Zhou, Jun Zhou, Xiumin Yan, Yidong Shen.
      Sensory perception and metabolic homeostasis are known to deteriorate with ageing, impairing the health of aged animals, while mechanisms underlying their deterioration remain poorly understood. The potential interplay between the declining sensory perception and the impaired metabolism during ageing is also barely explored. Here, we report that the intraflagellar transport (IFT) in the cilia of sensory neurons is impaired in the aged nematode Caenorhabditis elegans due to a daf-19/RFX-modulated decrease of IFT components. We find that the reduced IFT in sensory cilia thus impairs sensory perception with ageing. Moreover, we demonstrate that whereas the IFT-dependent decrease of sensory perception in aged worms has a mild impact on the insulin/IGF-1 signalling, it remarkably suppresses AMP-activated protein kinase (AMPK) signalling across tissues. We show that upregulating daf-19/RFX effectively enhances IFT, sensory perception, AMPK activity and autophagy, promoting metabolic homeostasis and longevity. Our study determines an ageing pathway causing IFT decay and sensory perception deterioration, which in turn disrupts metabolism and healthy ageing.
    DOI:  https://doi.org/10.1038/s41467-021-22065-8
  39. FEBS J. 2021 Mar 17.
    A Guide To… The Regulation Of Selective Autophagy Receptors.
    A Gubas, I Dikic.
      Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged, and excessive proteins, non-functional organelles, foreign pathogens, and other cellular components. Hence, autophagy can be non-selective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where pre-selected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications - phosphorylation, ubiquitination, acetylation, and oligomerisation - that are essential for autophagy receptor recruitment, function, and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.
    Keywords:  Autophagy; oligomerisation; phosphorylation; receptor; ubiquitination
    DOI:  https://doi.org/10.1111/febs.15824
  40. Br J Cancer. 2021 Mar 17.
    Cancer metastasis as a non-healing wound.
    Matthew Deyell, Christopher S Garris, Ashley M Laughney.
      Most cancer deaths are caused by metastasis: recurrence of disease by disseminated tumour cells at sites distant from the primary tumour. Large numbers of disseminated tumour cells are released from the primary tumour, even during the early stages of tumour growth. However, only a minority survive as potential seeds for future metastatic outgrowths. These cells must adapt to a relatively inhospitable microenvironment, evade immune surveillance and progress from the micro- to macro-metastatic stage to generate a secondary tumour. A pervasive driver of this transition is chronic inflammatory signalling emanating from tumour cells themselves. These signals can promote migration and engagement of stem and progenitor cell function, events that are also central to a wound healing response. In this review, we revisit the concept of cancer as a non-healing wound, first introduced by Virchow in the 19th century, with a new tumour cell-intrinsic perspective on inflammation and focus on metastasis. Cellular responses to inflammation in both wound healing and metastasis are tightly regulated by crosstalk with the surrounding microenvironment. Targeting or restoring canonical responses to inflammation could represent a novel strategy to prevent the lethal spread of cancer.
    DOI:  https://doi.org/10.1038/s41416-021-01309-w
  41. Methods Mol Biol. 2021 ;2294 17-26
    The Chicken Egg Chorioallantoic Membrane (CAM) Model as an In Vivo Method for the Investigation of the Invasion and Metastasis Cascade of Malignant Tumor Cells.
    Jörg H Leupold, Nitin Patil, Heike Allgayer.
      The CAM model enables an in vivo analysis of the individual sub-steps of the metastatic cascade like local invasion, intravasation, or the establishment of metastasis in particular organs. Incubated fertilized chicken eggs are inoculated with human tumor cells and further processed for up to 9-10 days. The invasion and metastasis of these cells is then detected quantitatively with high specificity and sensitivity by means of a PCR for human ALU sequences, using the genomic DNA isolated from distant portions of the CAM, as well as from diverse internal organs of the developing embryo.
    Keywords:  ALU elements; Chicken chorioallantoic membrane; DNA; In vivo model; Metastasis; Primer; Probe; Quantification; Real-time PCR; TaqMan
    DOI:  https://doi.org/10.1007/978-1-0716-1350-4_2
  42. Dev Cell. 2021 Mar 09. pii: S1534-5807(21)00164-7. [Epub ahead of print]
    Lipid metabolism in adaptation to extreme nutritional challenges.
    Luke Olsen, Edward Thum, Nicolas Rohner.
      Food shortages represent a common challenge for most animal species. As a consequence, many have evolved metabolic strategies encompassing extreme starvation-resistance capabilities, going without food for months or even years. One such strategy is to store substantial levels of fat when food is available and release these energy-rich lipids during periods of dearth. In this review, we provide an overview of the strategies and pathways underlying the extreme capacity for animals to store and mobilize lipids during nutritionally stressful environmental conditions and highlight accompanying resilience phenotypes that allow these animals to develop and tolerate such profound metabolic phenotypes.
    Keywords:  adaptation; cave dwelling; diapause; estivation; fasting resistance; hibernation; inflammation; lipid metabolism; migration; obesity
    DOI:  https://doi.org/10.1016/j.devcel.2021.02.024
  43. Proc Natl Acad Sci U S A. 2021 Apr 05. pii: e2102057118. [Epub ahead of print]118(14):
    Metabolic plasticity allows cancer cells to thrive under nutrient starvation.
    Wilhelm Palm.
      
    DOI:  https://doi.org/10.1073/pnas.2102057118
  44. JCI Insight. 2021 Mar 16. pii: 139793. [Epub ahead of print]
    Obesity results in adipose tissue T cell exhaustion.
    Cara E Porsche, Jennifer B DelProposto, Lynn Geletka, Robert O'Rourke, Carey N Lumeng.
      Despite studies implicating adipose tissue T cells (ATT) in the initiation and persistence of adipose tissue inflammation, fundamental gaps in knowledge regarding ATT function impedes progress towards understanding how obesity influences adaptive immunity. We hypothesized ATT activation and function would have tissue-resident specific properties and that obesity would potentiate their inflammatory properties. We assessed ATT activation and inflammatory potential within mouse and human stromal vascular fraction (SVF). Surprisingly, murine and human ATTs from obese visceral white adipose tissue exhibited impaired inflammatory characteristics. Both environmental and cell-intrinsic factors are implicated in ATT dysfunction. Soluble factors from obese SVF inhibit ATTs activation. Additionally, chronic signaling through the T cell receptor is necessary for ATT impairment in obese adipose tissue but is independent of increased PD1 expression. To assess intracellular signaling mechanisms responsible for ATT inflammation impairments, single-cell RNA sequencing of ATTs was performed. ATTs in obese adipose tissue exhibit gene expression resembling T cell exhaustion and increased expression of co-inhibitory receptor Btla. In sum, this work suggests that obesity-induced ATT cells have functional characteristics and gene expression resembling T cell exhaustion, which is dependent upon localized soluble factors and cell-to-cell interactions in adipose tissue.
    Keywords:  Adipose tissue; Inflammation; Metabolism; Obesity; T cells
    DOI:  https://doi.org/10.1172/jci.insight.139793
  45. EBioMedicine. 2021 Mar 10. pii: S2352-3964(21)00064-5. [Epub ahead of print]65 103271
    An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer.
    Zhijun Zhou, Junxia Zhang, Chao Xu, Jingxuan Yang, Yuqing Zhang, Mingyang Liu, Xiuhui Shi, Xiaoping Li, Hanxiang Zhan, Wei Chen, Lacey R McNally, Kar-Ming Fung, Wenyi Luo, Courtney W Houchen, Yulong He, Changhua Zhang, Min Li.
      BACKGROUND: N6-methyladenosine (m6A) is the most abundant mRNA modification. Whether m6A regulators can determine tumor aggressiveness and risk of immune evasion in pancreatic ductal adenocarcinoma (PDAC) remains unknown.METHODS: An integrated model named "m6Ascore" is constructed based on RNA-seq data of m6A regulators in PDAC. Association of m6Ascore and overall survival is validated across several different datasets. Overlaps of m6Ascore and established molecular classifications of PDAC is examined. Immune infiltration, enriched pathways, somatic copy number alterations (SCNAs), mutation profiles and response to immune checkpoint inhibitors are compared between m6Ascore-high and m6Ascore-low tumors.
    FINDINGS: m6Ascore is associated with dismal overall survival and increased tumor recurrence in PDAC as well as several other solid tumors including colorectal cancer and breast cancer. Basal-like (Squamous) PDAC has higher m6Ascore than that in the classical PDAC. Mechanism study showed m6Ascore-high tumors are characterized with reduced immune infiltration and T cells exhaustion. Meanwhile, m6Ascore is associated with genes regulating cachexia and chemoresistance in PDAC. Furthermore, distinct SCNAs patterns and mutation profiles of KRAS and TP53 are present in m6Ascore-high tumors, indicating immune evasion. m6Ascore-low tumors have higher response rates to immune checkpoint inhibitors (ICIs).
    INTERPRETATION: These findings indicate m6Ascore can predict aggressiveness and immune evasion in pancreatic cancer. This model has implications for pancreatic cancer prognosis and treatment response to ICIs.
    FUNDING: This work was supported in part by National Institutes of Health (NIH) grants to M. Li (R01 CA186338, R01 CA203108, R01 CA247234 and the William and Ella Owens Medical Research Foundation) and NIH/National Cancer Institute Q39 award P30CA225520 to Stephenson Cancer Center.
    Keywords:  Immune evasion; Immunotherapy; Pancreatic cancer, m6A regulators; RNA modification
    DOI:  https://doi.org/10.1016/j.ebiom.2021.103271
  46. EMBO J. 2021 Mar 19. e106632
    Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies.
    Xiancai Ma, Tao Chen, Zhilin Peng, Ziwen Wang, Jun Liu, Tao Yang, Liyang Wu, Guangyan Liu, Mo Zhou, Muye Tong, Yuanjun Guan, Xu Zhang, Yingtong Lin, Xiaoping Tang, Linghua Li, Zhonghui Tang, Ting Pan, Hui Zhang.
      HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
    Keywords:  CAF-1; HIV-1 latency; epigenetic regulation; nuclear body; phase separation
    DOI:  https://doi.org/10.15252/embj.2020106632
  47. J Cell Sci. 2021 Mar 18. pii: jcs.254185. [Epub ahead of print]
    De novo formation of early endosomes during Rab5 to Rab7 transition.
    Frode Miltzow Skjeldal, Linda Hofstad Haugen, Duarte Mateus, Dominik M Frei, Anna Vik Rødseth, Xian Hu, Oddmund Bakke.
      Rab5 and Rab7a are the main determinants of early and late endosomes and are important regulators of endosomal progression. The transport from early endosomes to late endosome seems to be regulated through an endosomal maturation switch where Rab5 is gradually exchanged with Rab7a on the same endosome. Here we provide new insight into the mechanism of endosomal maturation where we have discovered a stepwise Rab5 detachment, sequentially regulated by Rab7a. The initial detachment of Rab5 is Rab7a independent and demonstrate a diffusion-like exchange between cytosol and endosomal membrane, and a second phase where Rab5 converges into specific domains that detaches as a Rab5 indigenous endosome. Consequently, we show that early endosomal maturation regulated through the Rab5 to Rab7a switch induce the formation of new fully functional rab5 positive early endosomes. Progression through a stepwise early endosomal maturation regulates the direction of the transport and concomitantly regulates the homeostasis of early endosomes.
    Keywords:  Endosomal biogenesis; Endosome maturation; FRAP; Rab5; Rab7
    DOI:  https://doi.org/10.1242/jcs.254185
  48. Aging Cell. 2021 Mar 17. e13325
    Proteomics in aging research: A roadmap to clinical, translational research.
    Ruin Moaddel, Ceereena Ubaida-Mohien, Toshiko Tanaka, Alexey Lyashkov, Nathan Basisty, Birgit Schilling, Richard D Semba, Claudio Franceschi, Myriam Gorospe, Luigi Ferrucci.
      The identification of plasma proteins that systematically change with age and, independent of chronological age, predict accelerated decline of health is an expanding area of research. Circulating proteins are ideal translational "omics" since they are final effectors of physiological pathways and because physicians are accustomed to use information of plasma proteins as biomarkers for diagnosis, prognosis, and tracking the effectiveness of treatments. Recent technological advancements, including mass spectrometry (MS)-based proteomics, multiplexed proteomic assay using modified aptamers (SOMAscan), and Proximity Extension Assay (PEA, O-Link), have allowed for the assessment of thousands of proteins in plasma or other biological matrices, which are potentially translatable into new clinical biomarkers and provide new clues about the mechanisms by which aging is associated with health deterioration and functional decline. We carried out a detailed literature search for proteomic studies performed in different matrices (plasma, serum, urine, saliva, tissues) and species using multiple platforms. Herein, we identified 232 proteins that were age-associated across studies. Enrichment analysis of the 232 age-associated proteins revealed metabolic pathways previously connected with biological aging both in animal models and in humans, most remarkably insulin-like growth factor (IGF) signaling, mitogen-activated protein kinases (MAPK), hypoxia-inducible factor 1 (HIF1), cytokine signaling, Forkhead Box O (FOXO) metabolic pathways, folate metabolism, advance glycation end products (AGE), and receptor AGE (RAGE) metabolic pathway. Information on these age-relevant proteins, likely expanded and validated in longitudinal studies and examined in mechanistic studies, will be essential for patient stratification and the development of new treatments aimed at improving health expectancy.
    Keywords:  aging; geroscience; human; proteomics
    DOI:  https://doi.org/10.1111/acel.13325
  49. J Biol Chem. 2021 Mar 12. pii: S0021-9258(21)00317-3. [Epub ahead of print] 100539
    Choline restores respiration in Psd1-deficient yeast by replenishing mitochondrial phosphatidylethanolamine.
    Donna M Iadarola, Alaumy Joshi, Cameron B Caldwell, Vishal M Gohil.
      Phosphatidylethanolamine (PE) is essential for mitochondrial respiration in yeast Saccharomyces cerevisiae, whereas the most abundant mitochondrial phospholipid, phosphatidylcholine (PC), is largely dispensable. Surprisingly, choline (Cho), which is a biosynthetic precursor of PC, has been shown to rescue the respiratory growth of mitochondrial PE deficient yeast; however, the mechanism underlying this rescue has remained unknown. Using a combination of yeast genetics, lipid biochemistry, and cell biological approaches, we uncover the mechanism by showing that Cho rescues mitochondrial respiration by partially replenishing mitochondrial PE levels in yeast cells lacking the mitochondrial PE-biosynthetic enzyme Psd1. This rescue is dependent on the conversion of Cho to PC via the Kennedy pathway as well as on Psd2, an enzyme catalyzing PE biosynthesis in the endosome. Metabolic labeling experiments reveal that in the absence of exogenously supplied Cho, PE biosynthesized via Psd2 is mostly directed to the methylation pathway for PC biosynthesis and is unavailable for replenishing mitochondrial PE in Psd1-deleted cells. In this setting, stimulating the Kennedy pathway for PC biosynthesis by Cho spares Psd2-synthesized PE from the methylation pathway and redirects it to the mitochondria. Cho-mediated elevation in mitochondrial PE is dependent on Vps39, which has been recently implicated in PE trafficking to the mitochondria. Accordingly, epistasis experiments placed Vps39 downstream of Psd2 in choline-based rescue. Our work, thus, provides a mechanism of choline-based rescue of mitochondrial PE deficiency and uncovers an intricate inter-organelle phospholipid regulatory network that maintains mitochondrial PE homeostasis.
    Keywords:  Phospholipid; Psd1; Psd2; Vps39; choline; ethanolamine; mitochondria; phosphatidylethanolamine; yeast
    DOI:  https://doi.org/10.1016/j.jbc.2021.100539
  50. Biochim Biophys Acta Bioenerg. 2021 Mar 12. pii: S0005-2728(21)00043-8. [Epub ahead of print] 148410
    Metabolic implications of non-Electrogenic ATP/ADP exchange in Cancer cells: A mechanistic basis for the Warburg effect.
    John J Lemasters.
      In post-mitotic cells, mitochondrial ATP/ADP exchange occurs by the adenine nucleotide translocator (ANT). Driven by membrane potential (ΔΨ), ANT catalyzes electrogenic exchange of ATP4- for ADP3-, leading to higher ATP/ADP ratios in the cytosol than mitochondria. In cancer cells, ATP/ADP exchange occurs not by ANT but likely via the non-electrogenic ATP-Mg/phosphate carrier. Consequences of non-electrogenic exchange are: 1) Cytosolic ATP/ADP decreases to stimulate aerobic glycolysis. 2) Without proton utilization for exchange, ATP/O increases by 35% for complete glucose oxidation. 3) Decreased cytosolic ATP/ADP•Pi increases NAD(P)H/NAD(P)+. Increased NADH increases lactate/pyruvate, and increased NADPH promotes anabolic metabolism. Fourth, increased mitochondrial NADH/NAD+ magnifies the redox span across Complexes I and III, which increases ΔΨ, reactive oxygen species generation, and susceptibility to ferroptosis. 5) Increased mitochondrial NADPH/NADP+ favors a reverse isocitrate dehydrogenase-2 reaction with citrate accumulation and export for biomass formation. Consequently, 2-oxoglutarate formation occurs largely via oxidation of glutamine, the preferred respiratory substrate of cancer cells. Overall, non-electrogenic ATP/ADP exchange promotes aerobic glycolysis (Warburg effect) and confers growth advantages to cancer cells.
    Keywords:  ATP/ADP exchange; Aerobic glycolysis; Cancer; Glutamine; Mitochondria; Warburg effect
    DOI:  https://doi.org/10.1016/j.bbabio.2021.148410
  51. Gut. 2021 Mar 17. pii: gutjnl-2021-324460. [Epub ahead of print]
    Utility of mismatch repair protein expression screening via an endoscopic ultrasound assessment of treatment-naive pancreas ductal adenocarcinoma.
    Ana Garcia Garcia de Paredes, Rondell P Graham, Michael J Levy, Robert R McWilliams, Elizabeth Rajan, Lizhi Zhang, Ferga C Gleeson.
      
    Keywords:  DNA microsatellite instability; endoscopic ultrasonography; immunohistochemistry; pancreatic cancer
    DOI:  https://doi.org/10.1136/gutjnl-2021-324460
  52. Autophagy. 2021 Mar 09. 1-2
    VCP/p97 modulates PtdIns3P production and autophagy initiation.
    Lidia Wrobel, Sandra M Hill, Avraham Ashkenazi, David C Rubinsztein.
      VCP/p97 is an essential multifunctional protein implicated in a plethora of intracellular quality control systems, and abnormal function of VCP is the underlying cause of several neurodegenerative disorders. We reported that VCP regulates the levels of the macroautophagy/autophagy-inducing lipid phosphatidylinositol-3-phosphate (PtdIns3P) by modulating the activity of the BECN1 (beclin 1)-containing phosphatidylinositol 3-kinase (PtdIns3K) complex. VCP stimulates the deubiquitinase activity of ATXN3 (ataxin 3) to stabilize BECN1 protein levels and also interacts with and promotes the assembly and kinase activity of the PtdIns3K complex. Acute inhibition of VCP activity impairs autophagy induction, demonstrated by a diminished PtdIns3P production and decreased recruitment of early autophagy markers WIPI2 and ATG16L1. Thus, VCP promotes autophagosome biogenesis, in addition to its previously described role in autophagosome maturation.
    Keywords:  ATXN3; PI(3)P; PI3K; VCP/p97; autophagy initiation; beclin 1
    DOI:  https://doi.org/10.1080/15548627.2021.1898742
  53. Eur Radiol. 2021 Mar 19.
    Preoperative assessment of the resectability of pancreatic ductal adenocarcinoma on CT according to the NCCN Guidelines focusing on SMA/SMV branch invasion.
    Sae-Jin Park, Siwon Jang, Joon Koo Han, Hongbeom Kim, Wooil Kwon, Jin-Young Jang, Kyoung-Bun Lee, Haeryoung Kim, Dong Ho Lee.
      OBJECTIVES: For patients with pancreatic adenocarcinoma (PAC), adequate determination of disease extent is critical for optimal management. We aimed to evaluate diagnostic accuracy of CT in determining the resectability of PAC based on 2020 NCCN Guidelines.METHODS: We retrospectively enrolled 368 consecutive patients who underwent upfront surgery for PAC and preoperative pancreas protocol CT from January 2012 to December 2017. The resectability of PAC was assessed based on 2020 NCCN Guidelines and compared to 2017 NCCN Guidelines using chi-square tests. Overall survival (OS) was estimated using the Kaplan-Meier method and compared using log-rank test. R0 resection-associated factors were identified using logistic regression analysis.
    RESULTS: R0 rates were 80.8% (189/234), 67% (71/106), and 10.7% (3/28) for resectable, borderline resectable, and unresectable PAC according to 2020 NCCN Guidelines, respectively (p < 0.001). The estimated 3-year OS was 28.9% for borderline resectable PAC, which was significantly lower than for resectable PAC (43.6%) (p = 0.004) but significantly higher than for unresectable PAC (0.0%) (p < 0.001). R0 rate was significantly lower in patients with unresectable PAC according to 2020 NCCN Guidelines (10.7%, 3/28) than in those with unresectable PAC according to the previous version (31.7%, 20/63) (p = 0.038). In resectable PAC, tumor size ≥ 3 cm (p = 0.03) and abutment to portal vein (PV) (p = 0.04) were independently associated with margin-positive resection.
    CONCLUSIONS: The current NCCN Guidelines are useful for stratifying patients according to prognosis and perform better in R0 prediction in unresectable PAC than the previous version. Larger tumor size and abutment to PV were associated with margin-positive resection in patients with resectable PAC.
    KEY POINTS: • The updated 2020 NCCN Guidelines were useful for stratifying patients according to prognosis. • The updated 2020 NCCN Guidelines performed better in the prediction of margin-positive resection in unresectable cases than the previous version. • Tumor size ≥ 3 cm and abutment to the portal vein were associated with margin-positive resection in patients with resectable pancreatic adenocarcinoma.
    Keywords:  General surgery; Guideline; Pancreatic neoplasms; Survival
    DOI:  https://doi.org/10.1007/s00330-021-07847-4
  54. Trends Biochem Sci. 2021 Mar 16. pii: S0968-0004(21)00046-3. [Epub ahead of print]
    ATP Redux.
    Raymond S Ochs.
      The renaissance of interest in metabolism has focused mostly on techniques to measure massive numbers of metabolites. Yet, established metabolic theory has been abandoned. Here, I highlight one misconception: how ATP (and ADP and AMP) are currently understood. A critical point was established early on: cellular [ATP] is constant.
    Keywords:  ADP; AMP; ATP; kinase; metabolism
    DOI:  https://doi.org/10.1016/j.tibs.2021.03.001
  55. Semin Cell Dev Biol. 2021 Mar 16. pii: S1084-9521(21)00030-6. [Epub ahead of print]
    Aging: All roads lead to mitochondria.
    Jyung Mean Son, Changhan Lee.
      Mitochondria were described as early as 1890 as ubiquitous intracellular structures by Ernster and Schatz (1981) [1]. Since then, the accretion of knowledge in the past century has revealed much of the molecular details of mitochondria, ranging from mitochondrial origin, structure, metabolism, genetics, and signaling, and their implications in health and disease. We now know that mitochondria are remarkably multifunctional and deeply intertwined with many vital cellular processes. They are quasi-self organelles that still possess remnants of its bacterial ancestry, including an independent genome. The mitochondrial free radical theory of aging (MFRTA), which postulated that aging is a product of oxidative damage to mitochondrial DNA, provided a conceptual framework that put mitochondria on the map of aging research. However, several studies have more recently challenged the general validity of the theory, favoring novel ideas based on emerging evidence to understand how mitochondria contribute to aging and age-related diseases. One prominent topic of investigation lies on the fact that mitochondria are not only production sites for bioenergetics and macromolecules, but also regulatory hubs that communicate and coordinate many vital physiological processes at the cellular and organismal level. The bi-directional communication and coordination between the co-evolved mitochondrial and nuclear genomes is especially interesting in terms of cellular regulation. Mitochondria are dynamic and adaptive, rendering their function sensitive to cellular context. Tissues with high energy demands, such as the brain, seem to be uniquely affected by age-dependent mitochondrial dysfunction, providing a foundation for the development of novel mitochondrial-based therapeutics and diagnostics.
    Keywords:  Aging; Communication; Genomic instability; Immunity; Inflammation; Longevity; Mitochondria; Mitochondrial-derived peptides; Mitonuclear; Oxidative stress
    DOI:  https://doi.org/10.1016/j.semcdb.2021.02.006
  56. Nature. 2021 Mar 17.
    Abel Prize celebrates union of mathematics and computer science.
    Davide Castelvecchi.
      
    Keywords:  Mathematics and computing
    DOI:  https://doi.org/10.1038/d41586-021-00694-9
  57. Front Cell Dev Biol. 2021 ;9 613336
    Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.
    Paula Díaz, Alejandra Sandoval-Bórquez, Roberto Bravo-Sagua, Andrew F G Quest, Sergio Lavandero.
      In recent decades, compelling evidence has emerged showing that organelles are not static structures but rather form a highly dynamic cellular network and exchange information through membrane contact sites. Although high-throughput techniques facilitate identification of novel contact sites (e.g., organelle-organelle and organelle-vesicle interactions), little is known about their impact on cellular physiology. Moreover, even less is known about how the dysregulation of these structures impacts on cellular function and therefore, disease. Particularly, cancer cells display altered signaling pathways involving several cell organelles; however, the relevance of interorganelle communication in oncogenesis and/or cancer progression remains largely unknown. This review will focus on organelle contacts relevant to cancer pathogenesis. We will highlight specific proteins and protein families residing in these organelle-interfaces that are known to be involved in cancer-related processes. First, we will review the relevance of endoplasmic reticulum (ER)-mitochondria interactions. This section will focus on mitochondria-associated membranes (MAMs) and particularly the tethering proteins at the ER-mitochondria interphase, as well as their role in cancer disease progression. Subsequently, the role of Ca2+ at the ER-mitochondria interphase in cancer disease progression will be discussed. Members of the Bcl-2 protein family, key regulators of cell death, also modulate Ca2+ transport pathways at the ER-mitochondria interphase. Furthermore, we will review the role of ER-mitochondria communication in the regulation of proteostasis, focusing on the ER stress sensor PERK (PRKR-like ER kinase), which exerts dual roles in cancer. Second, we will review the relevance of ER and mitochondria interactions with other organelles. This section will focus on peroxisome and lysosome organelle interactions and their impact on cancer disease progression. In this context, the peroxisome biogenesis factor (PEX) gene family has been linked to cancer. Moreover, the autophagy-lysosome system is emerging as a driving force in the progression of numerous human cancers. Thus, we will summarize our current understanding of the role of each of these organelles and their communication, highlighting how alterations in organelle interfaces participate in cancer development and progression. A better understanding of specific organelle communication sites and their relevant proteins may help to identify potential pharmacological targets for novel therapies in cancer control.
    Keywords:  cancer; endoplasmic reticulum; interorganelle communication; lysosome; mitochondria; peroxisome
    DOI:  https://doi.org/10.3389/fcell.2021.613336
  58. J Clin Invest. 2021 Mar 15. pii: 143765. [Epub ahead of print]131(6):
    Leveraging microenvironmental synthetic lethalities to treat cancer.
    Kevin J Metcalf, Alaa Alazzeh, Zena Werb, Valerie M Weaver.
      Treatment resistance leads to cancer patient mortality. Therapeutic approaches that employ synthetic lethality to target mutational vulnerabilities in key tumor cell signaling pathways have proven effective in overcoming therapeutic resistance in some cancers. Yet, tumors are organs composed of malignant cells residing within a cellular and noncellular stroma. Tumor evolution and resistance to anticancer treatment are mediated through a dynamic and reciprocal dialogue with the tumor microenvironment (TME). Accordingly, expanding tumor cell synthetic lethality to encompass contextual synthetic lethality has the potential to eradicate tumors by targeting critical TME circuits that promote tumor progression and therapeutic resistance. In this Review, we summarize current knowledge about the TME and discuss its role in treatment. We outline the concept of tumor cell-specific synthetic lethality and describe therapeutic approaches to expand this paradigm to leverage TME synthetic lethality to improve cancer therapy.
    DOI:  https://doi.org/10.1172/JCI143765
  59. iScience. 2021 Mar 19. 24(3): 102179
    Engineered models of tumor metastasis with immune cell contributions.
    Pamela L Graney, Daniel Naveed Tavakol, Alan Chramiec, Kacey Ronaldson-Bouchard, Gordana Vunjak-Novakovic.
      Most cancer deaths are due to tumor metastasis rather than the primary tumor. Metastasis is a highly complex and dynamic process that requires orchestration of signaling between the tumor, its local environment, distant tissue sites, and immune system. Animal models of cancer metastasis provide the necessary systemic environment but lack control over factors that regulate cancer progression and often do not recapitulate the properties of human cancers. Bioengineered "organs-on-a-chip" that incorporate the primary tumor, metastatic tissue targets, and microfluidic perfusion are now emerging as quantitative human models of tumor metastasis. The ability of these systems to model tumor metastasis in individualized, patient-specific settings makes them uniquely suitable for studies of cancer biology and developmental testing of new treatments. In this review, we focus on human multi-organ platforms that incorporate circulating and tissue-resident immune cells in studies of tumor metastasis.
    Keywords:  biochemical assay; bioengineering; cancer; components of the immune system
    DOI:  https://doi.org/10.1016/j.isci.2021.102179
  60. Methods Mol Biol. 2021 ;2294 43-58
    Patient-Derived Xenografts from Solid Tumors (PDX) for Models of Metastasis.
    Annika Wulf-Goldenberg, Jens Hoffmann, Michael Becker, Bernadette Brzezicha, Wolfgang Walther.
      In cancer research, availability of clinically relevant tumor models is still essential for drug testing, proof of concept studies, and also molecular analyses. To achieve this, models are of advantage, which more closely reflect heterogeneity of tumors. In this regard, patient-derived xenograft (PDX) models more closely recapitulate the native tumor biology, tissue composition, and molecular characteristics. Since metastasis is still the major challenge of tumor therapy, models are pivotal, which resemble this particular property. In this context, PDX model-derived metastasis is of particular interest for testing antimetastatic therapies for their efficacy to better target this systemic disease. This protocol describes the establishment of PDX models from tumor specimen and their applicability for PDX-derived metastasis at metastatic sites such as liver and lung, which are also clinically relevant for the systemic spread of cancer. Analysis of metastasis and methods for quantification of metastatic spread are provided.
    Keywords:  Breast cancer; Colorectal cancer; Lung cancer; Metastasis; Patient-derived xenograft (PDX); Solid cancer
    DOI:  https://doi.org/10.1007/978-1-0716-1350-4_4
  61. FASEB J. 2021 Apr;35(4): e21456
    Reduced nicotinamide mononucleotide is a new and potent NAD+ precursor in mammalian cells and mice.
    Rubén Zapata-Pérez, Alessandra Tammaro, Bauke V Schomakers, Angelique M L Scantlebery, Simone Denis, Hyung L Elfrink, Judith Giroud-Gerbetant, Carles Cantó, Carmen López-Leonardo, Rebecca L McIntyre, Michel van Weeghel, Álvaro Sánchez-Ferrer, Riekelt H Houtkooper.
      Nicotinamide adenine dinucleotide (NAD+ ) homeostasis is constantly compromised due to degradation by NAD+ -dependent enzymes. NAD+ replenishment by supplementation with the NAD+ precursors nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR) can alleviate this imbalance. However, NMN and NR are limited by their mild effect on the cellular NAD+ pool and the need of high doses. Here, we report a synthesis method of a reduced form of NMN (NMNH), and identify this molecule as a new NAD+ precursor for the first time. We show that NMNH increases NAD+ levels to a much higher extent and faster than NMN or NR, and that it is metabolized through a different, NRK and NAMPT-independent, pathway. We also demonstrate that NMNH reduces damage and accelerates repair in renal tubular epithelial cells upon hypoxia/reoxygenation injury. Finally, we find that NMNH administration in mice causes a rapid and sustained NAD+ surge in whole blood, which is accompanied by increased NAD+ levels in liver, kidney, muscle, brain, brown adipose tissue, and heart, but not in white adipose tissue. Together, our data highlight NMNH as a new NAD+ precursor with therapeutic potential for acute kidney injury, confirm the existence of a novel pathway for the recycling of reduced NAD+ precursors and establish NMNH as a member of the new family of reduced NAD+ precursors.
    Keywords:  NAD+; NMNH; metabolism; nicotinamide mononucleotide
    DOI:  https://doi.org/10.1096/fj.202001826R
  62. Sci Adv. 2021 Mar;pii: eabe7520. [Epub ahead of print]7(12):
    Nuclear genome-wide associations with mitochondrial heteroplasmy.
    Priyanka Nandakumar, Chao Tian, Jared O'Connell, , David Hinds, Andrew D Paterson, Neal Sondheimer.
      The role of the nuclear genome in maintaining the stability of the mitochondrial genome (mtDNA) is incompletely known. mtDNA sequence variants can exist in a state of heteroplasmy, which denotes the coexistence of organellar genomes with different sequences. Heteroplasmic variants that impair mitochondrial capacity cause disease, and the state of heteroplasmy itself is deleterious. However, mitochondrial heteroplasmy may provide an intermediate state in the emergence of novel mitochondrial haplogroups. We used genome-wide genotyping data from 982,072 European ancestry individuals to evaluate variation in mitochondrial heteroplasmy and to identify the regions of the nuclear genome that affect it. Age, sex, and mitochondrial haplogroup were associated with the extent of heteroplasmy. GWAS identified 20 loci for heteroplasmy that exceeded genome-wide significance. This included a region overlapping mitochondrial transcription factor A (TFAM), which has multiple roles in mtDNA packaging, replication, and transcription. These results show that mitochondrial heteroplasmy has a heritable nuclear component.
    DOI:  https://doi.org/10.1126/sciadv.abe7520
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