bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–11–14
forty-one papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Dietary palmitic acid promotes a prometastatic memory via Schwann cells.
  2. Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
  3. Connecting copper and cancer: from transition metal signalling to metalloplasia.
  4. The biological role of metabolic reprogramming in pancreatic cancer.
  5. Skeletal muscle aging, cellular senescence, and senotherapeutics: Current knowledge and future directions.
  6. A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours.
  7. MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function.
  8. A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.
  9. Apoptotic stress-induced FGF signalling promotes non-cell autonomous resistance to cell death.
  10. IL-17B/RB Activation in Pancreatic Stellate Cells Promotes Pancreatic Cancer Metabolism and Growth.
  11. GRP75 mediates Endoplasmic Reticulum-Mitochondria coupling during palmitate-induced pancreatic β-cell apoptosis.
  12. The right time for senescence.
  13. Diverse alterations associated with resistance to KRAS(G12C) inhibition.
  14. The role of mitochondria in cellular senescence.
  15. CRISPR/Cas9-induced DNA damage enriches for mutations in a p53-linked interactome: implications for CRISPR-based therapies.
  16. Activation of Crtc2/Creb1 in skeletal muscle enhances weight loss during intermittent fasting.
  17. Unfolding the role of autophagy in the cancer metabolism.
  18. Computed structures of core eukaryotic protein complexes.
  19. Age-dependent prognostic value of KRAS mutation in metastatic colorectal cancer.
  20. Highly immunogenic cancer cells require activation of the WNT pathway for immunological escape.
  21. Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes.
  22. Diet composition influences the metabolic benefits of short cycles of very low caloric intake.
  23. Insular cortex neurons encode and retrieve specific immune responses.
  24. Single-cell transcriptomics reveals opposing roles of Shp2 in Myc-driven liver tumor cells and microenvironment.
  25. Transcriptional Control of Metastasis by Integrated Stress Response Signaling.
  26. A review of physical activity in pancreatic ductal adenocarcinoma: Epidemiology, intervention, animal models, and clinical trials.
  27. Protocol for the assessment of mTOR activity in mouse primary hepatocytes.
  28. Dynamic regulation of mitochondrial pyruvate metabolism is necessary for orthotopic pancreatic tumor growth.
  29. Stimulating TRPM7 suppresses cancer cell proliferation and metastasis by inhibiting autophagy.
  30. Disrupted mitochondrial homeostasis coupled with mitotic arrest generates antineoplastic oxidative stress.
  31. Cell size is a determinant of stem cell potential during aging.
  32. Pancreatic Ductal Adenocarcinoma: Preclinical in vitro and ex vivo Models.
  33. Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates.
  34. Molecular mechanisms of cancer metastasis via the lymphatic versus the blood vessels.
  35. Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses.
  36. Nuclear pores dilate and constrict in cellulo.
  37. Cell type ontologies of the Human Cell Atlas.
  38. Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin.
  39. Regulation of translation by site-specific ribosomal RNA methylation.
  40. A novel jamming phase diagram links tumor invasion to non-equilibrium phase separation.
  41. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
  1. Nature. 2021 Nov 10.
    Dietary palmitic acid promotes a prometastatic memory via Schwann cells.
    Gloria Pascual, Diana Domínguez, Marc Elosúa-Bayes, Felipe Beckedorff, Carmelo Laudanna, Claudia Bigas, Delphine Douillet, Carolina Greco, Aikaterini Symeonidi, Inmaculada Hernández, Sara Ruiz Gil, Neus Prats, Coro Bescós, Ramin Shiekhattar, Moran Amit, Holger Heyn, Ali Shilatifard, Salvador Aznar Benitah.
      Fatty acid uptake and altered metabolism constitute hallmarks of metastasis1,2, yet evidence of the underlying biology, as well as whether all dietary fatty acids are prometastatic, is lacking. Here we show that dietary palmitic acid (PA), but not oleic acid or linoleic acid, promotes metastasis in oral carcinomas and melanoma in mice. Tumours from mice that were fed a short-term palm-oil-rich diet (PA), or tumour cells that were briefly exposed to PA in vitro, remained highly metastatic even after being serially transplanted (without further exposure to high levels of PA). This PA-induced prometastatic memory requires the fatty acid transporter CD36 and is associated with the stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A (as part of the COMPASS complex (Set1A/COMPASS)). Bulk, single-cell and positional RNA-sequencing analyses indicate that genes with this prometastatic memory predominantly relate to a neural signature that stimulates intratumoural Schwann cells and innervation, two parameters that are strongly correlated with metastasis but are aetiologically poorly understood3,4. Mechanistically, tumour-associated Schwann cells secrete a specialized proregenerative extracellular matrix, the ablation of which inhibits metastasis initiation. Both the PA-induced memory of this proneural signature and its long-term boost in metastasis require the transcription factor EGR2 and the glial-cell-stimulating peptide galanin. In summary, we provide evidence that a dietary metabolite induces stable transcriptional and chromatin changes that lead to a long-term stimulation of metastasis, and that this is related to a proregenerative state of tumour-activated Schwann cells.
    DOI:  https://doi.org/10.1038/s41586-021-04075-0
  2. Nat Metab. 2021 Nov 11.
    Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
    Simon Schwörer, Natalya N Pavlova, Francesco V Cimino, Bryan King, Xin Cai, Gina M Sizemore, Craig B Thompson.
      The aberrant production of collagen by fibroblasts is a hallmark of many solid tumours and can influence cancer progression. How the mesenchymal cells in the tumour microenvironment maintain their production of extracellular matrix proteins as the vascular delivery of glutamine and glucose becomes compromised remains unclear. Here we show that pyruvate carboxylase (PC)-mediated anaplerosis in tumour-associated fibroblasts contributes to tumour fibrosis and growth. Using cultured mesenchymal and cancer cells, as well as mouse allograft models, we provide evidence that extracellular lactate can be utilized by fibroblasts to maintain tricarboxylic acid (TCA) cycle anaplerosis and non-essential amino acid biosynthesis through PC activity. Furthermore, we show that fibroblast PC is required for collagen production in the tumour microenvironment. These results establish TCA cycle anaplerosis as a determinant of extracellular matrix collagen production, and identify PC as a potential target to inhibit tumour desmoplasia.
    DOI:  https://doi.org/10.1038/s42255-021-00480-x
  3. Nat Rev Cancer. 2021 Nov 11.
    Connecting copper and cancer: from transition metal signalling to metalloplasia.
    Eva J Ge, Ashley I Bush, Angela Casini, Paul A Cobine, Justin R Cross, Gina M DeNicola, Q Ping Dou, Katherine J Franz, Vishal M Gohil, Sanjeev Gupta, Stephen G Kaler, Svetlana Lutsenko, Vivek Mittal, Michael J Petris, Roman Polishchuk, Martina Ralle, Michael L Schilsky, Nicholas K Tonks, Linda T Vahdat, Linda Van Aelst, Dan Xi, Peng Yuan, Donita C Brady, Christopher J Chang.
      Copper is an essential nutrient whose redox properties make it both beneficial and toxic to the cell. Recent progress in studying transition metal signalling has forged new links between researchers of different disciplines that can help translate basic research in the chemistry and biology of copper into clinical therapies and diagnostics to exploit copper-dependent disease vulnerabilities. This concept is particularly relevant in cancer, as tumour growth and metastasis have a heightened requirement for this metal nutrient. Indeed, the traditional view of copper as solely an active site metabolic cofactor has been challenged by emerging evidence that copper is also a dynamic signalling metal and metalloallosteric regulator, such as for copper-dependent phosphodiesterase 3B (PDE3B) in lipolysis, mitogen-activated protein kinase kinase 1 (MEK1) and MEK2 in cell growth and proliferation and the kinases ULK1 and ULK2 in autophagy. In this Perspective, we summarize our current understanding of the connection between copper and cancer and explore how challenges in the field could be addressed by using the framework of cuproplasia, which is defined as regulated copper-dependent cell proliferation and is a representative example of a broad range of metalloplasias. Cuproplasia is linked to a diverse array of cellular processes, including mitochondrial respiration, antioxidant defence, redox signalling, kinase signalling, autophagy and protein quality control. Identifying and characterizing new modes of copper-dependent signalling offers translational opportunities that leverage disease vulnerabilities to this metal nutrient.
    DOI:  https://doi.org/10.1038/s41568-021-00417-2
  4. MedComm (Beijing). 2020 Dec;1(3): 302-310
    The biological role of metabolic reprogramming in pancreatic cancer.
    Tatsunori Suzuki, Motoyuki Otsuka, Takahiro Seimiya, Takuma Iwata, Takahiro Kishikawa, Kazuhiko Koike.
      Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease and highly resistant to all forms of therapy. PDAC cells reprogram their metabolism extensively to promote their survival and growth. Reflecting the vital role of altered metabolism, experimental and clinical trials targeting the rewired metabolism are currently underway. In this review, we summarize the vital role of metabolic reprogramming in the development of PDAC and the future of novel therapeutic applications.
    Keywords:  autophagy; macropinocytosis; metabolism; pancreatic cancer; tumor microenvironment
    DOI:  https://doi.org/10.1002/mco2.37
  5. Mech Ageing Dev. 2021 Nov 03. pii: S0047-6374(21)00167-6. [Epub ahead of print]200 111595
    Skeletal muscle aging, cellular senescence, and senotherapeutics: Current knowledge and future directions.
    Davis A Englund, Xu Zhang, Zaira Aversa, Nathan K LeBrasseur.
      Cellular senescence is a state of cell cycle arrest induced by several forms of metabolic stress. Senescent cells accumulate with advancing age and have a distinctive phenotype, characterized by profound chromatin alterations and a robust senescence-associated secretory phenotype (SASP) that exerts negative effects on tissue health, both locally and systemically. In preclinical models, pharmacological agents that eliminate senescent cells (senotherapeutics) restore health and youthful properties in multiple tissues. To date, however, very little is understood about the vulnerability of terminally-differentiated skeletal muscle fibers and the resident mononuclear cells that populate the interstitial microenvironment of skeletal muscle to senescence, and their contribution to the onset and progression of skeletal muscle loss and dysfunction with aging. Scientific advances in these areas have the potential to highlight new therapeutic approaches to optimize late-life muscle health. To this end, this review highlights the current evidence and the key questions that need to be addressed to advance the field's understanding of cellular senescence as a mediator of skeletal muscle aging and the potential for emerging senescent cell-targeting therapies to counter age-related deficits in muscle mass, strength, and function.
    Keywords:  Fibroadipogenic progenitor cells; Muscle fiber; Sarcopenia; Satellite cells; Senescence-associated secretory phenotype; Senolytics
    DOI:  https://doi.org/10.1016/j.mad.2021.111595
  6. Nat Nanotechnol. 2021 Nov 11.
    A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours.
    Chang Cui, Kasturi Chakraborty, Xu Anna Tang, Kelly Q Schoenfelt, Alexandria Hoffman, Ariane Blank, Blake McBeth, Natalie Pulliam, Catherine A Reardon, Swati A Kulkarni, Tomas Vaisar, Andrea Ballabio, Yamuna Krishnan, Lev Becker.
      Activating CD8+ T cells by antigen cross-presentation is remarkably effective at eliminating tumours. Although this function is traditionally attributed to dendritic cells, tumour-associated macrophages (TAMs) can also cross-present antigens. TAMs are the most abundant tumour-infiltrating leukocyte. Yet, TAMs have not been leveraged to activate CD8+ T cells because mechanisms that modulate their ability to cross-present antigens are incompletely understood. Here we show that TAMs harbour hyperactive cysteine protease activity in their lysosomes, which impedes antigen cross-presentation, thereby preventing CD8+ T cell activation. We developed a DNA nanodevice (E64-DNA) that targets the lysosomes of TAMs in mice. E64-DNA inhibits the population of cysteine proteases that is present specifically inside the lysosomes of TAMs, improves their ability to cross-present antigens and attenuates tumour growth via CD8+ T cells. When combined with cyclophosphamide, E64-DNA showed sustained tumour regression in a triple-negative-breast-cancer model. Our studies demonstrate that DNA nanodevices can be targeted with organelle-level precision to reprogram macrophages and achieve immunomodulation in vivo.
    DOI:  https://doi.org/10.1038/s41565-021-00988-z
  7. Immunity. 2021 Nov 03. pii: S1074-7613(21)00448-9. [Epub ahead of print]
    MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function.
    Ayaka Sugiura, Gabriela Andrejeva, Kelsey Voss, Darren R Heintzman, Xincheng Xu, Matthew Z Madden, Xiang Ye, Katherine L Beier, Nowrin U Chowdhury, Melissa M Wolf, Arissa C Young, Dalton L Greenwood, Allison E Sewell, Shailesh K Shahi, Samantha N Freedman, Alanna M Cameron, Patrik Foerch, Tim Bourne, Juan C Garcia-Canaveras, John Karijolich, Dawn C Newcomb, Ashutosh K Mangalam, Joshua D Rabinowitz, Jeffrey C Rathmell.
      Antigenic stimulation promotes T cell metabolic reprogramming to meet increased biosynthetic, bioenergetic, and signaling demands. We show that the one-carbon (1C) metabolism enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) regulates de novo purine synthesis and signaling in activated T cells to promote proliferation and inflammatory cytokine production. In pathogenic T helper-17 (Th17) cells, MTHFD2 prevented aberrant upregulation of the transcription factor FoxP3 along with inappropriate gain of suppressive capacity. MTHFD2 deficiency also promoted regulatory T (Treg) cell differentiation. Mechanistically, MTHFD2 inhibition led to depletion of purine pools, accumulation of purine biosynthetic intermediates, and decreased nutrient sensor mTORC1 signaling. MTHFD2 was also critical to regulate DNA and histone methylation in Th17 cells. Importantly, MTHFD2 deficiency reduced disease severity in multiple in vivo inflammatory disease models. MTHFD2 is thus a metabolic checkpoint to integrate purine metabolism with pathogenic effector cell signaling and is a potential therapeutic target within 1C metabolism pathways.
    Keywords:  CD4(+) T cells; CRISPR screen; MTHFD2; T cell differentiation; inflammation; mTORC1; metabolic checkpoint; methylation; one carbon metabolism; purine metabolism
    DOI:  https://doi.org/10.1016/j.immuni.2021.10.011
  8. Nat Commun. 2021 Nov 11. 12(1): 6512
    A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.
    Sanju Sinha, Karina Barbosa, Kuoyuan Cheng, Mark D M Leiserson, Prashant Jain, Anagha Deshpande, David M Wilson, Bríd M Ryan, Ji Luo, Ze'ev A Ronai, Joo Sang Lee, Aniruddha J Deshpande, Eytan Ruppin.
      Recent studies have reported that genome editing by CRISPR-Cas9 induces a DNA damage response mediated by p53 in primary cells hampering their growth. This could lead to a selection of cells with pre-existing p53 mutations. In this study, employing an integrated computational and experimental framework, we systematically investigated the possibility of selection of additional cancer driver mutations during CRISPR-Cas9 gene editing. We first confirm the previous findings of the selection for pre-existing p53 mutations by CRISPR-Cas9. We next demonstrate that similar to p53, wildtype KRAS may also hamper the growth of Cas9-edited cells, potentially conferring a selective advantage to pre-existing KRAS-mutant cells. These selective effects are widespread, extending across cell-types and methods of CRISPR-Cas9 delivery and the strength of selection depends on the sgRNA sequence and the gene being edited. The selection for pre-existing p53 or KRAS mutations may confound CRISPR-Cas9 screens in cancer cells and more importantly, calls for monitoring patients undergoing CRISPR-Cas9-based editing for clinical therapeutics for pre-existing p53 and KRAS mutations.
    DOI:  https://doi.org/10.1038/s41467-021-26788-6
  9. Nat Commun. 2021 Nov 12. 12(1): 6572
    Apoptotic stress-induced FGF signalling promotes non-cell autonomous resistance to cell death.
    Florian J Bock, Egor Sedov, Elle Koren, Anna L Koessinger, Catherine Cloix, Désirée Zerbst, Dimitris Athineos, Jayanthi Anand, Kirsteen J Campbell, Karen Blyth, Yaron Fuchs, Stephen W G Tait.
      Damaged or superfluous cells are typically eliminated by apoptosis. Although apoptosis is a cell-autonomous process, apoptotic cells communicate with their environment in different ways. Here we describe a mechanism whereby cells under apoptotic stress can promote survival of neighbouring cells. We find that upon apoptotic stress, cells release the growth factor FGF2, leading to MEK-ERK-dependent transcriptional upregulation of pro-survival BCL-2 proteins in a non-cell autonomous manner. This transient upregulation of pro-survival BCL-2 proteins protects neighbouring cells from apoptosis. Accordingly, we find in certain cancer types a correlation between FGF-signalling, BCL-2 expression and worse prognosis. In vivo, upregulation of MCL-1 occurs in an FGF-dependent manner during skin repair, which regulates healing dynamics. Importantly, either co-treatment with FGF-receptor inhibitors or removal of apoptotic stress restores apoptotic sensitivity to cytotoxic therapy and delays wound healing. These data reveal a pathway by which cells under apoptotic stress can increase resistance to cell death in surrounding cells. Beyond mediating cytotoxic drug resistance, this process also provides a potential link between tissue damage and repair.
    DOI:  https://doi.org/10.1038/s41467-021-26613-0
  10. Cancers (Basel). 2021 Oct 24. pii: 5338. [Epub ahead of print]13(21):
    IL-17B/RB Activation in Pancreatic Stellate Cells Promotes Pancreatic Cancer Metabolism and Growth.
    Jiahui Li, Xiaolin Wu, Lars Schiffmann, Thomas MacVicar, Chenghui Zhou, Zhefang Wang, Dai Li, Oscar Velazquez Camacho, Reiner Heuchel, Margarete Odenthal, Axel Hillmer, Alexander Quaas, Yue Zhao, Christiane J Bruns, Felix C Popp.
      In pancreatic ductal adenocarcinoma (PDAC), the tumor stroma constitutes most of the cell mass and contributes to therapy resistance and progression. Here we show a hitherto unknown metabolic cooperation between pancreatic stellate cells (PSCs) and tumor cells through Interleukin 17B/Interleukin 17B receptor (IL-17B/IL-17RB) signaling. Tumor-derived IL-17B carrying extracellular vesicles (EVs) activated stromal PSCs and induced the expression of IL-17RB. PSCs increased oxidative phosphorylation while reducing mitochondrial turnover. PSCs activated tumor cells in a feedback loop. Tumor cells subsequently increased oxidative phosphorylation and decreased glycolysis partially via IL-6. In vivo, IL-17RB overexpression in PSCs accelerated tumor growth in a co-injection xenograft mouse model. Our results demonstrate a tumor-to-stroma feedback loop increasing tumor metabolism to accelerate tumor growth under optimal nutritional conditions.
    Keywords:  IL17B/RB; metabolism; pancreatic cancer; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers13215338
  11. J Biol Chem. 2021 Oct 28. pii: S0021-9258(21)01174-1. [Epub ahead of print] 101368
    GRP75 mediates Endoplasmic Reticulum-Mitochondria coupling during palmitate-induced pancreatic β-cell apoptosis.
    Shweta Tiwary, Arun Nandwani, Rukshar Khan, Malabika Datta.
      The endoplasmic reticulum (ER) and mitochondria are structurally connected with each other at specific sites termed mitochondria-associated membranes (MAM). These physical links are composed of several tethering proteins and are important during varied cellular processes, such as calcium homeostasis, lipid metabolism and transport, membrane biogenesis and organelle remodeling. However, the attributes of specific tethering proteins in these cellular functions remain debatable. Here, we present data to show that one such tether protein, GRP75, is essential in increasing ER-mitochondria contact during palmitate-induced apoptosis in pancreatic insulinoma cells. We demonstrate that palmitate increased GRP75 levels in mouse and rat pancreatic insulinoma cells as well as in mouse primary islet cells. This was associated with increased mitochondrial Ca2+ transfer, impaired mitochondrial membrane potential, increased ROS production, and enhanced physical coupling between the ER and mitochondria. Interestingly, GRP75 inhibition prevented these palmitate-induced cellular aberrations. Additionally, GRP75 overexpression alone was sufficient to impair mitochondrial membrane potential, increase mitochondrial Ca2+ levels and ROS generation, augment ER-mitochondria contact, and induce apoptosis in these cells. In vivo injection of palmitate induced hyperglycemia and hypertriglyceridemia, as well as impaired glucose and insulin tolerance in mice. These animals also exhibited elevated GRP75 levels accompanied by enhanced apoptosis within the pancreatic islets. Our findings suggest that GRP75 is critical in mediating palmitate-induced ER-mitochondrial interaction leading to apoptosis in pancreatic islet cells.
    Keywords:  ER-mitochondria contact; GRP75; calcium apoptosis; palmitate
    DOI:  https://doi.org/10.1016/j.jbc.2021.101368
  12. Elife. 2021 Nov 10. pii: e72449. [Epub ahead of print]10
    The right time for senescence.
    Diogo Paramos-de-Carvalho, Antonio Jacinto, Leonor Saúde.
      Cellular senescence is a highly complex and programmed cellular state with diverse and, at times, conflicting physiological and pathological roles across the lifespan of an organism. Initially considered a cell culture artifact, senescence evolved from an age-related circumstance to an intricate cellular defense mechanism in response to stress, implicated in a wide spectrum of biological processes like tissue remodelling, injury and cancer. The development of new tools to study senescence in vivo paved the way to uncover its functional roles in various frameworks, which are sometimes hard to reconcile. Here, we review the functional impact of senescent cells on different organismal contexts. We provide updated insights on the role of senescent cells in tissue repair and regeneration, in which they essentially modulate the levels of fibrosis and inflammation, discussing how "time" seems to be the key maestro of their effects. Finally, we overview the current clinical research landscape to target senescent cells and contemplate its repercussions on this fast-evolving field.
    Keywords:  cell biology; pathophysiology; senescence; senotherapies; time; tissue remodelling
    DOI:  https://doi.org/10.7554/eLife.72449
  13. Nature. 2021 Nov 10.
    Diverse alterations associated with resistance to KRAS(G12C) inhibition.
    Yulei Zhao, Yonina R Murciano-Goroff, Jenny Y Xue, Agnes Ang, Jessica Lucas, Trang T Mai, Arnaud F Da Cruz Paula, Anne Y Saiki, Deanna Mohn, Pragathi Achanta, Ann E Sisk, Kanika S Arora, Rohan S Roy, Dongsung Kim, Chuanchuan Li, Lee P Lim, Mark Li, Amber Bahr, Brian R Loomis, Elisa de Stanchina, Jorge S Reis-Filho, Britta Weigelt, Michael Berger, Gregory Riely, Kathryn C Arbour, J Russell Lipford, Bob T Li, Piro Lito.
      Inactive state-selective KRAS(G12C) inhibitors1-8 demonstrate a 30-40% response rate and result in approximately 6-month median progression-free survival in patients with lung cancer9. The genetic basis for resistance to these first-in-class mutant GTPase inhibitors remains under investigation. Here we evaluated matched pre-treatment and post-treatment specimens from 43 patients treated with the KRAS(G12C) inhibitor sotorasib. Multiple treatment-emergent alterations were observed across 27 patients, including alterations in KRAS, NRAS, BRAF, EGFR, FGFR2, MYC and other genes. In preclinical patient-derived xenograft and cell line models, resistance to KRAS(G12C) inhibition was associated with low allele frequency hotspot mutations in KRAS(G12V or G13D), NRAS(Q61K or G13R), MRAS(Q71R) and/or BRAF(G596R), mirroring observations in patients. Single-cell sequencing in an isogenic lineage identified secondary RAS and/or BRAF mutations in the same cells as KRAS(G12C), where they bypassed inhibition without affecting target inactivation. Genetic or pharmacological targeting of ERK signalling intermediates enhanced the antiproliferative effect of G12C inhibitor treatment in models with acquired RAS or BRAF mutations. Our study thus suggests a heterogenous pattern of resistance with multiple subclonal events emerging during G12C inhibitor treatment. A subset of patients in our cohort acquired oncogenic KRAS, NRAS or BRAF mutations, and resistance in this setting may be delayed by co-targeting of ERK signalling intermediates. These findings merit broader evaluation in prospective clinical trials.
    DOI:  https://doi.org/10.1038/s41586-021-04065-2
  14. FASEB J. 2021 Dec;35(12): e21991
    The role of mitochondria in cellular senescence.
    Shohini K Ghosh-Choudhary, Jie Liu, Toren Finkel.
      Mitochondria are intimately connected to cell fate and function. Here, we review how these intracellular organelles participate in the induction and maintenance of the senescent state. In particular, we discuss how alterations in mitochondrial metabolism, quality control and dynamics are all involved in various aspects of cellular senescence. Together, these observations suggest that mitochondria are active participants and are mechanistically linked to the unique biology of senescence. We further describe how these insights can be potentially exploited for therapeutic benefit.
    Keywords:  aging; metabolism; mitophagy; reactive oxygen species; senolytic
    DOI:  https://doi.org/10.1096/fj.202101462R
  15. Cancer Res. 2021 Nov 08. pii: canres.1692.2021. [Epub ahead of print]
    CRISPR/Cas9-induced DNA damage enriches for mutations in a p53-linked interactome: implications for CRISPR-based therapies.
    Long Jiang, Katrine Ingelshed, Yunbing Shen, Sanjaykumar V Boddul, Vaishnavi Srinivasan Iyer, Zsolt Kasza, Saikiran Sedimbi, David P Lane, Fredrik Wermeling.
      Inactivating p53 mutations are the most abundant genetic alterations found in cancer. Here we show that CRISPR/Cas9-induced double-stranded DNA breaks enrich for cells deficient in p53 as well as in genes of a core CRISPR-p53 tumor suppressor interactome. Such enrichment could predispose to cancer development and thus pose a challenge for clinical CRISPR use. Transient p53 inhibition could suppress the enrichment of cells with these mutations. The level of DNA damage response induced by an sgRNA influenced the enrichment of p53 deficient cells and could be a relevant parameter in sgRNA design to limit cellular enrichment. Furthermore, a dataset of >800 human cancer cell lines identified additional factors influencing the enrichment of p53 mutated cells, including strong baseline CDKN1A expression as a predictor for an active CRISPR-p53 axis. Taken together, these data provide details about p53 biology in the context of CRISPR-induced DNA damage and identify strategies to enable safer CRISPR use.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1692
  16. FASEB J. 2021 Dec;35(12): e21999
    Activation of Crtc2/Creb1 in skeletal muscle enhances weight loss during intermittent fasting.
    Nelson E Bruno, Jerome C Nwachukwu, David C Hughes, Sathish Srinivasan, Richard Hawkins, David Sturgill, Gordon L Hager, Stephen Hurst, Shey-Shing Sheu, Sue C Bodine, Michael D Conkright, Kendall W Nettles.
      The Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators drive Creb1-mediated transcription effects on metabolism in many tissues, but the in vivo effects of Crtc2/Creb1 transcription on skeletal muscle metabolism are not known. Skeletal muscle-specific overexpression of Crtc2 (Crtc2 mice) induced greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity, supported by upregulation of key metabolic genes. Crtc2 overexpression led to greater weight loss during alternate day fasting (ADF), selective loss of fat rather than lean mass, maintenance of higher energy expenditure during the fast and reduced binge-eating during the feeding period. ADF downregulated most of the mitochondrial electron transport genes, and other regulators of mitochondrial function, that were substantially reversed by Crtc2-driven transcription. Glucocorticoids acted with AMPK to drive atrophy and mitophagy, which was reversed by Crtc2/Creb1 signaling. Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb1 regulates metabolism and weight loss.
    Keywords:  Creb1; Crtc2; intermittent fasting; skeletal muscle
    DOI:  https://doi.org/10.1096/fj.202100171R
  17. Biochem Biophys Rep. 2021 Dec;28 101158
    Unfolding the role of autophagy in the cancer metabolism.
    Anchala Pandey, Pooja Yadav, Sanjeev Shukla.
      Autophagy is considered an indispensable process that scavenges toxins, recycles complex macromolecules, and sustains the essential cellular functions. In addition to its housekeeping role, autophagy plays a substantial role in many pathophysiological processes such as cancer. Certainly, it adapts cancer cells to thrive in the stress conditions such as hypoxia and starvation. Cancer cells indeed have also evolved by exploiting the autophagy process to fulfill energy requirements through the production of metabolic fuel sources and fundamentally altered metabolic pathways. Occasionally autophagy as a foe impedes tumorigenesis and promotes cell death. The complex role of autophagy in cancer makes it a potent therapeutic target and has been actively tested in clinical trials. Moreover, the versatility of autophagy has opened new avenues of effective combinatorial therapeutic strategies. Thereby, it is imperative to comprehend the specificity of autophagy in cancer-metabolism. This review summarizes the recent research and conceptual framework on the regulation of autophagy by various metabolic pathways, enzymes, and their cross-talk in the cancer milieu, including the implementation of altered metabolism and autophagy in clinically approved and experimental therapeutics.
    Keywords:  Autophagy; Cancer; Hypoxia; Metabolism; Starvation; Therapeutics
    DOI:  https://doi.org/10.1016/j.bbrep.2021.101158
  18. Science. 2021 Nov 11. eabm4805
    Computed structures of core eukaryotic protein complexes.
    Ian R Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov, Jing Zhang, Travis J Ness, Sudeep Banjade, Saket R Bagde, Viktoriya G Stancheva, Xiao-Han Li, Kaixian Liu, Zhi Zheng, Daniel J Barrero, Upasana Roy, Jochen Kuper, Israel S Fernández, Barnabas Szakal, Dana Branzei, Josep Rizo, Caroline Kisker, Eric C Greene, Sue Biggins, Scott Keeney, Elizabeth A Miller, J Christopher Fromme, Tamara L Hendrickson, Qian Cong, David Baker.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abm4805
  19. Future Oncol. 2021 Nov 11.
    Age-dependent prognostic value of KRAS mutation in metastatic colorectal cancer.
    Muhammet Ozer, Suleyman Yasin Goksu, Nina Niu Sanford, Chul Ahn, Muhammad Shaalan Beg, Syed Mohammad Ali Kazmi.
      Background: The age-dependent prognostic impact of KRAS status in metastatic colorectal cancer (mCRC) is unknown. Materials & Methods: We used the National Cancer Database to evaluate the survival by KRAS status for age-groups <50, 50-69 and ≥70, adjusting for relevant patient and tumor characteristics. Results: mCRC patients (n = 26,095; 33.5%) had KRAS status reported, and 11,338 of these patients (43.4%) had mutations in the KRAS gene. Patients with KRAS mutations had worse overall survival than wild-type KRAS patients. In age-groups <50 years (23 vs 29 months; p < 0.001) and 50-69 (21 vs 23.4 months; p < 0.001), KRAS mutations were significantly associated with worse survival, whereas in the ≥70-year age-group, there was no significant association (14 vs 14 months; p = 0.34). Conclusion: We conclude that the age of patients influences the prognostic value of KRAS mutation in metastatic colorectal cancer.
    Keywords:  KRAS; age of onset; colorectal neoplasms; database; metastasis
    DOI:  https://doi.org/10.2217/fon-2021-0650
  20. Sci Immunol. 2021 Nov 12. 6(65): eabc6424
    Highly immunogenic cancer cells require activation of the WNT pathway for immunological escape.
    Yoshiko Takeuchi, Tokiyoshi Tanegashima, Eiichi Sato, Takuma Irie, Atsuo Sai, Kota Itahashi, Shogo Kumagai, Yasuko Tada, Yosuke Togashi, Shohei Koyama, Esra A Akbay, Takahiro Karasaki, Keisuke Kataoka, Soichiro Funaki, Yasushi Shintani, Izumi Nagatomo, Hiroshi Kida, Genichiro Ishii, Tomohiro Miyoshi, Keiju Aokage, Kazuhiro Kakimi, Seishi Ogawa, Meinoshin Okumura, Masatoshi Eto, Atsushi Kumanogoh, Masahiro Tsuboi, Hiroyoshi Nishikawa.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciimmunol.abc6424
  21. Cell. 2021 Nov 04. pii: S0092-8674(21)01233-2. [Epub ahead of print]
    Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes.
    Suresh Kumar, Ruheena Javed, Michal Mudd, Sandeep Pallikkuth, Keith A Lidke, Ashish Jain, Karthikeyan Tangavelou, Sigurdur Runar Gudmundsson, Chunyan Ye, Tor Erik Rusten, Jan Haug Anonsen, Alf Håkon Lystad, Aurore Claude-Taupin, Anne Simonsen, Michelle Salemi, Brett Phinney, Jing Li, Lian-Wang Guo, Steven B Bradfute, Graham S Timmins, Eeva-Liisa Eskelinen, Vojo Deretic.
      The biogenesis of mammalian autophagosomes remains to be fully defined. Here, we used cellular and in vitro membrane fusion analyses to show that autophagosomes are formed from a hitherto unappreciated hybrid membrane compartment. The autophagic precursors emerge through fusion of FIP200 vesicles, derived from the cis-Golgi, with endosomally derived ATG16L1 membranes to generate a hybrid pre-autophagosomal structure, HyPAS. A previously unrecognized apparatus defined here controls HyPAS biogenesis and mammalian autophagosomal precursor membranes. HyPAS can be modulated by pharmacological agents whereas its formation is inhibited upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or by expression of SARS-CoV-2 nsp6. These findings reveal the origin of mammalian autophagosomal membranes, which emerge via convergence of secretory and endosomal pathways, and show that this process is targeted by microbial factors such as coronaviral membrane-modulating proteins.
    Keywords:  ATG16L1; Atg8ylation; COVID-19; FIP200; Golgi; SARS-CoV-2; Syntaxin 17; autophagy; coronavirus; endosome
    DOI:  https://doi.org/10.1016/j.cell.2021.10.017
  22. Nat Commun. 2021 Nov 09. 12(1): 6463
    Diet composition influences the metabolic benefits of short cycles of very low caloric intake.
    Alberto Diaz-Ruiz, Tyler Rhinesmith, Laura C D Pomatto-Watson, Nathan L Price, Farzin Eshaghi, Margaux R Ehrlich, Jacqueline M Moats, Melissa Carpenter, Annamaria Rudderow, Sebastian Brandhorst, Julie A Mattison, Miguel A Aon, Michel Bernier, Valter D Longo, Rafael de Cabo.
      Diet composition, calories, and fasting times contribute to the maintenance of health. However, the impact of very low-calorie intake (VLCI) achieved with either standard laboratory chow (SD) or a plant-based fasting mimicking diet (FMD) is not fully understood. Here, using middle-aged male mice we show that 5 months of short 4:10 VLCI cycles lead to decreases in both fat and lean mass, accompanied by improved physical performance and glucoregulation, and greater metabolic flexibility independent of diet composition. A long-lasting metabolomic reprograming in serum and liver is observed in mice on VLCI cycles with SD, but not FMD. Further, when challenged with an obesogenic diet, cycles of VLCI do not prevent diet-induced obesity nor do they elicit a long-lasting metabolic memory, despite achieving modest metabolic flexibility. Our results highlight the importance of diet composition in mediating the metabolic benefits of short cycles of VLCI.
    DOI:  https://doi.org/10.1038/s41467-021-26654-5
  23. Cell. 2021 Nov 03. pii: S0092-8674(21)01223-X. [Epub ahead of print]
    Insular cortex neurons encode and retrieve specific immune responses.
    Tamar Koren, Re'ee Yifa, Mariam Amer, Maria Krot, Nadia Boshnak, Tamar L Ben-Shaanan, Hilla Azulay-Debby, Itay Zalayat, Eden Avishai, Haitham Hajjo, Maya Schiller, Hedva Haykin, Ben Korin, Dorit Farfara, Fahed Hakim, Oren Kobiler, Kobi Rosenblum, Asya Rolls.
      Increasing evidence indicates that the brain regulates peripheral immunity, yet whether and how the brain represents the state of the immune system remains unclear. Here, we show that the brain's insular cortex (InsCtx) stores immune-related information. Using activity-dependent cell labeling in mice (FosTRAP), we captured neuronal ensembles in the InsCtx that were active under two different inflammatory conditions (dextran sulfate sodium [DSS]-induced colitis and zymosan-induced peritonitis). Chemogenetic reactivation of these neuronal ensembles was sufficient to broadly retrieve the inflammatory state under which these neurons were captured. Thus, we show that the brain can store and retrieve specific immune responses, extending the classical concept of immunological memory to neuronal representations of inflammatory information.
    Keywords:  engram; inflammation; insular cortex; memory; neurons; psychosomatic
    DOI:  https://doi.org/10.1016/j.cell.2021.10.013
  24. Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01453-4. [Epub ahead of print]37(6): 109974
    Single-cell transcriptomics reveals opposing roles of Shp2 in Myc-driven liver tumor cells and microenvironment.
    Wendy S Chen, Yan Liang, Min Zong, Jacey J Liu, Kota Kaneko, Kaisa L Hanley, Kun Zhang, Gen-Sheng Feng.
      The mechanisms of Myc-driven liver tumorigenesis are inadequately understood. Herein we show that Myc-driven hepatocellular carcinoma (HCC) is dramatically aggravated in mice with hepatocyte-specific Ptpn11/Shp2 deletion. However, Myc-induced tumors develop selectively from the rare Shp2-positive hepatocytes in Shp2-deficent liver, and Myc-driven oncogenesis depends on an intact Ras-Erk signaling promoted by Shp2 to sustain Myc stability. Despite a stringent requirement of Shp2 cell autonomously, Shp2 deletion induces an immunosuppressive environment, resulting in defective clearance of tumor-initiating cells and aggressive tumor progression. The basal Wnt/β-catenin signaling is upregulated in Shp2-deficient liver, which is further augmented by Myc transfection. Ablating Ctnnb1 suppresses Myc-induced HCC in Shp2-deficient livers, revealing an essential role of β-catenin. Consistently, Myc overexpression and CTNNB1 mutations are frequently co-detected in HCC patients with poor prognosis. These data elucidate complex mechanisms of liver tumorigenesis driven by cell-intrinsic oncogenic signaling in cooperation with a tumor-promoting microenvironment generated by disrupting the specific oncogenic pathway.
    Keywords:  Shp2; cMyc; hepatocellular carcinoma; macrophages; single cell RNA sequencing; tumor-promoting microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2021.109974
  25. Front Oncol. 2021 ;11 770843
    Transcriptional Control of Metastasis by Integrated Stress Response Signaling.
    Si Lu, Li-Xian Yang, Zi-Jian Cao, Jiang-Sha Zhao, Jia You, Yu-Xiong Feng.
      As a central cellular program to sense and transduce stress signals, the integrated stress response (ISR) pathway has been implicated in cancer initiation and progression. Depending on the genetic mutation landscape, cellular context, and differentiation states, there are emerging pieces of evidence showing that blockage of the ISR can selectively and effectively shift the balance of cancer cells toward apoptosis, rendering the ISR a promising target in cancer therapy. Going beyond its pro-survival functions, the ISR can also influence metastasis, especially via proteostasis-independent mechanisms. In particular, ISR can modulate metastasis via transcriptional reprogramming, in the help of essential transcription factors. In this review, we summarized the current understandings of ISR in cancer metastasis from the perspective of transcriptional regulation.
    Keywords:  EMT; cancer; integrated stress response (ISR); metastasis; transcription
    DOI:  https://doi.org/10.3389/fonc.2021.770843
  26. Pancreatology. 2021 Oct 26. pii: S1424-3903(21)00607-4. [Epub ahead of print]
    A review of physical activity in pancreatic ductal adenocarcinoma: Epidemiology, intervention, animal models, and clinical trials.
    Hsiang-Yin Hsueh, Valentina Pita-Grisanti, Kristyn Gumpper-Fedus, Ali Lahooti, Myrriah Chavez-Tomar, Keri Schadler, Zobeida Cruz-Monserrate.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer, and the increasing incidence of PDAC may be related to the prevalence of obesity. Physical activity (PA), a method known to mitigate obesity by increasing total energy expenditure, also modifies multiple cellular pathways associated with cancer hallmarks. Epidemiologic evidence has shown that PA can lower the risk of developing a variety of cancers, reduce some of the detrimental side effects of treatments, and improve patient's quality of life during cancer treatment. However, little is known about the pathways underlying the correlations observed between PA interventions and PDAC. Moreover, there is no standard dose of PA intervention that is ideal for PDAC prevention or as an adjuvant of cancer treatments. In this review, we summarize relevant literature showing how PDAC patients can benefit from PA, the potential of PA as an adjuvant treatment for PDAC, the studies using preclinical models of PDAC to study PA, and the clinical trials to date assessing the effects of PA in PDAC.
    Keywords:  Exercise; Pancreatic cancer; Pancreatic ductal adenocarcinoma; Physical activity; Translational research
    DOI:  https://doi.org/10.1016/j.pan.2021.10.004
  27. STAR Protoc. 2021 Dec 17. 2(4): 100918
    Protocol for the assessment of mTOR activity in mouse primary hepatocytes.
    Ana Belén Plata-Gómez, María Crespo, Celia de la Calle Arregui, Lucía de Prado-Rivas, Guadalupe Sabio, Alejo Efeyan.
      We present a protocol for measuring the activity of the mechanistic target of rapamycin (mTOR) pathway in ex vivo isolated mouse primary hepatocytes. It can be used as a tool for genetic, pharmacological, metabolomic, and signal transduction procedures. We discuss critical aspects for improving yield, viability, and modulation of the mTOR pathway. This protocol can be adapted to other signaling cascades and is compatible with multiple readouts. For complete details on the use and execution of this protocol, please refer to Ortega-Molina et al. (2021).
    Keywords:  Cell culture; Cell isolation; Cell-based Assays; Metabolism; Metabolomics; Signal Transduction
    DOI:  https://doi.org/10.1016/j.xpro.2021.100918
  28. Cancer Metab. 2021 Nov 08. 9(1): 39
    Dynamic regulation of mitochondrial pyruvate metabolism is necessary for orthotopic pancreatic tumor growth.
    Nancy P Echeverri Ruiz, Vijay Mohan, Jinghai Wu, Sabina Scott, McKenzie Kreamer, Martin Benej, Tereza Golias, Ioanna Papandreou, Nicholas C Denko.
       BACKGROUND: Pyruvate dehydrogenase complex (PDC) plays a central role in carbohydrate metabolism, linking cytoplasmic glycolysis to the mitochondrial tricarboxylic acid (TCA) cycle. PDC is a conserved E1-E2-E3 dehydrogenase with a PDHA1 and PDHB heterotetramer functioning as the E1 subunit. PDHA1 contains three serine residues that can be reversibly phosphorylated by a dedicated family of four inhibitory pyruvate dehydrogenase kinases (PDHK1-4) and two reactivating phosphatases (PDP1, 2). Hypoxia induces the expression of PDHK1 and PDHK3 and hyperphosphorylates PDHA1. The role of PDC in metabolic reprogramming and tumor progression appears to be for the integration of oncogenic and environmental signals which supports tumor growth.
    METHODS: To isolate the function of the serine-dependent regulation of PDC, we engineered MiaPaca2 cells to express PDHA1 protein with either intact serines at positions 232, 293, and 300 or all the combinations of non-phosphorylatable alanine substitution mutations. These lines were compared in vitro for biochemical response to hypoxia by western blot, metabolic activity by biochemical assay and Seahorse XF flux analysis, and growth in media with reduced exogenous metabolites. The lines were also tested for growth in vivo after orthotopic injection into the pancreata of immune-deficient mice.
    RESULTS: In this family of cells with non-phosphorylatable PDHA1, we found reduced hypoxic phosphorylation of PDHA1, decreased PDH enzymatic activity in normoxia and hypoxia, decreased mitochondrial function by Seahorse flux assay, reduced in vitro growth of cells in media depleted of lipids, and reduced growth of tumors after orthotopic transplantation of cells into the pancreata of immune-deficient mice.
    CONCLUSIONS: We found that any substitution of alanine for serine at regulatory sites generated a hypomorphic PDC. However, the reduced PDC activity was insensitive to further reduction in hypoxia. These cells had a very modest reduction of growth in vitro, but failed to grow as tumors indicating that dynamic PDC adaptation to microenvironmental conditions is necessary to support pancreatic cancer growth in vivo.
    Keywords:  Glucose metabolism; Hypoxia; Mitochondria; Orthotopic pancreatic tumors; Pyruvate dehydrogenase
    DOI:  https://doi.org/10.1186/s40170-021-00275-4
  29. Cancer Lett. 2021 Nov 06. pii: S0304-3835(21)00559-0. [Epub ahead of print]
    Stimulating TRPM7 suppresses cancer cell proliferation and metastasis by inhibiting autophagy.
    Yanhong Xing, Xiangqing Wei, Meng-Meng Wang, Yucheng Liu, Zhongheng Sui, Xinyan Wang, Yang Zhang, Yuan-Hui Fei, Yi Jiang, Chen Lu, Peng Zhang, Rong Chen, Nan Liu, Mengmei Wu, Lin Ding, Yuqing Wang, Feng Guo, Jun-Li Cao, Jiansong Qi, Wuyang Wang.
      The transient receptor potential melastatin-subfamily member 7 (TRPM7) is a ubiquitous cation channel possessing kinase activity. TRPM7 mediates a variety of physiological responses by conducting flow of cations such as Ca2+, Mg2+, and Zn2+. Here, we show that the activation of TRPM7 channel stimulated by chemical agonists of TRPM7, Clozapine or Naltriben, inhibited autophagy via mediating Zn2+ release to the cytosol, presumably from the intracellular Zn2+-accumulating vesicles where TRPM7 localizes. Zn2+ release following the activation of TRPM7 disrupted the fusion between autophagosomes and lysosomes by disturbing the interaction between Sxt17 and VAMP8 which determines fusion status of autophagosomes and lysosomes. Ultimately, the disrupted fusion resulting from stimulation of TRPM7 channels arrested autophagy. Functionally, we demonstrate that the autophagy inhibition mediated by TRPM7 triggered cell death and suppressed metastasis of cancer cells in vitro, more importantly, restricted tumor growth and metastasis in vivo, by evoking apoptosis, cell cycle arrest, and reactive oxygen species (ROS) elevation. These findings represent a strategy for stimulating TRPM7 to combat cancer.
    Keywords:  Autophagic arrest; TRPM7; Tumorigenesis; Zinc homeostasis
    DOI:  https://doi.org/10.1016/j.canlet.2021.10.043
  30. Oncogene. 2021 Nov 12.
    Disrupted mitochondrial homeostasis coupled with mitotic arrest generates antineoplastic oxidative stress.
    Xiaohe Hao, Wenqing Bu, Guosheng Lv, Limei Xu, Dong Hou, Jing Wang, Xiaojie Liu, Tingting Yang, Xiyu Zhang, Qiao Liu, Yaoqin Gong, Changshun Shao.
      Reactive oxygen species (ROS) serve as critical signals in various cellular processes. Excessive ROS cause cell death or senescence and mediates the therapeutic effect of many cancer drugs. Recent studies showed that ROS increasingly accumulate during G2/M arrest, the underlying mechanism, however, has not been fully elucidated. Here, we show that in cancer cells treated with anticancer agent TH287 or paclitaxel that causes M arrest, mitochondria accumulate robustly and produce excessive mitochondrial superoxide, which causes oxidative DNA damage and undermines cell survival and proliferation. While mitochondrial mass is greatly increased in cells arrested at M phase, the mitochondrial function is compromised, as reflected by reduced mitochondrial membrane potential, increased SUMOylation and acetylation of mitochondrial proteins, as well as an increased metabolic reliance on glycolysis. CHK1 functional disruption decelerates cell cycle, spares the M arrest and attenuates mitochondrial oxidative stress. Induction of mitophagy and blockade of mitochondrial biogenesis, measures that reduce mitochondrial accumulation, also decelerate cell cycle and abrogate M arrest-coupled mitochondrial oxidative stress. These results suggest that cell cycle progression and mitochondrial homeostasis are interdependent and coordinated, and that impairment of mitochondrial homeostasis and the associated redox signaling may mediate the antineoplastic effect of the M arrest-inducing chemotherapeutics. Our findings provide insights into the fate of cells arrested at M phase and have implications in cancer therapy.
    DOI:  https://doi.org/10.1038/s41388-021-02105-9
  31. Sci Adv. 2021 Nov 12. 7(46): eabk0271
    Cell size is a determinant of stem cell potential during aging.
    Jette Lengefeld, Chia-Wei Cheng, Pema Maretich, Marguerite Blair, Hannah Hagen, Melanie R McReynolds, Emily Sullivan, Kyra Majors, Christina Roberts, Joon Ho Kang, Joachim D Steiner, Teemu P Miettinen, Scott R Manalis, Adam Antebi, Sean J Morrison, Jacqueline A Lees, Laurie A Boyer, Ömer H Yilmaz, Angelika Amon.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abk0271
  32. Front Cell Dev Biol. 2021 ;9 741162
    Pancreatic Ductal Adenocarcinoma: Preclinical in vitro and ex vivo Models.
    Beate Gündel, Xinyuan Liu, Matthias Löhr, Rainer Heuchel.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most overlooked cancers despite its dismal median survival time of 6 months. The biggest challenges in improving patient survival are late diagnosis due to lack of diagnostic markers, and limited treatment options due to almost complete therapy resistance. The past decades of research identified the dense stroma and the complex interplay/crosstalk between the cancer- and the different stromal cells as the main culprits for the slow progress in improving patient outcome. For better ex vivo simulation of this complex tumor microenvironment the models used in PDAC research likewise need to become more diverse. Depending on the focus of the investigation, several in vitro and in vivo models for PDAC have been established in the past years. Particularly, 3D cell culture such as spheroids and organoids have become more frequently used. This review aims to examine current PDAC in vitro models, their inherent limitations, and their successful implementations in research.
    Keywords:  3D cell culture; organoids; pancreatic ductal adenocarcinoma; reporter assays; spheroid
    DOI:  https://doi.org/10.3389/fcell.2021.741162
  33. Elife. 2021 Nov 12. pii: e71982. [Epub ahead of print]10
    Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates.
    Xiao-Man Liu, Liang Ma, Randy Schekman.
      Exosomes may mediate cell-to-cell communication by transporting various proteins and nucleic acids to neighboring cells. Some protein and RNA cargoes are significantly enriched in exosomes. How cells efficiently and selectively sort them into exosomes remains incompletely explored. Previously we reported that YBX1 is required in sorting of miR-223 into exosomes. Here we show that YBX1 undergoes liquid-liquid phase separation (LLPS) in vitro and in cells. YBX1 condensates selectively recruit miR-223 in vitro and into exosomes secreted by cultured cells. Point mutations that inhibit YBX1 phase separation impair the incorporation of YBX1 protein into biomolecular condensates formed in cells, and perturb miR-233 sorting into exosomes. We propose that phase separation-mediated local enrichment of cytosolic RNA binding proteins and their cognate RNAs enables their targeting and packaging by vesicles that bud into multivesicular bodies. This provides a possible mechanism for efficient and selective engulfment of cytosolic proteins and RNAs into intraluminal vesicles which are then secreted as exosomes from cells.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.71982
  34. Clin Exp Metastasis. 2021 Nov 12.
    Molecular mechanisms of cancer metastasis via the lymphatic versus the blood vessels.
    Stanley P Leong, Kamila Naxerova, Laura Keller, Klaus Pantel, Marlys Witte.
      Cancer metastasis is the process by which primary cancer cells invade through the lymphatic or blood vessels to distant sites. The molecular mechanisms by which cancer cells spread either through the lymphatic versus blood vessels or both are not well established. Two major developments have helped us to understand the process more clearly. First, the development of the sentinel lymph node (SLN) concept which is well established in melanoma and breast cancer. The SLN is the first lymph node in the draining nodal basin to receive cancer cells. Patients with a negative SLN biopsy show a significantly lower incidence of distant metastasis, suggesting that the SLN may be the major gateway for cancer metastasis in these cancer types. Second, the discovery and characterization of several biomarkers including VEGF-C, LYVE-1, Podoplanin and Prox-1 have opened new vistas in the understanding of the induction of lymphangiogenesis by cancer cells. Cancer cells must complete multiple steps to invade the lymphatic system, some of which may be enabled by the evolution of new traits during cancer progression. Thus, cancer cells may spread initially through the main gateway of the SLN, from which evolving cancer clones can invade the blood vessels to distant sites. Cancer cells may also enter the blood vessels directly, bypassing the SLN to establish distant metastases. Future studies need to pinpoint the molecules that are used by cancer cells at different stages of metastasis via different routes so that specific therapies can be targeted against these molecules, with the goal of stopping or preventing cancer metastasis.
    Keywords:  Cancer metastasis; Cancer metastasis through the blood vessels; Cancer metastasis through the lymphatic vessels
    DOI:  https://doi.org/10.1007/s10585-021-10120-z
  35. Nat Commun. 2021 Nov 11. 12(1): 6522
    Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses.
    Humberto Contreras-Trujillo, Jiya Eerdeng, Samir Akre, Du Jiang, Jorge Contreras, Basia Gala, Mary C Vergel-Rodriguez, Yeachan Lee, Aparna Jorapur, Areen Andreasian, Lisa Harton, Charles S Bramlett, Anna Nogalska, Gang Xiao, Jae-Woong Lee, Lai N Chan, Markus Müschen, Akil A Merchant, Rong Lu.
      Cellular heterogeneity is a major cause of treatment resistance in cancer. Despite recent advances in single-cell genomic and transcriptomic sequencing, it remains difficult to relate measured molecular profiles to the cellular activities underlying cancer. Here, we present an integrated experimental system that connects single cell gene expression to heterogeneous cancer cell growth, metastasis, and treatment response. Our system integrates single cell transcriptome profiling with DNA barcode based clonal tracking in patient-derived xenograft models. We show that leukemia cells exhibiting unique gene expression respond to different chemotherapies in distinct but consistent manners across multiple mice. In addition, we uncover a form of leukemia expansion that is spatially confined to the bone marrow of single anatomical sites and driven by cells with distinct gene expression. Our integrated experimental system can interrogate the molecular and cellular basis of the intratumoral heterogeneity underlying disease progression and treatment resistance.
    DOI:  https://doi.org/10.1038/s41467-021-26771-1
  36. Science. 2021 Nov 11. eabd9776
    Nuclear pores dilate and constrict in cellulo.
    Christian E Zimmerli, Matteo Allegretti, Vasileios Rantos, Sara K Goetz, Agnieszka Obarska-Kosinska, Ievgeniia Zagoriy, Aliaksandr Halavatyi, Gerhard Hummer, Julia Mahamid, Jan Kosinski, Martin Beck.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abd9776
  37. Nat Cell Biol. 2021 Nov;23(11): 1129-1135
    Cell type ontologies of the Human Cell Atlas.
    David Osumi-Sutherland, Chuan Xu, Maria Keays, Adam P Levine, Peter V Kharchenko, Aviv Regev, Ed Lein, Sarah A Teichmann.
      Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body while at the same time raising the need to formalize this new knowledge. Here, we discuss current efforts to harmonize and integrate different sources of annotations of cell types and states into a reference cell ontology. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains.
    DOI:  https://doi.org/10.1038/s41556-021-00787-7
  38. Cancer Gene Ther. 2021 Nov 08.
    Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin.
    Dai Shimizu, Kenzui Taniue, Yusuke Matsui, Hiroshi Haeno, Hiromitsu Araki, Fumihito Miura, Mitsuko Fukunaga, Kenji Shiraishi, Yuji Miyamoto, Seiichi Tsukamoto, Aya Komine, Yuta Kobayashi, Akihiro Kitagawa, Yukihiro Yoshikawa, Kuniaki Sato, Tomoko Saito, Shuhei Ito, Takaaki Masuda, Atsushi Niida, Makoto Suzuki, Hideo Baba, Takashi Ito, Nobuyoshi Akimitsu, Yasuhiro Kodera, Koshi Mimori.
      The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.
    DOI:  https://doi.org/10.1038/s41417-021-00401-w
  39. Nat Struct Mol Biol. 2021 Nov;28(11): 889-899
    Regulation of translation by site-specific ribosomal RNA methylation.
    Martin D Jansson, Sophia J Häfner, Kübra Altinel, Disa Tehler, Nicolai Krogh, Emil Jakobsen, Jens V Andersen, Kasper L Andersen, Erwin M Schoof, Patrice Ménard, Henrik Nielsen, Anders H Lund.
      Ribosomes are complex ribozymes that interpret genetic information by translating messenger RNA (mRNA) into proteins. Natural variation in ribosome composition has been documented in several organisms and can arise from several different sources. A key question is whether specific control over ribosome heterogeneity represents a mechanism by which translation can be regulated. We used RiboMeth-seq to demonstrate that differential 2'-O-methylation of ribosomal RNA (rRNA) represents a considerable source of ribosome heterogeneity in human cells, and that modification levels at distinct sites can change dynamically in response to upstream signaling pathways, such as MYC oncogene expression. Ablation of one prominent methylation resulted in altered translation of select mRNAs and corresponding changes in cellular phenotypes. Thus, differential rRNA 2'-O-methylation can give rise to ribosomes with specialized function. This suggests a broader mechanism where the specific regulation of rRNA modification patterns fine tunes translation.
    DOI:  https://doi.org/10.1038/s41594-021-00669-4
  40. iScience. 2021 Nov 19. 24(11): 103252
    A novel jamming phase diagram links tumor invasion to non-equilibrium phase separation.
    Wenying Kang, Jacopo Ferruzzi, Catalina-Paula Spatarelu, Yu Long Han, Yasha Sharma, Stephan A Koehler, Jennifer A Mitchel, Adil Khan, James P Butler, Darren Roblyer, Muhammad H Zaman, Jin-Ah Park, Ming Guo, Zi Chen, Adrian F Pegoraro, Jeffrey J Fredberg.
      It is well established that the early malignant tumor invades surrounding extracellular matrix (ECM) in a manner that depends upon material properties of constituent cells, surrounding ECM, and their interactions. Recent studies have established the capacity of the invading tumor spheroids to evolve into coexistent solid-like, fluid-like, and gas-like phases. Using breast cancer cell lines invading into engineered ECM, here we show that the spheroid interior develops spatial and temporal heterogeneities in material phase which, depending upon cell type and matrix density, ultimately result in a variety of phase separation patterns at the invasive front. Using a computational approach, we further show that these patterns are captured by a novel jamming phase diagram. We suggest that non-equilibrium phase separation based upon jamming and unjamming transitions may provide a unifying physical picture to describe cellular migratory dynamics within, and invasion from, a tumor.
    Keywords:  Biophysics; Cancer; Mechanobiology
    DOI:  https://doi.org/10.1016/j.isci.2021.103252
  41. Nat Biomed Eng. 2021 Nov 08.
    Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
    Rumana Rashid, Yu-An Chen, John Hoffer, Jeremy L Muhlich, Jia-Ren Lin, Robert Krueger, Hanspeter Pfister, Richard Mitchell, Sandro Santagata, Peter K Sorger.
      Multiplexed tissue imaging facilitates the diagnosis and understanding of complex disease traits. However, the analysis of such digital images heavily relies on the experience of anatomical pathologists for the review, annotation and description of tissue features. In addition, the wider use of data from tissue atlases in basic and translational research and in classrooms would benefit from software that facilitates the easy visualization and sharing of the images and the results of their analyses. In this Perspective, we describe the ecosystem of software available for the analysis of tissue images and discuss the need for interactive online guides that help histopathologists make complex images comprehensible to non-specialists. We illustrate this idea via a software interface (Minerva), accessible via web browsers, that integrates multi-omic and tissue-atlas features. We argue that such interactive narrative guides can effectively disseminate digital histology data and aid their interpretation.
    DOI:  https://doi.org/10.1038/s41551-021-00789-8
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