bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒10‒10
thirty-six papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. An Oatp transporter-mediated steroid sink promotes tumor-induced cachexia in Drosophila.
  2. Rab9 mediates pancreatic autophagy switch from canonical to noncanonical, aggravating experimental pancreatitis.
  3. Labeling and Measuring Stressed Mitochondria Using a PINK1-Based Ratiometric Fluorescent Sensor.
  4. Oncogenic KRAS blockade therapy: renewed enthusiasm and persistent challenges.
  5. The interplay of immunology and cachexia in infection and cancer.
  6. IgE-based therapeutic combination enhances anti-tumor response in preclinical models of pancreatic cancer.
  7. PINK1 drives production of mtDNA-containing extracellular vesicles to promote invasiveness.
  8. Eicosanoid regulation of debris-stimulated metastasis.
  9. The assembly, regulation and function of the mitochondrial respiratory chain.
  10. Determinants of renal cell carcinoma invasion and metastatic competence.
  11. Single cell biology-a Keystone Symposia report.
  12. Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis.
  13. Metabolic Biomarkers for the Early Detection of Cancer Cachexia.
  14. Liquid-liquid phase separation: Orchestrating cell signaling through time and space.
  15. Metabolic regulation of the cancer-immunity cycle.
  16. Mucin Expression and Splicing Determine Novel Subtypes and Patient Mortality in Pancreatic Ductal Adenocarcinoma.
  17. Novel Models of Genetic Education and Testing for Pancreatic Cancer Interception: Preliminary Results from the GENERATE Study.
  18. Polygenic basis and biomedical consequences of telomere length variation.
  19. An open-access volume electron microscopy atlas of whole cells and tissues.
  20. Petasin potently inhibits mitochondrial complex I-based metabolism that supports tumor growth and metastasis.
  21. Autophagy deficiency activates rDNA transcription.
  22. Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex.
  23. High-resolution positron emission microscopy of patient-derived tumor organoids.
  24. Feasibility and efficacy of enteral tube feeding on weight stability, lean body mass, and patient-reported outcomes in pancreatic cancer cachexia.
  25. Collective regulation of chromatin modifications predicts replication timing during cell cycle.
  26. SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment.
  27. A multimodal whole-body atlas.
  28. Modulation of fracture healing by the transient accumulation of senescent cells.
  29. Raman microscopy-based quantification of the physical properties of intracellular lipids.
  30. ClusterMap for multi-scale clustering analysis of spatial gene expression.
  31. Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet.
  32. Novel oncogenic transcription factor cooperation in RB-deficient cancer.
  33. A randomized, feasibility trial of an exercise and nutrition-based rehabilitation programme (ENeRgy) in people with cancer.
  34. Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce.
  35. Visualizing formation of the active site in the mitochondrial ribosome.
  36. A Phase I, Open-Label, Dose-Escalation Study of the OX40 Agonist Ivuxolimab in Patients With Locally Advanced or Metastatic Cancers.
  1. Dev Cell. 2021 Oct 04. pii: S1534-5807(21)00727-9. [Epub ahead of print]
    An Oatp transporter-mediated steroid sink promotes tumor-induced cachexia in Drosophila.
    Paula Santabárbara-Ruiz, Pierre Léopold.
      Cancer cachexia is associated with many types of tumors and is characterized by a combination of anorexia, loss of body weight, catabolic alterations, and systemic inflammation. We developed a tumor model in Drosophila larvae that causies cachexia-like syndrome, and we found that cachectic larvae show reduced levels of the circulating steroid ecdysone (Ec). Artificially importing Ec in the tumor through the use of the EcI/Oatp74D importer aggravated cachexia, whereas feeding animals with Ec rescued cachectic defects. This suggests that a steroid sink induced by the tumor promotes catabolic alterations in healthy tissues. We found that Oatp33Eb, a member of the Oatp transporter family, is specifically induced in tumors promoting cachexia. The overexpression of Oatp33Eb in noncachectic tumors induced cachexia, whereas its inhibition in cachectic tumors restored circulating Ec and reversed cachectic alterations. Oatp transporters are induced in several types of hormone-dependent tumors, and this result suggests that a similar sink effect could modify hormonal balance in cachectic cancer patients.
    Keywords:  Drosophila; Oatp33Eb; SLCO transporters; cachexia; cancer; ecdysone; steroid hormones; tissue wasting; tumor
    DOI:  https://doi.org/10.1016/j.devcel.2021.09.009
  2. Cell Mol Gastroenterol Hepatol. 2021 Oct 02. pii: S2352-345X(21)00207-1. [Epub ahead of print]
    Rab9 mediates pancreatic autophagy switch from canonical to noncanonical, aggravating experimental pancreatitis.
    Olga A Mareninova, Dustin L Dillon, Carli J M Wightman, Iskandar Yakubov, Toshimasa Takahashi, Herbert Y Gaisano, Keith Munson, Masaki Ohmuraya, David Dawson, Ilya Gukovsky, Anna S Gukovskaya.
      BACKGROUND: Autophagosome, the central organelle in autophagy process, can assemble via canonical pathway mediated by LC3-II, the lipidated form of autophagy-related protein LC3/ATG8, or noncanonical pathway mediated by the small GTPase Rab9. Canonical autophagy is essential for exocrine pancreas homeostasis, and its disordering initiates and drives pancreatitis. The involvement of noncanonical autophagy has not been explored. We examine the role of Rab9 in pancreatic autophagy and pancreatitis severity.METHODS: We measured the effect of Rab9 on parameters of autophagy and pancreatitis responses using transgenic mice overexpressing Rab9 (Rab9TG) and adenoviral transduction of acinar cells. Effect of canonical autophagy on Rab9 was assessed in ATG5-deficient acinar cells.
    RESULTS: Pancreatic levels of Rab9 and its membrane-bound (active) form decreased in rodent pancreatitis models and in human disease. Rab9 overexpression stimulated noncanonical and inhibited canonical/LC3-mediated autophagosome formation in acinar cells through upregulation of ATG4B, the cysteine protease that delipidates LC3-II. Conversely, ATG5 deficiency caused Rab9 increase in acinar cells. Inhibition of canonical autophagy in Rab9TG pancreas was associated with accumulation of Rab9-positive vacuoles containing markers of mitochondria, protein aggregates and trans-Golgi. The shift to the noncanonical pathway caused pancreatitis-like damage in acinar cells and aggravated experimental pancreatitis.
    CONCLUSIONS: The results show that Rab9 regulates pancreatic autophagy and indicate a mutually antagonistic relationship between the canonical/LC3-mediated and noncanonical/Rab9-mediated autophagy pathways in pancreatitis. Noncanonical autophagy fails to substitute for its canonical counterpart in protecting against pancreatitis. Thus, Rab9 decrease in experimental and human pancreatitis is a protective response to sustain canonical autophagy and alleviate disease severity.
    Keywords:  Rab GTPase; RabGDI; alternative autophagy; autophagosome
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.09.017
  3. J Biol Chem. 2021 Oct 05. pii: S0021-9258(21)01082-6. [Epub ahead of print] 101279
    Labeling and Measuring Stressed Mitochondria Using a PINK1-Based Ratiometric Fluorescent Sensor.
    Rie Uesugi, Shunsuke Ishii, Akira Matsuura, Eisuke Itakura.
      Mitochondria are essential organelles that carry out a number of pivotal metabolic processes and maintain cellular homeostasis. Mitochondrial dysfunction caused by various stresses is associated with many diseases such as type 2 diabetes, obesity, cancer, heart failure, neurodegenerative disorders, and aging. Therefore, it is important to understand the stimuli that induce mitochondrial stress. However, broad analysis of mitochondrial stress has not been carried out to date. Here, we present a set of fluorescent tools, called mito-Pain (mitochondrial PINK1 accumulation index), which enables the labeling of stressed mitochondria. Mito-Pain utilizes PINK1 stabilization on mitochondria and quantifies mitochondrial stress levels by comparison with PINK1-GFP, which is stabilized under mitochondrial stress, and RFP-Omp25, which is constitutively localized on mitochondria. To identify compounds that induce mitochondrial stress, we screened a library of 3374 compounds using mito-Pain and identified 57 compounds as mitochondrial stress inducers. Furthermore, we classified each compound into several categories based on mitochondrial response: depolarization, mitochondrial morphology, or Parkin recruitment. Parkin recruitment to mitochondria was often associated with mitochondrial depolarization and aggregation, suggesting that Parkin is recruited to heavily damaged mitochondria. In addition, many of the compounds led to various mitochondrial morphological changes, including fragmentation, aggregation, elongation, and swelling, with or without Parkin recruitment or mitochondrial depolarization. We also found that several compounds induced an ectopic response of Parkin, leading to the formation of cytosolic puncta dependent on PINK1. Thus, mito-Pain enables the detection of stressed mitochondria under a wide variety of conditions and provide insights into mitochondrial quality control systems.
    Keywords:  PTEN‐induced putative kinase 1 (PINK1); Parkin; mitochondria; mitochondrial membrane potential; mitochondrial sensor; mitochondrial stress
    DOI:  https://doi.org/10.1016/j.jbc.2021.101279
  4. Mol Cancer. 2021 Oct 04. 20(1): 128
    Oncogenic KRAS blockade therapy: renewed enthusiasm and persistent challenges.
    Daolin Tang, Guido Kroemer, Rui Kang.
      Across a broad range of human cancers, gain-of-function mutations in RAS genes (HRAS, NRAS, and KRAS) lead to constitutive activity of oncoproteins responsible for tumorigenesis and cancer progression. The targeting of RAS with drugs is challenging because RAS lacks classic and tractable drug binding sites. Over the past 30 years, this perception has led to the pursuit of indirect routes for targeting RAS expression, processing, upstream regulators, or downstream effectors. After the discovery that the KRAS-G12C variant contains a druggable pocket below the switch-II loop region, it has become possible to design irreversible covalent inhibitors for the variant with improved potency, selectivity and bioavailability. Two such inhibitors, sotorasib (AMG 510) and adagrasib (MRTX849), were recently evaluated in phase I-III trials for the treatment of non-small cell lung cancer with KRAS-G12C mutations, heralding a new era of precision oncology. In this review, we outline the mutations and functions of KRAS in human tumors and then analyze indirect and direct approaches to shut down the oncogenic KRAS network. Specifically, we discuss the mechanistic principles, clinical features, and strategies for overcoming primary or secondary resistance to KRAS-G12C blockade.
    Keywords:  Covalent inhibitor; Drug resistance; Gene mutation; KRAS; Targeted therapy
    DOI:  https://doi.org/10.1186/s12943-021-01422-7
  5. Nat Rev Immunol. 2021 Oct 04.
    The interplay of immunology and cachexia in infection and cancer.
    Hatoon Baazim, Laura Antonio-Herrera, Andreas Bergthaler.
      Diverse inflammatory diseases, infections and malignancies are associated with wasting syndromes. In many of these conditions, the standards for diagnosis and treatment are lacking due to our limited understanding of the causative molecular mechanisms. Here, we discuss the complex immunological context of cachexia, a systemic catabolic syndrome that depletes both fat and muscle mass with profound consequences for patient prognosis. We highlight the main cytokine and immune cell-driven pathways that have been linked to weight loss and tissue wasting in the context of cancer-associated and infection-associated cachexia. Moreover, we discuss the potential immunometabolic consequences of cachexia on the basis of newly identified pathways and explore the multilayered area of immunometabolic crosstalk both upstream and downstream of tissue catabolism. Collectively, this Review highlights the intricate relationship of the immune system with cachexia in the context of malignant and infectious diseases.
    DOI:  https://doi.org/10.1038/s41577-021-00624-w
  6. Mol Cancer Ther. 2021 Oct 08. pii: molcanther.0368.2021. [Epub ahead of print]
    IgE-based therapeutic combination enhances anti-tumor response in preclinical models of pancreatic cancer.
    Spas Dimitrov Markov, Thomas C Caffrey, Kelly A O' Connell, James A Grunkemeyer, Simon Shin, Ryan Hanson, Prathamesh P Patil, Surendra K Shukla, Daisy Gonzalez, Ayrianne J Crawford, Krysten E Vance, Ying Huang, Kirsten C Eberle, Prakash Radhakrishnan, Paul M Grandgenett, Pankaj K Singh, Ragupathy Madiyalakan, Tracy R Daniels-Wells, Manuel L Penichet, Christopher F Nicodemus, Jill A Poole, Elizabeth M Jaffee, Michael A Hollingsworth, Kamiya Mehla.
      Pancreatic ductal adenocarcinoma (PDAC) represents 3% of all cancer cases and 7% of all cancer deaths in the United States. Late diagnosis and inadequate response to standard chemotherapies contribute to an unfavorable prognosis and an overall 5-year survival rate of less than 10% in PDAC. Despite recent advances in tumor immunology, tumor-induced immunosuppression attenuates the immunotherapy response in PDAC. To date, studies have focused on IgG-based therapeutic strategies in PDAC. With the recent interest in IgE-based therapies in multiple solid tumors, we explored the MUC1-targeted IgE antibody's potential against pancreatic cancer. Our study demonstrates the notable expression of FcεRI (receptor for IgE antibody) in PDAC patients. Our study showed that administration with a limited amount of MUC1 targeted-IgE (mouse/human chimeric anti-MUC1.IgE) antibody at intermittent levels in combination with checkpoint inhibitor (anti-PD-L1) and TLR3 agonist (PolyICLC) induces a robust anti-tumor response that is dependent on NK and CD8 T cells in pancreatic tumor-bearing mice. Subsequently, our study showed that IgE antibody's antigen specificity plays a vital role in executing the anti-tumor response as non-specific IgE, induced by ovalbumin (OVA), failed to restrict tumor growth in pancreatic tumor-bearing mice. Utilizing the OVA-induced allergic asthma-PDAC model, we demonstrate that allergic phenotype induced by OVA cannot restrain pancreatic tumor growth in orthotopic tumor-bearing mice. Together, our data demonstrate the novel tumor protective benefits of tumor antigen-specific IgE-based therapeutics in a preclinical model of pancreatic cancer, which can open new avenues for future clinical interventions.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-21-0368
  7. J Cell Biol. 2021 Dec 06. pii: e202006049. [Epub ahead of print]220(12):
    PINK1 drives production of mtDNA-containing extracellular vesicles to promote invasiveness.
    Nicolas Rabas, Sarah Palmer, Louise Mitchell, Shehab Ismail, Andrea Gohlke, Joel S Riley, Stephen W G Tait, Payam Gammage, Leandro Lemgruber Soares, Iain R Macpherson, Jim C Norman.
      The cystine-glutamate antiporter, xCT, supports a glutathione synthesis program enabling cancer cells to cope with metabolically stressful microenvironments. Up-regulated xCT, in combination with glutaminolysis, leads to increased extracellular glutamate, which promotes invasive behavior by activating metabotropic glutamate receptor 3 (mGluR3). Here we show that activation of mGluR3 in breast cancer cells activates Rab27-dependent release of extracellular vesicles (EVs), which can transfer invasive characteristics to "recipient" tumor cells. These EVs contain mitochondrial DNA (mtDNA), which is packaged via a PINK1-dependent mechanism. We highlight mtDNA as a key EV cargo necessary and sufficient for intercellular transfer of invasive behavior by activating Toll-like receptor 9 in recipient cells, and this involves increased endosomal trafficking of pro-invasive receptors. We propose that an EV-mediated mechanism, through which altered cellular metabolism in one cell influences endosomal trafficking in other cells, is key to generation and dissemination of pro-invasive microenvironments during mammary carcinoma progression.
    DOI:  https://doi.org/10.1083/jcb.202006049
  8. Proc Natl Acad Sci U S A. 2021 Oct 12. pii: e2107771118. [Epub ahead of print]118(41):
    Eicosanoid regulation of debris-stimulated metastasis.
    Jianjun Deng, Haixia Yang, Victoria M Haak, Jun Yang, Franciele C Kipper, Chantal Barksdale, Sung Hee Hwang, Allison Gartung, Diane R Bielenberg, Selvakumar Subbian, Koc-Kan Ho, Xiang Ye, Daidi Fan, Yongkui Sun, Bruce D Hammock, Dipak Panigrahy.
      Cancer therapy reduces tumor burden via tumor cell death ("debris"), which can accelerate tumor progression via the failure of inflammation resolution. Thus, there is an urgent need to develop treatment modalities that stimulate the clearance or resolution of inflammation-associated debris. Here, we demonstrate that chemotherapy-generated debris stimulates metastasis by up-regulating soluble epoxide hydrolase (sEH) and the prostaglandin E2 receptor 4 (EP4). Therapy-induced tumor cell debris triggers a storm of proinflammatory and proangiogenic eicosanoid-driven cytokines. Thus, targeting a single eicosanoid or cytokine is unlikely to prevent chemotherapy-induced metastasis. Pharmacological abrogation of both sEH and EP4 eicosanoid pathways prevents hepato-pancreatic tumor growth and liver metastasis by promoting macrophage phagocytosis of debris and counterregulating a protumorigenic eicosanoid and cytokine storm. Therefore, stimulating the clearance of tumor cell debris via combined sEH and EP4 inhibition is an approach to prevent debris-stimulated metastasis and tumor growth.
    Keywords:  autacoid; debris; inflammation resolution; prostaglandin E2 receptor 4; soluble epoxide hydrolase
    DOI:  https://doi.org/10.1073/pnas.2107771118
  9. Nat Rev Mol Cell Biol. 2021 Oct 07.
    The assembly, regulation and function of the mitochondrial respiratory chain.
    Irene Vercellino, Leonid A Sazanov.
      The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases.
    DOI:  https://doi.org/10.1038/s41580-021-00415-0
  10. Nat Commun. 2021 Oct 04. 12(1): 5760
    Determinants of renal cell carcinoma invasion and metastatic competence.
    Kangsan Kim, Qinbo Zhou, Alana Christie, Christina Stevens, Yuanqing Ma, Oreoluwa Onabolu, Suneetha Chintalapati, Tiffani Mckenzie, Vanina Toffessi Tcheuyap, Layton Woolford, He Zhang, Nirmish Singla, Pravat Kumar Parida, Mauricio Marquez-Palencia, Ivan Pedrosa, Vitaly Margulis, Arthur Sagalowsky, Zhiqun Xie, Tao Wang, Steffen Durinck, Zora Modrusan, Somasekar Seshagiri, Payal Kapur, James Brugarolas, Srinivas Malladi.
      Metastasis is the principal cause of cancer related deaths. Tumor invasion is essential for metastatic spread. However, determinants of invasion are poorly understood. We addressed this knowledge gap by leveraging a unique attribute of kidney cancer. Renal tumors invade into large vessels forming tumor thrombi (TT) that migrate extending sometimes into the heart. Over a decade, we prospectively enrolled 83 ethnically-diverse patients undergoing surgical resection for grossly invasive tumors at UT Southwestern Kidney Cancer Program. In this study, we perform comprehensive histological analyses, integrate multi-region genomic studies, generate in vivo models, and execute functional studies to define tumor invasion and metastatic competence. We find that invasion is not always associated with the most aggressive clone. Driven by immediate early genes, invasion appears to be an opportunistic trait attained by subclones with diverse oncogenomic status in geospatial proximity to vasculature. We show that not all invasive tumors metastasize and identify determinants of metastatic competency. TT associated with metastases are characterized by higher grade, mTOR activation and a particular immune contexture. Moreover, TT grade is a better predictor of metastasis than overall tumor grade, which may have implications for clinical practice.
    DOI:  https://doi.org/10.1038/s41467-021-25918-4
  11. Ann N Y Acad Sci. 2021 Oct 03.
    Single cell biology-a Keystone Symposia report.
    Jennifer Cable, Michael B Elowitz, Ana I Domingos, Naomi Habib, Shalev Itzkovitz, Homaira Hamidzada, Michael S Balzer, Itai Yanai, Prisca Liberali, Jessica Whited, Aaron Streets, Long Cai, Andrew B Stergachis, Clarice Kit Yee Hong, Leeat Keren, Martin Guilliams, Uri Alon, Alex K Shalek, Regan Hamel, Sarah J Pfau, Arjun Raj, Stephen R Quake, Nancy R Zhang, Jean Fan, Cole Trapnell, Bo Wang, Noah F Greenwald, Roser Vento-Tormo, Silvia D M Santos, Sabrina L Spencer, Hernan G Garcia, Geethika Arekatla, Federico Gaiti, Rinat Arbel-Goren, Steffen Rulands, Jan Philipp Junker, Allon M Klein, Samantha A Morris, John I Murray, Kate E Galloway, Michael Ratz, Merrit Romeike.
      Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
    Keywords:  development; differentiation; lineage tracing; reprogramming; single cell sequencing; spatial transcriptomics
    DOI:  https://doi.org/10.1111/nyas.14692
  12. Proc Natl Acad Sci U S A. 2021 Oct 12. pii: e2113174118. [Epub ahead of print]118(41):
    Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis.
    Bhavyashree Suresh, Anand Saminathan, Kasturi Chakraborty, Matthew Zajac, Chang Cui, Lev Becker, Yamuna Krishnan.
      Lysosomes adopt dynamic, tubular states that regulate antigen presentation, phagosome resolution, and autophagy. Tubular lysosomes are studied either by inducing autophagy or by activating immune cells, both of which lead to cell states where lysosomal gene expression differs from the resting state. Therefore, it has been challenging to pinpoint the biochemical properties lysosomes acquire upon tubulation that could drive their functionality. Here we describe a DNA-based assembly that tubulates lysosomes in macrophages without activating them. Proteolytic activity maps at single-lysosome resolution revealed that tubular lysosomes were less degradative and showed proximal to distal luminal pH and Ca2+ gradients. Such gradients had been predicted but never previously observed. We identify a role for tubular lysosomes in promoting phagocytosis and activating MMP9. The ability to tubulate lysosomes without starving or activating immune cells may help reveal new roles for tubular lysosomes.
    Keywords:  DNA nanotechnology; MMP9; lysosomes; macrophages; phagocytosis
    DOI:  https://doi.org/10.1073/pnas.2113174118
  13. Front Cell Dev Biol. 2021 ;9 720096
    Metabolic Biomarkers for the Early Detection of Cancer Cachexia.
    Thomas M O'Connell, Lilian Golzarri-Arroyo, Fabrizio Pin, Rafael Barreto, Stephanie L Dickinson, Marion E Couch, Andrea Bonetto.
      Background: Cancer cachexia is a severe metabolic disorder characterized by progressive weight loss along with a dramatic loss in skeletal muscle and adipose tissue. Like cancer, cachexia progresses in stages starting with pre-cachexia to cachexia and finally to refractory cachexia. In the refractory stage, patients are no longer responsive to therapy and management of weight loss is no longer possible. It is therefore critical to detect cachexia as early as possible. In this study we applied a metabolomics approach to search for early biomarkers of cachexia. Methods: Multi-platform metabolomics analyses were applied to the murine Colon-26 (C26) model of cachexia. Tumor bearing mice (n = 5) were sacrificed every other day over the 14-day time course and control mice (n = 5) were sacrificed every fourth day starting at day 2. Linear regression modeling of the data yielded metabolic trajectories that were compared with the trajectories of body weight and skeletal muscle loss to look for early biomarkers of cachexia. Results: Weight loss in the tumor-bearing mice became significant at day 9 as did the loss of tibialis muscle. The loss of muscle in the gastrocnemius and quadriceps was significant at day 7. Reductions in amino acids were among the earliest metabolic biomarkers of cachexia. The earliest change was in methionine at day 4. Significant alterations in acylcarnitines and lipoproteins were also detected several days prior to weight loss. Conclusion: The results of this study demonstrate that metabolic alterations appear well in advance of observable weight loss. The earliest and most significant alterations were found in amino acids and lipoproteins. Validation of these results in other models of cachexia and in clinical studies will pave the way for a clinical diagnostic panel for the early detection of cachexia. Such a panel would provide a tremendous advance in cachectic patient management and in the design of clinical trials for new therapeutic interventions.
    Keywords:  biomarkers; cancer cachexia; early detection; metabolomics; muscle wasting; pre-cachexia
    DOI:  https://doi.org/10.3389/fcell.2021.720096
  14. Mol Cell. 2021 Sep 28. pii: S1097-2765(21)00744-9. [Epub ahead of print]
    Liquid-liquid phase separation: Orchestrating cell signaling through time and space.
    Qi Su, Sohum Mehta, Jin Zhang.
      Cell signaling is a complex process. The faithful transduction of information into specific cellular actions depends on the synergistic effects of many regulatory molecules, nurtured by their strict spatiotemporal regulation. Over the years, we have gained copious insights into the subcellular architecture supporting this spatiotemporal control, including the roles of membrane-bound organelles and various signaling nanodomains. Recently, liquid-liquid phase separation (LLPS) has been recognized as another potentially ubiquitous framework for organizing signaling molecules with high specificity and precise spatiotemporal control in cells. Here, we review the pervasive role of LLPS in signal transduction, highlighting several key pathways that intersect with LLPS, including examples in which LLPS is controlled by signaling events. We also examine how LLPS orchestrates signaling by compartmentalizing signaling molecules, amplifying signals non-linearly, and moderating signaling dynamics. We focus on the specific molecules that drive LLPS and highlight the known functional and pathological consequences of LLPS in each pathway.
    Keywords:  Compartmentation; biomolecular condensates; membraneless organelle
    DOI:  https://doi.org/10.1016/j.molcel.2021.09.010
  15. Trends Immunol. 2021 Oct 02. pii: S1471-4906(21)00178-2. [Epub ahead of print]
    Metabolic regulation of the cancer-immunity cycle.
    Luis F Somarribas Patterson, Santosha A Vardhana.
      The cancer-immunity cycle (CIC) comprises a series of events that are required for immune-mediated control of tumor growth. Interruption of one or more steps of the CIC enables tumors to evade immunosurveillance. However, attempts to restore antitumor immunity by reactivating the CIC have had limited success thus far. Recently, numerous studies have implicated metabolic reprogramming of tumor and immune cells within the tumor microenvironment (TME) as key contributors to immune evasion. In this opinion, we propose that alterations in cellular metabolism during tumorigenesis promote both initiation and disruption of the CIC. We also provide a rationale for metabolically targeting the TME, which may assist in improving tumor responsiveness to chimeric antigen receptor (CAR)-transduced T cells or immune checkpoint blockade (ICB) therapies.
    Keywords:  CAR-T cells; PD-1; glycolysis; immunotherapy; lactate; metabolism; tumor immunology
    DOI:  https://doi.org/10.1016/j.it.2021.09.002
  16. Clin Cancer Res. 2021 Oct 06. pii: clincanres.1591.2021. [Epub ahead of print]
    Mucin Expression and Splicing Determine Novel Subtypes and Patient Mortality in Pancreatic Ductal Adenocarcinoma.
    Christopher M Thompson, Andrew Cannon, Sean West, Dario Ghersi, Pranita Atri, Rakesh Bhatia, Lynette Smith, Satyayanarayana Rachagani, Christopher Wichman, Sushil Kumar, Surinder K Batra.
      PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy demonstrating aberrant and progressive expression of mucins. The contribution of individual mucins has been extensively investigated in PDAC; however, comprehensive mucin profiling including splice variants in PDAC tumors has not been reported.EXPERIMENTAL DESIGN: Using publicly available RNA-Seq datasets, we assess the expression of mucin family members and their splice variants (SVs) in PDAC tumor samples for the first time. Mucin SVs that are correlated with PDAC patient survival are validated in a cohort of patient tumor samples. Further, we use computational methods to derive novel pancreatic tumor subtypes using mucin expression signatures and their associated activated pathways.
    RESULTS: Principal component analysis identified four novel mucin-based PDAC subtypes. Pathway analysis implicated specific biological signatures for each subtype, labeled 1) Immune Activated, 2) Progressive, 3) Pancreatitis-Initiated, and 4) Anti-Inflammatory/PanIN-Initiated. Assessing mucin SVs, significantly longer survival is observed with higher expression of four MUC1 and one MUC13 SVs, whereas patients expressing two MUC4 and one MUC16 SVs had shorter survival. Using a whole transcriptome correlation, a 3-gene panel, including ESRP2, PTK6, and MAGEH1, is designated to assess PDAC tumor sample cellularity by PCR. One MUC4 SV (MUC4Δ6) and one MUC13 SV (MUC13WT) are quantified in a separate PDAC patient cohort, and their effects on survival are experimentally validated.
    CONCLUSION: Altogether, we demonstrate the unique expression pattern of mucins, four mucins-based PDAC subtypes, and the contribution of MUC1, MUC4, and MUC16 SVs in PDAC patient survival.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-1591
  17. Cancer Prev Res (Phila). 2021 Oct 08.
    Novel Models of Genetic Education and Testing for Pancreatic Cancer Interception: Preliminary Results from the GENERATE Study.
    C Sloane Furniss, Matthew B Yurgelun, Chinedu Ukaegbu, Pamela E Constantinou, Catherine C Lafferty, Eliana R Talcove-Berko, Alison N Schwartz, Jill E Stopfer, Meghan Underhill-Blazey, Barbara Kenner, Scott H Nelson, Sydney Okumura, Sherman Law, Alicia Y Zhou, Tara B Coffin, Nicolette J Rodriguez, Hajime Uno, Allyson J Ocean, Florencia McAllister, Andrew M Lowy, Scott M Lippman, Alison P Klein, Lisa Madlensky, Gloria M Petersen, Judy E Garber, Michael G Goggins, Anirban Maitra, Sapna Syngal.
      Up to 10% of patients with pancreatic ductal adenocarcinoma (PDAC) carry underlying germline pathogenic variants in cancer susceptibility genes. The GENetic Education Risk Assessment and TEsting (GENERATE) study aimed to evaluate novel methods of genetic education and testing in relatives of patients with PDAC. Eligible individuals had a family history of PDAC and a relative with a germline pathogenic variant in APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, or TP53 genes. Participants were recruited at six academic cancer centers and through social media campaigns and patient advocacy efforts. Enrollment occurred via the study website (https://GENERATEstudy.org) and all participation, including collecting a saliva sample for genetic testing, could be done from home. Participants were randomized to one of two remote methods that delivered genetic education about the risks of inherited PDAC and strategies for surveillance. The primary outcome of the study was uptake of genetic testing. From 5/8/2019 to 5/6/2020, 49 participants were randomized to each of the intervention arms. Overall, 90 of 98 (92%) of randomized participants completed genetic testing. The most frequently detected pathogenic variants included those in BRCA2 (N = 15, 17%), ATM (N = 11, 12%), and CDKN2A (N = 4, 4%). Participation in the study remained steady throughout the onset of the Coronavirus disease (COVID-19) pandemic. Preliminary data from the GENERATE study indicate success of remote alternatives to traditional cascade testing, with genetic testing rates over 90% and a high rate of identification of germline pathogenic variant carriers who would be ideal candidates for PDAC interception approaches. PREVENTION RELEVANCE: Preliminary data from the GENERATE study indicate success of remote alternatives for pancreatic cancer genetic testing and education, with genetic testing uptake rates over 90% and a high rate of identification of germline pathogenic variant carriers who would be ideal candidates for pancreatic cancer interception.
    DOI:  https://doi.org/10.1158/1940-6207.CAPR-20-0642
  18. Nat Genet. 2021 Oct;53(10): 1425-1433
    Polygenic basis and biomedical consequences of telomere length variation.
    Veryan Codd, Qingning Wang, Elias Allara, Crispin Musicha, Stephen Kaptoge, Svetlana Stoma, Tao Jiang, Stephen E Hamby, Peter S Braund, Vasiliki Bountziouka, Charley A Budgeon, Matthew Denniff, Chloe Swinfield, Manolo Papakonstantinou, Shilpi Sheth, Dominika E Nanus, Sophie C Warner, Minxian Wang, Amit V Khera, James Eales, Willem H Ouwehand, John R Thompson, Emanuele Di Angelantonio, Angela M Wood, Adam S Butterworth, John N Danesh, Christopher P Nelson, Nilesh J Samani.
      Telomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.
    DOI:  https://doi.org/10.1038/s41588-021-00944-6
  19. Nature. 2021 Oct 06.
    An open-access volume electron microscopy atlas of whole cells and tissues.
    C Shan Xu, Song Pang, Gleb Shtengel, Andreas Müller, Alex T Ritter, Huxley K Hoffman, Shin-Ya Takemura, Zhiyuan Lu, H Amalia Pasolli, Nirmala Iyer, Jeeyun Chung, Davis Bennett, Aubrey V Weigel, Melanie Freeman, Schuyler B van Engelenburg, Tobias C Walther, Robert V Farese, Jennifer Lippincott-Schwartz, Ira Mellman, Michele Solimena, Harald F Hess.
      Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels1. Owing to advances in the precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle2) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and pose questions.
    DOI:  https://doi.org/10.1038/s41586-021-03992-4
  20. J Clin Invest. 2021 Sep 01. pii: e139933. [Epub ahead of print]131(17):
    Petasin potently inhibits mitochondrial complex I-based metabolism that supports tumor growth and metastasis.
    Kazuki Heishima, Nobuhiko Sugito, Tomoyoshi Soga, Masashi Nishikawa, Yuko Ito, Ryo Honda, Yuki Kuranaga, Hiroki Sakai, Ryo Ito, Takayuki Nakagawa, Hiroshi Ueda, Yukihiro Akao.
      Mitochondrial electron transport chain complex I (ETCC1) is the essential core of cancer metabolism, yet potent ETCC1 inhibitors capable of safely suppressing tumor growth and metastasis in vivo are limited. From a plant extract screening, we identified petasin (PT) as a highly potent ETCC1 inhibitor with a chemical structure distinct from conventional inhibitors. PT had at least 1700 times higher activity than that of metformin or phenformin and induced cytotoxicity against a broad spectrum of tumor types. PT administration also induced prominent growth inhibition in multiple syngeneic and xenograft mouse models in vivo. Despite its higher potency, it showed no apparent toxicity toward nontumor cells and normal organs. Also, treatment with PT attenuated cellular motility and focal adhesion in vitro as well as lung metastasis in vivo. Metabolome and proteome analyses revealed that PT severely depleted the level of aspartate, disrupted tumor-associated metabolism of nucleotide synthesis and glycosylation, and downregulated major oncoproteins associated with proliferation and metastasis. These findings indicate the promising potential of PT as a potent ETCC1 inhibitor to target the metabolic vulnerability of tumor cells.
    Keywords:  Amino acid metabolism; Cancer; Metabolism; Mitochondria; Oncology
    DOI:  https://doi.org/10.1172/JCI139933
  21. Autophagy. 2021 Oct 06. 1-12
    Autophagy deficiency activates rDNA transcription.
    Yinfeng Xu, Yaosen Wu, Lei Wang, Zhuo Ren, Lijiang Song, Hui Zhang, Chuying Qian, Qian Wang, Zhengfu He, Wei Wan.
      Macroautophagy/autophagy, a highly conserved lysosome-dependent degradation pathway, has been intensively studied in regulating cell metabolism by degradation of intracellular components. In this study, we link autophagy to RNA metabolism by uncovering a regulatory role of autophagy in ribosomal RNA (rRNA) synthesis. Autophagy-deficient cells exhibit much higher 47S precursor rRNA level, which is caused by the accumulation of SQSTM1/p62 (sequestosome 1) but not other autophagy receptors. Mechanistically, SQSTM1 accumulation potentiates the activation of MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) signaling and promotes the assembly of RNA polymerase I pre-initiation complex at ribosomal DNA (rDNA) promoters, which leads to an increase of 47S rRNA transcribed from rDNA. Functionally, autophagy deficiency promotes protein synthesis, cell growth and cell proliferation, both of which are dependent on SQSTM1 accumulation. Taken together, our findings suggest that autophagy deficiency is involved in RNA metabolism by activating rDNA transcription and provide novel mechanisms for the reprogramming of cell metabolism in autophagy-related diseases including multiple types of cancers.Abbreviations: 5-FUrd: 5-fluorouridine; AMPK: AMP-activated protein kinase; ATG: autophagy related; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; ChIP: chromatin immunoprecipitation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAPK/ERK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB/NF-κB: nuclear factor kappa B; NFE2L2/NRF2: nuclear factor, erythroid 2 like 2; OPTN: optineurin; PIC: pre-initiation complex; POLR1: RNA polymerase I; POLR1A/RPA194: RNA polymerase I subunit A; POLR2A: RNA polymerase II subunit A; rDNA: ribosomal DNA; RPS6KB1/S6K1: ribosomal protein S6 kinase B1; rRNA: ribosomal RNA; RUBCN/Rubicon: rubicon autophagy regulator; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; SUnSET: surface sensing of translation; TAX1BP1: Tax1 binding protein 1; UBTF/UBF1: upstream binding transcription factor; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild-type.
    Keywords:  Autophagy; MTORC1; SQSTM1/p62; rDNA; rRNA
    DOI:  https://doi.org/10.1080/15548627.2021.1974178
  22. EMBO J. 2021 Oct 06. e107958
    Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex.
    Dimitrios Papagiannidis, Peter W Bircham, Christian Lüchtenborg, Oliver Pajonk, Giulia Ruffini, Britta Brügger, Sebastian Schuck.
      Cells dynamically adapt organelle size to current physiological demand. Organelle growth requires membrane biogenesis and therefore needs to be coordinated with lipid metabolism. The endoplasmic reticulum (ER) can undergo massive expansion, but the underlying regulatory mechanisms are largely unclear. Here, we describe a genetic screen for factors involved in ER membrane expansion in budding yeast and identify the ER transmembrane protein Ice2 as a strong hit. We show that Ice2 promotes ER membrane biogenesis by opposing the phosphatidic acid phosphatase Pah1, called lipin in metazoa. Specifically, Ice2 inhibits the conserved Nem1-Spo7 complex and thus suppresses the dephosphorylation and activation of Pah1. Furthermore, Ice2 cooperates with the transcriptional regulation of lipid synthesis genes and helps to maintain cell homeostasis during ER stress. These findings establish the control of the lipin phosphatase complex as an important mechanism for regulating ER membrane biogenesis.
    Keywords:  Opi1; endoplasmic reticulum; lipid droplets; lipin; organelle biogenesis
    DOI:  https://doi.org/10.15252/embj.2021107958
  23. Nat Commun. 2021 Oct 07. 12(1): 5883
    High-resolution positron emission microscopy of patient-derived tumor organoids.
    Syamantak Khan, June Ho Shin, Valentina Ferri, Ning Cheng, Julia E Noel, Calvin Kuo, John B Sunwoo, Guillem Pratx.
      Tumor organoids offer new opportunities for translational cancer research, but unlike animal models, their broader use is hindered by the lack of clinically relevant imaging endpoints. Here, we present a positron-emission microscopy method for imaging clinical radiotracers in patient-derived tumor organoids with spatial resolution 100-fold better than clinical positron emission tomography (PET). Using this method, we quantify 18F-fluorodeoxyglucose influx to show that patient-derived tumor organoids recapitulate the glycolytic activity of the tumor of origin, and thus, could be used to predict therapeutic response in vitro. Similarly, we measure sodium-iodine symporter activity using 99mTc- pertechnetate and find that the iodine uptake pathway is functionally conserved in organoids derived from thyroid carcinomas. In conclusion, organoids can be imaged using clinical radiotracers, which opens new possibilities for identifying promising drug candidates and radiotracers, personalizing treatment regimens, and incorporating clinical imaging biomarkers in organoid-based co-clinical trials.
    DOI:  https://doi.org/10.1038/s41467-021-26081-6
  24. J Cachexia Sarcopenia Muscle. 2021 Oct 05.
    Feasibility and efficacy of enteral tube feeding on weight stability, lean body mass, and patient-reported outcomes in pancreatic cancer cachexia.
    Gillian Gresham, Veronica R Placencio-Hickok, Marie Lauzon, Tyra Nguyen, Haesoo Kim, Sejal Mehta, Shirley Paski, Stephen J Pandol, Arsen Osipov, Jun Gong, Laith H Jamil, Nicholas Nissen, Simon K Lo, Andrew E Hendifar.
      BACKGROUND: Advanced pancreatic ductal adenocarcinoma (PDAC) is characterized by progressive weight loss and nutritional deterioration. This wasting has been linked to poor survival outcomes, alterations in host defenses, decreased functional ability, and diminished health-related quality of life (HRQOL) in pancreatic cancer patients. There are currently no standardized approaches to the management of pancreatic cancer cachexia. This study explores the feasibility and efficacy of enteral tube feeding of a peptide-based formula to improve weight stability and patient-reported outcomes (PROs) in advanced PDAC patients with cachexia.METHODS: This was a single-institution, single-arm prospective trial conducted between April 2015 and March 2019. Eligible patients were adults (>18 years) diagnosed with advanced or locally advanced PDAC and cachexia, defined as greater than 5% unexplained weight loss within 6 months from screening. The study intervention included three 28 day cycles of a semi-elemental peptide-based formula, administered through a jejunal or gastrojejunal feeding tube. The primary outcome was weight stability at 3 months (Cycle 3), defined as weight change less than 0.1 kg/baseline BMI unit from baseline. Secondary outcomes included changes in lean body mass, appendicular lean mass, bone mineral density, fat mass, and percent body fat, as measured with a DEXA scan, HRQOL (EORTC QLQC30) and NIH PROMIS PROs assessed at each cycle. Daily activity (steps, distance, active minutes, heart rate, and sleep) were remotely monitored using a wearable activity monitor (Fitbit) over the 3 month study period.
    RESULTS: Thirty-six patients were screened for eligibility, 31 patients consented onto study and underwent jejunal tube placement, and 16 patients completed treatment: mean age 67 years (SD 9.3), 43.8% male. Among evaluable patients (n = 16), weight stability was achieved in 10 patients (62.5%), thus completing the trial early. Increases in lean body mass (1273.1, SD: 4078, P = 0.01) and appendicular lean mass (0.45, SD: 0.6, P = 0.02) were observed. Statistically significant improvements at Cycle 3 from baseline were also observed for QLQC30 role function [mean difference (MD): 20.1, P = 0.03], appetite (MD: 27.4, P = 0.02), and global health scores (MD: 13.3, P = 0.05) as well as for NIH PROMIS t-scores for depression (MD: -10.4, P = 0.006) and pain interference (MD: -7.5, P = 0.05). Objectively monitored (Fitbit) activity levels increased, although statistical significance was not reached.
    CONCLUSIONS: Our findings suggest that enteral nutrition support may improve weight stability, lean body mass, appendicular lean mass and PROs in PDAC patients with cachexia who completed treatment, representing a subsample of the study population. The feasibility and role of enteral feeding in routine care remain unclear, and larger and randomized controlled trials are warranted.
    Keywords:  Advanced pancreatic ductal adenocarcinoma; Cancer cachexia; Enteral nutrition; Lean body mass; Patient-reported outcomes; Weight stability
    DOI:  https://doi.org/10.1002/jcsm.12799
  25. Cell Rep. 2021 Oct 05. pii: S2211-1247(21)01259-6. [Epub ahead of print]37(1): 109799
    Collective regulation of chromatin modifications predicts replication timing during cell cycle.
    Capucine Van Rechem, Fei Ji, Damayanti Chakraborty, Joshua C Black, Ruslan I Sadreyev, Johnathan R Whetstine.
      Replication timing (RT) associates with genome architecture, while having a mixed relationship to histone marks. By profiling replication at high resolution and assessing broad histone marks across the cell cycle at the resolution of RT with and without genetic perturbation, we address the causal relationship between histone marks and RT. Four primary chromatin states, including an uncharacterized H3K36me2 state, emerge and define 97% of the mappable genome. RT and local replication patterns (e.g., initiation zones) quantitatively associate with chromatin states, histone mark dynamics, and spatial chromatin structure. Manipulation of broad histone marks and enhancer elements by overexpressing the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT across 11% of the genome. Broad histone modification changes were strong predictors of the observed RT alterations. Lastly, replication within H3K36me2-enriched neighborhoods is sensitive to KDM4A overexpression and is controlled at a megabase scale. These studies establish a role for collective chromatin mark regulation in modulating RT.
    Keywords:  ChIP-seq; H3K27me3; H3K36me2; KDM4A; Repli-seq; chromatin states; enhancers; heterochromatin; lysine demethylase; replication timing
    DOI:  https://doi.org/10.1016/j.celrep.2021.109799
  26. Nat Methods. 2021 Oct;18(10): 1223-1232
    SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment.
    Zhiyuan Yuan, Qiming Zhou, Lesi Cai, Lin Pan, Weiliang Sun, Shiwei Qumu, Si Yu, Jiaxin Feng, Hansen Zhao, Yongchang Zheng, Minglei Shi, Shao Li, Yang Chen, Xinrong Zhang, Michael Q Zhang.
      Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of computational algorithms that can display multiscale and multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We first applied SEAM to a range of wild-type mouse tissues, then delineated a consistent pattern of metabolic zonation in mouse liver. We further studied the spatial metabolic profile in the human fibrotic liver. We discovered subpopulations of hepatocytes with special metabolic features associated with their proximity to the fibrotic niche, and validated this finding by spatial transcriptomics with Geo-seq. These demonstrations highlighted SEAM's ability to explore the spatial metabolic profile and tissue histology at the single-cell level, leading to a deeper understanding of tissue metabolic organization.
    DOI:  https://doi.org/10.1038/s41592-021-01276-3
  27. Nat Methods. 2021 Oct;18(10): 1145
    A multimodal whole-body atlas.
    Rita Strack.
      
    DOI:  https://doi.org/10.1038/s41592-021-01293-2
  28. Elife. 2021 Oct 07. pii: e69958. [Epub ahead of print]10
    Modulation of fracture healing by the transient accumulation of senescent cells.
    Dominik Saul, David G Monroe, Jennifer L Rowsey, Robyn Laura Kosinsky, Stephanie J Vos, Madison L Doolittle, Joshua N Farr, Sundeep Khosla.
      Senescent cells have detrimental effects across tissues with aging but may have beneficial effects on tissue repair, specifically on skin wound healing. However, the potential role of senescent cells in fracture healing has not been defined. Here, we performed an in silico analysis of public mRNAseq data and found that senescence and senescence-associated secretory phenotype (SASP) markers increased during fracture healing. We next directly established that the expression of senescence biomarkers increased markedly during murine fracture healing. We also identified cells in the fracture callus that displayed hallmarks of senescence, including distension of satellite heterochromatin and telomeric DNA damage; the specific identity of these cells, however, requires further characterization. Then, using a genetic mouse model (Cdkn2aLUC) containing a Cdkn2aInk4a-driven luciferase reporter, we demonstrated transient in vivo senescent cell accumulation during callus formation. Finally, we intermittently treated young adult mice following fracture with drugs that selectively eliminate senescent cells ('senolytics', Dasatinib plus Quercetin), and showed that this regimen both decreased senescence and SASP markers in the fracture callus and significantly accelerated the time course of fracture healing. Our findings thus demonstrate that senescent cells accumulate transiently in the murine fracture callus and, in contrast to the skin, their clearance does not impair but rather improves fracture healing.
    Keywords:  medicine; mouse
    DOI:  https://doi.org/10.7554/eLife.69958
  29. Commun Biol. 2021 Oct 08. 4(1): 1176
    Raman microscopy-based quantification of the physical properties of intracellular lipids.
    Masaaki Uematsu, Takao Shimizu.
      The physical properties of lipids, such as viscosity, are homeostatically maintained in cells and are intimately involved in physiological roles. Measurement of the physical properties of plasma membranes has been achieved primarily through chemical or genetically encoded fluorescent probes. However, since most probes target plasma membranes, physical properties of lipids in intracellular organelles, including lipid droplets (LDs) are yet to be analyzed. Here, we present a novel Raman microscopy-based approach for quantifying the physical properties of intracellular lipids under deuterium-labeled fatty acid treatment conditions. Focusing on the fact that Raman spectra of carbon-deuterium vibration are altered depending on the surrounding lipid species, we quantitatively represented the physical properties of lipids as the gauche/trans conformational ratio of the introduced labeled fatty acids, which can be used as an indicator of viscosity. Intracellular Raman imaging revealed that the gauche/trans ratio of cytosolic regions was robustly preserved against perturbations attempting to alter the lipid composition. This was likely due to LDs functioning as a buffer against excess gauche/trans ratio, beyond its traditional role as an energy storage organelle. Our novel approach enables the observation of the physical properties of organelle lipids, which is difficult to perform with conventional probes, and is useful for quantitative assessment of the subcellular lipid environment.
    DOI:  https://doi.org/10.1038/s42003-021-02679-w
  30. Nat Commun. 2021 Oct 08. 12(1): 5909
    ClusterMap for multi-scale clustering analysis of spatial gene expression.
    Yichun He, Xin Tang, Jiahao Huang, Jingyi Ren, Haowen Zhou, Kevin Chen, Albert Liu, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Johain Ounadjela, Emanuelle I Grody, Jian Shu, Jia Liu, Xiao Wang.
      Quantifying RNAs in their spatial context is crucial to understanding gene expression and regulation in complex tissues. In situ transcriptomic methods generate spatially resolved RNA profiles in intact tissues. However, there is a lack of a unified computational framework for integrative analysis of in situ transcriptomic data. Here, we introduce an unsupervised and annotation-free framework, termed ClusterMap, which incorporates the physical location and gene identity of RNAs, formulates the task as a point pattern analysis problem, and identifies biologically meaningful structures by density peak clustering (DPC). Specifically, ClusterMap precisely clusters RNAs into subcellular structures, cell bodies, and tissue regions in both two- and three-dimensional space, and performs consistently on diverse tissue types, including mouse brain, placenta, gut, and human cardiac organoids. We demonstrate ClusterMap to be broadly applicable to various in situ transcriptomic measurements to uncover gene expression patterns, cell niche, and tissue organization principles from images with high-dimensional transcriptomic profiles.
    DOI:  https://doi.org/10.1038/s41467-021-26044-x
  31. iScience. 2021 Oct 22. 24(10): 103099
    Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet.
    Belinda Yau, Sheyda Naghiloo, Alexis Diaz-Vegas, Austin V Carr, Julian Van Gerwen, Elise J Needham, Dillon Jevon, Sing-Young Chen, Kyle L Hoehn, Amanda E Brandon, Laurance Macia, Gregory J Cooney, Michael R Shortreed, Lloyd M Smith, Mark P Keller, Peter Thorn, Mark Larance, David E James, Sean J Humphrey, Melkam A Kebede.
      Pancreatic islets are essential for maintaining physiological blood glucose levels, and declining islet function is a hallmark of type 2 diabetes. We employ mass spectrometry-based proteomics to systematically analyze islets from 9 genetic or diet-induced mouse models representing a broad cross-section of metabolic health. Quantifying the islet proteome to a depth of >11,500 proteins, this study represents the most detailed analysis of mouse islet proteins to date. Our data highlight that the majority of islet proteins are expressed in all strains and diets, but more than half of the proteins vary in expression levels, principally due to genetics. Associating these varied protein expression levels on an individual animal basis with individual phenotypic measures reveals islet mitochondrial function as a major positive indicator of metabolic health regardless of strain. This compendium of strain-specific and dietary changes to mouse islet proteomes represents a comprehensive resource for basic and translational islet cell biology.
    Keywords:  animal physiology; diabetology; proteomics
    DOI:  https://doi.org/10.1016/j.isci.2021.103099
  32. Cancer Res. 2021 Oct 08. pii: canres.1159.2021. [Epub ahead of print]
    Novel oncogenic transcription factor cooperation in RB-deficient cancer.
    Amy C Mandigo, Ayesha A Shafi, Jennifer J McCann, Wei Yuan, Talya S Laufer, Denisa Bogdan, Lewis Gallagher, Emanuela Dylgjeri, Galina Semenova, Irina A Vasilevskaya, Matthew J Schiewer, Christopher McNair, Johann S de Bono, Karen E Knudsen.
      The retinoblastoma tumor suppressor (RB) is a critical regulator of E2F-dependent transcription, controlling a multitude of pro-tumorigenic networks including but not limited to cell cycle control. Here, genome-wide assessment of E2F1 function after RB loss in isogenic models of prostate cancer revealed unexpected repositioning and cooperation with oncogenic transcription factors, including the major driver of disease progression, the androgen receptor (AR). Further investigation revealed that observed AR/E2F1 cooperation elicited novel transcriptional networks that promote cancer phenotypes, especially as related to evasion of cell death. These observations were reflected in assessment of human disease, indicating the clinical relevance of the AR/E2F1 cooperome in prostate cancer. Together, these studies reveal new mechanisms by which RB loss induces cancer progression and highlight the importance of understanding the targets of E2F1 function.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1159
  33. J Cachexia Sarcopenia Muscle. 2021 Oct 05.
    A randomized, feasibility trial of an exercise and nutrition-based rehabilitation programme (ENeRgy) in people with cancer.
    Charlie C Hall, Richard J E Skipworth, Honor Blackwood, Duncan Brown, Jane Cook, Katharina Diernberger, Elizabeth Dixon, Valerie Gibson, Catriona Graham, Peter Hall, Erna Haraldsdottir, Jane Hopkinson, Anna Lloyd, Matthew Maddocks, Lucy Norris, Sharon Tuck, Marie T Fallon, Barry J A Laird.
      BACKGROUND: Despite rehabilitation being increasingly advocated for people living with incurable cancer, there is limited evidence supporting efficacy or component parts. The progressive decline in function and nutritional in this population would support an approach that targets these factors. This trial aimed to assess the feasibility of an exercise and nutrition based rehabilitation programme in people with incurable cancer.METHODS: We randomized community dwelling adults with incurable cancer to either a personalized exercise and nutrition based programme (experimental arm) or standard care (control arm) for 8 weeks. Endpoints included feasibility, quality of life, physical activity (step count), and body weight. Qualitative and health economic analyses were also included.
    RESULTS: Forty-five patients were recruited (23 experimental arm, 22 control arm). There were 26 men (58%), and the median age was 78 years (IQR 69-84). At baseline, the median BMI was 26 kg/m2 (IQR: 22-29), and median weight loss in the previous 6 months was 5% (IQR: -12% to 0%). Adherence to the experimental arm was >80% in 16/21 (76%) patients. There was no statistically significant difference in the following between trial arms: step count - median % change from baseline to endpoint, per trial arm (experimental -18.5% [IQR: -61 to 65], control 5% [IQR: -32 to 50], P = 0.548); weight - median % change from baseline to endpoint, per trial arm (experimental 1%[IQR: -3 to 3], control -0.5% [IQR: -3 to 1], P = 0.184); overall quality of life - median % change from baseline to endpoint, per trial arm (experimental 0% [IQR: -20 to 19], control 0% [IQR: -23 to 33], P = 0.846). Qualitative findings observed themes of capability, opportunity, and motivation amongst patients in the experimental arm. The mean incremental cost of the experimental arm versus control was £-319.51 [CI -7593.53 to 6581.91], suggesting the experimental arm was less costly.
    CONCLUSIONS: An exercise and nutritional rehabilitation intervention is feasible and has potential benefits for people with incurable cancer. A larger trial is now warranted to test the efficacy of this approach.
    Keywords:  Cancer; Exercise; Nutrition; Rehabilitation
    DOI:  https://doi.org/10.1002/jcsm.12806
  34. Nat Med. 2021 Oct 04.
    Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce.
    Qian Li, Carolina E Hagberg, Helena Silva Cascales, Shuai Lang, Mervi T Hyvönen, Firoozeh Salehzadeh, Ping Chen, Ida Alexandersson, Eleni Terezaki, Matthew J Harms, Maria Kutschke, Nahida Arifen, Niels Krämer, Myriam Aouadi, Carole Knibbe, Jeremie Boucher, Anders Thorell, Kirsty L Spalding.
      Obesity is considered an important factor for many chronic diseases, including diabetes, cardiovascular disease and cancer. The expansion of adipose tissue in obesity is due to an increase in both adipocyte progenitor differentiation and mature adipocyte cell size. Adipocytes, however, are thought to be unable to divide or enter the cell cycle. We demonstrate that mature human adipocytes unexpectedly display a gene and protein signature indicative of an active cell cycle program. Adipocyte cell cycle progression associates with obesity and hyperinsulinemia, with a concomitant increase in cell size, nuclear size and nuclear DNA content. Chronic hyperinsulinemia in vitro or in humans, however, is associated with subsequent cell cycle exit, leading to a premature senescent transcriptomic and secretory profile in adipocytes. Premature senescence is rapidly becoming recognized as an important mediator of stress-induced tissue dysfunction. By demonstrating that adipocytes can activate a cell cycle program, we define a mechanism whereby mature human adipocytes senesce. We further show that by targeting the adipocyte cell cycle program using metformin, it is possible to influence adipocyte senescence and obesity-associated adipose tissue inflammation.
    DOI:  https://doi.org/10.1038/s41591-021-01501-8
  35. Elife. 2021 10 05. pii: e68806. [Epub ahead of print]10
    Visualizing formation of the active site in the mitochondrial ribosome.
    Viswanathan Chandrasekaran, Nirupa Desai, Nicholas O Burton, Hanting Yang, Jon Price, Eric A Miska, V Ramakrishnan.
      Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their Caenorhabditis elegans orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis.
    Keywords:  C. elegans; RNA modifications; biochemistry; chemical biology; cryo-EM; human; mitochondrial ribosome; molecular biophysics; peptidyl transferase center; structural biology
    DOI:  https://doi.org/10.7554/eLife.68806
  36. Clin Cancer Res. 2021 Oct 06. pii: clincanres.0845.2021. [Epub ahead of print]
    A Phase I, Open-Label, Dose-Escalation Study of the OX40 Agonist Ivuxolimab in Patients With Locally Advanced or Metastatic Cancers.
    Adi Diab, Omid Hamid, John A Thompson, Willeke Ros, Ferry A L M Eskens, Toshihiko Doi, Siwen Hu-Lieskovan, Samuel J Klempner, Bishu Ganguly, Catherine Fleener, Xiao Wang, Tenshang Jo, Ken Liao, Shahram Salek-Ardakani, Carrie Turich Taylor, Jeffrey Chou, Anthony B El-Khoueiry.
      PURPOSE: Stimulation of effector T cells is an appealing immunotherapeutic approach in oncology. OX40 (CD134) is a co-stimulatory receptor expressed on activated CD4+ and CD8+ T cells. Induction of OX40 following antigen recognition results in enhanced T-cell activation, proliferation, and survival, and OX40 targeting shows therapeutic efficacy in preclinical studies. We report the monotherapy dose-escalation portion of a multicenter, phase I trial (NCT02315066) of ivuxolimab (PF-04518600), a fully human immunoglobulin G2 agonistic monoclonal antibody specific for human OX40.EXPERIMENTAL DESIGN: Adult patients (N = 52) with selected locally advanced or metastatic cancers received ivuxolimab 0.01-10 mg/kg. Primary endpoints were safety and tolerability. Secondary/exploratory endpoints included preliminary assessment of antitumor activity, and biomarker analyses.
    RESULTS: The most common all-causality adverse events were fatigue (46.2%), nausea (28.8%), and decreased appetite (25.0%). Of 31 treatment-related adverse events, 30 (96.8%) were grade {less than or equal to}2. No dose-limiting toxicities occurred. Ivuxolimab exposure increased in a dose-proportionate manner from 0.3 to 10 mg/kg. Full peripheral blood target engagement occurred at {greater than or equal to}0.3 mg/kg. Three (5.8%) patients achieved a partial response, and disease control was achieved in 56% of patients. Increased CD4+ central memory T-cell proliferation and activation, and clonal expansion of CD4+ and CD8+ T cells in peripheral blood were observed at 0.1 to 3.0 mg/kg. Increased immune cell infiltrate and OX40 expression were evident in on-treatment tumor biopsies.
    CONCLUSIONS: Ivuxolimab was generally well tolerated with on-target immune activation at clinically relevant doses, showed preliminary anti-tumor activity, and may serve as a partner for combination studies.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-0845
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