bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–06–06
sixty-one papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Identification of prognostic lipid droplet-associated genes in pancreatic cancer patients via bioinformatics analysis.
  2. Mitochondrial Targeting Involving Cholesterol-Rich Lipid Rafts in the Mechanism of Action of the Antitumor Ether Lipid and Alkylphospholipid Analog Edelfosine.
  3. T cells armed with C-X-C chemokine receptor type 6 enhance adoptive cell therapy for pancreatic tumours.
  4. Does the Microenvironment Hold the Hidden Key for Functional Precision Medicine in Pancreatic Cancer?
  5. Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.
  6. Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.
  7. Targeting Fibrosis: The Bridge That Connects Pancreatitis and Pancreatic Cancer.
  8. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
  9. The pancreatic cancer genome revisited.
  10. Mitochondrial DNA: cellular genotoxic stress sentinel.
  11. CUX1 Enhances Pancreatic Cancer Formation by Synergizing with KRAS and Inducing MEK/ERK-Dependent Proliferation.
  12. KRAS, A Prime Mediator in Pancreatic Lipid Synthesis through Extra Mitochondrial Glutamine and Citrate Metabolism.
  13. Assessment of Mitochondrial Cell Metabolism by Respiratory Chain Electron Flow Assays.
  14. Targeting KRAS in Solid Tumors: Current Challenges and Future Opportunities of Novel KRAS Inhibitors.
  15. Autophagosome biogenesis and human health.
  16. Mitochondrial apoptotic priming is a key determinant of cell fate upon p53 restoration.
  17. Very-low-protein diets lead to reduced food intake and weight loss, linked to inhibition of hypothalamic mTOR signaling, in mice.
  18. LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis.
  19. The Golgi as a "Proton Sink" in Cancer.
  20. Cancer cell metabolic plasticity in migration and metastasis.
  21. Exploring the Complementarity of Pancreatic Ductal Adenocarcinoma Preclinical Models.
  22. Keratin 17 testing in pancreatic cancer needle aspiration biopsies predicts survival.
  23. Tracing oncogene-driven remodelling of the intestinal stem cell niche.
  24. TP53 missense mutations in PDAC are associated with enhanced fibrosis and an immunosuppressive microenvironment.
  25. Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing.
  26. Applications of Circulating Tumor DNA in a Cohort of Phase I Solid Tumor Patients Treated With Immunotherapy.
  27. Assessment of Mitochondrial Ca2+ Uptake.
  28. Mitochondrial Ca2+ Signaling in Health, Disease and Therapy.
  29. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
  30. Impact of Liver and Pancreas Diseases on Nutritional Status.
  31. Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase.
  32. Epithelial-to-Mesenchymal Transition in the Light of Plasticity and Hybrid E/M States.
  33. Drug Discovery Assay to Identify Modulators of the Mitochondrial Ca2+ Uniporter.
  34. Rodent studies of developmental programming and aging mechanisms.
  35. Accurate Measurement of Cellular and Cell-Free Circulating Mitochondrial DNA Content from Human Blood Samples Using Real-Time Quantitative PCR.
  36. Extracellular ATP and Adenosine in Cancer Pathogenesis and Treatment.
  37. Chromothripsis-Explosion in Genetic Science.
  38. Metabolic Response of Pancreatic Carcinoma Cells under Treatment with Dichloroacetate.
  39. Yorkie drives Ras-induced tumor progression by microRNA-mediated inhibition of cellular senescence.
  40. Pancreatic plasticity: Unlocking exocrine lineage specification.
  41. Hypoxic microenvironment induced spatial transcriptome changes in pancreatic cancer.
  42. The CD44/COL17A1 pathway promotes the formation of multilayered, transformed epithelia.
  43. The gate to metastasis: key players in cancer cell intravasation.
  44. Mitochondrial Dysfunction in Mitochondrial Medicine: Current Limitations, Pitfalls, and Tomorrow.
  45. Prevalence of proliferating CD8+ cells in normal lymphatic tissues, inflammation and cancer.
  46. KRAS Mutation Dictates the Cancer Immune Environment in Pancreatic Ductal Adenocarcinoma and Other Adenocarcinomas.
  47. The RAL signaling network: Cancer and beyond.
  48. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients.
  49. Choline kinase alpha 2 acts as a protein kinase to promote lipolysis of lipid droplets.
  50. Model-based analysis uncovers mutations altering autophagy selectivity in human cancer.
  51. Advances in neoadjuvant therapy for resectable pancreatic cancer over the past two decades.
  52. Mirtazapine in cancer-associated anorexia and cachexia: A double-blind placebo-controlled randomized trial.
  53. The bedside-bench-bedside cycle: Robert Lefkowitz and GPCRs.
  54. Human muscle stem cells are refractory to aging.
  55. Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs.
  56. Proteomic Analysis of Malignant Ascites From Patients With Pancreatic Ductal Adenocarcinoma.
  57. Vitamin D: Promises on the Horizon and Challenges Ahead for Fighting Pancreatic Cancer.
  58. Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy.
  59. Selective autophagy as the basis of autophagy-based degraders.
  60. Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma.
  61. Robustness of epithelial sealing is an emerging property of local ERK feedback driven by cell elimination.
  1. Lipids Health Dis. 2021 Jun 02. 20(1): 58
    Identification of prognostic lipid droplet-associated genes in pancreatic cancer patients via bioinformatics analysis.
    Rubing Bai, Artur Rebelo, Jörg Kleeff, Yoshiaki Sunami.
       BACKGROUND: Pancreatic cancer is the fourth leading cause of cancer deaths in the United States both in females and in males, and is projected to become the second deadliest cancer by 2030. The overall 5-year survival rate remains at around 10%. Cancer metabolism and specifically lipid metabolism plays an important role in pancreatic cancer progression and metastasis. Lipid droplets can not only store and transfer lipids, but also act as molecular messengers, and signaling factors. As lipid droplets are implicated in reprogramming tumor cell metabolism and in invasion and migration of pancreatic cancer cells, we aimed to identify lipid droplet-associated genes as prognostic markers in pancreatic cancer.
    METHODS: We performed a literature search on review articles related to lipid droplet-associated proteins. To select relevant lipid droplet-associated factors, bioinformatics analysis on the GEPIA platform (data are publicly available) was carried out for selected genes to identify differential expression in pancreatic cancer versus healthy pancreatic tissues. Differentially expressed genes were further analyzed regarding overall survival of pancreatic cancer patients.
    RESULTS: 65 factors were identified as lipid droplet-associated factors. Bioinformatics analysis of 179 pancreatic cancer samples and 171 normal pancreatic tissue samples on the GEPIA platform identified 39 deferentially expressed genes in pancreatic cancer with 36 up-regulated genes (ACSL3, ACSL4, AGPAT2, BSCL2, CAV1, CAV2, CAVIN1, CES1, CIDEC, DGAT1, DGAT2, FAF2, G0S2, HILPDA, HSD17B11, ICE2, LDAH, LIPE, LPCAT1, LPCAT2, LPIN1, MGLL, NAPA, NCEH1, PCYT1A, PLIN2, PLIN3, RAB5A, RAB7A, RAB8A, RAB18, SNAP23, SQLE, VAPA, VCP, VMP1) and 3 down-regulated genes (FITM1, PLIN4, PLIN5). Among 39 differentially expressed factors, seven up-regulated genes (CAV2, CIDEC, HILPDA, HSD17B11, NCEH1, RAB5A, and SQLE) and two down-regulation genes (BSCL2 and FITM1) were significantly associated with overall survival of pancreatic cancer patients. Multivariate Cox regression analysis identified CAV2 as the only independent prognostic factor.
    CONCLUSIONS: Through bioinformatics analysis, we identified nine prognostic relevant differentially expressed genes highlighting the role of lipid droplet-associated factors in pancreatic cancer.
    Keywords:  Bioinformatics; GEPIA; Lipid droplet-associated genes; Lipid metabolism; Pancreatic cancer
    DOI:  https://doi.org/10.1186/s12944-021-01476-y
  2. Pharmaceutics. 2021 May 20. pii: 763. [Epub ahead of print]13(5):
    Mitochondrial Targeting Involving Cholesterol-Rich Lipid Rafts in the Mechanism of Action of the Antitumor Ether Lipid and Alkylphospholipid Analog Edelfosine.
    Faustino Mollinedo, Consuelo Gajate.
      The ether lipid edelfosine induces apoptosis selectively in tumor cells and is the prototypic molecule of a family of synthetic antitumor compounds collectively known as alkylphospholipid analogs. Cumulative evidence shows that edelfosine interacts with cholesterol-rich lipid rafts, endoplasmic reticulum (ER) and mitochondria. Edelfosine induces apoptosis in a number of hematological cancer cells by recruiting death receptors and downstream apoptotic signaling into lipid rafts, whereas it promotes apoptosis in solid tumor cells through an ER stress response. Edelfosine-induced apoptosis, mediated by lipid rafts and/or ER, requires the involvement of a mitochondrial-dependent step to eventually elicit cell death, leading to the loss of mitochondrial membrane potential, cytochrome c release and the triggering of cell death. The overexpression of Bcl-2 or Bcl-xL blocks edelfosine-induced apoptosis. Edelfosine induces the redistribution of lipid rafts from the plasma membrane to the mitochondria. The pro-apoptotic action of edelfosine on cancer cells is associated with the recruitment of F1FO-ATP synthase into cholesterol-rich lipid rafts. Specific inhibition of the FO sector of the F1FO-ATP synthase, which contains the membrane-embedded c-subunit ring that constitutes the mitochondrial permeability transcription pore, hinders edelfosine-induced cell death. Taking together, the evidence shown here suggests that the ether lipid edelfosine could modulate cell death in cancer cells by direct interaction with mitochondria, and the reorganization of raft-located mitochondrial proteins that critically modulate cell death or survival. Here, we summarize and discuss the involvement of mitochondria in the antitumor action of the ether lipid edelfosine, pointing out the mitochondrial targeting of this drug as a major therapeutic approach, which can be extrapolated to other alkylphospholipid analogs. We also discuss the involvement of cholesterol transport and cholesterol-rich lipid rafts in the interactions between the organelles as well as in the role of mitochondria in the regulation of apoptosis in cancer cells and cancer therapy.
    Keywords:  alkylphospholipid analog; cholesterol; edelfosine; lipid raft; mitochondria; mitochondrial permeability transition pore
    DOI:  https://doi.org/10.3390/pharmaceutics13050763
  3. Nat Biomed Eng. 2021 Jun 03.
    T cells armed with C-X-C chemokine receptor type 6 enhance adoptive cell therapy for pancreatic tumours.
    Stefanie Lesch, Viktoria Blumenberg, Stefan Stoiber, Adrian Gottschlich, Justyna Ogonek, Bruno L Cadilha, Zahra Dantes, Felicitas Rataj, Klara Dorman, Johannes Lutz, Clara H Karches, Constanze Heise, Mathias Kurzay, Benjamin M Larimer, Simon Grassmann, Moritz Rapp, Alessia Nottebrock, Stephan Kruger, Nicholas Tokarew, Philipp Metzger, Christine Hoerth, Mohamed-Reda Benmebarek, Dario Dhoqina, Ruth Grünmeier, Matthias Seifert, Arman Oener, Öykü Umut, Sandy Joaquina, Lene Vimeux, Thi Tran, Thomas Hank, Taisuke Baba, Duc Huynh, Remco T A Megens, Klaus-Peter Janssen, Martin Jastroch, Daniel Lamp, Svenja Ruehland, Mauro Di Pilato, Jasper N Pruessmann, Moritz Thomas, Carsten Marr, Steffen Ormanns, Anna Reischer, Michael Hristov, Eric Tartour, Emmanuel Donnadieu, Simon Rothenfusser, Peter Duewell, Lars M König, Max Schnurr, Marion Subklewe, Andrew S Liss, Niels Halama, Maximilian Reichert, Thorsten R Mempel, Stefan Endres, Sebastian Kobold.
      The efficacy of adoptive cell therapy for solid tumours is hampered by the poor accumulation of the transferred T cells in tumour tissue. Here, we show that forced expression of C-X-C chemokine receptor type 6 (whose ligand is highly expressed by human and murine pancreatic cancer cells and tumour-infiltrating immune cells) in antigen-specific T cells enhanced the recognition and lysis of pancreatic cancer cells and the efficacy of adoptive cell therapy for pancreatic cancer. In mice with subcutaneous pancreatic tumours treated with T cells with either a transgenic T-cell receptor or a murine chimeric antigen receptor targeting the tumour-associated antigen epithelial cell adhesion molecule, and in mice with orthotopic pancreatic tumours or patient-derived xenografts treated with T cells expressing a chimeric antigen receptor targeting mesothelin, the T cells exhibited enhanced intratumoral accumulation, exerted sustained anti-tumoral activity and prolonged animal survival only when co-expressing C-X-C chemokine receptor type 6. Arming tumour-specific T cells with tumour-specific chemokine receptors may represent a promising strategy for the realization of adoptive cell therapy for solid tumours.
    DOI:  https://doi.org/10.1038/s41551-021-00737-6
  4. Cancers (Basel). 2021 May 17. pii: 2427. [Epub ahead of print]13(10):
    Does the Microenvironment Hold the Hidden Key for Functional Precision Medicine in Pancreatic Cancer?
    John Kokkinos, Anya Jensen, George Sharbeen, Joshua A McCarroll, David Goldstein, Koroush S Haghighi, Phoebe A Phillips.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers and no significant improvement in patient survival has been seen in the past three decades. Treatment options are limited and selection of chemotherapy in the clinic is usually based on the performance status of a patient rather than the biology of their disease. In recent years, research has attempted to unlock a personalised treatment strategy by identifying actionable molecular targets in tumour cells or using preclinical models to predict the effectiveness of chemotherapy. However, these approaches rely on the biology of PDAC tumour cells only and ignore the importance of the microenvironment and fibrotic stroma. In this review, we highlight the importance of the microenvironment in driving the chemoresistant nature of PDAC and the need for preclinical models to mimic the complex multi-cellular microenvironment of PDAC in the precision medicine pipeline. We discuss the potential for ex vivo whole-tissue culture models to inform precision medicine and their role in developing novel therapeutic strategies that hit both tumour and stromal compartments in PDAC. Thus, we highlight the critical role of the tumour microenvironment that needs to be addressed before a precision medicine program for PDAC can be implemented.
    Keywords:  microenvironment; pancreatic cancer; pre-clinical models; precision medicine
    DOI:  https://doi.org/10.3390/cancers13102427
  5. Cancer Cell. 2021 May 25. pii: S1535-6108(21)00268-3. [Epub ahead of print]
    Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.
    Toshiro Hara, Rony Chanoch-Myers, Nathan D Mathewson, Chad Myskiw, Lyla Atta, Lillian Bussema, Stephen W Eichhorn, Alissa C Greenwald, Gabriela S Kinker, Christopher Rodman, L Nicolas Gonzalez Castro, Hiroaki Wakimoto, Orit Rozenblatt-Rosen, Xiaowei Zhuang, Jean Fan, Tony Hunter, Inder M Verma, Kai W Wucherpfennig, Aviv Regev, Mario L Suvà, Itay Tirosh.
      The mesenchymal subtype of glioblastoma is thought to be determined by both cancer cell-intrinsic alterations and extrinsic cellular interactions, but remains poorly understood. Here, we dissect glioblastoma-to-microenvironment interactions by single-cell RNA sequencing analysis of human tumors and model systems, combined with functional experiments. We demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived oncostatin M (OSM) that interacts with its receptors (OSMR or LIFR) in complex with GP130 on glioblastoma cells and activates STAT3. We show that MES-like glioblastoma states are also associated with increased expression of a mesenchymal program in macrophages and with increased cytotoxicity of T cells, highlighting extensive alterations of the immune microenvironment with potential therapeutic implications.
    Keywords:  GBM; OSM; glioblastoma; macrophage; mesenchymal; scRNA-seq; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.ccell.2021.05.002
  6. Elife. 2021 Jun 04. pii: e62320. [Epub ahead of print]10
    Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.
    Timurs Maculins, Erik Verschueren, Trent Hinkle, Meena Choi, Patrick Chang, Cecile Chalouni, Shilpa Rao, Youngsu Kwon, Junghyun Lim, Anand Kumar Katakam, Ryan C Kunz, Brian K Erickson, Ting Huang, Tsung-Heng Tsai, Olga Vitek, Mike Reichelt, Yasin Senbabaoglu, Brent Mckenzie, John R Rohde, Ivan Dikic, Donald S Kirkpatrick, Aditya Murthy.
      Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core autophagy gene Atg16l1 increases risk for Crohn's disease in part by enhancing innate immunity through myeloid cells such as macrophages. However, autophagy is also recognized as a mechanism for clearance of certain intracellular pathogens. These divergent observations prompted a re-evaluation of ATG16L1 in innate antimicrobial immunity. In this study, we found that loss of Atg16l1 in myeloid cells enhanced the killing of virulent Shigella flexneri (S.flexneri), a clinically relevant enteric bacterium that resides within the cytosol by escaping from membrane-bound compartments. Quantitative multiplexed proteomics of murine bone marrow-derived macrophages revealed that ATG16L1 deficiency significantly upregulated proteins involved in the glutathione-mediated antioxidant response to compensate for elevated oxidative stress, which simultaneously promoted S.flexneri killing. Consistent with this, myeloid-specific deletion of Atg16l1 in mice accelerated bacterial clearance in vitro and in vivo. Pharmacological induction of oxidative stress through suppression of cysteine import enhanced microbial clearance by macrophages. Conversely, antioxidant treatment of macrophages permitted S.flexneri proliferation. These findings demonstrate that control of oxidative stress by ATG16L1 and autophagy regulates antimicrobial immunity against intracellular pathogens.
    Keywords:  autophagy; cell biology; immunology; inflammation; macrophages; mass spectrometry; mouse; oxidative damage; proteomics; shigella flexneri
    DOI:  https://doi.org/10.7554/eLife.62320
  7. Int J Mol Sci. 2021 May 07. pii: 4970. [Epub ahead of print]22(9):
    Targeting Fibrosis: The Bridge That Connects Pancreatitis and Pancreatic Cancer.
    Can Huang, Juan Iovanna, Patricia Santofimia-Castaño.
      Pancreatic fibrosis is caused by the excessive deposits of extracellular matrix (ECM) and collagen fibers during repeated necrosis to repair damaged pancreatic tissue. Pancreatic fibrosis is frequently present in chronic pancreatitis (CP) and pancreatic cancer (PC). Clinically, pancreatic fibrosis is a pathological feature of pancreatitis and pancreatic cancer. However, many new studies have found that pancreatic fibrosis is involved in the transformation from pancreatitis to pancreatic cancer. Thus, the role of fibrosis in the crosstalk between pancreatitis and pancreatic cancer is critical and still elusive; therefore, it deserves more attention. Here, we review the development of pancreatic fibrosis in inflammation and cancer, and we discuss the therapeutic strategies for alleviating pancreatic fibrosis. We further propose that cellular stress response might be a key driver that links fibrosis to cancer initiation and progression. Therefore, targeting stress proteins, such as nuclear protein 1 (NUPR1), could be an interesting strategy for pancreatic fibrosis and PC treatment.
    Keywords:  NUPR1; pancreatic cancer; pancreatic fibrosis; pancreatitis
    DOI:  https://doi.org/10.3390/ijms22094970
  8. Nat Biotechnol. 2021 Jun 03.
    Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
    Eleni P Mimitou, Caleb A Lareau, Kelvin Y Chen, Andre L Zorzetto-Fernandes, Yuhan Hao, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Z Yeung, Efthymia Papalexi, Pratiksha I Thakore, Tatsuya Kibayashi, James Badger Wing, Mayu Hata, Rahul Satija, Kristopher L Nazor, Shimon Sakaguchi, Leif S Ludwig, Vijay G Sankaran, Aviv Regev, Peter Smibert.
      Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.
    DOI:  https://doi.org/10.1038/s41587-021-00927-2
  9. Nat Rev Gastroenterol Hepatol. 2021 Jun 04.
    The pancreatic cancer genome revisited.
    Akimasa Hayashi, Jungeui Hong, Christine A Iacobuzio-Donahue.
      Pancreatic cancer is a genetic disease, and the recurrent genetic alterations characteristic of pancreatic cancer indicate the cellular processes that are targeted for malignant transformation. In addition to somatic alterations in the most common driver genes (KRAS, CDKN2A, TP53 and SMAD4), large-scale studies have revealed major roles for genetic alterations of the SWI/SNF and COMPASS complexes, copy number alterations in GATA6 and MYC that partially define phenotypes of pancreatic cancer, and the role(s) of polyploidy and chromothripsis as factors contributing to pancreatic cancer biology and progression. Germline variants that increase the risk of pancreatic cancer continue to be discovered along with a greater appreciation of the features of pancreatic cancers with mismatch repair deficiencies and homologous recombination deficiencies that confer sensitivity to therapeutic targeting. Wild-type KRAS pancreatic cancers, some of which are driven by alternative oncogenic events affecting NRG1 or NTRK1 - for which targeted therapies exist - further underscore that pancreatic cancer is formally entering the era of precision medicine. Given the vast developments within this field, here we review the wide-ranging and most current information related to pancreatic cancer genomics with the goal of integrating this information into a unifying description of the life history of pancreatic cancer.
    DOI:  https://doi.org/10.1038/s41575-021-00463-z
  10. Trends Biochem Sci. 2021 Jun 01. pii: S0968-0004(21)00106-7. [Epub ahead of print]
    Mitochondrial DNA: cellular genotoxic stress sentinel.
    Zheng Wu, Alva G Sainz, Gerald S Shadel.
      High copy number, damage prone, and lean on repair mechanisms are unique features of mitochondrial DNA (mtDNA) that are hard to reconcile with its essentiality for oxidative phosphorylation, the primary function ascribed to this maternally inherited component of our genome. We propose that mtDNA is also a genotoxic stress sentinel, as well as a direct second messenger of this type of cellular stress. Here, we discuss existing evidence for this sentinel/effector role through the ability of mtDNA to escape the confines of the mitochondrial matrix and activate nuclear DNA damage/repair responses via interferon-stimulated gene products and other downstream effectors. However, this arrangement may come at a cost, leading to cancer chemoresistance and contributing to inflammation, disease pathology, and aging.
    Keywords:  DNA repair; cGAS-STING; chemoresistance; interferon-stimulated gene (ISG); mtDNA; retrograde signaling
    DOI:  https://doi.org/10.1016/j.tibs.2021.05.004
  11. Cancers (Basel). 2021 May 18. pii: 2462. [Epub ahead of print]13(10):
    CUX1 Enhances Pancreatic Cancer Formation by Synergizing with KRAS and Inducing MEK/ERK-Dependent Proliferation.
    Heidi Griesmann, Sebastian Mühl, Jan Riedel, Katharina Theuerkorn, Bence Sipos, Irene Esposito, Gregory B Vanden Heuvel, Patrick Michl.
      The transcription factor CUX1 has been implicated in either tumor suppression or progression, depending on the cancer entity and the prevalent CUX1 isoform. Previously, we could show that CUX1 acts as an important mediator of tumor cell proliferation and resistance to apoptosis in pancreatic cancer cell lines. However, in vivo evidence for its impact on pancreatic carcinogenesis, isoform-specific effects and downstream signaling cascades are missing. We crossbred two different CUX1 isoform mouse models (p200 CUX1 and p110 CUX1) with KC (KrasLSL-G12D/+; Ptf1aCre/+) mice, a genetic model for pancreatic precursor lesions (PanIN). In the context of oncogenic KRASs, both mice KCCux1p200 and KCCux1p110 led to increased PanIN formation and development of invasive pancreatic ductal adenocarcinomata (PDAC). In KCCux1p110 mice, tumor development was dramatically more accelerated, leading to formation of invasive PDAC within 4 weeks. In vitro and in vivo, we could show that CUX1 enhanced proliferation by activating MEK-ERK signaling via an upstream increase of ADAM17 protein, which in turn led to an activation of EGFR. Additionally, CUX1 further enhanced MEK-ERK activation through upregulation of the serine/threonine kinase MOS, phosphorylating MEK in a KRAS-independent manner. We identified p110 CUX1 as major driver of pancreatic cancer formation in the context of mutant KRAS. These results provide the first in vivo evidence for the importance of CUX1 in the development of pancreatic cancer, and highlight the importance of CUX1-dependent signaling pathways as potential therapeutic targets.
    Keywords:  ADAM17; CUX1; EGFR; KRAS mutation; MEK-ERK; cell proliferation; pancreatic cancer; transgenic mice
    DOI:  https://doi.org/10.3390/cancers13102462
  12. Int J Mol Sci. 2021 May 11. pii: 5070. [Epub ahead of print]22(10):
    KRAS, A Prime Mediator in Pancreatic Lipid Synthesis through Extra Mitochondrial Glutamine and Citrate Metabolism.
    Isaac James Muyinda, Jae-Gwang Park, Eun-Jung Jang, Byong-Chul Yoo.
      Kirsten rat sarcoma viral oncogene homolog (KRAS)-driven pancreatic cancer is very lethal, with a five-year survival rate of <9%, irrespective of therapeutic advances. Different treatment modalities including chemotherapy, radiotherapy, and immunotherapy demonstrated only marginal efficacies because of pancreatic tumor specificities. Surgery at the early stage of the disease remains the only curative option, although only in 20% of patients with early stage disease. Clinical trials targeting the main oncogenic driver, KRAS, have largely been unsuccessful. Recently, global metabolic reprogramming has been identified in patients with pancreatic cancer and oncogenic KRAS mouse models. The newly reprogrammed metabolic pathways and oncometabolites affect the tumorigenic environment. The development of methods modulating metabolic reprogramming in pancreatic cancer cells might constitute a new approach to its therapy. In this review, we describe the major metabolic pathways providing acetyl-CoA and NADPH essential to sustain lipid synthesis and cell proliferation in pancreatic cancer cells.
    Keywords:  glutaminolysis; lipidomics; metabolomics; pancreatic cancer
    DOI:  https://doi.org/10.3390/ijms22105070
  13. Methods Mol Biol. 2021 ;2276 129-141
    Assessment of Mitochondrial Cell Metabolism by Respiratory Chain Electron Flow Assays.
    Flavia Radogna, Déborah Gérard, Mario Dicato, Marc Diederich.
      Cellular energy metabolism is regulated by complex metabolic pathways. Although anaerobic glycolysis was reported as a primary source of energy in cancer leading to a high rate of lactate production, current evidence shows that the main energy source supporting cancer cell metabolism relies on mitochondrial metabolism. Mitochondria are the key organelle maintaining optimal cellular energy levels. MitoPlate™ S-1 provides a highly reproducible bioenergetics tool to analyze the electron flow rate in live cells. Measuring the rates of electron flow into and through the electron transport chain using different NADH and FADH2-producing metabolic substrates enables the assessment of mitochondrial functionality. MitoPlate™ S-1 are 96-well microplates pre-coated with different substrates used as probes to examine the activity of mitochondrial metabolic pathways based on a colorimetric assay. A comparative metabolic analysis between cell lines or primary cells allows to establish a specific metabolic profile and to detect possible alterations of the mitochondrial function of a tumor cell. Moreover, the direct measurements of electron flux triggered by metabolic pathway activation could highlight targets for potential drug candidates.
    Keywords:  Bioinformatics; Cancer metabolism; Electron transport chain; Mitochondrial respiration; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1007/978-1-0716-1266-8_9
  14. Pharmaceutics. 2021 May 04. pii: 653. [Epub ahead of print]13(5):
    Targeting KRAS in Solid Tumors: Current Challenges and Future Opportunities of Novel KRAS Inhibitors.
    Alice Indini, Erika Rijavec, Michele Ghidini, Alessio Cortellini, Francesco Grossi.
      Activating mutations in RAS family proteins are found in ~25% of all human cancers. Different solid tumors are correlated with mutations in certain isoforms of RAS, with Kirsten RAS (KRAS) being the most frequently mutated isoform. Historically, KRAS has been acknowledged as "undruggable", largely because the RAS proteins do not appear to present suitable pockets to which small inhibitory molecules can bind. However, this scenario has changed over the last years with the advent of novel KRAS inhibitors. In this review, we describe the role of KRAS mutation across different solid tumors, providing data on novel KRAS inhibitors currently under development and an updated overview of ongoing research in this field. A literature search was performed to select papers, abstracts, and oral presentation on KRAS inhibitory strategies in KRAS mutated solid tumors. Overall, the most promising therapeutic results have been obtained with molecules targeting KRAS G12C, thus paving the way for a significant therapeutic improvement in non-small cell lung cancer. Unfortunately, KRAS G12C mutation is rather uncommon in other solid tumors, namely pancreatic ductal adenocarcinoma and colorectal cancer. Several combination strategies are currently under evaluation in clinical trials, in order to bypass the resistance mechanisms responsible for the intrinsic resistance of mutated KRAS to the main therapeutic strategies adopted to date. Results suggest that the therapeutic scenario of KRAS has started to change, and further research will bring therapeutic results in this field.
    Keywords:  AMG510; KRAS; LGSOC; NSCLC; colorectal cancer; endometrial cancer; pancreatic cancer; sotorasib
    DOI:  https://doi.org/10.3390/pharmaceutics13050653
  15. Cell Discov. 2020 Jun 02. 6(1): 33
    Autophagosome biogenesis and human health.
    Tsuyoshi Kawabata, Tamotsu Yoshimori.
      Autophagy degrades the cytoplasmic contents engulfed by autophagosomes. Besides providing energy and building blocks during starvation via random degradation, autophagy selectively targets cytotoxic components to prevent a wide range of diseases. This preventive activity of autophagy is supported by many studies using animal models and reports identifying several mutations in autophagy-related genes that are associated with human genetic disorders, which have been published in the past decade. Here, we summarize the molecular mechanisms of autophagosome biogenesis involving the proteins responsible for these genetic disorders, demonstrating a role for autophagy in human health. These findings will help elucidate the underlying mechanisms of autophagy-related diseases and develop future medications.
    DOI:  https://doi.org/10.1038/s41421-020-0166-y
  16. Proc Natl Acad Sci U S A. 2021 Jun 08. pii: e2019740118. [Epub ahead of print]118(23):
    Mitochondrial apoptotic priming is a key determinant of cell fate upon p53 restoration.
    Francisco J Sánchez-Rivera, Jeremy Ryan, Yadira M Soto-Feliciano, Mary Clare Beytagh, Lucius Xuan, David M Feldser, Michael T Hemann, Jesse Zamudio, Nadya Dimitrova, Anthony Letai, Tyler Jacks.
      Reactivation of p53 in established tumors typically results in one of two cell fates, cell cycle arrest or apoptosis, but it remains unclear how this cell fate is determined. We hypothesized that high mitochondrial priming prior to p53 reactivation would lead to apoptosis, while low priming would lead to survival and cell cycle arrest. Using a panel of Kras-driven, p53 restorable cell lines derived from genetically engineered mouse models of lung adenocarcinoma and sarcoma (both of which undergo cell cycle arrest upon p53 restoration), as well as lymphoma (which instead undergo apoptosis), we show that the level of mitochondrial apoptotic priming is a critical determinant of p53 reactivation outcome. Cells with high initial priming (e.g., lymphomas) lacked sufficient reserve antiapoptotic capacity and underwent apoptosis after p53 restoration. Forced BCL-2 or BCL-XL expression reduced priming and resulted in survival and cell cycle arrest. Cells with low initial priming (e.g., lung adenocarcinoma and sarcoma) survived and proceeded to arrest in the cell cycle. When primed by inhibition of their antiapoptotic proteins using genetic (BCL-2 or BCL-XL deletion or BAD overexpression) or pharmacologic (navitoclax) means, apoptosis resulted upon p53 restoration in vitro and in vivo. These data demonstrate that mitochondrial apoptotic priming is a key determining factor of cell fate upon p53 activation. Moreover, it is possible to enforce apoptotic cell fate following p53 activation in less primed cells using p53-independent drugs that increase apoptotic priming, including BH3 mimetic drugs.
    Keywords:  apoptosis; cell cycle arrest; cell fate; p53
    DOI:  https://doi.org/10.1073/pnas.2019740118
  17. Cell Metab. 2021 Jun 01. pii: S1550-4131(21)00182-0. [Epub ahead of print]33(6): 1264-1266
    Very-low-protein diets lead to reduced food intake and weight loss, linked to inhibition of hypothalamic mTOR signaling, in mice.
    Yingga Wu, Baoguo Li, Li Li, Sharon E Mitchell, Cara L Green, Giuseppe D'Agostino, Guanlin Wang, Lu Wang, Min Li, Jianbo Li, Chaoqun Niu, Zengguang Jin, Anyongqi Wang, Yu Zheng, Alex Douglas, John R Speakman.
      
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.016
  18. EMBO Rep. 2021 May 31. e51289
    LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis.
    Andrea Bast-Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schießl, Petra C Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor.
      The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remains largely unresolved. In this light, long noncoding RNAs (lncRNAs) emerged as a versatile class of modulators that control many steps within the differentiation machinery. Leveraging the naturally varying propensities of different inbred mouse strains for white adipose tissue browning, we identify the nuclear lncRNA Ctcflos as a pivotal orchestrator of thermogenic gene expression during brite adipocyte differentiation. Mechanistically, Ctcflos acts as a pleiotropic regulator, being essential for the transcriptional recruitment of the early core thermogenic regulatory program and the modulation of alternative splicing to drive brite adipogenesis. This is showcased by Ctcflos-regulated gene transcription and splicing of the key browning factor Prdm16 toward the isoform that is specific for the thermogenic gene program. Conclusively, our findings emphasize the mechanistic versatility of lncRNAs acting at several independent levels of gene expression for effective regulation of key differentiation factors to direct cell fate and function.
    Keywords:  Prdm16; Ucp1-dependent thermogenesis; brite adipocytes; long noncoding RNAs; splicing
    DOI:  https://doi.org/10.15252/embr.202051289
  19. Front Cell Dev Biol. 2021 ;9 664295
    The Golgi as a "Proton Sink" in Cancer.
    Koen M O Galenkamp, Cosimo Commisso.
      Cancer cells exhibit increased glycolytic flux and adenosine triphosphate (ATP) hydrolysis. These processes increase the acidic burden on the cells through the production of lactate and protons. Nonetheless, cancer cells can maintain an alkaline intracellular pH (pHi) relative to untransformed cells, which sets the stage for optimal functioning of glycolytic enzymes, evasion of cell death, and increased proliferation and motility. Upregulation of plasma membrane transporters allows for H+ and lactate efflux; however, recent evidence suggests that the acidification of organelles can contribute to maintenance of an alkaline cytosol in cancer cells by siphoning off protons, thereby supporting tumor growth. The Golgi is such an acidic organelle, with resting pH ranging from 6.0 to 6.7. Here, we posit that the Golgi represents a "proton sink" in cancer and delineate the proton channels involved in Golgi acidification and the ion channels that influence this process. Furthermore, we discuss ion channel regulators that can affect Golgi pH and Golgi-dependent processes that may contribute to pHi homeostasis in cancer.
    Keywords:  Golgi pH; cancer; intracellular pH; ion transport; pH homeostasis; proton sink
    DOI:  https://doi.org/10.3389/fcell.2021.664295
  20. Clin Exp Metastasis. 2021 Jun 02.
    Cancer cell metabolic plasticity in migration and metastasis.
    Jenna A Mosier, Samantha C Schwager, David A Boyajian, Cynthia A Reinhart-King.
      Metabolic reprogramming is a hallmark of cancer metastasis in which cancer cells manipulate their metabolic profile to meet the dynamic energetic requirements of the tumor microenvironment. Though cancer cell proliferation and migration through the extracellular matrix are key steps of cancer progression, they are not necessarily fueled by the same metabolites and energy production pathways. The two main metabolic pathways cancer cells use to derive energy from glucose, glycolysis and oxidative phosphorylation, are preferentially and plastically utilized by cancer cells depending on both their intrinsic metabolic properties and their surrounding environment. Mechanical factors in the microenvironment, such as collagen density, pore size, and alignment, and biochemical factors, such as oxygen and glucose availability, have been shown to influence both cell migration and glucose metabolism. As cancer cells have been identified as preferentially utilizing glycolysis or oxidative phosphorylation based on heterogeneous intrinsic or extrinsic factors, the relationship between cancer cell metabolism and metastatic potential is of recent interest. Here, we review current in vitro and in vivo findings in the context of cancer cell metabolism during migration and metastasis and extrapolate potential clinical applications of this work that could aid in diagnosing and tracking cancer progression in vivo by monitoring metabolism. We also review current progress in the development of a variety of metabolically targeted anti-metastatic drugs, both in clinical trials and approved for distribution, and highlight potential routes for incorporating our recent understanding of metabolic plasticity into therapeutic directions. By further understanding cancer cell energy production pathways and metabolic plasticity, more effective and successful clinical imaging and therapeutics can be developed to diagnose, target, and inhibit metastasis.
    Keywords:  ATP; Collective migration; Extracellular matrix; Glycolysis; Oxidative phosphorylation
    DOI:  https://doi.org/10.1007/s10585-021-10102-1
  21. Cancers (Basel). 2021 May 19. pii: 2473. [Epub ahead of print]13(10):
    Exploring the Complementarity of Pancreatic Ductal Adenocarcinoma Preclinical Models.
    Owen Hoare, Nicolas Fraunhoffer, Abdessamad Elkaoutari, Odile Gayet, Martin Bigonnet, Julie Roques, Rémy Nicolle, Colin McGuckin, Nico Forraz, Emilie Sohier, Laurie Tonon, Pauline Wajda, Sandrine Boyault, Valéry Attignon, Séverine Tabone-Eglinger, Sandrine Barbier, Caroline Mignard, Olivier Duchamp, Juan Iovanna, Nelson J Dusetti.
      Purpose: Compare pancreatic ductal adenocarcinoma (PDAC), preclinical models, by their transcriptome and drug response landscapes to evaluate their complementarity. Experimental Design: Three paired PDAC preclinical models-patient-derived xenografts (PDX), xenograft-derived pancreatic organoids (XDPO) and xenograft-derived primary cell cultures (XDPCC)-were derived from 20 patients and analyzed at the transcriptomic and chemosensitivity level. Transcriptomic characterization was performed using the basal-like/classical subtyping and the PDAC molecular gradient (PAMG). Chemosensitivity for gemcitabine, irinotecan, 5-fluorouracil and oxaliplatin was established and the associated biological pathways were determined using independent component analysis (ICA) on the transcriptome of each model. The selection criteria used to identify the different components was the chemosensitivity score (CSS) found for each drug in each model. Results: PDX was the most dispersed model whereas XDPO and XDPCC were mainly classical and basal-like, respectively. Chemosensitivity scoring determines that PDX and XDPO display a positive correlation for three out of four drugs tested, whereas PDX and XDPCC did not correlate. No match was observed for each tumor chemosensitivity in the different models. Finally, pathway analysis shows a significant association between PDX and XDPO for the chemosensitivity-associated pathways and PDX and XDPCC for the chemoresistance-associated pathways. Conclusions: Each PDAC preclinical model possesses a unique basal-like/classical transcriptomic phenotype that strongly influences their global chemosensitivity. Each preclinical model is imperfect but complementary, suggesting that a more representative approach of the clinical reality could be obtained by combining them. Translational Relevance: The identification of molecular signatures that underpin drug sensitivity to chemotherapy in PDAC remains clinically challenging. Importantly, the vast majority of studies using preclinical in vivo and in vitro models fail when transferred to patients in a clinical setting despite initially promising results. This study presents for the first time a comparison between three preclinical models directly derived from the same patients. We show that their applicability to preclinical studies should be considered with a complementary focus, avoiding tumor-based direct extrapolations, which might generate misleading conclusions and consequently the overlook of clinically relevant features.
    Keywords:  chemosensitivity prediction; in vitro models; in vivo models; pancreatic cancer; personalized medicine
    DOI:  https://doi.org/10.3390/cancers13102473
  22. Cancer Cytopathol. 2021 Jun 02.
    Keratin 17 testing in pancreatic cancer needle aspiration biopsies predicts survival.
    Lucia Roa-Peña, Sruthi Babu, Cindy V Leiton, Maoxin Wu, Sofia Taboada, Ali Akalin, Jonathan Buscaglia, Luisa F Escobar-Hoyos, Kenneth R Shroyer.
       BACKGROUND: Although pancreatic ductal adenocarcinoma (PDAC) has one of the lowest 5-year survival rates of all cancers, differences in survival exist between patients with clinically identical characteristics. The authors previously demonstrated that keratin 17 (K17) expression in PDAC, measured by RNA sequencing or immunohistochemistry (IHC), is an independent negative prognostic biomarker. Only 20% of cases are candidates for surgical resection, but most patients are diagnosed by needle aspiration biopsy (NAB). The aims of this study were to determine whether there was a correlation in K17 scores detected in matched NABs and surgical resection tissue sections and whether K17 IHC in NAB cell block specimens could be used as a negative prognostic biomarker in PDAC.
    METHODS: K17 IHC was performed for a cohort of 70 patients who had matched NAB cell block and surgical resection samples to analyze the correlation of K17 expression levels. K17 IHC was also performed in cell blocks from discovery and validation cohorts. Kaplan-Meier and Cox proportional hazards regression models were analyzed to determine survival differences in cases with different levels of K17 IHC expression.
    RESULTS: K17 IHC expression correlated in matched NABs and resection tissues. NAB samples were classified as high for K17 when ≥80% of tumor cells showed strong (2+) staining. High-K17 cases, including stage-matched cases, had shorter survival.
    CONCLUSIONS: K17 has been identified as a robust and independent prognostic biomarker that stratifies clinical outcomes for cases that are diagnosed by NAB. Testing for K17 also has the potential to inform clinical decisions for optimization of chemotherapeutic interventions.
    Keywords:  immunohistochemistry; keratin 17; needle aspiration biopsies; pancreatic ductal adenocarcinoma; prognostic biomarker
    DOI:  https://doi.org/10.1002/cncy.22438
  23. Nature. 2021 Jun 02.
    Tracing oncogene-driven remodelling of the intestinal stem cell niche.
    Min Kyu Yum, Seungmin Han, Juergen Fink, Szu-Hsien Sam Wu, Catherine Dabrowska, Teodora Trendafilova, Roxana Mustata, Lemonia Chatzeli, Roberta Azzarelli, Irina Pshenichnaya, Eunmin Lee, Frances England, Jong Kyoung Kim, Daniel E Stange, Anna Philpott, Joo-Hyeon Lee, Bon-Kyoung Koo, Benjamin D Simons.
      Interactions between tumour cells and the surrounding microenvironment contribute to tumour progression, metastasis and recurrence1-3. Although mosaic analyses in Drosophila have advanced our understanding of such interactions4,5, it has been difficult to engineer parallel approaches in vertebrates. Here we present an oncogene-associated, multicolour reporter mouse model-the Red2Onco system-that allows differential tracing of mutant and wild-type cells in the same tissue. By applying this system to the small intestine, we show that oncogene-expressing mutant crypts alter the cellular organization of neighbouring wild-type crypts, thereby driving accelerated clonal drift. Crypts that express oncogenic KRAS or PI3K secrete BMP ligands that suppress local stem cell activity, while changes in PDGFRloCD81+ stromal cells induced by crypts with oncogenic PI3K alter the WNT signalling environment. Together, these results show how oncogene-driven paracrine remodelling creates a niche environment that is detrimental to the maintenance of wild-type tissue, promoting field transformation dominated by oncogenic clones.
    DOI:  https://doi.org/10.1038/s41586-021-03605-0
  24. Proc Natl Acad Sci U S A. 2021 Jun 08. pii: e2025631118. [Epub ahead of print]118(23):
    TP53 missense mutations in PDAC are associated with enhanced fibrosis and an immunosuppressive microenvironment.
    Martino Maddalena, Giuseppe Mallel, Nishanth Belugali Nataraj, Michal Shreberk-Shaked, Ori Hassin, Saptaparna Mukherjee, Sharathchandra Arandkar, Ron Rotkopf, Abby Kapsack, Giuseppina Lambiase, Bianca Pellegrino, Eyal Ben-Isaac, Ofra Golani, Yoseph Addadi, Emma Hajaj, Raya Eilam, Ravid Straussman, Yosef Yarden, Michal Lotem, Moshe Oren.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, which is refractory to all currently available treatments and bears dismal prognosis. About 70% of all PDAC cases harbor mutations in the TP53 tumor suppressor gene. Many of those are missense mutations, resulting in abundant production of mutant p53 (mutp53) protein in the cancer cells. Analysis of human PDAC patient data from The Cancer Genome Atlas (TCGA) revealed a negative association between the presence of missense mutp53 and infiltration of CD8+ T cells into the tumor. Moreover, CD8+ T cell infiltration was negatively correlated with the expression of fibrosis-associated genes. Importantly, silencing of endogenous mutp53 in KPC cells, derived from mouse PDAC tumors driven by mutant Kras and mutp53, down-regulated fibrosis and elevated CD8+ T cell infiltration in the tumors arising upon orthotopic injection of these cells into the pancreas of syngeneic mice. Moreover, the tumors generated by mutp53-silenced KPC cells were markedly smaller than those elicited by mutp53-proficient control KPC cells. Altogether, our findings suggest that missense p53 mutations may contribute to worse PDAC prognosis by promoting a more vigorous fibrotic tumor microenvironment and impeding the ability of the immune system to eliminate the cancer cells.
    Keywords:  PDAC; fibrosis; immune infiltration; p53; tumor microenvironment
    DOI:  https://doi.org/10.1073/pnas.2025631118
  25. Nat Methods. 2021 May 31.
    Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing.
    Paul Datlinger, André F Rendeiro, Thorina Boenke, Martin Senekowitsch, Thomas Krausgruber, Daniele Barreca, Christoph Bock.
      Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed 'single-cell combinatorial fluidic indexing' (scifi). The scifi-RNA-seq assay combines one-step combinatorial preindexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. Preindexing allows us to load several cells per droplet and computationally demultiplex their individual expression profiles. Thereby, scifi-RNA-seq massively increases the throughput of droplet-based single-cell RNA-seq, and provides a straightforward way of multiplexing thousands of samples in a single experiment. Compared with multiround combinatorial indexing, scifi-RNA-seq provides an easy and efficient workflow. Compared to cell hashing methods, which flag and discard droplets containing more than one cell, scifi-RNA-seq resolves and retains individual transcriptomes from overloaded droplets. We benchmarked scifi-RNA-seq on various human and mouse cell lines, validated it for primary human T cells and applied it in a highly multiplexed CRISPR screen with single-cell transcriptome readout of T cell receptor activation.
    DOI:  https://doi.org/10.1038/s41592-021-01153-z
  26. JNCI Cancer Spectr. 2021 Jun;5(3): pkaa122
    Applications of Circulating Tumor DNA in a Cohort of Phase I Solid Tumor Patients Treated With Immunotherapy.
    Daniel V Araujo, Ao Wang, Dax Torti, Alberto Leon, Kayla Marsh, Aoife McCarthy, Hal Berman, Anna Spreafico, Aaron R Hansen, Albiruni-Abdul Razak, Philippe L Bedard, Lisa Wang, Eric Plackmann, Helen Chow, Hua Bao, Xue Wu, Trevor J Pugh, Lillian L Siu.
       Background: The correlation between blood-based tumor mutation burden (bTMB) and tissue-based tumor mutation burden(tTMB) has not been broadly tested in a multicancer cohort. Here, we assess the correlation between bTMB with tTMB in phase I trial patients treated with immunotherapy. As an exploratory analysis, we evaluated circulating tumor DNA (ctDNA) dynamics in responders.
    Methods: Patients treated with immunotherapy at the Princess Margaret phase I trials unit were enrolled. Pretreatment plasma ctDNA and matched normal blood controls were collected. Available archival tissue formalin-fixed paraffin-embedded (FFPE) samples were analyzed. A 425-gene panel was used to sequence both ctDNA and FFPE samples. Samples with TMB within the highest tertile were considered as high TMB.
    Results: Thirty-eight patients were accrued from 25 different trials, 86.8% of which involved an anti-PD-1/PD-L1 agent. Thirty patients (78.9%) had detectable mutations in ctDNA, of which the median (range) bTMB was 5 (1-53) mutations per megabase (mut/Mb). Of the 22 patients with available FFPE samples, mutations were detected in 21 (95.4%); the median (range) tTMB was 6 (2-124) mut/Mb. Among the 16 patients with detectable mutations in both FFPE and ctDNA, a statistically significant correlation between bTMB and tTMB was observed (ρ = 0.71; P = .002). High TMB was not associated with better survival. All 3 responders had a decrease in the variant allele frequency of mutations detected in ctDNA at a second timepoint relative to baseline, indicating a potential early marker of response.
    Conclusions: In this small series, bTMB correlated with tTMB. An on-treatment decrease in VAF of mutations detected in ctDNA at baseline was observed in responders. Larger studies to verify our findings are warranted.
    DOI:  https://doi.org/10.1093/jncics/pkaa122
  27. Methods Mol Biol. 2021 ;2276 173-191
    Assessment of Mitochondrial Ca2+ Uptake.
    András T Deak, Claire Jean-Quartier, Alexander I Bondarenko, Lukas N Groschner, Roland Malli, Wolfgang F Graier, Markus Waldeck-Weiermair.
      Mitochondrial Ca2+ uptake regulates mitochondrial function and contributes to cell signaling. Accordingly, quantifying mitochondrial Ca2+ signals and elaborating the mechanisms that accomplish mitochondrial Ca2+ uptake are essential to gain our understanding of cell biology. Here, we describe the benefits and drawbacks of various established old and new techniques to assess dynamic changes of mitochondrial Ca2+ concentration ([Ca2+]mito) in a wide range of applications.
    Keywords:  Ca2+ Imaging; Calcium Green; FRET; Fura-2; Mitochondrial Ca2+ uptake; Mitochondrial membrane potential; Mitoplast; Oxidative phosphorylation; Patch-clamp recording; Rhod-2
    DOI:  https://doi.org/10.1007/978-1-0716-1266-8_13
  28. Cells. 2021 May 25. pii: 1317. [Epub ahead of print]10(6):
    Mitochondrial Ca2+ Signaling in Health, Disease and Therapy.
    Lorenzo Modesti, Alberto Danese, Veronica Angela Maria Vitto, Daniela Ramaccini, Gianluca Aguiari, Roberta Gafà, Giovanni Lanza, Carlotta Giorgi, Paolo Pinton.
      The divalent cation calcium (Ca2+) is considered one of the main second messengers inside cells and acts as the most prominent signal in a plethora of biological processes. Its homeostasis is guaranteed by an intricate and complex system of channels, pumps, and exchangers. In this context, by regulating cellular Ca2+ levels, mitochondria control both the uptake and release of Ca2+. Therefore, at the mitochondrial level, Ca2+ plays a dual role, participating in both vital physiological processes (ATP production and regulation of mitochondrial metabolism) and pathophysiological processes (cell death, cancer progression and metastasis). Hence, it is not surprising that alterations in mitochondrial Ca2+ (mCa2+) pathways or mutations in Ca2+ transporters affect the activities and functions of the entire cell. Indeed, it is widely recognized that dysregulation of mCa2+ signaling leads to various pathological scenarios, including cancer, neurological defects and cardiovascular diseases (CVDs). This review summarizes the current knowledge on the regulation of mCa2+ homeostasis, the related mechanisms and the significance of this regulation in physiology and human diseases. We also highlight strategies aimed at remedying mCa2+ dysregulation as promising therapeutical approaches.
    Keywords:  Ca2+; cancer; cardiovascular diseases; mPTP; mitochondria; neurodegenerative diseases; therapy
    DOI:  https://doi.org/10.3390/cells10061317
  29. Science. 2021 Jun 04. 372(6546): 1085-1091
    Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
    Débora R Sobreira, Amelia C Joslin, Qi Zhang, Iain Williamson, Grace T Hansen, Kathryn M Farris, Noboru J Sakabe, Nasa Sinnott-Armstrong, Grazyna Bozek, Sharon O Jensen-Cody, Kyle H Flippo, Carole Ober, Wendy A Bickmore, Matthew Potthoff, Mengjie Chen, Melina Claussnitzer, Ivy Aneas, Marcelo A Nóbrega.
      Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and IRX5 from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
    DOI:  https://doi.org/10.1126/science.abf1008
  30. Nutrients. 2021 May 13. pii: 1650. [Epub ahead of print]13(5):
    Impact of Liver and Pancreas Diseases on Nutritional Status.
    Pablo Cañamares-Orbis, Vanesa Bernal-Monterde, Olivia Sierra-Gabarda, Diego Casas-Deza, Guillermo Garcia-Rayado, Luis Cortes, Alberto Lué.
      Liver and pancreatic diseases have significant consequences on nutritional status, with direct effects on clinical outcomes, survival, and quality of life. Maintaining and preserving an adequate nutritional status is crucial and should be one of the goals of patients with liver or pancreatic disease. Thus, the nutritional status of such patients should be systematically assessed at follow-up. Recently, great progress has been made in this direction, and the relevant pathophysiological mechanisms have been better established. While the spectrum of these diseases is wide, and the mechanisms of the onset of malnutrition are numerous and interrelated, clinical and nutritional manifestations are common. The main consequences include an impaired dietary intake, altered macro and micronutrient metabolism, energy metabolism disturbances, an increase in energy expenditure, nutrient malabsorption, sarcopenia, and osteopathy. In this review, we summarize the factors contributing to malnutrition, and the effects on nutritional status and clinical outcomes of liver and pancreatic diseases. We explain the current knowledge on how to assess malnutrition and the efficacy of nutritional interventions in these settings.
    Keywords:  liver cirrhosis; liver transplant; malabsorption; malnutrition; minerals; nutritional assessment; pancreatic exocrine insufficiency; sarcopenia; vitamins
    DOI:  https://doi.org/10.3390/nu13051650
  31. Proc Natl Acad Sci U S A. 2021 Jun 08. pii: e2104897118. [Epub ahead of print]118(23):
    Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase.
    Tae Hun Kim, Brandon J Payliss, Michael L Nosella, Ian T W Lee, Yuki Toyama, Julie D Forman-Kay, Lewis E Kay.
      The role of biomolecular condensates in regulating biological function and the importance of dynamic interactions involving intrinsically disordered protein regions (IDRs) in their assembly are increasingly appreciated. While computational and theoretical approaches have provided significant insights into IDR phase behavior, establishing the critical interactions that govern condensation with atomic resolution through experiment is more difficult, given the lack of applicability of standard structural biological tools to study these highly dynamic large-scale associated states. NMR can be a valuable method, but the dynamic and viscous nature of condensed IDRs presents challenges. Using the C-terminal IDR (607 to 709) of CAPRIN1, an RNA-binding protein found in stress granules, P bodies, and messenger RNA transport granules, we have developed and applied a variety of NMR methods for studies of condensed IDR states to provide insights into interactions driving and modulating phase separation. We identify ATP interactions with CAPRIN1 that can enhance or reduce phase separation. We also quantify specific side-chain and backbone interactions within condensed CAPRIN1 that define critical sequences for phase separation and that are reduced by O-GlcNAcylation known to occur during cell cycle and stress. This expanded NMR toolkit that has been developed for characterizing IDR condensates has generated detailed interaction information relevant for understanding CAPRIN1 biology and informing general models of phase separation, with significant potential future applications to illuminate dynamic structure-function relationships in other biological condensates.
    Keywords:  NMR methods for studying condensates; biomolecular condensates; intrinsically disordered protein regions; modification of phase separation by ATP and O-GlcNAcylation; site-specific intermolecular interactions
    DOI:  https://doi.org/10.1073/pnas.2104897118
  32. J Clin Med. 2021 May 29. pii: 2403. [Epub ahead of print]10(11):
    Epithelial-to-Mesenchymal Transition in the Light of Plasticity and Hybrid E/M States.
    Laura Bornes, Guillaume Belthier, Jacco van Rheenen.
      Epithelial-to-mesenchymal transition (EMT) is a cellular program which leads to cells losing epithelial features, including cell polarity, cell-cell adhesion and attachment to the basement membrane, while gaining mesenchymal characteristics, such as invasive properties and stemness. This program is involved in embryogenesis, wound healing and cancer progression. Over the years, the role of EMT in cancer progression has been heavily debated, and the requirement of this process in metastasis even has been disputed. In this review, we discuss previous discrepancies in the light of recent findings on EMT, plasticity and hybrid E/M states. Moreover, we highlight various tumor microenvironmental cues and cell intrinsic signaling pathways that induce and sustain EMT programs, plasticity and hybrid E/M states. Lastly, we discuss how recent findings on plasticity, especially on those that enable cells to switch between hybrid E/M states, have changed our understanding on the role of EMT in cancer metastasis, stemness and therapy resistance.
    Keywords:  EMP; epithelia-to-mesenchymal transition (EMT); hybrid E/M states; plasticity; stemness; therapy resistance; tumor progression
    DOI:  https://doi.org/10.3390/jcm10112403
  33. Methods Mol Biol. 2021 ;2277 69-89
    Drug Discovery Assay to Identify Modulators of the Mitochondrial Ca2+ Uniporter.
    Daniela M Arduino, Valerie Goh, Dejana Mokranjac, Fabiana Perocchi.
      The mitochondrial calcium uniporter (MCU ) is an essential protein of the inner mitochondrial membrane that mediates the uptake of calcium into mitochondria of virtually all mammalian tissues, regulating cell metabolism, signaling, and death. MCU-mediated calcium uptake has been shown to play a pathophysiological role in diverse human disease contexts, which qualifies this channel as a druggable target for therapeutic intervention.Here, we present a protocol to perform drug screens to identify effective and specific MCU-targeting inhibitors. The methodology is based on the use of cryopreserved mitochondria that are isolated from a yeast strain engineered to express the human MCU and its essential regulator EMRE together with the luminescence calcium sensor aequorin. Yeast mitochondria with a functionally reconstituted MCU-mediated calcium uptake are then employed as a ready-to-use screening reagent. False discovery rate is further minimized by energizing mitochondria with D-lactate in a mannitol/sucrose-based medium, which provides a mean to discriminate between direct and secondary effects of drugs on mitochondrial calcium uptake. This screening assay is sensitive and robust and can be easily implemented in any laboratory.
    Keywords:  Aequorin; Calcium; Drug screening; Luminescence assay; Mitochondria; Mitochondrial calcium uniporter; Yeast
    DOI:  https://doi.org/10.1007/978-1-0716-1270-5_5
  34. Eur J Clin Invest. 2021 Jun 01. e13631
    Rodent studies of developmental programming and aging mechanisms.
    Elena Zambrano, Consuelo Lomas Soria, Peter W Nathanielsz.
      Compelling evidence exists indicating that developmental programming influences aging. Programming alters life-course phenotype in multiple organs, predisposing to diseases such as diabetes, obesity and cardiovascular disease that shorten life-span. This review describes studies in rodents, the most commonly studied species, addressing interactions of programming challenges with aging. We first consider aging and programming of insulin function that has been clearly shown to decrease with age. It is important to evaluate aging in pancreatic islets isolated from other systems. Studies discussed show premature pancreatic islet aging resulting from both maternal under- and over nutrition. New ways to determine programming of adipose tissue and effects on fat storage are explored. Oxidative stress is a major factor that regulates aging in tissues. Oxidative stress is discussed in relation to reproductive and cardiovascular aging. Premature aging is associated with both low and high glucocorticoid function. Both over and undernutrition have offspring sex specific programming effects onlife-course glucocorticoid concentrations. Evidence is provided that maternal age at conception affects offspring endocrine and metabolism aging. Finally, the importance of matching fetal nutrition and energy availability with composition and energy content in the post-weaning diet is demonstrated. This mismatch can lead to a greatly shortened life span. General principles are discussed throughout. For example, sexual dimorphism of age-related outcomes can be marked. Accelerated aging occurs early in life. Improving knowledge on programming aging interactions will improve health span as well as life span. Finally, there are considerable similarities in outcomes programmed by maternal undernutrition and overnutrition.
    Keywords:  Developmental programming; aging; metabolism; oxidative stress; rodents; sexual dimorphism
    DOI:  https://doi.org/10.1111/eci.13631
  35. Methods Mol Biol. 2021 ;2277 247-268
    Accurate Measurement of Cellular and Cell-Free Circulating Mitochondrial DNA Content from Human Blood Samples Using Real-Time Quantitative PCR.
    Hannah Rosa, Afshan N Malik.
      Changes in circulating mitochondrial DNA (mtDNA) are widely used to indicate mitochondrial dysfunction in common non-genetic diseases where mitochondrial dysfunction may play a role. However, the methodology being used is not always specific and reproducible, and most studies use whole blood rather than evaluating cellular and cell-free mtDNA separately. Cellular mtDNA is contained within the mitochondrion and encodes vital subunits of the OXPHOS machinery. Conversely, cell-free mtDNA can have harmful effects, triggering inflammatory responses and potentially contributing to pathogenic processes. In this chapter, we describe a protocol to accurately measure the amount of cellular and cell-free human mtDNA in peripheral blood. Absolute quantification is carried out using real-time quantitative PCR (qPCR) to quantify cellular mtDNA, measured as the mitochondrial genome to nuclear genome ratio (designated the Mt/N ratio) in whole blood and peripheral blood mononuclear cells (PBMCs) and the number of mtDNA copies per μL in plasma and serum. We describe how to (1) separate whole blood into PBMCs, plasma, and serum fractions, (2) prepare DNA from each of these fractions, (3) prepare dilution standards for absolute quantification, (4) carry out qPCR for either relative or absolute quantification from test samples, (5) analyze qPCR data, and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use and can be modified to quantify mtDNA from other body fluids, human cells, and tissues.
    Keywords:  Absolute quantification; Circulating mtDNA; Mitochondrial DNA; Mt/N ratio; PBMCs; Plasma; Serum; mtDNA; mtDNA content; mtDNA copy number; qPCR
    DOI:  https://doi.org/10.1007/978-1-0716-1270-5_15
  36. Trends Cancer. 2021 May 29. pii: S2405-8033(21)00100-X. [Epub ahead of print]
    Extracellular ATP and Adenosine in Cancer Pathogenesis and Treatment.
    Anna M Chiarella, Yun K Ryu, Gulam A Manji, Anil K Rustgi.
      ATP hydrolysis and downstream signaling pathways in the extracellular space have a major impact upon tumor progression and metastasis. The complexity and interdependence of various cell types in the extracellular space have been increasingly appreciated in recent years. With increased awareness of the importance of this signaling pathway in the pathogenic development and progression of malignancies, there has been attention to therapeutic strategies targeting extracellular adenosine metabolism and signaling. This review summarizes the molecular and physiologic roles of extracellular ATP and adenosine in normal and disease states, and potential therapeutic applications.
    Keywords:  CD39; CD73; cancer; extracellular ATP; extracellular adenosine; purinergic signaling
    DOI:  https://doi.org/10.1016/j.trecan.2021.04.008
  37. Cells. 2021 May 04. pii: 1102. [Epub ahead of print]10(5):
    Chromothripsis-Explosion in Genetic Science.
    Mariia Shorokhova, Nikolay Nikolsky, Tatiana Grinchuk.
      Chromothripsis has been defined as complex patterns of alternating genes copy number changes (normal, gain or loss) along the length of a chromosome or chromosome segment (International System for Human Cytogenomic Nomenclature 2020). The phenomenon of chromothripsis was discovered in 2011 and changed the concept of genome variability, mechanisms of oncogenic transformation, and hereditary diseases. This review describes the phenomenon of chromothripsis, its prevalence in genomes, the mechanisms underlying this phenomenon, and methods of its detection. Due to the fact that most often the phenomenon of chromothripsis occurs in cancer cells, in this review, we will separately discuss the issue of the contribution of chromothripsis to the process of oncogenesis.
    Keywords:  cancer; chromosomal instability; chromothripsis; micronuclei; transformation
    DOI:  https://doi.org/10.3390/cells10051102
  38. Metabolites. 2021 May 30. pii: 350. [Epub ahead of print]11(6):
    Metabolic Response of Pancreatic Carcinoma Cells under Treatment with Dichloroacetate.
    Benedikt Feuerecker, Philipp Biechl, Christian Veltkamp, Dieter Saur, Wolfgang Eisenreich.
      In modern oncology, the analysis and evaluation of treatment response are still challenging. Hence, we used a 13C-guided approach to study the impacts of the small molecule dichloroacetate (DCA) upon the metabolic response of pancreatic cancer cells. Two different oncogenic PI3K-driven pancreatic cancer cell lines, 9580 and 10,158, respectively, were treated with 75 mM DCA for 18 h. In the presence of [U-13C6]glucose, the effects of DCA treatment in the core carbon metabolism were analyzed in these cells using gas chromatography-mass spectrometry (GC/MS). 13C-enrichments and isotopologue profiles of key amino acids revealed considerable effects of the DCA treatment upon glucose metabolism. The DCA treatment of the two pancreatic cell lines resulted in a significantly decreased incorporation of [U-13C6]glucose into the amino acids alanine, aspartate, glutamate, glycine, proline and serine in treated, but not in untreated, cancer cells. For both cell lines, the data indicated some activation of pyruvate dehydrogenase with increased carbon flux via the TCA cycle, but also massive inhibition of glycolytic flux and amino acid biosynthesis presumably by inhibition of the PI3K/Akt/mTORC axis. Together, it appears worthwhile to study the early treatment response in DCA-guided or accompanied cancer therapy in more detail, since it could open new avenues for improved diagnosis and therapeutic protocols of cancer.
    Keywords:  [U-13C6]glucose; dichloroacetate (DCA); isotopologue profiling; pancreatic cancer
    DOI:  https://doi.org/10.3390/metabo11060350
  39. Sci Signal. 2021 Jun 01. pii: eaaz3578. [Epub ahead of print]14(685):
    Yorkie drives Ras-induced tumor progression by microRNA-mediated inhibition of cellular senescence.
    Takao Ito, Tatsushi Igaki.
      The activation of Ras signaling is a major early event of oncogenesis in many contexts, yet paradoxically, Ras signaling induces cellular senescence, which prevents tumorigenesis. Thus, Ras-activated cells must overcome senescence to develop into cancer. Through a genetic screen in Drosophila melanogaster, we found that the ETS family transcriptional activator Pointed (Pnt) was necessary and sufficient to trigger cellular senescence upon Ras activation and blocked Ras-induced tumor growth in eye-antennal discs. Through analyses of mosaic discs using various genetic tools, we identified a mechanism of tumor progression in which loss of cell polarity, a common driver of epithelial oncogenesis, abrogated Ras-induced cellular senescence through microRNA-mediated inhibition of Pnt. Mechanistically, polarity defects in Ras-activated cells caused activation of the Hippo effector Yorkie (Yki), which induced the expression of the microRNA bantam bantam-mediated repression of the E3 ligase-associated protein Tribbles (Trbl) relieved Ras- and Akt-dependent inhibition of the transcription factor FoxO. The restoration of FoxO activity in Ras-activated cells induced the expression of the microRNAs miR-9c and miR-79, which led to reduced pnt expression, thereby abrogating cellular senescence and promoting tumor progression. Our findings provide a mechanistic explanation for how Ras-activated tumors progress toward malignancy by overcoming cellular senescence.
    DOI:  https://doi.org/10.1126/scisignal.aaz3578
  40. Cell Stem Cell. 2021 Jun 03. pii: S1934-5909(21)00224-1. [Epub ahead of print]28(6): 987-988
    Pancreatic plasticity: Unlocking exocrine lineage specification.
    Jason R Pitarresi, Anil K Rustgi.
      In this issue of Cell Stem Cell, Huang et al. (2021) and Breunig et al. (2021) developed human stem-cell-derived organoid culture systems to recapitulate pancreatic acinar and ductal lineages. This provides opportunities to study cellular plasticity and transformation in pancreatic cancer initiation and progression.
    DOI:  https://doi.org/10.1016/j.stem.2021.05.006
  41. Cancer Biol Med. 2021 Jun 04. pii: j.issn.2095-3941.2021.0158. [Epub ahead of print]
    Hypoxic microenvironment induced spatial transcriptome changes in pancreatic cancer.
    Huizhi Sun, Danfang Zhang, Chongbiao Huang, Yuhong Guo, Zhao Yang, Nan Yao, Xueyi Dong, Runfen Cheng, Nan Zhao, Jie Meng, Baocun Sun, Jihui Hao.
       OBJECTIVE: Hypoxia is a significant feature of solid tumors, including pancreatic ductal adenocarcinoma (PDAC). It is associated with tumor invasion, metastasis, and drug resistance. However, the spatial distribution of hypoxia-related heterogeneity in PDAC remains unclear.
    METHODS: Spatial transcriptomics (STs), a new technique, was used to investigate the ST features of engrafted human PDAC in the ischemic hind limbs of nude mice. Transcriptomes from ST spots in the hypoxic tumor and the control were clustered using differentially-expressed genes. These data were compared to determine the spatial organization of hypoxia-induced heterogeneity in PDAC. Clinical relevance was validated using the Tumor Cancer Genome Atlas and KM-plotter databases. The CMAP website was used to identify molecules that may serve as therapeutic targets for PDAC.
    RESULTS: ST showed that the tumor cell subgroups decreased to 7 subgroups in the hypoxia group, compared to 9 subgroups in the control group. Different subgroups showed positional characteristics and different gene signatures. Subgroup 6 located at the invasive front showed a higher proliferative ability under hypoxia. Subgroup 6 had active functions including cell proliferation, invasion, and response to stress. Expressions of hypoxia-related genes, LDHA, TPI1, and ENO1, induced changes. CMAP analysis indicated that ADZ-6482, a PI3K inhibitor, was targeted by the invasive subgroup in hypoxic tumors.
    CONCLUSIONS: This study is the first to describe hypoxic microenvironment-induced spatial transcriptome changes in PDAC, and to identify potential treatment targets for PDAC. These data will provide the basis for further investigations of the prognoses and treatments of hypoxic tumors.
    Keywords:  Pancreatic cancer; hypoxia; spatial transcriptomic
    DOI:  https://doi.org/10.20892/j.issn.2095-3941.2021.0158
  42. Curr Biol. 2021 May 28. pii: S0960-9822(21)00625-4. [Epub ahead of print]
    The CD44/COL17A1 pathway promotes the formation of multilayered, transformed epithelia.
    Kei Kozawa, Miho Sekai, Kenji Ohba, Shoko Ito, Hiroaki Sako, Takeshi Maruyama, Mai Kakeno, Takanobu Shirai, Keisuke Kuromiya, Tomoko Kamasaki, Koki Kohashi, Shinya Tanaka, Susumu Ishikawa, Nanami Sato, Shota Asano, Hironori Suzuki, Nobuyuki Tanimura, Yohei Mukai, Noriko Gotoh, Mishie Tanino, Shinya Tanaka, Ken Natsuga, Tomoyoshi Soga, Tomonori Nakamura, Yukihiro Yabuta, Mitinori Saitou, Takahiro Ito, Kenkyo Matsuura, Makoto Tsunoda, Toyone Kikumori, Tadashi Iida, Yasuyuki Mizutani, Yuki Miyai, Kozo Kaibuchi, Atsushi Enomoto, Yasuyuki Fujita.
      At the early stage of cancer development, oncogenic mutations often cause multilayered epithelial structures. However, the underlying molecular mechanism still remains enigmatic. By performing a series of screenings targeting plasma membrane proteins, we have found that collagen XVII (COL17A1) and CD44 accumulate in RasV12-, Src-, or ErbB2-transformed epithelial cells. In addition, the expression of COL17A1 and CD44 is also regulated by cell density and upon apical cell extrusion. We further demonstrate that the expression of COL17A1 and CD44 is profoundly upregulated at the upper layers of multilayered, transformed epithelia in vitro and in vivo. The accumulated COL17A1 and CD44 suppress mitochondrial membrane potential and reactive oxygen species (ROS) production. The diminished intracellular ROS level then promotes resistance against ferroptosis-mediated cell death upon cell extrusion, thereby positively regulating the formation of multilayered structures. To further understand the functional role of COL17A1, we performed comprehensive metabolome analysis and compared intracellular metabolites between RasV12 and COL17A1-knockout RasV12 cells. The data imply that COL17A1 regulates the metabolic pathway from the GABA shunt to mitochondrial complex I through succinate, thereby suppressing the ROS production. Moreover, we demonstrate that CD44 regulates membrane accumulation of COL17A1 in multilayered structures. These results suggest that CD44 and COL17A1 are crucial regulators for the clonal expansion of transformed cells within multilayered epithelia, thus being potential targets for early diagnosis and preventive treatment for precancerous lesions.
    Keywords:  CD44; COL17A1; GABA shunt; ROS; RasV12; cell extrusion; ferroptosis; multilayered epithelia; phage antibody display screening; precancerous lesion
    DOI:  https://doi.org/10.1016/j.cub.2021.04.078
  43. FEBS J. 2021 Jun 02.
    The gate to metastasis: key players in cancer cell intravasation.
    Magdalena Katarzyna Sznurkowska, Nicola Aceto.
      Metastasis is a leading cause of cancer-related death and consists of a sequence of events including tumor expansion, intravasation of cancer cells into the circulation, survival in the bloodstream, extravasation at distant sites and subsequent organ colonization. Particularly, intravasation is a process whereby cancer cells transverse the endothelium and leave the primary tumor site, pioneering the metastatic cascade. The identification of those mechanisms that trigger the entry of cancer cells into the bloodstream may reveal fundamentally novel ways to block metastasis at its start. Multiple factors have been implicated in cancer progression, yet, signals that unequivocally provoke the detachment of cancer cells from the primary tumor are still under investigation. Here, we discuss the role of intrinsic properties of cancer cells, tumor microenvironment and mechanical cues in the intravasation process, outlining studies that suggest the involvement of various factors and highlighting current understanding and open questions in the field.
    Keywords:  Cancer; Circulating tumor cells; Intravasation; Metastasis
    DOI:  https://doi.org/10.1111/febs.16046
  44. Methods Mol Biol. 2021 ;2276 1-29
    Mitochondrial Dysfunction in Mitochondrial Medicine: Current Limitations, Pitfalls, and Tomorrow.
    Naig Gueguen, Guy Lenaers, Pascal Reynier, Volkmar Weissig, Marvin Edeas.
      Until recently restricted to hereditary mitochondrial diseases, mitochondrial dysfunction is now recognized as a key player and strategic factor in the pathophysiological of many human diseases, ranging from the metabolism, vascular, cardiac, and neurodegenerative diseases to cancer. Because of their participation in a myriad of cellular functions and signaling pathways, precisely identifying the cause of mitochondrial "dysfunctions" can be challenging and requires robust and controlled techniques. Initially limited to the analysis of the respiratory chain functioning, these analytical techniques now enlarge to the analyses of mitochondrial and cellular metabolism, based on metabolomic approaches.Here, we address the methods used to assay mitochondrial dysfunction, with a highlight on the techniques used in diagnosis on tissues and cells derived from patients, the information they provide, and their strength and weakness.Targeting mitochondrial dysfunction by various strategies is a huge challenge, requires robust methods of evaluation, and should be able to take into consideration the mitochondria dynamics and localization. The future of mitochondrial medicine is strongly related to a perfect comprehension of its dysfunction.
    Keywords:  Bioenergetics; Devices; Metabolomics; Mitochondria evaluation; Mitochondrial dysfunctions
    DOI:  https://doi.org/10.1007/978-1-0716-1266-8_1
  45. Aging (Albany NY). 2021 Jun 03. 13
    Prevalence of proliferating CD8+ cells in normal lymphatic tissues, inflammation and cancer.
    Niclas C Blessin, Raed Abu-Hashem, Tim Mandelkow, Wenchao Li, Ronald Simon, Claudia Hube-Magg, Christina Möller-Koop, Melanie Witt, Alice Schmidt, Franziska Büscheck, Christoph Fraune, Andreas M Luebke, Katharina Möller, Frank Jacobsen, Florian Lutz, Maximilian Lennartz, Stefan Steurer, Guido Sauter, Doris Höflmayer, Maria Christina Tsourlakis, Andrea Hinsch, Eike Burandt, Waldemar Wilczak, Sarah Minner, Till S Clauditz.
      CD8+ cytotoxic T-lymphocytes are essential components of the anti-tumor immunity. To better understand the expansion of CD8+ T-cells we used multiplex fluorescence immunohistochemistry to study Ki67+CD8+ cells in normal lymphoid tissues, selected inflammatory diseases and cancers in 41 large sections/ microenvironment tissue microarrays (TMAs) as well as 765 samples in a conventional TMA format. The evaluation of more than 20 different compartments of normal lymphoid tissues revealed that the percentage of proliferating (ki67+) CD8+ cells did commonly not exceed 3%. In inflammations, the percentage of Ki67+CD8+ cells was more variable and higher compared to normal tissues. In cancers, the percentage of Ki67+CD8+ cells was higher in the tumor center than at the invasive margin. In the tumor center of 765 colorectal cancers, the density of Ki67+CD8+ cells and the percentage of proliferating CD8+ cytotoxic T-cells was significantly associated with microsatellite instability (p<0.0001), pT (p<0.0002) and pN category (p<0.0098). In summary, these data show that the percentage of Ki67+CD8+ cells is usually at a baseline proliferation rate below 3% in healthy secondary lymphoid organs. This rate is often markedly higher in inflammatory and neoplastic diseases compared to normal tissues. The striking link with unfavorable tumor features in colorectal cancer suggest a potential clinical utility of assessing the percentage of Ki67+CD8+ cells to predict patients outcome.
    Keywords:  CD8+ cytotoxic T cells; colorectal cancer; lymphatic tissue; tumor infiltrating lymphocytes; tumor microenvironment
    DOI:  https://doi.org/10.18632/aging.203113
  46. Cancers (Basel). 2021 May 18. pii: 2429. [Epub ahead of print]13(10):
    KRAS Mutation Dictates the Cancer Immune Environment in Pancreatic Ductal Adenocarcinoma and Other Adenocarcinomas.
    Meichen Gu, Yanli Gao, Pengyu Chang.
      Generally, patients with pancreatic ductal adenocarcinoma, especially those with wide metastatic lesions, have a poor prognosis. Recently, a breakthrough in improving their survival has been achieved by using first-line chemotherapy, such as gemcitabine plus nab-paclitaxel or oxaliplatin plus irinotecan plus 5-fluorouracil plus calcium folinate. Unfortunately, regimens with high effectiveness are still absent in second- or later-line settings. In addition, although immunotherapy using checkpoint inhibitors definitively represents a novel method for metastatic cancers, monotherapy using checkpoint inhibitors is almost completely ineffective for pancreatic ductal adenocarcinomas largely due to the suppressive immune milieu in such tumors. Critically, the genomic alteration pattern is believed to impact cancer immune environment. Surprisingly, KRAS gene mutation is found in almost all pancreatic ductal adenocarcinomas. Moreover, KRAS mutation is indispensable for pancreatic carcinogenesis. On these bases, a relationship likely exists between this oncogene and immunosuppression in this cancer. During pancreatic carcinogenesis, KRAS mutation-driven events, such as metabolic reprogramming, cell autophagy, and persistent activation of the yes-associated protein pathway, converge to cause immune evasion. However, intriguingly, KRAS mutation can dictate a different immune environment in other types of adenocarcinoma, such as colorectal adenocarcinoma and lung adenocarcinoma. Overall, the KRAS mutation can drive an immunosuppression in pancreatic ductal adenocarcinomas or in colorectal carcinomas, but this mechanism is not true in KRAS-mutant lung adenocarcinomas, especially in the presence of TP53 inactivation. As a result, the response of these adenocarcinomas to checkpoint inhibitors will vary.
    Keywords:  KRAS gene; cancer immunity; immune checkpoint blockade; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.3390/cancers13102429
  47. Int Rev Cell Mol Biol. 2021 ;pii: S1937-6448(20)30108-8. [Epub ahead of print]361 21-105
    The RAL signaling network: Cancer and beyond.
    Lisa H Apken, Andrea Oeckinghaus.
      The RAL proteins RALA and RALB belong to the superfamily of small RAS-like GTPases (guanosine triphosphatases). RAL GTPases function as molecular switches in cells by cycling through GDP- and GTP-bound states, a process which is regulated by several guanine exchange factors (GEFs) and two heterodimeric GTPase activating proteins (GAPs). Since their discovery in the 1980s, RALA and RALB have been established to exert isoform-specific functions in central cellular processes such as exocytosis, endocytosis, actin organization and gene expression. Consequently, it is not surprising that an increasing number of physiological functions are discovered to be controlled by RAL, including neuronal plasticity, immune response, and glucose and lipid homeostasis. The critical importance of RAL GTPases for oncogenic RAS-driven cellular transformation and tumorigenesis still attracts most research interest. Here, RAL proteins are key drivers of cell migration, metastasis, anchorage-independent proliferation, and survival. This chapter provides an overview of normal and pathological functions of RAL GTPases and summarizes the current knowledge on the involvement of RAL in human disease as well as current therapeutic targeting strategies. In particular, molecular mechanisms that specifically control RAL activity and RAL effector usage in different scenarios are outlined, putting a spotlight on the complexity of the RAL GTPase signaling network and the emerging theme of RAS-independent regulation and relevance of RAL.
    Keywords:  Exocyst functions; RAL GTPase signaling; RALGAP; RALGEF; RAS effector pathways; Ras-driven cancer; Regulation of RAL GTPase activity; Vesicle trafficking
    DOI:  https://doi.org/10.1016/bs.ircmb.2020.10.005
  48. Genome Med. 2021 May 31. 13(1): 96
    Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients.
    Dana W Y Tsui, Michael L Cheng, Maha Shady, Julie L Yang, Dennis Stephens, Helen Won, Preethi Srinivasan, Kety Huberman, Fanli Meng, Xiaohong Jing, Juber Patel, Maysun Hasan, Ian Johnson, Erika Gedvilaite, Brian Houck-Loomis, Nicholas D Socci, S Duygu Selcuklu, Venkatraman E Seshan, Hongxin Zhang, Debyani Chakravarty, Ahmet Zehir, Ryma Benayed, Maria Arcila, Marc Ladanyi, Samuel A Funt, Darren R Feldman, Bob T Li, Pedram Razavi, Jonathan Rosenberg, Dean Bajorin, Gopa Iyer, Wassim Abida, Howard I Scher, Dana Rathkopf, Agnes Viale, Michael F Berger, David B Solit.
       BACKGROUND: Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth.
    METHODS: Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES).
    RESULTS: cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches.
    CONCLUSIONS: cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
    Keywords:  Cancer; Liquid biopsy; Molecular diagnostic; Noninvasive; Plasma DNA; Sequencing
    DOI:  https://doi.org/10.1186/s13073-021-00898-8
  49. Mol Cell. 2021 May 25. pii: S1097-2765(21)00362-2. [Epub ahead of print]
    Choline kinase alpha 2 acts as a protein kinase to promote lipolysis of lipid droplets.
    Rui Liu, Jong-Ho Lee, Jingyi Li, Rilei Yu, Lin Tan, Yan Xia, Yanhua Zheng, Xue-Li Bian, Philip L Lorenzi, Qianming Chen, Zhimin Lu.
      Lipid droplets are important for cancer cell growth and survival. However, the mechanism underlying the initiation of lipid droplet lipolysis is not well understood. We demonstrate here that glucose deprivation induces the binding of choline kinase (CHK) α2 to lipid droplets, which is sequentially mediated by AMPK-dependent CHKα2 S279 phosphorylation and KAT5-dependent CHKα2 K247 acetylation. Importantly, CHKα2 with altered catalytic domain conformation functions as a protein kinase and phosphorylates PLIN2 at Y232 and PLIN3 at Y251. The phosphorylated PLIN2/3 dissociate from lipid droplets and are degraded by Hsc70-mediated autophagy, thereby promoting lipid droplet lipolysis, fatty acid oxidation, and brain tumor growth. In addition, levels of CHKα2 S279 phosphorylation, CHKα2 K247 acetylation, and PLIN2/3 phosphorylation are positively correlated with one another in human glioblastoma specimens and are associated with poor prognosis in glioblastoma patients. These findings underscore the role of CHKα2 as a protein kinase in lipolysis and glioblastoma development.
    Keywords:  AMPK; KAT5; PLIN2/3; acetylation; autophagy; choline kinase; lipid droplet; lipolysis; phosphorylation; tumorigenesis
    DOI:  https://doi.org/10.1016/j.molcel.2021.05.005
  50. Nat Commun. 2021 05 31. 12(1): 3258
    Model-based analysis uncovers mutations altering autophagy selectivity in human cancer.
    Zhu Han, Weizhi Zhang, Wanshan Ning, Chenwei Wang, Wankun Deng, Zhidan Li, Zehua Shang, Xiaofei Shen, Xiaohui Liu, Otto Baba, Tsuyoshi Morita, Lu Chen, Yu Xue, Da Jia.
      Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation. Aberrant regulation of autophagy promotes tumorigenesis, while it is far less clear whether and how tumor-specific alterations result in autophagic aberrance. To form a link between aberrant autophagy selectivity and human cancer, we establish a computational pipeline and prioritize 222 potential LIR (LC3-interacting region) motif-associated mutations (LAMs) in 148 proteins. We validate LAMs in multiple proteins including ATG4B, STBD1, EHMT2 and BRAF that impair their interactions with LC3 and autophagy activities. Using a combination of transcriptomic, metabolomic and additional experimental assays, we show that STBD1, a poorly-characterized protein, inhibits tumor growth via modulating glycogen autophagy, while a patient-derived W203C mutation on LIR abolishes its cancer inhibitory function. This work suggests that altered autophagy selectivity is a frequently-used mechanism by cancer cells to survive during various stresses, and provides a framework to discover additional autophagy-related pathways that influence carcinogenesis.
    DOI:  https://doi.org/10.1038/s41467-021-23539-5
  51. Ann Hepatobiliary Pancreat Surg. 2021 May 31. 25(2): 179-191
    Advances in neoadjuvant therapy for resectable pancreatic cancer over the past two decades.
    Alvaro Gregorio Morales Taboada, Pablo Lozano Lominchar, Lorena Martin Roman, Pilar García-Alfonso, Andres Jesús Muñoz Martin, Jose Antonio Blanco Rodriguez, Jose Manuel Asencio Pascual.
      In the last two decades, pancreatic cancer has been undergoing important changes in its perioperative management due to the great interest in multidisciplinary management and preoperative multimodal therapy, which in numerous studies have shown promising clinical results. Although the standard of treatment for resectable pancreatic ductal adenocarcinoma (PDAC) today is surgery followed by adjuvant therapy, as it is a biologically aggressive disease, even with complete resection, it has high rates of local and distant relapse. Several retrospective and prospective phase I/II studies have opened the window for neoadjuvant therapy with chemotherapy (CT), chemoradiotherapy (CRT), or both, as an alternative treatment for resectable pancreatic cancer, with promising results. Neoadjuvant therapy could has some advantages, including early administration of systemic treatment, in vivo assessment of response to treatment, increase resectability rate in borderline patients, increase resection rate with negative margin and survival benefit. While it seems clear that even potentially resectable disease would benefit from preoperative multimodal therapy, the optimal neoadjuvant therapeutic strategy is still controversial and currently there are only recommendations for neoadjuvant treatment, in clinical guidelines such as the NCCN and ESMO, for borderline and/or locally advanced PDAC. This review provides an overview of recent studies available and how they relate to systemic treatment of resectable PDAC in the neoadjuvant setting.
    Keywords:  Chemoradiotherapy; Chemotherapy; Neoadjuvant therapy; Pancreatic ductal adenocarcinoma; Resectable disease
    DOI:  https://doi.org/10.14701/ahbps.2021.25.2.179
  52. J Pain Symptom Manage. 2021 May 26. pii: S0885-3924(21)00369-9. [Epub ahead of print]
    Mirtazapine in cancer-associated anorexia and cachexia: A double-blind placebo-controlled randomized trial.
    Catherine N Hunter, Hesham H Abdel-Aal, Wessam A Elsherief, Dina E Farag, Nermine M Riad, Samy A Alsirafy.
       CONTEXT: Few pharmacological interventions are available for cancer-associated anorexia and cachexia. Mirtazapine has been suggested for use in cancer-associated anorexia and cachexia.
    OBJECTIVES: This study was conducted to assess the efficacy and tolerability of mirtazapine in cancer-associated anorexia and cachexia.
    METHODS: A double-blind placebo-controlled randomized trial. The study included 120 incurable solid tumour patients with anorexia (appetite loss ≥4 on 0-10 scale, 10= maximum appetite loss), cachexia (>5% body weight loss over 6 months or >2% plus body mass index <20) and depression score ≤3 on 0-6 scale (6= extreme feelings of depression). Patients were 1:1 randomized to receive mirtazapine 15mg daily at night for 8 weeks or placebo. The primary endpoint was change in appetite from baseline to day 28. Other outcomes included changes in quality-of-life, fatigue, depressive symptoms, body weight, lean body mass, handgrip strength, inflammatory markers, adverse events and survival.
    RESULTS: 48 (80%) patients in the mirtazapine arm and 52 (87%) in the placebo were assessable for the 1ry endpoint. Appetite score increased significantly with mirtazapine as well as with placebo (p<0.0001 each). The increase in appetite score did not differ significantly between the two arms in the per-protocol and intention-to-treat analysis (p=0.472 and 0.462, respectively). Mirtazapine was associated with significantly less increase in depressive symptoms and higher prevalence of somnolence. The change in other outcomes did not differ significantly between mirtazapine and placebo.
    CONCLUSION: Mirtazapine 15mg at night for 28 days is no better than placebo in improving the appetite of incurable solid tumor patients with cancer-associated anorexia and cachexia.
    Keywords:  Anorexia; Cachexia; Mirtazapine; Neoplasms; Randomized clinical trial
    DOI:  https://doi.org/10.1016/j.jpainsymman.2021.05.017
  53. Sci Signal. 2021 Jun 01. pii: eabj1753. [Epub ahead of print]14(685):
    The bedside-bench-bedside cycle: Robert Lefkowitz and GPCRs.
    Aaron Ciechanover.
      Biographies and autobiographies are important because they provide an account of history, social, cultural, and political developments, or discoveries and inventions, from a personal perspective. This is a review of the memoirs of Robert Lefkowitz (A Funny Thing Happened on the Way to Stockholm, with Randy Hall), who, together with Brian Kobilka, won the 2012 Nobel Prize in Chemistry for studies on G protein-coupled receptors.
    DOI:  https://doi.org/10.1126/scisignal.abj1753
  54. Aging Cell. 2021 Jun 05. e13411
    Human muscle stem cells are refractory to aging.
    James S Novak, Davi A G Mázala, Marie Nearing, Ravi Hindupur, Prech Uapinyoying, Nayab F Habib, Tessa Dickson, Olga B Ioffe, Brent T Harris, Marie N Fidelia-Lambert, Christopher T Rossi, D Ashely Hill, Kathryn R Wagner, Eric P Hoffman, Terence A Partridge.
      Age-related loss of muscle mass and strength is widely attributed to limitation in the capacity of muscle resident satellite cells to perform their myogenic function. This idea contains two notions that have not been comprehensively evaluated by experiment. First, it entails the idea that we damage and lose substantial amounts of muscle in the course of our normal daily activities. Second, it suggests that mechanisms of muscle repair are in some way exhausted, thus limiting muscle regeneration. A third potential option is that the aged environment becomes inimical to the conduct of muscle regeneration. In the present study, we used our established model of human muscle xenografting to test whether muscle samples taken from cadavers, of a range of ages, maintained their myogenic potential after being transplanted into immunodeficient mice. We find no measurable difference in regeneration across the range of ages investigated up to 78 years of age. Moreover, we report that satellite cells maintained their myogenic capacity even when muscles were grafted 11 days postmortem in our model. We conclude that the loss of muscle mass with increasing age is not attributable to any intrinsic loss of myogenicity and is most likely a reflection of progressive and detrimental changes in the muscle microenvironment such as to disfavor the myogenic function of these cells.
    Keywords:  aging; human satellite cells; muscle regeneration; myogenic capacity; sarcopenia
    DOI:  https://doi.org/10.1111/acel.13411
  55. J Clin Invest. 2021 Jun 01. pii: 135821. [Epub ahead of print]131(11):
    Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs.
    Francesca Solagna, Caterina Tezze, Maja T Lindenmeyer, Shun Lu, Guochao Wu, Shuya Liu, Yu Zhao, Robert Mitchell, Charlotte Meyer, Saleh Omairi, Temel Kilic, Andrea Paolini, Olli Ritvos, Arja Pasternack, Antonios Matsakas, Dominik Kylies, Julian Schulze Zur Wiesch, Jan-Eric Turner, Nicola Wanner, Viji Nair, Felix Eichinger, Rajasree Menon, Ina V Martin, Barbara M Klinkhammer, Elion Hoxha, Clemens D Cohen, Pierre-Louis Tharaux, Peter Boor, Tammo Ostendorf, Matthias Kretzler, Marco Sandri, Oliver Kretz, Victor G Puelles, Ketan Patel, Tobias B Huber.
      Skeletal muscle wasting is commonly associated with chronic kidney disease (CKD), resulting in increased morbidity and mortality. However, the link between kidney and muscle function remains poorly understood. Here, we took a complementary interorgan approach to investigate skeletal muscle wasting in CKD. We identified increased production and elevated blood levels of soluble pro-cachectic factors, including activin A, directly linking experimental and human CKD to skeletal muscle wasting programs. Single-cell sequencing data identified the expression of activin A in specific kidney cell populations of fibroblasts and cells of the juxtaglomerular apparatus. We propose that persistent and increased kidney production of pro-cachectic factors, combined with a lack of kidney clearance, facilitates a vicious kidney/muscle signaling cycle, leading to exacerbated blood accumulation and, thereby, skeletal muscle wasting. Systemic pharmacological blockade of activin A using soluble activin receptor type IIB ligand trap as well as muscle-specific adeno-associated virus-mediated downregulation of its receptor ACVR2A/B prevented muscle wasting in different mouse models of experimental CKD, suggesting that activin A is a key factor in CKD-induced cachexia. In summary, we uncovered a crosstalk between kidney and muscle and propose modulation of activin signaling as a potential therapeutic strategy for skeletal muscle wasting in CKD.
    Keywords:  Chronic kidney disease; Muscle; Muscle Biology; Nephrology
    DOI:  https://doi.org/10.1172/JCI135821
  56. Anticancer Res. 2021 Jun;41(6): 2895-2900
    Proteomic Analysis of Malignant Ascites From Patients With Pancreatic Ductal Adenocarcinoma.
    Fumimasa Kitamura, Tatsunori Miyata, Norio Uemura, Tomoyuki Uchihara, Katsunori Imai, Hiromitsu Hayashi, Yo-Ichi Yamashita, Keisuke Matsusaki, Takatsugu Ishimoto, Hideo Baba.
       BACKGROUND/AIM: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignant tumor. Research using an innovative research approach is needed to identify effective biomarkers or therapeutic targets for PDAC. We aimed to identify proteins related to the peritoneal dissemination of PDAC.
    MATERIALS AND METHODS: We performed proteomic analysis using ascites samples from patients with advanced PDAC and peritoneal dissemination and patients with liver cirrhosis (LC). Proteins specific to PDAC were identified in comparison to the findings for ascites from patients with LC as a control group.
    RESULTS: In total, 336 proteins were identified in ascites from patients with PDAC. We identified 18 specific proteins in ascites from patients with advanced PDAC. Among these proteins, CD13, lymphatic vessel endothelial hyaluronan receptor 1, ficolin-3, and V-set and immunoglobulin domain containing 4 were the most frequently detected. In addition, these 18 proteins could be classified into four categories: extracellular matrix, immunity, metabolism, and others.
    CONCLUSION: The identified proteins could be informative for developing treatment strategies for patients with PDAC and peritoneal dissemination.
    Keywords:  Biomarker; malignant ascites; pancreatic ductal adenocarcinoma; proteomics
    DOI:  https://doi.org/10.21873/anticanres.15071
  57. Cancers (Basel). 2021 May 31. pii: 2716. [Epub ahead of print]13(11):
    Vitamin D: Promises on the Horizon and Challenges Ahead for Fighting Pancreatic Cancer.
    Daoyan Wei, Liang Wang, Xiangsheng Zuo, Robert S Bresalier.
      Pancreatic cancer has a dismal prognosis, while its incidence is increasing. This is attributed, in part, to a profound desmoplastic and immunosuppressive tumor microenvironment associated with this cancer and resistance to current available therapies. Novel and effective intervention strategies are urgently needed to improve the outcomes of patients with pancreatic cancer. Vitamin D has pleiotropic functions beyond calcium-phosphate homeostasis and has been extensively studied both in the laboratory and clinic as a potential preventive agent or adjunct to standard therapies. Accumulating evidence from ecological, observational, and randomized controlled trials suggests that vitamin D has beneficial effects on risk, survival, and mortality in pancreatic cancer, although controversies still exist. Recent advances in demonstrating the important functions of vitamin D/vitamin D receptor (VDR) signaling in the regulation of stromal reprogramming, the microbiome, and immune response and the emergence of checkpoint immunotherapy provide opportunities for using vitamin D or its analogues as an adjunct for pancreatic cancer intervention. Many challenges lie ahead before the benefits of vitamin D can be fully realized in pancreatic cancer. These challenges include the need for randomized controlled trials of vitamin D to assess its impact on the risk and survival of pancreatic cancer, optimizing the timing and dosage of vitamin D or its analogues as an adjunct for pancreatic cancer intervention and elucidating the specific role of vitamin D/VDR signaling in the different stages of pancreatic cancer. Nevertheless, vitamin D holds great promise for reducing risk and improving outcomes of this disease.
    Keywords:  cancer risk; cancer survival; immunotherapy; pancreatic cancer; vitamin D
    DOI:  https://doi.org/10.3390/cancers13112716
  58. Nature. 2021 Jun 02.
    Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy.
    Ana Luísa Correia, Joao C Guimaraes, Priska Auf der Maur, Duvini De Silva, Marcel P Trefny, Ryoko Okamoto, Sandro Bruno, Alexander Schmidt, Kirsten Mertz, Katrin Volkmann, Luigi Terracciano, Alfred Zippelius, Marcus Vetter, Christian Kurzeder, Walter Paul Weber, Mohamed Bentires-Alj.
      The persistence of undetectable disseminated tumour cells (DTCs) after primary tumour resection poses a major challenge to effective cancer treatment1-3. These enduring dormant DTCs are seeds of future metastases, and the mechanisms that switch them from dormancy to outgrowth require definition. Because cancer dormancy provides a unique therapeutic window for preventing metastatic disease, a comprehensive understanding of the distribution, composition and dynamics of reservoirs of dormant DTCs is imperative. Here we show that different tissue-specific microenvironments restrain or allow the progression of breast cancer in the liver-a frequent site of metastasis4 that is often associated with a poor prognosis5. Using mouse models, we show that there is a selective increase in natural killer (NK) cells in the dormant milieu. Adjuvant interleukin-15-based immunotherapy ensures an abundant pool of NK cells that sustains dormancy through interferon-γ signalling, thereby preventing hepatic metastases and prolonging survival. Exit from dormancy follows a marked contraction of the NK cell compartment and the concurrent accumulation of activated hepatic stellate cells (aHSCs). Our proteomics studies on liver co-cultures implicate the aHSC-secreted chemokine CXCL12 in the induction of NK cell quiescence through its cognate receptor CXCR4. CXCL12 expression and aHSC abundance are closely correlated in patients with liver metastases. Our data identify the interplay between NK cells and aHSCs as a master switch of cancer dormancy, and suggest that therapies aimed at normalizing the NK cell pool might succeed in preventing metastatic outgrowth.
    DOI:  https://doi.org/10.1038/s41586-021-03614-z
  59. Cell Chem Biol. 2021 May 22. pii: S2451-9456(21)00223-3. [Epub ahead of print]
    Selective autophagy as the basis of autophagy-based degraders.
    Daiki Takahashi, Hirokazu Arimoto.
      Degrader technologies, which enable the chemical knockdown of disease-causing proteins, are promising for drug discovery. After two decades of research, degraders using the ubiquitin-proteasome system (UPS) are currently in clinical trials. However, the UPS substrates are mainly limited to soluble proteins. Autophagy-targeting chimeras and autophagosome-tethering compounds are degraders that use autophagy, which has functions complementary to the UPS. They can degrade organelles and aggregate-prone proteins, making them promising treatments against age-related conditions such as mitochondrial dysfunction and neurodegenerative diseases. The molecular mechanism of selective autophagy is an ongoing research topic, which explains why autophagy-based degraders were not available until recently. In this review, we introduce four classifications of selective autophagy mechanisms to facilitate the understanding of the degrader design.
    Keywords:  ATTEC; AUTAC; LLPS; S-guanylation; aggregates; autophagy; degrader; mitochondria; p62; ubiquitin
    DOI:  https://doi.org/10.1016/j.chembiol.2021.05.006
  60. Int J Mol Sci. 2021 May 20. pii: 5385. [Epub ahead of print]22(10):
    Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma.
    Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuss, Christiane Zgorzelski, Anne Kraft, Matthias M Gaida.
      Identification of pancreatic ductal adenocarcinoma (PDAC) and precursor lesions in histological tissue slides can be challenging and elaborate, especially due to tumor heterogeneity. Thus, supportive tools for the identification of anatomical and pathological tissue structures are desired. Deep learning methods recently emerged, which classify histological structures into image categories with high accuracy. However, to date, only a limited number of classes and patients have been included in histopathological studies. In this study, scanned histopathological tissue slides from tissue microarrays of PDAC patients (n = 201, image patches n = 81.165) were extracted and assigned to a training, validation, and test set. With these patches, we implemented a convolutional neuronal network, established quality control measures and a method to interpret the model, and implemented a workflow for whole tissue slides. An optimized EfficientNet algorithm achieved high accuracies that allowed automatically localizing and quantifying tissue categories including pancreatic intraepithelial neoplasia and PDAC in whole tissue slides. SmoothGrad heatmaps allowed explaining image classification results. This is the first study that utilizes deep learning for automatic identification of different anatomical tissue structures and diseases on histopathological images of pancreatic tissue specimens. The proposed approach is a valuable tool to support routine diagnostic review and pancreatic cancer research.
    Keywords:  artificial intelligence; convolutional neuronal networks; deep learning; pancreatic cancer
    DOI:  https://doi.org/10.3390/ijms22105385
  61. Dev Cell. 2021 May 28. pii: S1534-5807(21)00435-4. [Epub ahead of print]
    Robustness of epithelial sealing is an emerging property of local ERK feedback driven by cell elimination.
    Léo Valon, Anđela Davidović, Florence Levillayer, Alexis Villars, Mathilde Chouly, Fabiana Cerqueira-Campos, Romain Levayer.
      What regulates the spatiotemporal distribution of cell elimination in tissues remains largely unknown. This is particularly relevant for epithelia with high rates of cell elimination where simultaneous death of neighboring cells could impair epithelial sealing. Here, using the Drosophila pupal notum (a single-layer epithelium) and a new optogenetic tool to trigger caspase activation and cell extrusion, we first showed that death of clusters of at least three cells impaired epithelial sealing; yet, such clusters were almost never observed in vivo. Accordingly, statistical analysis and simulations of cell death distribution highlighted a transient and local protective phase occurring near every cell death. This protection is driven by a transient activation of ERK in cells neighboring extruding cells, which inhibits caspase activation and prevents elimination of cells in clusters. This suggests that the robustness of epithelia with high rates of cell elimination is an emerging property of local ERK feedback.
    Keywords:  Drosophila; ERK; apoptosis; caspase dynamics; cell extrusion; epithelium; optogenetics; self-organization; single-cell live imaging
    DOI:  https://doi.org/10.1016/j.devcel.2021.05.006
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