bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–08–08
35 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Squamousness gain defines pancreatic ductal adenocarcinoma hepatic metastases phenotype, and gemcitabine response.
  2. Uncertain beginnings: acinar and ductal cell plasticity in the development of pancreatic cancer.
  3. Drosophila Larval Models of Invasive Tumorigenesis for In Vivo Studies on Tumour/Peripheral Host Tissue Interactions during Cancer Cachexia.
  4. The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer.
  5. N-Acetylcysteine Reduces the Pro-Oxidant and Inflammatory Responses during Pancreatitis and Pancreas Tumorigenesis.
  6. Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control.
  7. N6-methyladenosine-mediated upregulation of WTAPP1 promotes WTAP translation and Wnt signaling to facilitate pancreatic cancer progression.
  8. LKB1 inactivation modulates chromatin accessibility to drive metastatic progression.
  9. Reductive stress in cancer.
  10. Impact of Senescent Cell Subtypes on Tissue Dysfunction and Repair: Importance and Research Questions.
  11. Apoptosis in the Pancreatic Cancer Tumor Microenvironment-The Double-Edged Sword of Cancer-Associated Fibroblasts.
  12. The Importance of Being PI3K in the RAS Signaling Network.
  13. Association of systemic inflammation with survival in patients with cancer cachexia: results from a multicentre cohort study.
  14. When fat talks, the gut listens: IRONing out metabolism.
  15. Perturbed BMP signaling and denervation promote muscle wasting in cancer cachexia.
  16. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers.
  17. Collagen Organization Does Not Influence T-Cell Distribution in Stroma of Human Pancreatic Cancer.
  18. ERK Inhibition Improves Anti-PD-L1 Immune Checkpoint Blockade in Preclinical Pancreatic Ductal Adenocarcinoma.
  19. Rapid interrogation of cancer cell of origin through CRISPR editing.
  20. Are cachexia-associated tumors transmitTERS of ER stress?
  21. Sequestration to lipid droplets promotes histone availability by preventing turnover of excess histones.
  22. Mitochondrial Dynamics and Mitophagy in Skeletal Muscle Health and Aging.
  23. Transgenic mice for in vivo epigenome editing with CRISPR-based systems.
  24. Dual targeting of CTLA-4 and CD47 on Treg cells promotes immunity against solid tumors.
  25. Spatial omics and multiplexed imaging to explore cancer biology.
  26. Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma.
  27. Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation.
  28. Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation.
  29. SCITO-seq: single-cell combinatorial indexed cytometry sequencing.
  30. Cancer as a Global Health Priority.
  31. Interconnections between circadian clocks and metabolism.
  32. Designer membraneless organelles sequester native factors for control of cell behavior.
  33. How lung cancer cells change identity.
  34. Exercise-induced angiogenesis is dependent on metabolically primed ATF3/4+ endothelial cells.
  35. Healthy Weight Loss Maintenance with Exercise, Liraglutide, or Both Combined.
  1. Eur J Cancer. 2021 Aug 01. pii: S0959-8049(21)00420-2. [Epub ahead of print]155 42-53
    Squamousness gain defines pancreatic ductal adenocarcinoma hepatic metastases phenotype, and gemcitabine response.
    Nicolas A Fraunhoffer, Analia M Abuelafia, Carlos Teyssedou, Eduardo Chuluyan, Martin Bigonnet, Laurent Palazzo, Odile Gayet, Remy Nicolle, Jerome Cros, Juan Iovanna, Nelson Dusetti.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a dismal disease with a survival rate of less than 7%, mainly due to the hepatic metastatic spread. Despite the importance of understanding PDAC metastases, central questions remain concerning their biology and chemosensitivity. Moreover, the transcriptomic divergence between primary tumor (PT) and hepatic metastases (HM) has been poorly studied and without a clear dissection of the confounding tumoral-surrounding tissue.
    METHODS: Here, to unravel key biological features not biased by the surrounding tissue, we implemented a blind source separation based on independent component analysis, ProDenICA, on a treatment-naïve cohort of PDAC paired samples and a cohort of 305 resectable patients. In addition, a time-lapse experiment was performed to assess the gemcitabine chemosensitivity profile between the PT and HM.
    RESULTS: We identified HM's specific transcriptomic characteristics related to the upregulation of cell cycle checkpoint, mitochondria activity, and extracellular matrix reorganization, which could be associated with metastatic niche adaptation mechanisms. Furthermore, squamous lineage emerged as a key feature linked with a downregulation in the epithelial-to-mesenchymal program that can stratifies PDAC HM independent of the classical/basal-like spectrum. Remarkably, we also demonstrated that gemcitabine response is influenced by the squamous profile, being the HM more refractory to the treatment than the PT.
    CONCLUSIONS: These results pointed out divergent HM aspects compared to PT and allowed their stratification through the squamous lineage. Moreover, we unravel a clinical actionable squamous signature that predicts the gemcitabine response.
    Keywords:  Chemosensitivity; Metastases; PDAC; Squamous lineage; Transcriptomic analysis
    DOI:  https://doi.org/10.1016/j.ejca.2021.06.038
  2. Cell Mol Gastroenterol Hepatol. 2021 Aug 02. pii: S2352-345X(21)00160-0. [Epub ahead of print]
    Uncertain beginnings: acinar and ductal cell plasticity in the development of pancreatic cancer.
    Adrien Grimont, Steven D Leach, Rohit Chandwani.
      The pancreas consists of several specialized cell types which display a remarkable ability to alter cellular identity in injury, regeneration, and repair. The abundant cellular plasticity within the pancreas appears to be exploited in tumorigenesis, with metaplastic, dedifferentiation, and transdifferentiation processes central to the development of pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary neoplasms (IPMNs), precursor lesions to pancreatic ductal adenocarcinoma (PDAC). In the face of shifting cellular identity, the cell-of-origin of pancreatic cancer has been difficult to elucidate. However, with the extensive utilization of in vivo lineage-traced mouse models coupled with insights from human samples, it has emerged that the acinar cell is most efficiently able to give rise to both IPMN and PanIN but that acinar and ductal cells can undergo malignant transformation to PDAC. In this review, we discuss the cellular reprogramming that takes place in both the normal and malignant pancreas and evaluate the current state of evidence that implicate both the acinar and ductal cell as context-dependent origins of this deadly disease.
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.07.014
  3. Int J Mol Sci. 2021 Aug 02. pii: 8317. [Epub ahead of print]22(15):
    Drosophila Larval Models of Invasive Tumorigenesis for In Vivo Studies on Tumour/Peripheral Host Tissue Interactions during Cancer Cachexia.
    Joseph A Hodgson, Jean-Philippe Parvy, Yachuan Yu, Marcos Vidal, Julia B Cordero.
      Cancer cachexia is a common deleterious paraneoplastic syndrome that represents an area of unmet clinical need, partly due to its poorly understood aetiology and complex multifactorial nature. We have interrogated multiple genetically defined larval Drosophila models of tumourigenesis against key features of human cancer cachexia. Our results indicate that cachectic tissue wasting is dependent on the genetic characteristics of the tumour and demonstrate that host malnutrition or tumour burden are not sufficient to drive wasting. We show that JAK/STAT and TNF-α/Egr signalling are elevated in cachectic muscle and promote tissue wasting. Furthermore, we introduce a dual driver system that allows independent genetic manipulation of tumour and host skeletal muscle. Overall, we present a novel Drosophila larval paradigm to study tumour/host tissue crosstalk in vivo, which may contribute to future research in cancer cachexia and impact the design of therapeutic approaches for this pathology.
    Keywords:  Drosophila larvae; Ras; Scribble; cancer cachexia; dual driver system
    DOI:  https://doi.org/10.3390/ijms22158317
  4. Cancer Cell. 2021 Jul 27. pii: S1535-6108(21)00384-6. [Epub ahead of print]
    The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer.
    William A Freed-Pastor, Laurens J Lambert, Zackery A Ely, Nimisha B Pattada, Arjun Bhutkar, George Eng, Kim L Mercer, Ana P Garcia, Lin Lin, William M Rideout, William L Hwang, Jason M Schenkel, Alex M Jaeger, Roderick T Bronson, Peter M K Westcott, Tyler D Hether, Prajan Divakar, Jason W Reeves, Vikram Deshpande, Toni Delorey, Devan Phillips, Omer H Yilmaz, Aviv Regev, Tyler Jacks.
      The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune-based strategies to combat this disease have been largely unsuccessful to date. We corroborate prior reports that a substantial portion of PDAC harbors predicted high-affinity MHC class I-restricted neoepitopes and extend these findings to advanced/metastatic disease. Using multiple preclinical models of neoantigen-expressing PDAC, we demonstrate that intratumoral neoantigen-specific CD8+ T cells adopt multiple states of dysfunction, resembling those in tumor-infiltrating lymphocytes of PDAC patients. Mechanistically, genetic and/or pharmacologic modulation of the CD155/TIGIT axis was sufficient to promote immune evasion in autochthonous neoantigen-expressing PDAC. Finally, we demonstrate that the CD155/TIGIT axis is critical in maintaining immune evasion in PDAC and uncover a combination immunotherapy (TIGIT/PD-1 co-blockade plus CD40 agonism) that elicits profound anti-tumor responses in preclinical models, now poised for clinical evaluation.
    Keywords:  CD155; TIGIT; immune evasion; immunotherapy; pancreatic cancer
    DOI:  https://doi.org/10.1016/j.ccell.2021.07.007
  5. Antioxidants (Basel). 2021 Jul 11. pii: 1107. [Epub ahead of print]10(7):
    N-Acetylcysteine Reduces the Pro-Oxidant and Inflammatory Responses during Pancreatitis and Pancreas Tumorigenesis.
    Marie-Albane Minati, Maxime Libert, Hajar Dahou, Patrick Jacquemin, Mohamad Assi.
      Pancreatitis, an inflammation of the pancreas, appears to be a main driver of pancreatic cancer when combined with Kras mutations. In this context, the exact redox mechanisms are not clearly elucidated. Herein, we treated mice expressing a KrasG12D mutation in pancreatic acinar cells with cerulein to induce acute pancreatitis. In the presence of KrasG12D, pancreatitis triggered significantly greater redox unbalance and oxidative damages compared to control mice expressing wild-type Kras alleles. Further analyses identified the disruption in glutathione metabolism as the main redox event occurring during pancreatitis. Compared to the wild-type background, KrasG12D-bearing mice showed a greater responsiveness to treatment with a thiol-containing compound, N-acetylcysteine (NAC). Notably, NAC treatment increased the pancreatic glutathione pool, reduced systemic markers related to pancreatic and liver damages, limited the extent of pancreatic edema and fibrosis as well as reduced systemic and pancreatic oxidative damages. The protective effects of NAC were, at least, partly due to a decrease in the production of tumor necrosis factor-α (TNF-α) by acinar cells, which was concomitant with the inhibition of NF-κB(p65) nuclear translocation. Our data provide a rationale to use thiol-containing compounds as an adjuvant therapy to alleviate the severity of inflammation during pancreatitis and pancreatic tumorigenesis.
    Keywords:  antioxidants; cancer; edema; inflammation; pancreas
    DOI:  https://doi.org/10.3390/antiox10071107
  6. EMBO Rep. 2021 Aug 02. e52289
    Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control.
    Alessio Reggio, Viviana Buonomo, Rayene Berkane, Ramachandra M Bhaskara, Mariana Tellechea, Ivana Peluso, Elena Polishchuk, Giorgia Di Lorenzo, Carmine Cirillo, Marianna Esposito, Adeela Hussain, Antje K Huebner, Christian A Hübner, Carmine Settembre, Gerhard Hummer, Paolo Grumati, Alexandra Stolz.
      Degradation of the endoplasmic reticulum (ER) via selective autophagy (ER-phagy) is vital for cellular homeostasis. We identify FAM134A/RETREG2 and FAM134C/RETREG3 as ER-phagy receptors, which predominantly exist in an inactive state under basal conditions. Upon autophagy induction and ER stress signal, they can induce significant ER fragmentation and subsequent lysosomal degradation. FAM134A, FAM134B/RETREG1, and FAM134C are essential for maintaining ER morphology in a LC3-interacting region (LIR)-dependent manner. Overexpression of any FAM134 paralogue has the capacity to significantly augment the general ER-phagy flux upon starvation or ER-stress. Global proteomic analysis of FAM134 overexpressing and knockout cell lines reveals several protein clusters that are distinctly regulated by each of the FAM134 paralogues as well as a cluster of commonly regulated ER-resident proteins. Utilizing pro-Collagen I, as a shared ER-phagy substrate, we observe that FAM134A acts in a LIR-independent manner and compensates for the loss of FAM134B and FAM134C, respectively. FAM134C instead is unable to compensate for the loss of its paralogues. Taken together, our data show that FAM134 paralogues contribute to common and unique ER-phagy pathways.
    Keywords:  Collagen; ER stress; ER-phagy; FAM134; autophagy
    DOI:  https://doi.org/10.15252/embr.202052289
  7. Cancer Res. 2021 Aug 06. pii: canres.0494.2021. [Epub ahead of print]
    N6-methyladenosine-mediated upregulation of WTAPP1 promotes WTAP translation and Wnt signaling to facilitate pancreatic cancer progression.
    Junge Deng, Jialiang Zhang, Ying Ye, Kaijing Liu, Lingxing Zeng, Jingyi Huang, Ling Pan, Mei Li, Ruihong Bai, Lisha Zhuang, Xudong Huang, Guandi Wu, Lusheng Wei, Yanfen Zheng, Jiachun Su, Shaoping Zhang, Rufu Chen, Dongxin Lin, Jian Zheng.
      Pseudogenes may play important roles in cancer. Here, we explore the mechanism and function of a pseudogene WTAPP1 in the progress of pancreatic ductal adenocarcinoma (PDAC). WTAPP1 RNA was significantly elevated in PDAC and was associated with poor prognosis in patients. Overexpression of WTAPP1 RNA promoted PDAC proliferation and invasiveness in vitro and in vivo. Mechanistically, N6-methyladenosine (m6A) modification stabilized WTAPP1 RNA via CCHC-type zinc finger nucleic acid binding protein (CNBP), resulting in increased levels of WTAPP1 RNA in PDAC cells. Excessive WTAPP1 RNA bound its protein-coding counterpart WT1 associated protein (WTAP) mRNA and recruited more EIF3 translation initiation complex to promote WTAP translation. Increased WTAP protein enhanced the activation of Wnt signaling and provoked the malignant phenotypes of PDAC. Decreasing WTAPP1 RNA significantly suppressed the in vivo growth and metastasis of PDAC cell lines and patient-derived xenografts. These results indicate that m6A-mediated increases in WTAPP1 expression promotes PDAC progression and thus may serve as a therapeutic target.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-0494
  8. Nat Cell Biol. 2021 Aug 02.
    LKB1 inactivation modulates chromatin accessibility to drive metastatic progression.
    Sarah E Pierce, Jeffrey M Granja, M Ryan Corces, Jennifer J Brady, Min K Tsai, Aubrey B Pierce, Rui Tang, Pauline Chu, David M Feldser, Howard Y Chang, Michael C Bassik, William J Greenleaf, Monte M Winslow.
      Metastasis is the leading cause of cancer-related deaths and enables cancer cells to compromise organ function by expanding in secondary sites. Since primary tumours and metastases often share the same constellation of driver mutations, the mechanisms that drive their distinct phenotypes are unclear. Here we show that inactivation of the frequently mutated tumour suppressor gene LKB1 (encoding liver kinase B1) has evolving effects throughout the progression of lung cancer, which leads to the differential epigenetic re-programming of early-stage primary tumours compared with late-stage metastases. By integrating genome-scale CRISPR-Cas9 screening with bulk and single-cell multi-omic analyses, we unexpectedly identify LKB1 as a master regulator of chromatin accessibility in lung adenocarcinoma primary tumours. Using an in vivo model of metastatic progression, we further show that loss of LKB1 activates the early endoderm transcription factor SOX17 in metastases and a metastatic-like sub-population of cancer cells within primary tumours. The expression of SOX17 is necessary and sufficient to drive a second wave of epigenetic changes in LKB1-deficient cells that enhances metastatic ability. Overall, our study demonstrates how the downstream effects of an individual driver mutation can change throughout cancer development, with implications for stage-specific therapeutic resistance mechanisms and the gene regulatory underpinnings of metastatic evolution.
    DOI:  https://doi.org/10.1038/s41556-021-00728-4
  9. Adv Cancer Res. 2021 ;pii: S0065-230X(21)00033-6. [Epub ahead of print]152 383-413
    Reductive stress in cancer.
    Leilei Zhang, Kenneth D Tew.
      Reductive stress is defined as a condition characterized by excess accumulation of reducing equivalents (e.g., NADH, NADPH, GSH), surpassing the activity of endogenous oxidoreductases. Excessive reducing equivalents can perturb cell signaling pathways, change the formation of disulfide bonding in proteins, disturb mitochondrial homeostasis or decrease metabolism. Reductive stress is influenced by cellular antioxidant load, its flux and a subverted homeostasis that paradoxically can result in excess ROS induction. Balanced reducing equivalents and antioxidant enzymes that contribute to reductive stress can be regulated by Nrf2, typically considered as an oxidative stress induced transcription factor. Cancer cells may coordinate distinct pools of redox couples under reductive stress and these may link to biological consequences from both molecular and translational standpoints. In cancer, there is recent interest in understanding how selective induction of reductive stress may influence therapeutic management and disease progression.
    Keywords:  Cellular homeostasis; GSH; NADH; NADPH; Oxidative stress; ROS; Reducing equivalents; Reductive stress
    DOI:  https://doi.org/10.1016/bs.acr.2021.03.009
  10. Mech Ageing Dev. 2021 Aug 02. pii: S0047-6374(21)00120-2. [Epub ahead of print]198 111548
    Impact of Senescent Cell Subtypes on Tissue Dysfunction and Repair: Importance and Research Questions.
    Utkarsh Tripathi, Avanish Misra, Tamar Tchkonia, James L Kirkland.
      Cellular senescence, first observed and defined through cell culture studies, is a cell fate associated with essentially permanent cell cycle arrest and that can be triggered by a variety of inducers. Emerging evidence suggests senescence is a dynamic process with diverse functional characteristics. Depending on the tissue, type of inducer, and time since induction, senescent cells can promote tissue repair and re-modeling, prevent tumor development, or contribute to age-related disorders and chronic diseases, including cancers. Senescent cell characteristics appear to depend on multiple factors and be influenced by the milieu and other senescent cells locally and at a distance. We review diverse phenotypes of senescent cells originating from different cell types, senescence inducers over time since induction of senescence, and across conditions and diseases. This background is essential to inform further understanding about senescent cell subtypes and will point towards rational senescence-modulating strategies for achieving therapeutic benefit.
    Keywords:  Cellular senescence; Deleterious senescent cell subtype; Helper senescent cell subtype; Senolytics
    DOI:  https://doi.org/10.1016/j.mad.2021.111548
  11. Cells. 2021 Jul 01. pii: 1653. [Epub ahead of print]10(7):
    Apoptosis in the Pancreatic Cancer Tumor Microenvironment-The Double-Edged Sword of Cancer-Associated Fibroblasts.
    Ester Pfeifer, Joy M Burchell, Francesco Dazzi, Debashis Sarker, Richard Beatson.
      Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis. This is attributed to the disease already being advanced at presentation and having a particularly aggressive tumor biology. The PDAC tumor microenvironment (TME) is characterized by a dense desmoplastic stroma, dominated by cancer-associated fibroblasts (CAF), extracellular matrix (ECM) and immune cells displaying immunosuppressive phenotypes. Due to the advanced stage at diagnosis, the depletion of immune effector cells and lack of actionable genomic targets, the standard treatment is still apoptosis-inducing regimens such as chemotherapy. Paradoxically, it has emerged that the direct induction of apoptosis of cancer cells may fuel oncogenic processes in the TME, including education of CAF and immune cells towards pro-tumorigenic phenotypes. The direct effect of cytotoxic therapies on CAF may also enhance tumorigenesis. With the awareness that CAF are the predominant cell type in PDAC driving tumorigenesis with various tumor supportive functions, efforts have been made to try to target them. However, efforts to target CAF have, to date, shown disappointing results in clinical trials. With the help of sophisticated single cell analyses it is now appreciated that CAF in PDAC are a heterogenous population with both tumor supportive and tumor suppressive functions. Hence, there remains a debate whether targeting CAF in PDAC is a valid therapeutic strategy. In this review we discuss how cytotoxic therapies and the induction of apoptosis in PDAC fuels oncogenesis by the education of surrounding stromal cells, with a particular focus on the potential pro-tumorigenic outcomes arising from targeting CAF. In addition, we explore therapeutic avenues to potentially avoid the oncogenic effects of apoptosis in PDAC CAF.
    Keywords:  CAF; PDAC; TME; apoptosis; fibroblasts; pancreatic cancer; stroma; tumor microenvironment
    DOI:  https://doi.org/10.3390/cells10071653
  12. Genes (Basel). 2021 Jul 19. pii: 1094. [Epub ahead of print]12(7):
    The Importance of Being PI3K in the RAS Signaling Network.
    Cristina Cuesta, Cristina Arévalo-Alameda, Esther Castellano.
      Ras proteins are essential mediators of a multitude of cellular processes, and its deregulation is frequently associated with cancer appearance, progression, and metastasis. Ras-driven cancers are usually aggressive and difficult to treat. Although the recent Food and Drug Administration (FDA) approval of the first Ras G12C inhibitor is an important milestone, only a small percentage of patients will benefit from it. A better understanding of the context in which Ras operates in different tumor types and the outcomes mediated by each effector pathway may help to identify additional strategies and targets to treat Ras-driven tumors. Evidence emerging in recent years suggests that both oncogenic Ras signaling in tumor cells and non-oncogenic Ras signaling in stromal cells play an essential role in cancer. PI3K is one of the main Ras effectors, regulating important cellular processes such as cell viability or resistance to therapy or angiogenesis upon oncogenic Ras activation. In this review, we will summarize recent advances in the understanding of Ras-dependent activation of PI3K both in physiological conditions and cancer, with a focus on how this signaling pathway contributes to the formation of a tumor stroma that promotes tumor cell proliferation, migration, and spread.
    Keywords:  PI3-Kinase; Ras oncogenes
    DOI:  https://doi.org/10.3390/genes12071094
  13. J Cachexia Sarcopenia Muscle. 2021 Aug 02.
    Association of systemic inflammation with survival in patients with cancer cachexia: results from a multicentre cohort study.
    Qi Zhang, Meng-Meng Song, Xi Zhang, Jia-Shan Ding, Guo-Tian Ruan, Xiao-Wei Zhang, Tong Liu, Ming Yang, Yi-Zhong Ge, Meng Tang, Xiang-Rui Li, Liang Qian, Chun-Hua Song, Hong-Xia Xu, Han-Ping Shi.
       BACKGROUND: Although systemic inflammation is an important feature of the cancer cachexia, studies on the association between systemic inflammation and prognostic of cancer cachexia are limited. The objective of this study is to evaluate whether the neutrophil-to-lymphocyte ratio (NLR) is associated with outcome and quality of life for patients with cancer cachexia and investigated any interaction between NLR and the clinical parameters.
    METHODS: This is a multicentre cohort study of 2612 cancer patients suffering from cachexia diagnosed between June 2012 and December 2019. The main parameters measured were overall survival (OS) time and all-cause mortality. The association between NLR and all-cause mortality was evaluated using hazard ratios (HRs) and the restricted cubic spline model with a two-sided P-value. Optimal stratification was used to solve threshold points. We also evaluated the cross-classification of NLR for each variable of survival.
    RESULTS: Of the 2612 participants diagnosed with cancer cachexia, 1533 (58.7%) were male, and the mean (SD) age was 58.7 (11.7) years. Over a median follow-up of 4.5 years, we observed 1189 deaths. The overall mortality rate for patients with cancer cachexia during the first 12 months was 30.2% (95%CI: 28.4%-32.0%), resulting in a rate of 226.07 events per 1000 patient-years. An increase in NLR had an inverted L-shaped dose-response association with all-cause mortality. The optimal cut-off point for NLR as a predictor of mortality in cancer patients with cachexia was 3.5. An NLR of 3.5 or greater could independently predict OS (HR, 1.51, 95%CI: 1.33-1.71). These associations were consistent across subtypes of cancer. Several potential effect modifiers were identified including gender, BMI, tumour type, KPS score and albumin in content. Increasing NLRs were independently associated with a worsening in the majority of EORTC QLQ-C30 domains. Elevated baseline NLR was associated with low response and poor survival in patients treated with immunotherapy.
    CONCLUSIONS: The baseline NLR status was found to be a significant negative prognostic biomarker for patients with cachexia; this effect was independent of other known prognostic factors.
    Keywords:  Cachexia; Neutrophil-to-lymphocyte ratio; Prognostic; Systemic inflammation
    DOI:  https://doi.org/10.1002/jcsm.12761
  14. Cell Metab. 2021 Aug 03. pii: S1550-4131(21)00328-4. [Epub ahead of print]33(8): 1505-1506
    When fat talks, the gut listens: IRONing out metabolism.
    Mirian Krystel De Siqueira, Claudio J Villanueva.
      In a new study, Zhang et al. (2021) show that reducing iron levels in adipose tissue improves metabolic function. This occurs through an interorgan communication system where signals from the adipocyte reduce intestinal lipid absorption.
    DOI:  https://doi.org/10.1016/j.cmet.2021.07.012
  15. Sci Transl Med. 2021 Aug 04. pii: eaay9592. [Epub ahead of print]13(605):
    Perturbed BMP signaling and denervation promote muscle wasting in cancer cachexia.
    Roberta Sartori, Adam Hagg, Sandra Zampieri, Andrea Armani, Catherine E Winbanks, Laís R Viana, Mouna Haidar, Kevin I Watt, Hongwei Qian, Camilla Pezzini, Pardis Zanganeh, Bradley J Turner, Anna Larsson, Gianpietro Zanchettin, Elisa S Pierobon, Lucia Moletta, Michele Valmasoni, Alberto Ponzoni, Shady Attar, Gianfranco Da Dalt, Cosimo Sperti, Monika Kustermann, Rachel E Thomson, Lars Larsson, Kate L Loveland, Paola Costelli, Aram Megighian, Stefano Merigliano, Fabio Penna, Paul Gregorevic, Marco Sandri.
      Most patients with advanced solid cancers exhibit features of cachexia, a debilitating syndrome characterized by progressive loss of skeletal muscle mass and strength. Because the underlying mechanisms of this multifactorial syndrome are incompletely defined, effective therapeutics have yet to be developed. Here, we show that diminished bone morphogenetic protein (BMP) signaling is observed early in the onset of skeletal muscle wasting associated with cancer cachexia in mouse models and in patients with cancer. Cancer-mediated factors including Activin A and IL-6 trigger the expression of the BMP inhibitor Noggin in muscle, which blocks the actions of BMPs on muscle fibers and motor nerves, subsequently causing disruption of the neuromuscular junction (NMJ), denervation, and muscle wasting. Increasing BMP signaling in the muscles of tumor-bearing mice by gene delivery or pharmacological means can prevent muscle wasting and preserve measures of NMJ function. The data identify perturbed BMP signaling and denervation of muscle fibers as important pathogenic mechanisms of muscle wasting associated with tumor growth. Collectively, these findings present interventions that promote BMP-mediated signaling as an attractive strategy to counteract the loss of functional musculature in patients with cancer.
    DOI:  https://doi.org/10.1126/scitranslmed.aay9592
  16. Cell Rep Med. 2021 Jul 20. 2(7): 100349
    Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers.
    CTD2 Research Network
      Uncoupling of mRNA expression from copy number (UECN) might be a strategy for cancer cells to a tolerate high degree of aneuploidy. To test the extent and role of UECN across cancers, we perform integrative multiomic analysis of The Cancer Genome Atlas (TCGA) dataset, encompassing ∼5,000 individual tumors. We find UECN is common in cancers and is associated with increased oncogenic signaling, proliferation, and immune suppression. UECN appears to be orchestrated by complex regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we develop a systems-biology approach to identify candidate TFs, which could serve as targets to disrupt UECN and reduce tumor fitness. Applying our approach to TCGA data, we identify 21 putative targets, 42.8% of which are validated by independent sources. Together, our study indicates that UECN is likely an important mechanism in development of aneuploid tumors and might be therapeutically targetable.
    Keywords:  CNVs; TCGA; aneuploidy; cancer biology; immune evasion; target discovery; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.xcrm.2021.100349
  17. Cancers (Basel). 2021 Jul 21. pii: 3648. [Epub ahead of print]13(15):
    Collagen Organization Does Not Influence T-Cell Distribution in Stroma of Human Pancreatic Cancer.
    Eva-Maria Kamionka, Baifeng Qian, Wolfgang Gross, Frank Bergmann, Thilo Hackert, Carlo A Beretta, Nicolas Dross, Eduard Ryschich.
      The dominant intrastromal T-cell infiltration in pancreatic cancer is mainly caused by the contact guidance through the excessive desmoplastic reaction and could represent one of the obstacles to an effective immune response in this tumor type. This study analyzed the collagen organization in normal and malignant pancreatic tissues as well as its influence on T-cell distribution in pancreatic cancer. Human pancreatic tissue was analyzed using immunofluorescence staining and multiphoton and SHG microscopy supported by multistep image processing. The influence of collagen alignment on activated T-cells was studied using 3D matrices and time-lapse microscopy. It was found that the stroma of malignant and normal pancreatic tissues was characterized by complex individual organization. T-cells were heterogeneously distributed in pancreatic cancer and there was no relationship between T-cell distribution and collagen organization. There was a difference in the angular orientation of collagen alignment in the peritumoral and tumor-cell-distant stroma regions in the pancreatic ductal adenocarcinoma tissue, but there was no correlation in the T-cell densities between these regions. The grade of collagen alignment did not influence the directionality of T-cell migration in the 3D collagen matrix. It can be concluded that differences in collagen organization do not change the spatial orientation of T-cell migration or influence stromal T-cell distribution in human pancreatic cancer. The results of the present study do not support the rationale of remodeling of stroma collagen organization for improvement of T-cell-tumor cell contact in pancreatic ductal adenocarcinoma.
    Keywords:  T-cell infiltration; chemokines; collagen organization; human pancreatic cancer; tumor stroma
    DOI:  https://doi.org/10.3390/cancers13153648
  18. Mol Cancer Ther. 2021 Aug 04. pii: molcanther.MCT-20-1112-A.2020. [Epub ahead of print]
    ERK Inhibition Improves Anti-PD-L1 Immune Checkpoint Blockade in Preclinical Pancreatic Ductal Adenocarcinoma.
    Kelly E Henry, Kyeara N Mack, Veronica L Nagle, Mike Cornejo, Adam O Michel, Ian L Fox, Maria Davydova, Thomas R Dilling, Nagavarakishore Pillarsetty, Jason S Lewis.
      Pancreatic ductal adenocarcinoma (PDAC) patients do not benefit from immune checkpoint blockade (ICB) along the PD-1/PD-L1 axis. Variable PD-L1 expression in PDAC indicates a potential access issue of PD-L1-targeted therapy. In order to monitor target engagement of PD-L1 targeted therapy, we generated a PD-L1 targeted PET tracer labeled with zirconium-89 (89Zr). As the MAPK signaling pathway (MEK and ERK) is known to modulate PD-L1 expression in other tumor types, we used [89Zr]Zr-DFO-anti-PD-L1 as a tool to non-invasively assess whether manipulation of the MAPK signaling cascade could be leveraged to modulate PD-L1 expression and thereby immunotherapeutic outcomes in PDAC. In this study, we observed that the inhibition of MEK or ERK is sufficient to increase PD-L1 expression, which we hypothesized could be leveraged for anti-PD-L1 immune checkpoint therapy. We found that the combination of ERK inhibition and anti-PD-L1 therapy indeed corresponded with a significant improvement of overall survival in a syngeneic mouse model of PDAC. Furthermore, immunohistochemical analysis indicates that the survival benefit may be CD8+ T-cell mediated. The therapeutic and molecular imaging tool kit developed could be exploited to better structure clinical trials and address the therapeutic gaps in challenging malignancies such as PDAC.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-20-1112
  19. Proc Natl Acad Sci U S A. 2021 Aug 10. pii: e2110344118. [Epub ahead of print]118(32):
    Rapid interrogation of cancer cell of origin through CRISPR editing.
    Weiran Feng, Zhen Cao, Pei Xin Lim, Huiyong Zhao, Hanzhi Luo, Ninghui Mao, Young Sun Lee, Aura Agudelo Rivera, Danielle Choi, Chao Wu, Teng Han, Rodrigo Romero, Elisa de Stanchina, Brett S Carver, Qiao Wang, Maria Jasin, Charles L Sawyers.
      The increasing complexity of different cell types revealed by single-cell analysis of tissues presents challenges in efficiently elucidating their functions. Here we show, using prostate as a model tissue, that primary organoids and freshly isolated epithelial cells can be CRISPR edited ex vivo using Cas9-sgRNA (guide RNA) ribotnucleoprotein complex technology, then orthotopically transferred in vivo into immunocompetent or immunodeficient mice to generate cancer models with phenotypes resembling those seen in traditional genetically engineered mouse models. Large intrachromosomal (∼2 Mb) or multigenic deletions can be engineered efficiently without the need for selection, including in isolated subpopulations to address cell-of-origin questions.
    Keywords:  CRISPR; cancer modeling; editing; organoids
    DOI:  https://doi.org/10.1073/pnas.2110344118
  20. Biochem Soc Trans. 2021 Aug 02. pii: BST20210496. [Epub ahead of print]
    Are cachexia-associated tumors transmitTERS of ER stress?
    Ana Sayuri Yamagata, Paula Paccielli Freire.
      Cancer cachexia is associated with deficient response to chemotherapy. On the other hand, the tumors of cachectic patients remarkably express more chemokines and have higher immune infiltration. For immunogenicity, a strong induction of the unfolded protein response (UPR) is necessary. UPR followed by cell surface exposure of calreticulin on the dying tumor cell is essential for its engulfment by macrophages and dendritic cells. However, some tumor cells upon endoplasmic reticulum (ER) stress can release factors that induce ER stress to other cells, in the so-called transmissible ER stress (TERS). The cells that received TERS produce more interleukin 6 (IL-6) and chemokines and acquire resistance to subsequent ER stress, nutrient deprivation, and genotoxic stress. Since ER stress enhances the release of extracellular vesicles (EVs), we suggest they can mediate TERS. It was found that ER stressed cachexia-inducing tumor cells transmit factors that trigger ER stress in other cells. Therefore, considering the role of EVs in cancer cachexia, the release of exosomes can possibly play a role in the process of blunting the immunogenicity of the cachexia-associated tumors. We propose that TERS can cause an inflammatory and immunosuppressive phenotype in cachexia-inducing tumors.
    Keywords:  ER stress; cachexia; cancer; immunology; tumor microenvironment
    DOI:  https://doi.org/10.1042/BST20210496
  21. Development. 2021 Aug 01. pii: dev199381. [Epub ahead of print]148(15):
    Sequestration to lipid droplets promotes histone availability by preventing turnover of excess histones.
    Roxan A Stephenson, Jonathon M Thomalla, Lili Chen, Petra Kolkhof, Roger P White, Mathias Beller, Michael A Welte.
      Because both dearth and overabundance of histones result in cellular defects, histone synthesis and demand are typically tightly coupled. In Drosophila embryos, histones H2B, H2A and H2Av accumulate on lipid droplets (LDs), which are cytoplasmic fat storage organelles. Without LD binding, maternally provided H2B, H2A and H2Av are absent; however, how LDs ensure histone storage is unclear. Using quantitative imaging, we uncover when during oogenesis these histones accumulate, and which step of accumulation is LD dependent. LDs originate in nurse cells (NCs) and are transported to the oocyte. Although H2Av accumulates on LDs in NCs, the majority of the final H2Av pool is synthesized in oocytes. LDs promote intercellular transport of the histone anchor Jabba and thus its presence in the ooplasm. Ooplasmic Jabba then prevents H2Av degradation, safeguarding the H2Av stockpile. Our findings provide insight into the mechanism for establishing histone stores during Drosophila oogenesis and shed light on the function of LDs as protein-sequestration sites.
    Keywords:   Drosophila oogenesis; Histones; Lipid droplets; Proteasome; Protein sequestration; Protein turnover
    DOI:  https://doi.org/10.1242/dev.199381
  22. Int J Mol Sci. 2021 Jul 30. pii: 8179. [Epub ahead of print]22(15):
    Mitochondrial Dynamics and Mitophagy in Skeletal Muscle Health and Aging.
    Jean-Philippe Leduc-Gaudet, Sabah N A Hussain, Esther Barreiro, Gilles Gouspillou.
      The maintenance of mitochondrial integrity is critical for muscle health. Mitochondria, indeed, play vital roles in a wide range of cellular processes, including energy supply, Ca2+ homeostasis, retrograde signaling, cell death, and many others. All mitochondria-containing cells, including skeletal muscle cells, dispose of several pathways to maintain mitochondrial health, including mitochondrial biogenesis, mitochondrial-derived vesicles, mitochondrial dynamics (fusion and fission process shaping mitochondrial morphology), and mitophagy-the process in charge of the removal of mitochondria though autophagy. The loss of skeletal muscle mass (atrophy) is a major health problem worldwide, especially in older people. Currently, there is no treatment to counteract the progressive decline in skeletal muscle mass and strength that occurs with aging, a process termed sarcopenia. There is increasing data, including our own, suggesting that accumulation of dysfunctional mitochondria contributes to the development of sarcopenia. Impairments in mitochondrial dynamics and mitophagy were recently proposed to contribute to sarcopenia. This review summarizes the current state of knowledge on the role played by mitochondrial dynamics and mitophagy in skeletal muscle health and in the development of sarcopenia. We also highlight recent studies showing that enhancing mitophagy in skeletal muscle is a promising therapeutic target to prevent or even treat skeletal muscle dysfunction in the elderly.
    Keywords:  aging; autophagy; mitochondrial dynamics; mitophagy; sarcopenia; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms22158179
  23. Nat Methods. 2021 Aug;18(8): 965-974
    Transgenic mice for in vivo epigenome editing with CRISPR-based systems.
    Matthew P Gemberling, Keith Siklenka, Erica Rodriguez, Katherine R Tonn-Eisinger, Alejandro Barrera, Fang Liu, Ariel Kantor, Liqing Li, Valentina Cigliola, Mariah F Hazlett, Courtney A Williams, Luke C Bartelt, Victoria J Madigan, Josephine C Bodle, Heather Daniels, Douglas C Rouse, Isaac B Hilton, Aravind Asokan, Maria Ciofani, Kenneth D Poss, Timothy E Reddy, Anne E West, Charles A Gersbach.
      CRISPR-Cas9 technologies have dramatically increased the ease of targeting DNA sequences in the genomes of living systems. The fusion of chromatin-modifying domains to nuclease-deactivated Cas9 (dCas9) has enabled targeted epigenome editing in both cultured cells and animal models. However, delivering large dCas9 fusion proteins to target cells and tissues is an obstacle to the widespread adoption of these tools for in vivo studies. Here, we describe the generation and characterization of two conditional transgenic mouse lines for epigenome editing, Rosa26:LSL-dCas9-p300 for gene activation and Rosa26:LSL-dCas9-KRAB for gene repression. By targeting the guide RNAs to transcriptional start sites or distal enhancer elements, we demonstrate regulation of target genes and corresponding changes to epigenetic states and downstream phenotypes in the brain and liver in vivo, and in T cells and fibroblasts ex vivo. These mouse lines are convenient and valuable tools for facile, temporally controlled, and tissue-restricted epigenome editing and manipulation of gene expression in vivo.
    DOI:  https://doi.org/10.1038/s41592-021-01207-2
  24. Sci Transl Med. 2021 Aug 04. pii: eabg8693. [Epub ahead of print]13(605):
    Dual targeting of CTLA-4 and CD47 on Treg cells promotes immunity against solid tumors.
    Anli Zhang, Zhenhua Ren, Kuo-Fu Tseng, Xiaojuan Liu, Huiyu Li, Changzheng Lu, Yueqi Cai, John D Minna, Yang-Xin Fu.
      Blockade of CD47, the "do not eat me" signal, has limited effects in solid tumors despite its potent antitumor effects in hematopoietic malignancies. Taking advantage of the high expression of cytotoxic T lymphocyte-associated protein 4 (CTLA-4) on Treg cells and abundant Fc receptor-expressing active phagocytes inside the tumor microenvironment (TME), we designed and tested a heterodimer combining an anti-CTLA-4 antibody, which targets Treg cells, with the CD47 ligand, signal regulatory protein α (SIRPα), to selectively block CD47 on intratumoral Treg cells. We hypothesized that heterodimer treatment would increase antibody-dependent cellular phagocytosis of the targeted Treg cells. We found that anti-CTLA-4×SIRPα preferentially depleted ICOShigh immunosuppressive Treg cells in the TME and enhanced immunity against solid tumors, including MC38 and CT26 murine colon cancers. Mechanistically, we found that CD47 expression on Treg cells limited anti-CTLA-4-mediated depletion and Fc on the heterodimer-enhanced depletion. Furthermore, anti-human CTLA-4×SIRPα depleted tumor Treg cells and exhibits less toxicity than anti-human CTLA-4 in a humanized mouse model. Collectively, these results demonstrate that simultaneously modulating both "eat me" and do not eat me signals induces Treg cell depletion inside the TME and may be an effective strategy for treating solid tumors.
    DOI:  https://doi.org/10.1126/scitranslmed.abg8693
  25. Nat Methods. 2021 Aug 02.
    Spatial omics and multiplexed imaging to explore cancer biology.
    Sabrina M Lewis, Marie-Liesse Asselin-Labat, Quan Nguyen, Jean Berthelet, Xiao Tan, Verena C Wimmer, Delphine Merino, Kelly L Rogers, Shalin H Naik.
      Understanding intratumoral heterogeneity-the molecular variation among cells within a tumor-promises to address outstanding questions in cancer biology and improve the diagnosis and treatment of specific cancer subtypes. Single-cell analyses, especially RNA sequencing and other genomics modalities, have been transformative in revealing novel biomarkers and molecular regulators associated with tumor growth, metastasis and drug resistance. However, these approaches fail to provide a complete picture of tumor biology, as information on cellular location within the tumor microenvironment is lost. New technologies leveraging multiplexed fluorescence, DNA, RNA and isotope labeling enable the detection of tens to thousands of cancer subclones or molecular biomarkers within their native spatial context. The expeditious growth in these techniques, along with methods for multiomics data integration, promises to yield a more comprehensive understanding of cell-to-cell variation within and between individual tumors. Here we provide the current state and future perspectives on the spatial technologies expected to drive the next generation of research and diagnostic and therapeutic strategies for cancer.
    DOI:  https://doi.org/10.1038/s41592-021-01203-6
  26. Cells. 2021 Jul 19. pii: 1821. [Epub ahead of print]10(7):
    Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma.
    Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Frank-Ulrich Weiss, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar Chromik, Markus Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers. Developing biomarkers for early detection and chemotherapeutic response prediction is crucial to improve the dismal prognosis of PDAC patients. However, molecular cancer signatures based on transcriptome analysis do not reflect intratumoral heterogeneity. To explore a more accurate stratification of PDAC phenotypes in an easily accessible matrix, plasma metabolome analysis using MxP® Global Profiling and MxP® Lipidomics was performed in 361 PDAC patients. We identified three metabolic PDAC subtypes associated with distinct complex lipid patterns. Subtype 1 was associated with reduced ceramide levels and a strong enrichment of triacylglycerols. Subtype 2 demonstrated increased abundance of ceramides, sphingomyelin and other complex sphingolipids, whereas subtype 3 showed decreased levels of sphingolipid metabolites in plasma. Pathway enrichment analysis revealed that sphingolipid-related pathways differ most among subtypes. Weighted correlation network analysis (WGCNA) implied PDAC subtypes differed in their metabolic programs. Interestingly, a reduced expression among related pathway genes in tumor tissue was associated with the lowest survival rate. However, our metabolic PDAC subtypes did not show any correlation to the described molecular PDAC subtypes. Our findings pave the way for further studies investigating sphingolipids metabolisms in PDAC.
    Keywords:  complex lipids; metabolic subtypes; pancreatic ductal adenocarcinoma; sphingolipids
    DOI:  https://doi.org/10.3390/cells10071821
  27. Cell Rep. 2021 Aug 03. pii: S2211-1247(21)00914-1. [Epub ahead of print]36(5): 109487
    Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation.
    Kevin B Koronowski, Carolina M Greco, He Huang, Jin-Kwang Kim, Jennifer L Fribourgh, Priya Crosby, Lavina Mathur, Xuelian Ren, Carrie L Partch, Cholsoon Jang, Feng Qiao, Yingming Zhao, Paolo Sassone-Corsi.
      Ketone bodies are bioactive metabolites that function as energy substrates, signaling molecules, and regulators of histone modifications. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, and associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification, and one-carbon metabolic pathways. Kbhb inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, in parallel with altered metabolite levels. Our results illuminate the role of Kbhb in hepatic metabolism under ketogenic conditions and demonstrate a functional consequence of this modification on a central metabolic enzyme.
    Keywords:  AHCY; S-adenosyl-L-homocysteine hydrolase; ketogenesis; ketogenic diet; liver metabolism; lysine acylation; methionine cycle; β-hydroxybutyrate; β-hydroxybutyrylation
    DOI:  https://doi.org/10.1016/j.celrep.2021.109487
  28. Cell Stem Cell. 2021 Jul 28. pii: S1934-5909(21)00287-3. [Epub ahead of print]
    Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation.
    Lucía Cordero-Espinoza, Anna M Dowbaj, Timo N Kohler, Bernhard Strauss, Olga Sarlidou, German Belenguer, Clare Pacini, Nuno P Martins, Ross Dobie, John R Wilson-Kanamori, Richard Butler, Nicole Prior, Palle Serup, Florian Jug, Neil C Henderson, Florian Hollfelder, Meritxell Huch.
      In the liver, ductal cells rarely proliferate during homeostasis but do so transiently after tissue injury. These cells can be expanded as organoids that recapitulate several of the cell-autonomous mechanisms of regeneration but lack the stromal interactions of the native tissue. Here, using organoid co-cultures that recapitulate the ductal-to-mesenchymal cell architecture of the portal tract, we demonstrate that a subpopulation of mouse periportal mesenchymal cells exerts dual control on proliferation of the epithelium. Ductal cell proliferation is either induced and sustained or, conversely, completely abolished, depending on the number of direct mesenchymal cell contacts, through a mechanism mediated, at least in part, by Notch signaling. Our findings expand the concept of the cellular niche in epithelial tissues, whereby not only soluble factors but also cell-cell contacts are the key regulatory cues involved in the control of cellular behaviors, suggesting a critical role for cell-cell contacts during regeneration.
    Keywords:  droplet microfluidics; flow-focussing device; liver; liver ductal cell; mesenchyme; multicellular co-culture; niche; organoid; organotypic co-culture; regeneration
    DOI:  https://doi.org/10.1016/j.stem.2021.07.002
  29. Nat Methods. 2021 Aug;18(8): 903-911
    SCITO-seq: single-cell combinatorial indexed cytometry sequencing.
    Byungjin Hwang, David S Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George C Hartoularos, Aidan Winters, Bertrand Z Yeung, Kristopher L Nazor, Yun S Song, Eric D Chow, Matthew H Spitzer, Chun Jimmie Ye.
      The development of DNA-barcoded antibodies to tag cell surface molecules has enabled the use of droplet-based single-cell sequencing (dsc-seq) to profile protein abundances from thousands of cells simultaneously. As compared to flow and mass cytometry, the high per cell cost of current dsc-seq-based workflows precludes their use in clinical applications and large-scale pooled screens. Here, we introduce SCITO-seq, a workflow that uses splint oligonucleotides (oligos) to enable combinatorially indexed dsc-seq of DNA-barcoded antibodies from over 105 cells per reaction using commercial microfluidics. By encoding sample barcodes into splint oligos, we demonstrate that multiplexed SCITO-seq produces reproducible estimates of cellular composition and surface protein expression comparable to those from mass cytometry. We further demonstrate two modified splint oligo designs that extend SCITO-seq to achieve compatibility with commercial DNA-barcoded antibodies and simultaneous expression profiling of the transcriptome and surface proteins from the same cell. These results demonstrate SCITO-seq as a flexible and ultra-high-throughput platform for sequencing-based single-cell protein and multimodal profiling.
    DOI:  https://doi.org/10.1038/s41592-021-01222-3
  30. JAMA. 2021 Aug 06.
    Cancer as a Global Health Priority.
    Satish Gopal, Norman E Sharpless.
      
    DOI:  https://doi.org/10.1001/jama.2021.12778
  31. J Clin Invest. 2021 Aug 02. pii: 148278. [Epub ahead of print]131(15):
    Interconnections between circadian clocks and metabolism.
    Dongyin Guan, Mitchell A Lazar.
      Circadian rhythms evolved through adaptation to daily light/dark changes in the environment; they are believed to be regulated by the core circadian clock interlocking feedback loop. Recent studies indicate that each core component executes general and specific functions in metabolism. Here, we review the current understanding of the role of these core circadian clock genes in the regulation of metabolism using various genetically modified animal models. Additionally, emerging evidence shows that exposure to environmental stimuli, such as artificial light, unbalanced diet, mistimed eating, and exercise, remodels the circadian physiological processes and causes metabolic disorders. This Review summarizes the reciprocal regulation between the circadian clock and metabolism, highlights remaining gaps in knowledge about the regulation of circadian rhythms and metabolism, and examines potential applications to human health and disease.
    DOI:  https://doi.org/10.1172/JCI148278
  32. Nat Chem Biol. 2021 Aug 02.
    Designer membraneless organelles sequester native factors for control of cell behavior.
    Mikael V Garabedian, Wentao Wang, Jorge B Dabdoub, Michelle Tong, Reese M Caldwell, William Benman, Benjamin S Schuster, Alexander Deiters, Matthew C Good.
      Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron-size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to 90% of targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.
    DOI:  https://doi.org/10.1038/s41589-021-00840-4
  33. Elife. 2021 Aug 04. pii: e71610. [Epub ahead of print]10
    How lung cancer cells change identity.
    Mitchell S von Itzstein, Benjamin J Drapkin, John D Minna.
      Changes in MAPK signaling allow lung cancer cells to transition between lineages that respond differently to treatment.
    Keywords:  ERK signaling; cancer biology; human; lineage switching; lineage transformation; lung cancer
    DOI:  https://doi.org/10.7554/eLife.71610
  34. Cell Metab. 2021 Jul 30. pii: S1550-4131(21)00331-4. [Epub ahead of print]
    Exercise-induced angiogenesis is dependent on metabolically primed ATF3/4+ endothelial cells.
    Zheng Fan, Guillermo Turiel, Raphaela Ardicoglu, Moheb Ghobrial, Evi Masschelein, Tea Kocijan, Jing Zhang, Ge Tan, Gillian Fitzgerald, Tatiane Gorski, Abdiel Alvarado-Diaz, Paola Gilardoni, Christopher M Adams, Bart Ghesquière, Katrien De Bock.
      Exercise is a powerful driver of physiological angiogenesis during adulthood, but the mechanisms of exercise-induced vascular expansion are poorly understood. We explored endothelial heterogeneity in skeletal muscle and identified two capillary muscle endothelial cell (mEC) populations that are characterized by differential expression of ATF3/4. Spatial mapping showed that ATF3/4+ mECs are enriched in red oxidative muscle areas while ATF3/4low ECs lie adjacent to white glycolytic fibers. In vitro and in vivo experiments revealed that red ATF3/4+ mECs are more angiogenic when compared with white ATF3/4low mECs. Mechanistically, ATF3/4 in mECs control genes involved in amino acid uptake and metabolism and metabolically prime red (ATF3/4+) mECs for angiogenesis. As a consequence, supplementation of non-essential amino acids and overexpression of ATF4 increased proliferation of white mECs. Finally, deleting Atf4 in ECs impaired exercise-induced angiogenesis. Our findings illustrate that spatial metabolic angiodiversity determines the angiogenic potential of muscle ECs.
    Keywords:  amino acid metabolism; endothelial heterogeneity; endothelial metabolism; exercise; muscle angiogenesis; single-cell RNA-seq
    DOI:  https://doi.org/10.1016/j.cmet.2021.07.015
  35. N Engl J Med. 2021 Aug 05. pii: 10.1056/NEJMc2109509#sa2. [Epub ahead of print]385(6): 572-573
    Healthy Weight Loss Maintenance with Exercise, Liraglutide, or Both Combined.
    Chidiebere E Okechukwu.
      
    DOI:  https://doi.org/10.1056/NEJMc2109509
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