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Houston J, Vissotsky C, Deep A, Hakozaki H, Crews E, Oegema K, Corbett KD, Lara-Gonzalez P, Kim T, Desai A. Phospho-KNL-1 recognition by a TPR domain targets the BUB-1-BUB-3 complex to C. elegans kinetochores. J Cell Biol 2024; 223:e202402036. [PMID: 38578284 PMCID: PMC10996584 DOI: 10.1083/jcb.202402036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024] Open
Abstract
During mitosis, the Bub1-Bub3 complex concentrates at kinetochores, the microtubule-coupling interfaces on chromosomes, where it contributes to spindle checkpoint activation, kinetochore-spindle microtubule interactions, and protection of centromeric cohesion. Bub1 has a conserved N-terminal tetratricopeptide repeat (TPR) domain followed by a binding motif for its conserved interactor Bub3. The current model for Bub1-Bub3 localization to kinetochores is that Bub3, along with its bound motif from Bub1, recognizes phosphorylated "MELT" motifs in the kinetochore scaffold protein Knl1. Motivated by the greater phenotypic severity of BUB-1 versus BUB-3 loss in C. elegans, we show that the BUB-1 TPR domain directly recognizes a distinct class of phosphorylated motifs in KNL-1 and that this interaction is essential for BUB-1-BUB-3 localization and function. BUB-3 recognition of phospho-MELT motifs additively contributes to drive super-stoichiometric accumulation of BUB-1-BUB-3 on its KNL-1 scaffold during mitotic entry. Bub1's TPR domain interacts with Knl1 in other species, suggesting that collaboration of TPR-dependent and Bub3-dependent interfaces in Bub1-Bub3 localization and functions may be conserved.
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Affiliation(s)
- Jack Houston
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | | | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Enice Crews
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Karen Oegema
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D. Corbett
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pablo Lara-Gonzalez
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Taekyung Kim
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Arshad Desai
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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Belle R, Saraç H, Salah E, Bhushan B, Szykowska A, Roper G, Tumber A, Kriaucionis S, Burgess-Brown N, Schofield CJ, Brown T, Kawamura A. Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate. J Med Chem 2024; 67:4525-4540. [PMID: 38294854 PMCID: PMC10983004 DOI: 10.1021/acs.jmedchem.3c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1-3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1-3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design.
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Affiliation(s)
- Roman Belle
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Hilal Saraç
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Aleksandra Szykowska
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Grace Roper
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig
Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Nicola Burgess-Brown
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Tom Brown
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
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3
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Dias D, Louphrasitthiphol P, Goding CR. TFE3 promotes ferroptosis in melanoma. Pigment Cell Melanoma Res 2024; 37:286-290. [PMID: 37953065 DOI: 10.1111/pcmr.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023]
Affiliation(s)
- Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Jones RA, Trejo B, Sil P, Little KA, Pasolli HA, Joyce B, Posfai E, Devenport D. An mTurq2-Col4a1 mouse model allows for live visualization of mammalian basement membrane development. J Cell Biol 2024; 223:e202309074. [PMID: 38051393 PMCID: PMC10697824 DOI: 10.1083/jcb.202309074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Basement membranes (BMs) are specialized sheets of extracellular matrix that underlie epithelial and endothelial tissues. BMs regulate the traffic of cells and molecules between compartments, and participate in signaling, cell migration, and organogenesis. The dynamics of mammalian BMs, however, are poorly understood, largely due to a lack of models in which core BM components are endogenously labeled. Here, we describe the mTurquoise2-Col4a1 mouse in which we fluorescently tag collagen IV, the main component of BMs. Using an innovative planar-sagittal live imaging technique to visualize the BM of developing skin, we directly observe BM deformation during hair follicle budding and basal progenitor cell divisions. The BM's inherent pliability enables dividing cells to remain attached to and deform the BM, rather than lose adhesion as generally thought. Using FRAP, we show BM collagen IV is extremely stable, even during periods of rapid epidermal growth. These findings demonstrate the utility of the mTurq2-Col4a1 mouse to shed new light on mammalian BM developmental dynamics.
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Affiliation(s)
- Rebecca A. Jones
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brandon Trejo
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Parijat Sil
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - H. Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Bradley Joyce
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Celià-Terrassa T, Kang Y. How important is EMT for cancer metastasis? PLoS Biol 2024; 22:e3002487. [PMID: 38324529 PMCID: PMC10849258 DOI: 10.1371/journal.pbio.3002487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
Epithelial-to-mesenchymal transition (EMT), a biological phenomenon of cellular plasticity initially reported in embryonic development, has been increasingly recognized for its importance in cancer progression and metastasis. Despite tremendous progress being made in the past 2 decades in our understanding of the molecular mechanism and functional importance of EMT in cancer, there are several mysteries around EMT that remain unresolved. In this Unsolved Mystery, we focus on the variety of EMT types in metastasis, cooperative and collective EMT behaviors, spatiotemporal characterization of EMT, and strategies of therapeutically targeting EMT. We also highlight new technical advances that will facilitate the efforts to elucidate the unsolved mysteries of EMT in metastasis.
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Affiliation(s)
- Toni Celià-Terrassa
- Cancer Research Program, Hospital del Mar Research Institute, Barcelona, Spain
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, New Jersey, United States of America
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Ferreira MT, Mendoza López RV, Gonçalves MG, Ferreira S, Sirak B, Baggio ML, Lazcano-Ponce E, Nyitray AG, Giuliano AR, Villa LL, Sichero L. Human Papillomavirus 16 Lineage A Variants Associated With Persistent Genital Infections in Men: The HPV Infection in Men (HIM) Study. J Infect Dis 2023; 228:1748-1757. [PMID: 37279655 PMCID: PMC10733738 DOI: 10.1093/infdis/jiad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/04/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) 16 non-A lineage variants have higher carcinogenic potential for cervical cancer. HPV-16 variants natural history among males is not established. We evaluated HPV-16 variants prevalence and persistence in the external genitalia of men enrolled in the prospective HPV Infection in Men (HIM) Study. METHODS The HIM Study included men from the United States, Brazil, and Mexico. HPV-16 variants were distinguished using polymerase chain reaction sequencing. The prevalence of HPV-16 variants was assessed, and associations with infection persistence were estimated. RESULTS We characterized the HPV-16 variants for 1700 genital swab samples from 753 men and 22 external genital lesions in 17 men. The prevalence of HPV-16 lineages differed by country and marital status (P < .001). Overall, 90.9% of participants harbored lineage A variants. The prevalence of non-A lineages was heterogenous among countries. HPV-16 lineage A variants were associated with a 2.69-fold increased risk of long-term persistent infections compared with non-A lineages. All high-grade penile intraepithelial neoplasia harbored lineage A variants and occurred in the context of long-term persistent infections with the same variants. CONCLUSIONS The prevalence and persistence of HPV-16 variants observed at the male external genitalia suggest differences in the natural history of these variants between men and women, which may be associated with intrinsic differences in the infected genital epithelia.
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Affiliation(s)
- Matthew Thomas Ferreira
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Rossana Veronica Mendoza López
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
| | - Milena Giulia Gonçalves
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
| | - Silvaneide Ferreira
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Bradley Sirak
- Center for Immunization and Infection Research in Cancer, and Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Maria Luizai Baggio
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Eduardo Lazcano-Ponce
- Center for Population Health Research, Instituto Nacional de Salud Pública, Instituto Mexicano del Seguro Social, Cuernavaca, Mexico
| | - Alan G Nyitray
- Health Intervention Sciences Group/Center for AIDS Intervention Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Clinical Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anna R Giuliano
- Center for Immunization and Infection Research in Cancer, and Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Luisa L Villa
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
- Department of Radiology and Oncology, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Laura Sichero
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
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7
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Pulver C, Grun D, Duc J, Sheppard S, Planet E, Coudray A, de Fondeville R, Pontis J, Trono D. Statistical learning quantifies transposable element-mediated cis-regulation. Genome Biol 2023; 24:258. [PMID: 37950299 PMCID: PMC10637000 DOI: 10.1186/s13059-023-03085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs). RESULTS Here, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 500 kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks. CONCLUSION Our results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.
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Affiliation(s)
- Cyril Pulver
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Raphaël de Fondeville
- Swiss Data Science Center, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| | - Julien Pontis
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- SOPHiA GENETICS SA, La Pièce 12, CH-1180, Rolle, Switzerland.
| | - Didier Trono
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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Gélabert C, Papoutsoglou P, Golán I, Ahlström E, Ameur A, Heldin CH, Caja L, Moustakas A. The long non-coding RNA LINC00707 interacts with Smad proteins to regulate TGFβ signaling and cancer cell invasion. Cell Commun Signal 2023; 21:271. [PMID: 37784093 PMCID: PMC10544626 DOI: 10.1186/s12964-023-01273-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/13/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) regulate cellular processes by interacting with RNAs or proteins. Transforming growth factor β (TGFβ) signaling via Smad proteins regulates gene networks that control diverse biological processes, including cancer cell migration. LncRNAs have emerged as TGFβ targets, yet, their mechanism of action and biological role in cancer remain poorly understood. METHODS Whole-genome transcriptomics identified lncRNA genes regulated by TGFβ. Protein kinase inhibitors and RNA-silencing, in combination with cDNA cloning, provided loss- and gain-of-function analyses. Cancer cell-based assays coupled to RNA-immunoprecipitation, chromatin isolation by RNA purification and protein screening sought mechanistic evidence. Functional validation of TGFβ-regulated lncRNAs was based on new transcriptomics and by combining RNAscope with immunohistochemical analysis in tumor tissue. RESULTS Transcriptomics of TGFβ signaling responses revealed down-regulation of the predominantly cytoplasmic long intergenic non-protein coding RNA 707 (LINC00707). Expression of LINC00707 required Smad and mitogen-activated protein kinase inputs. By limiting the binding of Krüppel-like factor 6 to the LINC00707 promoter, TGFβ led to LINC00707 repression. Functionally, LINC00707 suppressed cancer cell invasion, as well as key fibrogenic and pro-mesenchymal responses to TGFβ, as also attested by RNA-sequencing analysis. LINC00707 also suppressed Smad-dependent signaling. Mechanistically, LINC00707 interacted with and retained Smad proteins in the cytoplasm. Upon TGFβ stimulation, LINC00707 dissociated from the Smad complex, which allowed Smad accumulation in the nucleus. In vivo, LINC00707 expression was negatively correlated with Smad2 activation in tumor tissues. CONCLUSIONS LINC00707 interacts with Smad proteins and limits the output of TGFβ signaling, which decreases LINC00707 expression, thus favoring cancer cell invasion. Video Abstract.
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Affiliation(s)
- Caroline Gélabert
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden
| | - Panagiotis Papoutsoglou
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden
- Inserm, Centre de Lutte contre le Cancer Eugène Marquis, Université Rennes 1, OSS (Oncogenesis, Stress, Signalling) laboratory, UMR_S 1242, Rennes, F-35042, France
| | - Irene Golán
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden
| | - Eric Ahlström
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden
| | - Laia Caja
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden.
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 582, Uppsala, SE-75123, Sweden.
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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Malagón T, Trottier H, El-Zein M, Villa LL, Franco EL. Human Papillomavirus Intermittence and Risk Factors Associated With First Detections and Redetections in the Ludwig-McGill Cohort Study of Adult Women. J Infect Dis 2023; 228:402-411. [PMID: 36790831 PMCID: PMC10428201 DOI: 10.1093/infdis/jiad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND We assessed the incidence and risk factors for first detection and redetection with the same human papillomavirus (HPV) genotype, and prevalence of cytological lesions during HPV redetections. METHODS The Ludwig-McGill cohort study followed women aged 18-60 years from São Paulo, Brazil in 1993-1997 for up to 10 years. Women provided cervical samples for cytology testing and HPV DNA testing at each visit. A redetection was defined as a recurring genotype-specific HPV positive result after 1 or more intervening negative visits. Predictors of genotype-specific redetection were assessed using adjusted hazard ratios (aHR) with Cox regression modeling. RESULTS In total, 2184 women contributed 2368 incident HPV genotype-specific first detections and 308 genotype-specific redetections over a median follow-up of 6.5 years. The cumulative incidence of redetection with the same genotype was 6.6% at 1 year and 14.8% at 5 years after the loss of positivity of the first detection. Neither age (aHR 0.90; 95% confidence interval [CI], .54-1.47 for ≥45 years vs < 25 years) nor new sexual partner acquisition (aHR 0.98; 95% CI, .70-1.35) were statistically associated with genotype-specific redetection. High-grade squamous intraepithelial lesion prevalence was similar during first HPV detections (2.9%) and redetection (3.2%). CONCLUSIONS Our findings suggest many HPV redetections were likely reactivations of latent recurring infections.
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Affiliation(s)
- Talía Malagón
- Division of Cancer Epidemiology, Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Helen Trottier
- Département de Médecine Sociale et Préventive, Université de Montréal, Montréal, Canada
- Centre de Recherche, Centre Hospitalier Universitaire de Sainte-Justine, Montréal, Canada
| | - Mariam El-Zein
- Division of Cancer Epidemiology, Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Luisa L Villa
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Radiology and Oncology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Eduardo L Franco
- Division of Cancer Epidemiology, Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
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11
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Yang N, Wang Y, Liu S, Tariq SB, Luna JM, Mazo G, Tan A, Zhang T, Wang J, Yan W, Choi J, Rossi A, Xiang JZ, Rice CM, Merghoub T, Wolchok JD, Deng L. OX40L-expressing recombinant modified vaccinia virus Ankara induces potent antitumor immunity via reprogramming Tregs. J Exp Med 2023; 220:e20221166. [PMID: 37145142 PMCID: PMC10165539 DOI: 10.1084/jem.20221166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 03/05/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023] Open
Abstract
Effective depletion of immune suppressive regulatory T cells (Tregs) in the tumor microenvironment without triggering systemic autoimmunity is an important strategy for cancer immunotherapy. Modified vaccinia virus Ankara (MVA) is a highly attenuated, non-replicative vaccinia virus with a long history of human use. Here, we report rational engineering of an immune-activating recombinant MVA (rMVA, MVA∆E5R-Flt3L-OX40L) with deletion of the vaccinia E5R gene (encoding an inhibitor of the DNA sensor cyclic GMP-AMP synthase, cGAS) and expression of two membrane-anchored transgenes, Flt3L and OX40L. Intratumoral (IT) delivery of rMVA (MVA∆E5R-Flt3L-OX40L) generates potent antitumor immunity, dependent on CD8+ T cells, the cGAS/STING-mediated cytosolic DNA-sensing pathway, and type I IFN signaling. Remarkably, IT rMVA (MVA∆E5R-Flt3L-OX40L) depletes OX40hi regulatory T cells via OX40L/OX40 interaction and IFNAR signaling. Single-cell RNA-seq analyses of tumors treated with rMVA showed the depletion of OX40hiCCR8hi Tregs and expansion of IFN-responsive Tregs. Taken together, our study provides a proof-of-concept for depleting and reprogramming intratumoral Tregs via an immune-activating rMVA.
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Affiliation(s)
- Ning Yang
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Wang
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shuaitong Liu
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shanza Baseer Tariq
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph M. Luna
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Gregory Mazo
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrian Tan
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Tuo Zhang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | | | - Wei Yan
- IMVAQ Therapeutics, Sammamish, WA, USA
| | - John Choi
- IMVAQ Therapeutics, Sammamish, WA, USA
| | - Anthony Rossi
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Zhaoying Xiang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Charles M. Rice
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Taha Merghoub
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jedd D. Wolchok
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Liang Deng
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
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12
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Morgan KJ, Doggett K, Geng F, Mieruszynski S, Whitehead L, Smith KA, Hogan BM, Simons C, Baillie GJ, Molania R, Papenfuss AT, Hall TE, Ober EA, Stainier DYR, Gong Z, Heath JK. ahctf1 and kras mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma. eLife 2023; 12:73407. [PMID: 36648336 PMCID: PMC9897728 DOI: 10.7554/elife.73407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
The nucleoporin (NUP) ELYS, encoded by AHCTF1, is a large multifunctional protein with essential roles in nuclear pore assembly and mitosis. Using both larval and adult zebrafish models of hepatocellular carcinoma (HCC), in which the expression of an inducible mutant kras transgene (krasG12V) drives hepatocyte-specific hyperplasia and liver enlargement, we show that reducing ahctf1 gene dosage by 50% markedly decreases liver volume, while non-hyperplastic tissues are unaffected. We demonstrate that in the context of cancer, ahctf1 heterozygosity impairs nuclear pore formation, mitotic spindle assembly, and chromosome segregation, leading to DNA damage and activation of a Tp53-dependent transcriptional programme that induces cell death and cell cycle arrest. Heterozygous expression of both ahctf1 and ranbp2 (encoding a second nucleoporin), or treatment of heterozygous ahctf1 larvae with the nucleocytoplasmic transport inhibitor, Selinexor, completely blocks krasG12V-driven hepatocyte hyperplasia. Gene expression analysis of patient samples in the liver hepatocellular carcinoma (LIHC) dataset in The Cancer Genome Atlas shows that high expression of one or more of the transcripts encoding the 10 components of the NUP107-160 subcomplex, which includes AHCTF1, is positively correlated with worse overall survival. These results provide a strong and feasible rationale for the development of novel cancer therapeutics that target ELYS function and suggest potential avenues for effective combinatorial treatments.
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Affiliation(s)
- Kimberly J Morgan
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Karen Doggett
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Fansuo Geng
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Stephen Mieruszynski
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Lachlan Whitehead
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Centre for Dynamic Imaging, Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Kelly A Smith
- Department of Physiology, University of MelbourneParkvilleAustralia
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Benjamin M Hogan
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Peter MacCallum Cancer CentreMelbourneAustralia
| | - Cas Simons
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Murdoch Children's Research InstituteParkvilleAustralia
| | - Gregory J Baillie
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Ramyar Molania
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Anthony T Papenfuss
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Thomas E Hall
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Elke A Ober
- Danish Stem Cell Center, University of CopenhagenCopenhagenDenmark
| | - Didier YR Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Zhiyuan Gong
- Department of Biological Science, National University of SingaporeSingaporeSingapore
| | - Joan K Heath
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
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13
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Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX. Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology. Nucleic Acids Res 2022; 50:e104. [PMID: 35849350 PMCID: PMC9561279 DOI: 10.1093/nar/gkac612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.
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Affiliation(s)
- Jinfeng Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Masato Inoue
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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14
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Quail DF, Amulic B, Aziz M, Barnes BJ, Eruslanov E, Fridlender ZG, Goodridge HS, Granot Z, Hidalgo A, Huttenlocher A, Kaplan MJ, Malanchi I, Merghoub T, Meylan E, Mittal V, Pittet MJ, Rubio-Ponce A, Udalova IA, van den Berg TK, Wagner DD, Wang P, Zychlinsky A, de Visser KE, Egeblad M, Kubes P. Neutrophil phenotypes and functions in cancer: A consensus statement. J Exp Med 2022; 219:e20220011. [PMID: 35522219 PMCID: PMC9086501 DOI: 10.1084/jem.20220011] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
Neutrophils are the first responders to infection and inflammation and are thus a critical component of innate immune defense. Understanding the behavior of neutrophils as they act within various inflammatory contexts has provided insights into their role in sterile and infectious diseases; however, the field of neutrophils in cancer is comparatively young. Here, we summarize key concepts and current knowledge gaps related to the diverse roles of neutrophils throughout cancer progression. We discuss sources of neutrophil heterogeneity in cancer and provide recommendations on nomenclature for neutrophil states that are distinct in maturation and activation. We address discrepancies in the literature that highlight a need for technical standards that ought to be considered between laboratories. Finally, we review emerging questions in neutrophil biology and innate immunity in cancer. Overall, we emphasize that neutrophils are a more diverse population than previously appreciated and that their role in cancer may present novel unexplored opportunities to treat cancer.
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Affiliation(s)
- Daniela F. Quail
- Rosalind and Morris Goodman Cancer Institute, Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Borko Amulic
- Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Monowar Aziz
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, NY
| | - Betsy J. Barnes
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, Feinstein Institutes for Medical Research, Manhasset, NY
- Departments of Molecular Medicine and Pediatrics, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
| | - Evgeniy Eruslanov
- Division of Thoracic Surgery, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Zvi G. Fridlender
- Hadassah Medical Center, Institute of Pulmonary Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Helen S. Goodridge
- Board of Governors Regenerative Medicine Institute and Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Zvi Granot
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andrés Hidalgo
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Area of Cell and Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI
| | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, UK
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Etienne Meylan
- Lung Cancer and Immuno-Oncology Laboratory, Bordet Cancer Research Laboratories, Institut Jules Bordet, Université Libre de Bruxelles, Anderlecht, Belgium
- Laboratory of Immunobiology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Neuberger Berman Foundation Lung Cancer Research Center, Weill Cornell Medicine, New York, NY
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Mikael J. Pittet
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Andrea Rubio-Ponce
- Area of Cell and Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Irina A. Udalova
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, UK
| | - Timo K. van den Berg
- Laboratory of Immunotherapy, Sanquin Research, Amsterdam, Netherlands
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Denisa D. Wagner
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Ping Wang
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, NY
| | - Arturo Zychlinsky
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Karin E. de Visser
- Division of Tumour Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, Netherlands
- Banbury Center meeting organizers, Diverse Functions of Neutrophils in Cancer, Cold Spring Harbor Laboratory, New York, NY
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Banbury Center meeting organizers, Diverse Functions of Neutrophils in Cancer, Cold Spring Harbor Laboratory, New York, NY
| | - Paul Kubes
- Department of Pharmacology and Physiology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Banbury Center meeting organizers, Diverse Functions of Neutrophils in Cancer, Cold Spring Harbor Laboratory, New York, NY
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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15
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Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M, Hirschhorn D, Budhu S, Amisaki M, Arniella M, Redmond D, Chaft J, Forde PM, Gainor JF, Hellmann MD, Balachandran V, Shah S, Smith KN, Pardoll D, Elemento O, Wolchok JD, Merghoub T. Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. J Exp Med 2022; 219:e20212169. [PMID: 35604411 PMCID: PMC9130031 DOI: 10.1084/jem.20212169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 11/04/2022] Open
Abstract
Transcription factors ThPOK and Runx3 regulate the differentiation of "helper" CD4+ and "cytotoxic" CD8+ T cell lineages respectively, inducing single positive (SP) T cells that enter the periphery with the expression of either the CD4 or CD8 co-receptor. Despite the expectation that these cell fates are mutually exclusive and that mature CD4+CD8+ double positive (DP) T cells are present in healthy individuals and augmented in the context of disease, yet their molecular features and pathophysiologic role are disputed. Here, we show DP T cells in murine and human tumors as a heterogenous population originating from SP T cells which re-express the opposite co-receptor and acquire features of the opposite cell type's phenotype and function following TCR stimulation. We identified distinct clonally expanded DP T cells in human melanoma and lung cancer by scRNA sequencing and demonstrated their tumor reactivity in cytotoxicity assays. Our findings indicate that antigen stimulation induces SP T cells to differentiate into DP T cell subsets gaining in polyfunctional characteristics.
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Affiliation(s)
- Sara E. Schad
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Levi Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Heng Pan
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jiajia Zhang
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justina X. Caushi
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicole Malandro
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Roberta Zappasodi
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Mathieu Gigoux
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Masataka Amisaki
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Jamie Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Patrick M. Forde
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Justin F. Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vinod Balachandran
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kellie N. Smith
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Drew Pardoll
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Olivier Elemento
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jedd D. Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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16
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He C, Maniyar RR, Avraham Y, Zappasodi R, Rusinova R, Newman W, Heath H, Wolchok JD, Dahan R, Merghoub T, Meyerson JR. Therapeutic antibody activation of the glucocorticoid-induced TNF receptor by a clustering mechanism. Sci Adv 2022; 8:eabm4552. [PMID: 35213218 PMCID: PMC8880771 DOI: 10.1126/sciadv.abm4552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/12/2022] [Indexed: 05/11/2023]
Abstract
GITR is a TNF receptor, and its activation promotes immune responses and drives antitumor activity. The receptor is activated by the GITR ligand (GITRL), which is believed to cluster receptors into a high-order array. Immunotherapeutic agonist antibodies also activate the receptor, but their mechanisms are not well characterized. We solved the structure of full-length mouse GITR bound to Fabs from the antibody DTA-1. The receptor is a dimer, and each subunit binds one Fab in an orientation suggesting that the antibody clusters receptors. Binding experiments with purified proteins show that DTA-1 IgG and GITRL both drive extensive clustering of GITR. Functional data reveal that DTA-1 and the anti-human GITR antibody TRX518 activate GITR in their IgG forms but not as Fabs. Thus, the divalent character of the IgG agonists confers an ability to mimic GITRL and cluster and activate GITR. These findings will inform the clinical development of this class of antibodies for immuno-oncology.
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Affiliation(s)
- Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Rachana R. Maniyar
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yahel Avraham
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Roberta Zappasodi
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Jedd D. Wolchok
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rony Dahan
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel R. Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
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17
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Sarri N, Wang K, Tsioumpekou M, Castillejo-López C, Lennartsson J, Heldin CH, Papadopoulos N. Deubiquitinating enzymes USP4 and USP17 finetune the trafficking of PDGFRβ and affect PDGF-BB-induced STAT3 signalling. Cell Mol Life Sci 2022; 79:85. [PMID: 35064336 PMCID: PMC8782881 DOI: 10.1007/s00018-022-04128-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022]
Abstract
Interaction of platelet-derived growth factor (PDGF) isoforms with their receptors results in activation and internalization of receptors, with a concomitant activation of downstream signalling pathways. Ubiquitination of PDGFRs serves as a mark to direct the internalization and sorting of the receptors. By overexpressing a panel of deubiquitinating enzymes (DUBs), we found that USP17 and USP4 efficiently deubiquitinate PDGF receptor β (PDGFRβ) and are able to remove both Lys63 and Lys48-linked polyubiquitin chains from the receptor. Deubiquitination of PDGFRβ did not affect its stability, but regulated the timing of its trafficking, whereby USP17 prolonged the presence of the receptor at the cell surface, while USP4 affected the speed of trafficking towards early endosomes. Induction of each of the DUBs in BJhTERT fibroblasts and U2OS osteosarcoma cells led to prolonged and/or shifted activation of STAT3 in response to PDGF-BB stimulation, which in turn led to increased transcriptional activity of STAT3. Induction of USP17 promoted acute upregulation of the mRNA expression of STAT3-inducible genes STAT3, CSF1, junB and c-myc, while causing long-term changes in the expression of myc and CDKN1A. Deletion of USP17 was lethal to fibroblasts, while deletion of USP4 led to a decreased proliferative response to stimulation by PDGF-BB. Thus, USP17- and USP4-mediated changes in ubiquitination of PDFGRβ lead to dysregulated signalling and transcription downstream of STAT3, resulting in defects in the control of cell proliferation.
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Affiliation(s)
- Niki Sarri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Kehuan Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
| | - Maria Tsioumpekou
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | - Johan Lennartsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
| | - Natalia Papadopoulos
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
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18
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Tsutsumi N, Maeda S, Qu Q, Vögele M, Jude KM, Suomivuori CM, Panova O, Waghray D, Kato HE, Velasco A, Dror RO, Skiniotis G, Kobilka BK, Garcia KC. Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins. Sci Adv 2022; 8:eabl5442. [PMID: 35061538 PMCID: PMC8782444 DOI: 10.1126/sciadv.abl5442] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/29/2021] [Indexed: 05/12/2023]
Abstract
Human cytomegalovirus (HCMV) encodes G protein-coupled receptors (GPCRs) US28 and US27, which facilitate viral pathogenesis through engagement of host G proteins. Here we report cryo-electron microscopy structures of US28 and US27 forming nonproductive and productive complexes with Gi and Gq, respectively, exhibiting unusual features with functional implications. The "orphan" GPCR US27 lacks a ligand-binding pocket and has captured a guanosine diphosphate-bound inactive Gi through a tenuous interaction. The docking modes of CX3CL1-US28 and US27 to Gi favor localization to endosome-like curved membranes, where US28 and US27 can function as nonproductive Gi sinks to attenuate host chemokine-dependent Gi signaling. The CX3CL1-US28-Gq/11 complex likely represents a trapped intermediate during productive signaling, providing a view of a transition state in GPCR-G protein coupling for signaling. Our collective results shed new insight into unique G protein-mediated HCMV GPCR structural mechanisms, compared to mammalian GPCR counterparts, for subversion of host immunity.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Vögele
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hideaki E. Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Velasco
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ron O. Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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19
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Ding H, Chen Z, Wu K, Huang SM, Wu WL, LeBoeuf SE, Pillai RG, Rabinowitz JD, Papagiannakopoulos T. Activation of the NRF2 antioxidant program sensitizes tumors to G6PD inhibition. Sci Adv 2021; 7:eabk1023. [PMID: 34788087 PMCID: PMC8598006 DOI: 10.1126/sciadv.abk1023] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 05/20/2023]
Abstract
The KEAP1/NRF2 pathway promotes metabolic rewiring to support redox homeostasis. Activation of NRF2 occurs in many cancers, often due to KEAP1 mutations, and is associated with more aggressive disease and treatment resistance. To identify metabolic dependencies in cancers with NRF2 activation, we performed a metabolism-focused CRISPR screen. Glucose-6-phosphate dehydrogenase (G6PD), which was recently shown to be dispensable in Ras-driven tumors, was a top dependency. G6PD catalyzes the committed step of the oxidative pentose phosphate pathway that produces NADPH and nucleotide precursors, but neither antioxidants nor nucleosides rescued. Instead, G6PD loss triggered tricarboxylic acid (TCA) intermediate depletion because of up-regulation of the alternative NADPH-producing enzymes malic enzyme and isocitrate dehydrogenase. In vivo, G6PD impairment markedly suppressed KEAP1 mutant tumor growth, and this suppression was further augmented by TCA depletion by glutaminase inhibition. Thus, G6PD inhibition–induced TCA depletion is a therapeutic vulnerability of NRF2-activated cancer.
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Affiliation(s)
- Hongyu Ding
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Zihong Chen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, 91 Prospect Avenue, Princeton, NJ 08544, USA
| | - Katherine Wu
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Shih Ming Huang
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Warren L. Wu
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Sarah E. LeBoeuf
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Ray G. Pillai
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, VA New York Harbor Healthcare System, 423 East 23rd Avenue, New York, NY 10016, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, 91 Prospect Avenue, Princeton, NJ 08544, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA
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20
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Stump CT, Roehle K, Manjarrez Orduno N, Dougan SK. Radiation combines with immune checkpoint blockade to enhance T cell priming in a murine model of poorly immunogenic pancreatic cancer. Open Biol 2021; 11:210245. [PMID: 34784792 PMCID: PMC8595997 DOI: 10.1098/rsob.210245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 02/06/2023] Open
Abstract
Radiation has been a pillar of cancer therapy for decades. The effects of radiation on the anti-tumour immune response are variable across studies and have not been explicitly defined in poorly immunogenic tumour types. Here, we employed combination checkpoint blockade immunotherapy with stereotactic body radiation therapy and examined the effect on tumour growth and immune infiltrates in subcutaneous and orthotopic mouse models of pancreatic cancer. Although immune checkpoint blockade and radiation were ineffective alone, their combination produced a modest growth delay in both irradiated and non-irradiated tumours that corresponded with significant increases in CD8+ T cells, CD4+ T cells and tumour-specific T cells as identified by IFNγ ELISpot. We conclude that radiation enhances priming of tumour-specific T cells in poorly immunogenic tumours and that the frequency of these T cells can be further increased by combination with immune checkpoint blockade.
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Affiliation(s)
- Courtney T. Stump
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA 02215, USA
| | - Kevin Roehle
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02215, USA
| | | | - Stephanie K. Dougan
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02215, USA
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21
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Gutiontov SI, Turchan WT, Spurr LF, Rouhani SJ, Chervin CS, Steinhardt G, Lager AM, Wanjari P, Malik R, Connell PP, Chmura SJ, Juloori A, Hoffman PC, Ferguson MK, Donington JS, Patel JD, Vokes EE, Weichselbaum RR, Bestvina CM, Segal JP, Pitroda SP. CDKN2A loss-of-function predicts immunotherapy resistance in non-small cell lung cancer. Sci Rep 2021; 11:20059. [PMID: 34625620 PMCID: PMC8501138 DOI: 10.1038/s41598-021-99524-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/28/2021] [Indexed: 01/10/2023] Open
Abstract
Immune checkpoint blockade (ICB) improves outcomes in non-small cell lung cancer (NSCLC) though most patients progress. There are limited data regarding molecular predictors of progression. In particular, there is controversy regarding the role of CDKN2A loss-of-function (LOF) in ICB resistance. We analyzed 139 consecutive patients with advanced NSCLC who underwent NGS prior to ICB initiation to explore the association of CDKN2A LOF with clinical outcomes. 73% were PD-L1 positive (≥ 1%). 48% exhibited high TMB (≥ 10 mutations/megabase). CDKN2A LOF was present in 26% of patients and was associated with inferior PFS (multivariate hazard ratio [MVA-HR] 1.66, 95% CI 1.02-2.63, p = 0.041) and OS (MVA-HR 2.08, 95% CI 1.21-3.49, p = 0.0087) when compared to wild-type (WT) patients. These findings held in patients with high TMB (median OS, LOF vs. WT 10.5 vs. 22.3 months; p = 0.069) and PD-L1 ≥ 50% (median OS, LOF vs. WT 11.1 vs. 24.2 months; p = 0.020), as well as in an independent dataset. CDKN2A LOF vs. WT tumors were twice as likely to experience disease progression following ICB (46% vs. 21%; p = 0.021). CDKN2A LOF negatively impacts clinical outcomes in advanced NSCLC treated with ICB, even in high PD-L1 and high TMB tumors. This novel finding should be prospectively validated and presents a potential therapeutic target.
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Affiliation(s)
- Stanley I Gutiontov
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - William Tyler Turchan
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - Liam F Spurr
- Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - Sherin J Rouhani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Carolina Soto Chervin
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - George Steinhardt
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Angela M Lager
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Pankhuri Wanjari
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Renuka Malik
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - Steven J Chmura
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - Aditya Juloori
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
| | - Philip C Hoffman
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Mark K Ferguson
- Section of Thoracic Surgery, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Jessica S Donington
- Section of Thoracic Surgery, Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Jyoti D Patel
- Section of Hematology/Oncology, Department of Medicine, Northwestern University, Evanston, IL, USA
| | - Everett E Vokes
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA
| | - Christine M Bestvina
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jeremy P Segal
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Sean P Pitroda
- Department of Radiation and Cellular Oncology, The University of Chicago, 5758 S Maryland Ave, MC 9006, Chicago, IL, 60637, USA.
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA.
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22
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Turchan WT, Pitroda SP, Weichselbaum RR. Treatment of Cancer with Radio-Immunotherapy: What We Currently Know and What the Future May Hold. Int J Mol Sci 2021; 22:9573. [PMID: 34502479 PMCID: PMC8431248 DOI: 10.3390/ijms22179573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Radiotherapy and immunotherapy are most effective as cancer therapies in the setting of low-volume disease. Although initial studies of radio-immunotherapy in patients with metastatic cancer have not confirmed the efficacy of this approach, the role of radio-immunotherapy in patients with limited metastatic burden is unclear. We propose that further investigation of radio-immunotherapy in metastatic patients should focus upon patients with oligometastatic disease.
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Affiliation(s)
| | | | - Ralph R. Weichselbaum
- Department of Radiation and Cellular Oncology and the Ludwig Center for Metastasis Research, University of Chicago, 5758 S Maryland Ave, Chicago, IL 60637, USA; (W.T.T.); (S.P.P.)
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23
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Siejka-Zielińska P, Cheng J, Jackson F, Liu Y, Soonawalla Z, Reddy S, Silva M, Puta L, McCain MV, Culver EL, Bekkali N, Schuster-Böckler B, Palamara PF, Mann D, Reeves H, Barnes E, Sivakumar S, Song CX. Cell-free DNA TAPS provides multimodal information for early cancer detection. Sci Adv 2021; 7:eabh0534. [PMID: 34516908 PMCID: PMC8442905 DOI: 10.1126/sciadv.abh0534] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/14/2021] [Indexed: 05/05/2023]
Abstract
Multimodal, genome-wide characterization of epigenetic and genetic information in circulating cell-free DNA (cfDNA) could enable more sensitive early cancer detection, but it is technologically challenging. Recently, we developed TET-assisted pyridine borane sequencing (TAPS), which is a mild, bisulfite-free method for base-resolution direct DNA methylation sequencing. Here, we optimized TAPS for cfDNA (cfTAPS) to provide high-quality and high-depth whole-genome cell-free methylomes. We applied cfTAPS to 85 cfDNA samples from patients with hepatocellular carcinoma (HCC) or pancreatic ductal adenocarcinoma (PDAC) and noncancer controls. From only 10 ng of cfDNA (1 to 3 ml of plasma), we generated the most comprehensive cfDNA methylome to date. We demonstrated that cfTAPS provides multimodal information about cfDNA characteristics, including DNA methylation, tissue of origin, and DNA fragmentation. Integrated analysis of these epigenetic and genetic features enables accurate identification of early HCC and PDAC.
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Affiliation(s)
- Paulina Siejka-Zielińska
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Felix Jackson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Srikanth Reddy
- Oxford Transplant Centre, Churchill Hospital, Oxford, UK
| | - Michael Silva
- Department of HPB Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Luminita Puta
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Misti Vanette McCain
- Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Newcastle University Centre for Cancer, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Emma L. Culver
- Peter Medawar Building and Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Noor Bekkali
- Department of Gastroenterology, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Derek Mann
- Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Reeves
- Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Newcastle University Centre for Cancer, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Liver Unit, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Eleanor Barnes
- Peter Medawar Building and Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford, Oxford, UK
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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24
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Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Res 2021; 49:e76. [PMID: 33905495 PMCID: PMC8287915 DOI: 10.1093/nar/gkab291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
Whole genome base-resolution methylome sequencing allows for the most comprehensive analysis of DNA methylation, however, the considerable sequencing cost often limits its applications. While reduced representation sequencing can be an affordable alternative, over 80% of CpGs in the genome are not covered. Building on our recently developed TET-assisted pyridine borane sequencing (TAPS) method, we here described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-cleaving endonuclease digestion of TAPS-converted DNA to enrich methylated CpG sites (mCpGs). eeTAPS can accurately detect 87% of mCpGs in the mouse genome with a sequencing depth equivalent to 4× whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of mCpGs with 2.5× sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.
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Affiliation(s)
- Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paulina Siejka-Zielińska
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Anandhakumar Chandran
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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Di Giovannantonio M, Harris BH, Zhang P, Kitchen-Smith I, Xiong L, Sahgal N, Stracquadanio G, Wallace M, Blagden S, Lord S, Harris D, Harris AHL, Buffa FM, Bond GL. Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits. J Med Genet 2021; 58:392-399. [PMID: 32591342 PMCID: PMC8142426 DOI: 10.1136/jmedgenet-2019-106799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Height and other anthropometric measures are consistently found to associate with differential cancer risk. However, both genetic and mechanistic insights into these epidemiological associations are notably lacking. Conversely, inherited genetic variants in tumour suppressors and oncogenes increase cancer risk, but little is known about their influence on anthropometric traits. METHODS By integrating inherited and somatic cancer genetic data from the Genome-Wide Association Study Catalog, expression Quantitative Trait Loci databases and the Cancer Gene Census, we identify SNPs that associate with different cancer types and differential gene expression in at least one tissue type, and explore the potential pleiotropic associations of these SNPs with anthropometric traits through SNP-wise association in a cohort of 500,000 individuals. RESULTS We identify three regulatory SNPs for three important cancer genes, FANCA, MAP3K1 and TP53 that associate with both anthropometric traits and cancer risk. Of particular interest, we identify a previously unrecognised strong association between the rs78378222[C] SNP in the 3' untranslated region (3'-UTR) of TP53 and both increased risk for developing non-melanomatous skin cancer (OR=1.36 (95% 1.31 to 1.41), adjusted p=7.62E-63), brain malignancy (OR=3.12 (2.22 to 4.37), adjusted p=1.43E-12) and increased standing height (adjusted p=2.18E-24, beta=0.073±0.007), lean body mass (adjusted p=8.34E-37, beta=0.073±0.005) and basal metabolic rate (adjusted p=1.13E-31, beta=0.076±0.006), thus offering a novel genetic link between these anthropometric traits and cancer risk. CONCLUSION Our results clearly demonstrate that heritable variants in key cancer genes can associate with both differential cancer risk and anthropometric traits in the general population, thereby lending support for a genetic basis for linking these human phenotypes.
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Affiliation(s)
- Matteo Di Giovannantonio
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Benjamin Hl Harris
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
| | - Ping Zhang
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Isaac Kitchen-Smith
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Lingyun Xiong
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Natasha Sahgal
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Giovanni Stracquadanio
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Marsha Wallace
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Sarah Blagden
- Cancer Therapeutics and mRNA Dysregulation, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Simon Lord
- Early Phase Clinical Trials Unit, Department of Oncology, Medical Siences Division, University of Oxford, Oxford, UK
| | - David Harris
- St Anne's College, University of Oxford, Oxford, UK
| | - Adrian H L Harris
- Molecular Oncology Laboratories, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
| | - Gareth L Bond
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
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Cachot A, Bilous M, Liu YC, Li X, Saillard M, Cenerenti M, Rockinger GA, Wyss T, Guillaume P, Schmidt J, Genolet R, Ercolano G, Protti MP, Reith W, Ioannidou K, de Leval L, Trapani JA, Coukos G, Harari A, Speiser DE, Mathis A, Gfeller D, Altug H, Romero P, Jandus C. Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. Sci Adv 2021; 7:7/9/eabe3348. [PMID: 33637530 PMCID: PMC7909889 DOI: 10.1126/sciadv.abe3348] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/14/2021] [Indexed: 05/04/2023]
Abstract
CD4 T cells have been implicated in cancer immunity for their helper functions. Moreover, their direct cytotoxic potential has been shown in some patients with cancer. Here, by mining single-cell RNA-seq datasets, we identified CD4 T cell clusters displaying cytotoxic phenotypes in different human cancers, resembling CD8 T cell profiles. Using the peptide-MHCII-multimer technology, we confirmed ex vivo the presence of cytolytic tumor-specific CD4 T cells. We performed an integrated phenotypic and functional characterization of these cells, down to the single-cell level, through a high-throughput nanobiochip consisting of massive arrays of picowells and machine learning. We demonstrated a direct, contact-, and granzyme-dependent cytotoxic activity against tumors, with delayed kinetics compared to classical cytotoxic lymphocytes. Last, we found that this cytotoxic activity was in part dependent on SLAMF7. Agonistic engagement of SLAMF7 enhanced cytotoxicity of tumor-specific CD4 T cells, suggesting that targeting these cells might prove synergistic with other cancer immunotherapies.
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Affiliation(s)
- Amélie Cachot
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Mariia Bilous
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Yen-Cheng Liu
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Xiaokang Li
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Margaux Saillard
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Mara Cenerenti
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, CH-1211, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, CH-1066, Switzerland
| | - Georg Alexander Rockinger
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Tania Wyss
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Philippe Guillaume
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Julien Schmidt
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Raphaël Genolet
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Giuseppe Ercolano
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, CH-1211, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, CH-1066, Switzerland
| | - Maria Pia Protti
- Tumor Immunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Walter Reith
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, CH-1211, Switzerland
| | - Kalliopi Ioannidou
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Joseph A Trapani
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne 3000, Australia
| | - George Coukos
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Alexandre Harari
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Daniel E Speiser
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Alexander Mathis
- Harvard University, Cambridge, MA, USA
- Center for Neuroprosthetics, Center for Intelligent Systems, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, CH-1015, Switzerland
| | - David Gfeller
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Hatice Altug
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Pedro Romero
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, CH-1066, Switzerland
| | - Camilla Jandus
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, CH-1211, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, CH-1066, Switzerland
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27
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Canè S, Van Snick J, Uyttenhove C, Pilotte L, Van den Eynde BJ. TGFβ1 neutralization displays therapeutic efficacy through both an immunomodulatory and a non-immune tumor-intrinsic mechanism. J Immunother Cancer 2021; 9:e001798. [PMID: 33637600 PMCID: PMC7919595 DOI: 10.1136/jitc-2020-001798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Transforming growth factor-β (TGFβ) is emerging as a promising target for cancer therapy, given its ability to promote progression of advanced tumors and to suppress anti-tumor immune responses. However, TGFβ also plays multiple roles in normal tissues, particularly during organogenesis, raising toxicity concerns about TGFβ blockade. Dose-limiting cardiovascular toxicity was observed, possibly due to the blockade of all three TGFβ isoforms. The dominant isoform in tumors is TGFβ1, while TGFβ2 and TGFβ3 seem to be more involved in cardiovascular development. Recent data indicated that selective targeting of TGFβ1 promoted the efficacy of checkpoint inhibitor anti-PD1 in transplanted preclinical tumor models, without cardiovascular toxicity. METHODS To further explore the therapeutic potential of isoform-specific TGFβ blockade, we developed neutralizing mAbs targeting mature TGFβ1 or TGFβ3, and tested them, in parallel with anti-panTGFβ mAb 1D11, in two preclinical models: the transplanted colon cancer model CT26, and the autochthonous melanoma model TiRP. RESULTS We observed that the blockade of TGFβ1, but not that of TGFβ3, increased the efficacy of a prophylactic cellular vaccine against colon cancer CT26. This effect was similar to pan-TGFβ blockade, and was associated with increased infiltration of activated CD8 T cells in the tumor, and reduced levels of regulatory T cells and myeloid-derived suppressor cells. In contrast, in the autochthonous TiRP melanoma model, we observed therapeutic efficacy of the TGFβ1-specific mAb as a single agent, while the TGFβ3 mAb was inactive. In this model, the anti-tumor effect of TGFβ1 blockade was tumor intrinsic rather than immune mediated, as it was also observed in T-cell depleted mice. Mechanistically, TGFβ1 blockade increased mouse survival by delaying the phenotype switch, akin to epithelial-to-mesenchymal transition (EMT), which transforms initially pigmented tumors into highly aggressive unpigmented tumors. CONCLUSIONS Our results confirm TGFβ1 as the relevant isoform to target for cancer therapy, not only in combination with checkpoint inhibitors, but also with other immunotherapies such as cancer vaccines. Moreover, TGFβ1 blockade can also act as a monotherapy, through a tumor-intrinsic effect blocking the EMT-like transition. Because human melanomas that resist therapy often express a gene signature that links TGFβ1 with EMT-related genes, these results support the clinical development of TGFβ1-specific mAbs in melanoma.
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Affiliation(s)
- Stefania Canè
- Ludwig Institute for Cancer Research, De Duve Institute, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
- Department of Medicine, Immunology Section, University of Verona, Verona, Italy
| | - Jacques Van Snick
- Ludwig Institute for Cancer Research, De Duve Institute, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
| | - Catherine Uyttenhove
- Ludwig Institute for Cancer Research, De Duve Institute, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
| | - Luc Pilotte
- Ludwig Institute for Cancer Research, De Duve Institute, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
- WELBIO, UCLouvain, Brussels, Belgium
| | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, De Duve Institute, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
- WELBIO, UCLouvain, Brussels, Belgium
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28
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Watanabe S, Meitinger F, Shiau AK, Oegema K, Desai A. Centriole-independent mitotic spindle assembly relies on the PCNT-CDK5RAP2 pericentriolar matrix. J Cell Biol 2020; 219:e202006010. [PMID: 33170211 PMCID: PMC7658699 DOI: 10.1083/jcb.202006010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/27/2020] [Accepted: 10/06/2020] [Indexed: 01/04/2023] Open
Abstract
Centrosomes, composed of centrioles that recruit a pericentriolar material (PCM) matrix assembled from PCNT and CDK5RAP2, catalyze mitotic spindle assembly. Here, we inhibit centriole formation and/or remove PCNT-CDK5RAP2 in RPE1 cells to address their relative contributions to spindle formation. While CDK5RAP2 and PCNT are normally dispensable for spindle formation, they become essential when centrioles are absent. Acentriolar spindle assembly is accompanied by the formation of foci containing PCNT and CDK5RAP2 via a microtubule and Polo-like kinase 1-dependent process. Foci formation and spindle assembly require PCNT-CDK5RAP2-dependent matrix assembly and the ability of CDK5RAP2 to recruit γ-tubulin complexes. Thus, the PCM matrix can self-organize independently of centrioles to generate microtubules for spindle assembly; conversely, an alternative centriole-anchored mechanism supports spindle assembly when the PCM matrix is absent. Extension to three cancer cell lines revealed similar results in HeLa cells, whereas DLD1 and U2OS cells could assemble spindles in the absence of centrioles and PCNT-CDK5RAP2, suggesting cell type variation in spindle assembly mechanisms.
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Affiliation(s)
- Sadanori Watanabe
- Ludwig Institute for Cancer Research, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Franz Meitinger
- Ludwig Institute for Cancer Research, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Andrew K. Shiau
- Ludwig Institute for Cancer Research, La Jolla, CA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA
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29
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Pan L, Lemieux ME, Thomas T, Rogers JM, Lipper CH, Lee W, Johnson C, Sholl LM, South AP, Marto JA, Adelmant GO, Blacklow SC, Aster JC. IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation. eLife 2020; 9:e58081. [PMID: 32936072 PMCID: PMC7529455 DOI: 10.7554/elife.58081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Notch signaling regulates squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is tumor suppressive. Here, we show that conditional activation of Notch in squamous cells activates a context-specific gene expression program through lineage-specific regulatory elements. Among direct Notch target genes are multiple DNA damage response genes, including IER5, which we show is required for Notch-induced differentiation of squamous carcinoma cells and TERT-immortalized keratinocytes. IER5 is epistatic to PPP2R2A, a gene that encodes the PP2A B55α subunit, which we show interacts with IER5 in cells and in purified systems. Thus, Notch and DNA-damage response pathways converge in squamous cells on common genes that promote differentiation, which may serve to eliminate damaged cells from the proliferative pool. We further propose that crosstalk involving Notch and PP2A enables tuning and integration of Notch signaling with other pathways that regulate squamous differentiation.
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Affiliation(s)
- Li Pan
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | | | - Tom Thomas
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Julia M Rogers
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Winston Lee
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Carl Johnson
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Jarrod A Marto
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
- Departmentof Oncologic Pathology and Blais Proteomics Center, Dana FarberCancer Institute, HarvardMedical SchoolBostonUnited States
| | - Guillaume O Adelmant
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
- Departmentof Oncologic Pathology and Blais Proteomics Center, Dana FarberCancer Institute, HarvardMedical SchoolBostonUnited States
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Jon C Aster
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
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30
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Tsutsumi N, Mukherjee S, Waghray D, Janda CY, Jude KM, Miao Y, Burg JS, Aduri NG, Kossiakoff AA, Gati C, Garcia KC. Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. eLife 2020; 9:e58464. [PMID: 32762848 PMCID: PMC7442489 DOI: 10.7554/elife.58464] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/06/2020] [Indexed: 01/19/2023] Open
Abstract
Frizzleds (Fzd) are the primary receptors for Wnt morphogens, which are essential regulators of stem cell biology, yet the structural basis of Wnt signaling through Fzd remains poorly understood. Here we report the structure of an unliganded human Fzd5 determined by single-particle cryo-EM at 3.7 Å resolution, with the aid of an antibody chaperone acting as a fiducial marker. We also analyzed the topology of low-resolution XWnt8/Fzd5 complex particles, which revealed extreme flexibility between the Wnt/Fzd-CRD and the Fzd-TM regions. Analysis of Wnt/β-catenin signaling in response to Wnt3a versus a 'surrogate agonist' that cross-links Fzd to LRP6, revealed identical structure-activity relationships. Thus, canonical Wnt/β-catenin signaling appears to be principally reliant on ligand-induced Fzd/LRP6 heterodimerization, versus the allosteric mechanisms seen in structurally analogous class A G protein-coupled receptors, and Smoothened. These findings deepen our mechanistic understanding of Wnt signal transduction, and have implications for harnessing Wnt agonism in regenerative medicine.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
| | - Claudia Y Janda
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Princess Máxima Center for Pediatric OncologyUtrechtNetherlands
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - John S Burg
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Nanda Gowtham Aduri
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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31
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Fenech EJ, Lari F, Charles PD, Fischer R, Laétitia-Thézénas M, Bagola K, Paton AW, Paton JC, Gyrd-Hansen M, Kessler BM, Christianson JC. Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. eLife 2020; 9:e57306. [PMID: 32614325 PMCID: PMC7332293 DOI: 10.7554/elife.57306] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
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Affiliation(s)
- Emma J Fenech
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Federica Lari
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Philip D Charles
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Marie Laétitia-Thézénas
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Katrin Bagola
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of AdelaideAdelaideAustralia
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Botnar Research CentreOxfordUnited Kingdom
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32
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Gutiérrez-Salmerón M, García-Martínez JM, Martínez-Useros J, Fernández-Aceñero MJ, Viollet B, Olivier S, Chauhan J, Lucena SR, De la Vieja A, Goding CR, Chocarro-Calvo A, García-Jiménez C. Paradoxical activation of AMPK by glucose drives selective EP300 activity in colorectal cancer. PLoS Biol 2020; 18:e3000732. [PMID: 32603375 PMCID: PMC7326158 DOI: 10.1371/journal.pbio.3000732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
Coordination of gene expression with nutrient availability supports proliferation and homeostasis and is shaped by protein acetylation. Yet how physiological/pathological signals link acetylation to specific gene expression programs and whether such responses are cell-type–specific is unclear. AMP-activated protein kinase (AMPK) is a key energy sensor, activated by glucose limitation to resolve nutrient supply–demand imbalances, critical for diabetes and cancer. Unexpectedly, we show here that, in gastrointestinal cancer cells, glucose activates AMPK to selectively induce EP300, but not CREB-binding protein (CBP). Consequently, EP300 is redirected away from nuclear receptors that promote differentiation towards β-catenin, a driver of proliferation and colorectal tumorigenesis. Importantly, blocking glycogen synthesis permits reactive oxygen species (ROS) accumulation and AMPK activation in response to glucose in previously nonresponsive cells. Notably, glycogen content and activity of the ROS/AMPK/EP300/β-catenin axis are opposite in healthy versus tumor sections. Glycogen content reduction from healthy to tumor tissue may explain AMPK switching from tumor suppressor to activator during tumor evolution. Metabolic context determines whether the key energy sensor AMPK is a tumor suppressor or tumor promoter. This paradoxical behavior is explained through glucose inhibition of AMPK in healthy tissue versus glucose induction of AMPK in cancer colon epithelial cells.
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Affiliation(s)
- María Gutiérrez-Salmerón
- Area of Physiology, Faculty of Health Sciences, University Rey Juan Carlos, Alcorcón, Madrid, Spain
| | | | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute-University Hospital Fundación Jiménez Diaz-UAM, Madrid, Spain
| | | | - Benoit Viollet
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Severine Olivier
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia R. Lucena
- Area of Physiology, Faculty of Health Sciences, University Rey Juan Carlos, Alcorcón, Madrid, Spain
| | - Antonio De la Vieja
- Unidad de Tumores Endocrinos (UFIEC), Instituto de Salud Carlos III and CiberOnc, Majadahonda, Madrid, Spain
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Chocarro-Calvo
- Area of Physiology, Faculty of Health Sciences, University Rey Juan Carlos, Alcorcón, Madrid, Spain
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail: (ACC); (CGJ)
| | - Custodia García-Jiménez
- Area of Physiology, Faculty of Health Sciences, University Rey Juan Carlos, Alcorcón, Madrid, Spain
- * E-mail: (ACC); (CGJ)
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33
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Cheng X, Prange-Barczynska M, Fielding JW, Zhang M, Burrell AL, Lima JD, Eckardt L, Argles IL, Pugh CW, Buckler KJ, Robbins PA, Hodson EJ, Bruick RK, Collinson LM, Rastinejad F, Bishop T, Ratcliffe PJ. Marked and rapid effects of pharmacological HIF-2α antagonism on hypoxic ventilatory control. J Clin Invest 2020; 130:2237-2251. [PMID: 31999648 PMCID: PMC7190921 DOI: 10.1172/jci133194] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022] Open
Abstract
Hypoxia-inducible factor (HIF) is strikingly upregulated in many types of cancer, and there is great interest in applying inhibitors of HIF as anticancer therapeutics. The most advanced of these are small molecules that target the HIF-2 isoform through binding the PAS-B domain of HIF-2α. These molecules are undergoing clinical trials with promising results in renal and other cancers where HIF-2 is considered to be driving growth. Nevertheless, a central question remains as to whether such inhibitors affect physiological responses to hypoxia at relevant doses. Here, we show that pharmacological HIF-2α inhibition with PT2385, at doses similar to those reported to inhibit tumor growth, rapidly impaired ventilatory responses to hypoxia, abrogating both ventilatory acclimatization and carotid body cell proliferative responses to sustained hypoxia. Mice carrying a HIF-2α PAS-B S305M mutation that disrupts PT2385 binding, but not dimerization with HIF-1β, did not respond to PT2385, indicating that these effects are on-target. Furthermore, the finding of a hypomorphic ventilatory phenotype in untreated HIF-2α S305M mutant mice suggests a function for the HIF-2α PAS-B domain beyond heterodimerization with HIF-1β. Although PT2385 was well tolerated, the findings indicate the need for caution in patients who are dependent on hypoxic ventilatory drive.
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Affiliation(s)
- Xiaotong Cheng
- Target Discovery Institute and
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Maria Prange-Barczynska
- Target Discovery Institute and
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - James W. Fielding
- Target Discovery Institute and
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | | | | - Keith J. Buckler
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Richard K. Bruick
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | | | | | - Peter J. Ratcliffe
- Target Discovery Institute and
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
- Francis Crick Institute, London, United Kingdom
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34
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Cebon JS, Gore M, Thompson JF, Davis ID, McArthur GA, Walpole E, Smithers M, Cerundolo V, Dunbar PR, MacGregor D, Fisher C, Millward M, Nathan P, Findlay MPN, Hersey P, Evans TRJ, Ottensmeier CH, Marsden J, Dalgleish AG, Corrie PG, Maria M, Brimble M, Williams G, Winkler S, Jackson HM, Endo-Munoz L, Tutuka CSA, Venhaus R, Old LJ, Haack D, Maraskovsky E, Behren A, Chen W. Results of a randomized, double-blind phase II clinical trial of NY-ESO-1 vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in participants with high-risk resected melanoma. J Immunother Cancer 2020; 8:e000410. [PMID: 32317292 PMCID: PMC7204806 DOI: 10.1136/jitc-2019-000410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND To compare the clinical efficacy of New York Esophageal squamous cell carcinoma-1 (NY-ESO-1) vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in a randomized, double-blind phase II study in participants with fully resected melanoma at high risk of recurrence. METHODS Participants with resected stage IIc, IIIb, IIIc and IV melanoma expressing NY-ESO-1 were randomized to treatment with three doses of NY-ESO-1/ISCOMATRIX or ISCOMATRIX adjuvant administered intramuscularly at 4-week intervals, followed by a further dose at 6 months. Primary endpoint was the proportion free of relapse at 18 months in the intention-to-treat (ITT) population and two per-protocol populations. Secondary endpoints included relapse-free survival (RFS) and overall survival (OS), safety and NY-ESO-1 immunity. RESULTS The ITT population comprised 110 participants, with 56 randomized to NY-ESO-1/ISCOMATRIX and 54 to ISCOMATRIX alone. No significant toxicities were observed. There were no differences between the study arms in relapses at 18 months or for median time to relapse; 139 vs 176 days (p=0.296), or relapse rate, 27 (48.2%) vs 26 (48.1%) (HR 0.913; 95% CI 0.402 to 2.231), respectively. RFS and OS were similar between the study arms. Vaccine recipients developed strong positive antibody responses to NY-ESO-1 (p≤0.0001) and NY-ESO-1-specific CD4+ and CD8+ responses. Biopsies following relapse did not demonstrate differences in NY-ESO-1 expression between the study populations although an exploratory study demonstrated reduced (NY-ESO-1)+/Human Leukocyte Antigen (HLA) class I+ double-positive cells in biopsies from vaccine recipients performed on relapse in 19 participants. CONCLUSIONS The vaccine was well tolerated, however, despite inducing antigen-specific immunity, it did not affect survival endpoints. Immune escape through the downregulation of NY-ESO-1 and/or HLA class I molecules on tumor may have contributed to relapse.
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MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Immunologic/adverse effects
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biopsy
- Cancer Vaccines/administration & dosage
- Cancer Vaccines/adverse effects
- Cancer Vaccines/genetics
- Cancer Vaccines/immunology
- Chemotherapy, Adjuvant/adverse effects
- Chemotherapy, Adjuvant/methods
- Cholesterol/administration & dosage
- Cholesterol/adverse effects
- Dermatologic Surgical Procedures
- Disease-Free Survival
- Double-Blind Method
- Drug Combinations
- Female
- Follow-Up Studies
- Humans
- Immunogenicity, Vaccine
- Male
- Melanoma/diagnosis
- Melanoma/immunology
- Melanoma/mortality
- Melanoma/therapy
- Membrane Proteins/genetics
- Membrane Proteins/immunology
- Middle Aged
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/epidemiology
- Neoplasm Recurrence, Local/prevention & control
- Neoplasm Staging
- Phospholipids/administration & dosage
- Phospholipids/adverse effects
- Saponins/administration & dosage
- Saponins/adverse effects
- Skin/pathology
- Skin Neoplasms/diagnosis
- Skin Neoplasms/immunology
- Skin Neoplasms/mortality
- Skin Neoplasms/therapy
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Affiliation(s)
- Jonathan S Cebon
- Cancer Immunobiology Programme, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University at Austin Health, Heidelberg, Victoria, Australia
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
| | - Martin Gore
- Oncology, Royal Marsden Hospital NHS Trust, London, UK
| | - John F Thompson
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
| | - Ian D Davis
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
- Monash University Eastern Health Clinical School, Box Hill, Victoria, Australia
| | - Grant A McArthur
- Melanona and Skin Service, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Euan Walpole
- Cancer Services Division, Princess Alexandra Hospital Health Service District, Woolloongabba, Queensland, Australia
| | - Mark Smithers
- Oncology Services Unit, Princess Alexandra Hospital Health Service District, Woolloongabba, Queensland, Australia
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, Oxfordshire, UK
| | - P Rod Dunbar
- School of Biological Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Duncan MacGregor
- Department of Anatomical Pathology, Austin Health, Heidelberg, Victoria, Australia
| | - Cyril Fisher
- Oncology, Royal Marsden Hospital NHS Trust, London, UK
| | - Michael Millward
- School of Medicine and Pharmacology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Paul Nathan
- Mount Vernon Cancer Centre, Mount Vernon Hospital, Northwood, London, UK
| | - Michael P N Findlay
- School of Medicine and Health Science, The University of Auckland, Auckland, New Zealand
| | - Peter Hersey
- Melanoma Immunology and Oncology Group, Centenary Institute, Newtown, New South Wales, Australia
| | - T R Jeffry Evans
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Jeremy Marsden
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Angus G Dalgleish
- Cell and Molecular Sciences, Division of Oncology, St Georges Hospital Medical School, London, UK
| | - Pippa G Corrie
- West Anglia Cancer Research Network Oncology Centre, Addenbrooke's Hospital, Cambridge, Cambridgeshire, UK
| | - Marples Maria
- The Cancer Research Centre, Weston Park Hospital, Sheffield, UK
| | - Margaret Brimble
- School of Biological Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Geoff Williams
- School of Biological Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Sintia Winkler
- School of Biological Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Heather M Jackson
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
| | - Liliana Endo-Munoz
- Cancer Immunobiology Programme, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University at Austin Health, Heidelberg, Victoria, Australia
| | - Candani S A Tutuka
- Cancer Immunobiology Programme, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University at Austin Health, Heidelberg, Victoria, Australia
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
| | - Ralph Venhaus
- Ludwig Institute for Cancer Research, New York, New York, USA
| | - Lloyd J Old
- Ludwig Institute for Cancer Research, New York, New York, USA
| | - Dennis Haack
- Versagenics Inc, Morrisville, North Carolina, USA
| | | | - Andreas Behren
- Cancer Immunobiology Programme, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University at Austin Health, Heidelberg, Victoria, Australia
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
| | - Weisan Chen
- Ludwig Institute for Cancer Research Austin Branch, Heidelberg, Victoria, Australia
- Biochemistry and Genetics, La Trobe University, Melbourne, Victoria, Australia
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35
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Abstract
Transforming growth factor-β (TGF-β) represents an evolutionarily conserved family of secreted polypeptide factors that regulate many aspects of physiological embryogenesis and adult tissue homeostasis. The TGF-β family members are also involved in pathophysiological mechanisms that underlie many diseases. Although the family comprises many factors, which exhibit cell type-specific and developmental stage-dependent biological actions, they all signal via conserved signaling pathways. The signaling mechanisms of the TGF-β family are controlled at the extracellular level, where ligand secretion, deposition to the extracellular matrix and activation prior to signaling play important roles. At the plasma membrane level, TGF-βs associate with receptor kinases that mediate phosphorylation-dependent signaling to downstream mediators, mainly the SMAD proteins, and mediate oligomerization-dependent signaling to ubiquitin ligases and intracellular protein kinases. The interplay between SMADs and other signaling proteins mediate regulatory signals that control expression of target genes, RNA processing at multiple levels, mRNA translation and nuclear or cytoplasmic protein regulation. This article emphasizes signaling mechanisms and the importance of biochemical control in executing biological functions by the prototype member of the family, TGF-β.
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36
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Srinivasan R, Nady N, Arora N, Hsieh LJ, Swigut T, Narlikar GJ, Wossidlo M, Wysocka J. Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage. Sci Adv 2020; 6:eaaz9115. [PMID: 32219172 PMCID: PMC7083622 DOI: 10.1126/sciadv.aaz9115] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/02/2020] [Indexed: 05/07/2023]
Abstract
Zinc finger protein Zscan4 is selectively expressed in mouse two-cell (2C) embryos undergoing zygotic genome activation (ZGA) and in a rare subpopulation of embryonic stem cells with 2C-like features. Here, we show that Zscan4 specifically recognizes a subset of (CA)n microsatellites, repeat sequences prone to genomic instability. Zscan4-associated microsatellite regions are characterized by low nuclease sensitivity and high histone occupancy. In vitro, Zscan4 binds nucleosomes and protects them from disassembly upon torsional strain. Furthermore, Zscan4 depletion leads to elevated DNA damage in 2C mouse embryos in a transcription-dependent manner. Together, our results identify Zscan4 as a DNA sequence-dependent microsatellite binding factor and suggest a developmentally regulated mechanism, which protects fragile genomic regions from DNA damage at a time of embryogenesis associated with high transcriptional burden and genomic stress.
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Affiliation(s)
- Rajini Srinivasan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nataliya Nady
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura J. Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark Wossidlo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Cell and Developmental Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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37
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Ali S, Zhou F, Braden B, Bailey A, Yang S, Cheng G, Zhang P, Li X, Kayser M, Soberanis-Mukul RD, Albarqouni S, Wang X, Wang C, Watanabe S, Oksuz I, Ning Q, Yang S, Khan MA, Gao XW, Realdon S, Loshchenov M, Schnabel JA, East JE, Wagnieres G, Loschenov VB, Grisan E, Daul C, Blondel W, Rittscher J. An objective comparison of detection and segmentation algorithms for artefacts in clinical endoscopy. Sci Rep 2020; 10:2748. [PMID: 32066744 PMCID: PMC7026422 DOI: 10.1038/s41598-020-59413-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
We present a comprehensive analysis of the submissions to the first edition of the Endoscopy Artefact Detection challenge (EAD). Using crowd-sourcing, this initiative is a step towards understanding the limitations of existing state-of-the-art computer vision methods applied to endoscopy and promoting the development of new approaches suitable for clinical translation. Endoscopy is a routine imaging technique for the detection, diagnosis and treatment of diseases in hollow-organs; the esophagus, stomach, colon, uterus and the bladder. However the nature of these organs prevent imaged tissues to be free of imaging artefacts such as bubbles, pixel saturation, organ specularity and debris, all of which pose substantial challenges for any quantitative analysis. Consequently, the potential for improved clinical outcomes through quantitative assessment of abnormal mucosal surface observed in endoscopy videos is presently not realized accurately. The EAD challenge promotes awareness of and addresses this key bottleneck problem by investigating methods that can accurately classify, localize and segment artefacts in endoscopy frames as critical prerequisite tasks. Using a diverse curated multi-institutional, multi-modality, multi-organ dataset of video frames, the accuracy and performance of 23 algorithms were objectively ranked for artefact detection and segmentation. The ability of methods to generalize to unseen datasets was also evaluated. The best performing methods (top 15%) propose deep learning strategies to reconcile variabilities in artefact appearance with respect to size, modality, occurrence and organ type. However, no single method outperformed across all tasks. Detailed analyses reveal the shortcomings of current training strategies and highlight the need for developing new optimal metrics to accurately quantify the clinical applicability of methods.
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Affiliation(s)
- Sharib Ali
- Institute of Biomedical Engineering, Big Data Institute, Department of Engineering Science, University of Oxford, Oxford, UK.
| | - Felix Zhou
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Barbara Braden
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Div., John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Adam Bailey
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Div., John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Suhui Yang
- Ping An Technology (Shenzhen) Co. Ltd, Shenzhen, China
| | - Guanju Cheng
- Ping An Technology (Shenzhen) Co. Ltd, Shenzhen, China
| | | | | | | | | | | | - Xiaokang Wang
- Department of Biomedical Engineering, University of California, Davis, USA
| | - Chunqing Wang
- Department of Ultrasound Imaging, Tiantan Hospital, Beijing, China
| | - Seiryo Watanabe
- Department of Bioinformatic Engineering, Osaka University, Suita, Osaka, Japan
| | - Ilkay Oksuz
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Computer Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Qingtian Ning
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
| | - Shufan Yang
- School of Engineering, University of Glasgow, Glasgow, UK
| | - Mohammad Azam Khan
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Xiaohong W Gao
- Department of Computer Science, Middlesex University, London, UK
| | | | - Maxim Loshchenov
- A.M. Prokhorov General Physics Institute, Russian Academy of Science, Moscow, Russia
| | - Julia A Schnabel
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - James E East
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Div., John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Georges Wagnieres
- Swiss Federal Institute of Technology in Lausanne (EPFL), Lausanne, Switzerland
| | - Victor B Loschenov
- A.M. Prokhorov General Physics Institute, Russian Academy of Science, Moscow, Russia
| | - Enrico Grisan
- Department of Information Engineering, University of Padova, Padova, Italy
- School of Engineering, London South Bank University, London, UK
| | - Christian Daul
- CRAN UMR 7039, University of Lorraine, CNRS, Nancy, France
| | - Walter Blondel
- CRAN UMR 7039, University of Lorraine, CNRS, Nancy, France
| | - Jens Rittscher
- Institute of Biomedical Engineering, Big Data Institute, Department of Engineering Science, University of Oxford, Oxford, UK
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38
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Coe EA, Tan JY, Shapiro M, Louphrasitthiphol P, Bassett AR, Marques AC, Goding CR, Vance KW. The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor. PLoS Genet 2019; 15:e1008501. [PMID: 31881017 PMCID: PMC6934268 DOI: 10.1371/journal.pgen.1008501] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/30/2019] [Indexed: 01/14/2023] Open
Abstract
The MITF and SOX10 transcription factors regulate the expression of genes important for melanoma proliferation, invasion and metastasis. Despite growing evidence of the contribution of long noncoding RNAs (lncRNAs) in cancer, including melanoma, their functions within MITF-SOX10 transcriptional programmes remain poorly investigated. Here we identify 245 candidate melanoma associated lncRNAs whose loci are co-occupied by MITF-SOX10 and that are enriched at active enhancer-like regions. Our work suggests that one of these, Disrupted In Renal Carcinoma 3 (DIRC3), may be a clinically important MITF-SOX10 regulated tumour suppressor. DIRC3 depletion in human melanoma cells leads to increased anchorage-independent growth, a hallmark of malignant transformation, whilst melanoma patients classified by low DIRC3 expression have decreased survival. DIRC3 is a nuclear lncRNA that activates expression of its neighbouring IGFBP5 tumour suppressor through modulating chromatin structure and suppressing SOX10 binding to putative regulatory elements within the DIRC3 locus. In turn, DIRC3 dependent regulation of IGFBP5 impacts the expression of genes involved in cancer associated processes and is needed for DIRC3 control of anchorage-independent growth. Our work indicates that lncRNA components of MITF-SOX10 networks are an important new class of melanoma regulators and candidate therapeutic targets that can act not only as downstream mediators of MITF-SOX10 function but as feedback regulators of MITF-SOX10 activity.
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Affiliation(s)
- Elizabeth A. Coe
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jennifer Y. Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Michael Shapiro
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Andrew R. Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ana C. Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Keith W. Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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39
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Yuan F, Bi Y, Zhang JY, Zhou YL, Zhang XX, Song CX. 5-Carboxylcytosine is resistant towards phosphodiesterase I digestion: implications for epigenetic modification quantification by mass spectrometry. RSC Adv 2019; 9:29010-29014. [PMID: 35528408 PMCID: PMC9071843 DOI: 10.1039/c9ra04375f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/08/2019] [Indexed: 12/29/2022] Open
Abstract
DNA cytosine modifications are important epigenetic modifications in gene regulation and pathogenesis. DNA hydrolysis followed by HPLC-MS/MS is the gold standard in DNA modification quantification. In particular, it is the only sensitive and accurate method for low abundance modifications, such as 5-carboxylcytosine (5caC). Here, we report the discovery of the nuclease resistance property of 5caC to snake venom phosphodiesterase I (PDE1), a 3' to 5' exonuclease commonly used in several DNA hydrolysis protocols. We conducted a systematic evaluation of six commonly used hydrolysis protocols and found that all protocols that use PDE1 underestimate the level of 5caC. Finally, we identified the best method for cytosine modification quantification of biological samples, which leads to an over 10-fold higher amount of 5caC being detected compared with other methods. Our results highlight that caution should be taken when choosing a DNA hydrolysis protocol to quantify certain DNA modifications.
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Affiliation(s)
- Fang Yuan
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford OX3 7FZ UK
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University Beijing 100871 China
| | - Ying Bi
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford OX3 7FZ UK
| | - Jia-Yuan Zhang
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford OX3 7FZ UK
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University Beijing 100871 China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University Beijing 100871 China
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford OX3 7FZ UK
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40
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Cockman ME, Lippl K, Tian YM, Pegg HB, Figg WD, Abboud MI, Heilig R, Fischer R, Myllyharju J, Schofield CJ, Ratcliffe PJ. Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates. eLife 2019; 8:e46490. [PMID: 31500697 PMCID: PMC6739866 DOI: 10.7554/elife.46490] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
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Affiliation(s)
| | - Kerstin Lippl
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Ya-Min Tian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - William D Figg
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Peter J Ratcliffe
- The Francis Crick InstituteLondonUnited Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
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41
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Wang S, Ochoa SD, Khaliullin RN, Gerson-Gurwitz A, Hendel JM, Zhao Z, Biggs R, Chisholm AD, Desai A, Oegema K, Green RA. A high-content imaging approach to profile C. elegans embryonic development. Development 2019; 146:dev174029. [PMID: 30890570 PMCID: PMC6467471 DOI: 10.1242/dev.174029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
The Caenorhabditis elegans embryo is an important model for analyzing mechanisms of cell fate specification and tissue morphogenesis. Sophisticated lineage-tracing approaches for analyzing embryogenesis have been developed but are labor intensive and do not naturally integrate morphogenetic readouts. To enable the rapid classification of developmental phenotypes, we developed a high-content method that employs two custom strains: a Germ Layer strain that expresses nuclear markers in the ectoderm, mesoderm and endoderm/pharynx; and a Morphogenesis strain that expresses markers labeling epidermal cell junctions and the neuronal cell surface. We describe a procedure that allows simultaneous live imaging of development in 80-100 embryos and provide a custom program that generates cropped, oriented image stacks of individual embryos to facilitate analysis. We demonstrate the utility of our method by perturbing 40 previously characterized developmental genes in variants of the two strains containing RNAi-sensitizing mutations. The resulting datasets yielded distinct, reproducible signature phenotypes for a broad spectrum of genes that are involved in cell fate specification and morphogenesis. In addition, our analysis provides new in vivo evidence for MBK-2 function in mesoderm fate specification and LET-381 function in elongation.
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Affiliation(s)
- Shaohe Wang
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacy D Ochoa
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Renat N Khaliullin
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Adina Gerson-Gurwitz
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeffrey M Hendel
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhiling Zhao
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Biggs
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew D Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Rebecca A Green
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
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42
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Zhou FY, Ruiz-Puig C, Owen RP, White MJ, Rittscher J, Lu X. Motion sensing superpixels (MOSES) is a systematic computational framework to quantify and discover cellular motion phenotypes. eLife 2019; 8:e40162. [PMID: 30803483 PMCID: PMC6391079 DOI: 10.7554/elife.40162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022] Open
Abstract
Correct cell/cell interactions and motion dynamics are fundamental in tissue homeostasis, and defects in these cellular processes cause diseases. Therefore, there is strong interest in identifying factors, including drug candidates that affect cell/cell interactions and motion dynamics. However, existing quantitative tools for systematically interrogating complex motion phenotypes in timelapse datasets are limited. We present Motion Sensing Superpixels (MOSES), a computational framework that measures and characterises biological motion with a unique superpixel 'mesh' formulation. Using published datasets, MOSES demonstrates single-cell tracking capability and more advanced population quantification than Particle Image Velocimetry approaches. From > 190 co-culture videos, MOSES motion-mapped the interactions between human esophageal squamous epithelial and columnar cells mimicking the esophageal squamous-columnar junction, a site where Barrett's esophagus and esophageal adenocarcinoma often arise clinically. MOSES is a powerful tool that will facilitate unbiased, systematic analysis of cellular dynamics from high-content time-lapse imaging screens with little prior knowledge and few assumptions.
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Affiliation(s)
- Felix Y Zhou
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Carlos Ruiz-Puig
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Richard P Owen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Michael J White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Jens Rittscher
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Institute of Biomedical Engineering, Department of EngineeringUniversity of OxfordOxfordUnited Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and DiscoveryUniversity of OxfordOxfordUnited Kingdom
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
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43
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West AMV, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. eLife 2019; 8:e40372. [PMID: 30657449 PMCID: PMC6349405 DOI: 10.7554/elife.40372] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 11/30/2022] Open
Abstract
The meiotic chromosome axis plays key roles in meiotic chromosome organization and recombination, yet the underlying protein components of this structure are highly diverged. Here, we show that 'axis core proteins' from budding yeast (Red1), mammals (SYCP2/SYCP3), and plants (ASY3/ASY4) are evolutionarily related and play equivalent roles in chromosome axis assembly. We first identify 'closure motifs' in each complex that recruit meiotic HORMADs, the master regulators of meiotic recombination. We next find that axis core proteins form homotetrameric (Red1) or heterotetrameric (SYCP2:SYCP3 and ASY3:ASY4) coiled-coil assemblies that further oligomerize into micron-length filaments. Thus, the meiotic chromosome axis core in fungi, mammals, and plants shares a common molecular architecture, and likely also plays conserved roles in meiotic chromosome axis assembly and recombination control.
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Affiliation(s)
- Alan MV West
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Scott C Rosenberg
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
| | - Sarah N Ur
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - Madison K Lehmer
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Qiaozhen Ye
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Götz Hagemann
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Iracema Caballero
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
| | - Isabel Usón
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Amy J MacQueen
- Department of Molecular Biology and BiochemistryWesleyan UniversityMiddletownUnited States
| | - Franz Herzog
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Kevin D Corbett
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
- Ludwig Institute for Cancer ResearchLa JollaUnited States
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44
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Martin Lluesma S, Graciotti M, Chiang CLL, Kandalaft LE. Does the Immunocompetent Status of Cancer Patients Have an Impact on Therapeutic DC Vaccination Strategies? Vaccines (Basel) 2018; 6:E79. [PMID: 30477198 PMCID: PMC6313858 DOI: 10.3390/vaccines6040079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/09/2018] [Accepted: 11/21/2018] [Indexed: 12/24/2022] Open
Abstract
Although different types of therapeutic vaccines against established cancerous lesions in various indications have been developed since the 1990s, their clinical benefit is still very limited. This observed lack of effectiveness in cancer eradication may be partially due to the often deficient immunocompetent status of cancer patients, which may facilitate tumor development by different mechanisms, including immune evasion. The most frequently used cellular vehicle in clinical trials are dendritic cells (DCs), thanks to their crucial role in initiating and directing immune responses. Viable vaccination options using DCs are available, with a positive toxicity profile. For these reasons, despite their limited therapeutic outcomes, DC vaccination is currently considered an additional immunotherapeutic option that still needs to be further explored. In this review, we propose potential actions aimed at improving DC vaccine efficacy by counteracting the detrimental mechanisms recognized to date and implicated in establishing a poor immunocompetent status in cancer patients.
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Affiliation(s)
- Silvia Martin Lluesma
- Center of Experimental Therapeutics, Ludwig Center for Cancer Research, Department of Oncology, University of Lausanne, Lausanne 1011, Switzerland.
| | - Michele Graciotti
- Vaccine development laboratory, Ludwig Center for Cancer Research, Lausanne 1011, Switzerland.
| | - Cheryl Lai-Lai Chiang
- Vaccine development laboratory, Ludwig Center for Cancer Research, Lausanne 1011, Switzerland.
| | - Lana E Kandalaft
- Center of Experimental Therapeutics, Ludwig Center for Cancer Research, Department of Oncology, University of Lausanne, Lausanne 1011, Switzerland.
- Vaccine development laboratory, Ludwig Center for Cancer Research, Lausanne 1011, Switzerland.
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45
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Wang Y, Zhong S, Schofield CJ, Ratcliffe PJ, Lu X. Nuclear entry and export of FIH are mediated by HIF1α and exportin1, respectively. J Cell Sci 2018; 131:jcs219782. [PMID: 30333145 PMCID: PMC6250434 DOI: 10.1242/jcs.219782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022] Open
Abstract
Hypoxia plays a crucial role at cellular and physiological levels in all animals. The responses to chronic hypoxia are, at least substantially, orchestrated by activation of the hypoxia inducible transcription factors (HIFs), whose stability and subsequent transcriptional activation are regulated by HIF hydroxylases. Factor inhibiting HIF (FIH), initially isolated as a HIFα interacting protein following a yeast two-hybrid screen, is an asparaginyl hydroxylase that negatively regulates transcriptional activation by HIF. This study aimed to define the mechanisms that govern transitions of FIH between the nucleus and cytoplasm. We report that FIH accumulates in the nucleus within a short time window during hypoxia treatment. We provide evidence, based on the application of genetic interventions and small molecule inhibition of the HIF hydroxylases, that the nuclear localization of FIH is governed by two opposing processes: nuclear entry by 'coupling' with HIF1α for importin β1-mediated nuclear import and active export via a Leptomycin B-sensitive exportin1-dependent pathway.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yihua Wang
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Shan Zhong
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, NDM Research Building, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Xin Lu
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
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46
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Motnenko A, Liang CC, Yang D, Lopez-Martinez D, Yoshikawa Y, Zhan B, Ward KE, Tian J, Haas W, Spingardi P, Kessler BM, Kriaucionis S, Gygi SP, Cohn MA. Identification of UHRF2 as a novel DNA interstrand crosslink sensor protein. PLoS Genet 2018; 14:e1007643. [PMID: 30335751 PMCID: PMC6193622 DOI: 10.1371/journal.pgen.1007643] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/17/2018] [Indexed: 02/04/2023] Open
Abstract
The Fanconi Anemia (FA) pathway is important for repairing interstrand crosslinks (ICLs) between the Watson-Crick strands of the DNA double helix. An initial and essential stage in the repair process is the detection of the ICL. Here, we report the identification of UHRF2, a paralogue of UHRF1, as an ICL sensor protein. UHRF2 is recruited to ICLs in the genome within seconds of their appearance. We show that UHRF2 cooperates with UHRF1, to ensure recruitment of FANCD2 to ICLs. A direct protein-protein interaction is formed between UHRF1 and UHRF2, and between either UHRF1 and UHRF2, and FANCD2. Importantly, we demonstrate that the essential monoubiquitination of FANCD2 is stimulated by UHRF1/UHRF2. The stimulation is mediating by a retention of FANCD2 on chromatin, allowing for its monoubiquitination by the FA core complex. Taken together, we uncover a mechanism of ICL sensing by UHRF2, leading to FANCD2 recruitment and retention at ICLs, in turn facilitating activation of FANCD2 by monoubiquitination.
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Affiliation(s)
- Anna Motnenko
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Di Yang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Yasunaga Yoshikawa
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Bao Zhan
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Katherine E. Ward
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jiayang Tian
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Wilhelm Haas
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States of America Medicine, Kitasato University, Aomori, Japan
| | - Paolo Spingardi
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States of America Medicine, Kitasato University, Aomori, Japan
| | - Martin A. Cohn
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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47
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Tomkova M, Tomek J, Kriaucionis S, Schuster-Böckler B. Mutational signature distribution varies with DNA replication timing and strand asymmetry. Genome Biol 2018; 19:129. [PMID: 30201020 PMCID: PMC6130095 DOI: 10.1186/s13059-018-1509-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. CONCLUSIONS Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jakub Tomek
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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48
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Muir A, Danai LV, Vander Heiden MG. Microenvironmental regulation of cancer cell metabolism: implications for experimental design and translational studies. Dis Model Mech 2018; 11:dmm035758. [PMID: 30104199 PMCID: PMC6124553 DOI: 10.1242/dmm.035758] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cancers have an altered metabolism, and there is interest in understanding precisely how oncogenic transformation alters cellular metabolism and how these metabolic alterations can translate into therapeutic opportunities. Researchers are developing increasingly powerful experimental techniques to study cellular metabolism, and these techniques have allowed for the analysis of cancer cell metabolism, both in tumors and in ex vivo cancer models. These analyses show that, while factors intrinsic to cancer cells such as oncogenic mutations, alter cellular metabolism, cell-extrinsic microenvironmental factors also substantially contribute to the metabolic phenotype of cancer cells. These findings highlight that microenvironmental factors within the tumor, such as nutrient availability, physical properties of the extracellular matrix, and interactions with stromal cells, can influence the metabolic phenotype of cancer cells and might ultimately dictate the response to metabolically targeted therapies. In an effort to better understand and target cancer metabolism, this Review focuses on the experimental evidence that microenvironmental factors regulate tumor metabolism, and on the implications of these findings for choosing appropriate model systems and experimental approaches.
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Affiliation(s)
- Alexander Muir
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laura V Danai
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
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49
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Mangal S, Sacher J, Kim T, Osório DS, Motegi F, Carvalho AX, Oegema K, Zanin E. TPXL-1 activates Aurora A to clear contractile ring components from the polar cortex during cytokinesis. J Cell Biol 2018; 217:837-848. [PMID: 29311228 PMCID: PMC5839786 DOI: 10.1083/jcb.201706021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 11/13/2017] [Accepted: 12/01/2017] [Indexed: 02/07/2023] Open
Abstract
During cytokinesis, a signal from the central spindle that forms between the separating anaphase chromosomes promotes the accumulation of contractile ring components at the cell equator, while a signal from the centrosomal microtubule asters inhibits accumulation of contractile ring components at the cell poles. However, the molecular identity of the inhibitory signal has remained unknown. To identify molecular components of the aster-based inhibitory signal, we developed a means to monitor the removal of contractile ring proteins from the polar cortex after anaphase onset. Using this assay, we show that polar clearing is an active process that requires activation of Aurora A kinase by TPXL-1. TPXL-1 concentrates on astral microtubules coincident with polar clearing in anaphase, and its ability to recruit Aurora A and activate its kinase activity are essential for clearing. In summary, our data identify Aurora A kinase as an aster-based inhibitory signal that restricts contractile ring components to the cell equator during cytokinesis.
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Affiliation(s)
- Sriyash Mangal
- Center for Integrated Protein Science, Department Biology II, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Jennifer Sacher
- Center for Integrated Protein Science, Department Biology II, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Taekyung Kim
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA
| | - Daniel Sampaio Osório
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Fumio Motegi
- Research Link, National University of Singapore, Singapore
| | - Ana Xavier Carvalho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Karen Oegema
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA
| | - Esther Zanin
- Center for Integrated Protein Science, Department Biology II, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
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50
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Chiang IKN, Fritzsche M, Pichol-Thievend C, Neal A, Holmes K, Lagendijk A, Overman J, D'Angelo D, Omini A, Hermkens D, Lesieur E, Liu K, Ratnayaka I, Corada M, Bou-Gharios G, Carroll J, Dejana E, Schulte-Merker S, Hogan B, Beltrame M, De Val S, Francois M. SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development. Development 2017; 144:2629-2639. [PMID: 28619820 PMCID: PMC5536923 DOI: 10.1242/dev.146241] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 06/07/2017] [Indexed: 12/30/2022]
Abstract
Arterial specification and differentiation are influenced by a number of regulatory pathways. While it is known that the Vegfa-Notch cascade plays a central role, the transcriptional hierarchy controlling arterial specification has not been fully delineated. To elucidate the direct transcriptional regulators of Notch receptor expression in arterial endothelial cells, we used histone signatures, DNaseI hypersensitivity and ChIP-seq data to identify enhancers for the human NOTCH1 and zebrafish notch1b genes. These enhancers were able to direct arterial endothelial cell-restricted expression in transgenic models. Genetic disruption of SoxF binding sites established a clear requirement for members of this group of transcription factors (SOX7, SOX17 and SOX18) to drive the activity of these enhancers in vivo Endogenous deletion of the notch1b enhancer led to a significant loss of arterial connections to the dorsal aorta in Notch pathway-deficient zebrafish. Loss of SoxF function revealed that these factors are necessary for NOTCH1 and notch1b enhancer activity and for correct endogenous transcription of these genes. These findings position SoxF transcription factors directly upstream of Notch receptor expression during the acquisition of arterial identity in vertebrates.
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MESH Headings
- Amino Acid Sequence
- Animals
- Animals, Genetically Modified
- Arteries/embryology
- Arteries/metabolism
- Arteriovenous Malformations/embryology
- Arteriovenous Malformations/genetics
- Arteriovenous Malformations/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Expression Regulation, Developmental
- Human Umbilical Vein Endothelial Cells
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Pregnancy
- Receptor, Notch1/deficiency
- Receptor, Notch1/genetics
- Receptor, Notch1/metabolism
- SOXF Transcription Factors/deficiency
- SOXF Transcription Factors/genetics
- SOXF Transcription Factors/metabolism
- Sequence Homology, Amino Acid
- Signal Transduction
- Zebrafish
- Zebrafish Proteins/deficiency
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Ivy Kim-Ni Chiang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Martin Fritzsche
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, The University of Oxford, Oxford OX3 7DQ, UK
| | - Cathy Pichol-Thievend
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alice Neal
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, The University of Oxford, Oxford OX3 7DQ, UK
| | - Kelly Holmes
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anne Lagendijk
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeroen Overman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Donatella D'Angelo
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Alice Omini
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Dorien Hermkens
- University of Münster, 48149 Münster, Germany Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Westfälische Wilhelms-Universität Münster (WWU), Mendelstrasse 7, 48149 Münster and CiM Cluster of Excellence, Germany
| | - Emmanuelle Lesieur
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ke Liu
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool L69 3GA, UK
| | - Indrika Ratnayaka
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, The University of Oxford, Oxford OX3 7DQ, UK
| | - Monica Corada
- IFOM, FIRC Institute of Molecular Oncology, 1620139 Milan, Italy
| | - George Bou-Gharios
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool L69 3GA, UK
| | - Jason Carroll
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Elisabetta Dejana
- IFOM, FIRC Institute of Molecular Oncology, 1620139 Milan, Italy
- Department of Immunology Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
| | - Stefan Schulte-Merker
- University of Münster, 48149 Münster, Germany Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Westfälische Wilhelms-Universität Münster (WWU), Mendelstrasse 7, 48149 Münster and CiM Cluster of Excellence, Germany
| | - Benjamin Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Monica Beltrame
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sarah De Val
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, The University of Oxford, Oxford OX3 7DQ, UK
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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