1
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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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2
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Wragg JW, White PL, Hadzhiev Y, Wanigasooriya K, Stodolna A, Tee L, Barros-Silva JD, Beggs AD, Müller F. Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism. Nat Struct Mol Biol 2023; 30:1970-1984. [PMID: 37996663 PMCID: PMC10716046 DOI: 10.1038/s41594-023-01156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023]
Abstract
Global changes in transcriptional regulation and RNA metabolism are crucial features of cancer development. However, little is known about the role of the core promoter in defining transcript identity and post-transcriptional fates, a potentially crucial layer of transcriptional regulation in cancer. In this study, we use CAGE-seq analysis to uncover widespread use of dual-initiation promoters in which non-canonical, first-base-cytosine (C) transcription initiation occurs alongside first-base-purine initiation across 59 human cancers and healthy tissues. C-initiation is often followed by a 5' terminal oligopyrimidine (5'TOP) sequence, dramatically increasing the range of genes potentially subjected to 5'TOP-associated post-transcriptional regulation. We show selective, dynamic switching between purine and C-initiation site usage, indicating transcription initiation-level regulation in cancers. We additionally detail global metabolic changes in C-initiation transcripts that mark differentiation status, proliferative capacity, radiosensitivity, and response to irradiation and to PI3K-Akt-mTOR and DNA damage pathway-targeted radiosensitization therapies in colorectal cancer organoids and cancer cell lines and tissues.
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Affiliation(s)
- Joseph W Wragg
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Paige-Louise White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kasun Wanigasooriya
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Agata Stodolna
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Louise Tee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joao D Barros-Silva
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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3
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Ben-Oz BM, Machour FE, Nicola M, Argoetti A, Polyak G, Hanna R, Kleifeld O, Mandel-Gutfreund Y, Ayoub N. A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response. Nat Commun 2023; 14:7628. [PMID: 37993446 PMCID: PMC10665399 DOI: 10.1038/s41467-023-43495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
p53-mediated cell cycle arrest during DNA damage is dependent on the induction of p21 protein, encoded by the CDKN1A gene. p21 inhibits cyclin-dependent kinases required for cell cycle progression to guarantee accurate repair of DNA lesions. Hence, fine-tuning of p21 levels is crucial to preserve genomic stability. Currently, the multilayered regulation of p21 levels during DNA damage is not fully understood. Herein, we identify the human RNA binding motif protein 42 (RBM42) as a regulator of p21 levels during DNA damage. Genome-wide transcriptome and interactome analysis reveals that RBM42 alters the expression of p53-regulated genes during DNA damage. Specifically, we demonstrate that RBM42 facilitates CDKN1A splicing by counteracting the splicing inhibitory effect of RBM4 protein. Unexpectedly, we also show that RBM42, underpins translation of various splicing targets, including CDKN1A. Concordantly, transcriptome-wide mapping of RBM42-RNA interactions using eCLIP further substantiates the dual function of RBM42 in regulating splicing and translation of its target genes, including CDKN1A. Collectively, our data show that RBM42 couples splicing and translation machineries to fine-tune gene expression during DNA damage response.
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Affiliation(s)
- Bella M Ben-Oz
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Feras E Machour
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Marian Nicola
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Amir Argoetti
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Galia Polyak
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Rawad Hanna
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Oded Kleifeld
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
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4
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Prochownik EV, Wang H. Lessons in aging from Myc knockout mouse models. Front Cell Dev Biol 2023; 11:1244321. [PMID: 37621775 PMCID: PMC10446843 DOI: 10.3389/fcell.2023.1244321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Despite MYC being among the most intensively studied oncogenes, its role in normal development has not been determined as Myc-/- mice do not survival beyond mid-gestation. Myc ± mice live longer than their wild-type counterparts and are slower to accumulate many age-related phenotypes. However, Myc haplo-insufficiency likely conceals other important phenotypes as many high-affinity Myc targets genes continue to be regulated normally. By delaying Myc inactivation until after birth it has recently been possible to study the consequences of its near-complete total body loss and thus to infer its normal function. Against expectation, these "MycKO" mice lived significantly longer than control wild-type mice but manifested a marked premature aging phenotype. This seemingly paradoxical behavior was potentially explained by a >3-fold lower lifetime incidence of cancer, normally the most common cause of death in mice and often Myc-driven. Myc loss accelerated the accumulation of numerous "Aging Hallmarks", including the loss of mitochondrial and ribosomal structural and functional integrity, the generation of reactive oxygen species, the acquisition of genotoxic damage, the detrimental rewiring of metabolism and the onset of senescence. In both mice and humans, normal aging in many tissues was accompaniued by the downregulation of Myc and the loss of Myc target gene regulation. Unlike most mouse models of premature aging, which are based on monogenic disorders of DNA damage recognition and repair, the MycKO mouse model directly impacts most Aging Hallmarks and may therefore more faithfully replicate the normal aging process of both mice and humans. It further establishes that the strong association between aging and cancer can be genetically separated and is maintained by a single gene.
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Affiliation(s)
- Edward V. Prochownik
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
- The Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA, United States
- The Hillman Cancer Center of UPMC, Pittsburgh, PA, United States
- The Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA, United States
| | - Huabo Wang
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
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5
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Zhang W, Cao X, Zhong X, Wu H, Shi Y, Feng M, Wang YC, Ann D, Gwack Y, Yuan YC, Shang W, Sun Z. SRC2 controls CD4 + T cell activation via stimulating c-Myc-mediated upregulation of amino acid transporter Slc7a5. Proc Natl Acad Sci U S A 2023; 120:e2221352120. [PMID: 37094160 PMCID: PMC10160970 DOI: 10.1073/pnas.2221352120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/16/2023] [Indexed: 04/26/2023] Open
Abstract
T cell activation stimulates substantially increased protein synthesis activity to accumulate sufficient biomass for cell proliferation. The protein synthesis is fueled by the amino acids transported from the environment. Steroid nuclear receptor coactivator 2 (SRC2) is a member of a family of transcription coactivators. Here, we show that SRC2 recruited by c-Myc enhances CD4+ T cell activation to stimulate immune responses via upregulation of amino acid transporter Slc7a5. Mice deficient of SRC2 in T cells (SRC2fl/fl/CD4Cre) are resistant to the induction of experimental autoimmune encephalomyelitis (EAE) and susceptible to Citrobacter rodentium (C. rodentium) infection. Adoptive transfer of naive CD4+ T cells from SRC2fl/fl/CD4Cre mice fails to elicit EAE and colitis in Rag1/ recipients. Further, CD4+ T cells from SRC2fl/fl/CD4Cre mice display defective T cell proliferation, cytokine production, and differentiation both in vitro and in vivo. Mechanically, SRC2 functions as a coactivator to work together with c-Myc to stimulate the expression of amino acid transporter Slc7a5 required for T cell activation. Slc7a5 fails to be up-regulated in CD4+ T cells from SRC2fl/fl/CD4Cre mice, and forced expression of Slc7a5 rescues proliferation, cytokine production, and the ability of SRC2fl/fl/CD4Cre CD4+ T cells to induce EAE. Therefore, SRC2 is essential for CD4+ T cell activation and, thus, a potential drug target for controlling CD4+ T cell-mediated autoimmunity.
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Affiliation(s)
- Wencan Zhang
- Department of Immunology & Theranostics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Xu Cao
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Xiancai Zhong
- Department of Immunology & Theranostics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Hongmin Wu
- Department of Immunology & Theranostics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Yun Shi
- Department of Immunology & Theranostics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Mingye Feng
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Yi-Chang Wang
- Department of Diabetes Complication and Metabolism, Arthur Rigs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - David Ann
- Department of Diabetes Complication and Metabolism, Arthur Rigs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
| | - Yousang Gwack
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Yate-Ching Yuan
- Division of Translational Bioinformatic, Bioinformatics Core, City of Hope, Duarte, CA91010
| | - Weirong Shang
- Department of Gynecology and Obsterics, School of Medicine, Emory University, Atlanta, GA30322
| | - Zuoming Sun
- Department of Immunology & Theranostics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA91010
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6
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Vähätupa M, Nättinen J, Aapola U, Uusitalo-Järvinen H, Uusitalo H, Järvinen TAH. Proteomics Analysis of R-Ras Deficiency in Oxygen Induced Retinopathy. Int J Mol Sci 2023; 24:ijms24097914. [PMID: 37175621 PMCID: PMC10178533 DOI: 10.3390/ijms24097914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Small GTPase R-Ras regulates vascular permeability in angiogenesis. In the eye, abnormal angiogenesis and hyperpermeability are the leading causes of vision loss in several ischemic retinal diseases such as proliferative diabetic retinopathy (PDR), retinal vein occlusion (RVO), and retinopathy of prematurity (ROP). Oxygen-induced retinopathy (OIR) is the most widely used experimental model for these ischemic retinopathies. To shed more light on how the R-Ras regulates vascular permeability in pathological angiogenesis, we performed a comprehensive (>2900 proteins) characterization of OIR in R-Ras knockout (KO) and wild-type (WT) mice by sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics. OIR and age-matched normoxic control retinas were collected at P13, P17, and P42 from R-Ras KO and WT mice and were subjected to SWATH-MS and data analysis. The most significant difference between the R-Ras KO and WT retinas was an accumulation of plasma proteins. The pathological vascular hyperpermeability during OIR in the R-Ras KO retina took place very early, P13. This led to simultaneous hypoxic cell injury/death (ferroptosis), glycolytic metabolism as well compensatory mechanisms to counter the pathological leakage from angiogenic blood vessels in the OIR retina of R-Ras deficient mice.
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Affiliation(s)
- Maria Vähätupa
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
| | - Janika Nättinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Ulla Aapola
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Hannele Uusitalo-Järvinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Hannu Uusitalo
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
| | - Tero A H Järvinen
- Faculty of Medicine and Health Technology, Tampere University, 33521 Tampere, Finland
- Tampere University Hospital, 33520 Tampere, Finland
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7
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Cieśla M, Ngoc PCT, Muthukumar S, Todisco G, Madej M, Fritz H, Dimitriou M, Incarnato D, Hellström-Lindberg E, Bellodi C. m 6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis. Mol Cell 2023; 83:1165-1179.e11. [PMID: 36944332 DOI: 10.1016/j.molcel.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 01/07/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDSs), which are clonal hematopoietic disorders with variable risk of leukemic transformation. Although tumorigenic SF3B1 mutations have been extensively characterized, the role of "non-mutated" wild-type SF3B1 in cancer remains largely unresolved. Here, we identify a conserved epitranscriptomic program that steers SF3B1 levels to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals dynamic regulation of SF3B1 protein abundance, which affects MDS-to-leukemia progression in vivo. Mechanistically, ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation directing splicing of central DNA repair and epigenetic regulators during transformation. This impacts genome stability and leukemia progression in vivo, supporting an integrative analysis in humans that SF3B1 molecular signatures may predict mutational variability and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.
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Affiliation(s)
- Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden; International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland.
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Gabriele Todisco
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Helena Fritz
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Marios Dimitriou
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184 Lund, Sweden.
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8
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Zhou X, Fu C, Chen X. The role of ubiquitin pathway-mediated regulation of immune checkpoints in cancer immunotherapy. Cancer 2023; 129:1649-1661. [PMID: 36857206 DOI: 10.1002/cncr.34729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
Abstract
With the continuous cognition of the relationship between tumor cells and tumor immune microenvironment, immunotherapy based on the immune checkpoint blockade has achieved great breakthroughs, led to improved clinical outcomes, and prolonged survival for cancer patients in recent years. Nevertheless, the de novo or acquired resistance to immunotherapy has greatly counteracted the efficacy, leading to a 20%-40% overall response rate. Thus, further in-depth understanding of the regulation of the tumor microenvironment and antitumor immunity is urgently warranted. Ubiquitination-mediated protein degradation plays vital roles in protein stabilization, activation, and dynamics as well as in cellular homeostasis modulation. The dysregulated ubiquitination and deubiquitination are closely related to the changes in physiological and pathological processes, which subsequently result in a variety of diseases including cancer. In this review, the authors first summarize the current knowledge about the involvement of the ubiquitin-proteasome system in tumor development with the ubiquitin conjugation-regulated stability of p53, phosphatase and tensin homolog, and Myc protein as examples, then dissect the potential implications of ubiquitination-mediated immune checkpoints degradation in tumor microenvironment and immune responses, and finally discuss the effects of therapeutically targeting the ubiquitin-proteasome pathway on immunotherapy, with the goal of providing deep insights into the exploitation of more precise and effective combinational therapy against cancer.
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Affiliation(s)
- Xiaoming Zhou
- Cancer Research Institute, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Department of Pharmacy, School of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Chengxiao Fu
- Cancer Research Institute, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Department of Pharmacy, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xisha Chen
- Cancer Research Institute, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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9
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Parry EM, Leshchiner I, Guièze R, Johnson C, Tausch E, Parikh SA, Lemvigh C, Broséus J, Hergalant S, Messer C, Utro F, Levovitz C, Rhrissorrakrai K, Li L, Rosebrock D, Yin S, Deng S, Slowik K, Jacobs R, Huang T, Li S, Fell G, Redd R, Lin Z, Knisbacher BA, Livitz D, Schneider C, Ruthen N, Elagina L, Taylor-Weiner A, Persaud B, Martinez A, Fernandes SM, Purroy N, Anandappa AJ, Ma J, Hess J, Rassenti LZ, Kipps TJ, Jain N, Wierda W, Cymbalista F, Feugier P, Kay NE, Livak KJ, Danysh BP, Stewart C, Neuberg D, Davids MS, Brown JR, Parida L, Stilgenbauer S, Getz G, Wu CJ. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome. Nat Med 2023; 29:158-169. [PMID: 36624313 PMCID: PMC10155825 DOI: 10.1038/s41591-022-02113-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 10/28/2022] [Indexed: 01/11/2023]
Abstract
Richter syndrome (RS) arising from chronic lymphocytic leukemia (CLL) exemplifies an aggressive malignancy that develops from an indolent neoplasm. To decipher the genetics underlying this transformation, we computationally deconvoluted admixtures of CLL and RS cells from 52 patients with RS, evaluating paired CLL-RS whole-exome sequencing data. We discovered RS-specific somatic driver mutations (including IRF2BP2, SRSF1, B2M, DNMT3A and CCND3), recurrent copy-number alterations beyond del(9p21)(CDKN2A/B), whole-genome duplication and chromothripsis, which were confirmed in 45 independent RS cases and in an external set of RS whole genomes. Through unsupervised clustering, clonally related RS was largely distinct from diffuse large B cell lymphoma. We distinguished pathways that were dysregulated in RS versus CLL, and detected clonal evolution of transformation at single-cell resolution, identifying intermediate cell states. Our study defines distinct molecular subtypes of RS and highlights cell-free DNA analysis as a potential tool for early diagnosis and monitoring.
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Affiliation(s)
- Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Romain Guièze
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- CHU de Clermont-Ferrand, Clermont-Ferrand, France
- Université Clermont Auvergne, EA7453 CHELTER, Clermont-Ferrand, France
| | | | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | | | - Camilla Lemvigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julien Broséus
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU-Nancy, service d'hématologie biologique, pôle laboratoires, Nancy, France
| | - Sébastien Hergalant
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
| | - Conor Messer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Filippo Utro
- IBM Research, Yorktown Heights, New York, NY, USA
| | | | | | - Liang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Stephanie Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kara Slowik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raquel Jacobs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Geoff Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robert Redd
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziao Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Christof Schneider
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Neil Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Bria Persaud
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aina Martinez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Annabelle J Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jialin Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julian Hess
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Z Rassenti
- Moores Cancer Center, Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Kipps
- Moores Cancer Center, Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nitin Jain
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florence Cymbalista
- Laboratoire d'hématologie, Hôpital Avicenne-AP-HP, INSERM U978- Université Sorbonne Paris Nord, Bobigny, France
| | - Pierre Feugier
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU Nancy, service d'hématologie clinique, Nancy, France
| | - Neil E Kay
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laxmi Parida
- IBM Research, Yorktown Heights, New York, NY, USA
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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10
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Zhang J, Wang Z, Wang K, Xin D, Wang L, Fan Y, Xu Y. Increased Expression of SRSF1 Predicts Poor Prognosis in Multiple Myeloma. JOURNAL OF ONCOLOGY 2023; 2023:9998927. [PMID: 37206090 PMCID: PMC10191755 DOI: 10.1155/2023/9998927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/11/2022] [Accepted: 01/19/2023] [Indexed: 05/21/2023]
Abstract
Background Multiple myeloma (MM) is a clonal plasma cell disorder which still lacks sufficient prognostic factors. The serine/arginine-rich splicing factor (SRSF) family serves as an important splicing regulator in organ development. Among all members, SRSF1 plays an important role in cell proliferation and renewal. However, the role of SRSF1 in MM is still unknown. Methods SRSF1 was selected from the primary bioinformatics analysis of SRSF family members, and then we integrated 11 independent datasets and analyzed the relationship between SRSF1 expression and MM clinical characteristics. Gene set enrichment analysis (GSEA) was conducted to explore the potential mechanism of SRSF1 in MM progression. ImmuCellAI was used to estimate the abundance of immune infiltrating cells between the SRSF1high and SRSF1low groups. The ESTIMATE algorithm was used to evaluate the tumor microenvironment in MM. The expression of immune-related genes was compared between the groups. Additionally, SRSF1 expression was validated in clinical samples. SRSF1 knockdown was conducted to explore the role of SRSF1 in MM development. Results SRSF1 expression showed an increasing trend with the progression of myeloma. Besides, SRSF1 expression increased as the age, ISS stage, 1q21 amplification level, and relapse times increased. MM patients with higher SRSF1 expression had worse clinical features and poorer outcomes. Univariate and multivariate analysis indicated that upregulated SRSF1 expression was an independent poor prognostic factor for MM. Enrichment pathway analysis confirmed that SRSF1 takes part in the myeloma progression via tumor-associated and immune-related pathways. Several checkpoints and immune-activating genes were significantly downregulated in the SRSF1high groups. Furthermore, we detected that SRSF1 expression was significantly higher in MM patients than that in control donors. SRSF1 knockdown resulted in proliferation arrest in MM cell lines. Conclusion The expression value of SRSF1 is positively associated with myeloma progression, and high SRSF1 expression might be a poor prognostic biomarker in MM patients.
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Affiliation(s)
- Jiawei Zhang
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Zhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zanzan Wang
- Department of Hematology, Ningbo First Hospital, Ningbo 315010, China
| | - Kailai Wang
- Zhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Dijia Xin
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Luyao Wang
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yili Fan
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yang Xu
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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11
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Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. Deciphering the role of RNA structure in translation efficiency. BMC Bioinformatics 2022; 23:559. [PMID: 36564729 PMCID: PMC9783404 DOI: 10.1186/s12859-022-05037-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. RESULTS Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3' untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5' UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. CONCLUSIONS Our results suggest the openness of the 3' UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3' UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation.
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Affiliation(s)
- Jianan Lin
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Yang Chen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Center for Quantitative Medicine, University of Connecticut, Farmington, CT, 06030, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, CT, 06520, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA.
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12
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Larionova TD, Bastola S, Aksinina TE, Anufrieva KS, Wang J, Shender VO, Andreev DE, Kovalenko TF, Arapidi GP, Shnaider PV, Kazakova AN, Latyshev YA, Tatarskiy VV, Shtil AA, Moreau P, Giraud F, Li C, Wang Y, Rubtsova MP, Dontsova OA, Condro M, Ellingson BM, Shakhparonov MI, Kornblum HI, Nakano I, Pavlyukov MS. Alternative RNA splicing modulates ribosomal composition and determines the spatial phenotype of glioblastoma cells. Nat Cell Biol 2022; 24:1541-1557. [PMID: 36192632 PMCID: PMC10026424 DOI: 10.1038/s41556-022-00994-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/15/2022] [Indexed: 02/08/2023]
Abstract
Glioblastoma (GBM) is characterized by exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here, we found that the compositions of ribosomes of GBM cells in the tumour core and edge differ due to alternative RNA splicing. The acidic pH in the core switches before messenger RNA splicing of the ribosomal gene RPL22L1 towards the RPL22L1b isoform. This allows cells to survive acidosis, increases stemness and correlates with worse patient outcome. Mechanistically, RPL22L1b promotes RNA splicing by interacting with lncMALAT1 in the nucleus and inducing its degradation. Contrarily, in the tumour edge region, RPL22L1a interacts with ribosomes in the cytoplasm and upregulates the translation of multiple messenger RNAs including TP53. We found that the RPL22L1 isoform switch is regulated by SRSF4 and identified a compound that inhibits this process and decreases tumour growth. These findings demonstrate how distinct GBM cell populations arise during tumour growth. Targeting this mechanism may decrease GBM heterogeneity and facilitate therapy.
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Affiliation(s)
- Tatyana D Larionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Soniya Bastola
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Tatiana E Aksinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Jia Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Victoria O Shender
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Dmitriy E Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Tatiana F Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Georgij P Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Yaroslav A Latyshev
- N.N. Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Pascale Moreau
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Francis Giraud
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chaoxi Li
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yichan Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maria P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Olga A Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Michael Condro
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Ellingson
- Brain Tumor Imaging Laboratory, Center for Computer Vision and Imaging Biomarkers, University of California Los Angeles, Los Angeles, CA, USA
- Department of Radiological Sciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Harley I Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ichiro Nakano
- Department of Neurosurgery, Medical Institute of Hokuto, Hokkaido, Japan.
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
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13
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Demel UM, Wirth M, Yousefian S, Zhang L, Isaakidis K, Dönig J, Böger M, Singh N, Köse H, Haas S, Müller S, Schick M, Keller U. Small-molecule SUMO inhibition for biomarker-informed B-cell lymphoma therapy. Haematologica 2022; 108:555-567. [PMID: 36134453 PMCID: PMC9890013 DOI: 10.3324/haematol.2022.280995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 02/03/2023] Open
Abstract
Aberrant activity of the SUMOylation pathway has been associated with MYC overexpression and poor prognosis in aggressive B-cell lymphoma (BCL) and other malignancies. Recently developed small-molecule inhibitors of SUMOylation (SUMOi) target the heterodimeric E1 SUMO activation complex (SAE1/UBA2). Here, we report that activated MYC signaling is an actionable molecular vulnerability in vitro and in a preclinical murine in vivo model of MYC-driven BCL. While SUMOi conferred direct effects on MYC-driven lymphoma cells, SUMO inhibition also resulted in substantial remodeling of various subsets of the innate and specific immunity in vivo. Specifically, SUMOi increased the number of memory B cells as well as cytotoxic and memory T cells, subsets that are attributed a key role within a coordinated anti-tumor immune response. In summary, our data constitute pharmacologic SUMOi as a powerful therapy in a subset of BCL causing massive remodeling of the normal B-cell and T-cell compartment.
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Affiliation(s)
- Uta M. Demel
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin,Clinician Scientist Program, Berlin Institute of Health (BIH), Berlin
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Schayan Yousefian
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin
| | - Le Zhang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Konstandina Isaakidis
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Judith Dönig
- Institute of Biochemistry II, Goethe University Frankfurt, Medical School, Frankfurt
| | - Marlitt Böger
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Nikita Singh
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Hazal Köse
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Simon Haas
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg,Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University Frankfurt, Medical School, Frankfurt
| | - Markus Schick
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin,Max-Delbrück-Center for Molecular Medicine, Berlin
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg.
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14
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Salloum D, Singh K, Davidson NR, Cao L, Kuo D, Sanghvi VR, Jiang M, Lafoz MT, Viale A, Ratsch G, Wendel HG. A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1189-1199. [PMID: 36002234 PMCID: PMC9492650 DOI: 10.4049/jimmunol.2100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/25/2022] [Indexed: 01/04/2023]
Abstract
The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
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Affiliation(s)
- Darin Salloum
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY
| | - Natalie R Davidson
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Linlin Cao
- Swiss Institute for Experimental Cancer Research, EPFL, Lausanne, Switzerland
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami FL
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Tello Lafoz
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Ratsch
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY;
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15
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Mohan P, Pasion J, Ciriello G, Lailler N, de Stanchina E, Viale A, van den Berg A, Diepstra A, Wendel HG, Sanghvi VR, Singh K. Frequent 4EBP1 Amplification Induces Synthetic Dependence on FGFR Signaling in Cancer. Cancers (Basel) 2022; 14:2397. [PMID: 35626002 PMCID: PMC9139685 DOI: 10.3390/cancers14102397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
The eIF4E translation initiation factor has oncogenic properties and concordantly, the inhibitory eIF4E-binding protein (4EBP1) is considered a tumor suppressor. The exact molecular effects of 4EBP1 activation in cancer are still unknown. Surprisingly, 4EBP1 is a target of genomic copy number gains (Chr. 8p11) in breast and lung cancer. We noticed that 4EBP1 gains are genetically linked to gains in neighboring genes, including WHSC1L1 and FGFR1. Our results show that FGFR1 gains act to attenuate the function of 4EBP1 via PI3K-mediated phosphorylation at Thr37/46, Ser65, and Thr70 sites. This implies that not 4EBP1 but instead FGFR1 is the genetic target of Chr. 8p11 gains in breast and lung cancer. Accordingly, these tumors show increased sensitivity to FGFR1 and PI3K inhibition, and this is a therapeutic vulnerability through restoring the tumor-suppressive function of 4EBP1. Ribosome profiling reveals genes involved in insulin signaling, glucose metabolism, and the inositol pathway to be the relevant translational targets of 4EBP1. These mRNAs are among the top 200 translation targets and are highly enriched for structure and sequence motifs in their 5'UTR, which depends on the 4EBP1-EIF4E activity. In summary, we identified the translational targets of 4EBP1-EIF4E that facilitate the tumor suppressor function of 4EBP1 in cancer.
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Affiliation(s)
- Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Joyce Pasion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, CH-1005 Lausanne, Switzerland;
| | - Nathalie Lailler
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA;
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.v.d.B.); (A.D.)
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.v.d.B.); (A.D.)
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Viraj R. Sanghvi
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Kamini Singh
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY 10461, USA
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16
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Surya A, Sarinay-Cenik E. Cell autonomous and non-autonomous consequences of deviations in translation machinery on organism growth and the connecting signalling pathways. Open Biol 2022; 12:210308. [PMID: 35472285 PMCID: PMC9042575 DOI: 10.1098/rsob.210308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/31/2022] [Indexed: 01/09/2023] Open
Abstract
Translation machinery is responsible for the production of cellular proteins; thus, cells devote the majority of their resources to ribosome biogenesis and protein synthesis. Single-copy loss of function in the translation machinery components results in rare ribosomopathy disorders, such as Diamond-Blackfan anaemia in humans and similar developmental defects in various model organisms. Somatic copy number alterations of translation machinery components are also observed in specific tumours. The organism-wide response to haploinsufficient loss-of-function mutations in ribosomal proteins or translation machinery components is complex: variations in translation machinery lead to reduced ribosome biogenesis, protein translation and altered protein homeostasis and cellular signalling pathways. Cells are affected both autonomously and non-autonomously by changes in translation machinery or ribosome biogenesis through cell-cell interactions and secreted hormones. We first briefly introduce the model organisms where mutants or knockdowns of protein synthesis and ribosome biogenesis are characterized. Next, we specifically describe observations in Caenorhabditis elegans and Drosophila melanogaster, where insufficient protein synthesis in a subset of cells triggers cell non-autonomous growth or apoptosis responses that affect nearby cells and tissues. We then cover the characterized signalling pathways that interact with ribosome biogenesis/protein synthesis machinery with an emphasis on their respective functions during organism development.
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Affiliation(s)
- Agustian Surya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elif Sarinay-Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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17
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Cannons JL, Villarino AV, Kapnick SM, Preite S, Shih HY, Gomez-Rodriguez J, Kaul Z, Shibata H, Reilley JM, Huang B, Handon R, McBain IT, Gossa S, Wu T, Su HC, McGavern DB, O'Shea JJ, McGuire PJ, Uzel G, Schwartzberg PL. PI3Kδ coordinates transcriptional, chromatin, and metabolic changes to promote effector CD8 + T cells at the expense of central memory. Cell Rep 2021; 37:109804. [PMID: 34644563 PMCID: PMC8582080 DOI: 10.1016/j.celrep.2021.109804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 07/15/2021] [Accepted: 09/16/2021] [Indexed: 01/05/2023] Open
Abstract
Patients with activated phosphatidylinositol 3-kinase delta (PI3Kδ) syndrome (APDS) present with sinopulmonary infections, lymphadenopathy, and cytomegalvirus (CMV) and/or Epstein-Barr virus (EBV) viremia, yet why patients fail to clear certain chronic viral infections remains incompletely understood. Using patient samples and a mouse model (Pik3cdE1020K/+ mice), we demonstrate that, upon activation, Pik3cdE1020K/+ CD8+ T cells exhibit exaggerated features of effector populations both in vitro and after viral infection that are associated with increased Fas-mediated apoptosis due to sustained FoxO1 phosphorylation and Fasl derepression, enhanced mTORC1 and c-Myc signatures, metabolic perturbations, and an altered chromatin landscape. Conversely, Pik3cdE1020K/+ CD8+ cells fail to sustain expression of proteins critical for central memory, including TCF1. Strikingly, activated Pik3cdE1020K/+ CD8+ cells exhibit altered transcriptional and epigenetic circuits characterized by pronounced interleukin-2 (IL-2)/STAT5 signatures and heightened IL-2 responses that prevent differentiation to memory-like cells in IL-15. Our data position PI3Kδ as integrating multiple signaling nodes that promote CD8+ T cell effector differentiation, providing insight into phenotypes of patients with APDS.
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Affiliation(s)
- Jennifer L Cannons
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
| | - Alejandro V Villarino
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA; Department of Microbiology & Immunology and Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Senta M Kapnick
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Silvia Preite
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Julio Gomez-Rodriguez
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; TCR2 Therapeutics, Cambridge, MA 02142, USA
| | - Zenia Kaul
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Hirofumi Shibata
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Julie M Reilley
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bonnie Huang
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Handon
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ian T McBain
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Selamawit Gossa
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Tuoqi Wu
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; University of Colorado, Department of Immunology, Denver, CO 80204, USA; Department of Immunology and Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390
| | - Helen C Su
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Dorian B McGavern
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - John J O'Shea
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Peter J McGuire
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Gulbu Uzel
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Pamela L Schwartzberg
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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18
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Donati G, Ravà M, Filipuzzi M, Nicoli P, Cassina L, Verrecchia A, Doni M, Rodighiero S, Parodi F, Boletta A, Vellano CP, Marszalek JR, Draetta GF, Amati B. Targeting mitochondrial respiration and the BCL2 family in high-grade MYC-associated B-cell lymphoma. Mol Oncol 2021; 16:1132-1152. [PMID: 34632715 PMCID: PMC8895457 DOI: 10.1002/1878-0261.13115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 01/02/2023] Open
Abstract
Multiple molecular features, such as activation of specific oncogenes (e.g., MYC, BCL2) or a variety of gene expression signatures, have been associated with disease course in diffuse large B‐cell lymphoma (DLBCL), although their relationships and implications for targeted therapy remain to be fully unraveled. We report that MYC activity is closely correlated with—and most likely a driver of—gene signatures related to oxidative phosphorylation (OxPhos) in DLBCL, pointing to OxPhos enzymes, in particular mitochondrial electron transport chain (ETC) complexes, as possible therapeutic targets in high‐grade MYC‐associated lymphomas. In our experiments, indeed, MYC sensitized B cells to the ETC complex I inhibitor IACS‐010759. Mechanistically, IACS‐010759 triggered the integrated stress response (ISR) pathway, driven by the transcription factors ATF4 and CHOP, which engaged the intrinsic apoptosis pathway and lowered the apoptotic threshold in MYC‐overexpressing cells. In line with these findings, the BCL2‐inhibitory compound venetoclax synergized with IACS‐010759 against double‐hit lymphoma (DHL), a high‐grade malignancy with concurrent activation of MYC and BCL2. In BCL2‐negative lymphoma cells, instead, killing by IACS‐010759 was potentiated by the Mcl‐1 inhibitor S63845. Thus, combining an OxPhos inhibitor with select BH3‐mimetic drugs provides a novel therapeutic principle against aggressive, MYC‐associated DLBCL variants.
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Affiliation(s)
- Giulio Donati
- European Institute of Oncology (IEO)-IRCCS, Milan, Italy
| | - Micol Ravà
- European Institute of Oncology (IEO)-IRCCS, Milan, Italy
| | | | - Paola Nicoli
- European Institute of Oncology (IEO)-IRCCS, Milan, Italy
| | - Laura Cassina
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Mirko Doni
- European Institute of Oncology (IEO)-IRCCS, Milan, Italy
| | | | | | | | - Christopher P Vellano
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION), Houston, TX, USA
| | - Joseph R Marszalek
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION), Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bruno Amati
- European Institute of Oncology (IEO)-IRCCS, Milan, Italy
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19
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Abstract
A central component of Myc's role as a master coordinator of energy metabolism and biomass accumulation is its ability to increase the rate of protein synthesis, driving cell cycle progression, and proliferation. Importantly, Myc-induced alterations in both global and specific mRNA translation is a key determinant of Myc's oncogenic function. Herein, we provide five assays to enable researchers to measure global protein synthesis changes, to identify the translatome uniquely regulated by Myc and to investigate the mechanisms generating the tailored Myc translation network. Metabolic labeling of cells with 35S-containing methionine and cysteine in culture and O-propargyl-puromycin (OP-Puro) incorporation in vivo are presented as methods to measure the overall rate of global protein synthesis. Isolation of polysome-associated mRNAs followed by quantitative real-time PCR (qRT-PCR) and the toeprint assay enable the detection of altered translation of specific mRNAs and isoforms, and visualization of differential ribosomal engagement at start codons uniquely mediated by Myc activation, respectively. Finally, the translation initiation reporter assay is utilized to uncover the molecular mechanism mediating altered translation initiation of a specific mRNA. Together, the protocols detailed in this chapter can be used to illuminate how and to what degree Myc-dependent regulation of translation influences homeostatic cellular functions as well as tumorigenesis.
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20
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Suresh S, O'Donnell KA. Translational Control of Immune Evasion in Cancer. Trends Cancer 2021; 7:580-582. [PMID: 33972197 PMCID: PMC8262573 DOI: 10.1016/j.trecan.2021.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022]
Abstract
Mechanisms that control translation play important roles in tumor progression and metastasis. Emerging evidence has revealed that dysregulated translation also impacts immune evasion in response to cellular or oncogenic stress. Here, we summarize current knowledge regarding the translational control of immune checkpoints and implications for cancer immunotherapies.
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Affiliation(s)
- Shruthy Suresh
- Department of Molecular Biology, University of Texas Southwestern (UTSW) Medical Center, Dallas, TX 75390, USA
| | - Kathryn A O'Donnell
- Department of Molecular Biology, University of Texas Southwestern (UTSW) Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UTSW Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, UTSW Medical Center, Dallas, TX 75390, USA.
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21
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JAK2 activation promotes tumorigenesis in ALK-negative anaplastic large cell lymphoma via regulating oncogenic STAT1-PVT1 lncRNA axis. Blood Cancer J 2021; 11:56. [PMID: 33712566 PMCID: PMC7955124 DOI: 10.1038/s41408-021-00447-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/15/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
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22
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Duffy MJ, O'Grady S, Tang M, Crown J. MYC as a target for cancer treatment. Cancer Treat Rev 2021; 94:102154. [PMID: 33524794 DOI: 10.1016/j.ctrv.2021.102154] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 02/06/2023]
Abstract
The MYC gene which consists of 3 paralogs, C-MYC, N-MYC and L-MYC, is one of the most frequently deregulated driver genes in human cancer. Because of its high prevalence of deregulation and its causal role in cancer formation, maintenance and progression, targeting MYC is theoretically an attractive strategy for treating cancer. As a potential anticancer target, MYC was traditionally regarded as undruggable due to the absence of a suitable pocket for high-affinity binding by low molecular weight inhibitors. In recent years however, several compounds that directly or indirectly inhibit MYC have been shown to have anticancer activity in preclinical tumor models. Amongst the most detailed investigated strategies for targeting MYC are inhibition of its binding to its obligate interaction partner MAX, prevention of MYC expression and blocking of genes exhibiting synthetic lethality with overexpression of MYC. One of the most extensively investigated MYC inhibitors is a peptide/mini-protein known as OmoMYC. OmoMYC, which acts by blocking the binding of all 3 forms of MYC to their target promoters, has been shown to exhibit anticancer activity in a diverse range of preclinical models, with minimal side effects. Based on its broad efficacy and limited toxicity, OmoMYC is currently being developed for evaluation in clinical trials. Although no compound directly targeting MYC has yet progressed to clinical testing, APTO-253, which partly acts by decreasing expression of MYC, is currently undergoing a phase I clinical trial in patients with relapsed/refractory acute myeloid leukemia or myelodysplastic syndrome.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland; UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland.
| | - Shane O'Grady
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Minhong Tang
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin 4, Ireland
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23
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Wu G, Suo C, Yang Y, Shen S, Sun L, Li ST, Zhou Y, Yang D, Wang Y, Cai Y, Wang N, Zhang H, Yang YG, Cao J, Gao P. MYC promotes cancer progression by modulating m 6 A modifications to suppress target gene translation. EMBO Rep 2021; 22:e51519. [PMID: 33426808 DOI: 10.15252/embr.202051519] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022] Open
Abstract
The MYC oncoprotein activates and represses gene expression in a transcription-dependent or transcription-independent manner. Modification of mRNA emerges as a key gene expression regulatory nexus. We sought to determine whether MYC alters mRNA modifications and report here that MYC promotes cancer progression by down-regulating N6-methyladenosine (m6 A) preferentially in transcripts of a subset of MYC-repressed genes (MRGs). We find that MYC activates the expression of ALKBH5 and reduces m6 A levels in the mRNA of the selected MRGs SPI1 and PHF12. We also show that MYC-regulated m6 A controls the translation of MRG mRNA via the specific m6 A reader YTHDF3. Finally, we find that inhibition of ALKBH5, or overexpression of SPI1 or PHF12, effectively suppresses the growth of MYC-deregulated B-cell lymphomas, both in vitro and in vivo. Our findings uncover a novel mechanism by which MYC suppresses gene expression by altering m6 A modifications in selected MRG transcripts promotes cancer progression.
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Affiliation(s)
- Gongwei Wu
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.,CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Caixia Suo
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.,School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, CAS Center for Excellence in Molecular Cell Science, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shengqi Shen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Linchong Sun
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.,School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China
| | - Shi-Ting Li
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yingli Zhou
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Dongdong Yang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yan Wang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yongping Cai
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Nana Wang
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Huafeng Zhang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, CAS Center for Excellence in Molecular Cell Science, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Jie Cao
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.,School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China
| | - Ping Gao
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.,CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China.,School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
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24
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de Jonge AV, Mutis T, Roemer MGM, Scheijen B, Chamuleau MED. Impact of MYC on Anti-Tumor Immune Responses in Aggressive B Cell Non-Hodgkin Lymphomas: Consequences for Cancer Immunotherapy. Cancers (Basel) 2020; 12:cancers12103052. [PMID: 33092116 PMCID: PMC7589056 DOI: 10.3390/cancers12103052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 02/08/2023] Open
Abstract
Simple Summary The human immune system has several mechanisms to attack and eliminate lymphomas. However, the MYC oncogene is thought to facilitate escape from this anti-tumor immune response. Since patients with MYC overexpressing lymphomas face a significant dismal prognosis after treatment with standard immunochemotherapy, understanding the role of MYC in regulating the anti-tumor immune response is highly relevant. In this review, we describe the mechanisms by which MYC attenuates the anti-tumor immune responses in B cell non-Hodgkin lymphomas. We aim to implement this knowledge in the deployment of novel immunotherapeutic approaches. Therefore, we also provide a comprehensive overview of current immunotherapeutic options and we discuss potential future treatment strategies for MYC overexpressing lymphomas. Abstract Patients with MYC overexpressing high grade B cell lymphoma (HGBL) face significant dismal prognosis after treatment with standard immunochemotherapy regimens. Recent preclinical studies indicate that MYC not only contributes to tumorigenesis by its effects on cell proliferation and differentiation, but also plays an important role in promoting escape from anti-tumor immune responses. This is of specific interest, since reversing tumor immune inhibition with immunotherapy has shown promising results in the treatment of both solid tumors and hematological malignancies. In this review, we outline the current understanding of impaired immune responses in B cell lymphoid malignancies with MYC overexpression, with a particular emphasis on diffuse large B cell lymphoma. We also discuss clinical consequences of MYC overexpression in the treatment of HGBL with novel immunotherapeutic agents and potential future treatment strategies.
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Affiliation(s)
- A. Vera de Jonge
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, 1081HV Amsterdam, The Netherlands; (T.M.); (M.E.D.C.)
- Correspondence:
| | - Tuna Mutis
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, 1081HV Amsterdam, The Netherlands; (T.M.); (M.E.D.C.)
| | - Margaretha G. M. Roemer
- Department of Pathology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, 1081HV Amsterdam, The Netherlands;
| | - Blanca Scheijen
- Department of Pathology, Radboud UMC, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands;
| | - Martine E. D. Chamuleau
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, 1081HV Amsterdam, The Netherlands; (T.M.); (M.E.D.C.)
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25
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Duffy MJ, Crown J. Drugging "undruggable" genes for cancer treatment: Are we making progress? Int J Cancer 2020; 148:8-17. [PMID: 32638380 DOI: 10.1002/ijc.33197] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
RAS, TP53 (p53) and MYC are among the most frequently altered driver genes in cancer. Thus, RAS is the most frequently mutated oncogene, MYC the most frequently amplified gene and TP53 the most frequently mutated tumor suppressor gene and overall the most frequently mutated gene in cancer. Theoretically, therefore, these genes are highly attractive targets for cancer treatment. However, as the protein products of each of these genes lack an accessible hydrophobic pocket into which low molecular weight compounds might bind with high affinity, they have proved difficult to target and have traditionally been referred to as "undruggable." Despite this branding, several low molecular weight compounds targeting each of these proteins have recently been reported to have anticancer activity in preclinical models. Indeed, several drugs inhibiting mutant KRAS, MYC overexpression or reactivating mutant p53 have undergone or are currently undergoing clinical trials. For targeting mutant KRAS and reactivating mutant p53, trials have progressed to a Phase III stage, that is, the mutant-p53 reactivating drug, APR-246 is currently being investigated in patients with myelodysplastic syndrome (MDS) and the RAS inhibitor, rigosertib is also undergoing evaluation in patients with MDS. Although there appears to be no directly acting MYC inhibitor currently being tested in a clinical trial, an anti-MYC compound, known as OmoMYC has been extensively validated in multiple preclinical models and is being developed for clinical evaluation. Based on current evidence, the traditional perception of RAS, p53 and MYC as being "undruggable" would appear to be coming to an end.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.,UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin 4, Ireland
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26
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Liu Y, Shi Y. Mitochondria as a target in cancer treatment. MedComm (Beijing) 2020; 1:129-139. [PMID: 34766113 PMCID: PMC8491233 DOI: 10.1002/mco2.16] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Yu'e Liu
- Tongji University Cancer Center Shanghai Tenth People's Hospital of Tongji University School of Medicine Tongji University Shanghai China
| | - Yufeng Shi
- Tongji University Cancer Center Shanghai Tenth People's Hospital of Tongji University School of Medicine Tongji University Shanghai China
- Center for Brain and Spinal Cord Research School of Medicine Tongji University Shanghai China
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27
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Parsa S, Ortega-Molina A, Ying HY, Jiang M, Teater M, Wang J, Zhao C, Reznik E, Pasion JP, Kuo D, Mohan P, Wang S, Camarillo JM, Thomas PM, Jain N, Garcia-Bermudez J, Cho BK, Tam W, Kelleher NL, Socci N, Dogan A, De Stanchina E, Ciriello G, Green MR, Li S, Birsoy K, Melnick AM, Wendel HG. The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing. ACTA ACUST UNITED AC 2020; 1:653-664. [PMID: 33569544 DOI: 10.1038/s43018-020-0080-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer cells adapt their metabolic activities to support growth and proliferation. However, increased activity of metabolic enzymes is not usually considered an initiating event in the malignant process. Here, we investigate the possible role of the enzyme serine hydroxymethyltransferase-2 (SHMT2) in lymphoma initiation. SHMT2 localizes to the most frequent region of copy number gains at chromosome 12q14.1 in lymphoma. Elevated expression of SHMT2 cooperates with BCL2 in lymphoma development; loss or inhibition of SHMT2 impairs lymphoma cell survival. SHMT2 catalyzes the conversion of serine to glycine and produces an activated one-carbon unit that can be used to support S-adenosyl methionine synthesis. SHMT2 induces changes in DNA and histone methylation patterns leading to promoter silencing of previously uncharacterized mutational genes, such as SASH1 and PTPRM. Together, our findings reveal that amplification of SHMT2 in cooperation with BCL2 is sufficient in the initiation of lymphomagenesis through epigenetic tumor suppressor silencing.
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Affiliation(s)
- Sara Parsa
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ana Ortega-Molina
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Hsia-Yuan Ying
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Man Jiang
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Matt Teater
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jiahui Wang
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Chunying Zhao
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Joyce P Pasion
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Prathibha Mohan
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Shenqiu Wang
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Neeraj Jain
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Javier Garcia-Bermudez
- Laboratory of Metabolic Regulation and Genetics, Rockefeller University, New York, NY, USA
| | - Byoung-Kyu Cho
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Nicholas Socci
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Departments of Pathology and Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Elisa De Stanchina
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheng Li
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Kivanc Birsoy
- Laboratory of Metabolic Regulation and Genetics, Rockefeller University, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Quatrini L, Vacca P, Tumino N, Besi F, Di Pace AL, Scordamaglia F, Martini S, Munari E, Mingari MC, Ugolini S, Moretta L. Glucocorticoids and the cytokines IL-12, IL-15, and IL-18 present in the tumor microenvironment induce PD-1 expression on human natural killer cells. J Allergy Clin Immunol 2020; 147:349-360. [PMID: 32417134 DOI: 10.1016/j.jaci.2020.04.044] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/28/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Programmed cell death protein 1 (PD-1)-immune checkpoint blockade has provided significant clinical efficacy across various types of cancer by unleashing both T and natural killer (NK) cell-mediated antitumor responses. However, resistance to immunotherapy occurs for many patients, rendering the identification of the mechanisms that control PD-1 expression extremely important to increase the response to the therapy. OBJECTIVE We sought to identify the stimuli and the molecular mechanisms that induce the de novo PD-1 expression on human NK cells in the tumor setting. METHODS NK cells freshly isolated from peripheral blood of healthy donors were stimulated with different combinations of molecules, and PD-1 expression was studied at the mRNA and protein levels. Moreover, ex vivo analysis of tumor microenvironment and NK cell phenotype was performed. RESULTS Glucocorticoids are indispensable for PD-1 induction on human NK cells, in cooperation with a combination of cytokines that are abundant at the tumor site. Mechanistically, glucocorticoids together with IL-12, IL-15, and IL-18 not only upregulate PDCD1 transcription, but also activate a previously unrecognized transcriptional program leading to enhanced mRNA translation and resulting in an increased PD-1 amount in NK cells. CONCLUSIONS These results provide evidence of a novel immune suppressive mechanism of glucocorticoids involving the transcriptional and translational control of an important immune checkpoint.
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Affiliation(s)
- Linda Quatrini
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy.
| | - Paola Vacca
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy
| | - Nicola Tumino
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Besi
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy
| | - Anna Laura Di Pace
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Stefania Martini
- Immunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
| | - Enrico Munari
- Department of Pathology, Sacro Cuore Don Calabria, Negrar, Italy
| | - Maria Cristina Mingari
- Immunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy; Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | - Sophie Ugolini
- Aix-Marseille Université, Centre National de la Recherche Scientifique, Istitut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Lorenzo Moretta
- Department of Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Bambino Gesù Children's Hospital, Rome, Italy.
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29
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Marchingo JM, Sinclair LV, Howden AJ, Cantrell DA. Quantitative analysis of how Myc controls T cell proteomes and metabolic pathways during T cell activation. eLife 2020; 9:53725. [PMID: 32022686 PMCID: PMC7056270 DOI: 10.7554/elife.53725] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
T cell expansion and differentiation are critically dependent on the transcription factor c-Myc (Myc). Herein we use quantitative mass-spectrometry to reveal how Myc controls antigen receptor driven cell growth and proteome restructuring in murine T cells. Analysis of copy numbers per cell of >7000 proteins provides new understanding of the selective role of Myc in controlling the protein machinery that govern T cell fate. The data identify both Myc dependent and independent metabolic processes in immune activated T cells. We uncover that a primary function of Myc is to control expression of multiple amino acid transporters and that loss of a single Myc-controlled amino acid transporter effectively phenocopies the impact of Myc deletion. This study provides a comprehensive map of how Myc selectively shapes T cell phenotypes, revealing that Myc induction of amino acid transport is pivotal for subsequent bioenergetic and biosynthetic programs and licences T cell receptor driven proteome reprogramming.
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Affiliation(s)
- Julia M Marchingo
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Linda V Sinclair
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andrew Jm Howden
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Doreen A Cantrell
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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30
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Abstract
New role for an old molecule: c-Myc and translation Members of the MYC family of oncogenes are master regulators of mRNA translation. In this issue of JEM, Singh et al. (https://doi.org/10.1084/jem.20181726) demonstrate that c-Myc governs protein synthesis in lymphoma cells by interfering with SRSF1- and RBM42-mediated suppression of mRNA translation and by altering selection of translation initiation sites.
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Affiliation(s)
- Marie Cargnello
- Cancer Research Center of Toulouse, Institut National de la Santé et de la Recherche Médicale UMR 1037, University of Toulouse, Toulouse, France
| | - Ivan Topisirovic
- Lady Davis Institute, Sir Mortimor B. Davis Jewish General Hospital, Montreal, Quebec, Canada .,Gerald Bronfman Department of Oncology, Division of Experimental Medicine and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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