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Soumerai JD, Diefenbach CS, Jagadeesh D, Asch A, Kumar A, Tsai ML, Jandl TA, Lossos IS, Kenkre VP, Awan F, Novotny W, Huang J, Miao L, Rajagopalan P, Ghalie RG, Zelenetz AD. Safety and efficacy of zandelisib plus zanubrutinib in previously treated follicular and mantle cell lymphomas. Br J Haematol 2024; 204:1762-1770. [PMID: 38500476 DOI: 10.1111/bjh.19419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
The combination of the phosphatidylinositol 3-kinase delta (PI3Kδ) inhibitor zandelisib with the Bruton's tyrosine kinase (BTK) inhibitor zanubrutinib was hypothesized to be synergistic and prevent resistance to single-agent therapy. This phase 1 study (NCT02914938) included a dose-finding stage in patients with relapsed/refractory (R/R) B-cell malignancies (n = 20) and disease-specific expansion cohorts in follicular lymphoma (FL; n = 31) or mantle cell lymphoma (MCL; n = 19). The recommended phase 2 dose was zandelisib 60 mg on Days 1-7 plus zanubrutinib 80 mg twice daily continuously in 28-day cycle. In the total population, the most common adverse events (AEs; all grades/grade 3-4) were neutropenia (35%/24%), diarrhoea (33%/2%), thrombocytopenia (32%/8%), anaemia (27%/8%), increased creatinine (25%/0%), contusion (21%/0%), fatigue (21%/2%), nausea (21%/2%) and increased aspartate aminotransferase (24%/6%). Three patients discontinued due to AEs. The overall response rate was 87% (complete response [CR] = 33%) for FL and 74% (CR = 47%) for MCL. The median duration of response and progression-free survival (PFS) were not reached in either group. The estimated 1-year PFS was 72.3% (95% confidence interval [CI], 51.9-85.1) for FL and 56.3% (95% CI, 28.9-76.7) for MCL (median follow-up: 16.5 and 10.9 months respectively). Zandelisib plus zanubrutinib was associated with high response rates and no increased toxicity compared to either agent alone.
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Affiliation(s)
- Jacob D Soumerai
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | | | - Deepa Jagadeesh
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Adam Asch
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | | | - Thomas A Jandl
- Stony Brook University Hospital, Stony Brook, New York, USA
| | - Izidore S Lossos
- Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, Florida, USA
| | | | - Farrukh Awan
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Jane Huang
- BeiGene, LTD, Cambridge, Massachusetts, USA
| | - Lu Miao
- MEI Pharma, Inc., San Diego, California, USA
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2
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Liao Y, Yan J, Beri NR, Giulino-Roth L, Cesarman E, Gewurz BE. Germinal center cytokine driven epigenetic control of Epstein-Barr virus latency gene expression. PLoS Pathog 2024; 20:e1011939. [PMID: 38683861 PMCID: PMC11081508 DOI: 10.1371/journal.ppat.1011939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Epstein-Barr virus (EBV) persistently infects 95% of adults worldwide and is associated with multiple human lymphomas that express characteristic EBV latency programs used by the virus to navigate the B-cell compartment. Upon primary infection, the EBV latency III program, comprised of six Epstein-Barr Nuclear Antigens (EBNA) and two Latent Membrane Protein (LMP) antigens, drives infected B-cells into germinal center (GC). By incompletely understood mechanisms, GC microenvironmental cues trigger the EBV genome to switch to the latency II program, comprised of EBNA1, LMP1 and LMP2A and observed in GC-derived Hodgkin lymphoma. To gain insights into pathways and epigenetic mechanisms that control EBV latency reprogramming as EBV-infected B-cells encounter microenvironmental cues, we characterized GC cytokine effects on EBV latency protein expression and on the EBV epigenome. We confirmed and extended prior studies highlighting GC cytokine effects in support of the latency II transition. The T-follicular helper cytokine interleukin 21 (IL-21), which is a major regulator of GC responses, and to a lesser extent IL-4 and IL-10, hyper-induced LMP1 expression, while repressing EBNA expression. However, follicular dendritic cell cytokines including IL-15 and IL-27 downmodulate EBNA but not LMP1 expression. CRISPR editing highlighted that STAT3 and STAT5 were necessary for cytokine mediated EBNA silencing via epigenetic effects at the EBV genomic C promoter. By contrast, STAT3 was instead necessary for LMP1 promoter epigenetic remodeling, including gain of activating histone chromatin marks and loss of repressive polycomb repressive complex silencing marks. Thus, EBV has evolved to coopt STAT signaling to oppositely regulate the epigenetic status of key viral genomic promoters in response to GC cytokine cues.
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Affiliation(s)
- Yifei Liao
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jinjie Yan
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Nina R. Beri
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lisa Giulino-Roth
- Weill Cornell Medical College, New York, New York, United States of America
| | - Ethel Cesarman
- Weill Cornell Medical College, New York, New York, United States of America
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
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3
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Preston JD, Jansen CS, Kosaraju S, Niyogusaba T, Zhuang TZ, Iwamoto SW, Hutto SK, Lechowicz MJ, Allen PB. Cutaneous T-cell lymphoma with CNS involvement: a case series and review of the literature. CNS Oncol 2023; 12:CNS105. [PMID: 37877303 PMCID: PMC10701703 DOI: 10.2217/cns-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a rare hematologic malignancy that traditionally presents with cutaneous lesions, though metastases are not uncommon in progressive disease. We describe four cases of CTCL with central nervous system (CNS) involvement, detailing the history, pathological characteristics, treatment response, and progression. Median time from initial diagnosis to CNS metastasis was ∼5.4 years (range 3.4-15.5 years) and survival after metastasis was ∼160 days (range 19 days-4.4 years). No patients achieved long-term (>5 years) survival, though some displayed varying degrees of remission following CNS-directed therapy. We conclude that clinicians must be attentive to the development of CNS metastases in patients with CTCL. The growing body of literature on such cases will inform evolving therapeutic guidelines on this rare CTCL complication.
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Affiliation(s)
- Joshua D Preston
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA 30322, USA
- Nutrition & Health Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Caroline S Jansen
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Siddhartha Kosaraju
- Division of Neuroradiology, Department of Radiology & Imaging Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tim Niyogusaba
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tony Z Zhuang
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sally W Iwamoto
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Spencer K Hutto
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary Jo Lechowicz
- Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Pamela B Allen
- Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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4
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Tschernia NP, Heiling H, Deal AM, Cheng C, Babinec C, Gonzalez M, Morrison JK, Dittus C, Dotti G, Beaven AW, Serody JS, Wood WA, Savoldo B, Grover NS. Patient-reported outcomes in CD30-directed CAR-T cells against relapsed/refractory CD30+ lymphomas. J Immunother Cancer 2023; 11:e006959. [PMID: 37527906 PMCID: PMC10394544 DOI: 10.1136/jitc-2023-006959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Chimeric antigen receptor (CAR)-T cells targeting CD30 have demonstrated high response rates with durable remissions observed in a subset of patients with relapsed/refractory CD30+ hematologic malignancies, particularly classical Hodgkin lymphoma. This therapy has low rates of toxicity including cytokine release syndrome with no neurotoxicity observed in our phase 2 study. We collected patient-reported outcomes (PROs) on patients treated with CD30 directed CAR-T cells to evaluate the impact of this therapy on their symptom experience. We collected PROs including PROMIS (Patient-Reported Outcomes Measurement Information System) Global Health and Physical Function questionnaires and selected symptom questions from the NCI PRO-CTCAE in patients enrolled on our clinical trial of CD30-directed CAR-T cells at procurement, at time of CAR-T cell infusion, and at various time points post treatment. We compared PROMIS scores and overall symptom burden between pre-procurement, time of infusion, and at 4 weeks post infusion. At least one PRO measurement during the study period was found in 23 out of the 28 enrolled patients. Patient overall symptom burden, global health and mental health, and physical function were at or above baseline levels at 4 weeks post CAR-T cell infusion. In addition, PROMIS scores for patients who participated in the clinical trial were similar to the average healthy population. CD30 CAR-T cell therapy has a favorable toxicity profile with patient physical function and symptom burden recovering to at least their baseline pretreatment health by 1 month post infusion. Trial registration number: NCT02690545.
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Affiliation(s)
- Nicholas P Tschernia
- Medical Oncology Service, National Institutes of Health, Bethesda, Maryland, USA
| | - Hillary Heiling
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allison M Deal
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine Cheng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Caroline Babinec
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Megan Gonzalez
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J Kaitlin Morrison
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Christopher Dittus
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Gianpietro Dotti
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Anne W Beaven
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - William A Wood
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Barbara Savoldo
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Natalie S Grover
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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Anderson KG, Braun DA, Buqué A, Gitto SB, Guerriero JL, Horton B, Keenan BP, Kim TS, Overacre-Delgoffe A, Ruella M, Triplett TA, Veeranki O, Verma V, Zhang F. Leveraging immune resistance archetypes in solid cancer to inform next-generation anticancer therapies. J Immunother Cancer 2023; 11:e006533. [PMID: 37399356 PMCID: PMC10314654 DOI: 10.1136/jitc-2022-006533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 07/05/2023] Open
Abstract
Anticancer immunotherapies, such as immune checkpoint inhibitors, bispecific antibodies, and chimeric antigen receptor T cells, have improved outcomes for patients with a variety of malignancies. However, most patients either do not initially respond or do not exhibit durable responses due to primary or adaptive/acquired immune resistance mechanisms of the tumor microenvironment. These suppressive programs are myriad, different between patients with ostensibly the same cancer type, and can harness multiple cell types to reinforce their stability. Consequently, the overall benefit of monotherapies remains limited. Cutting-edge technologies now allow for extensive tumor profiling, which can be used to define tumor cell intrinsic and extrinsic pathways of primary and/or acquired immune resistance, herein referred to as features or feature sets of immune resistance to current therapies. We propose that cancers can be characterized by immune resistance archetypes, comprised of five feature sets encompassing known immune resistance mechanisms. Archetypes of resistance may inform new therapeutic strategies that concurrently address multiple cell axes and/or suppressive mechanisms, and clinicians may consequently be able to prioritize targeted therapy combinations for individual patients to improve overall efficacy and outcomes.
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Affiliation(s)
- Kristin G Anderson
- Department of Microbiology, Immunology and Cancer Biology, Obstetrics and Gynecology, Carter Center for Immunology Research, University of Virginia, Charlottesville, Virginia, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - David A Braun
- Center of Molecular and Cellular Oncology, Yale University Yale Cancer Center, New Haven, Connecticut, USA
| | - Aitziber Buqué
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York, USA
| | - Sarah B Gitto
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Brendan Horton
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bridget P Keenan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California, USA
| | - Teresa S Kim
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Abigail Overacre-Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Marco Ruella
- Department of Medicine, Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Todd A Triplett
- Department of Immunotherapeutics and Biotechnology, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, Texas, USA
| | - Omkara Veeranki
- Medical Affairs and Clinical Development, Caris Life Sciences Inc, Irving, Texas, USA
| | - Vivek Verma
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Fan Zhang
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, USA
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6
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Lee YG, Yang N, Chun I, Porazzi P, Carturan A, Paruzzo L, Sauter CT, Guruprasad P, Pajarillo R, Ruella M. Apoptosis: a Janus bifrons in T-cell immunotherapy. J Immunother Cancer 2023; 11:e005967. [PMID: 37055217 PMCID: PMC10106075 DOI: 10.1136/jitc-2022-005967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2023] [Indexed: 04/15/2023] Open
Abstract
Immunotherapy has revolutionized the treatment of cancer. In particular, immune checkpoint blockade, bispecific antibodies, and adoptive T-cell transfer have yielded unprecedented clinical results in hematological malignancies and solid cancers. While T cell-based immunotherapies have multiple mechanisms of action, their ultimate goal is achieving apoptosis of cancer cells. Unsurprisingly, apoptosis evasion is a key feature of cancer biology. Therefore, enhancing cancer cells' sensitivity to apoptosis represents a key strategy to improve clinical outcomes in cancer immunotherapy. Indeed, cancer cells are characterized by several intrinsic mechanisms to resist apoptosis, in addition to features to promote apoptosis in T cells and evade therapy. However, apoptosis is double-faced: when it occurs in T cells, it represents a critical mechanism of failure for immunotherapies. This review will summarize the recent efforts to enhance T cell-based immunotherapies by increasing apoptosis susceptibility in cancer cells and discuss the role of apoptosis in modulating the survival of cytotoxic T lymphocytes in the tumor microenvironment and potential strategies to overcome this issue.
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Affiliation(s)
- Yong Gu Lee
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Nicholas Yang
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Inkook Chun
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Patrizia Porazzi
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alberto Carturan
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Luca Paruzzo
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Oncology, University of Turin, Torino, Piemonte, Italy
| | - Christopher Tor Sauter
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Puneeth Guruprasad
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Raymone Pajarillo
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Hinds JW, Feris EJ, Wilkins OM, Deary LT, Wang X, Cole MD. S146L in MYC is a context-dependent activating substitution in cancer development. PLoS One 2022; 17:e0272771. [PMID: 36018850 PMCID: PMC9417018 DOI: 10.1371/journal.pone.0272771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/26/2022] [Indexed: 11/19/2022] Open
Abstract
MYC is one of the most dysregulated oncogenes and is thought to be fundamental to tumor formation and/or maintenance in many cancer types. This dominant pro-tumor activity makes MYC an attractive target for cancer therapy. However, MYC is a transcription factor lacking enzymatic activity, and the structure of one of its two domains is unknown e.g., its transactivation domain. Consequently, few direct MYC-targeting therapies have been developed, and none have been successful in the clinic. Nevertheless, significant effort has been devoted to understanding the mechanisms of oncogenic MYC activity with the objective of uncovering novel vulnerabilities of MYC-dependent cancers. These extensive investigations have revealed in detail how MYC translocation, amplification, and other upstream perturbations contribute to MYC activity in cancer. However, missense mutations of the MYC gene have remained relatively understudied for their potential role in MYC-mediated oncogenesis. While the function of several low-frequency mutations in MYC have been described, our understanding of other equally or more frequent mutations is incomplete. Herein, we define the function of a recurrent missense mutation in MYC resulting in the substitution S146L. This mutation enhances the interaction between MYC and its cofactor TRRAP and may enhance oncogenic MYC activity in certain cellular contexts.
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Affiliation(s)
- John W. Hinds
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Edmond J. Feris
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Owen M. Wilkins
- Center for Quantitative Biology (CQB), Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, Unites States of America
| | - Luke T. Deary
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Xiaofeng Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Michael D. Cole
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
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8
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Meier JA, Savoldo B, Grover NS. The Emerging Role of CAR T Cell Therapy in Relapsed/Refractory Hodgkin Lymphoma. J Pers Med 2022; 12:jpm12020197. [PMID: 35207685 PMCID: PMC8877886 DOI: 10.3390/jpm12020197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Treatment for Hodgkin lymphoma (HL) has evolved considerably from the time it was originally described in the 19th century with many patients now being cured with frontline therapy. Despite these advances, upwards of 10% of patients experience progressive disease after initial therapy with an even higher percentage relapsing. Until recently there had been limited therapeutic options for relapsed and/or refractory HL outside of highly intensive chemotherapy with stem cell rescue. Improved understanding of the pathophysiology of HL, coupled with the emergence of more targeted therapeutics, has reshaped how we view the treatment of relapsed/refractory HL and its prognosis. With this, there has been an increased focus on immunotherapies that can reprogram the immune system to better overcome the immunosuppressive milieu found in HL for improved cancer cell killing. In particular, chimeric antigen receptor (CAR) T cells are emerging as a valuable therapeutic tool in this area. Building on the success of antibody-drug conjugates directed against CD30, CAR T cells engineered to recognize the same antigen are now reaching patients. Though still in its infancy, CAR T therapy for relapsed/refractory HL has shown exceptional promise in early-stage clinical trials with the potential for durable responses even in patients who had progressed through multiple lines of prior therapy. Here we will review currently available data on the use of CAR T cells in HL, strategies to optimize their effectiveness, and how this therapy may fit into the treatment paradigm of HL going forward.
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Affiliation(s)
- Jeremy A. Meier
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (J.A.M.); (B.S.)
- Department of Medicine, Division of Hematology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara Savoldo
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (J.A.M.); (B.S.)
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie S. Grover
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (J.A.M.); (B.S.)
- Department of Medicine, Division of Hematology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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9
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Shouse G, Herrera AF. Advances in Immunotherapy for Diffuse Large B Cell Lymphoma. BioDrugs 2021; 35:517-528. [PMID: 34264504 DOI: 10.1007/s40259-021-00491-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 11/25/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is a heterogeneous disease that is normally treated with combination chemotherapy combined with the anti-CD20 monoclonal antibody rituximab. Although about two-thirds of patients are cured with initial chemo-immunotherapy, a sizable minority of patients will have relapsed or refractory (r/r) DLBCL. Standard therapy for r/r DLBCL is salvage chemotherapy followed by autologous stem cell transplantation (ASCT); however, a minority of patients have long-term remission with this approach. In recent years, there has been a proliferation of immunotherapies for the treatment of DLBCL that have expanded our treatment options for these patients, providing the opportunity for durable remissions that were not previously possible. In this review, we discuss these novel immunotherapies, including monoclonal antibodies, antibody-drug conjugates, bispecific antibodies and chimeric antigen receptor (CAR) T cells. The plethora of novel agents leaves patients with more therapeutic options, but leaves the practitioner faced with challenging decisions regarding the timing and indications for use of these immunotherapies. Although studies are ongoing, no agents have been verified as alternatives to standard salvage therapy followed by ASCT at first relapse. The opportunity for durable response and broad age range eligibility makes a strong case for CAR T cells to be used as third-line therapy. The remainder of the agents discussed can be useful in specific clinical scenarios including in patients who are not candidates for ASCT or CAR T cells, as bridging therapy to CAR T cells, or in the r/r setting after CAR T cell therapy failure.
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Affiliation(s)
- Geoffrey Shouse
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Alex F Herrera
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, 1500 E. Duarte Road, Duarte, CA, 91010, USA.
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10
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 PMCID: PMC8130916 DOI: 10.1371/journal.ppat.1009217] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response. Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular miRNA targets and the relative abundance of each miRNA-mRNA interaction. We also show that viral miRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular miRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (ST); (EKF)
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
- * E-mail: (ST); (EKF)
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11
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Guruprasad P, Lee YG, Kim KH, Ruella M. The current landscape of single-cell transcriptomics for cancer immunotherapy. J Exp Med 2021; 218:e20201574. [PMID: 33601414 PMCID: PMC7754680 DOI: 10.1084/jem.20201574] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022] Open
Abstract
Immunotherapies such as immune checkpoint blockade and adoptive cell transfer have revolutionized cancer treatment, but further progress is hindered by our limited understanding of tumor resistance mechanisms. Emerging technologies now enable the study of tumors at the single-cell level, providing unprecedented high-resolution insights into the genetic makeup of the tumor microenvironment and immune system that bulk genomics cannot fully capture. Here, we highlight the recent key findings of the use of single-cell RNA sequencing to deconvolute heterogeneous tumors and immune populations during immunotherapy. Single-cell RNA sequencing has identified new crucial factors and cellular subpopulations that either promote tumor progression or leave tumors vulnerable to immunotherapy. We anticipate that the strategic use of single-cell analytics will promote the development of the next generation of successful, rationally designed immunotherapeutics.
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Affiliation(s)
- Puneeth Guruprasad
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ki Hyun Kim
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Marco Ruella
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
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Rosikiewicz W, Chen X, Dominguez PM, Ghamlouch H, Aoufouchi S, Bernard OA, Melnick A, Li S. TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis. Sci Adv 2020; 6:eaay5872. [PMID: 32596441 PMCID: PMC7299612 DOI: 10.1126/sciadv.aay5872] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/25/2020] [Indexed: 05/22/2023]
Abstract
The TET2 DNA hydroxymethyltransferase is frequently disrupted by somatic mutations in diffuse large B cell lymphomas (DLBCLs), a tumor that originates from germinal center (GC) B cells. Here, we show that TET2 deficiency leads to DNA hypermethylation of regulatory elements in GC B cells, associated with silencing of the respective genes. This hypermethylation affects the binding of transcription factors including those involved in exit from the GC reaction and involves pathways such as B cell receptor, antigen presentation, CD40, and others. Normal GC B cells manifest a typical hypomethylation signature, which is caused by AID, the enzyme that mediates somatic hypermutation. However, AID-induced demethylation is markedly impaired in TET2-deficient GC B cells, suggesting that AID epigenetic effects are partially dependent on TET2. Last, we find that TET2 mutant DLBCLs also manifest the aberrant TET2-deficient GC DNA methylation signature, suggesting that this epigenetic pattern is maintained during and contributes to lymphomagenesis.
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Affiliation(s)
- Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xiaowen Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Pilar M. Dominguez
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Hussein Ghamlouch
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Said Aoufouchi
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Olivier A. Bernard
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
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13
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Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med 2019; 216:1509-1524. [PMID: 31142587 PMCID: PMC6605752 DOI: 10.1084/jem.20181726] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/22/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. Specifically, MYC drives the translation of most protein components of the electron transport chain in lymphoma cells, and many of these effects are independent from proliferation. Specific interactions of MYC-sensitive RNA-binding proteins (e.g., SRSF1/RBM42) with 5'UTR sequence motifs mediate many of these changes. Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. Together, our findings reveal MYC effects on the translation of key metabolic enzymes and immune receptors in lymphoma cells.
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Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald C Hendrickson
- Proteomics and Microchemistry, Memorial Sloan- Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
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Ungerleider N, Flemington E. SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. BMC Bioinformatics 2019; 20:231. [PMID: 31068132 PMCID: PMC6507234 DOI: 10.1186/s12859-019-2865-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited. RESULTS Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward- and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript. CONCLUSIONS SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Erik Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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15
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Bonora G, Rubbi L, Morselli M, Ma F, Chronis C, Plath K, Pellegrini M. DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS). PLoS One 2019; 14:e0214368. [PMID: 30946758 PMCID: PMC6448829 DOI: 10.1371/journal.pone.0214368] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/12/2019] [Indexed: 11/18/2022] Open
Abstract
Whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used for measuring DNA methylation levels on a genome-wide scale. Both methods have limitations: WGBS is expensive and prohibitive for most large-scale projects; RRBS only interrogates 6-12% of the CpGs in the human genome. Here, we introduce methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) which has the reduced sequencing requirements of RRBS, but significantly expands the coverage of CpG sites in the genome. We built a multiple regression model that combines the two features of MREBS: the bisulfite conversion ratios of single cytosines (as in WGBS and RRBS) as well as the number of reads that cover each locus (as in MRE-seq). This combined approach allowed us to estimate differential methylation across 60% of the genome using read count data alone, and where counts were sufficiently high in both samples (about 1.5% of the genome), our estimates were significantly improved by the single CpG conversion information. We show that differential DNA methylation values based on MREBS data correlate well with those based on WGBS and RRBS. This newly developed technique combines the sequencing cost of RRBS and DNA methylation estimates on a portion of the genome similar to WGBS, making it ideal for large-scale projects of mammalian genomes.
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Affiliation(s)
- Giancarlo Bonora
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, United States of America
- Department of Biological Chemistry, University of California, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Liudmilla Rubbi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Marco Morselli
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Feiyang Ma
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Constantinos Chronis
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Department of Biological Chemistry, University of California, Los Angeles, California, United States of America
| | - Kathrin Plath
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, United States of America
- Department of Biological Chemistry, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center at the David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail: (KP); (MP)
| | - Matteo Pellegrini
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center at the David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail: (KP); (MP)
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Ren Y, Bi C, Zhao X, Lwin T, Wang C, Yuan J, Silva AS, Shah BD, Fang B, Li T, Koomen JM, Jiang H, Chavez JC, Pham LV, Sudalagunta PR, Wan L, Wang X, Dalton WS, Moscinski LC, Shain KH, Vose J, Cleveland JL, Sotomayor EM, Fu K, Tao J. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. J Clin Invest 2018; 128:5517-5530. [PMID: 30260324 PMCID: PMC6264635 DOI: 10.1172/jci122533] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
Concordant activation of MYC and BCL-2 oncoproteins in double-hit lymphoma (DHL) results in aggressive disease that is refractory to treatment. By integrating activity-based proteomic profiling and drug screens, polo-like kinase-1 (PLK1) was identified as an essential regulator of the MYC-dependent kinome in DHL. Notably, PLK1 was expressed at high levels in DHL, correlated with MYC expression, and connoted poor outcome. Further, PLK1 signaling augmented MYC protein stability, and in turn, MYC directly induced PLK1 transcription, establishing a feed-forward MYC-PLK1 circuit in DHL. Finally, inhibition of PLK1 triggered degradation of MYC and of the antiapoptotic protein MCL-1, and PLK1 inhibitors showed synergy with BCL-2 antagonists in blocking DHL cell growth, survival, and tumorigenicity, supporting clinical targeting of PLK1 in DHL.
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Affiliation(s)
- Yuan Ren
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Chengfeng Bi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Xiaohong Zhao
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tint Lwin
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Cheng Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ji Yuan
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | | | - Bin Fang
- Proteomics Core Facility, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tao Li
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - John M. Koomen
- Proteomics Core Facility, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Huijuan Jiang
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
- Tianjin Medical School, Tianjin, China
| | | | - Lan V. Pham
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Lixin Wan
- Department of Molecular Oncology and
| | - Xuefeng Wang
- Department of Biostatics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | | | - Lynn C. Moscinski
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | | | - Julie Vose
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - John L. Cleveland
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Eduardo M. Sotomayor
- Department of Hematology & Oncology, George Washington University, Washington, DC, USA
| | - Kai Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jianguo Tao
- Department of Laboratory Medicine and Hematopathology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
- Department of Malignant Hematology, and
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