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Caria CA, Faà V, Porcu S, Marongiu MF, Poddie D, Perseu L, Meloni A, Vaccargiu S, Ristaldi MS. Post-GWAS Validation of Target Genes Associated with HbF and HbA 2 Levels. Cells 2024; 13:1185. [PMID: 39056767 PMCID: PMC11274989 DOI: 10.3390/cells13141185] [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: 05/21/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Genome-Wide Association Studies (GWASs) have identified a huge number of variants associated with different traits. However, their validation through in vitro and in vivo studies often lags well behind their identification. For variants associated with traits or diseases of biomedical interest, this gap delays the development of possible therapies. This issue also impacts beta-hemoglobinopathies, such as beta-thalassemia and sickle cell disease (SCD). The definitive cures for these diseases are currently bone marrow transplantation and gene therapy. However, limitations regarding their effective use restrict their worldwide application. Great efforts have been made to identify whether modulators of fetal hemoglobin (HbF) and, to a lesser extent, hemoglobin A2 (HbA2) are possible therapeutic targets. Herein, we performed the post-GWAS in vivo validation of two genes, cyclin D3 (CCND3) and nuclear factor I X (NFIX), previously associated with HbF and HbA2 levels. The absence of Ccnd3 expression in vivo significantly increased g (HbF) and d (HbA2) globin gene expression. Our data suggest that CCND3 is a possible therapeutic target in sickle cell disease. We also confirmed the association of Nfix with γ-globin gene expression and present data suggesting a possible role for Nfix in regulating Kruppel-like transcription factor 1 (Klf1), a master regulator of hemoglobin switching. This study contributes to filling the gap between GWAS variant identification and target validation for beta-hemoglobinopathies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maria Serafina Ristaldi
- Istituto di Ricerca Genetica e Biomedica, Cittadella Universitaria di Monserrato, SS 554, Bivio Sestu Km 4,500, 09042 Cagliari, Italy; (C.A.C.); (V.F.); (S.P.); (M.F.M.); (D.P.); (L.P.); (A.M.); (S.V.)
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2
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Witte H, Künstner A, Gebauer N. Update: The molecular spectrum of virus-associated high-grade B-cell non-Hodgkin lymphomas. Blood Rev 2024; 65:101172. [PMID: 38267313 DOI: 10.1016/j.blre.2024.101172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
The vast spectrum of aggressive B-cell non-Hodgkin neoplasms (B-NHL) encompasses several infrequent entities occurring in association with viral infections, posing diagnostic challenges for practitioners. In the emerging era of precision oncology, the molecular characterization of malignancies has acquired paramount significance. The pathophysiological comprehension of specific entities and the identification of targeted therapeutic options have seen rapid development. However, owing to their rarity, not all entities have undergone exhaustive molecular characterization. Considerable heterogeneity exists in the extant body of work, both in terms of employed methodologies and the scale of cases studied. Presently, therapeutic strategies are predominantly derived from observations in diffuse large B-cell lymphoma (DLBCL), the most prevalent subset of aggressive B-NHL. Ongoing investigations into the molecular profiles of these uncommon virus-associated entities are progressively facilitating a clearer distinction from DLBCL, ultimately paving the way towards individualized therapeutic approaches. This review consolidates the current molecular insights into aggressive and virus-associated B-NHL, taking into consideration the recently updated 5th edition of the WHO classification of hematolymphoid tumors (WHO-5HAEM) and the International Consensus Classification (ICC). Additionally, potential therapeutically targetable susceptibilities are highlighted, offering a comprehensive overview of the present scientific landscape in the field.
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Affiliation(s)
- H Witte
- Department of Hematology and Oncology, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081 Ulm, Germany; Department of Hematology and Oncology, University Hospital Schleswig-Holstein (UKSH) Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
| | - A Künstner
- University Cancer Center Schleswig-Holstein (UCCSH), Ratzeburger Allee 160, 23538 Lübeck, Germany; Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - N Gebauer
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein (UKSH) Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; University Cancer Center Schleswig-Holstein (UCCSH), Ratzeburger Allee 160, 23538 Lübeck, Germany
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3
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Wan Q, Tavakoli L, Wang TY, Tucker AJ, Zhou R, Liu Q, Feng S, Choi D, He Z, Gack MU, Zhao J. Hijacking of nucleotide biosynthesis and deamidation-mediated glycolysis by an oncogenic herpesvirus. Nat Commun 2024; 15:1442. [PMID: 38365882 PMCID: PMC10873312 DOI: 10.1038/s41467-024-45852-5] [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: 06/21/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS) and multiple types of B cell malignancies. Emerging evidence demonstrates that KSHV reprograms host-cell central carbon metabolic pathways, which contributes to viral persistence and tumorigenesis. However, the mechanisms underlying KSHV-mediated metabolic reprogramming remain poorly understood. Carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) is a key enzyme of the de novo pyrimidine synthesis, and was recently identified to deamidate the NF-κB subunit RelA to promote aerobic glycolysis and cell proliferation. Here we report that KSHV infection exploits CAD for nucleotide synthesis and glycolysis. Mechanistically, KSHV vCyclin binds to and hijacks cyclin-dependent kinase CDK6 to phosphorylate Ser-1900 on CAD, thereby activating CAD-mediated pyrimidine synthesis and RelA-deamidation-mediated glycolytic reprogramming. Correspondingly, genetic depletion or pharmacological inhibition of CDK6 and CAD potently impeded KSHV lytic replication and thwarted tumorigenesis of primary effusion lymphoma (PEL) cells in vitro and in vivo. Altogether, our work defines a viral metabolic reprogramming mechanism underpinning KSHV oncogenesis, which may spur the development of new strategies to treat KSHV-associated malignancies and other diseases.
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Affiliation(s)
- Quanyuan Wan
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Leah Tavakoli
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Ting-Yu Wang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Andrew J Tucker
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Ruiting Zhou
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Qizhi Liu
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- State Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, China
| | - Shu Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- Department of Diabetes & Cancer Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Dongwon Choi
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhiheng He
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Jun Zhao
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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Hogan CH, Owens SM, Reynoso GV, Liao Y, Meyer TJ, Zelazowska MA, Liu B, Li X, Grosskopf AK, Khairallah C, Kirillov V, Reich NC, Sheridan BS, McBride KM, Gewurz BE, Hickman HD, Forrest JC, Krug LT. Multifaceted roles for STAT3 in gammaherpesvirus latency revealed through in vivo B cell knockout models. mBio 2024; 15:e0299823. [PMID: 38170993 PMCID: PMC10870824 DOI: 10.1128/mbio.02998-23] [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: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Cancers associated with the oncogenic gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus, are notable for their constitutive activation of the transcription factor signal transducer and activator of transcription 3 (STAT3). To better understand the role of STAT3 during gammaherpesvirus latency and the B cell response to infection, we used the model pathogen murine gammaherpesvirus 68 (MHV68). Genetic deletion of STAT3 in B cells of CD19cre/+Stat3f/f mice reduced peak MHV68 latency approximately sevenfold. However, infected CD19cre/+Stat3f/f mice exhibited disordered germinal centers and heightened virus-specific CD8 T cell responses compared to wild-type (WT) littermates. To circumvent the systemic immune alterations observed in the B cell-STAT3 knockout mice and more directly evaluate intrinsic roles for STAT3, we generated mixed bone marrow chimeric mice consisting of WT and STAT3 knockout B cells. We discovered a dramatic reduction in latency in STAT3 knockout B cells compared to their WT B cell counterparts in the same lymphoid organ. RNA sequencing of sorted germinal center B cells revealed that MHV68 infection shifts the gene signature toward proliferation and away from type I and type II IFN responses. Loss of STAT3 largely reversed the virus-driven transcriptional shift without impacting the viral gene expression program. STAT3 promoted B cell processes of the germinal center, including IL-21-stimulated downregulation of surface CD23 on B cells infected with MHV68 or EBV. Together, our data provide mechanistic insights into the role of STAT3 as a latency determinant in B cells for oncogenic gammaherpesviruses.IMPORTANCEThere are no directed therapies to the latency program of the human gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus. Activated host factor signal transducer and activator of transcription 3 (STAT3) is a hallmark of cancers caused by these viruses. We applied the murine gammaherpesvirus pathogen system to explore STAT3 function upon primary B cell infection in the host. Since STAT3 deletion in all CD19+ B cells of infected mice led to altered B and T cell responses, we generated chimeric mice with both normal and STAT3-deleted B cells. B cells lacking STAT3 failed to support virus latency compared to normal B cells from the same infected animal. Loss of STAT3 impaired B cell proliferation and differentiation and led to a striking upregulation of interferon-stimulated genes. These findings expand our understanding of STAT3-dependent processes that are key to its function as a pro-viral latency determinant for oncogenic gammaherpesviruses in B cells and may provide novel therapeutic targets.
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Affiliation(s)
- Chad H. Hogan
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, USA
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Shana M. Owens
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Glennys V. Reynoso
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Yifei Liao
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas J. Meyer
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Monika A. Zelazowska
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaofan Li
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Anna K. Grosskopf
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Camille Khairallah
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Varvara Kirillov
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Nancy C. Reich
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Brian S. Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Kevin M. McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Heather D. Hickman
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - J. Craig Forrest
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laurie T. Krug
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
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5
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He F, Hu S, Liu R, Li X, Guo S, Wang H, Tian G, Qi Y, Wang T. Decoding the biological toxicity of phenanthrene on intestinal cells of Eisenia fetida: Effects, toxicity pathways and corresponding mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166903. [PMID: 37683861 DOI: 10.1016/j.scitotenv.2023.166903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Phenanthrene is frequently detected and exists extensively in the soil environment, and its residues inevitably impose a significant threat to soil organisms. Exposure to and toxicity of phenanthrene on earthworms has been extensively studied before, however, the possible mechanisms and related pathways associated with phenanthrene-triggered toxicity at the intestinal cell level remain unclear. Herein, primary intestinal cells isolated from Eisenia fetida (Annelida, Oligochaeta) intestine were used as targeted receptors to probe the molecular mechanisms involved in ROS-mediated damaging effects and the potential pathways of phenanthrene-induced toxicity at cellular and sub-cellular levels. Results indicated that phenanthrene exposure induced oxidative stress by activating intracellular ROS (elevated O2-, H2O2, and OH- content) bursts in E. fetida intestinal cells, causing various oxidative damage effects, including lipid peroxidation (increased MDA content), protein oxidation (enhanced PCO levels), and DNA damage (enhanced 8-OHdG levels). The enzymatic and non-enzymatic strategies in earthworm cells were activated to mitigate these detrimental effects by regulating ROS-mediated pathways involving defense regulation. Also, phenanthrene stress destroyed the cell membrane of E. fetida intestinal cells, resulting in cellular calcium homeostasis disruption and cellular energetic alteration, ultimately causing cytotoxicity and cell apoptosis/death. More importantly, the mitochondrial dysfunction in E. fetida cells was induced by phenanthrene-caused mitochondrial membrane depolarization, which in turn caused un-controlled ROS burst and induced apoptosis through mitochondria-mediated caspase-3 activation and ROS-mediated mitochondrial-dependent pathway. Furthermore, exposure to phenanthrene activated an abnormal mRNA expression profile associated with defense regulation (e.g., Hsp70, MT, CRT, SOD, CAT, and GST genes) in E. fetida intestinal cells, resulting in various cellular dysfunctions and pathological conditions, eventually, apoptotic cell death. Taken together, this study offers valuable insights for probing the toxic effects and underlying mechanisms posed by phenanthrene at the intestinal cell level, and is of great significance to estimate the detrimental side effects of phenanthrene on soil ecological health.
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Affiliation(s)
- Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shaoyang Hu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shuqi Guo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Hao Wang
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Guang Tian
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Yuntao Qi
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Tingting Wang
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
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6
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Ramaswami R, Tagawa T, Mahesh G, Serquina A, Koparde V, Lurain K, Dremel S, Li X, Mungale A, Beran A, Ohler ZW, Bassel L, Warner A, Mangusan R, Widell A, Ekwede I, Krug LT, Uldrick TS, Yarchoan R, Ziegelbauer JM. Transcriptional landscape of Kaposi sarcoma tumors identifies unique immunologic signatures and key determinants of angiogenesis. J Transl Med 2023; 21:653. [PMID: 37740179 PMCID: PMC10517594 DOI: 10.1186/s12967-023-04517-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/09/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Kaposi sarcoma (KS) is a multicentric tumor caused by Kaposi sarcoma herpesvirus (KSHV) that leads to morbidity and mortality among people with HIV worldwide. KS commonly involves the skin but can occur in the gastrointestinal tract (GI) in severe cases. METHODS RNA sequencing was used to compare the cellular and KSHV gene expression signatures of skin and GI KS lesions in 44 paired samples from 19 participants with KS alone or with concurrent KSHV-associated diseases. Analyses of KSHV expression from KS lesions identified transcriptionally active areas of the viral genome. RESULTS The transcript of an essential viral lytic gene, ORF75, was detected in 91% of KS lesions. Analyses of host genes identified 370 differentially expressed genes (DEGs) unique to skin KS and 58 DEGs unique to GI KS lesions as compared to normal tissue. Interleukin (IL)-6 and IL-10 gene expression were higher in skin lesions as compared to normal skin but not in GI KS lesions. Twenty-six cellular genes were differentially expressed in both skin and GI KS tissues: these included Fms-related tyrosine kinase 4 (FLT4), encoding an angiogenic receptor, and Stanniocalcin 1 (STC1), a secreted glycoprotein. FLT4 and STC1 were further investigated in functional studies using primary lymphatic endothelial cells (LECs). In these models, KSHV infection of LECs led to increased tubule formation that was impaired upon knock-down of STC1 or FLT4. CONCLUSIONS This study of transcriptional profiling of KS tissue provides novel insights into the characteristics and pathogenesis of this unique virus-driven neoplasm.
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Affiliation(s)
- Ramya Ramaswami
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Guruswamy Mahesh
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Anna Serquina
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Vishal Koparde
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Sarah Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Xiaofan Li
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ameera Mungale
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Alex Beran
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Zoe Weaver Ohler
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Laura Bassel
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew Warner
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph Mangusan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Anaida Widell
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Irene Ekwede
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Laurie T Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Thomas S Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Joseph M Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
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7
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Tantawy SI, Timofeeva N, Sarkar A, Gandhi V. Targeting MCL-1 protein to treat cancer: opportunities and challenges. Front Oncol 2023; 13:1226289. [PMID: 37601693 PMCID: PMC10436212 DOI: 10.3389/fonc.2023.1226289] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Evading apoptosis has been linked to tumor development and chemoresistance. One mechanism for this evasion is the overexpression of prosurvival B-cell lymphoma-2 (BCL-2) family proteins, which gives cancer cells a survival advantage. Mcl-1, a member of the BCL-2 family, is among the most frequently amplified genes in cancer. Targeting myeloid cell leukemia-1 (MCL-1) protein is a successful strategy to induce apoptosis and overcome tumor resistance to chemotherapy and targeted therapy. Various strategies to inhibit the antiapoptotic activity of MCL-1 protein, including transcription, translation, and the degradation of MCL-1 protein, have been tested. Neutralizing MCL-1's function by targeting its interactions with other proteins via BCL-2 interacting mediator (BIM)S2A has been shown to be an equally effective approach. Encouraged by the design of venetoclax and its efficacy in chronic lymphocytic leukemia, scientists have developed other BCL-2 homology (BH3) mimetics-particularly MCL-1 inhibitors (MCL-1i)-that are currently in clinical trials for various cancers. While extensive reviews of MCL-1i are available, critical analyses focusing on the challenges of MCL-1i and their optimization are lacking. In this review, we discuss the current knowledge regarding clinically relevant MCL-1i and focus on predictive biomarkers of response, mechanisms of resistance, major issues associated with use of MCL-1i, and the future use of and maximization of the benefits from these agents.
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Affiliation(s)
- Shady I. Tantawy
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalia Timofeeva
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Aloke Sarkar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Varsha Gandhi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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8
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Patel R, Lurain K, Yarchoan R, Ramaswami R. Clinical management of Kaposi sarcoma herpesvirus-associated diseases: an update on disease manifestations and treatment strategies. Expert Rev Anti Infect Ther 2023; 21:929-941. [PMID: 37578202 PMCID: PMC10529793 DOI: 10.1080/14787210.2023.2247161] [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: 04/11/2023] [Revised: 07/08/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
INTRODUCTION Kaposi sarcoma herpes virus (KSHV) is associated with several diseases including Kaposi sarcoma, a form of multicentric Castleman's disease, primary effusion lymphoma, and an inflammatory cytokine syndrome. These KSHV-associated diseases (KAD) can present with heterogenous signs and symptoms that are often associated with cytokine dysregulation that may result in multiorgan dysfunction. The inability to promptly diagnose and treat these conditions can result in long-term complications and mortality. AREAS COVERED Existing epidemiological subtypes of existing KSHV-associated diseases, specifically Kaposi sarcoma as well as the incidence of several KSHV-associated disorders are described. We review the KSHV latent and lytic phases as they correlate with KSHV-associated diseases. Given the complicated presentations, we discuss the clinical manifestations, current diagnostic criteria, existing treatment algorithms for individual KAD, and when they occur concurrently. With emerging evidence on the virus and host interactions, we evaluate novel approaches for the treatment of KAD. An extensive literature search was conducted to support these findings. EXPERT OPINION KSHV leads to complex and concurrent disease processes that are often underdiagnosed both in the United States and worldwide. New therapies that exist for many of these conditions focus on chemotherapy-sparing options that seek to target the underlying viral pathogenesis or immunotherapy strategies.
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Affiliation(s)
- Roshani Patel
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Kuehnle N, Osborne SM, Liang Z, Manzano M, Gottwein E. CRISPR screens identify novel regulators of cFLIP dependency and ligand-independent, TRAIL-R1-mediated cell death. Cell Death Differ 2023; 30:1221-1234. [PMID: 36801923 PMCID: PMC10154404 DOI: 10.1038/s41418-023-01133-0] [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: 08/16/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival, although KSHV encodes a viral homolog of this protein (vFLIP). Cellular and viral FLIP proteins have several functions, including, most importantly, the inhibition of pro-apoptotic caspase 8 and modulation of NF-κB signaling. To investigate the essential role of cFLIP and its potential redundancy with vFLIP in PEL cells, we first performed rescue experiments with human or viral FLIP proteins known to affect FLIP target pathways differently. The long and short isoforms of cFLIP and molluscum contagiosum virus MC159L, which are all strong caspase 8 inhibitors, efficiently rescued the loss of endogenous cFLIP activity in PEL cells. KSHV vFLIP was unable to fully rescue the loss of endogenous cFLIP and is therefore functionally distinct. Next, we employed genome-wide CRISPR/Cas9 synthetic rescue screens to identify loss of function perturbations that can compensate for cFLIP knockout. Results from these screens and our validation experiments implicate the canonical cFLIP target caspase 8 and TRAIL receptor 1 (TRAIL-R1 or TNFRSF10A) in promoting constitutive death signaling in PEL cells. However, this process was independent of TRAIL receptor 2 or TRAIL, the latter of which is not detectable in PEL cell cultures. The requirement for cFLIP is also overcome by inactivation of the ER/Golgi resident chondroitin sulfate proteoglycan synthesis and UFMylation pathways, Jagunal homolog 1 (JAGN1) or CXCR4. UFMylation and JAGN1, but not chondroitin sulfate proteoglycan synthesis or CXCR4, contribute to TRAIL-R1 expression. In sum, our work shows that cFLIP is required in PEL cells to inhibit ligand-independent TRAIL-R1 cell death signaling downstream of a complex set of ER/Golgi-associated processes that have not previously been implicated in cFLIP or TRAIL-R1 function.
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Affiliation(s)
- Neil Kuehnle
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Tarry 6-735, Chicago, IL, 60611, USA
| | - Scout Mask Osborne
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Tarry 6-735, Chicago, IL, 60611, USA
| | - Ziyan Liang
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Tarry 6-735, Chicago, IL, 60611, USA
| | - Mark Manzano
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eva Gottwein
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Tarry 6-735, Chicago, IL, 60611, USA.
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10
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Moore LN, Holmes DL, Sharma A, Landazuri Vinueza J, Lagunoff M. Bcl-xL is required to protect endothelial cells latently infected with KSHV from virus induced intrinsic apoptosis. PLoS Pathog 2023; 19:e1011385. [PMID: 37163552 PMCID: PMC10202281 DOI: 10.1371/journal.ppat.1011385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/22/2023] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
Kaposi's Sarcoma herpesvirus (KSHV) is the etiologic agent of Kaposi's Sarcoma (KS), a highly vascularized tumor common in AIDS patients and many countries in Africa. KSHV is predominantly in the latent state in the main KS tumor cell, the spindle cell, a cell expressing endothelial cell markers. To identify host genes important for KSHV latent infection of endothelial cells we previously used a global CRISPR/Cas9 screen to identify genes necessary for the survival or proliferation of latently infected cells. In this study we rescreened top hits and found that the highest scoring gene necessary for infected cell survival is the anti-apoptotic Bcl-2 family member Bcl-xL. Knockout of Bcl-xL or treatment with a Bcl-xL inhibitor leads to high levels of cell death in latently infected endothelial cells but not their mock counterparts. Cell death occurs through apoptosis as shown by increased PARP cleavage and activation of caspase-3/7. Knockout of the pro-apoptotic protein, Bax, eliminates the requirement for Bcl-xL. Interestingly, neither Bcl-2 nor Mcl-1, related and often redundant anti-apoptotic proteins of the Bcl-2 protein family, are necessary for the survival of latently infected endothelial cells, likely due to their lack of expression in all the endothelial cell types we have examined. Bcl-xL is not required for the survival of latently infected primary effusion lymphoma (PEL) cells or other cell types tested. Expression of the KSHV major latent locus alone in the absence of KSHV infection led to sensitivity to the absence of Bcl-xL, indicating that viral gene expression from the latent locus induces intrinsic apoptosis leading to the requirement for Bcl-xL in endothelial cells. The critical requirement of Bcl-xL during KSHV latency makes it an intriguing therapeutic target for KS tumors.
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Affiliation(s)
- Lyndsey N. Moore
- University of Washington Department of Microbiology, Seattle, Washington, United States of America
| | - Daniel L. Holmes
- University of Washington Department of Microbiology, Seattle, Washington, United States of America
| | - Anjali Sharma
- University of Washington Department of Microbiology, Seattle, Washington, United States of America
| | | | - Michael Lagunoff
- University of Washington Department of Microbiology, Seattle, Washington, United States of America
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11
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Hogan CH, Owens SM, Reynoso GV, Kirillov V, Meyer TJ, Zelazowska MA, Liu B, Li X, Chikhalya A, Dong Q, Khairallah C, Reich NC, Sheridan B, McBride KM, Hearing P, Hickman HD, Forrest JC, Krug LT. B cell-intrinsic STAT3-mediated support of latency and interferon suppression during murine gammaherpesvirus 68 infection revealed through an in vivo competition model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533727. [PMID: 36993230 PMCID: PMC10055336 DOI: 10.1101/2023.03.22.533727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cancers associated with the oncogenic gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus, are notable for their constitutive activation of the transcription factor STAT3. To better understand the role of STAT3 during gammaherpesvirus latency and immune control, we utilized murine gammaherpesvirus 68 (MHV68) infection. Genetic deletion of STAT3 in B cells of CD19cre/+Stat3f/f mice reduced peak latency approximately 7-fold. However, infected CD19cre/+Stat3f/f mice exhibited disordered germinal centers and heightened virus-specific CD8 T cell responses compared to WT littermates. To circumvent the systemic immune alterations observed in the B cell-STAT3 knockout mice and more directly evaluate intrinsic roles for STAT3, we generated mixed bone marrow chimeras consisting of WT and STAT3-knockout B cells. Using a competitive model of infection, we discovered a dramatic reduction in latency in STAT3-knockout B cells compared to their WT B cell counterparts in the same lymphoid organ. RNA sequencing of sorted germinal center B cells revealed that STAT3 promotes proliferation and B cell processes of the germinal center but does not directly regulate viral gene expression. Last, this analysis uncovered a STAT3-dependent role for dampening type I IFN responses in newly infected B cells. Together, our data provide mechanistic insight into the role of STAT3 as a latency determinant in B cells for oncogenic gammaherpesviruses.
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Affiliation(s)
- Chad H. Hogan
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, USA
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Shana M. Owens
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Glennys V. Reynoso
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Varvara Kirillov
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Thomas J. Meyer
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Monika A. Zelazowska
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaofan Li
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Aniska Chikhalya
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Qiwen Dong
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Graduate Program of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York, USA
| | - Camille Khairallah
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Nancy C. Reich
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Brian Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Kevin M. McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hearing
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Heather D. Hickman
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - J. Craig Forrest
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laurie T. Krug
- HIV & AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
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12
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Tagawa T, Oh D, Dremel S, Mahesh G, Koparde VN, Duncan G, Andresson T, Ziegelbauer JM. A virus-induced circular RNA maintains latent infection of Kaposi's sarcoma herpesvirus. Proc Natl Acad Sci U S A 2023; 120:e2212864120. [PMID: 36724259 PMCID: PMC9963958 DOI: 10.1073/pnas.2212864120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/08/2022] [Indexed: 02/03/2023] Open
Abstract
Non-coding RNAs (ncRNAs) play important roles in host-pathogen interactions; oncogenic viruses like Kaposi's sarcoma herpesvirus (KSHV) employ ncRNAs to establish a latent reservoir and persist for the life of the host. We previously reported that KSHV infection alters a novel class of RNA, circular RNAs (circRNAs). CircRNAs are alternative splicing isoforms and regulate gene expression, but their importance in infection is largely unknown. Here, we showed that a human circRNA, hsa_circ_0001400, is induced by various pathogenic viruses, namely KSHV, Epstein-Barr virus, and human cytomegalovirus. The induction of circRNAs including circ_0001400 by KSHV is co-transcriptionally regulated, likely at splicing. Consistently, screening for circ_0001400-interacting proteins identified a splicing factor, PNISR. Functional studies using infected primary endothelial cells revealed that circ_0001400 inhibits KSHV lytic transcription and virus production. Simultaneously, the circRNA promoted cell cycle, inhibited apoptosis, and induced immune genes. RNA-pull down assays identified transcripts interacting with circ_0001400, including TTI1, which is a component of the pro-growth mTOR complexes. We thus identified a circRNA that is pro-growth and anti-lytic replication. These results support a model in which KSHV induces circ_0001400 expression to maintain latency. Since circ_0001400 is induced by multiple viruses, this novel viral strategy may be widely employed by other viruses.
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Affiliation(s)
- Takanobu Tagawa
- HIV and AIDS Malignancy Branch, Center of Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Daniel Oh
- HIV and AIDS Malignancy Branch, Center of Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Sarah Dremel
- HIV and AIDS Malignancy Branch, Center of Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Guruswamy Mahesh
- HIV and AIDS Malignancy Branch, Center of Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Vishal N. Koparde
- Center for Cancer Research Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD21701
| | - Gerard Duncan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD21701
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD21701
| | - Joseph M. Ziegelbauer
- HIV and AIDS Malignancy Branch, Center of Cancer Research, National Cancer Institute, Bethesda, MD20892
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13
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Dunham D, Viswanathan P, Gill J, Manzano M. Expression Ratios of the Antiapoptotic BCL2 Family Members Dictate the Selective Addiction of Kaposi's Sarcoma-Associated Herpesvirus-Transformed Primary Effusion Lymphoma Cell Lines to MCL1. J Virol 2022; 96:e0136022. [PMID: 36416587 PMCID: PMC9749474 DOI: 10.1128/jvi.01360-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes several malignancies in people living with HIV, including primary effusion lymphoma (PEL). PEL cell lines exhibit oncogene addictions to both viral and cellular genes. Using CRISPR screens, we previously identified cellular oncogene addictions in PEL cell lines, including MCL1. MCL1 is a member of the BCL2 family, which functions to prevent intrinsic apoptosis and has been implicated in several cancers. Despite the overlapping functions of the BCL2 family members, PEL cells are dependent only on MCL1, suggesting that MCL1 may have nonredundant functions. To investigate why PEL cells exhibit selective addiction to MCL1, we inactivated the intrinsic apoptosis pathway by engineering BAX/BAK1 double knockout cells. In this context, PEL cells become resistant to MCL1 knockdown or MCL1 inactivation by the MCL1 inhibitor S63845, indicating that the main function of MCL1 in PEL cells is to prevent BAX/BAK1-mediated apoptosis. The selective requirement to MCL1 is due to MCL1 being expressed in excess over the BCL2 family. Ectopic expression of several BCL2 family proteins, as well as the KSHV BCL2 homolog, significantly decreased basal caspase 3/7 activity and buffered against staurosporine-induced apoptosis. Finally, overexpressed BCL2 family members can functionally substitute for MCL1, when it is inhibited by S63845. Together, our data indicate that the expression levels of the BCL2 family likely explain why PEL tumor cells are highly addicted to MCL1. Importantly, our results suggest that caution should be taken when considering MCL1 inhibitors as a monotherapy regimen for PEL because resistance can develop easily. IMPORTANCE Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus. We showed previously that PEL cell lines require the antiapoptotic protein MCL1 for survival but not the other BCL2 family proteins. This selective dependence on MCL1 is unexpected as the BCL2 family functions similarly in preventing intrinsic apoptosis. Recently, new roles for MCL1 not shared with the BCL2 family have emerged. Here, we show that noncanonical functions of MCL1 are unlikely essential. Instead, MCL1 functions mainly to prevent apoptosis. The specific requirement to MCL1 is due to MCL1 being expressed in excess over the BCL2 family. Consistent with this model, shifting these expression ratios changes the requirement away from MCL1 and toward the dominant BCL2 family gene. Together, our results indicate that although MCL1 is an attractive chemotherapeutic target to treat PEL, careful consideration must be taken, as resistance to MCL1-specific inhibitors easily develops through BCL2 family overexpression.
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Affiliation(s)
- Daniel Dunham
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Prasanth Viswanathan
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jackson Gill
- Department of Biological Sciences, Henderson State University, Arkadelphia, Arkansas, USA
| | - Mark Manzano
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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14
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Kuehnle N, Gottwein E. Druggable host gene dependencies in primary effusion lymphoma. Curr Opin Virol 2022; 56:101270. [PMID: 36182745 PMCID: PMC10043043 DOI: 10.1016/j.coviro.2022.101270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). Here, we review what is known about human gene essentiality in PEL-derived cell lines. We provide an updated list of PEL-specific human gene dependencies, based on the improved definition of core essential genes across human cancer types. The requirements of PEL cell lines for interferon regulatory factor 4 (IRF4), basic leukine zipper ATF-like transcription factor (BATF), G1/S cyclin D2 (CCND2), CASP8 and FADD like apoptosis regulator (CFLAR), MCL1 apoptosis regulator (MCL1), and murine double minute 2 (MDM2) have been confirmed experimentally. KSHV co-opts IRF4 and BATF to drive superenhancer (SE)-mediated expression of IRF4 itself, MYC, and CCND2. IRF4 dependency of SE-mediated gene expression is shared with Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) and human T-cell leukemia virus type 1-transformed adult T-cell leukemia/lymphoma (ATLL) cell lines, as well as several B-cell lymphomas of nonviral etiology. LCLs and ATLL cell lines similarly share dependencies on CCND2 and CFLAR with PEL, but also have distinct gene dependencies. Genetic dependencies could be exploited for therapeutic intervention in PEL and other cancers.
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Affiliation(s)
- Neil Kuehnle
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eva Gottwein
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
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15
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Guo X, Zhou X. Risk stratification of acute myeloid leukemia: Assessment using a novel prediction model based on ferroptosis-immune related genes. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:11821-11839. [PMID: 36653976 DOI: 10.3934/mbe.2022551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In acute myeloid leukemia (AML), the link between ferroptosis and the immune microenvironment has profound clinical significance. The objective of this study was to investigate the role of ferroptosis-immune related genes (FIRGs) in predicting the prognosis and therapeutic sensitivity in patients with AML. Using The Cancer Genome Atlas dataset, single sample gene set enrichment analysis was performed to calculate the ferroptosis score of AML samples. To search for FIRGs, differentially expressed genes between the high- and low-ferroptosis score groups were identified and then cross-screened with immune related genes. Univariate Cox and LASSO regression analyses were performed on the FIRGs to establish a prognostic risk score model with five signature FIRGs (BMP2, CCL3, EBI3, ELANE, and S100A6). The prognostic risk score model was then used to divide the patients into high- and low-risk groups. For external validation, two Gene Expression Omnibus cohorts were employed. Overall survival was poorer in the high-risk group than in the low-risk group. The novel risk score model was an independent prognostic factor for overall survival in patients with AML. Infiltrating immune cells were also linked to high-risk scores. Treatment targeting programmed cell death protein 1 may be more effective in high-risk patients. This FIRG-based prognostic risk model may aid in optimizing prognostic risk stratification and treatment of AML.
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Affiliation(s)
- Xing Guo
- Department of Hematology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Xiaogang Zhou
- Department of Hematology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
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16
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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17
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Wu Y, Shrestha P, Heape NM, Yarchoan R. CDK4/6 inhibitors sensitize gammaherpesvirus-infected tumor cells to T-cell killing by enhancing expression of immune surface molecules. J Transl Med 2022; 20:217. [PMID: 35562811 PMCID: PMC9101822 DOI: 10.1186/s12967-022-03400-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The two oncogenic human gammaherpesviruses, Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), both downregulate immune surface molecules, such as MHC-I, ICAM-1, and B7-2, enabling them to evade T-cell and natural killer cell immunity. Both also either encode for human cyclin homologues or promote cellular cyclin activity, and this has been shown to be important for proliferation and survival of gammaherpesvirus-induced tumors. CDK4/6 inhibitors, which are approved for certain breast cancers, have been shown to enhance expression of MHC-I in cell lines and murine models of breast cancer, and this was attributed to activation of interferons by endogenous retrovirus elements. However, it was not known if this would occur in gammaherpesvirus-induced tumors in which interferons are already activated. METHODS Multiple KSHV/EBV-infected cell lines were treated with CDK4/6 inhibitors. The growth of viable cells and expression of surface markers was assessed. T cell activation stimulated by the treated cells was assayed by a T-cell activation bioassay. Both viral and host gene expression was surveyed using RT-qPCR. RESULTS Three CDK4/6 inhibitors, abemaciclib, palbociclib, and ribociclib, inhibited cell growth in KSHV-induced primary effusion lymphoma (PEL) and EBV positive Burkitt's lymphoma (BL) cell lines, and KSHV-infected human umbilical vein endothelial cells (HUVECs). Moreover, CDK4/6 inhibitors increased mRNA and surface expression of MHC-I in all three and prevented downregulation of MHC-I surface expression during lytic replication in KSHV-infected cells. CDK4/6 inhibitors also variably increased mRNA and surface expression of ICAM-1 and B7-2 in the tested lines. Abemaciclib also significantly enhanced T-cell activation induced by treated PEL and BL cells. Certain gammaherpesvirus genes as well as endogenous retrovirus (ERV) 3-1 genes were enhanced by CDK4/6 inhibitors in most PEL and BL lines and this enhancement was associated with expression of gamma interferon-induced genes including MHC-I. CONCLUSIONS These observations provide evidence that CDK4/6 inhibitors can induce expression of surface immune markers MHC-I, B7-2, and ICAM-1 in gammaherpesvirus-infected cell lines and induce virus-specific immunity. They can thus thwart virus-induced immune evasion. These effects, along with their direct effects on KSHV- or EBV-induced tumors, provide a rational for the clinical testing of these drugs in these tumors.
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Affiliation(s)
- Yiquan Wu
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Building 10, Rm. 6N106, MSC 1868, 10 Center Drive, Bethesda, MD, 20892-1868, USA
| | - Prabha Shrestha
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Building 10, Rm. 6N106, MSC 1868, 10 Center Drive, Bethesda, MD, 20892-1868, USA
| | - Natalie M Heape
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Building 10, Rm. 6N106, MSC 1868, 10 Center Drive, Bethesda, MD, 20892-1868, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Building 10, Rm. 6N106, MSC 1868, 10 Center Drive, Bethesda, MD, 20892-1868, USA.
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18
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Calvani J, Gérard L, Fadlallah J, Poullot E, Galicier L, Robe C, Garzaro M, Bertinchamp R, Boutboul D, Cuccuini W, Cayuela JM, Gaulard P, Oksenhendler É, Meignin V. A Comprehensive Clinicopathologic and Molecular Study of 19 Primary Effusion Lymphomas in HIV-infected Patients. Am J Surg Pathol 2022; 46:353-362. [PMID: 34560683 DOI: 10.1097/pas.0000000000001813] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Primary effusion lymphoma (PEL) is associated with human herpesvirus 8 and frequently with Epstein-Barr virus (EBV). We report here a single-center series of 19 human immunodeficiency virus-associated PELs, including 14 EBV+ and 5 EBV- PELs. The objectives were to describe the clinicopathologic features of PELs, with a focus on programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) expression, to search for genetic alterations by targeted deep sequencing analysis, and to compare the features between EBV+ and EBV- cases. All the patients were male, and the median age at diagnosis was 47 years old (interquartile range: 40 to 56 y). Reflecting the terminal B-cell differentiation, immunophenotypic profiles showed low expression levels of B-cell markers, including CD19 (0/19), CD20 (1/19), CD79a (0/19), PAX5 (1/19), BOB1 (3/19), and OCT2 (4/19), contrasting with a common expression of CD38 (10/19), CD138 (7/19), and IRF4/MUM1 (18/19). We observed a frequent aberrant expression of T-cell markers, especially CD3 (10/19), and less frequently CD2 (2/19), CD4 (3/19), CD5 (1/19), and CD8 (0/19). Only 2 cases were PD-L1 positive on tumor cells and none PD-1 positive. With respect to immune cells, 3 samples tested positive for PD-L1 and 5 for PD-1. Our 36-gene lymphopanel revealed 7 distinct variants in 5/10 PELs, with either a single or 2 mutations per sample: B2M (n=2), CD58 (n=1), EP300 (n=1), TNFAIP3 (n=1), ARID1A (n=1), and TP53 (n=1). Finally, we did not observe any major clinical, pathologic, or immunohistochemical differences between EBV+ and EBV- PELs and the outcome was similar (2-y overall survival probability of 61.9% [95% confidence interval, 31.2-82.1] vs. 60.0% [95% confidence interval, 12.6-88.2], respectively, P=0.62).
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Affiliation(s)
| | | | | | - Elsa Poullot
- Department of Pathology, Henri Mondor Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP)
- INSERM U955, University Paris-Est Créteil, Créteil, France
| | | | - Cyrielle Robe
- Department of Pathology, Henri Mondor Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP)
- INSERM U955, University Paris-Est Créteil, Créteil, France
| | | | | | | | | | - Jean-Michel Cayuela
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP)
- University of Paris, Paris
| | - Philippe Gaulard
- Department of Pathology, Henri Mondor Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP)
- INSERM U955, University Paris-Est Créteil, Créteil, France
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19
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Cesarman E, Chadburn A, Rubinstein PG. KSHV/HHV8-mediated hematologic diseases. Blood 2022; 139:1013-1025. [PMID: 34479367 PMCID: PMC8854683 DOI: 10.1182/blood.2020005470] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Kaposi sarcoma (KS) herpesvirus (KSHV), also known as human herpesvirus 8, is the causal agent of KS but is also pathogenetically related to several lymphoproliferative disorders, including primary effusion lymphoma (PEL)/extracavitary (EC) PEL, KSHV-associated multicentric Castleman disease (MCD), KSHV+ diffuse large B-cell lymphoma, and germinotropic lymphoproliferative disorder. These different KSHV-associated diseases may co-occur and may have overlapping features. KSHV, similar to Epstein-Barr virus (EBV), is a lymphotropic gammaherpesvirus that is preferentially present in abnormal lymphoid proliferations occurring in immunecompromised individuals. Notably, both KSHV and EBV can infect and transform the same B cell, which is frequently seen in KSHV+ EBV+ PEL/EC-PEL. The mechanisms by which KSHV leads to lymphoproliferative disorders is thought to be related to the expression of a few transforming viral genes that can affect cellular proliferation and survival. There are critical differences between KSHV-MCD and PEL/EC-PEL, the 2 most common KSHV-associated lymphoid proliferations, including viral associations, patterns of viral gene expression, and cellular differentiation stage reflected by the phenotype and genotype of the infected abnormal B cells. Advances in treatment have improved outcomes, but mortality rates remain high. Our deepening understanding of KSHV biology, clinical features of KSHV-associated diseases, and newer clinical interventions should lead to improved and increasingly targeted therapeutic interventions.
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Affiliation(s)
- Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Paul G Rubinstein
- Section of Hematology/Oncology, Department of Medicine, John H. Stroger Jr Hospital of Cook County, Chicago, IL; and
- Department of Medicine, Ruth M. Rothstein CORE Center, Rush University Medical Center, Chicago, IL
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20
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Inhibition of MCL1 induces apoptosis in anaplastic large cell lymphoma and in primary effusion lymphoma. Sci Rep 2022; 12:1085. [PMID: 35058488 PMCID: PMC8776734 DOI: 10.1038/s41598-022-04916-6] [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: 09/09/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
AbstractOverexpression of antiapoptotic BCL2 family proteins occurs in various hematologic malignancies and contributes to tumorigenesis by inhibiting the apoptotic machinery of the cells. Antagonizing BH3 mimetics provide an option for medication, with venetoclax as the first drug applied for chronic lymphocytic leukemia and for acute myeloid leukemia. To find additional hematologic entities with ectopic expression of BCL2 family members, we performed expression screening of cell lines applying the LL-100 panel. Anaplastic large cell lymphoma (ALCL) and primary effusion lymphoma (PEL), 2/22 entities covered by this panel, stood out by high expression of MCL1 and low expression of BCL2. The MCL1 inhibitor AZD-5991 induced apoptosis in cell lines from both malignancies, suggesting that this BH3 mimetic might be efficient as drug for these diseases. The ALCL cell lines also expressed BCLXL and BCL2A1, both contributing to survival of the cells. The combination of specific BH3 mimetics yielded synergistic effects, pointing to a novel strategy for the treatment of ALCL. The PI3K/mTOR inhibitor BEZ-235 could also efficiently be applied in combination with AZD-5991, offering an alternative to avoid thrombocytopenia which is associated with the use of BCLXL inhibitors.
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21
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Gaglia MM. Kaposi's sarcoma-associated herpesvirus at 27. Tumour Virus Res 2021; 12:200223. [PMID: 34153523 PMCID: PMC8250455 DOI: 10.1016/j.tvr.2021.200223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/25/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) was discovered 27 years ago and its link to several pathologies - Kaposi's sarcoma, primary effusion lymphoma, and the B cell variant of Multicentric Castleman disease - is now well established. However, many questions remain about how KSHV causes tumors. Here, I will review studies from the last few years (primarily 2019-2021) that report new information about KSHV biology and tumorigenesis, including new results about KSHV proteins implicated in tumorigenesis, genetic and environmental variability in KSHV-related tumor development, and potential vulnerabilities of KSHV-caused tumors that could be novel therapeutic targets.
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Affiliation(s)
- Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA.
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22
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Sittithumcharee G, Kariya R, Kasemsuk T, Saeeng R, Okada S. Antitumor effect of acanthoic acid against primary effusion lymphoma via inhibition of c-FLIP. Phytother Res 2021; 35:7018-7026. [PMID: 34779075 DOI: 10.1002/ptr.7322] [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: 04/30/2021] [Revised: 09/29/2021] [Accepted: 10/17/2021] [Indexed: 11/10/2022]
Abstract
Acanthoic acid (AA) is an active substance that is extracted from Croton oblongifolius Roxb., a traditional plant in Thailand. The antiinflammatory effect of AA on NF-κB pathway has been exclusively reported, however, its anticancer effect is still lacking. PEL is a B cell lymphoma that is mostly found in HIV patients. The prognosis and progression of PEL patients are terribly poor with a median survival time less than 6 months, so the new effective treatment is urgently needed. In this study, we found that AA effectively inhibited PEL cell proliferation with IC50s at 120-130 μM in well-representative cells, while the IC50s of AA in PBMC were higher (>200 μM). AA increased percentages of Annexin V/PI positive cells, whereas adding of caspase inhibitor (Q-VD-OPh) prevented AA-induced cell death. The antiapoptotic protein, c-FLIP, was downregulated by AA which leading to the activation of caspase-8 and -3. Combination of AA and TRAIL dramatically enhanced apoptotic cell death. In PEL xenograft model, AA at the dose of 250 mg/kg effectively inhibited PEL tumor growth without detectable toxicities assessed by mice weight and appearance.
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Affiliation(s)
- Gunya Sittithumcharee
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Division of Hematopoiesis, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryusho Kariya
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Teerapich Kasemsuk
- Department of Chemistry, Faculty of Science and Technology, Rambhai Barni Rajabhat University, Chanthaburi, Thailand
| | - Rungnapha Saeeng
- Department of Chemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Division of Hematopoiesis, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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23
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Kim YJ, Kim Y, Kumar A, Kim CW, Toth Z, Cho NH, Lee HR. Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen dysregulates expression of MCL-1 by targeting FBW7. PLoS Pathog 2021; 17:e1009179. [PMID: 33471866 PMCID: PMC7816990 DOI: 10.1371/journal.ppat.1009179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022] Open
Abstract
Primary effusion lymphoma (PEL) is an aggressive B cell lymphoma that is etiologically linked to Kaposi’s sarcoma-associated herpesvirus (KSHV). Despite standard multi-chemotherapy treatment, PEL continues to cause high mortality. Thus, new strategies to control PEL are needed urgently. Here, we show that a phosphodegron motif within the KSHV protein, latency-associated nuclear antigen (LANA), specifically interacts with E3 ubiquitin ligase FBW7, thereby competitively inhibiting the binding of the anti-apoptotic protein MCL-1 to FBW7. Consequently, LANA-FBW7 interaction enhances the stability of MCL-1 by preventing its proteasome-mediated degradation, which inhibits caspase-3-mediated apoptosis in PEL cells. Importantly, MCL-1 inhibitors markedly suppress colony formation on soft agar and tumor growth of KSHV+PEL/BCBL-1 in a xenograft mouse model. These results strongly support the conclusion that high levels of MCL-1 expression enable the oncogenesis of PEL cells and thus, MCL-1 could be a potential drug target for KSHV-associated PEL. This work also unravels a mechanism by which an oncogenic virus perturbs a key component of the ubiquitination pathway to induce tumorigenesis. Primary effusion lymphoma (PEL), a highly aggressive B cell lymphoma, is associated with Kaposi’s sarcoma-associated herpesvirus (KSHV). However, the underlying mechanisms that govern the aggressiveness of KSHV-associated PEL are poorly understood. Here, we demonstrate that KSHV LANA interacts with cellular ubiquitin E3 ligase FBW7, sequestering MCL-1 from FBW7, which reduces MCL-1 ubiquitination. As such, LANA potently stabilizes and increases MCL-1 protein, leading to inhibition of caspase-3-mediated apoptosis in PEL cells. Furthermore, MCL-1 inhibitors efficiently blocked PEL progression in mouse xenograft model. These results suggest that LANA acts as a proto-oncogene via deregulating tumor suppressor FBW7, which upregulates anti-apoptotic MCL-1 expression. This study suggests drugs that target MCL-1 may serve as an effective therapy against KSHV+ PEL.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Apoptosis
- Cell Proliferation
- F-Box-WD Repeat-Containing Protein 7/genetics
- F-Box-WD Repeat-Containing Protein 7/metabolism
- Female
- Herpesvirus 8, Human/physiology
- Humans
- Lymphoma, Primary Effusion/genetics
- Lymphoma, Primary Effusion/metabolism
- Lymphoma, Primary Effusion/pathology
- Lymphoma, Primary Effusion/virology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphorylation
- Sarcoma, Kaposi/genetics
- Sarcoma, Kaposi/metabolism
- Sarcoma, Kaposi/pathology
- Sarcoma, Kaposi/virology
- Tumor Cells, Cultured
- Ubiquitination
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Yeong Jun Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University college of Medicine, Seoul, South Korea
| | - Abhishek Kumar
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Chan Woo Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Nam Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University college of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University college of Medicine, Seoul, South Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
- Department of Lab Medicine, College of Medicine, Korea University, Seoul, South Korea
- * E-mail:
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24
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Interdiction at a protein-protein interface: MCL-1 inhibitors for oncology. Bioorg Med Chem Lett 2021; 32:127717. [DOI: 10.1016/j.bmcl.2020.127717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 01/19/2023]
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25
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Hollingworth R, Stewart GS, Grand RJ. Productive herpesvirus lytic replication in primary effusion lymphoma cells requires S-phase entry. J Gen Virol 2020; 101:873-883. [PMID: 32501196 PMCID: PMC7641394 DOI: 10.1099/jgv.0.001444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gammaherpesviruses establish lifelong latent infection in B lymphocytes and are the causative agent of several B-cell malignancies and lymphoproliferative disorders. While a quiescent latent infection allows these pathogens to evade immune detection, initiation of an alternative lifecycle stage, known as lytic replication, is an essential step in the production and dissemination of infectious progeny. Although cessation of cellular proliferation is an eventual consequence of lytic induction, exactly how gammaherpesviruses manipulate the cell cycle prior to amplification of viral DNA remains under debate. Here we show that the onset of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation in B cells leads to S-phase accumulation and that exit from G1 is required for efficient viral DNA replication. We also show that lytic replication leads to an S-phase-specific activation of the DNA damage response (DDR) that is abrogated when lytic replication is restricted to G0/G1. Finally, we observe that expression of early lytic viral genes results in cellular replication stress with increased stalling of DNA replication forks. Overall, we demonstrate that S-phase entry is important for optimal KSHV replication, that G1 arresting compounds are effective inhibitors of viral propagation, and that lytic-induced cell-cycle arrest could occur through the obstruction of cellular replication forks and subsequent activation of the DDR.
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Affiliation(s)
- Robert Hollingworth
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Roger J Grand
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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26
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Bolomsky A, Vogler M, Köse MC, Heckman CA, Ehx G, Ludwig H, Caers J. MCL-1 inhibitors, fast-lane development of a new class of anti-cancer agents. J Hematol Oncol 2020; 13:173. [PMID: 33308268 PMCID: PMC7731749 DOI: 10.1186/s13045-020-01007-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/22/2020] [Indexed: 12/24/2022] Open
Abstract
Cell death escape is one of the most prominent features of tumor cells and closely linked to the dysregulation of members of the Bcl-2 family of proteins. Among those, the anti-apoptotic family member myeloid cell leukemia-1 (MCL-1) acts as a master regulator of apoptosis in various human malignancies. Irrespective of its unfavorable structure profile, independent research efforts recently led to the generation of highly potent MCL-1 inhibitors that are currently evaluated in clinical trials. This offers new perspectives to target a so far undruggable cancer cell dependency. However, a detailed understanding about the tumor and tissue type specific implications of MCL-1 are a prerequisite for the optimal (i.e., precision medicine guided) use of this novel drug class. In this review, we summarize the major functions of MCL-1 with a special focus on cancer, provide insights into its different roles in solid vs. hematological tumors and give an update about the (pre)clinical development program of state-of-the-art MCL-1 targeting compounds. We aim to raise the awareness about the heterogeneous role of MCL-1 as drug target between, but also within tumor entities and to highlight the importance of rationale treatment decisions on a case by case basis.
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Affiliation(s)
- Arnold Bolomsky
- Wilhelminen Cancer Research Institute, Wilhelminenspital, Vienna, Austria
| | - Meike Vogler
- Department of Clinical Hematology, GIGA-I3, University of Liège, CHU De Liège, 35, Dom Univ Sart Tilman B, 4000, Liège, Belgium
| | - Murat Cem Köse
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Grégory Ehx
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - Heinz Ludwig
- Wilhelminen Cancer Research Institute, Wilhelminenspital, Vienna, Austria
| | - Jo Caers
- Department of Clinical Hematology, GIGA-I3, University of Liège, CHU De Liège, 35, Dom Univ Sart Tilman B, 4000, Liège, Belgium.
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27
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Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors. Nat Commun 2020; 11:6318. [PMID: 33298918 PMCID: PMC7726151 DOI: 10.1038/s41467-020-20136-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Primary effusion lymphoma (PEL) has a very poor prognosis. To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in PEL cells. This allows us to generate the PEL enhancer connectome, which links enhancers and promoters in PEL genome-wide. We identify more than 8000 genomic interactions in each PEL cell line. By incorporating HiChIP data with H3K27ac ChIP-seq data, we identify interactions between enhancers/enhancers, enhancers/promoters, and promoters/promoters. HiChIP further links PEL super-enhancers to PEL dependency factors MYC, IRF4, MCL1, CCND2, MDM2, and CFLAR. CRISPR knock out of MEF2C and IRF4 significantly reduces MYC and IRF4 super-enhancer H3K27ac signal. Knock out also reduces MYC and IRF4 expression. CRISPRi perturbation of these super-enhancers by tethering transcription repressors to enhancers significantly reduces target gene expression and reduces PEL cell growth. These data provide insights into PEL molecular pathogenesis.
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28
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Calderon A, Soldan SS, De Leo A, Deng Z, Frase DM, Anderson EM, Zhang Y, Vladimirova O, Lu F, Leung JC, Murphy ME, Lieberman PM. Identification of Mubritinib (TAK 165) as an inhibitor of KSHV driven primary effusion lymphoma via disruption of mitochondrial OXPHOS metabolism. Oncotarget 2020; 11:4224-4242. [PMID: 33245718 PMCID: PMC7679036 DOI: 10.18632/oncotarget.27815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
KSHV-associated cancers have poor prognoses and lack therapeutics that selectively target viral gene functions. We developed a screening campaign to identify known drugs that could be repurposed for the treatment of KSHV-associated cancers. We focused on primary effusion lymphoma (PEL), which has particularly poor treatment outcomes. We developed a luciferase reporter assay to test the ability of drugs to inhibit DNA binding of the KSHV LANA DNA binding domain (DBD). In parallel, we screened drugs for selective inhibition of a KSHV+ PEL cells. While potent hits were identified in each assay, only one hit, Mubritinib, was found to score in both assays. Mubritinib caused PEL cells to undergo cell cycle arrest with accumulation of sub-G1 population and Annexin V. Mubritinib inhibited LANA binding to KSHV terminal repeat (TR) DNA in KSHV+ PEL cells, but did not lead to KSHV lytic cycle reactivation. Mubritinib was originally identified as a receptor tyrosine kinase (RTK) inhibitor selective for HER2/ErbB2. But recent studies have revealed that Mubritinib can also inhibit the electron transport chain (ETC) complex at nanomolar concentrations. We found that other related ETC complex inhibitors (Rotenone and Deguelin) exhibited PEL cell growth inhibition while RTK inhibitors failed. Seahorse analysis demonstrated that Mubritinib selectively inhibits the maximal oxygen consumption (OCR) in PEL cells and metabolomics revealed changes in ATP/ADP and ATP/AMP ratios. These findings indicate that PEL cells are selectively sensitive to ETC complex inhibitors and provide a rationale for repurposing Mubritinib for selective treatment of PEL.
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Affiliation(s)
| | | | | | - Zhong Deng
- The Wistar Institute, Philadelphia, PA 19146, USA
| | | | | | - Yue Zhang
- The Wistar Institute, Philadelphia, PA 19146, USA
| | | | - Fang Lu
- The Wistar Institute, Philadelphia, PA 19146, USA
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29
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Holmes DL, Vogt DT, Lagunoff M. A CRISPR-Cas9 screen identifies mitochondrial translation as an essential process in latent KSHV infection of human endothelial cells. Proc Natl Acad Sci U S A 2020; 117:28384-28392. [PMID: 33122441 PMCID: PMC7668072 DOI: 10.1073/pnas.2011645117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL). The main proliferating component of KS tumors is a cell of endothelial origin termed the spindle cell. Spindle cells are predominantly latently infected with only a small percentage of cells undergoing viral replication. As there is no direct treatment for latent KSHV, identification of host vulnerabilities in latently infected endothelial cells could be exploited to inhibit KSHV-associated tumor cells. Using a pooled CRISPR-Cas9 lentivirus library, we identified host factors that are essential for the survival or proliferation of latently infected endothelial cells in culture, but not their uninfected counterparts. Among the many host genes identified, there was an enrichment in genes localizing to the mitochondria, including genes involved in mitochondrial translation. Antibiotics that inhibit bacterial and mitochondrial translation specifically inhibited the expansion of latently infected endothelial cells and led to increased cell death in patient-derived PEL cell lines. Direct inhibition of mitochondrial respiration or ablation of mitochondrial genomes leads to increased death in latently infected cells. KSHV latent infection decreases mitochondrial numbers, but there are increases in mitochondrial size, genome copy number, and transcript levels. We found that multiple gene products of the latent locus localize to the mitochondria. During latent infection, KSHV significantly alters mitochondrial biology, leading to enhanced sensitivity to inhibition of mitochondrial respiration, which provides a potential therapeutic avenue for KSHV-associated cancers.
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Affiliation(s)
- Daniel L Holmes
- Department of Microbiology, University of Washington, Seattle, WA 98109
| | - Daniel T Vogt
- Department of Microbiology, University of Washington, Seattle, WA 98109
| | - Michael Lagunoff
- Department of Microbiology, University of Washington, Seattle, WA 98109
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The Oncogenic Kaposi's Sarcoma-Associated Herpesvirus Encodes a Mimic of the Tumor-Suppressive miR-15/16 miRNA Family. Cell Rep 2020; 29:2961-2969.e6. [PMID: 31801064 PMCID: PMC6939447 DOI: 10.1016/j.celrep.2019.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/07/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Many tumor viruses encode oncogenes of cellular origin. Here, we report an oncoviral mimic of a cellular tumor suppressor. The Kaposi’s sarcoma-associated herpesvirus (KSHV) microRNA (miRNA) miR-K6-5p shares sequence similarity to the tumor-suppressive cellular miR-15/16 miRNA family. We show that miR-K6-5p inhibits cell cycle progression, a hallmark function of miR-16. miR-K6-5p regulates conserved miR-15/16 family miRNA targets, including many cell cycle regulators. Inhibition of miR-K6-5p in KSHV-transformed B cells confers a significant growth advantage. Altogether, our data show that KSHV encodes a functional mimic of miR-15/16 family miRNAs. While it is exceedingly well established that oncogenic viruses encode oncogenes of cellular origin, this is an unusual example of an oncogenic virus that encodes a viral mimic of a cellular tumor suppressor. Encoding a tumor-suppressive miRNA could help KSHV balance viral oncogene expression and thereby avoid severe pathogenesis in the healthy host. Morrison et al. report that the tumor virus KSHV encodes a mimic of a cellular tumor suppressor. KSHV miR-K6-5p phenocopies miR-16-induced cell cycle inhibition, shares mRNA targets and binding sites with miR-16, and negatively regulates proliferation in KSHV-infected cells.
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Xue VW, Wong SCC, Cho WCS. Genome-wide CRISPR screens for the identification of therapeutic targets for cancer treatment. Expert Opin Ther Targets 2020; 24:1147-1158. [PMID: 32893711 DOI: 10.1080/14728222.2020.1820986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Exploring the function of every gene is a challenging task. There is a paradigm shift of RNA interference with the introduction of clustered regularly interspaced short palindromic repeat (CRISPR)-based genome-wide screening. CRISPR-based screening can detect the loss-of-function and gain-of-function targets. Many DNA-binding proteins are engineered as effective tools for modulating gene expression and for investigating therapeutic targets for a spectrum of diseases. Among them, CRISPR-Cas9 has received extensive attention with its potential for screening cancer treatment targets. AREAS COVERED This article reviews CRISPR toolkit and its applications in screening cancer therapeutic targets, especially genome-wide screens using different CRISPR-Cas9 systems. We compare and summarize the characteristics of CRISPR systems, which would be helpful for understanding and optimizing current CRISPR toolkits, as well as reflecting on the potential future development and clinical applications of CRISPR screens. EXPERT OPINION The application of CRISPR-based therapeutic target screening is broadly used in cancer drug development. Its application in cancer immunotherapy and precision oncology is blooming. Nevertheless, more effective methods of Cas protein delivery and the development of more accurate and efficient genome-editing tools are needed.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Anatomical and Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong , Hong Kong, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University , Hong Kong, China
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Park A, Oh S, Jung KL, Choi UY, Lee HR, Rosenfeld MG, Jung JU. Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs. Proc Natl Acad Sci U S A 2020; 117:21618-21627. [PMID: 32817485 PMCID: PMC7474655 DOI: 10.1073/pnas.1922216117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. Active enhancers and superenhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II activity. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic gamma-2 herpesvirus that causes Kaposi's sarcoma and primary effusion lymphoma (PEL). It is well characterized that KSHV utilizes host epigenetic machineries to control the switch between two lifecycles, latency and lytic replication. However, how KSHV impacts host epigenome at different stages of viral lifecycle is not well understood. Using global run-on sequencing (GRO-seq) and chromatin-immunoprecipitation sequencing (ChIP-seq), we profiled the dynamics of host transcriptional regulatory elements during latency and lytic replication of KSHV-infected PEL cells. This revealed that a number of critical host genes for KSHV latency, including MYC proto-oncogene, were under the control of superenhancers whose activities were globally repressed upon viral reactivation. The eRNA-expressing MYC superenhancers were located downstream of the MYC gene in KSHV-infected PELs and played a key role in MYC expression. RNAi-mediated depletion or dCas9-KRAB CRISPR inhibition of eRNA expression significantly reduced MYC mRNA level in PELs, as did the treatment of an epigenomic drug that globally blocks superenhancer function. Finally, while cellular IRF4 acted upon eRNA expression and superenhancer function for MYC expression during latency, KSHV viral IRF4 repressed cellular IRF4 expression, decreasing MYC expression and thereby, facilitating lytic replication. These results indicate that KSHV acts as an epigenomic driver that modifies host epigenomic status upon reactivation by effectively regulating host enhancer function.
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Affiliation(s)
- Angela Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Soohwan Oh
- Graduate Program of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kyle L Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Un Yung Choi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, 30019 Sejong, South Korea
| | - Michael G Rosenfeld
- HHMI, University of California San Diego, La Jolla, CA 92093;
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
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Kaposi's Sarcoma-Associated Herpesvirus Drives a Super-Enhancer-Mediated Survival Gene Expression Program in Primary Effusion Lymphoma. mBio 2020; 11:mBio.01457-20. [PMID: 32843547 PMCID: PMC7448273 DOI: 10.1128/mbio.01457-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). The cellular transcription factor (TF) interferon (IFN) regulatory factor 4 (IRF4) is an essential oncogene in PEL, but its specific role in PEL and how KSHV deregulates IRF4 remain unknown. Here, we report that the KSHV latency protein viral interferon regulatory factor 3 (vIRF3) cooperates with IRF4 and cellular BATF (basic leucine zipper ATF-like TF) to drive a super-enhancer (SE)-mediated oncogenic transcriptional program in PEL. Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-Seq) experiments demonstrated that IRF4, vIRF3, and BATF cooccupy the SEs of key survival genes, in a pattern that is distinct from those seen with other IRF4-driven malignancies. All three proteins cooperatively drive SE-mediated IRF4 overexpression. Inactivation of vIRF3 and, to a lesser extent, BATF phenocopies the gene expression changes and loss of cellular viability observed upon inactivation of IRF4. In sum, this work suggests that KSHV vIRF3 and cellular IRF4 and BATF cooperate as oncogenic transcription factors on SEs to promote cellular survival and proliferation in KSHV-associated lymphomas.IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) causes the aggressive disease primary effusion lymphoma (PEL). Here, we show that a viral transcription factor (vIRF3) cooperates with the cellular transcription factor IRF4 to control an oncogenic gene expression program in PEL cells. These proteins promote KSHV-mediated B cell transformation by activating the expression of prosurvival genes through super-enhancers. Our report thus demonstrates that this DNA tumor virus encodes a transcription factor that functions with cellular IRF4 to drive oncogenic transcriptional reprogramming.
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Genome-wide CRISPR screens reveal genetic mediators of cereblon modulator toxicity in primary effusion lymphoma. Blood Adv 2020; 3:2105-2117. [PMID: 31300418 DOI: 10.1182/bloodadvances.2019031732] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 12/25/2022] Open
Abstract
Genome-wide CRISPR/Cas9 screens represent a powerful approach to studying mechanisms of drug action and resistance. Cereblon modulating agents (CMs) have recently emerged as candidates for therapeutic intervention in primary effusion lymphoma (PEL), a highly aggressive cancer caused by Kaposi's sarcoma-associated herpesvirus. CMs bind to cereblon (CRBN), the substrate receptor of the cullin-RING type E3 ubiquitin ligase CRL4CRBN, and thereby trigger the acquisition and proteasomal degradation of neosubstrates. Downstream mechanisms of CM toxicity are incompletely understood, however. To identify novel CM effectors and mechanisms of CM resistance, we performed positive selection CRISPR screens using 3 CMs with increasing toxicity in PEL: lenalidomide (LEN), pomalidomide (POM), and CC-122. Results identified several novel modulators of the activity of CRL4CRBN The number of genes whose inactivation confers resistance decreases with increasing CM efficacy. Only inactivation of CRBN conferred complete resistance to CC-122. Inactivation of the E2 ubiquitin conjugating enzyme UBE2G1 also conferred robust resistance against LEN and POM. Inactivation of additional genes, including the Nedd8-specific protease SENP8, conferred resistance to only LEN. SENP8 inactivation indirectly increased levels of unneddylated CUL4A/B, which limits CRL4CRBN activity in a dominant negative manner. Accordingly, sensitivity of SENP8-inactivated cells to LEN is restored by overexpression of CRBN. In sum, our screens identify several novel players in CRL4CRBN function and define pathways to CM resistance in PEL. These results provide rationale for increasing CM efficacy on patient relapse from a less-efficient CM. Identified genes could finally be developed as biomarkers to predict CM efficacy in PEL and other cancers.
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Fu M, Mani M, Bradford J, Chen W, Chen M, Fuda F. Application of flow cytometry in the analysis of lymphoid disease in the lung and pleural space. Semin Diagn Pathol 2020; 37:303-320. [PMID: 32768250 DOI: 10.1053/j.semdp.2020.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 11/11/2022]
Abstract
Various types of lymphoid neoplasms can occur in the lung. Lung parenchyma, the pleura or the pleural cavity can be the primary site of a lymphoid neoplasm or can be involved secondarily as a result of systemic dissemination from a separate primary site. Recognition of pulmonary lymphoid neoplasms (PLN) has increased secondary to technological advances in the medical field. Multiparameter flow cytometry (FC) is a one of the diagnostic tools that serves an essential role in the detecting and categorizing PLNs. FC allows for rapid identification and immunophenotypic characterization of PLN. In this article, we discuss the role of FC in the diagnosis of the most commonly encountered PLNs as well as their basic clinicopathologic features. We briefly discuss the role of FC in identifying non-hematolymphoid neoplasms in lung specimens as well.
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Affiliation(s)
- May Fu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Malary Mani
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jaclyn Bradford
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Weina Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Franklin Fuda
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.
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Seltzer J, Moorad R, Schifano JM, Landis JT, Dittmer DP. Interleukin-1 Receptor-Associated Kinase (IRAK) Signaling in Kaposi Sarcoma-Associated Herpesvirus-Induced Primary Effusion Lymphoma. J Virol 2020; 94:e02123-19. [PMID: 32161170 PMCID: PMC7199399 DOI: 10.1128/jvi.02123-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) is necessary but not sufficient for primary effusion lymphoma (PEL) development. Alterations in cellular signaling pathways are also a characteristic of PEL. Other B cell lymphomas have acquired an oncogenic mutation in the myeloid differentiation primary response 88 (MYD88) gene. The MYD88 L265P mutant results in the activation of interleukin-1 receptor associated kinase (IRAK). To probe IRAK/MYD88 signaling in PEL, we employed CRISPR/Cas9 technology to generate stable deletion clones in BCBL-1Cas9 and BC-1Cas9 cells. To look for off-target effects, we determined the complete exome of the BCBL-1Cas9 and BC-1Cas9 cells. Deletion of either MYD88, IRAK4, or IRAK1 abolished interleukin-1 beta (IL-1β) signaling; however, we were able to grow stable subclones from each population. Transcriptome sequencing (RNA-seq) analysis of IRAK4 knockout cell lines (IRAK4 KOs) showed that the IRAK pathway induced cellular signals constitutively, independent of IL-1β stimulation, which was abrogated by deletion of IRAK4. Transient complementation with IRAK1 increased NF-κB activity in MYD88 KO, IRAK1 KO, and IRAK4 KO cells even in the absence of IL-1β. IL-10, a hallmark of PEL, was dependent on the IRAK pathway, as IRAK4 KOs showed reduced IL-10 levels. We surmise that, unlike B cell receptor (BCR) signaling, MYD88/IRAK signaling is constitutively active in PEL, but that under cell culture conditions, PEL rapidly became independent of this pathway.IMPORTANCE One hundred percent of primary effusion lymphoma (PEL) cases are associated with Kaposi sarcoma-associated herpesvirus (KSHV). PEL cell lines, such as BCBL-1, are the workhorse for understanding this human oncovirus and the host pathways that KSHV dysregulates. Understanding their function is important for developing new therapies as well as identifying high-risk patient groups. The myeloid differentiation primary response 88 (MYD88)/interleukin-1 receptor associated kinase (IRAK) pathway, which has progrowth functions in other B cell lymphomas, has not been fully explored in PEL. By performing CRISPR/Cas9 knockout (KO) studies targeting the IRAK pathway in PEL, we were able to determine that established PEL cell lines can circumvent the loss of IRAK1, IRAK4, and MYD88; however, the deletion clones are deficient in interleukin-10 (IL-10) production. Since IL-10 suppresses T cell function, this suggests that the IRAK pathway may serve a function in vivo and during early-stage development of PEL.
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Affiliation(s)
- Jedediah Seltzer
- Department of Microbiology and Immunology, Center for AIDS Research, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Razia Moorad
- Department of Microbiology and Immunology, Center for AIDS Research, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason M Schifano
- Department of Microbiology and Immunology, Center for AIDS Research, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin T Landis
- Department of Microbiology and Immunology, Center for AIDS Research, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, Center for AIDS Research, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Sadek J, Wuo MG, Rooklin D, Hauenstein A, Hong SH, Gautam A, Wu H, Zhang Y, Cesarman E, Arora PS. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat Commun 2020; 11:1786. [PMID: 32286300 PMCID: PMC7156456 DOI: 10.1038/s41467-020-15576-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein. NF-κB signalling involves the scaffold protein NEMO, which can be bound by the oncoprotein vFLIP to promote cell survival and oncogenic transformation. Here the authors rationally engineer a tertiary protein mimic of NEMO to disrupt the vFLIP-NEMO interaction to induce cell death.
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Affiliation(s)
- Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Michael G Wuo
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - David Rooklin
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Arthur Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Archana Gautam
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, USA.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, 200122, Shanghai, China
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, 10003, USA.
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Sukswai N, Lyapichev K, Khoury JD, Medeiros LJ. Diffuse large B-cell lymphoma variants: an update. Pathology 2019; 52:53-67. [PMID: 31735345 DOI: 10.1016/j.pathol.2019.08.013] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoma, representing approximately one-third of all cases worldwide. In the World Health Organization (WHO) classification of lymphomas, most cases of DLBCL are designated as not otherwise specified (NOS). About 20% of cases, however, are designated as specific variants of DLBCL. These variants, 13 in total, are specified on the basis of distinctive morphological or immunophenotypic findings or distinctive biological or clinical issues associated with their diagnoses. In this review we discuss the following variants: T-cell/histiocyte-rich large B-cell lymphoma; ALK-positive large B-cell lymphoma; plasmablastic lymphoma; intravascular large B-cell lymphoma; large B-cell lymphoma with IRF4 rearrangement; primary mediastinal large B-cell lymphoma; primary cutaneous diffuse large B-cell lymphoma, leg type; primary diffuse large B-cell lymphoma of the central nervous system; diffuse large B-cell lymphoma associated with chronic inflammation; lymphomatoid granulomatosis; primary effusion lymphoma; and HHV8-positive diffuse large B-cell lymphoma, NOS. Two additional variants recognised in the WHO classification, EBV-positive diffuse large B-cell lymphoma and EBV-positive mucocutaneous ulcer are discussed elsewhere in another review within this issue of Pathology. Although not recognised as a specific variant in the current WHO classification, primary testicular diffuse large B-cell lymphoma also has unique biological features and requires some modification of the standard treatment approach for patients with DLBCL. Therefore, we suggest that primary testicular diffuse large B-cell lymphoma also should be recognised as a specific variant of DLBCL in a future version of the WHO classification.
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Affiliation(s)
- Narittee Sukswai
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kirill Lyapichev
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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BeltCappellino A, Majerciak V, Lobanov A, Lack J, Cam M, Zheng ZM. CRISPR/Cas9-Mediated Knockout and In Situ Inversion of the ORF57 Gene from All Copies of the Kaposi's Sarcoma-Associated Herpesvirus Genome in BCBL-1 Cells. J Virol 2019; 93:e00628-19. [PMID: 31413125 PMCID: PMC6803266 DOI: 10.1128/jvi.00628-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV)-transformed primary effusion lymphoma cell lines contain ∼70 to 150 copies of episomal KSHV genomes per cell and have been widely used for studying the mechanisms of KSHV latency and lytic reactivation. Here, we report the first complete knockout (KO) of viral ORF57 gene from all ∼100 copies of KSHV genome per cell in BCBL-1 cells. This was achieved by a modified CRISPR/Cas9 technology to simultaneously express two guide RNAs (gRNAs) and Cas9 from a single expression vector in transfected cells in combination with multiple rounds of cell selection and single-cell cloning. CRISPR/Cas9-mediated genome engineering induces the targeted gene deletion and inversion in situ We found the inverted ORF57 gene in the targeted site in the KSHV genome in one of two characterized single cell clones. Knockout of ORF57 from the KSHV genome led to viral genome instability, thereby reducing viral genome copies and expression of viral lytic genes in BCBL-1-derived single-cell clones. The modified CRISPR/Cas9 technology was very efficient in knocking out the ORF57 gene in iSLK/Bac16 and HEK293/Bac36 cells, where each cell contains only a few copies of the KSHV genome. The ORF57 KO genome was stable in iSLK/Bac16 cells, and, upon lytic induction, was partially rescued by ectopic ORF57 to express viral lytic gene ORF59 and produce infectious virions. Together, the technology developed in this study has paved the way to express two separate gRNAs and the Cas9 enzyme simultaneously in the same cell and could be efficiently applied to any genetic alterations from various genomes, including those in extreme high copy numbers.IMPORTANCE This study provides the first evidence that CRISPR/Cas9 technology can be applied to knock out the ORF57 gene from all ∼100 copies of the KSHV genome in primary effusion lymphoma (PEL) cells by coexpressing two guide RNAs (gRNAs) and Cas9 from a single expression vector in combination with single-cell cloning. The gene knockout efficiency in this system was evaluated rapidly using a direct cell PCR screening. The current CRISPR/Cas9 technology also mediated ORF57 inversion in situ in the targeted site of the KSHV genome. The successful rescue of viral lytic gene expression and infectious virion production from the ORF57 knockout (KO) genome further reiterates the essential role of ORF57 in KSHV infection and multiplication. This modified technology should be useful for knocking out any viral genes from a genome to dissect functions of individual viral genes in the context of the virus genome and to understand their contributions to viral genetics and the virus life cycle.
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Affiliation(s)
- Andrew BeltCappellino
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Justin Lack
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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Transcription Factor IRF4 Dysfunction Affects the Immunosuppressive Function of Treg Cells in Patients with Primary Immune Thrombocytopenia. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1050285. [PMID: 31380412 PMCID: PMC6652070 DOI: 10.1155/2019/1050285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/12/2019] [Accepted: 06/13/2019] [Indexed: 01/16/2023]
Abstract
Background Th17/Treg balance skews towards Th17 in ITP patient. IRF4 has been highlighted for its close relationship to the immunosuppressive function of Treg cells and the IL-17 synthesis in CD4+ T cells. This study was aimed at examining the effects of IRF4 to the Th17/Treg cells in patients with ITP. Methods Treg and Teff cells were isolated from PBMCs of newly diagnosed ITP patients. The percentages of CD4+CD25hiFoxp3+Treg cells and the CD3+CD4+IL-17+Th17 cells were detected by flow cytometry. After being cultured, the supernatants of Tregs were collected for IL-10 concentration test. The IRF4 levels of Tregs were measured. Teffs were cultured alone or with Tregs for 24 hours. Then the supernatants were collected for IL-17 concentration test. The binding intensity of IRF4 to the gene IL-10 in Treg cells was detected by ChIP-qPCR. Metabolic assays for Teffs and Tregs were performed with Agilent Seahorse XF96 Analyzer. Results The secretion of IL-10 by Tregs was decreased in ITP patients. The intensity of IRF4 binding to IL-10 DNA of Tregs in patients was higher than that of normal controls and Teffs in ITP patients. The expressions of IRF4 of Tregs in ITP patients were remarkably lower than that of healthy controls. The percentage of Th17 cells in healthy controls was significantly increased after IRF4 mRNA silencing. Abnormal metabolism of Treg and Teff cells was found in ITP patients. Conclusion The skewed ratio of Th17/Treg cells and dysfunction of Treg cells in newly diagnosed ITP patients was at least partly caused by IRF4 dysfunction. The underlying mechanism might be the impact of IRF4 on the metabolism of Treg and Teff cells.
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Gruffaz M, Yuan H, Meng W, Liu H, Bae S, Kim JS, Lu C, Huang Y, Gao SJ. CRISPR-Cas9 Screening of Kaposi's Sarcoma-Associated Herpesvirus-Transformed Cells Identifies XPO1 as a Vulnerable Target of Cancer Cells. mBio 2019; 10:e00866-19. [PMID: 31088931 PMCID: PMC6520457 DOI: 10.1128/mbio.00866-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 02/05/2023] Open
Abstract
The abnormal proliferation of cancer cells is driven by deregulated oncogenes or tumor suppressors, among which the cancer-vulnerable genes are attractive therapeutic targets. Targeting mislocalization of oncogenes and tumor suppressors resulting from aberrant nuclear export is effective for inhibiting growth transformation of cancer cells. We performed a clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) screening in a unique model of matched primary and oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV)-transformed cells and identified genes that were growth promoting and growth suppressive for both types of cells, among which exportin XPO1 was demonstrated to be critical for the survival of transformed cells. Using XPO1 inhibitor KPT-8602 and by small interfering RNA (siRNA) knockdown, we confirmed the essential role of XPO1 in cell proliferation and growth transformation of KSHV-transformed cells and in cell lines of other cancers, including gastric cancer and liver cancer. XPO1 inhibition induced cell cycle arrest through p53 activation, but the mechanisms of p53 activation differed among the different types of cancer cells. p53 activation depended on the formation of promyelocytic leukemia (PML) nuclear bodies in gastric cancer and liver cancer cells. Mechanistically, XPO1 inhibition induced relocalization of autophagy adaptor protein p62 (SQSTM1), recruiting p53 for activation in PML nuclear bodies. Taken the data together, we have identified novel growth-promoting and growth-suppressive genes of primary and cancer cells and have demonstrated that XPO1 is a vulnerable target of cancer cells. XPO1 inhibition induces cell arrest through a novel PML- and p62-dependent mechanism of p53 activation in some types of cancer cells.IMPORTANCE Using a model of oncogenic virus KSHV-driven cellular transformation of primary cells, we have performed a genome-wide CRISPR-Cas9 screening to identify vulnerable genes of cancer cells. This screening is unique in that this virus-induced oncogenesis model does not depend on any cellular genetic alterations and has matched primary and KSHV-transformed cells, which are not available for similar screenings in other types of cancer. We have identified genes that are both growth promoting and growth suppressive in primary and transformed cells, some of which could represent novel proto-oncogenes and tumor suppressors. In particular, we have demonstrated that the exportin XPO1 is a critical factor for the survival of transformed cells. Using a XPO1 inhibitor (KPT-8602) and siRNA-mediated knockdown, we have confirmed the essential role of XPO1 in cell proliferation and in growth transformation of KSHV-transformed cells, as well as of gastric and liver cancer cells. XPO1 inhibition induces cell cycle arrest by activating p53, but the mechanisms of p53 activation differed among different types of cancer cells. p53 activation is dependent on the formation of PML nuclear bodies in gastric and liver cancer cells. Mechanistically, XPO1 inhibition induces relocalization of autophagy adaptor protein p62 (SQSTM1), recruiting p53 for activation in PML nuclear bodies. These results illustrate that XPO1 is a vulnerable target of cancer cells and reveal a novel mechanism for blocking cancer cell proliferation by XPO1 inhibition as well as a novel PML- and p62-mediated mechanism of p53 activation in some types of cancer cells.
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Affiliation(s)
- Marion Gruffaz
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hongfeng Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Wen Meng
- UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hui Liu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejon, South Korea
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Chun Lu
- Nanjing Medical University, Nanjing, China
| | - Yufei Huang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Shou-Jiang Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Nanjing Medical University, Nanjing, China
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
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Hird AW, Tron AE. Recent advances in the development of Mcl-1 inhibitors for cancer therapy. Pharmacol Ther 2019; 198:59-67. [PMID: 30790641 DOI: 10.1016/j.pharmthera.2019.02.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/11/2019] [Indexed: 01/08/2023]
Abstract
Dysregulation of the mitochondrial apoptotic pathway controlled by members of the Bcl-2 protein family plays a central role in cancer development and resistance to conventional cytotoxic as well as targeted therapies. Hence, selective inhibition of pro-survival Bcl-2 family of proteins to activate apoptosis in malignant cells represents an exciting anti-cancer strategy. The remarkable clinical performance of the selective Bcl-2 antagonist venetoclax has highlighted the potential for selective inhibitors of the other pro-survival members of the Bcl-2 family, particularly Mcl-1. Here we review the latest progress on the discovery and development of selective inhibitors of Mcl-1 that are undergoing clinical evaluation for cancer therapy.
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Fortin JP, Tan J, Gascoigne KE, Haverty PM, Forrest WF, Costa MR, Martin SE. Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens. Genome Biol 2019; 20:21. [PMID: 30683138 PMCID: PMC6346559 DOI: 10.1186/s13059-019-1621-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed. RESULTS In this work, we analyze CRISPR essentiality screen data from 391 cancer cell lines to characterize biases induced by multi-target sgRNAs. We investigate two types of multi-targets: on-targets predicted through perfect sequence complementarity and off-targets predicted through sequence complementarity with up to two nucleotide mismatches. We find that the number of on-targets and off-targets both increase sgRNA activity in a cell line-specific manner and that existing additive models of gene knockout effects fail at capturing genetic interactions that may occur between co-targeted genes. We use synthetic lethality between paralog genes to show that genetic interactions can introduce biases in essentiality scores estimated from multi-target sgRNAs. We further show that single-mismatch tolerant sgRNAs can confound the analysis of gene essentiality and lead to incorrect co-essentiality functional networks. Lastly, we also find that single nucleotide polymorphisms located in protospacer regions can impair on-target activity as a result of mismatch tolerance. CONCLUSION We show the impact of multi-target effects on estimating cancer cell dependencies and the impact of off-target effects caused by mismatch tolerance in sgRNA-DNA binding.
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Affiliation(s)
- Jean-Philippe Fortin
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.
| | - Jenille Tan
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
| | - Karen E Gascoigne
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
| | - Peter M Haverty
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
| | - William F Forrest
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
| | - Scott E Martin
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA
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CK1α and IRF4 are essential and independent effectors of immunomodulatory drugs in primary effusion lymphoma. Blood 2018; 132:577-586. [PMID: 29954751 DOI: 10.1182/blood-2018-01-828418] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Primary effusion lymphoma (PEL) is an aggressive cancer with few treatment options. The immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide have recently been shown to kill PEL cell lines, and lenalidomide is in clinical trials against PEL. IMiDs bind to the CRL4CRBN E3 ubiquitin ligase complex, leading to the acquisition of the Ikaros family zinc finger proteins 1 and 3 (IKZF1 and IKZF3), casein kinase 1 α (CK1α), and zinc finger protein 91 (ZFP91) as neosubstrates. IMiDs are effective against multiple myeloma because of degradation of IKZF1 and IKZF3 and the consequent loss of interferon regulatory factor 4 (IRF4) and MYC expression. Lenalidomide is also effective in chromosome 5q deletion-associated myelodysplastic syndrome as a result of degradation of CK1α. An essential IKZF1-IRF4-MYC axis has recently been proposed to underlie the toxicity of IMiDs in PEL. Here, we further investigate IMiD effectors in PEL cell lines, based on genome-wide CRISPR/Cas9 screens for essential human genes. These screens and extensive validation experiments show that, of the 4 neosubstrates, only CK1α is essential for the survival of PEL cell lines. In contrast, IKZF1 and IKZF3 are dispensable, individually or in combination. IRF4 was critical in all 8 PEL cell lines tested, and surprisingly, IMiDs triggered downregulation of IRF4 expression independently of both IKZF1 and IKZF3. Reexpression of CK1α and/or IRF4 partially rescued PEL cell lines from IMiD-mediated toxicity. In conclusion, IMiD toxicity in PEL cell lines is independent of IKZF1 and IKZF3 but proceeds through degradation of the neosubstrate CK1α and downregulation of IRF4.
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