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Forberg AL, Unrau J, Weber KS, Rutz AC, Lund S, Guidinger J, Pelzel A, Hauge J, Hemmen AJ, Hartert KT. Integrative analyses reveal outcome-associated and targetable molecular partnerships between TP53, BRD4, TNFRSF10B, and CDKN1A in diffuse large B-cell lymphoma. Ann Hematol 2024; 103:199-209. [PMID: 37792064 DOI: 10.1007/s00277-023-05478-x] [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: 05/22/2023] [Accepted: 09/23/2023] [Indexed: 10/05/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a common, genomically heterogenous disease that presents a clinical challenge despite the success of frontline regimens and second-line chimeric antigen receptor T-cell (CAR-T) therapy. Recently, genomic alterations and tumor microenvironment features associated with poor CAR-T response have been identified, namely those to the TP53 tumor suppressor gene. This retrospective analysis aimed to integrate various data to identify genomic partnerships capable of providing further clarity and actionable treatment targets within this population. Publicly available data were analyzed for differential expression based on TP53 and 24-month event-free survival (EFS24) status, revealing enrichments of the BRD4 bromodomain oncogene (p < 0.0001, p = 0.001). High-BRD4 and TP53 alterations were significantly associated with lower CDKN1A (p21) and TNFRSF10B (TRAIL-R2), a key tumor suppressor and CAR-T modulator, respectively. Significant loss of CD8 T-cell presence within low-TNFRSF0B (p = 0.0042) and altered-TP53 (p = 0.0424) patients showcased relevant outcome-associated tumor microenvironment features. Furthermore, reduced expression of CDKN1A was associated with low TNFRSF10B (FDR < 0.0001) and increased BRD4 interactant genes (FDR < 0.0001). Promisingly, in vitro MDM2 inhibition with Idasnutlin and TP53 reactivation via Eprenetapopt was able to renew TNFRSF10B protein expression. Additionally, applying the BRD4-degrading PROTAC ARV-825 and the CDK4/6 inhibitor Abemaciclib as single-agents and in synergistic combination significantly reduced TP53-altered DLBCL cell line viability. Our analysis presents key associations within a genomic network of actionable targets capable of providing clarity within the evolving precision CAR-T treatment landscape.
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Affiliation(s)
- Aidan L Forberg
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Jordan Unrau
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Kennedee S Weber
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Alison C Rutz
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Shelby Lund
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Jinda Guidinger
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Andrew Pelzel
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Jackson Hauge
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Ainslee J Hemmen
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA
| | - Keenan T Hartert
- Department of Biological Sciences, Minnesota State University Mankato, Mankato, MN, 56001, USA.
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Aliyath A, Eni-Olotu A, Donaldson N, Trivedi P. Malignancy-associated immune responses: Lessons from human inborn errors of immunity. Immunology 2023; 170:319-333. [PMID: 37335539 DOI: 10.1111/imm.13675] [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: 03/03/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023] Open
Abstract
It is widely understood that cancer is a significant cause of morbidity and mortality worldwide. Despite numerous available treatments, prognosis for many remains poor, thus, the development of novel therapies remains essential. Given the incredible success of many immunotherapies in this field, the important contribution of the immune system to the control, and elimination, of malignancy is clear. While many immunotherapies target higher-order pathways, for example, through promoting T-cell activation via immune checkpoint blockade, the potential to target specific immunological pathways is largely not well researched. Precisely understanding how immunity can be tailored to respond to specific challenges is an exciting idea with great potential, and may trigger the development of new therapies for cancer. Inborn Errors of Immunity (IEI) are a group of rare congenital disorders caused by gene mutations that result in immune dysregulation. This heterogeneous group, spanning widespread, multisystem immunopathology to specific immune cell defects, primarily manifest in immunodeficiency symptoms. Thus, these patients are particularly susceptible to life-threatening infection, autoimmunity and malignancy, making IEI an especially complex group of diseases. While precise mechanisms of IEI-induced malignancy have not yet been fully elucidated, analysis of these conditions can highlight the importance of particular genes, and downstream immune responses, in carcinogenesis and may help inform mechanisms which can be utilised in novel immunotherapies. In this review, we examine the links between IEIs and cancer, establishing potential connections between immune dysfunction and malignancy and suggesting roles for specific immunological mechanisms involved in preventing carcinogenesis, thus, guiding essential future research focused on cancer immunotherapy and providing valuable insight into the workings of the immune system in both health and disease.
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3
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Turi M, Anilkumar Sithara A, Hofmanová L, Žihala D, Radhakrishnan D, Vdovin A, Knápková S, Ševčíková T, Chyra Z, Jelínek T, Šimíček M, Gullà A, Anderson KC, Hájek R, Hrdinka M. Transcriptome Analysis of Diffuse Large B-Cell Lymphoma Cells Inducibly Expressing MyD88 L265P Mutation Identifies Upregulated CD44, LGALS3, NFKBIZ, and BATF as Downstream Targets of Oncogenic NF-κB Signaling. Int J Mol Sci 2023; 24:ijms24065623. [PMID: 36982699 PMCID: PMC10057398 DOI: 10.3390/ijms24065623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
During innate immune responses, myeloid differentiation primary response 88 (MyD88) functions as a critical signaling adaptor protein integrating stimuli from toll-like receptors (TLR) and the interleukin-1 receptor (IL-1R) family and translates them into specific cellular outcomes. In B cells, somatic mutations in MyD88 trigger oncogenic NF-κB signaling independent of receptor stimulation, which leads to the development of B-cell malignancies. However, the exact molecular mechanisms and downstream signaling targets remain unresolved. We established an inducible system to introduce MyD88 to lymphoma cell lines and performed transcriptomic analysis (RNA-seq) to identify genes differentially expressed by MyD88 bearing the L265P oncogenic mutation. We show that MyD88L265P activates NF-κB signaling and upregulates genes that might contribute to lymphomagenesis, including CD44, LGALS3 (coding Galectin-3), NFKBIZ (coding IkBƺ), and BATF. Moreover, we demonstrate that CD44 can serve as a marker of the activated B-cell (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) and that CD44 expression is correlated with overall survival in DLBCL patients. Our results shed new light on the downstream outcomes of MyD88L265P oncogenic signaling that might be involved in cellular transformation and provide novel therapeutical targets.
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Affiliation(s)
- Marcello Turi
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Anjana Anilkumar Sithara
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Lucie Hofmanová
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - David Žihala
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Dhwani Radhakrishnan
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Alexander Vdovin
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Sofija Knápková
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Tereza Ševčíková
- Faculty of Science, University of Ostrava, 70100 Ostrava, Czech Republic
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Zuzana Chyra
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Tomáš Jelínek
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Michal Šimíček
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Annamaria Gullà
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Kenneth Carl Anderson
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Roman Hájek
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
| | - Matouš Hrdinka
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, 70300 Ostrava, Czech Republic
- Department of Haematooncology, University Hospital Ostrava, 70800 Ostrava, Czech Republic
- Correspondence:
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Xu L, Mu X, Liu M, Wang Z, Shen C, Mu Q, Feng B, Xu Y, Hou T, Gao L, Jiang H, Li J, Zhou Y, Wang W. Novel thieno[2,3-b]quinoline-procaine hybrid molecules: A new class of allosteric SHP-1 activators evolved from PTP1B inhibitors. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Cekic S, Huriyet H, Hortoglu M, Kasap N, Ozen A, Karakoc-Aydiner E, Metin A, Ocakoglu G, Demiroz Abakay C, Temel SG, Ozemri Sag S, Baris S, Cavas T, Kilic SS. Full Increased radiosensitivity and impaired DNA repair in patients with STAT3-LOF and ZNF341 deficiency, potentially contributing to malignant transformations. Clin Exp Immunol 2022; 209:83-89. [PMID: 35511492 PMCID: PMC9307231 DOI: 10.1093/cei/uxac041] [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: 08/15/2021] [Revised: 04/03/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
STAT3 plays an important role in various complex and sometimes contradictory pathways such as proliferation, differentiation, migration, inflammation, and apoptosis. The transcriptional activity of the STAT3 gene is controlled by a transcription factor called ZNF341. There is insufficient data on radiation sensitivity and post-radiation DNA repair in STAT3- loss-of-function (LOF) patients. We aimed to investigate the radiosensitivity in patients with STAT3-LOF and ZNF341 deficiency. Twelve patients with STAT3-LOF and four ZNF341-deficiency patients were recruited from three clinical immunology centers in Turkey and evaluated for radiosensitivity by the Comet assay, comparing to 14 age- and sex-matched healthy controls. The Tail length (μm), Tail DNA (%), Olive Tail Moment (OTM) (arbitrary units) were evaluated at the same time for baseline (spontaneous), initial (immediately after 2Gy irradiation), and recovery (2h after irradiation) periods by using a computerized image-analysis system, estimating DNA damage. Except for a patient with ZNF341 deficiency who developed nasal cell primitive neuroendocrine tumor and papillary thyroid cancer during the follow-up, there was no cancer in both groups. During the recovery period of irradiation, TL, TDNA%, and OTM values of healthy controls decreased rapidly towards the baseline, while these values of patients with STAT3-LOF and ZNF341 deficiency continued to increase, implying impaired DNA repair mechanisms. Increased radiosensitivity and impaired DNA repair were demonstrated in patients diagnosed with STAT3-LOF and ZNF341 deficiency, potentially explaining the susceptibility to malignant transformation.
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Affiliation(s)
- Sukru Cekic
- Division of Pediatric Immunology, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
| | - Huzeyfe Huriyet
- Faculty of Sciences and Letters, Biology Department, Uludag University, Bursa, Turkey
| | - Melika Hortoglu
- Faculty of Sciences and Letters, Biology Department, Uludag University, Bursa, Turkey
| | - Nurhan Kasap
- Division of Pediatric Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ayse Metin
- Division of Pediatric Allergy and Immunology, University of Health Sciences/Ankara City Hospital/Children's Hospital, Ankara, Turkey
| | - Gokhan Ocakoglu
- Department of Biostatistics, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
| | - Candan Demiroz Abakay
- Department of Radiation Oncology, Uludag University Faculty of Medicine, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Tolga Cavas
- Faculty of Sciences and Letters, Biology Department, Uludag University, Bursa, Turkey
| | - Sara Sebnem Kilic
- Division of Pediatric Immunology, Bursa Uludag University Faculty of Medicine, Bursa, Turkey.,Bursa Uludag University, Translational Medicine, Bursa, Turkey
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6
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Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep 2021; 11:15463. [PMID: 34326396 PMCID: PMC8322331 DOI: 10.1038/s41598-021-94805-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.
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Affiliation(s)
- Arno Meiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Manuela Weitkunat
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.
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7
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Gao Y, Ding X. miR-145-5p exerts anti-tumor effects in diffuse large B-cell lymphoma by regulating S1PR1/STAT3/AKT pathway. Leuk Lymphoma 2021; 62:1884-1891. [PMID: 33715582 DOI: 10.1080/10428194.2021.1894642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
To investigate the molecular mechanism of miR-145-5p in diffuse large B-cell lymphoma (DLBCL) tissues and cells. The tissues from patients with DLBCL were collected for RT-qPCR or immunohistochemistry. Cell viability, proliferation, migration, invasion, the relationship between miR-145-5p and S1PR1, and proteins related pathway were detected using CCK-8, BrdU staining, Transwell assay, dual luciferase report assay, and western blotting, respectively. The results showed that miR-145-5p was down-regulated and positively correlated with the survival of DLBCL patients. Overexpression of miR-145-5p inhibited cell proliferation, migration, and invasion in cell model. miR-145-5p directly targeted S1PR1. miR-145-5p down-regulated S1PR1, p-AKT/AKT, and p-STAT3 expression. The reduction of miR-145-5p-induced cell movement was reversed by S1PR1 overexpression. Moreover, S1PR1-induced addition of cell growth was clearly alleviated in LY294002 or S3I-201 treated cells. S1PR1 was up-regulated in the tissues of DLBCL patients. In conclusion, miR-145-5p regulated DLBCL cell growth and movement through suppressing S1PR1/STAT3/AKT pathway.
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Affiliation(s)
- Yuanmei Gao
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojuan Ding
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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8
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Hartert KT, Wenzl K, Krull JE, Manske M, Sarangi V, Asmann Y, Larson MC, Maurer MJ, Slager S, Macon WR, King RL, Feldman AL, Gandhi AK, Link BK, Habermann TM, Yang ZZ, Ansell SM, Cerhan JR, Witzig TE, Nowakowski GS, Novak AJ. Targeting of inflammatory pathways with R2CHOP in high-risk DLBCL. Leukemia 2021; 35:522-533. [PMID: 32139889 PMCID: PMC7483252 DOI: 10.1038/s41375-020-0766-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/17/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma, and front line therapies have not improved overall outcomes since the advent of immunochemotherapy. By pairing DNA and gene expression data with clinical response data, we identified a high-risk subset of non-GCB DLBCL patients characterized by genomic alterations and expression signatures capable of sustaining an inflammatory environment. These mutational alterations (PIM1, SPEN, and MYD88 [L265P]) and expression signatures (NF-κB, IRF4, and JAK-STAT engagement) were associated with proliferative signaling, and were found to be enriched in patients treated with RCHOP that experienced unfavorable outcomes. However, patients with these high-risk mutations had more favorable outcomes when the immunomodulatory agent lenalidomide was added to RCHOP (R2CHOP). We are the first to report the genomic validation of a high-risk phenotype with a preferential response towards R2CHOP therapy in non-GCB DLBCL patients. These conclusions could be translated to a clinical setting to identify the ~38% of non-GCB patients that could be considered high-risk, and would benefit from alternative therapies to standard RCHOP based on personalized genomic data.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cyclophosphamide/administration & dosage
- Doxorubicin/administration & dosage
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Lenalidomide/administration & dosage
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Prednisone/administration & dosage
- Prognosis
- Retrospective Studies
- Rituximab/administration & dosage
- Survival Rate
- Vincristine/administration & dosage
- Young Adult
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Yan Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Melissa C Larson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Maurer
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - William R Macon
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Rebecca L King
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Brian K Link
- Division of Hematology, Oncology, and Bone & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | | | | | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | | | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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9
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Gouveia GR, Ferreira SC, Siqueira SAC, de Pádua Covas Lage LA, Hallack Neto AE, de Oliveira Costa R, Pereira J. Overexpression of OCT-1 gene is a biomarker of adverse prognosis for diffuse large B-cell lymphoma (DLBCL): data from a retrospective cohort of 77 Brazilian patients. BMC Cancer 2020; 20:1041. [PMID: 33121489 PMCID: PMC7596969 DOI: 10.1186/s12885-020-07553-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND OCT-1 gene is a member of the POU-homeodomain family of transcriptional regulators of B-lymphocyte differentiation by controlling expression of B-cell specific genes. BCL-2 gene is a potent inhibitor of apoptosis and it is essential during B-cell differentiation into germinal center. These genes may be expressed in diffuse large B-cell lymphoma (DLBCL), but the role of BCL-2 in its prognosis has been contradictory, and OCT-1 has yet to be tested. METHODS In this study, we aimed to investigate the prognostic impact of OCT-1 and BCL-2 expression in DLBCL treated in the real world with immunochemotherapy in a single center. BCL-2 and OCT-1 genes were available in 78.5% (77/98) DLBCL patients, and the RNA for quantitative real-time PCR was isolated from formalin-fixed paraffin-embedded samples. The values obtained for gene expression were transformed in categorical variable according to their median. RESULTS Cohort median age was 54.5 years (15-84), 49 (50%) were male, 38/77 (49.4%) and 40/77 (51.9%) presented OCT-1 and BCL-2 expression ≥ median, respectively. The overall response rate (ORR) in all patients was 68.4% (67/98), 65,3% (64/98) of patients acquired complete response, and 3.1% (3/98) partial response, while 6.1% (6/98) were primary refractory. The median follow-up was 3.77 years (95% CI: 3.2-4.1), with 5.43 (95% CI: 2.2-NR) of overall survival (OS) and 5.15 years (95% CI: 2.9-NA) of progression free survival (PFS). OCT-1 ≥ median was associated with shorter OS at univariate analysis (p = 0.013; [HR] 2.450, 95% CI: 1.21-4.96) and PFS (p = 0.019; [HR] 2.270, 95%CI: 1.14-4.51) and BCL-2 gene overexpression presented worse PFS (p = 0.043, [HR] 2.008, 95% CI: 1.02-3.95). At multivariate analysis, OCT-1 overexpression was associated with poor PFS (p = 0.035, [HR] 2.22, 95% CI: 1.06-4.67). CONCLUSION In this study, we showed that overexpression of OCT1 gene was an independent prognostic factor of adverse outcomes in DLBCL.
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Affiliation(s)
- Gisele R Gouveia
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Faculty of Medicine, University of Sao Paulo's Medical School (FM-USP), Av. Dr. Enéas Carvalho de Aguiar, 155, Cerqueira César, São Paulo, Brazil
| | - Suzete C Ferreira
- Department of Molecular Biology, Pró-Sangue Foundation, Sao Paulo Blood Bank, São Paulo, Brazil
| | - Sheila A C Siqueira
- Department of Pathology, Hospital das Clínicas - Faculty of Medicine, Sao Paulo University (HC-FM-USP), São Paulo, Brazil
| | - Luis Alberto de Pádua Covas Lage
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Faculty of Medicine, University of Sao Paulo's Medical School (FM-USP), Av. Dr. Enéas Carvalho de Aguiar, 155, Cerqueira César, São Paulo, Brazil. .,Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University (FM-USP), São Paulo, Brazil.
| | - Abrahão E Hallack Neto
- Department of Hematology and Hemotherapy, University of Juiz de Fora (UJF), Juiz de Fora, Brazil
| | - Renata de Oliveira Costa
- Department of Hematology and Hemotherapy, Centro Universitário Lusíadas (FCMS/UNILUS), Santos, Brazil
| | - Juliana Pereira
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University (FM-USP), São Paulo, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Nucleus of non-Hodgkin's Lymphomas & Histiocytic Disorders (LIM-31/FM-USP), São Paulo, Brazil
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10
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Cancer Tendency in a Patient with ZNF341 Deficiency. J Clin Immunol 2020; 40:534-538. [PMID: 31980991 DOI: 10.1007/s10875-020-00756-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
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11
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Zhou C, Bi F, Yuan J, Yang F, Sun S. Gain of UBE2D1 facilitates hepatocellular carcinoma progression and is associated with DNA damage caused by continuous IL-6. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:290. [PMID: 30482241 PMCID: PMC6260761 DOI: 10.1186/s13046-018-0951-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
Abstract
Background Hepatocellular carcinoma (HCC) is the most common type of liver cancer with increasing incidence and poor prognosis. Ubiquitination regulators are reported to play crucial roles in HCC carcinogenesis. UBE2D1, one of family member of E2 ubiquitin conjugating enzyme, mediates the ubiquitination and degradation of tumor suppressor protein p53. However, the expression and functional roles of UBE2D1 in HCC was unknown. Methods Immunohistochemistry (IHC), western blotting, and real-time PCR were used to detect the protein, transcription and genomic levels of UBE2D1 in HCC tissues with paired nontumor tissues, precancerous lesions and hepatitis liver tissues. Four HCC cell lines and two immortalized hepatic cell lines were used to evaluate the functional roles and underlying mechanisms of UBE2D1 in HCC initiation and progression in vitro and in vivo. The contributors to UBE2D1 genomic amplification were first evaluated by performing a correlation analysis between UBE2D1 genomic levels with clinical data of HCC patients, and then evaluated in HCC and hepatic cell lines. Results Expression of UBE2D1 was significantly increased in HCC tissues and precancerous lesions and was associated with reduced survival of HCC patients. Upregulation of UBE2D1 promoted HCC growth in vitro and in vivo by decreasing the p53 in ubiquitination-dependent pathway. High expression of UBE2D1 was attributed to the recurrent genomic copy number gain, which was associated with high serum IL-6 level of HCC patients. Further experiments showed that continuous IL-6 activated the DNA damage response and genomic instability by repressing DNA damage checkpoint protein RAD51B. Moreover, continuous IL-6 could significantly facilitate the HCC growth especially with the genomic gain of UBE2D1. Conclusions Our findings showed that UBE2D1 played a crucial role in HCC progression, and suggested a novel pattern of continuous IL-6 to promote cancers by inducing the genomic alterations of specific oncogenes. Electronic supplementary material The online version of this article (10.1186/s13046-018-0951-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuanchuan Zhou
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China.,Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510000, China
| | - Fengrui Bi
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China
| | - Jihang Yuan
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China
| | - Shuhan Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China.
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12
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Kwon HJ, Yang JM, Lee JO, Lee JS, Paik JH. Clinicopathologic implication of PD-L1 and phosphorylated STAT3 expression in diffuse large B cell lymphoma. J Transl Med 2018; 16:320. [PMID: 30458835 PMCID: PMC6245852 DOI: 10.1186/s12967-018-1689-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Antitumor immune response of programmed cell death ligand (PD-L1) has shown clinical value not only in Hodgkin lymphoma and EBV-associated lymphomas but also in EBV-negative diffuse large B cell lymphoma (DLBCL) of non-germinal center B cell-like (non-GCB) subtype. Signal transducer and activator of transcription 3 (STAT3) is known to induce PD-L1 in immune cells and its activated form, phosphorylated STAT3 (pSTAT3), is also frequently expressed in non-GCB DLBCL. Herein, we investigated associations between PD-L1 expression/gene alteration, pSTAT3 expression and clinicopathologic variables in EBV-negative DLBCL. METHODS In 107 cases of DLBCLs with non-GCB subtype (67%; 72/107), GCB subtype (25%; 27/107) and unclassifiable cases (8%; 8/107), we performed PD-L1 and pSTAT3 immunohistochemistry and fluorescence in situ hybridization for PD-L1 gene translocation and copy number gain/amplification. RESULTS PD-L1 was expressed in tumor cells (PD-L1t) in 21% (23/107; 30% cutoff), immune cells (PD-L1i) in 36% (38/107; 20% cutoff), and pSTAT3 in tumor nuclei in 41% (44/107; 40% cutoff). PD-L1 gene alteration was observed in 10% (10/102) including translocation in 6% (6/102) and copy number gain/amplification in 4% (4/102). Non-GCB subtype was associated with PD-L1t and pSTAT3 (p = 0.006 and p = 0.042), and tended to have PD-L1 gene alteration (p = 0.058). Tumoral PD-L1 expression without gene alteration (PD-L1t+ GA-) correlated with pSTAT3-positive tumor cell proportions (%) (p = 0.033). In survival analysis, pSTAT3 expression independently predicted shorter PFS in total cohort (p = 0.017) and R-CHOP-treated group (p = 0.007), and in pSTAT3-negative R-CHOP-treated subset, PD-L1 expression in immune cells (PD-L1i) correlated with shorter PFS (p = 0.042). CONCLUSIONS Gene alteration and protein expression of PD-L1 and pSTAT3 expression were closely related in DLBCL and constituted features of non-GCB subtype. In addition to known clinical significance of pSTAT3, immune cell expression of PD-L1 (PD-L1i) had also clinical value in pSTAT3-dependent manner. These findings may provide an insight into immunotherapeutic strategy and risk stratification in DLBCL patients.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- B7-H1 Antigen/genetics
- B7-H1 Antigen/metabolism
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cohort Studies
- Disease-Free Survival
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Kaplan-Meier Estimate
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Phosphorylation/drug effects
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
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Affiliation(s)
- Hyun Jung Kwon
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707 South Korea
| | - Jeong Mi Yang
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707 South Korea
| | - Jeong-Ok Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jong Seok Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jin Ho Paik
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707 South Korea
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13
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RA, Drexler HG. Aberrant expression of NKL homeobox gene HLX in Hodgkin lymphoma. Oncotarget 2018; 9:14338-14353. [PMID: 29581848 PMCID: PMC5865674 DOI: 10.18632/oncotarget.24512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
NKL homeobox genes are basic regulators of cell and tissue differentiation, many acting as oncogenes in T-cell leukemia. Recently, we described an hematopoietic NKL-code comprising six particular NKL homeobox genes expressed in hematopoietic stem cells and lymphoid progenitors, unmasking their physiological roles in the development of these cell types. Hodgkin lymphoma (HL) is a B-cell malignancy showing aberrant activity of several developmental genes resulting in disturbed B-cell differentiation. To examine potential concordances in abnormal lymphoid differentiation of T- and B-cell malignancies we analyzed the expression of the hematopoietic NKL-code associated genes in HL, comprising HHEX, HLX, MSX1, NKX2-3, NKX3-1 and NKX6-3. Our approach revealed aberrant HLX activity in 8 % of classical HL patients and additionally in HL cell line L-540. Accordingly, to identify upstream regulators and downstream target genes of HLX we used L-540 cells as a model and performed chromosome and genome analyses, comparative expression profiling and functional assays via knockdown and overexpression experiments therein. These investigations excluded chromosomal rearrangements of the HLX locus at 1q41 and demonstrated that STAT3 operated directly as transcriptional activator of the HLX gene. Moreover, subcellular analyses showed highly enriched STAT3 protein in the nucleus of L-540 cells which underwent cytoplasmic translocation by repressing deacetylation. Finally, HLX inhibited transcription of B-cell differentiation factors MSX1, BCL11A and SPIB and of pro-apoptotic factor BCL2L11/BIM, thereby suppressing Etoposide-induced cell death. Collectively, we propose that aberrantly expressed NKL homeobox gene HLX is part of a pathological gene network in HL, driving deregulated B-cell differentiation and survival.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A.F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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14
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Zhao X, Zhang Z, Moreira D, Su YL, Won H, Adamus T, Dong Z, Liang Y, Yin HH, Swiderski P, Pillai RK, Kwak L, Forman S, Kortylewski M. B Cell Lymphoma Immunotherapy Using TLR9-Targeted Oligonucleotide STAT3 Inhibitors. Mol Ther 2018; 26:695-707. [PMID: 29433938 PMCID: PMC5910676 DOI: 10.1016/j.ymthe.2018.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 01/22/2023] Open
Abstract
Growing evidence links the aggressiveness of non-Hodgkin’s lymphoma, especially the activated B cell-like type diffuse large B cell lymphomas (ABC-DLBCLs) to Toll-like receptor 9 (TLR9)/MyD88 and STAT3 transcription factor signaling. Here, we describe a dual-function molecule consisting of a clinically relevant TLR9 agonist (CpG7909) and a STAT3 inhibitor in the form of a high-affinity decoy oligodeoxynucleotide (dODN). The CpG-STAT3dODN blocked STAT3 DNA binding and activity, thus reducing expression of downstream target genes, such as MYC and BCL2L1, in human and mouse lymphoma cells. We further demonstrated that injections (i.v.) of CpG-STAT3dODN inhibited growth of human OCI-Ly3 lymphoma in immunodeficient mice. Moreover, systemic CpG-STAT3dODN administration induced complete regression of the syngeneic A20 lymphoma, resulting in long-term survival of immunocompetent mice. Both TLR9 stimulation and concurrent STAT3 inhibition were critical for immune-mediated therapeutic effects, since neither CpG7909 alone nor CpG7909 co-injected with unconjugated STAT3dODN extended mouse survival. The CpG-STAT3dODN induced expression of genes critical to antigen-processing/presentation and Th1 cell activation while suppressing survival signaling. These effects resulted in the generation of lymphoma cell-specific CD8/CD4-dependent T cell immunity protecting mice from tumor rechallenge. Our results suggest that CpG-STAT3dODN as a systemic/local monotherapy or in combination with PD1 blockade can provide an opportunity for treating patients with B cell NHL.
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Affiliation(s)
- Xingli Zhao
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300020, China
| | - Zhuoran Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Dayson Moreira
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yu-Lin Su
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Haejung Won
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Tomasz Adamus
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Zhenyuan Dong
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yong Liang
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Hongwei H Yin
- Molecular Pathology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Piotr Swiderski
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Raju K Pillai
- Molecular Pathology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Larry Kwak
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Stephen Forman
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
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15
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Gene regulation and suppression of type I interferon signaling by STAT3 in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2018; 115:E498-E505. [PMID: 29295936 DOI: 10.1073/pnas.1715118115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
STAT3 is constitutively activated in many cancers and regulates gene expression to promote cancer cell survival, proliferation, invasion, and migration. In diffuse large B cell lymphoma (DLBCL), activation of STAT3 and its kinase JAK1 is caused by autocrine production of IL-6 and IL-10 in the activated B cell-like subtype (ABC). However, the gene regulatory mechanisms underlying the pathogenesis of this aggressive lymphoma by STAT3 are not well characterized. Here we performed genome-wide analysis and identified 2,251 STAT3 direct target genes, which involve B cell activation, survival, proliferation, differentiation, and migration. Whole-transcriptome profiling revealed that STAT3 acts as both a transcriptional activator and a suppressor, with a comparable number of up- and down-regulated genes. STAT3 regulates multiple oncogenic signaling pathways, including NF-κB, a cell-cycle checkpoint, PI3K/AKT/mTORC1, and STAT3 itself. In addition, STAT3 negatively regulates the lethal type I IFN signaling pathway by inhibiting expression of IRF7, IRF9, STAT1, and STAT2 Inhibition of STAT3 activity by ruxolitinib synergizes with the type I IFN inducer lenalidomide in growth inhibition of ABC DLBCL cells in vitro and in a xenograft mouse model. Therefore, this study provides a mechanistic rationale for clinical trials to evaluate ruxolitinib or a specific JAK1 inhibitor combined with lenalidomide in ABC DLBCL.
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16
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Coordinate Regulation of TET2 and EBNA2 Controls the DNA Methylation State of Latent Epstein-Barr Virus. J Virol 2017; 91:JVI.00804-17. [PMID: 28794029 DOI: 10.1128/jvi.00804-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) latency and its associated carcinogenesis are regulated by dynamic changes in DNA methylation of both virus and host genomes. We show here that the ten-eleven translocation 2 (TET2) gene, implicated in hydroxymethylation and active DNA demethylation, is a key regulator of EBV latency type DNA methylation patterning. EBV latency types are defined by DNA methylation patterns that restrict expression of viral latency genes. We show that TET2 mRNA and protein expression correlate with the highly demethylated EBV type III latency program permissive for expression of EBNA2, EBNA3s, and LMP transcripts. We show that short hairpin RNA (shRNA) depletion of TET2 results in a decrease in latency gene expression but can also trigger a switch to lytic gene expression. TET2 depletion results in the loss of hydroxymethylated cytosine and a corresponding increase in cytosine methylation at key regulatory regions on the viral and host genomes. This also corresponded to a loss of RBP-jκ binding and decreased histone H3K4 trimethylation at these sites. Furthermore, we show that the TET2 gene itself is regulated in a fashion similar to that of the EBV genome. Chromatin immunoprecipitation high-throughput sequencing (ChIP-seq) revealed that the TET2 gene contains EBNA2-dependent RBP-jκ and EBF1 binding sites and is subject to DNA methylation-associated transcriptional silencing similar to what is seen in EBV latency type III genomes. Finally, we provide evidence that TET2 colocalizes with EBNA2-EBF1-RBP-jκ binding sites and can interact with EBNA2 by coimmunoprecipitation. Taken together, these findings indicate that TET2 gene transcripts are regulated similarly to EBV type III latency genes and that TET2 protein is a cofactor of EBNA2 and coregulator of the EBV type III latency program and DNA methylation state.IMPORTANCE Epstein-Barr virus (EBV) latency and carcinogenesis involve the selective epigenetic modification of viral and cellular genes. Here, we show that TET2, a cellular tumor suppressor involved in active DNA demethylation, plays a central role in regulating the DNA methylation state during EBV latency. TET2 is coordinately regulated and functionally interacts with the viral oncogene EBNA2. TET2 and EBNA2 function cooperatively to demethylate genes important for EBV-driven B-cell growth transformation.
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17
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Restricted TET2 Expression in Germinal Center Type B Cells Promotes Stringent Epstein-Barr Virus Latency. J Virol 2017; 91:JVI.01987-16. [PMID: 28003489 DOI: 10.1128/jvi.01987-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Epstein-Barr virus (EBV) latently infects normal B cells and contributes to the development of certain human lymphomas. Newly infected B cells support a highly transforming form (type III) of viral latency; however, long-term EBV infection in immunocompetent hosts is limited to B cells with a more restricted form of latency (type I) in which most viral gene expression is silenced by promoter DNA methylation. How EBV converts latency type is unclear, although it is known that type I latency is associated with a germinal center (GC) B cell phenotype, and type III latency with an activated B cell (ABC) phenotype. In this study, we have examined whether expression of TET2, a cellular enzyme that initiates DNA demethylation by converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates EBV latency type in B cells. We found that TET2 expression is inhibited in normal GC cells and GC type lymphomas. In contrast, TET2 is expressed in normal naive B cells and ABC type lymphomas. We also demonstrate that GC type cell lines have increased 5mC levels and reduced 5hmC levels in comparison to those of ABC type lines. Finally, we show that TET2 promotes the ability of the EBV transcription factor EBNA2 to convert EBV-infected cells from type I to type III latency. These findings demonstrate that TET2 expression is repressed in GC cells independent of EBV infection and suggest that TET2 promotes type III EBV latency in B cells with an ABC or naive phenotype by enhancing EBNA2 activation of methylated EBV promoters.IMPORTANCE EBV establishes several different types of viral latency in B cells. However, cellular factors that determine whether EBV enters the highly transforming type III latency, versus the more restricted type I latency, have not been well characterized. Here we show that TET2, a cellular enzyme that initiates DNA demethylation by converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates EBV latency type in B cells by enhancing the ability of the viral transcription factor EBNA2 to activate methylated viral promoters that are expressed in type III (but not type I) latency. Furthermore, we demonstrate that (independent of EBV) TET2 is turned off in normal and malignant germinal center (GC) B cells but expressed in other B cell types. Thus, restricted TET2 expression in GC cells may promote type I EBV latency.
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18
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Epigenetic gene regulation by Janus kinase 1 in diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A 2016; 113:E7260-E7267. [PMID: 27799566 DOI: 10.1073/pnas.1610970113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Janus kinases (JAKs) classically signal by activating STAT transcription factors but can also regulate gene expression by epigenetically phosphorylating histone H3 on tyrosine 41 (H3Y41-P). In diffuse large B-cell lymphomas (DLBCLs), JAK signaling is a feature of the activated B-cell (ABC) subtype and is triggered by autocrine production of IL-6 and IL-10. Whether this signaling involves STAT activation, epigenetic modification of chromatin, or both mechanisms is unknown. Here we use genetic and pharmacological inhibition to show that JAK1 signaling sustains the survival of ABC DLBCL cells. Whereas STAT3 contributed to the survival of ABC DLBCL cell lines, forced STAT3 activity could not protect these cells from death following JAK1 inhibition, suggesting epigenetic JAK1 action. JAK1 regulated the expression of nearly 3,000 genes in ABC DLBCL cells, and the chromatin surrounding many of these genes was modified by H3Y41-P marks that were diminished by JAK1 inhibition. These JAK1 epigenetic target genes encode important regulators of ABC DLBCL proliferation and survival, including IRF4, MYD88, and MYC. A small molecule JAK1 inhibitor cooperated with the BTK inhibitor ibrutinib in reducing IRF4 levels and acted synergistically to kill ABC DLBCL cells, suggesting that this combination should be evaluated in clinical trials.
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19
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Feist M, Kemper J, Taruttis F, Rehberg T, Engelmann JC, Gronwald W, Hummel M, Spang R, Kube D. Synergy of interleukin 10 and toll-like receptor 9 signalling in B cell proliferation: Implications for lymphoma pathogenesis. Int J Cancer 2016; 140:1147-1158. [PMID: 27668411 DOI: 10.1002/ijc.30444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/02/2016] [Indexed: 12/18/2022]
Abstract
A network of autocrine and paracrine signals defines B cell homeostasis and is thought to be involved in transformation processes. Investigating interactions of these microenvironmental factors and their relation to proto-oncogenes as c-Myc (MYC) is fundamental to understand the biology of B cell lymphoma. Therefore, B cells with conditional MYC expression were stimulated with CD40L, insulin-like growth factor 1, α-IgM, Interleukin-10 (IL10) and CpG alone or in combination. The impact of forty different interventions on cell proliferation was investigated in MYC deprived cells and calculated by linear regression. Combination of CpG and IL10 led to a strong synergistic activation of cell proliferation (S-phase/doubling of total cell number) comparable to cells with high MYC expression. A synergistic up-regulation of CDK4, CDK6 and CCND3 expression by IL10 and CpG treatment was causal for this proliferative effect as shown by qRT-PCR analysis and inhibition of the CDK4/6 complex by PD0332991. Furthermore, treatment of stimulated MYC deprived cells with MLN120b, ACHP, Pyridone 6 or Ruxolitinib showed that IL10/CpG induced proliferation and CDK4 expression were JAK/STAT3 and IKK/NF-κB dependent. This was further supported by STAT3 and p65/RELA knockdown experiments, showing strongest effects on cell proliferation and CDK4 expression after double knockdown. Additionally, chromatin immunoprecipitation revealed a dual binding of STAT3 and p65 to the proximal promotor of CDK4 after IL10/CpG treatment. Therefore, the observed synergism of IL10R and TLR9 signalling was able to induce proliferation in a comparable way as aberrant MYC and might play a role in B cell homeostasis or transformation.
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Affiliation(s)
- Maren Feist
- Clinic of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,BMBF e:Bio Network, MMML-Myc-Sys
| | - Judith Kemper
- Clinic of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany
| | - Franziska Taruttis
- BMBF e:Bio Network, MMML-Myc-Sys.,Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Germany
| | - Thorsten Rehberg
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Germany
| | - Julia C Engelmann
- BMBF e:Bio Network, MMML-Myc-Sys.,Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Germany
| | - Wolfram Gronwald
- BMBF e:Bio Network, MMML-Myc-Sys.,Institute of Functional Genomics, University of Regensburg, Germany
| | - Michael Hummel
- BMBF e:Bio Network, MMML-Myc-Sys.,Institute for Pathology, Campus Benjamin Franklin, Charité Berlin, Germany
| | - Rainer Spang
- BMBF e:Bio Network, MMML-Myc-Sys.,Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Germany
| | - Dieter Kube
- Clinic of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,BMBF e:Bio Network, MMML-Myc-Sys
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Brown PJ, Gascoyne DM, Lyne L, Spearman H, Felce SL, McFadden N, Chakravarty P, Barrans S, Lynham S, Calado DP, Ward M, Banham AH. N-terminally truncated FOXP1 protein expression and alternate internal FOXP1 promoter usage in normal and malignant B cells. Haematologica 2016; 101:861-71. [PMID: 27056922 PMCID: PMC5004466 DOI: 10.3324/haematol.2016.142141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/04/2016] [Indexed: 12/20/2022] Open
Abstract
Strong FOXP1 protein expression is a poor risk factor in diffuse large B-cell lymphoma and has been linked to an activated B-cell-like subtype, which preferentially expresses short FOXP1 (FOXP1S) proteins. However, both short isoform generation and function are incompletely understood. Here we prove by mass spectrometry and N-terminal antibody staining that FOXP1S proteins in activated B-cell-like diffuse large B-cell lymphoma are N-terminally truncated. Furthermore, a rare strongly FOXP1-expressing population of normal germinal center B cells lacking the N-terminus of the regular long protein (FOXP1L) was identified. Exon-targeted silencing and transcript analyses identified three alternate 5' non-coding exons [FOXP1-Ex6b(s), FOXP1-Ex7b and FOXP1-Ex7c], downstream of at least two predicted promoters, giving rise to FOXP1S proteins. These were differentially controlled by B-cell activation and methylation, conserved in murine lymphoma cells, and significantly correlated with FOXP1S protein expression in primary diffuse large B-cell lymphoma samples. Alternatively spliced isoforms lacking exon 9 (e.g. isoform 3) did not encode FOXP1S, and an alternate long human FOXP1 protein (FOXP1AL) likely generated from a FOXP1-Ex6b(L) transcript was detected. The ratio of FOXP1L:FOXP1S isoforms correlated with differential expression of plasmacytic differentiation markers in U-2932 subpopulations, and altering this ratio was sufficient to modulate CD19 expression in diffuse large B-cell lymphoma cell lines. Thus, the activity of multiple alternate FOXP1 promoters to produce multiple protein isoforms is likely to regulate B-cell maturation.
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MESH Headings
- Alternative Splicing
- Animals
- Antigens, CD19/genetics
- Antigens, CD19/metabolism
- B-Lymphocytes/metabolism
- Cell Line, Tumor
- Exons
- Forkhead Transcription Factors/chemistry
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice
- Promoter Regions, Genetic
- Protein Interaction Domains and Motifs/genetics
- Protein Isoforms
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Philip J Brown
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
| | - Duncan M Gascoyne
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
| | - Linden Lyne
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
| | - Hayley Spearman
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
| | - Suet Ling Felce
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
| | - Nora McFadden
- Immunity and Cancer Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, Lincoln's Inn Fields, London, UK
| | - Probir Chakravarty
- Computational Biology Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, Lincoln's Inn Fields, London, UK
| | - Sharon Barrans
- Leeds Teaching Hospitals NHS Trust, HMDS, Leeds Cancer Centre, Kings College London, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK
| | - Dinis P Calado
- Immunity and Cancer Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, Lincoln's Inn Fields, London, UK Peter Gorer Department of Immunobiology, Kings College London, UK
| | - Malcolm Ward
- Centre of Excellence for Mass Spectrometry, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK
| | - Alison H Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, London, UK
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21
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Pinno J, Bongartz H, Klepsch O, Wundrack N, Poli V, Schaper F, Dittrich A. Interleukin-6 influences stress-signalling by reducing the expression of the mTOR-inhibitor REDD1 in a STAT3-dependent manner. Cell Signal 2016; 28:907-16. [PMID: 27094713 DOI: 10.1016/j.cellsig.2016.04.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/05/2016] [Accepted: 04/09/2016] [Indexed: 11/30/2022]
Abstract
Interleukin 6 (IL-6) is a pleiotropic cytokine and a strong activator of Mammalian Target of Rapamycin (mTOR). In contrast, mTOR activity is negatively regulated by Regulated in Development and DNA Damage Responses 1 (REDD1). Expression of REDD1 is induced by cellular stressors such as glucocorticoids and DNA damaging agents. We show that the expression of basal as well as stress-induced REDD1 is reduced by IL-6. The reduction of REDD1 expression by IL-6 is independent of proteasomal or caspase-mediated degradation of REDD1 protein. Instead, induction of REDD1 mRNA is reduced by IL-6. The regulation of REDD1 expression by IL-6 is independent of Phosphatidylinositide-3-Kinase (PI3K) and Mitogen-Activated Protein Kinase (MAPK) signalling but depends on the expression and activation of Signal Transducer and Activator of Transcription 3 (STAT3). Furthermore, the reduction of basal REDD1 expression by IL-6 correlates with IL-6-induced activation of mTOR signalling. Inhibition of STAT3 activation blocks IL-6-induced mTOR activation. In summary, we present a novel STAT3-dependent mechanism of both IL-6-induced activation of mTOR and IL-6-dependent reversion of stress-induced inhibition of mTOR activity.
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Affiliation(s)
- Jessica Pinno
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
| | - Hannes Bongartz
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
| | - Oliver Klepsch
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
| | - Nicole Wundrack
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
| | - Valeria Poli
- Molecular Biotechnology Center (MBC), Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy.
| | - Fred Schaper
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
| | - Anna Dittrich
- Institute of Biology, Department of Systems Biology, Otto-von-Guericke University, Universitätsplatz 2, Gebäude 28, 39106 Magdeburg, Germany.
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22
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Zheng M, Turton KB, Zhu F, Li Y, Grindle KM, Annis DS, Lu L, Drennan AC, Tweardy DJ, Bharadwaj U, Mosher DF, Rui L. A mix of S and ΔS variants of STAT3 enable survival of activated B-cell-like diffuse large B-cell lymphoma cells in culture. Oncogenesis 2016; 4:e184. [PMID: 26727576 PMCID: PMC4728674 DOI: 10.1038/oncsis.2015.44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/29/2015] [Accepted: 11/12/2015] [Indexed: 12/13/2022] Open
Abstract
Activated B-cell-like diffuse large B-cell lymphoma (ABC DLBCL) is characterized by increased expression and activator of signal transducer and activator of transcription 3 (STAT3). ABC DLBCL cells require STAT3 for growth in culture. In ABC DLBCL cells, eosinophils and perhaps all cells, four variant STAT3 mRNAs (Sα, ΔSα, Sβ and ΔSβ) are present as a result of two alternative splicing events, one that results in the inclusion of a 55-residue C-terminal transactivation domain (α) or a truncated C-terminal domain with 7 unique residues (β) and a second that includes (S) or excludes (ΔS) the codon for Ser-701 in the linker between the SH2 and C-terminal domains. A substantial literature indicates that both α and β variants are required for optimal STAT3 function, but nothing is known about functions of ΔS variants. We used a knockdown/re-expression strategy to explore whether survival of ABC DLBCL cells requires that the four variants be in an appropriate ratio. No single variant rescued survival as well as STAT3Sα-C, Sα with activating mutations (A661C and N663C) in the SH2 domain. Better rescue was achieved when all four variants were re-expressed or Sα and ΔSα or Sβ and ΔSβ were re-expressed in pairs. Rescue correlated with expression of STAT3-sensitive genes NFKBIA and NFKBIZ. We consider a variety of explanations why a mix of S and ΔS variants of STAT3 should enable survival of ABC DLBCL cells.
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Affiliation(s)
- M Zheng
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - K B Turton
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - F Zhu
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Y Li
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - K M Grindle
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - D S Annis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - L Lu
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - A C Drennan
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - D J Tweardy
- Department of Internal Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - U Bharadwaj
- Department of Internal Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - D F Mosher
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - L Rui
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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23
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Fan Y, Timani KA, He JJ. STAT3 and its phosphorylation are involved in HIV-1 Tat-induced transactivation of glial fibrillary acidic protein. Curr HIV Res 2015; 13:55-63. [PMID: 25613134 DOI: 10.2174/1570162x13666150121115804] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 01/31/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) Tat protein is a major pathogenic factor in HIV-associated neurological diseases; it exhibits direct neurotoxicity and indirect astrocyte-mediated neurotoxicity. We have shown that Tat alone is capable of activating glial fibrillary acidic protein (GFAP) expression and inducing astrocytosis involving sequential activation of early growth response protein 1 (Egr-1) and p300. In this study, we determined the roles of signal transducer and activator of transcription 3 (STAT3) in Tat-induced GFAP transactivation. STAT3 expression and phosphorylation led to significant increases in GFAP transcription and protein expression. Tat expression was associated with increased STAT3 expression and phosphorylation in Tat-expressing astrocytes and HIV-infected astrocytes. GFAP, Egr-1 and p300 transcription and protein expression all showed positive response to STAT3 and its phosphorylation. Importantly, knockdown of STAT3 resulted in significant decreases in Tat-induced GFAP and Egr-1 transcription and protein expression. Taken together, these findings show that STAT3 is involved in and acts upstream of Egr1 and p300 in the Tat-induced GFAP transactivation cascade and suggest important roles of STAT3 in controlling astrocyte proliferation and activation in the HIV-infected central nervous system.
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Affiliation(s)
| | | | - Johnny J He
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
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24
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Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O. Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma. Genome Med 2015; 7:110. [PMID: 26521025 PMCID: PMC4628784 DOI: 10.1186/s13073-015-0230-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/08/2015] [Indexed: 12/14/2022] Open
Abstract
Background Gene profiling of diffuse large B cell lymphoma (DLBCL) has revealed broad gene expression deregulation compared to normal B cells. While many studies have interrogated well known and annotated genes in DLBCL, none have yet performed a systematic analysis to uncover novel unannotated long non-coding RNAs (lncRNA) in DLBCL. In this study we sought to uncover these lncRNAs by examining RNA-seq data from primary DLBCL tumors and performed supporting analysis to identify potential role of these lncRNAs in DLBCL. Methods We performed a systematic analysis of novel lncRNAs from the poly-adenylated transcriptome of 116 primary DLBCL samples. RNA-seq data were processed using de novo transcript assembly pipeline to discover novel lncRNAs in DLBCL. Systematic functional, mutational, cross-species, and co-expression analyses using numerous bioinformatics tools and statistical analysis were performed to characterize these novel lncRNAs. Results We identified 2,632 novel, multi-exonic lncRNAs expressed in more than one tumor, two-thirds of which are not expressed in normal B cells. Long read single molecule sequencing supports the splicing structure of many of these lncRNAs. More than one-third of novel lncRNAs are differentially expressed between the two major DLBCL subtypes, ABC and GCB. Novel lncRNAs are enriched at DLBCL super-enhancers, with a fraction of them conserved between human and dog lymphomas. We see transposable elements (TE) overlap in the exonic regions; particularly significant in the last exon of the novel lncRNAs suggest potential usage of cryptic TE polyadenylation signals. We identified highly co-expressed protein coding genes for at least 88 % of the novel lncRNAs. Functional enrichment analysis of co-expressed genes predicts a potential function for about half of novel lncRNAs. Finally, systematic structural analysis of candidate point mutations (SNVs) suggests that such mutations frequently stabilize lncRNA structures instead of destabilizing them. Conclusions Discovery of these 2,632 novel lncRNAs in DLBCL significantly expands the lymphoma transcriptome and our analysis identifies potential roles of these lncRNAs in lymphomagenesis and/or tumor maintenance. For further studies, these novel lncRNAs also provide an abundant source of new targets for antisense oligonucleotide pharmacology, including shared targets between human and dog lymphomas. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0230-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akanksha Verma
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Yanwen Jiang
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Wei Du
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Lauren Fairchild
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA. .,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA. .,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.
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25
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Sorafenib improves rituximab and ofatumumab efficacy by decreasing the expression of complement regulatory proteins. Blood Cancer J 2015; 5:e300. [PMID: 25860291 PMCID: PMC4450327 DOI: 10.1038/bcj.2015.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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26
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Paik JH, Nam SJ, Kim TM, Heo DS, Kim CW, Jeon YK. Overexpression of sphingosine-1-phosphate receptor 1 and phospho-signal transducer and activator of transcription 3 is associated with poor prognosis in rituximab-treated diffuse large B-cell lymphomas. BMC Cancer 2014; 14:911. [PMID: 25472725 PMCID: PMC4265452 DOI: 10.1186/1471-2407-14-911] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 11/22/2014] [Indexed: 11/16/2022] Open
Abstract
Background Sphingosine-1-phosphate receptor-1 (S1PR1) and signal transducer and activator of transcription-3 (STAT3) play important roles in immune responses with potential oncogenic roles. Methods We analyzed S1PR1/STAT3 pathway activation using immunohistochemistry in rituximab-treated diffuse large B-cell lymphomas (DLBCL; N = 103). Results Nuclear expression of pSTAT3 (but not S1PR1) was associated with non-GCB phenotype (p = 0.010). In univariate survival analysis, S1PR1 expression (S1PR1+) was a poor prognostic factor in total DLBCLs (p = 0.018), as well as in nodal (p = 0.041), high-stage (III, IV) (p = 0.002), and high-international prognostic index (IPI; 3–5) (p = 0.014) subgroups, while nuclear expression of pSTAT3 (pSTAT3+) was associated with poor prognosis in the low-stage (I, II) subgroup (p = 0.022). The S1PR1/pSTAT3 risk-categories, containing high-risk (S1PR1+), intermediate-risk (S1PR1-/pSTAT3+), and low-risk (S1PR1-/pSTAT3-), predicted overall survival (p = 0.010). This prognostication tended to be valid in each stage (p = 0.059 in low-stage; p = 0.006 in high-stage) and each IPI subgroups (p = 0.055 [low-IPI]; p = 0.034 [high-IPI]). S1PR1 alone and S1PR1/pSTAT3 risk-category were significant independent prognostic indicators in multivariate analyses incorporating IPI and B symptoms (S1PR1 [p = 0.005; HR = 3.0]; S1PR1/pSTAT3 risk-category [p = 0.019: overall; p = 0.024, HR = 2.7 for S1PR1-/pSTAT3+ vs. S1PR1+; p = 0.021, HR = 3.8 for S1PR1-/pSTAT3- vs. S1PR1+]). Conclusions Therefore, S1PR1 and S1PR1/pSTAT3 risk-category may contribute to risk stratification in rituximab-treated DLBCLs, and S1PR1 and STAT3 might be therapeutic targets for DLBCL.
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Affiliation(s)
| | | | | | | | | | - Yoon Kyung Jeon
- Tumor Immunity Medical Research Center, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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27
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Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A. The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinformatics 2014; 15:79. [PMID: 24650281 PMCID: PMC4000056 DOI: 10.1186/1471-2105-15-79] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/11/2014] [Indexed: 11/13/2022] Open
Abstract
Background Identifying differentially expressed genes (DEG) is a fundamental step in studies that perform genome wide expression profiling. Typically, DEG are identified by univariate approaches such as Significance Analysis of Microarrays (SAM) or Linear Models for Microarray Data (LIMMA) for processing cDNA microarrays, and differential gene expression analysis based on the negative binomial distribution (DESeq) or Empirical analysis of Digital Gene Expression data in R (edgeR) for RNA-seq profiling. Results Here we present a new geometrical multivariate approach to identify DEG called the Characteristic Direction. We demonstrate that the Characteristic Direction method is significantly more sensitive than existing methods for identifying DEG in the context of transcription factor (TF) and drug perturbation responses over a large number of microarray experiments. We also benchmarked the Characteristic Direction method using synthetic data, as well as RNA-Seq data. A large collection of microarray expression data from TF perturbations (73 experiments) and drug perturbations (130 experiments) extracted from the Gene Expression Omnibus (GEO), as well as an RNA-Seq study that profiled genome-wide gene expression and STAT3 DNA binding in two subtypes of diffuse large B-cell Lymphoma, were used for benchmarking the method using real data. ChIP-Seq data identifying DNA binding sites of the perturbed TFs, as well as known drug targets of the perturbing drugs, were used as prior knowledge silver-standard for validation. In all cases the Characteristic Direction DEG calling method outperformed other methods. We find that when drugs are applied to cells in various contexts, the proteins that interact with the drug-targets are differentially expressed and more of the corresponding genes are discovered by the Characteristic Direction method. In addition, we show that the Characteristic Direction conceptualization can be used to perform improved gene set enrichment analyses when compared with the gene-set enrichment analysis (GSEA) and the hypergeometric test. Conclusions The application of the Characteristic Direction method may shed new light on relevant biological mechanisms that would have remained undiscovered by the current state-of-the-art DEG methods. The method is freely accessible via various open source code implementations using four popular programming languages: R, Python, MATLAB and Mathematica, all available at: http://www.maayanlab.net/CD.
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Affiliation(s)
| | | | | | | | | | | | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY 10029, USA.
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