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Castrogiovanni P, Sanfilippo C, Imbesi R, Lazzarino G, Li Volti G, Tibullo D, Vicario N, Parenti R, Giuseppe L, Barbagallo I, Alanazi AM, Vecchio M, Cappello F, Musumeci G, Di Rosa M. Skeletal muscle of young females under resistance exercise exhibits a unique innate immune cell infiltration profile compared to males and elderly individuals. J Muscle Res Cell Motil 2024:10.1007/s10974-024-09668-6. [PMID: 38578562 DOI: 10.1007/s10974-024-09668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Muscle damage resulting from physical activities such as exercise triggers an immune response crucial for tissue repair and recovery. This study investigates the immune cell profiles in muscle biopsies of individuals engaged in resistance exercise (RE) and explores the impact of age and sex on the immune response following exercise-induced muscle damage. Microarray datasets from muscle biopsies of young and old subjects were analyzed, focusing on the gene expression patterns associated with immune cell activation. Genes were compared with immune cell signatures to reveal the cellular landscape during exercise. Results show that the most significant modulated gene after RE was Folliculin Interacting Protein 2 (FNIP2) a crucial regulator in cellular homeostasis. Moreover, the transcriptome was stratified based on the expression of FNIP2 and the 203 genes common to the groups obtained based on sex and age. Gene ontology analysis highlighted the FLCN-FNIP1-FNIP2 complex, which exerts as a negative feedback loop to Pi3k-Akt-mTORC1 pathway. Furthermore, we highlighted that the young females exhibit a distinct innate immune cell activation signature compared to males after a RE session. Specifically, young females demonstrate a notable overlap with dendritic cells (DCs), M1 macrophages, M2 macrophages, and neutrophils, while young males overlap with M1 macrophages, M2 macrophages, and motor neurons. Interestingly, in elderly subjects, both sexes display M1 macrophage activation signatures. Comparison of young and elderly signatures reveals an increased M1 macrophage percentage in young subjects. Additionally, common genes were identified in both sexes across different age groups, elucidating biological functions related to cell remodeling and immune activation. This study underscores the intricate interplay between sex, age, and the immune response in muscle tissue following RE, offering potential directions for future research. Nevertheless, there is a need for further studies to delve deeper and confirm the dynamics of immune cells in response to exercise-induced muscle damage.
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Affiliation(s)
- Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, 95125, Italy
| | - Cristina Sanfilippo
- Neurologic Unit, Department of Medical, Surgical Sciences and Advanced Technologies, AOU "Policlinico-San Marco", University of Catania, Via Santa Sofia n.78, Sicily, GF, Ingrassia, Catania, 95100, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, 95125, Italy
| | - Giacomo Lazzarino
- UniCamillus-Saint Camillus International University of Health Sciences, Via di Sant'Alessandro 8, Rome, 00131, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, Catania, 95123, Italy
| | - Daniele Tibullo
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, Catania, 95123, Italy
| | - Nunzio Vicario
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, 95123, Italy
| | - Rosalba Parenti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, 95123, Italy
| | - Lazzarino Giuseppe
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, Catania, 95123, Italy
| | - Ignazio Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, Catania, 95123, Italy
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Michele Vecchio
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, 95124, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, Palermo, 90127, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, 90139, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, 95125, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, 95125, Italy.
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Chen Q, Hong Y, Chen W, Lin F, Zeng J, Huang Y, Zhang L, Yao J, Xu B. Prognostic implications of cGAS and STING gene expression in acute myeloid leukemia. Exp Biol Med (Maywood) 2024; 249:10108. [PMID: 38510490 PMCID: PMC10954193 DOI: 10.3389/ebm.2024.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/25/2023] [Indexed: 03/22/2024] Open
Abstract
Acute myeloid leukemia (AML) is one of the most threatening hematological malignances. cGAS-STING pathway plays an important role in tumor immunity and development. However, the prognostic role of cGAS-STING pathway in AML remains unknown. Firstly, The expression of cGAS and STING was analyzed by bioinformatics analysis. Subsequently, Bone marrow samples were collected from 120 AML patients and 15 healthy individuals in an independent cohort. The cGAS and STING expression was significantly elevated in AML patients compared with healthy controls. Patients with high cGAS and STING expression had a higher NRAS/KRAS mutation rate and lower complete remission (CR) rate. High cGAS and STING expression was significantly associated with lower overall survival (OS) and disease-free survival (DFS). Our findings revealed that the expression levels of cGAS and STING in AML are elevated. High expression of cGAS and STING correlated with worse OS and DFS and may be a useful biomarker for inferior prognosis in AML patients.
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Affiliation(s)
- Qiuling Chen
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Yan Hong
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - WeiFeng Chen
- Department of Hematology, Shantou Central Hospital, Shantou, Guangdong, China
| | - Feng Lin
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
- Department of Hematology, Shantou Central Hospital, Shantou, Guangdong, China
| | - Jiawei Zeng
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Yueting Huang
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Li Zhang
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Jingwei Yao
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
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Coats JT, Tauro S, Sutherland C. Elraglusib (formerly 9-ING-41) possesses potent anti-lymphoma properties which cannot be attributed to GSK3 inhibition. Cell Commun Signal 2023; 21:131. [PMID: 37316860 DOI: 10.1186/s12964-023-01147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
Elraglusib (formerly 9-ING-41) is an ATP-competitive inhibitor of glycogen synthase kinase-3β (GSK3β) undergoing clinical trials for the treatment of various cancers including non-Hodgkin lymphoma (NHL). The drug reduces proliferation of several NHL cell lines and has efficacy in xenograft models of the disease. To confirm the importance of its action on GSK3β, we treated 3 lymphoma cell lines with selective, structurally distinct GSK3 inhibitors: CT99021, SB216763, LY2090314, tideglusib, and elraglusib. Stabilization of β-catenin and reduced phosphorylation of CRMP2, two validated targets of GSK3, were used as functional read-outs for GSK3 inhibition. CT99021, SB216763, and LY2090314 failed to reduce proliferation or viability in any cell line at concentrations that stabilized β-catenin and reduced CRMP2 phosphorylation. There was partial reduction of CRMP2 phosphorylation but no significant effect on β-catenin at cytotoxic doses of elraglusib. There was no indication of GSK3 inhibition at doses of tideglusib that affected cell viability and apoptosis. Cell-free kinase screening confirmed several other targets of elraglusib, distinct from the GSK3 inhibitors with no anti-lymphoma actions, including PIM kinases and MST2. These data question GSK3 as the target of elraglusib in lymphoma, and hence the utility of GSK3 expression as a 'stand-alone', therapeutic biomarker in NHL. Video Abstract.
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Affiliation(s)
- Josh T Coats
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Sudhir Tauro
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Calum Sutherland
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK.
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Davies AJ, Barrans S, Stanton L, Caddy J, Wilding S, Saunders G, Mamot C, Novak U, McMillan A, Fields P, Collins GP, Stephens R, Cucco F, Sha C, van Hoppe M, Tooze R, Davies JR, Griffiths G, Schuh A, Burton C, Westhead DR, Du MQ, Johnson PW. Differential Efficacy From the Addition of Bortezomib to R-CHOP in Diffuse Large B-Cell Lymphoma According to the Molecular Subgroup in the REMoDL-B Study With a 5-Year Follow-Up. J Clin Oncol 2023; 41:2718-2723. [PMID: 36972491 PMCID: PMC10414744 DOI: 10.1200/jco.23.00033] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/10/2023] [Indexed: 03/29/2023] Open
Abstract
Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.The REMoDL-B phase III adaptive trial compared rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP) versus R-CHOP + bortezomib (RB-CHOP) in patients with diffuse large B-cell lymphoma (DLBCL), stratified by molecular subtype. Primary analysis at a median follow-up of 30 months found no effect of bortezomib on progression-free survival (PFS) or overall survival (OS). Retrospective analysis using a gene expression-based classifier identified a molecular high-grade (MHG) group with worse outcomes. We present an updated analysis for patients successfully classified by the gene expression profile (GEP). Eligible patients were age older than 18 years with untreated DLBCL, fit enough for full-dose chemotherapy, and with adequate biopsies for GEP. Of 1,077 patients registered, 801 were identified with Activated B-Cell (ABC), Germinal Center B-cell, or MHG lymphoma. At a median follow-up of 64 months, there was no overall benefit of bortezomib on PFS or OS (5-year PFS hazard ratio [HR], 0.81; P = .085; OS HR, 0.86; P = .32). However, improved PFS and OS were seen in ABC lymphomas after RB-CHOP: 5-year OS 67% with R-CHOP versus 80% with RB-CHOP (HR, 0.58; 95% CI, 0.35 to 0.95; P = .032). Five-year PFS was higher in MHG lymphomas: 29% versus 55% (HR, 0.46; 95% CI, 0.26 to 0.84). Patients with ABC and MHG DLBCL may benefit from the addition of bortezomib to R-CHOP in initial therapy.
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Affiliation(s)
- Andrew J. Davies
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Louise Stanton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Josh Caddy
- Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Sam Wilding
- Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Geoff Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | | | - Urban Novak
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrew McMillan
- Department of Haematology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Paul Fields
- Department of Haematology, Guy's and St Thomas's Hospitals NHS Trust, Kings Health Partners, London, United Kingdom
| | - Graham P. Collins
- Oxford Cancer and Haematology Centre, Churchill Hospital, Oxford, United Kingdom
| | - Richard Stephens
- National Cancer Research Institute Consumer Forum, London, United Kingdom
| | - Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Chulin Sha
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Moniek van Hoppe
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Reuben Tooze
- Section of Experimental Haematology, University of Leeds, Leeds, United Kingdom
| | - John R. Davies
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - David R. Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Peter W.M. Johnson
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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Sanfilippo C, Castrogiovanni P, Vinciguerra M, Imbesi R, Ulivieri M, Fazio F, Cantarella A, Nunnari G, Di Rosa M. Neuro-immune deconvolution analysis of OAS3 as a transcriptomic central node in HIV-associated neurocognitive disorders. J Neurol Sci 2023; 446:120562. [PMID: 36706688 DOI: 10.1016/j.jns.2023.120562] [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: 08/13/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Neurological complications of AIDS (NeuroAIDS) include primary HIV-associated neurocognitive disorder (HAND). OAS3 is an enzyme belonging to the 2', 5' oligoadenylate synthase family induced by type I interferons and involved in the degradation of both viral and endogenous RNA. Here, we used microarray datasets from NCBI of brain samples of non-demented HIV-negative controls (NDC), HIV, deceased patients with HAND and encephalitis (HIVE) (treated and untreated with antiretroviral therapy, ART), and with HAND without HIVE. The HAND/HIVE patients were stratified according to the OAS3 gene expression. The genes positively and negatively correlated to the OAS3 gene expression were used to perform a genomic deconvolution analysis using neuroimmune signatures (NIS) belonging to sixteen signatures. Expression analysis revealed significantly higher OAS3 expression in HAND/HIVE and HAND/HIVE/ART compared with NDC. OAS3 expressed an excellent diagnostic ability to discriminate NDC from HAND/HIVE, HAND from HAND/HIVE, HAND from HAND/HIVE/ART, and HIV from HAND/HIVE. Noteworthy, OAS3 expression levels in the brains of HAND/HIVE patients were positively correlated with viral load in both peripheral blood and cerebrospinal fluid (CSF). Furthermore, deconvolution analysis revealed that the genes positively correlated to OAS3 expression were associated with inflammatory signatures. Neuronal activation profiles were significantly activated by the genes negatively correlated to OAS3 expression levels. Moreover, gene ontology analysis performed on genes characterizing the microglia signature highlighted an immune response as a main biological process. According to our results, genes positively correlated to OAS3 gene expression in the brains of HAND/HIVE patients are associated with inflammatory transcriptomic signatures and likely worse cognitive impairment.
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Affiliation(s)
- Cristina Sanfilippo
- Neurologic Unit, AOU "Policlinico-San Marco", Department of Medical, Surgical Sciences and Advanced Technologies, GF, Ingrassia, University of Catania, Via Santa Sofia n.78, 95100 Catania, Sicily, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic; Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria; Liverpool Center for Cardiovascular Science, Liverpool Johns Moore University & University of Liverpool, Liverpool, UK
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Martina Ulivieri
- University of California San Diego, Department of Psychiatry, Health Science, San Diego La Jolla, CA, USA
| | - Francesco Fazio
- University of California San Diego, Department of Psychiatry, Health Science, San Diego La Jolla, CA, USA
| | - Antonio Cantarella
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, 98124 Messina, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy.
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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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Resistin-like beta reduction is associated to low survival rate and is downregulated by adjuvant therapy in colorectal cancer patients. Sci Rep 2023; 13:1490. [PMID: 36707698 PMCID: PMC9883247 DOI: 10.1038/s41598-023-28450-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Colorectal Cancer (CRC) is one of the most common cancers accounting for 1.8 million new cases worldwide every year. Therefore, the identification of new potential therapeutic targets represents a continuous challenge to improve survival and quality of CRC patient's life. We performed a microarray analysis dataset consisting of colon biopsies of healthy subjects (HS) and CRC patients. These results were further confirmed in a clinical setting evaluating a series of CRC patients to assess the expression of Resistin-Like Beta (RETNLB) and to correlate it with their clinical data. Our results showed a significant reduction of RETNLB expression in CRC biopsies compared to the HS mucosa. Furthermore, such reduction was significantly associated with the TNM grade and patients' age. Furthermore, a significantly positive correlation was found within mutated subjects for KRAS, TP53, and BRAF. In particular, patients with poor prognosis at 5 years exhibited RETNLB lower levels. In-silico analysis data were confirmed by histochemical analysis in a series of CRC patients recruited by our group. The results obtained provided that RETNLB low levels are associated with an unfavorable prognosis in CRC patients and its expression is also dependent on adjuvant therapy. Further studies are warranted in order to evaluate the molecular mechanisms underlying the role of RETNLB in CRC progression.
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Meta-Analysis of MS-Based Proteomics Studies Indicates Interferon Regulatory Factor 4 and Nucleobindin1 as Potential Prognostic and Drug Resistance Biomarkers in Diffuse Large B Cell Lymphoma. Cells 2023; 12:cells12010196. [PMID: 36611989 PMCID: PMC9818977 DOI: 10.3390/cells12010196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The prognosis of diffuse large B cell lymphoma (DLBCL) is inaccurately predicted using clinical features and immunohistochemistry (IHC) algorithms. Nomination of a panel of molecules as the target for therapy and predicting prognosis in DLBCL is challenging because of the divergences in the results of molecular studies. Mass spectrometry (MS)-based proteomics in the clinic represents an analytical tool with the potential to improve DLBCL diagnosis and prognosis. Previous proteomics studies using MS-based proteomics identified a wide range of proteins. To achieve a consensus, we reviewed MS-based proteomics studies and extracted the most consistently significantly dysregulated proteins. These proteins were then further explored by analyzing data from other omics fields. Among all significantly regulated proteins, interferon regulatory factor 4 (IRF4) was identified as a potential target by proteomics, genomics, and IHC. Moreover, annexinA5 (ANXA5) and nucleobindin1 (NUCB1) were two of the most up-regulated proteins identified in MS studies. Functional enrichment analysis identified the light zone reactions of the germinal center (LZ-GC) together with cytoskeleton locomotion functions as enriched based on consistent, significantly dysregulated proteins. In this study, we suggest IRF4 and NUCB1 proteins as potential biomarkers that deserve further investigation in the field of DLBCL sub-classification and prognosis.
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9
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Sanfilippo C, Castrogiovanni P, Imbesi R, Musumeci G, Vecchio M, Li Volti G, Tibullo D, Broggi G, Caltabiano R, Ulivieri M, Kazakova M, Parenti R, Vicario N, Fazio F, Di Rosa M. Sex-dependent neuro-deconvolution analysis of Alzheimer's disease brain transcriptomes according to CHI3L1 expression levels. J Neuroimmunol 2022; 373:577977. [PMID: 36228382 DOI: 10.1016/j.jneuroim.2022.577977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/29/2022] [Accepted: 10/01/2022] [Indexed: 11/07/2022]
Abstract
Glial activation and related neuroinflammatory processes play a key role in the aging and progression of Alzheimer's disease (AD). CHI3L1/ YKL40 is a widely investigated chitinase in neurodegenerative diseases and recent studies have shown its involvement in aging and AD. Nevertheless, the biological function of CHI3L1 in AD is still unknown. Here, we collected microarray datasets from the National Center for Biotechnology Information (NCBI) brain samples of not demented healthy controls (NDHC) who died from causes not attributable to neurodegenerative disorders (n = 460), and of deceased patients suffering from Alzheimer's disease (AD) (n = 697). The NDHC and AD patients were stratified according to CHI3L1 expression levels as a cut-off. We identified two groups both males and females, subsequently used for our statistical comparisons: the high CHI3L1 expression group (HCEG) and the low CHI3L1 expression group (LCEG). Comparing HCEG to LCEG, we attained four signatures according to the sex of patients, in order to identify the healthy and AD brain cellular architecture, performing a genomic deconvolution analysis. We used neurological signatures (NS) belonging to six neurological cells populations and nine signatures that included the main physiological neurological processes. We discovered that, in the brains of NDHC the high expression levels of CHI3L1 were associated with astrocyte activation profile, while in AD males and females we showed an inflammatory profile microglia-mediated. The low CHI3L1 brain expression levels in NDHC and AD patients highlighted a neuronal activation profile. Furthermore, using drugs opposing CHI3L1 transcriptomic signatures, we found a specific drug profile for AD males and females characterized by high levels of CHI3L1 composed of fostamatinib, rucaparib, cephaeline, prednisolone, and dinoprostone. Brain levels of CHI3L1 in AD patients represent a biological signature that allows distinguishing between males and females and their likely cellular brain architecture.
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Affiliation(s)
- Cristina Sanfilippo
- Neurologic Unit, AOU "Policlinico-San Marco", Department of Medical, Surgical Sciences and Advanced Technologies, GF, Ingrassia, University of Catania, Via Santa Sofia n.78, 95100 Catania, Sicily, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Michele Vecchio
- Rehabilitation Unit, "AOU Policlinico Vittorio Emanuele", Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania 95123, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123, Catania, Italy
| | - Daniele Tibullo
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123, Catania, Italy
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Martina Ulivieri
- University of California San Diego, Department of Psychiatry, Health Science, San Diego, La Jolla, CA, USA
| | - Maria Kazakova
- Department of Medical Biology, Medical University, Plovdiv, 4002 Plovdiv, Bulgaria; Research Institute, Medical University-, Plovdiv, 4002 Plovdiv, Bulgaria
| | - Rosalba Parenti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Nunzio Vicario
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Francesco Fazio
- University of California San Diego, Department of Psychiatry, Health Science, San Diego, La Jolla, CA, USA
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy.
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10
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Sanfilippo C, Castrogiovanni P, Vinciguerra M, Imbesi R, Ulivieri M, Fazio F, Blennow K, Zetterberg H, Di Rosa M. A sex-stratified analysis of neuroimmune gene expression signatures in Alzheimer's disease brains. GeroScience 2022; 45:523-541. [PMID: 36136224 PMCID: PMC9886773 DOI: 10.1007/s11357-022-00664-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/14/2022] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of progressively disabling dementia. The chitinases CHI3L1 and CHI3L2 have long been known as biomarkers for microglial and astrocytic activation in neurodegeneration. Here, we collected microarray datasets from the National Center for Biotechnology Information (NCBI) brain samples of non-demented controls (NDC) (n = 460), and of deceased patients with AD (n = 697). The AD patients were stratified according to sex. Comparing the high CHI3L1 and CHI3L2 expression group (75th percentile), and low CHI3L1 and CHI3L2 expression group (25th percentile), we obtained eight signatures according to the sex of patients and performed a genomic deconvolution analysis using neuroimmune signatures (NIS) belonging to twelve cell populations. Expression analysis revealed significantly higher CHI3L1 and CHI3L2 expression in AD compared with NDC, and positive correlations of these genes with GFAP and TMEM119. Furthermore, deconvolution analysis revealed that CHI3L1 and CHI3L2 high expression was associated with inflammatory signatures in both sexes. Neuronal activation profiles were significantly activated in AD patients with low CHI3L1 and CHI3L2 expression levels. Furthermore, gene ontology analysis of common genes regulated by the two chitinases unveiled immune response as a main biological process. Finally, microglia NIS significantly correlated with CHI3L2 expression levels and were more than 98% similar to microglia NIS determined by CHI3L1. According to our results, high levels of CHI3L1 and CHI3L2 in the brains of AD patients are associated with inflammatory transcriptomic signatures. The high correlation between CHI3L1 and CHI3L2 suggests strong co-regulation.
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Affiliation(s)
- Cristina Sanfilippo
- Neurologic Unit, AOU “Policlinico-San Marco”, Department of Medical, Surgical Sciences and Advanced Technologies, GF, Ingrassia, University of Catania, Catania, Sicily Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic ,Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, Italy
| | - Martina Ulivieri
- Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Francesco Fazio
- Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden ,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden ,UK Dementia Research Institute at UCL, London, UK ,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, Catania, Italy.
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11
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GJA1/CX43 High Expression Levels in the Cervical Spinal Cord of ALS Patients Correlate to Microglia-Mediated Neuroinflammatory Profile. Biomedicines 2022; 10:biomedicines10092246. [PMID: 36140348 PMCID: PMC9496195 DOI: 10.3390/biomedicines10092246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder affecting motoneurons (MNs) with a fatal outcome. The typical degeneration of cortico-spinal, spinal, and bulbar MNs, observed in post-mortem biopsies, is associated with the activation of neuroimmune cells. GJA1, a member of the connexins (Cxs) gene family, encodes for connexin 43 (Cx43), a core gap junctions (GJs)- and hemichannels (HCs)-forming protein, involved in cell death, proliferation, and differentiation. Recently, Cx43 expression was found to play a role in ALS pathogenesis. Here, we used microarray and RNA-seq datasets from the NCBI of the spinal cord of control (NDC) and ALS patients, which were stratified according to the GJA1 gene expression. Genes that positively or negatively correlated to GJA1 expression were used to perform a genomic deconvolution analysis (GDA) using neuroimmune signatures. Expression analysis revealed a significantly higher GJA1 expression in the MNs of ALS patients as compared to NDC. Gene deconvolution analysis revealed that positively correlated genes were associated with microglia activation, whereas negatively correlated genes were associated with neuronal activation profiles. Moreover, gene ontology analysis, performed on genes characterizing either microglia or neuronal signature, indicated immune activation or neurogenesis as main biological processes. Finally, using a synthetic analysis of drugs able to revert the GJA1 transcriptomic signatures, we found a specific drug profile for ALS patients with high GJA1 expression levels, composed of amlodipine, sertraline, and prednisolone. In conclusion, our exploratory study suggests GJA1 as a new neuro-immunological gene correlated to microglial cellular profile in the spinal cord of ALS patients. Further studies are warranted to confirm these results and to evaluate the therapeutic potential of drugs able to revert typical GJA1/CX43 signature in ALS patients
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12
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Castrogiovanni P, Barbagallo I, Imbesi R, Musumeci G, Sanfilippo C, Broggi G, Caltabiano R, Tibullo D, Giallongo C, Forte S, Li Volti G, Di Rosa M. Chitinase domain containing 1 increase is associated with low survival rate and M0 macrophages infiltrates in colorectal cancer patients. Pathol Res Pract 2022; 237:154038. [DOI: 10.1016/j.prp.2022.154038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 02/08/2023]
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13
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Longhitano L, Vicario N, Tibullo D, Giallongo C, Broggi G, Caltabiano R, Barbagallo GMV, Altieri R, Baghini M, Di Rosa M, Parenti R, Giordano A, Mione MC, Li Volti G. Lactate Induces the Expressions of MCT1 and HCAR1 to Promote Tumor Growth and Progression in Glioblastoma. Front Oncol 2022; 12:871798. [PMID: 35574309 PMCID: PMC9097945 DOI: 10.3389/fonc.2022.871798] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/23/2022] [Indexed: 12/04/2022] Open
Abstract
The tumor microenvironment (TME) plays a pivotal role in establishing malignancy, and it is associated with high glycolytic metabolism and lactate release through monocarboxylate transporters (MCTs). Several lines of evidence suggest that lactate also serves as a signaling molecule through its receptor hydroxycarboxylic acid receptor 1 (HCAR1/GPR81), thus functioning as a paracrine and autocrine signaling molecule. The aim of the present study was to investigate the role of lactate in glioblastoma (GBM) progression and metabolic reprogramming in an in vitro and in vivo model. The cell proliferation, migration, and clonogenicity were tested in vitro in three different human GBM cell lines. The expressions of MCT1, MCT4, and HCAR1 were evaluated both in vitro and in a zebrafish GBM model. The results were further validated in patient-derived GBM biopsies. Our results showed that lactate significantly increased the cell proliferation, migration, and colony formation capacity of GBM cells, both in vitro and in vivo. We also showed that lactate increased the expressions of MCT1 and HCAR1. Moreover, lactate modulated the epithelial–mesenchymal transition protein markers E-cadherin and β-catenin. Interestingly, lactate induced mitochondrial mass and the OXPHOS gene, suggesting improved mitochondrial fitness. Similar effects were observed after treatment with 3,5-dihydroxybenzoic acid, a known agonist of HCAR1. Consistently, the GBM zebrafish model exhibited an altered metabolism and increased expressions of MCT1 and HCAR1, leading to high levels of extracellular lactate and, thus, supporting tumor cell proliferation. Our data from human GBM biopsies also showed that, in high proliferative GBM biopsies, Ki67-positive cells expressed significantly higher levels of MCT1 compared to low proliferative GBM cells. In conclusion, our data suggest that lactate and its transporter and receptor play a major role in GBM proliferation and migration, thus representing a potential target for new therapeutic strategies to counteract tumor progression and recurrence.
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Affiliation(s)
- Lucia Longhitano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Nunzio Vicario
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Daniele Tibullo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cesarina Giallongo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Catania, Italy
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Catania, Italy
| | - Giuseppe Maria Vincenzo Barbagallo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia" Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy.,Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, Catania, Italy
| | - Roberto Altieri
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia" Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy.,Interdisciplinary Research Center on Brain Tumors Diagnosis and Treatment, University of Catania, Catania, Italy
| | - Marta Baghini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Rosalba Parenti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine and Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Maria Caterina Mione
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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14
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Wu Z, Zhang X, Chen D, Li Z, Wu X, Wang J, Deng Y. N6-Methyladenosine-Related LncRNAs Are Potential Remodeling Indicators in the Tumor Microenvironment and Prognostic Markers in Osteosarcoma. Front Immunol 2022; 12:806189. [PMID: 35095893 PMCID: PMC8790065 DOI: 10.3389/fimmu.2021.806189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022] Open
Abstract
N6-Adenosine methylation, yielding N6-methyladenosine (m6A), is a reversible epigenetic modification found in messenger RNAs and long non-coding RNAs (lncRNAs), which affects the fate of modified RNA molecules and is essential for the development and differentiation of immune cells in the tumor microenvironment (TME). Osteosarcoma (OS) is the most common primary bone tumor in children and adolescents, and is characterized by high mortality. Currently, the possible role of m6A modifications in the prognosis of OS is unclear. In the present study, we investigated the correlation between m6A-related lncRNA expression and the clinical outcomes of OS patients via a comprehensive analysis. Clinical and workflow-type data were obtained from the Genotype-Tissue Expression Program and The Cancer Genome Atlas. We examined the relationship between m6A modifications and lncRNA expression, conducted Kyoto Encyclopedia of Genes analysis and also gene set enrichment analysis (GSEA), implemented survival analysis to investigate the association of clinical survival data with the expression of m6A-related lncRNAs, and utilized Lasso regression to model the prognosis of OS. Furthermore, we performed immune correlation analysis and TME differential analysis to investigate the infiltration levels of immune cells and their relationship with clinical prognosis. LncRNA expression and m6A levels were closely associated in co-expression analysis. The expression of m6A-related lncRNAs was quite low in tumor tissues; this appeared to be a predicting factor of OS in a prognostic model, independent of other clinical features. The NOD-like receptor signaling pathway was the most significantly enriched pathway in GSEA. In tumor tissues, SPAG4 was overexpressed while ZBTB32 and DEPTOR were downregulated. Tissues in cluster 2 were highly infiltrated by plasma cells. Cluster 2 presented higher ESTIMATE scores and stromal scores, showing a lower tumor cell purity in the TME. In conclusion, m6A-related lncRNA expression is strongly associated with the occurrence and development of OS, and can be used to as a prognostic factor of OS. Moreover, m6A-related lncRNAs and infiltrating immune cells in the TME could serve as new therapeutic targets and prognostic biomarkers for OS.
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Affiliation(s)
- Zhongguang Wu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Zhang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Dongjie Chen
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zian Li
- Department of Clinical Laboratory, Qinghai Provincial People's Hospital, Xining, China
| | - Xin Wu
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianlong Wang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Youwen Deng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
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15
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Morin RD, Arthur SE, Hodson DJ. Molecular profiling in diffuse large B-cell lymphoma: why so many types of subtypes? Br J Haematol 2021; 196:814-829. [PMID: 34467527 DOI: 10.1111/bjh.17811] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The term diffuse large B-cell lymphoma (DLBCL) includes a heterogeneous collection of biologically distinct tumours. This heterogeneity currently presents a barrier to the successful deployment of novel, biologically targeted therapies. Molecular profiling studies have recently proposed new molecular classification systems. These have the potential to resolve the biological heterogeneity of DLBCL into manageable subgroups of tumours that rely on shared oncogenic programmes. In many cases these biological programmes straddle the boundaries of our existing systems for classifying B-cell lymphomas. Here we review the findings from these major molecular profiling studies with a specific focus on those that propose new genetic subgroups of DLBCL. We highlight the areas of consensus and discordance between these studies and discuss the implications for current clinical practice and for clinical trials. Finally, we address the outstanding challenges and solutions to the introduction of genomic subtyping and precision medicine in DLBCL.
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Affiliation(s)
- Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
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16
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Sanfilippo C, Castrogiovanni P, Imbesi R, Lazzarino G, Di Pietro V, Li Volti G, Tibullo D, Barbagallo I, Lazzarino G, Avola R, Musumeci G, Fazio F, Vinciguerra M, Di Rosa M. Sex-dependent monoamine oxidase isoforms expression patterns during human brain ageing. Mech Ageing Dev 2021; 197:111516. [PMID: 34097937 DOI: 10.1016/j.mad.2021.111516] [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: 08/27/2020] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 10/21/2022]
Abstract
Human behavior is influenced by both genetic and environmental factors. Monoamine oxidase A (MAOA) is among the most investigated genetic determinants of violent behaviors, while the monoamine oxidase B (MAOB) is explored in Parkinson's disease. We collected twenty-four post-mortem brain tissue datasets of 3871 and 1820 non-demented males and females, respectively, who died from causes not attributable to neurodegenerative diseases. The gene expressions of MAOA and MAOB (MAO genes) were analyzed in these subjects, who were further stratified according to age into eleven groups ranging from late Infancy (5-9 months) to centenarians (>100 years). MAO genes were differently expressed in brains during the entire life span. In particular, maximal and minimal expression levels were found in early life and around the teen years. Females tended to have higher MAO gene levels throughout their lives than those found in age-matched males, even when expressions were separately measured in different brain regions. We demonstrated the existence of age- and sex- related variations in the MAO transcript levels in defined brain regions. More in-depth protein studies are needed to confirm our preliminary results obtained only on messenger RNAs in order to establish the role played by MAO genes in human development.
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Affiliation(s)
- Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, School of Medicine, University of Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, School of Medicine, University of Catania, Italy
| | - Giuseppe Lazzarino
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123 Catania, Italy
| | - Valentina Di Pietro
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Aging, University of Birmingham, Birmingham B15 2TT, UK
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123 Catania, Italy
| | - Daniele Tibullo
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123 Catania, Italy
| | - Ignazio Barbagallo
- Section of Biochemistry, Department of Drug Sciences, University of Catania, 95123 Catania, Italy
| | - Giacomo Lazzarino
- UniCamillus - Saint Camillus International University of Health Sciences, Via di Sant'Alessandro 8, 00131, Rome, Italy
| | - Roberto Avola
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, 95123 Catania, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, School of Medicine, University of Catania, Italy
| | - Francesco Fazio
- University of California San Diego, Department of Psychiatry, Health Science, San Diego La Jolla, CA, USA
| | - Manlio Vinciguerra
- International Clinical Research Center (FNUSA-ICRC), St' Anne University Hospital, Brno, Czech Republic
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Sciences, School of Medicine, University of Catania, Italy.
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17
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Cherng HJJ, Westin J. Why R-CHOP + X is not enough: lessons learned and next steps in the mission to improve frontline therapy for diffuse large B-cell lymphoma. Leuk Lymphoma 2021; 62:1302-1312. [PMID: 33403905 PMCID: PMC9153122 DOI: 10.1080/10428194.2020.1869228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Two-thirds of newly diagnosed cases of diffuse large B-cell lymphoma (DLBCL) are cured with R-CHOP, an immunochemotherapy regimen that has been the standard of care for almost two decades. Ongoing molecular characterization of DLBCL has revealed a heterogeneous disease comprised of multiple subtypes based on putative cell of origin or somatic mutations with unique oncogenic signaling pathways. The door has been opened to the use of novel agents that target the specific molecular vulnerabilities of DLBCL, but despite this, multiple randomized studies have not identified a suitable drug 'X' to combine with R-CHOP. This report will review recent attempts to add individual novel agents to R-CHOP in the mission to improve frontline treatment for DLBCL and discuss promising ongoing studies. It will offer potential strategies to explore when designing future clinical trials, including exploiting synergy between multiple novel agents.
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Affiliation(s)
- Hua-Jay J. Cherng
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
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18
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Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients. Cells 2021; 10:cells10040882. [PMID: 33924468 PMCID: PMC8069241 DOI: 10.3390/cells10040882] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease is a progressive, devastating, and irreversible brain disorder that, day by day, destroys memory skills and social behavior. Despite this, the number of known genes suitable for discriminating between AD patients is insufficient. Among the genes potentially involved in the development of AD, there are the chitinase-like proteins (CLPs) CHI3L1, CHI3L2, and CHID1. The genes of the first two have been extensively investigated while, on the contrary, little information is available on CHID1. In this manuscript, we conducted transcriptome meta-analysis on an extensive sample of brains of healthy control subjects (n = 1849) (NDHC) and brains of AD patients (n = 1170) in order to demonstrate CHID1 involvement. Our analysis revealed an inverse correlation between the brain CHID1 expression levels and the age of NDHC subjects. Significant differences were highlighted comparing CHID1 expression of NDHC subjects and AD patients. Exclusive in AD patients, the CHID1 expression levels were correlated positively to calcium-binding adapter molecule 1 (IBA1) levels. Furthermore, both in NDHC and in AD patient’s brains, the CHID1 expression levels were directly correlated with calbindin 1 (CALB1) and neurogranin (NRGN). According to brain regions, correlation differences were shown between the expression levels of CHID1 in prefrontal, frontal, occipital, cerebellum, temporal, and limbic system. Sex-related differences were only highlighted in NDHC. CHID1 represents a new chitinase potentially involved in the principal processes underlying Alzheimer’s disease.
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19
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Ahmed S, Glover P, Taylor J, Sha C, Care MA, Tooze R, Davies A, Westhead DR, Johnson PWM, Burton C, Barrans SL. Comparative analysis of gene expression platforms for cell-of-origin classification of diffuse large B-cell lymphoma shows high concordance. Br J Haematol 2020; 192:599-604. [PMID: 33249557 DOI: 10.1111/bjh.17246] [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] [Received: 09/23/2020] [Accepted: 11/01/2020] [Indexed: 12/21/2022]
Abstract
Cell-of-origin subclassification of diffuse large B cell lymphoma (DLBCL) into activated B cell-like (ABC), germinal centre B cell-like (GCB) and unclassified (UNC) or type III by gene expression profiling is recommended in the latest update of the World Health Organization's classification of lymphoid neoplasms. There is, however, no accepted gold standard method or dataset for this classification. Here, we compare classification results using gene expression data for 68 formalin-fixed paraffin-embedded DLBCL samples measured on four different gene expression platforms (Illumina wG-DASLTM arrays, Affymetrix PrimeView arrays, Illumina TrueSeq RNA sequencing and the HTG EdgeSeq DLBCL Cell of Origin Assay EU using an established platform agnostic classification algorithm (DAC) and the classifier native to the HTG platform, which is CE marked for in vitro diagnostic use (CE-IVD). Classification methods and platforms show a high level of concordance, with agreement in at least 80% of cases and rising to much higher levels for classifications of high confidence. Our results demonstrate that cell-of-origin classification by gene expression profiling on different platforms is robust, and that the use of the confidence value alongside the classification result is important in clinical applications.
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Affiliation(s)
- Sophia Ahmed
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Paul Glover
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Jan Taylor
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Chulin Sha
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
- Faculty of Medicine, University of Leeds, Leeds, UK
| | - Andrew Davies
- Cancer Research UK Centre, Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | - Peter W M Johnson
- Cancer Research UK Centre, Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Sharon L Barrans
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
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20
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Sanfilippo C, Musumeci G, Kazakova M, Mazzone V, Castrogiovanni P, Imbesi R, Di Rosa M. GNG13 Is a Potential Marker of the State of Health of Alzheimer's Disease Patients' Cerebellum. J Mol Neurosci 2020; 71:1046-1060. [PMID: 33057964 DOI: 10.1007/s12031-020-01726-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Brain regions such as the cerebellum (CB) have been neglected for a long time in the study of Alzheimer's disease (AD) pathogenesis. In reference to a new emerging hypothesis according to which there is an altered cerebellar synaptic processing in AD, we verified the possible role played by new biomarkers in the CB of AD patients compared with not-demented healthy control subjects (NDHS). Using a bioinformatics approach, we have collected several microarray datasets and obtained 626 cerebella sample biopsies belonging to subjects who did not die from causes related to neurological diseases and 199 cerebella belonging to AD. The analysis of logical relations between the transcriptome dataset highlighted guanine nucleotide-binding protein (G protein) gamma 13 (GNG13) as a potential new biomarker for Purkinje cells (PCs). We have correlated GNG13 expression levels with already widely existing bibliography of PC marker genes, such as Purkinje cell protein 2 (PCP2), Purkinje cell protein 4 (PCP4), and cerebellin 3 (CBLN3). We showed that expression levels of GNG13 and PCP2, PCP4, and CBLN3 were significantly correlated with each other in NDHS and in AD and significantly reduced in AD patients compared with NDHS subjects. In addition, we highlighted a negative correlation between the expression levels of PC biomarkers and age. From the outcome of our investigation, it is possible to conclude that the identification of GNG13 as a potentially biomarker in PCs represents also a state of health of CB, in association with the expression of PCP2, PCP4, and CBLN3.
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Affiliation(s)
- Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124, Messina, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Maria Kazakova
- Department of Medical Biology, Medical Faculty, Medical University, Plovdiv, Bulgaria
| | - Venera Mazzone
- Department G.F. Ingrassia, Anatomy, School of Medicine, University of Catania, Catania, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy.
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21
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Cocco M, Care MA, Saadi A, Al-Maskari M, Doody G, Tooze R. A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition. Life Sci Alliance 2020; 3:e202000654. [PMID: 32843533 PMCID: PMC7471511 DOI: 10.26508/lsa.202000654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/22/2023] Open
Abstract
The activated B-cell (ABC) to plasmablast transition encompasses the cusp of antibody-secreting cell (ASC) differentiation. We explore this transition with integrated analysis in human cells, focusing on changes that follow removal from CD40-mediated signals. Within hours of input signal loss, cell growth programs shift toward enhanced proliferation, accompanied by ER-stress response, and up-regulation of ASC features. Clustering of genomic occupancy for IRF4, BLIMP1, XBP1, and CTCF with histone marks identifies a dichotomy: XBP1 and IRF4 link to induced but not repressed gene modules in plasmablasts, whereas BLIMP1 links to modules of ABC genes that are repressed, but not to activated genes. Between ABC and plasmablast states, IRF4 shifts away from AP1/IRF composite elements while maintaining occupancy at IRF and ETS/IRF elements. This parallels the loss of BATF expression, which is identified as a potential BLIMP1 target. In plasmablasts, IRF4 acquires an association with CTCF, a feature maintained in plasma cell myeloma lines. Thus, shifting occupancy links IRF4 to both ABC and ASC gene expression, whereas BLIMP1 occupancy links to repression of the activation state.
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Affiliation(s)
- Mario Cocco
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Matthew A Care
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Bioinformatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Amel Saadi
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Muna Al-Maskari
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Gina Doody
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reuben Tooze
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
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22
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Sanfilippo C, Castrogiovanni P, Imbesi R, Nunnari G, Di Rosa M. Postsynaptic damage and microglial activation in AD patients could be linked CXCR4/CXCL12 expression levels. Brain Res 2020; 1749:147127. [PMID: 32949560 DOI: 10.1016/j.brainres.2020.147127] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/26/2020] [Accepted: 09/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the most common forms of dementia with still unknown pathogenesis. Several cytokines and chemokines are involved in the pathogenesis of AD. Among the chemokines, the CXCR4/CXCL12 complex has been shown to play an important role in the pathogenetic development of AD. We investigated the expression levels of CXCR4 / CXCL12 in fifteen brain regions of healthy non-demented subjects (NDHC) (2139 sample) and AD patients (1170 sample) stratified according to sex and age. Furthermore, we correlated their expressions with the Neurogranin (NRGN) and CHI3L1 levels, two inflamm-aging markers. We highlighted that CXCR4 gene expression levels were age-correlated in the brain of NDHC subjects and that AD nullified this correlation. A similar trend, but diametrically opposite was observed for CXCL12. Its expression was decreased during the aging in both sexes, and in the brains of AD patients, it underwent an inversion of the trend, only and exclusively in females. Brains of AD patients expressed high CXCR4 and CHI3L1, and low CXCL12 and Neurogranin levels compared to NDHC subjects. Both CXCR4 and CXCL12 correlated significantly with CHI3L1 and Neurogranin expression levels, regardless of disease. Furthermore, we showed a selective modulation of CXCL12 and CXCR4 only in specific brain regions. Taken together our results demonstrate that CXCL12 and CXCR4 are linked to Neurogranin and CHI3L1 expression levels and the relationship between postsynaptic damage and microglial activation in AD could be shown using all these genes. Further confirmations are needed to demonstrate the close link between these genes.
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Affiliation(s)
- Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy.
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23
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Nunnari G, Sanfilippo C, Castrogiovanni P, Imbesi R, Li Volti G, Barbagallo I, Musumeci G, Di Rosa M. Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection. Exp Cell Res 2020; 395:112204. [PMID: 32735892 PMCID: PMC7386311 DOI: 10.1016/j.yexcr.2020.112204] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 11/24/2022]
Abstract
Background SARS-CoV2, the agent responsible for the current pandemic, is also causing respiratory distress syndrome (RDS), hyperinflammation and high mortality. It is critical to dissect the pathogenetic mechanisms in order to reach a targeted therapeutic approach. Methods In the present investigation, we evaluated the effects of SARS-CoV2 on human bronchial epithelial cells (HBEC). We used RNA-seq datasets available online for identifying SARS-CoV2 potential genes target on human bronchial epithelial cells. RNA expression levels and potential cellular gene pathways have been analyzed. In order to identify possible common strategies among the main pandemic viruses, such as SARS-CoV2, SARS-CoV1, MERS-CoV, and H1N1, we carried out a hypergeometric test of the main genes transcribed in the cells of the respiratory tract exposed to these viruses. Results The analysis showed that two mechanisms are highly regulated in HBEC: the innate immunity recruitment and the disassembly of cilia and cytoskeletal structure. The granulocyte colony-stimulating factor (CSF3) and dynein heavy chain 7, axonemal (DNAH7) represented respectively the most upregulated and downregulated genes belonging to the two mechanisms highlighted above. Furthermore, the carcinoembryonic antigen-related cell adhesion molecule 7 (CEACAM7) that codifies for a surface protein is highly specific of SARS-CoV2 and not for SARS-CoV1, MERS-CoV, and H1N1, suggesting a potential role in viral entry. In order to identify potential new drugs, using a machine learning approach, we highlighted Flunisolide, Thalidomide, Lenalidomide, Desoximetasone, xylazine, and salmeterol as potential drugs against SARS-CoV2 infection. Conclusions Overall, lung involvement and RDS could be generated by the activation and down regulation of diverse gene pathway involving respiratory cilia and muscle contraction, apoptotic phenomena, matrix destructuration, collagen deposition, neutrophil and macrophages recruitment. SARS-CoV2 causing respiratory distress syndrome, hyperinflammation and high mortality. In NHBEC, SARS-CoV2 highly regulated the innate immunity recruitment and the disassembly of cilia and cytoskeletal structure. The granulocyte colony-stimulating factor (CSF3) is the most upregulated gene by SARS-CoV2. The dynein heavy chain 7, axonemal (DNAH7) represented the most downregulated genes by SARS-CoV2. Flunisolide, Thalidomide, Lenalidomide, Desoximetasone, xylazine, and salmeterol as potential drugs against SARS-CoV-2.
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Affiliation(s)
- Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy.
| | - Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124, Messina, Italy.
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy.
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy.
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95125, Catania, Italy.
| | - Ignazio Barbagallo
- Department of Drug Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy.
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy.
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy.
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24
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CHI3L2 Expression Levels Are Correlated with AIF1, PECAM1, and CALB1 in the Brains of Alzheimer's Disease Patients. J Mol Neurosci 2020; 70:1598-1610. [PMID: 32705525 DOI: 10.1007/s12031-020-01667-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) represents one of the main forms of dementia that afflicts our society. The expression of several genes has been associated with disease development. Despite this, the number of genes known to be capable of discriminating between AD patients according to sex remains deficient. In our study, we performed a transcriptomes meta-analysis on a large court of brains of healthy control subjects (n = 2139) (NDHC) and brains of AD patients (n = 1170). Our aim was to verify the brain expression levels of CHI3L2 and its correlation with genes associated with microglia-mediated neuroinflammation (IBA1), alteration of the blood-brain barrier (PECAM1), and neuronal damage (CALB1). We showed that the CHI3L2, IBA1, PECAM1, and CALB1 expression levels were modulated in the brains of patients with AD compared to NDHC subjects. Furthermore, both in NDHC and in AD patient's brains, the CHI3L2 expression levels were directly correlated with IBA1 and PECAM1 and inversely with CALB1. Additionally, the expression levels of CHI3L2, PECAM1, and CALB1 but not of IBA1 were sex-depended. By stratifying the samples according to age and sex, correlation differences emerged between the expression levels of CHI3L2, IBA1, PECAM1, and CALB1 and the age of NDHC subjects and AD patients. CHI3L2 represents a promising gene potentially involved in the key processes underlying Alzheimer's disease. Its expression in the brains of sex-conditioned AD patients opens up new possible sex therapeutic strategies aimed at controlling imbalance in disease progression.
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25
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Cucco F, Barrans S, Sha C, Clipson A, Crouch S, Dobson R, Chen Z, Thompson JS, Care MA, Cummin T, Caddy J, Liu H, Robinson A, Schuh A, Fitzgibbon J, Painter D, Smith A, Roman E, Tooze R, Burton C, Davies AJ, Westhead DR, Johnson PWM, Du MQ. Distinct genetic changes reveal evolutionary history and heterogeneous molecular grade of DLBCL with MYC/BCL2 double-hit. Leukemia 2020; 34:1329-1341. [PMID: 31844144 PMCID: PMC7192846 DOI: 10.1038/s41375-019-0691-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 11/22/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
Using a Burkitt lymphoma-like gene expression signature, we recently defined a high-risk molecular high-grade (MHG) group mainly within germinal centre B-cell like diffuse large B-cell lymphomas (GCB-DLBCL), which was enriched for MYC/BCL2 double-hit (MYC/BCL2-DH). The genetic basis underlying MHG-DLBCL and their aggressive clinical behaviour remain unknown. We investigated 697 cases of DLBCL, particularly those with MYC/BCL2-DH (n = 62) by targeted sequencing and gene expression profiling. We showed that DLBCL with MYC/BCL2-DH, and those with BCL2 translocation, harbour the characteristic mutation signatures that are associated with follicular lymphoma and its high-grade transformation. We identified frequent MYC hotspot mutations that affect the phosphorylation site (T58) and its adjacent amino acids, which are important for MYC protein degradation. These MYC mutations were seen in a subset of cases with MYC translocation, but predominantly in those of MHG. The mutations were more frequent in double-hit lymphomas with IG as the MYC translocation partner, and were associated with higher MYC protein expression and poor patient survival. DLBCL with MYC/BCL2-DH and those with BCL2 translocation alone are most likely derived from follicular lymphoma or its precursor lesion, and acquisition of MYC pathogenic mutations may augment MYC function, resulting in aggressive clinical behaviour.
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Affiliation(s)
- Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Chulin Sha
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Simon Crouch
- Department of Health Sciences, University of York, York, UK
| | - Rachel Dobson
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Matthew A Care
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas Cummin
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Josh Caddy
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Anne Robinson
- Haematopathology and Oncology Diagnostics Service, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - Daniel Painter
- Department of Health Sciences, University of York, York, UK
| | | | - Eve Roman
- Department of Health Sciences, University of York, York, UK
| | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Andrew J Davies
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | - Peter W M Johnson
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK.
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26
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Jash A, Zhou YW, Gerardo DK, Ripperger TJ, Parikh BA, Piersma S, Jamwal DR, Kiela PR, Boon ACM, Yokoyama WM, Hsieh CS, Bhattacharya D. ZBTB32 restrains antibody responses to murine cytomegalovirus infections, but not other repetitive challenges. Sci Rep 2019; 9:15257. [PMID: 31649328 PMCID: PMC6813321 DOI: 10.1038/s41598-019-51860-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/01/2019] [Indexed: 02/06/2023] Open
Abstract
ZBTB32 is a transcription factor that is highly expressed by a subset of memory B cells and restrains the magnitude and duration of recall responses against hapten-protein conjugates. To define physiological contexts in which ZBTB32 acts, we assessed responses by Zbtb32-/- mice or bone marrow chimeras against a panel of chronic and acute challenges. Mixed bone marrow chimeras were established in which all B cells were derived from either Zbtb32-/- mice or control littermates. Chronic infection of Zbtb32-/- chimeras with murine cytomegalovirus led to nearly 20-fold higher antigen-specific IgG2b levels relative to controls by week 9 post-infection, despite similar viral loads. In contrast, IgA responses and specificities in the intestine, where memory B cells are repeatedly stimulated by commensal bacteria, were similar between Zbtb32-/- mice and control littermates. Finally, an infection and heterologous booster vaccination model revealed no role for ZBTB32 in restraining primary or recall antibody responses against influenza viruses. Thus, ZBTB32 does not limit recall responses to a number of physiological acute challenges, but does restrict antibody levels during chronic viral infections that periodically engage memory B cells. This restriction might selectively prevent recall responses against chronic infections from progressively overwhelming other antibody specificities.
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Affiliation(s)
- Arijita Jash
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - You W Zhou
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Division of Rheumatology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Diana K Gerardo
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Tyler J Ripperger
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Sytse Piersma
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Division of Rheumatology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Deepa R Jamwal
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Pawel R Kiela
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Wayne M Yokoyama
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Division of Rheumatology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Chyi S Hsieh
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America.,Division of Rheumatology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America
| | - Deepta Bhattacharya
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States of America. .,Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, 85724, USA.
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27
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Nowakowski GS, Feldman T, Rimsza LM, Westin JR, Witzig TE, Zinzani PL. Integrating precision medicine through evaluation of cell of origin in treatment planning for diffuse large B-cell lymphoma. Blood Cancer J 2019; 9:48. [PMID: 31097684 PMCID: PMC6522601 DOI: 10.1038/s41408-019-0208-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Precision medicine is modernizing strategies for clinical study design to help improve diagnoses guiding individualized treatment based on genetic or phenotypic characteristics that discriminate between patients with similar clinical presentations. Methodology to personalize treatment choices is being increasingly employed in clinical trials, yielding favorable correlations with improved response rates and survival. In patients with diffuse large B-cell lymphoma (DLBCL), disease characteristics and outcomes may vary widely, underscoring the importance of patient classification through identification of sensitive prognostic features. The discovery of distinct DLBCL molecular subtypes based on cell of origin (COO) is redefining the prognosis and treatment of this heterogeneous cancer. Owing to significant molecular and clinical differences between activated B-cell-like (ABC)- and germinal center B-cell-like (GCB)-DLBCL subtypes, COO identification offers opportunities to optimize treatment selection. Widespread adoption of COO classification would greatly improve treatment and prognosis; however, limitations in interlaboratory concordance between immunohistochemistry techniques, cost, and availability of gene expression profiling tools undermine universal integration in the clinical setting. With advanced methodology to determine COO in a real-world clinical setting, therapies targeted to specific subtypes are under development. The focus here is to review applications of precision medicine exemplified by COO determination in DLBCL patients.
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Affiliation(s)
| | - Tatyana Feldman
- Division of Lymphoma, John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Jason R Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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28
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Davies A, Cummin TE, Barrans S, Maishman T, Mamot C, Novak U, Caddy J, Stanton L, Kazmi-Stokes S, McMillan A, Fields P, Pocock C, Collins GP, Stephens R, Cucco F, Clipson A, Sha C, Tooze R, Care MA, Griffiths G, Du MQ, Westhead DR, Burton C, Johnson PWM. Gene-expression profiling of bortezomib added to standard chemoimmunotherapy for diffuse large B-cell lymphoma (REMoDL-B): an open-label, randomised, phase 3 trial. Lancet Oncol 2019; 20:649-662. [PMID: 30948276 PMCID: PMC6494978 DOI: 10.1016/s1470-2045(18)30935-5] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Biologically distinct subtypes of diffuse large B-cell lymphoma can be identified using gene-expression analysis to determine their cell of origin, corresponding to germinal centre or activated B cell. We aimed to investigate whether adding bortezomib to standard therapy could improve outcomes in patients with these subtypes. METHODS In a randomised evaluation of molecular guided therapy for diffuse large B-cell lymphoma with bortezomib (REMoDL-B), an open-label, adaptive, randomised controlled, phase 3 superiority trial, participants were recruited from 107 cancer centres in the UK (n=94) and Switzerland (n=13). Eligible patients had previously untreated, histologically confirmed diffuse large B-cell lymphoma with sufficient diagnostic material from initial biopsies for gene-expression profiling and pathology review; were aged 18 years or older; had ECOG performance status of 2 or less; had bulky stage I or stage II-IV disease requiring full-course chemotherapy; had measurable disease; and had cardiac, lung, renal, and liver function sufficient to tolerate chemotherapy. Patients initially received one 21-day cycle of standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP; rituximab 375 mg/m2, cyclophosphamide 750 mg/m2, doxorubicin 50 mg/m2, and vincristine 1·4 mg/m2 [to a maximum of 2 mg total dose] intravenously on day 1 of the cycle, and prednisolone 100 mg orally once daily on days 1-5). During this time, we did gene-expression profiling using whole genome cDNA-mediated annealing, selection, extension, and ligation assay of tissue from routine diagnostic biopsy samples to determine the cell-of-origin subtype of each participant (germinal centre B cell, activated B cell, or unclassified). Patients were then centrally randomly assigned (1:1) via a web-based system, with block randomisation stratified by international prognostic index score and cell-of-origin subtype, to continue R-CHOP alone (R-CHOP group; control), or with bortezomib (RB-CHOP group; experimental; 1·3 mg/m2 intravenously or 1·6 mg/m2 subcutaneously) on days 1 and 8 for cycles two to six. If RNA extracted from the diagnostic tissues was of insufficient quality or quantity, participants were given R-CHOP as per the control group. The primary endpoint was 30-month progression-free survival, for the germinal centre and activated B-cell population. The primary analysis was on the modified intention-to-treat population of activated and germinal centre B-cell population. Safety was assessed in all participants who were given at least one dose of study drug. We report the progression-free survival and safety outcomes for patients in the follow-up phase after the required number of events occurred. This study was registered at ClinicalTrials.gov, number NCT01324596, and recruitment and treatment has completed for all participants, with long-term follow-up ongoing. FINDINGS Between June 2, 2011, and June 10, 2015, 1128 eligible patients were registered, of whom 918 (81%) were randomly assigned to receive treatment (n=459 to R-CHOP, n=459 to RB-CHOP), comprising 244 (26·6%) with activated B-cell disease, 475 (51·7%) with germinal centre B cell disease, and 199 (21·7%) with unclassified disease. At a median follow-up of 29·7 months (95% CI 29·0-32·0), we saw no evidence for a difference in progression-free survival in the combined germinal centre and activated B-cell population between R-CHOP and RB-CHOP (30-month progression-free survival 70·1%, 95% CI 65·0-74·7 vs 74·3%, 69·3-78·7; hazard ratio 0·86, 95% CI 0·65-1·13; p=0·28). The most common grade 3 or worse adverse event was haematological toxicity, reported in 178 (39·8%) of 447 patients given R-CHOP and 187 (42·1%) of 444 given RB-CHOP. However, RB-CHOP was not associated with increased haematological toxicity and 398 [87·1%] of 459 participants assigned to receive RB-CHOP completed six cycles of treatment. Grade 3 or worse neuropathy occurred in 17 (3·8%) patients given RB-CHOP versus eight (1·8%) given R-CHOP. Serious adverse events occurred in 190 (42·5%) patients given R-CHOP, including five treatment-related deaths, and 223 (50·2%) given RB-CHOP, including four treatment-related deaths. INTERPRETATION This is the first large-scale study in diffuse large B-cell lymphoma to use real-time molecular characterisation for prospective stratification, randomisation, and subsequent analysis of biologically distinct subgroups of patients. The addition of bortezomib did not improve progression-free survival. FUNDING Janssen-Cilag, Bloodwise, and Cancer Research UK.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Biomarkers, Tumor/genetics
- Bortezomib/administration & dosage
- Bortezomib/adverse effects
- Cyclophosphamide/administration & dosage
- Cyclophosphamide/adverse effects
- Disease Progression
- Doxorubicin/administration & dosage
- Doxorubicin/adverse effects
- Female
- Gene Expression Profiling
- Humans
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/mortality
- Male
- Middle Aged
- Prednisone/administration & dosage
- Prednisone/adverse effects
- Progression-Free Survival
- Proteasome Inhibitors/administration & dosage
- Proteasome Inhibitors/adverse effects
- Rituximab/administration & dosage
- Rituximab/adverse effects
- Switzerland
- Time Factors
- Transcriptome
- United Kingdom
- Vincristine/administration & dosage
- Vincristine/adverse effects
- Young Adult
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Affiliation(s)
- Andrew Davies
- Cancer Research UK Centre, University of Southampton, Southampton, UK; Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Thomas E Cummin
- Cancer Research UK Centre, University of Southampton, Southampton, UK; Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, UK
| | - Tom Maishman
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | - Urban Novak
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Josh Caddy
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Louise Stanton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | - Andrew McMillan
- Department of Haematology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Paul Fields
- Department of Haematology, Guy's and St Thomas' Hospitals NHS Trust, Kings Health Partners, London, UK
| | - Christopher Pocock
- Department of Haematology, East Kent Hospitals University Foundation Trust, Canterbury, UK
| | - Graham P Collins
- Oxford Cancer and Haematology Centre, Churchill Hospital, Oxford, UK
| | | | - Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Chulin Sha
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, UK; Section of Experimental Haematology, University of Leeds, Leeds, UK
| | - Matthew A Care
- Section of Experimental Haematology, University of Leeds, Leeds, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, UK
| | - Peter W M Johnson
- Cancer Research UK Centre, University of Southampton, Southampton, UK.
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29
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Kane E, Painter D, Smith A, Crouch S, Oliver S, Patmore R, Roman E. The impact of rheumatological disorders on lymphomas and myeloma: a report on risk and survival from the UK's population-based Haematological Malignancy Research Network. Cancer Epidemiol 2019; 59:236-243. [PMID: 30844679 PMCID: PMC6452783 DOI: 10.1016/j.canep.2019.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/05/2019] [Accepted: 02/09/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Autoimmune inflammatory disease increases the risk of diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL), but findings for other mature B-cell malignancies are equivocal. Furthermore, it has been suggested that the increase in DLBCL is due to the activated B-cell (ABC) subtype; but data on this, and the impact of inflammatory co-morbidities on survival, are sparse and contradictory. METHODS Data are from an established UK population-based cohort. Patients (n = 6834) diagnosed between 01/2009 and 08/2015 are included; DLBCL (n = 1771), myeloma (n = 1760), chronic lymphocytic leukaemia (CLL, n = 1580), MZL (n = 936), and follicular lymphoma (FL, n = 787). Information on rheumatological disorders and deaths was obtained by record-linkage to nationally compiled Hospital Episode Statistics, with age-and sex-matched individuals (n = 68,340) from the same catchment population (˜4 million people) providing the comparator. RESULTS Significantly increased risks for DLBCL (OR = 2.3, 95% CI 1.8-2.8) and MZL (OR = 2.0, 95% CI 1.5-2.7) were found for those with rheumatological disorders; the site distribution of those with/without rheumatological conditions differing for DLBCL (p = 0.007) and MZL (p = 0.002). No increases in risk were observed for the remaining mature B-cell malignancies, and no associations with survival were detected for DLBCL (age-adjusted HR = 1.2, 95% CI 0.9-1.6) or MZL (age-adjusted HR = 1.0, 95% CI 0.6-1.9). Furthermore, whilst our findings provide evidence for an association with rheumatological disease severity for DLBCL, they offer little support for the notion that the association is driven by an increase in the incidence of the ABC subtype. CONCLUSION Our findings support the hypothesis that the chronic activation and proliferation of specific B-cell populations which characterize autoimmune disease increase the potential for the lymphomagenic events that lead to DLBCL and MZL in both males and females; but have no impact on the development of CLL, FL or MM, or on survival.
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MESH Headings
- Aged
- Aged, 80 and over
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell
- Lymphoma/epidemiology
- Lymphoma/mortality
- Lymphoma/pathology
- Lymphoma, B-Cell, Marginal Zone/epidemiology
- Lymphoma, B-Cell, Marginal Zone/mortality
- Lymphoma, Follicular/epidemiology
- Lymphoma, Follicular/mortality
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/epidemiology
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Multiple Myeloma/epidemiology
- Multiple Myeloma/mortality
- Multiple Myeloma/pathology
- Rheumatic Diseases/epidemiology
- Rheumatic Diseases/mortality
- Rheumatic Diseases/pathology
- United Kingdom/epidemiology
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Affiliation(s)
- Eleanor Kane
- Department of Health Sciences, University of York, York, UK.
| | - Daniel Painter
- Department of Health Sciences, University of York, York, UK
| | | | - Simon Crouch
- Department of Health Sciences, University of York, York, UK
| | - Steven Oliver
- Department of Health Sciences, University of York, York, UK; Hull York Medical School, York, UK
| | | | - Eve Roman
- Department of Health Sciences, University of York, York, UK
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30
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Sha C, Barrans S, Cucco F, Bentley MA, Care MA, Cummin T, Kennedy H, Thompson JS, Uddin R, Worrillow L, Chalkley R, van Hoppe M, Ahmed S, Maishman T, Caddy J, Schuh A, Mamot C, Burton C, Tooze R, Davies A, Du MQ, Johnson PW, Westhead DR. Molecular High-Grade B-Cell Lymphoma: Defining a Poor-Risk Group That Requires Different Approaches to Therapy. J Clin Oncol 2019; 37:202-212. [PMID: 30523719 PMCID: PMC6338391 DOI: 10.1200/jco.18.01314] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Biologic heterogeneity is a feature of diffuse large B-cell lymphoma (DLBCL), and the existence of a subgroup with poor prognosis and phenotypic proximity to Burkitt lymphoma is well known. Conventional cytogenetics identifies some patients with rearrangements of MYC and BCL2 and/or BCL6 (double-hit lymphomas) who are increasingly treated with more intensive chemotherapy, but a more biologically coherent and clinically useful definition of this group is required. PATIENTS AND METHODS We defined a molecular high-grade (MHG) group by applying a gene expression-based classifier to 928 patients with DLBCL from a clinical trial that investigated the addition of bortezomib to standard rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) therapy. The prognostic significance of MHG was compared with existing biomarkers. We performed targeted sequencing of 70 genes in 400 patients and explored molecular pathology using gene expression signature databases. Findings were validated in an independent data set. RESULTS The MHG group comprised 83 patients (9%), with 75 in the cell-of-origin germinal center B-cell-like group. MYC rearranged and double-hit groups were strongly over-represented in MHG but comprised only one half of the total. Gene expression analysis revealed a proliferative phenotype with a relationship to centroblasts. Progression-free survival rate at 36 months after R-CHOP in the MHG group was 37% (95% CI, 24% to 55%) compared with 72% (95% CI, 68% to 77%) for others, and an analysis of treatment effects suggested a possible positive effect of bortezomib. Double-hit lymphomas lacking the MHG signature showed no evidence of worse outcome than other germinal center B-cell-like cases. CONCLUSION MHG defines a biologically coherent high-grade B-cell lymphoma group with distinct molecular features and clinical outcomes that effectively doubles the size of the poor-prognosis, double-hit group. Patients with MHG may benefit from intensified chemotherapy or novel targeted therapies.
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MESH Headings
- Antibodies, Monoclonal, Murine-Derived/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Bortezomib/administration & dosage
- Cyclophosphamide/administration & dosage
- Databases, Genetic
- Doxorubicin/administration & dosage
- Female
- Humans
- 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
- Neoplasm Grading
- Prednisone/administration & dosage
- Proportional Hazards Models
- Randomized Controlled Trials as Topic
- Retrospective Studies
- Rituximab/administration & dosage
- Transcriptome
- Vincristine/administration & dosage
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Affiliation(s)
- Chulin Sha
- University of Leeds, Leeds, United Kingdom
| | | | | | | | | | - Thomas Cummin
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | | | | | | | | | | | | | | | - Tom Maishman
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Josh Caddy
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Anna Schuh
- University of Oxford, Oxford, United Kingdom
| | - Christoph Mamot
- Cantonal Hospital Aarau, Aarau/Swiss Group for Clinical Cancer Research, Switzerland
| | | | | | - Andrew Davies
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
| | - Ming-Qing Du
- University of Cambridge, Cambridge, United Kingdom
| | - Peter W.M. Johnson
- Cancer Research UK Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, United Kingdom
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31
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Painter D, Barrans S, Lacy S, Smith A, Crouch S, Westhead D, Sha C, Patmore R, Tooze R, Burton C, Roman E. Cell-of-origin in diffuse large B-cell lymphoma: findings from the UK's population-based Haematological Malignancy Research Network. Br J Haematol 2018; 185:781-784. [PMID: 30408148 DOI: 10.1111/bjh.15619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Daniel Painter
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Stuart Lacy
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Alexandra Smith
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Simon Crouch
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - David Westhead
- Bioinfomatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Chulin Sha
- Bioinfomatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Russell Patmore
- Queen's Centre for Oncology and Haematology, Hull and East Yorkshire Hospitals, Cottingham, UK
| | - Reuben Tooze
- Section of Experimental Haematology, University of Leeds, Leeds, UK
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Eve Roman
- Epidemiology & Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
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32
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Al-Maskari M, Care MA, Robinson E, Cocco M, Tooze RM, Doody GM. Site-1 protease function is essential for the generation of antibody secreting cells and reprogramming for secretory activity. Sci Rep 2018; 8:14338. [PMID: 30254311 PMCID: PMC6156501 DOI: 10.1038/s41598-018-32705-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/11/2018] [Indexed: 01/08/2023] Open
Abstract
The unfolded protein response (UPR) and activation of XBP1 is necessary for high secretory efficiency and functional differentiation of antibody secreting cells (ASCs). The UPR additionally includes a branch in which membrane-bound transcription factors, exemplified by ATF6, undergo intramembrane-proteolysis by the sequential action of site-1 (MBTPS1/S1P) and site-2 proteases (MBTPS2/S2P) and release of the cytoplasmic domain as an active transcription factor. Such regulation is shared with a family of CREB3-related transcription factors and sterol regulatory element-binding proteins (SREBPs). Of these, we identify that the CREB3 family member CREB3L2 is strongly induced and activated during the transition from B-cell to plasma cell state. Inhibition of site-1 protease leads to a profound reduction in plasmablast number linked to induction of autophagy. Plasmablasts generated in the presence of site-1 protease inhibitor segregated into CD38high and CD38low populations, the latter characterized by a marked reduction in the capacity to secrete IgG. Site-1 protease inhibition is accompanied by a distinctive change in gene expression associated with amino acid, steroid and fatty acid synthesis pathways. These results demonstrate that transcriptional control of metabolic programs necessary for secretory activity can be targeted via site-1 protease inhibition during ASC differentiation.
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Affiliation(s)
- Muna Al-Maskari
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Matthew A Care
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Emily Robinson
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Mario Cocco
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Gina M Doody
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom.
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33
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Zhu C, Chen G, Zhao Y, Gao XM, Wang J. Regulation of the Development and Function of B Cells by ZBTB Transcription Factors. Front Immunol 2018; 9:580. [PMID: 29616049 PMCID: PMC5869932 DOI: 10.3389/fimmu.2018.00580] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/07/2018] [Indexed: 12/20/2022] Open
Abstract
The large ZBTB family comprises a diverse group of transcriptional factors. Several ZBTB proteins have emerged as critical factors that regulate the lineage commitment, differentiation, and function of lymphoid cells as well as many other developmental events. For instance, dysfunctions of ZBTB20 or ZBTB24 have been linked to multisystem failures in humans. Within the B-cell lineage, BCL6, ZBTB7A, ZBTB17, and ZBTB1 regulate the development/differentiation of B cells in both bone marrow and peripheral lymphoid organs, while ZBTB20 and ZBTB32 seem to mainly impact the maintenance of terminal plasma cells. Given the importance of B cells in the prevention and treatment of infectious or autoimmune disorders, we herein summarize the roles of seven ZBTB family members (BCL6, ZBTB7A, ZBTB17, ZBTB20, ZBTB32, ZBTB1, and ZBTB24) in the development, differentiation, and function of B cells as well as the underlying molecular mechanisms.
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Affiliation(s)
- Can Zhu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ge Chen
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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34
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Guo L, Lin P, Xiong H, Tu S, Chen G. Molecular heterogeneity in diffuse large B-cell lymphoma and its implications in clinical diagnosis and treatment. Biochim Biophys Acta Rev Cancer 2018; 1869:85-96. [PMID: 29337112 DOI: 10.1016/j.bbcan.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over half of patients with diffuse large B-cell lymphoma (DLBCL) can be cured by standard R-CHOP treatment (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone). However, the remaining patients are refractory and ultimately succumb to progressive or relapsed disease. During the past decade, there has been significant progress in the understanding of molecular mechanisms in DLBCL, largely owing to collaborative efforts in large-scale gene expression profiling and deep sequencing, which have identified genetic alterations critical in lymphomagenesis through activation of key signaling transduction pathways in DLBCL. These discoveries have not only led to the development of targeted therapies, including several currently in clinical trials, but also laid a solid foundation for the future identification of more effective therapies for patients not curable by R-CHOP. This review summarizes the recent advances in our understanding of the molecular characterization and pathogenesis of DLBCL and new treatment directions.
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Affiliation(s)
- Lingchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, Jiangsu 215000, China.
| | - Pei Lin
- Department of Hematopathology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 72, Houston, TX 77030, USA.
| | - Hui Xiong
- Shanghai Righton Biotechnology Co., Ltd, 1698 Wangyuan Road, Building 12, Fengxian District, Shanghai 201403, China.
| | - Shichun Tu
- Shanghai Righton Biotechnology Co., Ltd, 1698 Wangyuan Road, Building 12, Fengxian District, Shanghai 201403, China; Scintillon Institute for Biomedical and Bioenergy Research, 6888 Nancy Ridge Dr., San Diego, CA 92121, USA; Allele Biotechnology & Pharmaceuticals, Inc., 6404 Nancy Ridge Drive, San Diego, CA 92121, USA.
| | - Gang Chen
- Department of Pathology of Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China.
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35
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Loo SK, Ch'ng ES, Md Salleh MS, Banham AH, Pedersen LM, Møller MB, Green TM, Wong KK. TRPM4 expression is associated with activated B cell subtype and poor survival in diffuse large B cell lymphoma. Histopathology 2017; 71:98-111. [DOI: 10.1111/his.13204] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Suet K Loo
- Department of Immunology; School of Medical Sciences; Universiti Sains Malaysia; Kelantan Malaysia
| | - Ewe S Ch'ng
- Advanced Medical and Dental Institute; Universiti Sains Malaysia; Bertam Malaysia
| | - Md Salzihan Md Salleh
- Department of Pathology; School of Medical Sciences; Universiti Sains Malaysia; Kelantan Malaysia
| | - Alison H Banham
- Nuffield Division of Clinical Laboratory Sciences; Radcliffe Department of Medicine; University of Oxford; John Radcliffe Hospital; Oxford UK
| | - Lars M Pedersen
- Department of Haematology; Herlev University Hospital; Copenhagen Denmark
| | - Michael B Møller
- Department of Pathology; Odense University Hospital; Odense Denmark
| | - Tina M Green
- Department of Pathology; Odense University Hospital; Odense Denmark
| | - Kah K Wong
- Department of Immunology; School of Medical Sciences; Universiti Sains Malaysia; Kelantan Malaysia
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36
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Abstract
Diffuse large B-cell lymphoma (DLBCL) is the commonest aggressive non-Hodgkin lymphoma with approximately 5,000 cases annually in the UK. The R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone) regimen has become the international standard of care with cure rates of around 75% and despite extensive studies aimed at improving the outcomes, R-CHOP has not been superseded. Those patients that do not respond to R-CHOP have a poor outlook. DLBCL is a disease with marked molecular heterogeneity; advances in gene expression profiling and mutational analysis can be used to increase our understanding of the disease and identify new therapeutic targets. Precision medicine using new agents, including small molecule inhibitors, is now being investigated for DLBCL. Progress in this disease is likely to come by targeting heterogeneous subtypes through novel combinations. Where R-CHOP fails, we hope that these new approaches can succeed by providing personalised medicine using precision diagnostics to guide new treatment paradigms.
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37
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Cummin T, Johnson P. Lymphoma: turning biology into cures. Clin Med (Lond) 2016; 16. [PMID: 27956453 PMCID: PMC6329566 DOI: 10.7861/clinmedicine.16-6s-s125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the commonest aggressive non-Hodgkin lymphoma with approximately 5,000 cases annually in the UK. The R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone) regimen has become the international standard of care with cure rates of around 75% and despite extensive studies aimed at improving the outcomes, R-CHOP has not been superseded. Those patients that do not respond to R-CHOP have a poor outlook. DLBCL is a disease with marked molecular heterogeneity; advances in gene expression profiling and mutational analysis can be used to increase our understanding of the disease and identify new therapeutic targets. Precision medicine using new agents, including small molecule inhibitors, is now being investigated for DLBCL. Progress in this disease is likely to come by targeting heterogeneous subtypes through novel combinations. Where R-CHOP fails, we hope that these new approaches can succeed by providing personalised medicine using precision diagnostics to guide new treatment paradigms.
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Affiliation(s)
- Thomas Cummin
- AUniversity of Southampton, Southampton, UK,Address for correspondence: Dr T Cummin, Somers Cancer Research Building MP824, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
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Falgreen S, Ellern Bilgrau A, Brøndum RF, Hjort Jakobsen L, Have J, Lindblad Nielsen K, El-Galaly TC, Bødker JS, Schmitz A, H. Young K, Johnsen HE, Dybkær K, Bøgsted M. hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PLoS One 2016; 11:e0163711. [PMID: 27701436 PMCID: PMC5049784 DOI: 10.1371/journal.pone.0163711] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background Dozens of omics based cancer classification systems have been introduced with prognostic, diagnostic, and predictive capabilities. However, they often employ complex algorithms and are only applicable on whole cohorts of patients, making them difficult to apply in a personalized clinical setting. Results This prompted us to create hemaClass.org, an online web application providing an easy interface to one-by-one RMA normalization of microarrays and subsequent risk classifications of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin and chemotherapeutic sensitivity classes. Classification results for one-by-one array pre-processing with and without a laboratory specific RMA reference dataset were compared to cohort based classifiers in 4 publicly available datasets. Classifications showed high agreement between one-by-one and whole cohort pre-processsed data when a laboratory specific reference set was supplied. The website is essentially the R-package hemaClass accompanied by a Shiny web application. The well-documented package can be used to run the website locally or to use the developed methods programmatically. Conclusions The website and R-package is relevant for biological and clinical lymphoma researchers using affymetrix U-133 Plus 2 arrays, as it provides reliable and swift methods for calculation of disease subclasses. The proposed one-by-one pre-processing method is relevant for all researchers using microarrays.
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Affiliation(s)
- Steffen Falgreen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Anders Ellern Bilgrau
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Lasse Hjort Jakobsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Jonas Have
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Kasper Lindblad Nielsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Ken H. Young
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- * E-mail:
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Araf S, Korfi K, Rahim T, Davies A, Fitzgibbon J. Advances in the molecular diagnosis of diffuse large B-cell lymphoma in the era of precision medicine. Expert Rev Mol Diagn 2016; 16:1093-1102. [PMID: 27648481 DOI: 10.1080/14737159.2016.1235974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The adoption of high-throughput technologies has led to a transformation in our ability to classify diffuse large B-cell lymphoma (DLBCL) into unique molecular subtypes. In parallel, the expansion of agents targeting key genetic and gene expression signatures has led to an unprecedented opportunity to personalize cancer therapies, paving the way for precision medicine. Areas covered: This review summarizes the key molecular subtypes of DLBCL and outlines the novel technology platforms in development to discriminate clinically relevant subtypes. Expert commentary: The application of emerging diagnostic tests into routine clinical practise is gaining momentum following the demonstration of subtype specific activity by novel agents. Co-ordinated efforts are required to ensure that these state of the art technologies provide reliable and clinically meaningful results accessible to the wider haematology community.
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MESH Headings
- Biomarkers, Tumor
- Gene Expression
- Genes, bcl-2
- Genes, myc
- High-Throughput Nucleotide Sequencing
- Humans
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/therapy
- Molecular Diagnostic Techniques
- Mutation
- Precision Medicine/methods
- Prognosis
- Transcriptome
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Affiliation(s)
- Shamzah Araf
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Koorosh Korfi
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Tahrima Rahim
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Andrew Davies
- b Cancer Sciences Unit, Faculty of Medicine , University of Southampton , Southampton , UK
| | - Jude Fitzgibbon
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
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Jash A, Wang Y, Weisel FJ, Scharer CD, Boss JM, Shlomchik MJ, Bhattacharya D. ZBTB32 Restricts the Duration of Memory B Cell Recall Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 197:1159-68. [PMID: 27357154 PMCID: PMC4975986 DOI: 10.4049/jimmunol.1600882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/06/2016] [Indexed: 11/19/2022]
Abstract
Memory B cell responses are more rapid and of greater magnitude than are primary Ab responses. The mechanisms by which these secondary responses are eventually attenuated remain unknown. We demonstrate that the transcription factor ZBTB32 limits the rapidity and duration of Ab recall responses. ZBTB32 is highly expressed by mouse and human memory B cells but not by their naive counterparts. Zbtb32(-/-) mice mount normal primary Ab responses to T-dependent Ags. However, Zbtb32(-/-) memory B cell-mediated recall responses occur more rapidly and persist longer than do control responses. Microarray analyses demonstrate that Zbtb32(-/-) secondary bone marrow plasma cells display elevated expression of genes that promote cell cycle progression and mitochondrial function relative to wild-type controls. BrdU labeling and adoptive transfer experiments confirm more rapid production and a cell-intrinsic survival advantage of Zbtb32(-/-) secondary plasma cells relative to wild-type counterparts. ZBTB32 is therefore a novel negative regulator of Ab recall responses.
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Affiliation(s)
- Arijita Jash
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Yinan Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Florian J Weisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Christopher D Scharer
- Department of Microbiology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
| | - Jeremy M Boss
- Department of Microbiology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Deepta Bhattacharya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
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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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Scott DW. Cell-of-Origin in Diffuse Large B-Cell Lymphoma: Are the Assays Ready for the Clinic? Am Soc Clin Oncol Educ Book 2016:e458-66. [PMID: 25993210 DOI: 10.14694/edbook_am.2015.35.e458] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma worldwide and consists of a heterogeneous group of cancers classified together on the basis of shared morphology, immunophenotype, and aggressive clinical behavior. It is now recognized that this malignancy comprises at least two distinct molecular subtypes identified by gene expression profiling: the activated B-cell-like (ABC) and the germinal center B-cell-like (GCB) groups-the cell-of-origin (COO) classification. These two groups have different genetic mutation landscapes, pathobiology, and outcomes following treatment. Evidence is accumulating that novel agents have selective activity in one or the other COO group, making COO a predictive biomarker. Thus, there is now a pressing need for accurate and robust methods to assign COO, to support clinical trials, and ultimately guide treatment decisions for patients. The "gold standard" methods for COO are based on gene expression profiling (GEP) of RNA from fresh frozen tissue using microarray technology, which is an impractical solution when formalin-fixed paraffin-embedded tissue (FFPET) biopsies are the standard diagnostic material. This review outlines the history of the COO classification before examining the practical implementation of COO assays applicable to FFPET biopsies. The immunohistochemistry (IHC)-based algorithms and gene expression-based assays suitable for the highly degraded RNA from FFPET are discussed. Finally, the technical and practical challenges that still need to be addressed are outlined before robust gene expression-based assays are used in the routine management of patients with DLBCL.
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Affiliation(s)
- David W Scott
- From the Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1. Proc Natl Acad Sci U S A 2016; 113:E577-86. [PMID: 26787899 DOI: 10.1073/pnas.1524677113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High expression of the forkhead box P1 (FOXP1) transcription factor distinguishes the aggressive activated B cell (ABC) diffuse large B-cell lymphoma (DLBCL) subtype from the better prognosis germinal center B-cell (GCB)-DLBCL subtype and is highly correlated with poor outcomes. A genetic or functional role for FOXP1 in lymphomagenesis, however, remains unknown. Here, we report that sustained FOXP1 expression is vital for ABC-DLBCL cell-line survival. Genome-wide analyses revealed direct and indirect FOXP1 transcriptional enforcement of ABC-DLBCL hallmarks, including the classical NF-κB and MYD88 (myeloid differentiation primary response gene 88) pathways. FOXP1 promoted gene expression underlying transition of the GCB cell to the plasmablast--the transient B-cell stage targeted in ABC-DLBCL transformation--by antagonizing pathways distinctive of GCB-DLBCL, including that of the GCB "master regulator," BCL6 (B-cell lymphoma 6). Cell-line derived FOXP1 target genes that were highly correlated with FOXP1 expression in primary DLBCL accurately segregated the corresponding clinical subtypes of a large cohort of primary DLBCL isolates and identified conserved pathways associated with ABC-DLBCL pathology.
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Kreuz S, Holmes KB, Tooze RM, Lefevre PF. Loss of PIM2 enhances the anti-proliferative effect of the pan-PIM kinase inhibitor AZD1208 in non-Hodgkin lymphomas. Mol Cancer 2015; 14:205. [PMID: 26643319 PMCID: PMC4672512 DOI: 10.1186/s12943-015-0477-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Background A promising therapeutic approach for aggressive B-cell Non-Hodgkin lymphoma (NHL), including diffuse large B-cell lymphoma (DLBCL), and Burkitt lymphoma (BL) is to target kinases involved in signal transduction and gene regulation. PIM1/2 serine/threonine kinases are highly expressed in activated B-cell-like DLBCL (ABC-DLBCL) with poor prognosis. In addition, both PIM kinases have a reported synergistic effect with c-MYC in mediating tumour development in several cancers, c-MYC gene being translocated to one of the immunoglobulin loci in nearly all BLs. Methods For these reasons, we tested the efficiency of several PIM kinase inhibitors (AZD1208, SMI4a, PIM1/2 inhibitor VI and Quercetagetin) in preventing proliferation of aggressive NHL-derived cell lines and compared their efficiency with PIM1 and/or PIM2 knockdown. Results We observed that most of the anti-proliferative potential of these inhibitors in NHL was due to an off-target effect. Interestingly, we present evidence of a kinase-independent function of PIM2 in regulating cell cycle. Moreover, combining AZD1208 treatment and PIM2 knockdown additively repressed cell proliferation. Conclusion Taken together, this study suggests that at least a part of PIM1/2 oncogenic potential could be independent of their kinase activity, justifying the limited anti-tumorigenic outcome of PIM-kinase inhibitors in NHL. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0477-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- S Kreuz
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - K B Holmes
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - R M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - P F Lefevre
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
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Wong KK, Ch'ng ES, Loo SK, Husin A, Muruzabal MA, Møller MB, Pedersen LM, Pomposo MP, Gaafar A, Banham AH, Green TM, Lawrie CH. Low HIP1R mRNA and protein expression are associated with worse survival in diffuse large B-cell lymphoma patients treated with R-CHOP. Exp Mol Pathol 2015; 99:537-45. [DOI: 10.1016/j.yexmp.2015.08.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
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46
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Dias LM, Thodima V, Friedman J, Ma C, Guttapalli A, Mendiratta G, Siddiqi IN, Syrbu S, Chaganti RSK, Houldsworth J. Cross-platform assessment of genomic imbalance confirms the clinical relevance of genomic complexity and reveals loci with potential pathogenic roles in diffuse large B-cell lymphoma. Leuk Lymphoma 2015; 57:899-908. [PMID: 26294112 DOI: 10.3109/10428194.2015.1080364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genomic copy number alterations (CNAs) in diffuse large B-cell lymphoma (DLBCL) have roles in disease pathogenesis, but overall clinical relevance remains unclear. Herein, an unbiased algorithm was uniformly applied across three genome profiling datasets comprising 392 newly-diagnosed DLBCL specimens that defined 32 overlapping CNAs, involving 36 minimal common regions (MCRs). Scoring criteria were established for 50 aberrations within the MCRs while considering peak gains/losses. Application of these criteria to independent datasets revealed novel candidate genes with coordinated expression, such as CNOT2, potentially with pathogenic roles. No one single aberration significantly associated with patient outcome across datasets, but genomic complexity, defined by imbalance in more than one MCR, significantly portended adverse outcome in two of three independent datasets. Thus, the standardized scoring of CNAs currently developed can be uniformly applied across platforms, affording robust validation of genomic imbalance and complexity in DLBCL and overall clinical utility as biomarkers of patient outcome.
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Affiliation(s)
| | | | | | - Charles Ma
- a Cancer Genetics, Inc. , Rutherford , NJ , USA
| | | | | | - Imran N Siddiqi
- b Hematopathology Section , University of Southern California Keck School of Medicine , CA , USA
| | - Sergei Syrbu
- c Department of Pathology, Carver College of Medicine , University of Iowa , Iowa City , IA , USA
| | - R S K Chaganti
- d Cell Biology Program , Memorial Sloan-Kettering Cancer Center , New York , NY , USA ;,e Department of Medicine , Memorial Sloan-Kettering Cancer Center , New York , NY , USA
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Care MA, Westhead DR, Tooze RM. Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma. Genome Med 2015; 7:96. [PMID: 26362649 PMCID: PMC4566848 DOI: 10.1186/s13073-015-0218-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Cancers adapt to immune-surveillance through evasion. Immune responses against carcinoma and melanoma converge on cytotoxic effectors and IFNγ-STAT1-IRF1 signalling. Local IFN-driven immune checkpoint expression can mediate feedback inhibition and adaptive immune resistance. Whether such coupled immune polarization and adaptive resistance is generalisable to lymphoid malignancies is incompletely defined. The host response in diffuse large B-cell lymphoma (DLBCL), the commonest aggressive lymphoid malignancy, provides an empirical model. METHODS Using ten publicly available gene expression data sets encompassing 2030 cases we explore the nature of host response in DLBCL. Starting from the "cell of origin" paradigm for DLBCL classification, we use the consistency of differential expression to define polarized patterns of immune response genes in DLBCL, and derive a linear classifier of immune response gene expression. We validate and extend the results in an approach independent of "cell of origin" classification based on gene expression correlations across all data sets. RESULTS T-cell and cytotoxic gene expression with polarization along the IFNγ-STAT1-IRF1 axis provides a defining feature of the immune response in DLBCL. This response is associated with improved outcome, particularly in the germinal centre B-cell subsets of DLBCL. Analysis of gene correlations across all data sets, independent of "cell of origin" class, demonstrates a consistent association with a hierarchy of immune-regulatory gene expression that places IDO1, LAG3 and FGL2 ahead of PD1-ligands CD274 and PDCD1LG2. CONCLUSION Immune responses in DLBCL converge onto the IFNγ-STAT1-IRF1 axis and link to diverse potential mediators of adaptive immune resistance identifying future therapeutic targets.
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Affiliation(s)
- Matthew A Care
- Section of Experimental Haematology, Wellcome Trust Brenner Building, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - David R Westhead
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Reuben M Tooze
- Section of Experimental Haematology, Wellcome Trust Brenner Building, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.
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Sha C, Barrans S, Care MA, Cunningham D, Tooze RM, Jack A, Westhead DR. Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas. Genome Med 2015; 7:64. [PMID: 26207141 PMCID: PMC4512160 DOI: 10.1186/s13073-015-0187-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases where traditional diagnosis is difficult. Transfer of these research classifiers into a clinical setting is challenging because there are competing classifiers in the literature based on different methodology and gene sets with no clear best choice; classifiers based on one expression measurement platform may not transfer effectively to another; and, classifiers developed using fresh frozen samples may not work effectively with the commonly used and more convenient formalin fixed paraffin-embedded samples used in routine diagnosis. METHODS Here we thoroughly compared two published high profile classifiers developed on data from different Affymetrix array platforms and fresh-frozen tissue, examining their transferability and concordance. Based on this analysis, a new Burkitt and diffuse large B cell lymphoma classifier (BDC) was developed and employed on Illumina DASL data from our own paraffin-embedded samples, allowing comparison with the diagnosis made in a central haematopathology laboratory and evaluation of clinical relevance. RESULTS We show that both previous classifiers can be recapitulated using very much smaller gene sets than originally employed, and that the classification result is closely dependent on the Burkitt lymphoma criteria applied in the training set. The BDC classification on our data exhibits high agreement (~95 %) with the original diagnosis. A simple outcome comparison in the patients presenting intermediate features on conventional criteria suggests that the cases classified as Burkitt lymphoma by BDC have worse response to standard diffuse large B cell lymphoma treatment than those classified as diffuse large B cell lymphoma. CONCLUSIONS In this study, we comprehensively investigate two previous Burkitt lymphoma molecular classifiers, and implement a new gene expression classifier, BDC, that works effectively on paraffin-embedded samples and provides useful information for treatment decisions. The classifier is available as a free software package under the GNU public licence within the R statistical software environment through the link http://www.bioinformatics.leeds.ac.uk/labpages/softwares/ or on github https://github.com/Sharlene/BDC.
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Affiliation(s)
- Chulin Sha
- />School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, LS2 9JT UK
| | - Sharon Barrans
- />Haematological, Malignancy Diagnostic Service, St James’s University Hospital, Leeds, UK
| | - Matthew A. Care
- />Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | - Reuben M. Tooze
- />Haematological, Malignancy Diagnostic Service, St James’s University Hospital, Leeds, UK
- />Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Andrew Jack
- />Haematological, Malignancy Diagnostic Service, St James’s University Hospital, Leeds, UK
| | - David R. Westhead
- />School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, LS2 9JT UK
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Clipson A, Barrans S, Zeng N, Crouch S, Grigoropoulos NF, Liu H, Kocialkowski S, Wang M, Huang Y, Worrillow L, Goodlad J, Buxton J, Neat M, Fields P, Wilkins B, Grant JW, Wright P, Ei-Daly H, Follows GA, Roman E, Watkins AJ, Johnson PWM, Jack A, Du MQ. The prognosis of MYC translocation positive diffuse large B-cell lymphoma depends on the second hit. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2015; 1:125-133. [PMID: 27347428 PMCID: PMC4915334 DOI: 10.1002/cjp2.10] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/23/2014] [Indexed: 12/14/2022]
Abstract
A proportion of MYC translocation positive diffuse large B‐cell lymphomas (DLBCL) harbour a BCL2 and/or BCL6 translocation, known as double‐hit DLBCL, and are clinically aggressive. It is unknown whether there are other genetic abnormalities that cooperate with MYC translocation and form double‐hit DLBCL, and whether there is a difference in clinical outcome between the double‐hit DLBCL and those with an isolated MYC translocation. We investigated TP53 gene mutations along with BCL2 and BCL6 translocations in a total of 234 cases of DLBCL, including 81 with MYC translocation. TP53 mutations were investigated by PCR and sequencing, while BCL2 and BCL6 translocation was studied by interphase fluorescence in situ hybridization. The majority of MYC translocation positive DLBCLs (60/81 = 74%) had at least one additional genetic hit. In MYC translocation positive DLBCL treated by R‐CHOP (n = 67), TP53 mutation and BCL2, but not BCL6 translocation had an adverse effect on patient overall survival. In comparison with DLBCL with an isolated MYC translocation, cases with MYC/TP53 double‐hits had the worst overall survival, followed by those with MYC/BCL2 double‐hits. In MYC translocation negative DLBCL treated by R‐CHOP (n = 101), TP53 mutation, BCL2 and BCL6 translocation had no impact on patient survival. The prognosis of MYC translocation positive DLBCL critically depends on the second hit, with TP53 mutations and BCL2 translocation contributing to an adverse prognosis. It is pivotal to investigate both TP53 mutations and BCL2 translocations in MYC translocation positive DLBCL, and to distinguish double‐hit DLBCLs from those with an isolated MYC translocation.
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Affiliation(s)
- Alexandra Clipson
- Division of Molecular Histopathology Department of Pathology University of Cambridge UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service St. James's Institute of Oncology Leeds UK
| | - Naiyan Zeng
- Division of Molecular Histopathology Department of Pathology University of Cambridge UK
| | - Simon Crouch
- Department of Health Sciences Epidemiology and Cancer Statistics Group University of York York UK
| | - Nicholas F Grigoropoulos
- Division of Molecular HistopathologyDepartment of PathologyUniversity of CambridgeUK; Department of HaematologyAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Hongxiang Liu
- Department of Histopathology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Sylvia Kocialkowski
- Division of Molecular Histopathology Department of Pathology University of Cambridge UK
| | - Ming Wang
- Division of Molecular Histopathology Department of Pathology University of Cambridge UK
| | - Yuanxue Huang
- Division of Molecular Histopathology Department of Pathology University of Cambridge UK
| | - Lisa Worrillow
- Haematological Malignancy Diagnostic Service St. James's Institute of Oncology Leeds UK
| | - John Goodlad
- Department of Pathology Western General Hospital Edinburgh UK
| | - Jenny Buxton
- Department of Haematology Western General Hospital Edinburgh UK
| | - Michael Neat
- Department of Haematology and Department of Cytogenetics GSTS Pathology Guy's and St. Thomas NHS Foundation Trust London UK
| | - Paul Fields
- Department of Haematology GSST Kings Health Partners London UK
| | - Bridget Wilkins
- Histopathology Department St Thomas' Hospital and King's College London UK
| | - John W Grant
- Department of Histopathology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Penny Wright
- Department of Histopathology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Hesham Ei-Daly
- Department of Haematology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - George A Follows
- Department of Haematology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Eve Roman
- Department of Health Sciences Epidemiology and Cancer Statistics Group University of York York UK
| | - A James Watkins
- Department of Haematology Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Peter W M Johnson
- Cancer Research UK Centre University of Southampton Southampton United Kingdom
| | - Andrew Jack
- Haematological Malignancy Diagnostic Service St. James's Institute of Oncology Leeds UK
| | - Ming-Qing Du
- Division of Molecular HistopathologyDepartment of PathologyUniversity of CambridgeUK; Department of HistopathologyAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
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Dybkær K, Bøgsted M, Falgreen S, Bødker JS, Kjeldsen MK, Schmitz A, Bilgrau AE, Xu-Monette ZY, Li L, Bergkvist KS, Laursen MB, Rodrigo-Domingo M, Marques SC, Rasmussen SB, Nyegaard M, Gaihede M, Møller MB, Samworth RJ, Shah RD, Johansen P, El-Galaly TC, Young KH, Johnsen HE. Diffuse large B-cell lymphoma classification system that associates normal B-cell subset phenotypes with prognosis. J Clin Oncol 2015; 33:1379-88. [PMID: 25800755 DOI: 10.1200/jco.2014.57.7080] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Current diagnostic tests for diffuse large B-cell lymphoma use the updated WHO criteria based on biologic, morphologic, and clinical heterogeneity. We propose a refined classification system based on subset-specific B-cell-associated gene signatures (BAGS) in the normal B-cell hierarchy, hypothesizing that it can provide new biologic insight and diagnostic and prognostic value. PATIENTS AND METHODS We combined fluorescence-activated cell sorting, gene expression profiling, and statistical modeling to generate BAGS for naive, centrocyte, centroblast, memory, and plasmablast B cells from normal human tonsils. The impact of BAGS-assigned subtyping was analyzed using five clinical cohorts (treated with cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP], n = 270; treated with rituximab plus CHOP [R-CHOP], n = 869) gathered across geographic regions, time eras, and sampling methods. The analysis estimated subtype frequencies and drug-specific resistance and included a prognostic meta-analysis of patients treated with first-line R-CHOP therapy. RESULTS Similar BAGS subtype frequencies were assigned across 1,139 samples from five different cohorts. Among R-CHOP-treated patients, BAGS assignment was significantly associated with overall survival and progression-free survival within the germinal center B-cell-like subclass; the centrocyte subtype had a superior prognosis compared with the centroblast subtype. In agreement with the observed therapeutic outcome, centrocyte subtypes were estimated as being less resistant than the centroblast subtype to doxorubicin and vincristine. The centroblast subtype had a complex genotype, whereas the centrocyte subtype had high TP53 mutation and insertion/deletion frequencies and expressed LMO2, CD58, and stromal-1-signature and major histocompatibility complex class II-signature genes, which are known to have a positive impact on prognosis. CONCLUSION Further development of a diagnostic platform using BAGS-assigned subtypes may allow pathogenetic studies to improve disease management.
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Affiliation(s)
- Karen Dybkær
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Martin Bøgsted
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Steffen Falgreen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Julie S Bødker
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Malene K Kjeldsen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Alexander Schmitz
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Anders E Bilgrau
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Zijun Y Xu-Monette
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Ling Li
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Kim S Bergkvist
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Maria B Laursen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Maria Rodrigo-Domingo
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Sara C Marques
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Sophie B Rasmussen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Mette Nyegaard
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Michael Gaihede
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Michael B Møller
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Richard J Samworth
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Rajen D Shah
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Preben Johansen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Tarec C El-Galaly
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Ken H Young
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom
| | - Hans E Johnsen
- Karen Dybkær, Martin Bøgsted, Steffen Falgreen, Julie S. Bødker, Malene K. Kjeldsen, Alexander Schmitz, Anders E. Bilgrau, Kim S. Bergkvist, Maria B. Laursen, Maria Rodrigo-Domingo, Sara C. Marques, Sophie B. Rasmussen, Mette Nyegaard, Michael Gaihede, Preben Johansen, Tarec C. El-Galaly, and Hans E. Johnsen, Aalborg University Hospital; Karen Dybkær, Martin Bøgsted, Anders E. Bilgrau, Maria Rodrigo-Domingo, Michael Gaihede, and Hans E. Johnsen, Aalborg University, Aalborg; Michael B. Møller, Odense University Hospital, Odense, Denmark; Zijun Y. Xu-Monette, Ling Li, and Ken H. Young, The University of Texas MD Anderson Cancer Center, Houston, TX; and Richard J. Samworth and Rajen D. Shah, University of Cambridge, Cambridge, United Kingdom.
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