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      Genomic abnormalities of TP53 define distinct risk groups of paediatric B-cell non-Hodgkin lymphoma

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          Abstract

          Children with B-cell non-Hodgkin lymphoma (B-NHL) have an excellent chance of survival, however, current clinical risk stratification places as many as half of patients in a high-risk group receiving very intensive chemo-immunotherapy. TP53 alterations are associated with adverse outcome in many malignancies; however, whilst common in paediatric B-NHL, their utility as a risk classifier is unknown. We evaluated the clinical significance of TP53 abnormalities (mutations, deletion and/or copy number neutral loss of heterozygosity) in a large UK paediatric B-NHL cohort and determined their impact on survival. TP53 abnormalities were present in 54.7% of cases and were independently associated with a significantly inferior survival compared to those without a TP53 abnormality (PFS 70.0% vs 100%, p < 0.001, OS 78.0% vs 100%, p = 0.002). Moreover, amongst patients clinically defined as high-risk (stage III with high LDH or stage IV), those without a TP53 abnormality have superior survival compared to those with TP53 abnormalities (PFS 100% vs 55.6%, p = 0.005, OS 100% vs 66.7%, p = 0.019). Biallelic TP53 abnormalities were either maintained from the presentation or acquired at progression in all paired diagnosis/progression Burkitt lymphoma cases. TP53 abnormalities thus define clinical risk groups within paediatric B-NHL and offer a novel molecular risk stratifier, allowing more personalised treatment protocols.

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          Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma

          BACKGROUND Diffuse large B-cell lymphomas (DLBCLs) are phenotypically and genetically heterogeneous. Gene-expression profiling has identified subgroups of DLBCL (activated B-cell–like [ABC], germinal-center B-cell–like [GCB], and unclassified) according to cell of origin that are associated with a differential response to chemotherapy and targeted agents. We sought to extend these findings by identifying genetic subtypes of DLBCL based on shared genomic abnormalities and to uncover therapeutic vulnerabilities based on tumor genetics. METHODS We studied 574 DLBCL biopsy samples using exome and transcriptome sequencing, array-based DNA copy-number analysis, and targeted amplicon resequencing of 372 genes to identify genes with recurrent aberrations. We developed and implemented an algorithm to discover genetic subtypes based on the co-occurrence of genetic alterations. RESULTS We identified four prominent genetic subtypes in DLBCL, termed MCD (based on the co-occurrence of MYD88 L265P and CD79B mutations), BN2 (based on BCL6 fusions and NOTCH2 mutations), N1 (based on NOTCH1 mutations), and EZB (based on EZH2 mutations and BCL2 translocations). Genetic aberrations in multiple genes distinguished each genetic subtype from other DLBCLs. These subtypes differed phenotypically, as judged by differences in gene-expression signatures and responses to immunochemotherapy, with favorable survival in the BN2 and EZB subtypes and inferior outcomes in the MCD and N1 subtypes. Analysis of genetic pathways suggested that MCD and BN2 DLBCLs rely on “chronic active” B-cell receptor signaling that is amenable to therapeutic inhibition. CONCLUSIONS We uncovered genetic subtypes of DLBCL with distinct genotypic, epigenetic, and clinical characteristics, providing a potential nosology for precision-medicine strategies in DLBCL. (Funded by the Intramural Research Program of the National Institutes of Health and others.)
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            Putting p53 in Context.

            TP53 is the most frequently mutated gene in human cancer. Functionally, p53 is activated by a host of stress stimuli and, in turn, governs an exquisitely complex anti-proliferative transcriptional program that touches upon a bewildering array of biological responses. Despite the many unveiled facets of the p53 network, a clear appreciation of how and in what contexts p53 exerts its diverse effects remains unclear. How can we interpret p53's disparate activities and the consequences of its dysfunction to understand how cell type, mutation profile, and epigenetic cell state dictate outcomes, and how might we restore its tumor-suppressive activities in cancer?
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              Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

              Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B cell (ABC) and germinal center B cell (GCB) subtypes. We carried out a comprehensive genetic analysis of 304 primary DLBCLs and identified low-frequency alterations, captured recurrent mutations, somatic copy number alterations, and structural variants, and defined coordinate signatures in patients with available outcome data. We integrated these genetic drivers using consensus clustering and identified five robust DLBCL subsets, including a previously unrecognized group of low-risk ABC-DLBCLs of extrafollicular/marginal zone origin; two distinct subsets of GCB-DLBCLs with different outcomes and targetable alterations; and an ABC/GCB-independent group with biallelic inactivation of TP53, CDKN2A loss, and associated genomic instability. The genetic features of the newly characterized subsets, their mutational signatures, and the temporal ordering of identified alterations provide new insights into DLBCL pathogenesis. The coordinate genetic signatures also predict outcome independent of the clinical International Prognostic Index and suggest new combination treatment strategies. More broadly, our results provide a roadmap for an actionable DLBCL classification.
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                Author and article information

                Contributors
                v.rand@tees.ac.uk
                Journal
                Leukemia
                Leukemia
                Leukemia
                Nature Publishing Group UK (London )
                0887-6924
                1476-5551
                21 October 2021
                21 October 2021
                2022
                : 36
                : 3
                : 781-789
                Affiliations
                [1 ]GRID grid.26597.3f, ISNI 0000 0001 2325 1783, School of Health & Life Sciences, , Teesside University, ; Middlesbrough, UK
                [2 ]GRID grid.26597.3f, ISNI 0000 0001 2325 1783, National Horizons Centre, , Teesside University, ; 38 John Dixon Lane, Darlington, UK
                [3 ]GRID grid.1006.7, ISNI 0000 0001 0462 7212, Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, , Newcastle University, ; Newcastle upon Tyne, UK
                [4 ]GRID grid.420004.2, ISNI 0000 0004 0444 2244, Newcastle Genetics Laboratory, , Newcastle upon Tyne Hospitals NHS Foundation Trust, ; Newcastle upon Tyne, UK
                [5 ]GRID grid.424926.f, ISNI 0000 0004 0417 0461, Department of Paediatric Oncology, , Royal Marsden Hospital, ; Sutton, Surrey UK
                [6 ]GRID grid.420004.2, ISNI 0000 0004 0444 2244, Department of Cellular Pathology, , Newcastle upon Tyne Hospitals NHS Foundation Trust, ; Newcastle upon Tyne, UK
                [7 ]GRID grid.120073.7, ISNI 0000 0004 0622 5016, Division of Cellular and Molecular Pathology, Department of Pathology, , University of Cambridge, Addenbrooke’s Hospital, ; Cambridge, UK
                [8 ]GRID grid.497421.d, CEITEC, Masaryk University, ; Brno, Czech Republic
                [9 ]GRID grid.24029.3d, ISNI 0000 0004 0383 8386, Department of Paediatric Haematology, Oncology and Palliative Care, Addenbrooke’s Hospital, , Cambridge University Hospitals NHS Foundation Trust, ; Cambridge, UK
                [10 ]GRID grid.459561.a, ISNI 0000 0004 4904 7256, Department of Paediatric and Adolescent Haematology and Oncology, , The Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, ; Newcastle upon Tyne, UK
                Author information
                http://orcid.org/0000-0001-8045-822X
                http://orcid.org/0000-0002-8439-4507
                http://orcid.org/0000-0003-2671-9972
                http://orcid.org/0000-0002-2198-8949
                Article
                1444
                10.1038/s41375-021-01444-6
                8885412
                34675373
                ef21a380-ed7d-4cd1-90c3-c014a42eb169
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 2 March 2021
                : 26 September 2021
                : 29 September 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000265, RCUK | Medical Research Council (MRC);
                Funded by: Good Will Cause
                Funded by: MRC/EPSRC Newcastle Pathology Node
                Funded by: FundRef https://doi.org/10.13039/501100003776, Newcastle upon Tyne Hospitals NHS Foundation Trust (Newcastle upon Tyne Hospitals NHS Trust);
                Funded by: Blood Cancer UK - Senior Bennett Fellowship #12005 North East Promenaders Against Cancer (NEPAC) The Little Princess Trust JGW Patterson Foundation
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

                Oncology & Radiotherapy
                cancer genomics,b-cell lymphoma
                Oncology & Radiotherapy
                cancer genomics, b-cell lymphoma

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