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Berrino E, Bellomo SE, Chesta A, Detillo P, Bragoni A, Gagliardi A, Naccarati A, Cereda M, Witel G, Sapino A, Bussolati B, Bussolati G, Marchiò C. Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling. J Transl Med 2024; 104:100280. [PMID: 38345263 DOI: 10.1016/j.labinv.2023.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 02/15/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
| | | | - Anita Chesta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | | | - Alberto Bragoni
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Amedeo Gagliardi
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Alessio Naccarati
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Matteo Cereda
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
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Tzioni M, Wotherspoon A, Chen Z, Cucco F, Makker J, Du M. Divergent evolution of metachronous follicular lymphoma and extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue from a common precursor. J Pathol 2023; 261:11-18. [PMID: 37345526 PMCID: PMC10952687 DOI: 10.1002/path.6143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/14/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
The translocation t(14;18)(q32:q21)/IGH::BCL2 occurs at the pre-B stage of B-cell development in the bone marrow and is insufficient for malignant transformation, although it leads to the formation of in situ follicular B-cell neoplasia (ISFN). Despite that, the translocation is the genetic hallmark of follicular lymphoma (FL), it occurs infrequently in metachronous/synchronous lymphomas, including extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (EMZL), mantle cell lymphoma, and Hodgkin's lymphoma. In each of these scenarios, the two lymphomas often appear to be clonally related by analyses of IGH::BCL2 and/or rearranged IG genes. However, it remains largely unknown whether one lymphoma originates from the other or they develop independently. We studied five cases of metachronous EMZL and FL. In four cases, the two lymphomas were clonally related, as shown by identical IGH::BCL2 and/or rearranged IG genes or shared mutations. There were common and unique mutations between the paired EMZL and FL, indicating that they developed independently from a common premalignant cell population, harbouring IGH::BCL2 in three cases. Furthermore, case 1 presented with three metachronous FLs, and all of them originated from a common precursor cell population via divergent evolution. Our findings highlight the multi-malignant potential of IGH::BCL2-positive B-cells. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Maria‐Myrsini Tzioni
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Francesco Cucco
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Jasmine Makker
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Ming‐Qing Du
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
- Department of Histopathology, Addenbrooke's HospitalCambridge University Hospitals NHS Foundation TrustCambridgeUK
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Attygalle AD, Dobson R, Chak PK, Vroobel KM, Wren D, Mugalaasi H, Morgan Y, Kaur M, Ahmad R, Chen Z, Naresh KN, Du M. Parallel evolution of two distinct lymphoid proliferations in clonal haematopoiesis. Histopathology 2022; 80:847-858. [PMID: 35064935 PMCID: PMC9310594 DOI: 10.1111/his.14619] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
Abstract
AIMS Angioimmunoblastic T-cell lymphoma (AITL) is genetically characterized by TET2 and DNMT3A mutations occurring in haematopoietic progenitor cells, and late events (e.g. the RHOA-G17V mutation) associated with malignant transformation. As TET2/DNMT3A-mutated progenitor cells can differentiate into multilineage progenies and give rise to both AITL and myeloid neoplasms, they may also have the potential to lead to other metachronous/synchronous neoplasms. We report two cases showing parallel evolution of two distinct potentially neoplastic lymphoid proliferations from a common mutated haematopoietic progenitor cell population. METHODS AND RESULTS Both cases presented with generalized lymphadenopathy. In case 1 (a 67-year-old female), an initial lymph node (LN) biopsy was dismissed as reactive, but a repeat biopsy showed a nodal marginal zone lymphoma (NMZL)-like proliferation with an increase in the number of T-follicular helper (TFH) cells. Immunohistochemistry, and clonality and mutational analyses by targeted sequencing of both whole tissue sections and microdissected NMZL-like lesions, demonstrated a clonal B-cell proliferation that harboured the BRAF-G469R mutation and shared TET2 and DNMT3A mutations with an underlying RHOA-G17V-mutant TFH proliferation. Review of the original LN biopsy showed histological and immunophenotypic features of AITL. In case 2 (a 66-year-old male), cytotoxic T-cell lymphoma with an increase in the number of Epstein-Barr virus-positive large B cells was diagnosed on initial biopsy. On review together with the relapsed biopsy, we identified an additional occult neoplastic TFH proliferation/smouldering AITL. Both T-cell proliferations shared TET2 and DNMT3A mutations while RHOA-G17V was confined to the smouldering AITL. CONCLUSIONS In addition to demonstrating diagnostic challenges, these cases expand the potential of clonal haematopoiesis in the development of different lineage neoplastic proliferations.
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Affiliation(s)
| | - Rachel Dobson
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Pui Kwan Chak
- Department of Anatomical and Cellular PathologyPrince of Wales HospitalShatinNew TerritoriesHong Kong
| | | | - Dorte Wren
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic MedicineManchester University NHS Foundation Trust, Saint Mary's HospitalManchesterUK
| | - Hood Mugalaasi
- Clinical Genomics, Haematological Diagnostic Malignancy ServiceThe Royal Marsden HospitalSuttonUK
| | - Yvonne Morgan
- Clinical Genomics, Haematological Diagnostic Malignancy ServiceThe Royal Marsden HospitalSuttonUK
| | - Manmit Kaur
- Department of HaematologyLuton & Dunstable University HospitalLutonUK
| | - Raida Ahmad
- Department of Cellular PathologyImperial College Healthcare NHS Trust, Charing Cross HospitalLondonUK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Kikkeri N Naresh
- Centre for HaematologyImperial College LondonLondonUK
- Clinical Research DivisionFred Hutchison Cancer Research CenterSeattleWAUSA
| | - Ming‐Qing Du
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
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Dobson R, Wotherspoon A, Liu SA, Cucco F, Chen Z, Tang Y, Du M. Widespread in situ follicular neoplasia in patients who subsequently developed follicular lymphoma. J Pathol 2022; 256:369-377. [PMID: 34957565 PMCID: PMC9310836 DOI: 10.1002/path.5861] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/07/2021] [Accepted: 12/23/2021] [Indexed: 02/05/2023]
Abstract
In situ follicular neoplasia (ISFN) is usually an occasional incidental finding in lymph nodes by BCL2 immunohistochemistry, and its true scale is unknown. We have identified six cases of follicular lymphoma (FL) with a history of solid neoplasm 4-16 years ago, from which ISFN was identified widely in the surgically cleared lymph nodes (LNs). Using clone-specific PCR and BaseScope in situ hybridisation with primers or probes specific to the VDJ or BCL2-IGHJ junction sequence, we confirmed the clonal identity among different ISFNs and overt-FL in each of the four cases successfully investigated. Mutation analyses of overt-FL by targeted next-generation sequencing identified multiple potential pathogenic changes involving CREBBP, EZH2, KMT2D, TNFRS14, and STAT6. Further investigations of these mutations in paired ISFNs using Fluidigm PCR and Illumina sequencing showed the presence of the FL-associated mutations in early lesions for two of the six cases investigated (CREBBP and KMT2D in one case and STAT6 in the other), with one case displaying stepwise accumulation of its observed mutations. Remarkably, there were considerable divergences in BCL2 variants among different ISFN-involved lymph nodes in all four cases successfully investigated, indicating ongoing intraclonal diversification by somatic hypermutation machinery. Our findings demonstrate widespread distribution of ISFN lesions, further implicating their dynamic nature with the neoplastic cells undergoing active trafficking and clonal evolution. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Rachel Dobson
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Shizhang Alexander Liu
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Francesco Cucco
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Yuan Tang
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
- Department of Pathology, West China HospitalSichuan UniversityChengduPR China
| | - Ming‐Qing Du
- Division of Cellular and Molecular Pathology, Department of PathologyUniversity of CambridgeCambridgeUK
- Department of Histopathology, Addenbrooke’s HospitalCambridge University Hospitals NHS Foundation TrustCambridgeUK
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Genetic Characterization and Clinical Features of Helicobacter pylori Negative Gastric Mucosa-Associated Lymphoid Tissue Lymphoma. Cancers (Basel) 2021; 13:cancers13122993. [PMID: 34203889 PMCID: PMC8232676 DOI: 10.3390/cancers13122993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The pathogenesis of H. pylori-associated gastric MALT lymphoma has been well characterized, but the genetic basis and clinical features of H. pylori negative gastric cases remain elusive. In the present study, we investigated the genetic profiles of a large series of H. pylori negative gastric MALT lymphoma by targeted sequencing for a panel of genes specifically designed for marginal zone lymphoma, together with assessment of common translocations and comprehensive clinical data. Targeted sequencing confirmed that NF-κB activation is a major driver in the pathogenesis of H. pylori negative MALT lymphoma, as shown by frequent TNFAIP3 inactivating mutations and also by translocations of MALT1/IGH. This study adds new insights into the genetic background of H. pylori negative MALT lymphoma and will potentially allow us to more specifically target the underlying molecular pathways in future therapeutic concepts. Abstract Background: In Western countries, the prevalence of gastric mucosa-associated lymphoid tissue (MALT) lymphoma has declined over the last three decades. Contemporaneously, H. pylori negative gastric MALT lymphoma is increasingly encountered, and their genetic basis and clinical features remain elusive. Methods: A total of 57 cases of H. pylori negative gastric MALT lymphoma were reviewed and investigated for chromosome translocation by fluorescence in-situ hybridization and for somatic mutations by the targeted sequencing of 93 genes. Results: MALT1 translocation, most likely t(11;18)(q21;q21)/BIRC3-MALT1, was detected in 39% (22/57) cases, and IGH translocation was further seen in 12 MALT1-negative cases, together accounting for 60% of the cohort. Targeted sequencing was successful in 35 cases, and showed frequent mutations in NF-κB signaling pathways (TNFAIP3 = 23%, CARD11 = 9%, MAP3K14 = 9%), together affecting 14 cases (40%). The NF-κB pathway mutations were mutually exclusive from MALT1, albeit not IGH translocation, altogether occurring in 86% of cases. There was no significant correlation between the genetic changes and clinicopathological parameters. The patients showed a median of progression-free survival (PFS) of 66.3 months, and a significant superior PFS when treated with systemic versus antibiotic therapy (p = 0.004). Conclusion: H. pylori negative gastric MALT lymphoma is characterized by highly frequent genetic changes in the NF-κB signaling pathways.
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Thyroid MALT lymphoma: self-harm to gain potential T-cell help. Leukemia 2021; 35:3497-3508. [PMID: 34021249 PMCID: PMC8632687 DOI: 10.1038/s41375-021-01289-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
The development of extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) is driven by chronic inflammatory responses and acquired genetic changes. To investigate its genetic bases, we performed targeted sequencing of 93 genes in 131 MALT lymphomas including 76 from the thyroid. We found frequent deleterious mutations of TET2 (86%), CD274 (53%), TNFRSF14 (53%), and TNFAIP3 (30%) in thyroid MALT lymphoma. CD274 was also frequently deleted, together with mutation seen in 68% of cases. There was a significant association between CD274 mutation/deletion and TNFRSF14 mutation (p = 0.001). CD274 (PD-L1) and TNFRSF14 are ligands for the co-inhibitory receptor PD1 and BTLA on T-helper cells, respectively, their inactivation may free T-cell activities, promoting their help to malignant B-cells. In support of this, both the proportion of activated T-cells (CD4+CD69+/CD4+) within the proximity of malignant B-cells, and the level of transformed blasts were significantly higher in cases with CD274/TNFRSF14 genetic abnormalities than those without these changes. Both CD274 and TNFRSF14 genetic changes were significantly associated with Hashimoto’s thyroiditis (p = 0.01, p = 0.04, respectively), and CD274 mutation/deletion additionally associated with increased erythrocyte sedimentation rate (p = 0.0001). In conclusion, CD274/TNFRSF14 inactivation in thyroid MALT lymphoma B-cells may deregulate their interaction with T-cells, promoting co-stimulations and impairing peripheral tolerance.
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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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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Yao WQ, Wu F, Zhang W, Chuang SS, Thompson JS, Chen Z, Zhang SW, Clipson A, Wang M, Liu H, Bibawi H, Huang Y, Campos L, Grant JW, Wright P, Ei-Daly H, Rásó-Barnett L, Farkas L, Follows GA, Gao Z, Attygalle AD, Ashton-Key M, Liu W, Du MQ. Angioimmunoblastic T-cell lymphoma contains multiple clonal T-cell populations derived from a common TET2 mutant progenitor cell. J Pathol 2020; 250:346-357. [PMID: 31859368 PMCID: PMC7064999 DOI: 10.1002/path.5376] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/28/2019] [Accepted: 12/12/2019] [Indexed: 02/05/2023]
Abstract
Angioimmunoblastic T‐cell lymphoma (AITL) is a neoplastic proliferation of T follicular helper cells with clinical and histological presentations suggesting a role of antigenic drive in its development. Genetically, it is characterized by a stepwise acquisition of somatic mutations, with early mutations involving epigenetic regulators (TET2, DNMT3A) and occurring in haematopoietic stem cells, with subsequent changes involving signaling molecules (RHOA, VAV1, PLCG1, CD28) critical for T‐cell biology. To search for evidence of potential oncogenic cooperation between genetic changes and intrinsic T cell receptor (TCR) signaling, we investigated somatic mutations and T‐cell receptor β (TRB) rearrangement in 119 AITL, 11 peripheral T‐cell lymphomas with T follicular helper phenotype (PTCL‐TFH), and 25 PTCL‐NOS using Fluidigm polymerase chain reaction (PCR) and Illumina MiSeq sequencing. We confirmed frequent TET2, DNMT3A, and RHOA mutations in AITL (72%, 34%, 61%) and PTCL‐TFH (73%, 36%, 45%) and showed multiple TET2 mutations (2 or 3) in 57% of the involved AITL and PTCL‐TFH. Clonal TRB rearrangement was seen in 76 cases with multiple functional rearrangements (2–4) in 18 cases (24%). In selected cases, we confirmed bi‐clonal T‐cell populations and further demonstrated that these independent T‐cell populations harboured identical TET2 mutations by using BaseScope in situ hybridization, suggesting their derivation from a common TET2 mutant progenitor cell population. Furthermore, both T‐cell populations expressed CD4. Finally, in comparison with tonsillar TFH cells, both AITL and PTCL‐TFH showed a significant overrepresentation of several TRB variable family members, particularly TRBV19*01. Our findings suggest the presence of parallel neoplastic evolutions from a common TET2 mutant haematopoietic progenitor pool in AITL and PTCL‐TFH, albeit to be confirmed in a large series of cases. The biased TRBV usage in these lymphomas suggests that antigenic stimulation may play an important role in predilection of T cells to clonal expansion and malignant transformation. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Wen-Qing Yao
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Fangtian Wu
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Haematology, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, PR China
| | - Wenyan Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | | | - Joe S Thompson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shao-Wei Zhang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Alexandra Clipson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ming Wang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Hongxiang Liu
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hani Bibawi
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yuanxue Huang
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Luis Campos
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, 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
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lívia Rásó-Barnett
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lorant Farkas
- The Haematopathology and Oncology Diagnostic Service, 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
| | - Zifen Gao
- Department of Pathology, Health Science Centre, Peking University, Beijing, PR China
| | | | - Margaret Ashton-Key
- Department of Cellular Pathology, Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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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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