1
|
Leich E, Brodtkorb M, Schmidt T, Altenbuchinger M, Lingjærde OC, Lockmer S, Holte H, Nedeva T, Grieb T, Sander B, Sundström C, Spang R, Kimby E, Rosenwald A. Gene expression and copy number profiling of follicular lymphoma biopsies from patients treated with first-line rituximab without chemotherapy. Leuk Lymphoma 2023; 64:1927-1937. [PMID: 37683053 DOI: 10.1080/10428194.2023.2240462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 09/10/2023]
Abstract
The Nordic Lymphoma Study Group has performed two randomized clinical trials with chemotherapy-free first-line treatment (rituximab +/- interferon) in follicular lymphoma (FL), with 73% of patients alive and 38% without any need of chemotherapy after 10.6 years median follow-up. In order to identify predictive markers, that may also serve as therapeutic targets, gene expression- and copy number profiles were obtained from 97 FL patients using whole genome microarrays. Copy number alterations (CNAs) were identified, e.g. by GISTIC. Cox Lasso Regression and Lasso logistic regression were used to determine molecular features predictive of time to next therapy (TTNT). A few molecular changes were associated with TTNT (e.g. increased expression of INPP5B, gains in 12q23/q24), but were not significant after adjusting for multiple testing. Our findings suggest that there are no strong determinants of patient outcome with respect to GE data and CNAs in FL patients treated with a chemotherapy-free regimen (i.e. rituximab +/- interferon).
Collapse
Affiliation(s)
- E Leich
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | | | - T Schmidt
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - M Altenbuchinger
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
| | - Ole Christian Lingjærde
- Division of Biomedical Informatics, Department of Computer Science, University of Oslo, Norway
| | - S Lockmer
- Division of Hematology, Department of Medicine at Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - H Holte
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - T Nedeva
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - T Grieb
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - B Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - C Sundström
- Department of Pathology, Uppsala University Hospital, Uppsala University, Uppsala, Sweden
| | - R Spang
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - E Kimby
- Division of Hematology, Department of Medicine at Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| |
Collapse
|
2
|
Mozas P, López C, Grau M, Nadeu F, Clot G, Valle S, Kulis M, Navarro A, Ramis-Zaldivar JE, González-Farré B, Rivas-Delgado A, Rivero A, Frigola G, Balagué O, Giné E, Delgado J, Villamor N, Matutes E, Magnano L, García-Sanz R, Huet S, Russell RB, Campo E, López-Guillermo A, Beà S. Genomic landscape of follicular lymphoma across a wide spectrum of clinical behaviors. Hematol Oncol 2023; 41:631-643. [PMID: 36994552 DOI: 10.1002/hon.3132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/31/2023]
Abstract
While some follicular lymphoma (FL) patients do not require treatment or experience prolonged responses, others relapse early, and little is known about genetic alterations specific to patients with a particular clinical behavior. We selected 56 grade 1-3A FL patients according to their need of treatment or timing of relapse: never treated (n = 7), non-relapsed (19), late relapse (14), early relapse or POD24 (11), and primary refractory (5). We analyzed 56 diagnostic and 12 paired relapse lymphoid tissue biopsies and performed copy number alteration (CNA) analysis and next generation sequencing (NGS). We identified six focal driver losses (1p36.32, 6p21.32, 6q14.1, 6q23.3, 9p21.3, 10q23.33) and 1p36.33 copy-neutral loss of heterozygosity (CN-LOH). By integrating CNA and NGS results, the most frequently altered genes/regions were KMT2D (79%), CREBBP (67%), TNFRSF14 (46%) and BCL2 (40%). Although we found that mutations in PIM1, FOXO1 and TMEM30A were associated with an adverse clinical behavior, definitive conclusions cannot be drawn, due to the small sample size. We identified common precursor cells harboring early oncogenic alterations of the KMT2D, CREBBP, TNFRSF14 and EP300 genes and 16p13.3-p13.2 CN-LOH. Finally, we established the functional consequences of mutations by means of protein modeling (CD79B, PLCG2, PIM1, MCL1 and IRF8). These data expand the knowledge on the genomics behind the heterogeneous FL population and, upon replication in larger cohorts, could contribute to risk stratification and the development of targeted therapies.
Collapse
Affiliation(s)
- Pablo Mozas
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Cristina López
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Marta Grau
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Ferran Nadeu
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Guillem Clot
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Sara Valle
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Marta Kulis
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Alba Navarro
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Joan Enric Ramis-Zaldivar
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Blanca González-Farré
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Andrea Rivero
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Olga Balagué
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Eva Giné
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Julio Delgado
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Neus Villamor
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Estella Matutes
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Laura Magnano
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ramón García-Sanz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Haematology, University Hospital of Salamanca (HUS/IBSAL) and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Sarah Huet
- Team LIB, ISEM 1111 International Center for Research in Infectiology, Université Claude Bernard Lyon I, Pierre-Bénite, France
- France and Department of Biological Haematology, Hôpital Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Robert B Russell
- Biochemie Zentrum Heidelberg (BZH) and Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Elías Campo
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Armando López-Guillermo
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Department of Pathology, Haematopathology Section, Hospital Clínic de Barcelona, Barcelona, Spain
| |
Collapse
|
3
|
Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, Wlodarska I. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity. Genes Chromosomes Cancer 2022; 61:603-615. [PMID: 35611992 DOI: 10.1002/gcc.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/07/2022] Open
Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
Collapse
Affiliation(s)
| | - Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jonas Demeulemeester
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Daan Dierickx
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Free University Hospital, Brussels, Belgium
| | - Karen Deraedt
- Anatomo-Pathology, Hospital East Limburg, Genk, Belgium
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | | | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | |
Collapse
|
4
|
Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia 2021; 35:2002-2016. [PMID: 33953289 PMCID: PMC8257491 DOI: 10.1038/s41375-021-01251-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 02/03/2023]
Abstract
B cells have the unique property to somatically alter their immunoglobulin (IG) genes by V(D)J recombination, somatic hypermutation (SHM) and class-switch recombination (CSR). Aberrant targeting of these mechanisms is implicated in lymphomagenesis, but the mutational processes are poorly understood. By performing whole genome and transcriptome sequencing of 181 germinal center derived B-cell lymphomas (gcBCL) we identified distinct mutational signatures linked to SHM and CSR. We show that not only SHM, but presumably also CSR causes off-target mutations in non-IG genes. Kataegis clusters with high mutational density mainly affected early replicating regions and were enriched for SHM- and CSR-mediated off-target mutations. Moreover, they often co-occurred in loci physically interacting in the nucleus, suggesting that mutation hotspots promote increased mutation targeting of spatially co-localized loci (termed hypermutation by proxy). Only around 1% of somatic small variants were in protein coding sequences, but in about half of the driver genes, a contribution of B-cell specific mutational processes to their mutations was found. The B-cell-specific mutational processes contribute to both lymphoma initiation and intratumoral heterogeneity. Overall, we demonstrate that mutational processes involved in the development of gcBCL are more complex than previously appreciated, and that B cell-specific mutational processes contribute via diverse mechanisms to lymphomagenesis.
Collapse
|
5
|
CREBBP and STAT6 co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma. Blood Cancer J 2020; 10:69. [PMID: 32555149 PMCID: PMC7299932 DOI: 10.1038/s41408-020-0335-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
The diffuse variant of follicular lymphoma (dFL) is a rare variant of FL lacking t(14;18) that was first described in 2009. In this study, we use a comprehensive approach to define unifying pathologic and genetic features through gold-standard pathologic review, FISH, SNP-microarray, and next-generation sequencing of 16 cases of dFL. We found unique morphologic features, including interstitial sclerosis, microfollicle formation, and rounded nuclear cytology, confirmed absence of t(14;18) and recurrent deletion of 1p36, and showed a novel association with deletion/CN-LOH of 16p13 (inclusive of CREBBP, CIITA, and SOCS1). Mutational profiling demonstrated near-uniform mutations in CREBBP and STAT6, with clonal dominance of CREBBP, among other mutations typical of germinal-center B-cell lymphomas. Frequent CREBBP and CIITA codeletion/mutation suggested a mechanism for immune evasion, while subclonal STAT6 activating mutations with concurrent SOCS1 loss suggested a mechanism of BCL-xL/BCL2L1 upregulation in the absence of BCL2 rearrangements. A review of the literature showed significant enrichment for 16p13 and 1p36 loss/CN-LOH, STAT6 mutation, and CREBBP and STAT6 comutation in dFL, as compared with conventional FL. With this comprehensive approach, our study demonstrates confirmatory and novel genetic associations that can aid in the diagnosis and subclassification of this rare type of lymphoma.
Collapse
|
6
|
Augustus GJ, Xicola RM, Llor X, Ellis NA. Decreased copy-neutral loss of heterozygosity in African American colorectal cancers. Genes Chromosomes Cancer 2020; 59:454-464. [PMID: 32293075 DOI: 10.1002/gcc.22851] [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: 09/17/2019] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 11/11/2022] Open
Abstract
Despite improvements over the past 20 years, African Americans continue to have the highest incidence and mortality rates of colorectal cancer (CRC) in the United States. While previous studies have found that copy number variations (CNVs) occur at similar frequency in African American and White CRCs, copy-neutral loss of heterozygosity (cnLOH) has not been investigated. In the present study, we used publicly available data from The Cancer Genome Atlas (TCGA) as well as data from an African American CRC cohort, the Chicago Colorectal Cancer Consortium (CCCC), to compare frequencies of CNVs and cnLOH events in CRCs in the two racial groups. Using genotype microarray data, we analyzed large-scale CNV and cnLOH events from 166 microsatellite stable CRCs-31 and 39 African American CRCs from TCGA and the CCCC, respectively, and 96 White CRCs from TCGA. As reported previously, the frequencies of CNVs were similar between African American and White CRCs; however, there was a significantly lower frequency of cnLOH events in African American CRCs compared to White CRCs, even after adjusting for demographic and clinical covariates. Although larger differences for chromosome 18 were observed, a lower frequency of cnLOH events in African American CRCs was observed for nearly all chromosomes. These results suggest that mechanistic differences, including differences in the frequency of cnLOH, could contribute to clinicopathological disparities between African Americans and Whites. Additionally, we observed a previously uncharacterized phenomenon we refer to as small interstitial cnLOH, in which segments of chromosomes from 1 to 5 Mb long were affected by cnLOH.
Collapse
Affiliation(s)
- Gaius J Augustus
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA
| | - Rosa M Xicola
- Department of Internal Medicine and Yale Cancer Center, Yale University, Hew Haven, Connecticut, USA
| | - Xavier Llor
- Department of Internal Medicine and Yale Cancer Center, Yale University, Hew Haven, Connecticut, USA
| | - Nathan A Ellis
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA.,Department of Cellular and Molecular Medicine and University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
| |
Collapse
|
7
|
Zhu Z, Li T, Zhang X, Zhang Z, Zhu D, Lin P, Tu S, Ren W. Molecular and clinical progress in follicular lymphoma lacking the t(14;18) translocation (Review). Int J Oncol 2019; 56:7-17. [PMID: 31789408 DOI: 10.3892/ijo.2019.4917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/25/2019] [Indexed: 11/05/2022] Open
Abstract
Although the majority of patients with follicular lymphoma (FL) harbor the t(14;18)(q32;q21) IGH/BCL2 gene rearrangement that leads to the overexpression of BCL2 protein, approximately 20% of FL cases lack t(14;18)(q32;q21). It is considered that BCL2 overexpression underscores the development of the majority of cases of FL and their transformation to more aggressive lymphoma [known as transformed FL (tFL)]. However, FL cases lacking the t(14;18)(q32;q21) translocation exhibit symptoms analogous to their t(14;18)‑positive counterparts. An important goal of recent research on FL has been to clarify the distinctions between the two different forms of FL. Numerous studies have shed light onto the genetic and molecular features of t(14;18)‑negative FL and the related clinical manifestations. In this review, we summarize the current knowledge of t(14;18)‑negative FL occurring in the lymph nodes with an emphasis on the underlying molecular and clinical features. In addition, novel treatment directions are discussed.
Collapse
Affiliation(s)
- Zunmin Zhu
- Institute of Hematology, Henan Renmin Hospital, Zhengzhou, Henan 475000, P.R. China
| | - Tao Li
- Laboratory of Hematology, The First Affiliated Hospital of Zhenzhou University, Zhengzhou, Henan 475000, P.R. China
| | - Xuran Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450000, P.R. China
| | - Zhengqiang Zhang
- Immunology Laboratory of Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, Henan 450008, P.R. China
| | - Dandan Zhu
- Zhengzhou Shenyou Biotechnology, Zhengzhou, Henan 450000, P.R. China
| | - Pei Lin
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shichun Tu
- Scintillon Institute for Biomedical and Bioenergy Research, San Diego, CA 92121, USA
| | - Weihong Ren
- Department of Laboratory Medicine, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450000, P.R. China
| |
Collapse
|
8
|
Gascoyne RD, Nadel B, Pasqualucci L, Fitzgibbon J, Payton JE, Melnick A, Weigert O, Tarte K, Gribben JG, Friedberg JW, Seymour JF, Cavalli F, Zucca E. Follicular lymphoma: State-of-the-art ICML workshop in Lugano 2015. Hematol Oncol 2017; 35:397-407. [PMID: 28378425 DOI: 10.1002/hon.2411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/25/2022]
Abstract
The 13th International Conference on Malignant Lymphoma held in Lugano in June 2015 was preceded by a closed workshop (organized in collaboration with the American Association for Cancer Research and the European School of Oncology) with the aim of developing an up-to-date understanding of the biology of follicular lymphoma and the clinical implications of new findings in the field. Discussed topics included the mutational spectrum at diagnosis, the clinical correlates of genetic and epigenetic alterations, the mechanisms of clonal evolution and histological transformation, the cross talk between tumor cells and microenvironment, and the development of novel treatments. This report represents a summary of the workshop.
Collapse
Affiliation(s)
- Randy D Gascoyne
- Department of Pathology and the Centre for Lymphoid Cancer, British Columbia Cancer Agency and University of BC, Vancouver, BC, Canada
| | - Bertrand Nadel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Marseille, France
| | - Laura Pasqualucci
- Institute of Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jacqueline E Payton
- Department of Pathology and Immunology and Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ari Melnick
- Weill Cornell Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Karin Tarte
- UMR INSERM U917, Equipe Labellisée Ligue Contre le Cancer, Université Rennes 1, Rennes, France
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - John F Seymour
- Department of Haematology, Peter MacCallum Cancer Centre, and University of Melbourne, Parkville, Victoria, Australia
| | - Franco Cavalli
- Oncology Institute of Southern Switzerland, Ospedale San Giovanni, Bellinzona, Switzerland
| | - Emanuele Zucca
- Oncology Institute of Southern Switzerland, Ospedale San Giovanni, Bellinzona, Switzerland
| |
Collapse
|
9
|
Bouska A, Zhang W, Gong Q, Iqbal J, Scuto A, Vose J, Ludvigsen M, Fu K, Weisenburger DD, Greiner TC, Gascoyne RD, Rosenwald A, Ott G, Campo E, Rimsza LM, Delabie J, Jaffe ES, Braziel RM, Connors JM, Wu CI, Staudt LM, D'Amore F, McKeithan TW, Chan WC. Combined copy number and mutation analysis identifies oncogenic pathways associated with transformation of follicular lymphoma. Leukemia 2017; 31:83-91. [PMID: 27389057 PMCID: PMC5214175 DOI: 10.1038/leu.2016.175] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 12/31/2022]
Abstract
Follicular lymphoma (FL) is typically an indolent disease, but 30-40% of FL cases transform into an aggressive lymphoma (tFL) with a poor prognosis. To identify the genetic changes that drive this transformation, we sequenced the exomes of 12 cases with paired FL and tFL biopsies and identified 45 recurrently mutated genes in the FL-tFL data set and 39 in the tFL cases. We selected 496 genes of potential importance in transformation and sequenced them in 23 additional tFL cases. Integration of the mutation data with copy-number abnormality (CNA) data provided complementary information. We found recurrent mutations of miR-142, which has not been previously been reported to be mutated in FL/tFL. The genes most frequently mutated in tFL included KMT2D (MLL2), CREBBP, EZH2, BCL2 and MEF2B. Many recurrently mutated genes are involved in epigenetic regulation, the Janus-activated kinase-signal transducer and activator of transcription (STAT) or the nuclear factor-κB pathways, immune surveillance and cell cycle regulation or are TFs involved in B-cell development. Of particular interest are mutations and CNAs affecting S1P-activated pathways through S1PR1 or S1PR2, which likely regulate lymphoma cell migration and survival outside of follicles. Our custom gene enrichment panel provides high depth of coverage for the study of clonal evolution or divergence.
Collapse
Affiliation(s)
- Alyssa Bouska
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Weiwei Zhang
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Qiang Gong
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Javeed Iqbal
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Anna Scuto
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Julie Vose
- Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE
| | | | - Kai Fu
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | | | - Timothy C. Greiner
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Randy D. Gascoyne
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Elias Campo
- Hematopathology Unit, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Lisa M. Rimsza
- Department of Pathology, University of Arizona, Tucson, AZ
| | - Jan Delabie
- Department of Pathology, University of Toronto, Toronto, Canada
| | - Elaine S. Jaffe
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Joseph M. Connors
- Division of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Chung-I Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Louis M. Staudt
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | | | - Wing C. Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| |
Collapse
|
10
|
Characterization of a variant of t(14;18) negative nodal diffuse follicular lymphoma with CD23 expression, 1p36/TNFRSF14 abnormalities, and STAT6 mutations. Mod Pathol 2016; 29:570-81. [PMID: 26965583 DOI: 10.1038/modpathol.2016.51] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 01/08/2023]
Abstract
A predominantly diffuse growth pattern and CD23 co-expression are uncommon findings in nodal follicular lymphoma and can create diagnostic challenges. A single case series in 2009 (Katzenberger et al) proposed a unique morphologic variant of nodal follicular lymphoma, characterized by a predominantly diffuse architecture, lack of the t(14;18) IGH/BCL2 translocation, presence of 1p36 deletion, frequent inguinal lymph node involvement, CD23 co-expression, and low clinical stage. Other studies on CD23+ follicular lymphoma, while associating inguinal location, have not specifically described this architecture. In addition, no follow-up studies have correlated the histopathologic and cytogenetic/molecular features of these cases, and they remain a diagnostic problem. We identified 11 cases of diffuse, CD23+ follicular lymphoma with histopathologic features similar to those described by Katzenberger et al. Along with pertinent clinical information, we detail their histopathology, IGH/BCL2 translocation status, lymphoma-associated chromosomal gains/losses, and assessment of mutations in 220 lymphoma-associated genes by massively parallel sequencing. All cases showed a diffuse growth pattern around well- to ill-defined residual germinal centers, uniform CD23 expression, mixed centrocytic/centroblastic cytology, and expression of at least one germinal center marker. Ten of 11 involved inguinal lymph nodes, 5 solely. By fluorescence in situ hybridization analysis, the vast majority lacked IGH/BCL2 translocation (9/11). Deletion of 1p36 was observed in five cases and included TNFRSF14. Of the six cases lacking 1p36 deletion, TNFRSF14 mutations were identified in three, highlighting the strong association of 1p36/TNFRSF14 abnormalities with this follicular lymphoma variant. In addition, 9 of the 11 cases tested (82%) had STAT6 mutations and nuclear P-STAT6 expression was detectable in the mutated cases by immunohistochemistry. The proportion of STAT6 mutations is higher than recently reported in conventional follicular lymphoma (11%). These findings lend support for a clinicopathologic variant of t(14;18) negative nodal follicular lymphoma and suggests importance of the interleukin (IL)-4/JAK/STAT6 pathway in this variant.
Collapse
|
11
|
Thomas R, Demeter Z, Kennedy KA, Borst L, Singh K, Valli VE, Le Boedec K, Breen M. Integrated immunohistochemical and DNA copy number profiling analysis provides insight into the molecular pathogenesis of canine follicular lymphoma. Vet Comp Oncol 2016; 15:852-867. [PMID: 27135201 DOI: 10.1111/vco.12227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/21/2016] [Accepted: 02/22/2016] [Indexed: 12/16/2022]
Abstract
Follicular lymphomas (FLs) typically exhibit a chromosome translocation that induces constitutive expression of the anti-apoptotic bcl2 protein and accumulation of additional molecular defects. This rearrangement offers a promising therapeutic target, but its nature as a fundamental driver of FL pathogenesis remains unclear as 15% of cases lack the translocation. We performed an integrated immunohistochemical and genomic investigation of 10 naturally occurring FL cases from domestic dogs, showing that, as with human tumours, they exhibit marked heterogeneity in the frequency and intensity of bcl2 protein expression. Genomic copy number aberrations were infrequent and broadly consistent with those of other canine B-cell lymphoma subtypes. None of the canine FL specimens exhibited a rearrangement consistent with the hallmark translocation of human FL, despite their remarkable histomorphologic similarity. Parallel exploration of canine and human cases may reveal alternative tumour-initiating mechanisms other than BCL2 disruption, yielding a more complete definition of the molecular pathogenesis of FL.
Collapse
Affiliation(s)
- R Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
| | - Z Demeter
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.,IDEXX Reference Laboratories Inc., West Sacramento, CA, USA
| | - K A Kennedy
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - L Borst
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - K Singh
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - V E Valli
- Visalia Pathology Medical Group, Visalia, CA, USA
| | - K Le Boedec
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - M Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| |
Collapse
|
12
|
Szablewski V, Ingen-Housz-Oro S, Baia M, Delfau-Larue MH, Copie-Bergman C, Ortonne N. Primary Cutaneous Follicle Center Lymphomas Expressing BCL2 Protein Frequently Harbor BCL2 Gene Break and May Present 1p36 Deletion: A Study of 20 Cases. Am J Surg Pathol 2016; 40:127-36. [PMID: 26658664 DOI: 10.1097/pas.0000000000000567] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The classification of cutaneous follicular lymphoma (CFL) into primary cutaneous follicle center lymphoma (PCFCL) or secondary cutaneous follicular lymphoma (SCFL) is challenging. SCFL is suspected when tumor cells express BCL2 protein, reflecting a BCL2 translocation. However, BCL2 expression is difficult to assess in CFLs because of numerous BCL2+ reactive T cells. To investigate these issues and to further characterize PCFCL, we studied a series of 25 CFLs without any extracutaneous disease at diagnosis, selected on the basis of BCL2 protein expression using 2 BCL2 antibodies (clones 124 and E17) and BOB1/BCL2 double immunostaining. All cases were studied using interphase fluorescence in situ hybridization with BCL2, BCL6, IGH, IGK, IGL breakapart, IGH-BCL2 fusion, and 1p36/1q25 dual-color probes. Nineteen CFLs were BCL2 positive, and 6 were negative. After a medium follow-up of 24 (6 to 96) months, 5 cases were reclassified as SCFL and were excluded from a part of our analyses. Among BCL2+ PCFCLs, 60% (9/15) demonstrated a BCL2 break. BCL2-break-positive cases had a tendency to occur in the head and neck and showed the classical phenotype of nodal follicular lymphoma (CD10+, BCL6+, BCL2+, STMN+) compared with BCL2-break-negative PCFCLs. Del 1p36 was observed in 1 PCFCL. No significant clinical differences were observed between BCL2+ or BCL2- PCFCL. In conclusion, we show that a subset of PCFCLs harbor similar genetic alterations, as observed in nodal follicular lymphomas, including BCL2 breaks and 1p36 deletion. As BCL2 protein expression is usually associated with the presence of a BCL2 translocation, fluorescence in situ hybridization should be performed to confirm this hypothesis.
Collapse
Affiliation(s)
- Vanessa Szablewski
- *Pathology Department, CHU Montpellier, Gui de Chauliac Hospital, Montpellier †Dermatology Department §Immunology and Hematology Department ¶Pathology Department, AP-HP, Groupe Henri Mondor-Albert Chenevier ‡INSERM, U955 team 9 ∥Medical University, Paris Est Creteil university (UPEC), UMR-S, Créteil, France
| | | | | | | | | | | |
Collapse
|
13
|
Iqbal J, Naushad H, Bi C, Yu J, Bouska A, Rohr J, Chao W, Fu K, Chan WC, Vose JM. Genomic signatures in B-cell lymphoma: How can these improve precision in diagnosis and inform prognosis? Blood Rev 2016; 30:73-88. [DOI: 10.1016/j.blre.2015.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 01/07/2023]
|
14
|
Song J, Shao H. SNP Array in Hematopoietic Neoplasms: A Review. MICROARRAYS 2015; 5:microarrays5010001. [PMID: 27600067 PMCID: PMC5003446 DOI: 10.3390/microarrays5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 12/03/2022]
Abstract
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.
Collapse
Affiliation(s)
- Jinming Song
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | - Haipeng Shao
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| |
Collapse
|
15
|
Forero-Castro M, Robledo C, Lumbreras E, Benito R, Hernández-Sánchez JM, Hernández-Sánchez M, García JL, Corchete-Sánchez LA, Tormo M, Barba P, Menárguez J, Ribera J, Grande C, Escoda L, Olivier C, Carrillo E, García de Coca A, Ribera JM, Hernández-Rivas JM. The presence of genomic imbalances is associated with poor outcome in patients with burkitt lymphoma treated with dose-intensive chemotherapy including rituximab. Br J Haematol 2015; 172:428-38. [DOI: 10.1111/bjh.13849] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Maribel Forero-Castro
- Cancer Research Centre; IBSAL; IBMCC; University of Salamanca; CSIC; Salamanca Spain
- School of Biological Sciences (GEBIMOL); Pedagogical and Technological University of Colombia (UPTC); Colombia IN USA
| | - Cristina Robledo
- Cancer Research Centre; IBSAL; IBMCC; University of Salamanca; CSIC; Salamanca Spain
| | - Eva Lumbreras
- Cancer Research Centre; IBSAL; IBMCC; University of Salamanca; CSIC; Salamanca Spain
| | - Rocio Benito
- Cancer Research Centre; IBSAL; IBMCC; University of Salamanca; CSIC; Salamanca Spain
| | | | | | - Juan L. García
- Studies Institute of Health Sciences of Castilla and León (IESCYL); Salamanca Spain
| | | | - Mar Tormo
- Haematology Department; Clinical University Hospital of Valencia; Valencia Spain
| | - Pere Barba
- Haematology Department; Vall d'Hebron Hospital; Barcelona Spain
| | | | - Jordi Ribera
- Clinical Haematology Department ICO-Hospital Germans Trias i Pujol; Jose Carreras Research Institute; Badalona Spain
| | - Carlos Grande
- Haematology Department; University Hospital October 12; Madrid Spain
| | - Lourdes Escoda
- Haematology Department; University Hospital of Tarragona Joan XXIII; Tarragona Spain
| | - Carmen Olivier
- Haematology Department; General Hospital of Segovia; Segovia Spain
| | - Estrella Carrillo
- Haematology Department; University Hospital Virgen del Rocío; Seville Spain
| | | | - Josep-María Ribera
- Clinical Haematology Department ICO-Hospital Germans Trias i Pujol; Jose Carreras Research Institute; Badalona Spain
| | - Jesús M. Hernández-Rivas
- Cancer Research Centre; IBSAL; IBMCC; University of Salamanca; CSIC; Salamanca Spain
- Haematology Department; University Hospital of Salamanca; Salamanca Spain
| |
Collapse
|
16
|
Etebari M, Navari M, Piccaluga PP. SNPs Array Karyotyping in Non-Hodgkin Lymphoma. MICROARRAYS 2015; 4:551-69. [PMID: 27600240 PMCID: PMC4996401 DOI: 10.3390/microarrays4040551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
The traditional methods for detection of chromosomal aberrations, which included cytogenetic or gene candidate solutions, suffered from low sensitivity or the need for previous knowledge of the target regions of the genome. With the advent of single nucleotide polymorphism (SNP) arrays, genome screening at global level in order to find chromosomal aberrations like copy number variants, DNA amplifications, deletions, and also loss of heterozygosity became feasible. In this review, we present an update of the knowledge, gained by SNPs arrays, of the genomic complexity of the most important subtypes of non-Hodgkin lymphomas.
Collapse
Affiliation(s)
- Maryam Etebari
- Department of Experimental, Diagnostic, and Specialty Medicine; Hematopathology Unit, S. Orsola-Malpighi Hospital, Bologna 40138, Italy.
| | - Mohsen Navari
- Department of Experimental, Diagnostic, and Specialty Medicine; Hematopathology Unit, S. Orsola-Malpighi Hospital, Bologna 40138, Italy.
| | - Pier Paolo Piccaluga
- Department of Experimental, Diagnostic, and Specialty Medicine; Hematopathology Unit, S. Orsola-Malpighi Hospital, Bologna 40138, Italy.
| |
Collapse
|
17
|
Shiseki M, Masuda A, Yoshinaga K, Mori N, Okada M, Motoji T, Tanaka J. Identification of the SOX5 gene as a novel IGH-involved translocation partner in BCL2-negative follicular lymphoma with t(12;14)(p12.2;q32). Int J Hematol 2015; 102:633-8. [DOI: 10.1007/s12185-015-1823-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
|
18
|
Abstract
Follicular lymphoma (FL) is the most common indolent lymphoma. The vast majority of cases are associated with the chromosome translocation t(14;18), a somatic rearrangement that leads to constitutive expression of the anti-apoptotic BCL2 protein. Although t(14;18) clearly represents an important early event in FL pathogenesis, abundant evidence indicates that it is not sufficient. In particular, the recent application of next-generation DNA sequencing technology has uncovered numerous recurrent somatic genomic alterations associated with FL, most of which affect tumor suppressor genes (TSGs). In this article we review the existing literature on TSGs involved in the development and progression of FL. We consider the genes that are most frequently targeted by deleterious mutation, deletion or epigenetic silencing, along with strategies for developing new treatments that exploit the susceptibilities that may be conferred on lymphoma cells by the loss of particular TSGs.
Collapse
|
19
|
Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H. Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest 2014; 124:4529-38. [PMID: 25244093 DOI: 10.1172/jci74747] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/10/2014] [Indexed: 12/13/2022] Open
Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a nonmalignant clonal disease of hematopoietic stem cells that is associated with hemolysis, marrow failure, and thrombophilia. PNH has been considered a monogenic disease that results from somatic mutations in the gene encoding PIGA, which is required for biosynthesis of glycosylphosphatidylinisotol-anchored (GPI-anchored) proteins. The loss of certain GPI-anchored proteins is hypothesized to provide the mutant clone with an extrinsic growth advantage, but some features of PNH argue that there are intrinsic drivers of clonal expansion. Here, we performed whole-exome sequencing of paired PNH+ and PNH- fractions on samples taken from 12 patients as well as targeted deep sequencing of an additional 36 PNH patients. We identified additional somatic mutations that resulted in a complex hierarchical clonal architecture, similar to that observed in myeloid neoplasms. In addition to mutations in PIGA, mutations were found in genes known to be involved in myeloid neoplasm pathogenesis, including TET2, SUZ12, U2AF1, and JAK2. Clonal analysis indicated that these additional mutations arose either as a subclone within the PIGA-mutant population, or prior to PIGA mutation. Together, our data indicate that in addition to PIGA mutations, accessory genetic events are frequent in PNH, suggesting a stepwise clonal evolution derived from a singular stem cell clone.
Collapse
|
20
|
Abstract
B cell lymphomas are cancers that arise from cells that depend on numerous highly orchestrated interactions with immune and stromal cells in the course of normal development. Despite the recent focus on dissecting the genetic aberrations within cancer cells, it has been increasingly recognized that tumour cells retain a range of dependence on interactions with the non-malignant cells and stromal elements that constitute the tumour microenvironment. A fundamental understanding of these interactions gives insight into the pathogenesis of most B cell lymphomas and, moreover, identifies novel therapeutic opportunities for targeting oncogenic pathways, both now and in the future.
Collapse
Affiliation(s)
- David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Randy D Gascoyne
- 1] Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada. [2] Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| |
Collapse
|
21
|
Gibson SE, Luo J, Sathanoori M, Liao J, Surti U, Swerdlow SH. Whole-genome single nucleotide polymorphism array analysis is complementary to classical cytogenetic analysis in the evaluation of lymphoid proliferations. Am J Clin Pathol 2014; 141:247-55. [PMID: 24436273 DOI: 10.1309/ajcprhght28duwla] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. METHODS Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA). RESULTS Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. CONCLUSIONS The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.
Collapse
Affiliation(s)
- Sarah E. Gibson
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Malini Sathanoori
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Jun Liao
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Steven H. Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| |
Collapse
|
22
|
Alhejaily A, Day AG, Feilotter HE, Baetz T, Lebrun DP. Inactivation of the CDKN2A tumor-suppressor gene by deletion or methylation is common at diagnosis in follicular lymphoma and associated with poor clinical outcome. Clin Cancer Res 2014; 20:1676-86. [PMID: 24449825 DOI: 10.1158/1078-0432.ccr-13-2175] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Follicular lymphoma, the most common indolent lymphoma, is clinically heterogeneous. CDKN2A encodes the tumor suppressors p16(INK4a) and p14(ARF) and frequently suffers deleterious alterations in cancer. We investigated the hypothesis that deletion or hypermethylation of CDKN2A might identify follicular lymphoma cases with distinct clinical or pathologic features potentially amenable to tailored clinical management. EXPERIMENTAL DESIGN Deletion of CDKN2A was detected in pretreatment biopsy specimens using a single nucleotide polymorphism-based approach or endpoint PCR, and methylation of CpG elements in CDKN2A was quantified by methylation-specific PCR. Correlations between CDKN2A status and pathologic or clinical characteristics, including overall survival (OS), were investigated in 106 cases using standard statistical methods. RESULTS Deletion of CDKN2A was detected in 9 of 111 samples (8%) and methylation was detectable in 22 of 113 (19%). CDKN2A was either deleted or methylated in 29 of 106 cases (27%) and this status was associated with inferior OS especially among patients treated with rituximab (P = 0.004). CDKN2A deletion or methylation was associated with more advanced age (P = 0.012) and normal hemoglobin (P = 0.05) but not with sex, FLIPI score, ECOG stage, LDH, performance status, number of involved nodal sites, B symptoms, histologic grade, the presence of a component of diffuse large B-cell lymphoma, proliferation index, or other pathologic factors. CONCLUSIONS Our results show that deletion or methylation of CDKN2A is relatively common in pretreatment follicular lymphoma biopsy specimens and defines a group of cases associated with reduced survival in the rituximab era presumably on the basis of more aggressive disease biology.
Collapse
Affiliation(s)
- Abdulmohsen Alhejaily
- Authors' Affiliations: Department of Pathology and Molecular Medicine, Queen's University; Clinical Research Centre; and Cancer Centre of Southeastern Ontario, Kingston General Hospital, Kingston, Ontario, Canada
| | | | | | | | | |
Collapse
|
23
|
Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood 2014; 123:1487-98. [PMID: 24435047 DOI: 10.1182/blood-2013-05-500264] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Follicular lymphoma (FL) constitutes the second most common non-Hodgkin lymphoma in the western world. FL carries characteristic recurrent structural genomic aberrations. However, information regarding the coding genome in FL is still evolving. Here, we describe the results of massively parallel exome sequencing and single nucleotide polymorphism 6.0 array genomic profiling of 11 highly purified FL cases, and 1 transformed FL case and the validation of selected mutations in 102 FL cases. We report the identification of 15 novel recurrently mutated genes in FL. These include frequent mutations in the linker histone genes HIST1H1 B-E (27%) and mutations in OCT2 (also known as POU2F2; 8%), IRF8 (6%), and ARID1A (11%). A subset of the mutations in HIST1H1 B-E affected binding to DNMT3B, and mutations in HIST1H1 B-E and in EZH2 or ARID1A were largely mutually exclusive, implicating HIST1H1 B-E in epigenetic deregulation in FL. Mutations in OCT2 (POU2F2) affected its transcriptional and functional properties as measured through luciferase assays, the biological analysis of stably transduced cell lines, and global expression profiling. Finally, multiple novel mutated genes located within regions of acquired uniparental disomy in FL are identified. In aggregate, these data substantially broaden our understanding of the genomic pathogenesis of FL.
Collapse
|
24
|
Mamessier E, Song JY, Eberle FC, Pack S, Drevet C, Chetaille B, Abdullaev Z, Adelaïde J, Birnbaum D, Chaffanet M, Pittaluga S, Roulland S, Chott A, Jaffe ES, Nadel B. Early lesions of follicular lymphoma: a genetic perspective. Haematologica 2013; 99:481-8. [PMID: 24162788 DOI: 10.3324/haematol.2013.094474] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The pathogenesis of follicular lymphoma is a multi-hit process progressing over many years through the accumulation of numerous genetic alterations. Besides the hallmark t(14;18), it is still unclear which other oncogenic hits contribute to the early steps of transformation and in which precursor stages these occur. To address this issue, we performed high-resolution comparative genomic hybridization microarrays on laser-capture micro-dissected cases of follicular lymphoma in situ (n=4), partial involvement by follicular lymphoma (n=4), and duodenal follicular lymphoma (n=4), assumed to represent, potentially, the earliest stages in the evolution of follicular lymphoma. Cases of reactive follicular hyperplasia (n=2), uninvolved areas from follicular lymphoma in situ lymph nodes, follicular lymphoma grade 1-2 (n=5) and follicular lymphoma grade 3A (n=5) were used as controls. Surprisingly, alterations involving several relevant (onco)genes were found in all entities, but at significantly lower proportions than in overt follicular lymphoma. While the number of alterations clearly assigns all these entities as precursors, the pattern of partial involvement by follicular lymphoma alterations was quantitatively and qualitatively closer to that of follicular lymphoma, indicating significant selective pressure in line with its faster rate of progression. Among the most notable alterations, we observed and validated deletions of 1p36 and gains of the 7p and 12q chromosomes and related oncogenes, which include some of the most recurrent oncogenic alterations in overt follicular lymphoma (TNFRSF14, EZH2, MLL2). By further delineating distinctive and hierarchical molecular and genetic features of early follicular lymphoma entities, our analysis underlines the importance of applying appropriate criteria for the differential diagnosis. It also provides a first set of candidates likely to be involved in the cascade of hits that pave the path of the various progression phases to follicular lymphoma development.
Collapse
|
25
|
Genome-wide copy-number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma. Blood 2013; 123:1681-90. [PMID: 24037725 DOI: 10.1182/blood-2013-05-500595] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Follicular lymphoma (FL), the second most common type of non-Hodgkin lymphoma in the western world, is characterized by the t(14;18) translocation, which is present in up to 90% of cases. We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma. Common recurrent chromosomal abnormalities in FL included gains of 2, 5, 7, 6p, 8, 12, 17q, 18, 21, and X and losses on 6q and 17p. We also observed many frequent small abnormalities, including losses of 1p36.33-p36.31, 6q23.3-q24.1, and 10q23.1-q25.1 and gains of 2p16.1-p15, 8q24.13-q24.3, and 12q12-q13.13, and identified candidate genes that may be driving this selection. Recurrent abnormalities more frequent in tFL samples included gains of 3q27.3-q28 and chromosome 11 and losses of 9p21.3 and 15q. Four abnormalities, gain of X or Xp and losses of 6q23.2-24.1 or 6q13-15, predicted overall survival. Abnormalities associated with transformation of the disease likely impair immune surveillance, activate the nuclear factor-κB pathway, and deregulate p53 and B-cell transcription factors.
Collapse
|
26
|
Martin-Guerrero I, Salaverria I, Burkhardt B, Szczepanowski M, Baudis M, Bens S, de Leval L, Garcia-Orad A, Horn H, Lisfeld J, Pellissery S, Klapper W, Oschlies I, Siebert R. Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas. Haematologica 2013; 98:1237-41. [PMID: 23445872 DOI: 10.3324/haematol.2012.073916] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pediatric follicular lymphoma is a rare disease that differs genetically and clinically from its adult counterpart. With the exception of pediatric follicular lymphoma with IRF4-translocation, the genetic events associated with these lymphomas have not yet been defined. We applied array-comparative genomic hybridization and molecular inversion probe assay analyses to formalin-fixed paraffin-embedded tissues from 18 patients aged 18 years and under with IRF4 translocation negative follicular lymphoma. All evaluable cases lacked t(14;18). Only 6 of 16 evaluable cases displayed chromosomal imbalances with gains or amplifications of 6pter-p24.3 (including IRF4) and deletion and copy number neutral-loss of heterozygosity in 1p36 (including TNFRSF14) being most frequent. Sequencing of TNFRSF14 located in the minimal region of loss in 1p36.32 showed nine mutations in 7 cases from our series. Two subsets of pediatric follicular lymphoma were delineated according to the presence of molecular alterations, one with genomic aberrations associated with higher grade and/or diffuse large B-cell lymphoma component and more widespread disease, and another one lacking genetic alterations associated with more limited disease.
Collapse
Affiliation(s)
- Idoia Martin-Guerrero
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Kiel, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Banerjee D. Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. Methods Mol Biol 2013; 973:1-13. [PMID: 23412780 DOI: 10.1007/978-1-62703-281-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and correspondingly the size of the datasets generated has grown exponentially such that computational methods required to handle massive datasets have had to be devised. This chapter provides a brief synopsis of the evolution of such techniques as an introduction to the subsequent chapters that provide methods and applications, relevant to research, and clinical diagnostics.
Collapse
Affiliation(s)
- Diponkar Banerjee
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, BC, Canada.
| |
Collapse
|
28
|
Lundin C, Hjorth L, Behrendtz M, Ehinger M, Biloglav A, Johansson B. Submicroscopic genomic imbalances in burkitt lymphomas/leukemias: Association with age and further evidence that 8q24/MYCtranslocations are not sufficient for leukemogenesis. Genes Chromosomes Cancer 2012; 52:370-7. [DOI: 10.1002/gcc.22034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 10/23/2012] [Indexed: 01/13/2023] Open
|
29
|
Gru AA, Hussaini M, Nguyen T, Frater JL, Kreisel F, Hassan A. High prevalence of 1p36 microdeletions in B-cell non-Hodgkin lymphomas (NHL) is associated with PAX7 loss. Int J Lab Hematol 2012. [PMID: 23205730 DOI: 10.1111/ijlh.12034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Kumar N, Cai H, von Mering C, Baudis M. Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data. PLoS One 2012; 7:e43689. [PMID: 22937079 PMCID: PMC3427184 DOI: 10.1371/journal.pone.0043689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/23/2012] [Indexed: 12/02/2022] Open
Abstract
Background Regional genomic copy number alterations (CNA) are observed in the vast majority of cancers. Besides specifically targeting well-known, canonical oncogenes, CNAs may also play more subtle roles in terms of modulating genetic potential and broad gene expression patterns of developing tumors. Any significant differences in the overall CNA patterns between different cancer types may thus point towards specific biological mechanisms acting in those cancers. In addition, differences among CNA profiles may prove valuable for cancer classifications beyond existing annotation systems. Principal Findings We have analyzed molecular-cytogenetic data from 25579 tumors samples, which were classified into 160 cancer types according to the International Classification of Disease (ICD) coding system. When correcting for differences in the overall CNA frequencies between cancer types, related cancers were often found to cluster together according to similarities in their CNA profiles. Based on a randomization approach, distance measures from the cluster dendrograms were used to identify those specific genomic regions that contributed significantly to this signal. This approach identified 43 non-neutral genomic regions whose propensity for the occurrence of copy number alterations varied with the type of cancer at hand. Only a subset of these identified loci overlapped with previously implied, highly recurrent (hot-spot) cytogenetic imbalance regions. Conclusions Thus, for many genomic regions, a simple null-hypothesis of independence between cancer type and relative copy number alteration frequency can be rejected. Since a subset of these regions display relatively low overall CNA frequencies, they may point towards second-tier genomic targets that are adaptively relevant but not necessarily essential for cancer development.
Collapse
Affiliation(s)
- Nitin Kumar
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | | | | |
Collapse
|
31
|
Single nucleotide polymorphism microarray analysis in cortisol-secreting adrenocortical adenomas identifies new candidate genes and pathways. Neoplasia 2012; 14:206-18. [PMID: 22496620 DOI: 10.1593/neo.111758] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/13/2012] [Accepted: 02/13/2012] [Indexed: 02/04/2023] Open
Abstract
The genetic mechanisms underlying adrenocortical tumor development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays (Affymetrix SNP 6.0) to detect copy number alterations (CNAs) and copy-neutral losses of heterozygosity (cnLOH) in 15 cortisol-secreting adrenocortical adenomas with matched blood samples. We focused on microalterations aiming to discover new candidate genes involved in early tumorigenesis and/or autonomous cortisol secretion. We identified 962 CNAs with a median of 18 CNAs per sample. Half of them involved noncoding regions, 89% were less than 100 kb, and 28% were found in at least two samples. The most frequently gained regions were 5p15.33, 6q16.1, 7p22.3-22.2, 8q24.3, 9q34.2-34.3, 11p15.5, 11q11, 12q12, 16q24.3, 20p11.1-20q21.11, and Xq28 (≥20% of cases), most of them being identified in the same three adenomas. These regions contained among others genes like NOTCH1, CYP11B2, HRAS, and IGF2. Recurrent losses were less common and smaller than gains, being mostly localized at 1p, 6q, and 11q. Pathway analysis revealed that Notch signaling was the most frequently altered. We identified 46 recurrent CNAs that each affected a single gene (31 gains and 15 losses), including genes involved in steroidogenesis (CYP11B1) or tumorigenesis (CTNNB1, EPHA7, SGK1, STIL, FHIT). Finally, 20 small cnLOH in four cases affecting 15 known genes were found. Our findings provide the first high-resolution genome-wide view of chromosomal changes in cortisol-secreting adenomas and identify novel candidate genes, such as HRAS, EPHA7, and SGK1. Furthermore, they implicate that the Notch1 signaling pathway might be involved in the molecular pathogenesis of adrenocortical tumors.
Collapse
|
32
|
Cheung KJ, Rogic S, Ben-Neriah S, Boyle M, Connors JM, Gascoyne RD, Horsman DE. SNP analysis of minimally evolved t(14;18)(q32;q21)-positive follicular lymphomas reveals a common copy-neutral loss of heterozygosity pattern. Cytogenet Genome Res 2011; 136:38-43. [PMID: 22104078 DOI: 10.1159/000334265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2011] [Indexed: 01/11/2023] Open
Abstract
Follicular lymphoma (FL) cases with a t(14;18)(q32;q21) and minimal or no additional karyotypic alterations, such as copy number gains and losses and/or chromosomal rearrangements, may exhibit pathologic features and a clinical behavior similar to those with more complex karyotypes. This study sought to investigate whether the copy-neutral loss of heterozygosity (cnLOH) profiles of these minimally evolved t(14;18)(q32;q21)-positive follicular lymphoma (MEV-FL) cases are similar to or different from the majority of FL cases with more karyotypic alterations. Affymetrix SNP 6.0 array analysis was applied to the tumor genomes of 23 MEV-FL biopsy samples to assess for the presence of cnLOH. These cases carried either a single or no chromosomal abnormality in addition to t(14;18)(q32;q21) as determined by karyotyping. We found that, although these MEV-FL cases had simple karyotypes, they showed very similar cnLOH profiles as compared to cytogenetically complex cases. The most frequent regions affected by cnLOH were 1p (17%), 6p (17%), 12q (13%) and 16p (13%). Our study suggests that cnLOH alterations may serve as important contributors to the pathological and clinical manifestations of FL.
Collapse
Affiliation(s)
- K J Cheung
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada.
| | | | | | | | | | | | | |
Collapse
|
33
|
Duhoux FP, Ameye G, Lambot V, Herens C, Lambert F, Raynaud S, Wlodarska I, Michaux L, Roche-Lestienne C, Labis E, Taviaux S, Chapiro E, Nguyen-Khac F, Khac FN, Struski S, Dobbelstein S, Dastugue N, Lippert E, Speleman F, Van Roy N, De Weer A, Rack K, Talmant P, Richebourg S, Mugneret F, Tigaud I, Mozziconacci MJ, Laibe S, Nadal N, Terré C, Libouton JM, Decottignies A, Vikkula M, Poirel HA. Refinement of 1p36 alterations not involving PRDM16 in myeloid and lymphoid malignancies. PLoS One 2011; 6:e26311. [PMID: 22039459 PMCID: PMC3198844 DOI: 10.1371/journal.pone.0026311] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 09/23/2011] [Indexed: 01/06/2023] Open
Abstract
Fluorescence in situ hybridization was performed to characterize 81 cases of myeloid and lymphoid malignancies with cytogenetic 1p36 alterations not affecting the PRDM16 locus. In total, three subgroups were identified: balanced translocations (N = 27) and telomeric rearrangements (N = 15), both mainly observed in myeloid disorders; and unbalanced non-telomeric rearrangements (N = 39), mainly observed in lymphoid proliferations and frequently associated with a highly complex karyotype. The 1p36 rearrangement was isolated in 12 cases, mainly myeloid disorders. The breakpoints on 1p36 were more widely distributed than previously reported, but with identifiable rare breakpoint cluster regions, such as the TP73 locus. We also found novel partner loci on 1p36 for the known multi-partner genes HMGA2 and RUNX1. We precised the common terminal 1p36 deletion, which has been suggested to have an adverse prognosis, in B-cell lymphomas [follicular lymphomas and diffuse large B-cell lymphomas with t(14;18)(q32;q21) as well as follicular lymphomas without t(14;18)]. Intrachromosomal telomeric repetitive sequences were detected in at least half the cases of telomeric rearrangements. It is unclear how the latter rearrangements occurred and whether they represent oncogenic events or result from chromosomal instability during oncogenesis.
Collapse
Affiliation(s)
- Francois P Duhoux
- Center for Human Genetics, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
High rate of TNFRSF14 gene alterations related to 1p36 region in de novo follicular lymphoma and impact on prognosis. Leukemia 2011; 26:559-62. [DOI: 10.1038/leu.2011.266] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
Leich E, Ott G, Rosenwald A. Pathology, pathogenesis and molecular genetics of follicular NHL. Best Pract Res Clin Haematol 2011; 24:95-109. [PMID: 21658611 DOI: 10.1016/j.beha.2011.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Follicular lymphoma (FL) is a germinal centre-derived indolent B-cell lymphoma representing the second most common Non Hodgkin lymphoma in the Western world. This chapter focuses on the pathology of FL and summarizes the current knowledge about genetic and molecular features that are relevant for the pathogenesis of this neoplasm. The translocation t(14;18) is present in approximately 90% of FL leading to the upregulation of the anti-apoptotic protein BCL2, that may constitute a promising molecular target for therapeutic approaches. FL lacking the t(14;18) also exist, and B-cells carrying the t(14;18) can be detected in a subset of healthy individuals. In addition to the t(14;18), secondary genetic alterations are present in most FL and, more recently, deeper insights into the methylation and microRNA expression patterns in the tumour cells have been gained. The tumour microenvironment appears to be particularly important for the biology and the clinical course of FL.
Collapse
Affiliation(s)
- E Leich
- Institute of Pathology, University of Würzburg, Josef-Schneider-Str 2, 97080 Würzburg, Germany.
| | | | | |
Collapse
|
36
|
Li X, Tan X, Yu Y, Chen H, Chang W, Hou J, Xu D, Ma L, Cao G. D9S168 microsatellite alteration predicts a poor prognosis in patients with clear cell renal cell carcinoma and correlates with the down-regulation of protein tyrosine phosphatase receptor delta. Cancer 2011; 117:4201-11. [DOI: 10.1002/cncr.26028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/12/2011] [Accepted: 01/18/2011] [Indexed: 11/09/2022]
|
37
|
van Krieken JH. New developments in the pathology of malignant lymphoma. A review of the literature published from August 2010–October 2010. J Hematop 2010. [DOI: 10.1007/s12308-010-0078-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|