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Panicker S, Chengizkhan G, Gor R, Ramachandran I, Ramalingam S. Exploring the Relationship between Fusion Genes and MicroRNAs in Cancer. Cells 2023; 12:2467. [PMID: 37887311 PMCID: PMC10605240 DOI: 10.3390/cells12202467] [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: 08/31/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Fusion genes are key cancer driver genes that can be used as potential drug targets in precision therapies, and they can also serve as accurate diagnostic and prognostic biomarkers. The fusion genes can cause microRNA (miRNA/miR) aberrations in many types of cancer. Nevertheless, whether fusion genes incite miRNA aberrations as one of their many critical oncogenic functionalities for driving carcinogenesis needs further investigation. Recent discoveries of miRNA genes that are present within the regions of genomic rearrangements that initiate fusion gene-based intronic miRNA dysregulation have brought the fusion genes into the limelight and revealed their unexplored potential in the field of cancer biology. Fusion gene-based 'promoter-switch' event aberrantly activate the miRNA-related upstream regulatory signals, while fusion-based coding region alterations disrupt the original miRNA coding loci. Fusion genes can potentially regulate the miRNA aberrations regardless of the protein-coding capability of the resultant fusion transcript. Studies on out-of-frame fusion and nonrecurrent fusion genes that cause miRNA dysregulation have attracted the attention of researchers on fusion genes from an oncological perspective and therefore could have potential implications in cancer therapies. This review will provide insights into the role of fusion genes and miRNAs, and their possible interrelationships in cancer.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Gautham Chengizkhan
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Ravi Gor
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Ilangovan Ramachandran
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
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Lebrun L, Allard-Demoustiez S, Salmon I. Pathology and new insights in central nervous system lymphomas. Curr Opin Oncol 2023; 35:347-356. [PMID: 37439536 PMCID: PMC10408733 DOI: 10.1097/cco.0000000000000978] [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] [Indexed: 07/14/2023]
Abstract
PURPOSE OF REVIEW Primary central nervous system lymphoma (PCNSL) is a rare central nervous system (CNS) malignancy, which represents a heterogenous group of tumors. Among PCNSL, diffuse large B-cell lymphoma of the CNS (CNS-DLBCL) represents the most common tumor type. Multiomics studies have recently revealed the complex genomic landscape of these rare diseases. These findings lead to a potential new molecular and epigenetic classification. RECENT FINDINGS Our review is focused on CNS-DLBCL in immunocompetent patients. CNS-DLBCL are derived from self-reactive/polyreactive precursor cells. An early molecular event such as MYD88 mutation leads to escape elimination of precursor cells, which, by a dysregulated GC reaction, acquire auto-/polyreactivity of the B-cell tumoral cells for antigens physiologically expressed in the CNS. Most of CNS-DLBCL tumor cells harbor a non-GCB, ABC-like immunophenotype associated with a late GC (exit) B-cells genotype by gene expression profiling. Various mechanisms of genetic alterations are involved in the pathogenesis of PCNSL, including point mutations [nonsomatic hypermutation (SHM), aberrant SHM (aSHM)], SHM/aSHM, chromosome copy gains or losses, and DNA hypermethylation. Constitutive NFκB activation plays a key role in lymphoma cell proliferation and survival by dysregulation of toll-like receptor (mutations of CARD11 and MYD88 ), BCR ( CD79B ), JAK-STAT, and NFκB signaling pathways. SUMMARY Multiomics approaches have succeeded to substantially improve the understanding of the pathogenesis, as well as the molecular and epigenetic events in PCNSL. Challenges remain due to the obvious heterogeneity of CNS-DLBCL, and improvement is needed for their classification.
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Affiliation(s)
- Laetitia Lebrun
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, Erasme University Hospital, Department of Pathology, Brussels
| | - Sacha Allard-Demoustiez
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, Erasme University Hospital, Department of Pathology, Brussels
| | - Isabelle Salmon
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, Erasme University Hospital, Department of Pathology, Brussels
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
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Ohno H, Maekawa F, Nakagawa M, Chagi Y, Nakagawa M, Kishimori C, Fukutsuka K, Hayashida M, Takeoka K, Maruyama W, Ukyo N, Sumiyoshi S. Two cases of primary diffuse large B-cell lymphoma of the CNS associated with t(8;14)(q24;q32) or t(3;14)(q27;q32) identified by G-banding and fluorescence in situ hybridization applied to metaphase spreads. J Clin Exp Hematop 2022; 62:242-248. [PMID: 36436932 PMCID: PMC9898718 DOI: 10.3960/jslrt.22019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We describe two patients with primary diffuse large B-cell lymphoma of the central nervous system (PCNS-DLBCL). The first patient (case 1) was a woman in her late 70s who presented with a tumor in the left frontal lobe, whereas the second patient (case 2) was a man in his early 70s who presented with a left frontal lobe tumor associated with intratumoral hemorrhage. The histopathology of the tumor specimen disclosed the proliferation of large cells with centroblastic (case 1) or immunoblastic/plasmablastic (case 2) cytomorphology and an accumulation of the tumor cells within the perivascular space. The cells in both cases were positive for CD20, CD79a, BCL6, IRF4/MUM1, MYC, and BCL2 and negative for CD5 and CD10. G-banding revealed t(8;14)(q24;q32) in case 1, and the tetraploid-range karyotype including two or three copies of der(3)t(3;14)(q27;q32) and der(14)t(3;14)(q27;q32) in case 2. Fluorescence in situ hybridization applied to metaphase spreads confirmed colocalization of MYC and IGH (case 1) and BCL6 and IGH (case 2) hybridization signals on the relevant derivative chromosomes. Case 1 carried the MYD88L265P mutation. This case report provides clear evidence for the occurrence of t(8;14)(q24;q32) and t(3;14)(q27;q32) in PCNS-DLBCL using metaphase-based cytogenetic analysis.
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Affiliation(s)
- Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Fumiyo Maekawa
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Misumi Nakagawa
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Yoshinari Chagi
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Miho Nakagawa
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Chiyuki Kishimori
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | | | | | - Kayo Takeoka
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Wataru Maruyama
- Department of Hematology, Tenri Hospital, Tenri, Nara, Japan
| | - Naoya Ukyo
- Department of Hematology, Tenri Hospital, Tenri, Nara, Japan
| | - Shinji Sumiyoshi
- Department of Diagnostic Pathology, Tenri Hospital, Tenri, Nara, Japan
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The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat Commun 2022; 13:2558. [PMID: 35538064 PMCID: PMC9091224 DOI: 10.1038/s41467-022-30050-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS. We find recurrent mutations in JAK-STAT, NFkB, and B-cell receptor signaling pathways, including hallmark mutations in MYD88 L265P (67%) and CD79B (63%), and CDKN2A deletions (83%). PCNSLs exhibit significantly more focal deletions of HLA-D (6p21) locus as a potential mechanism of immune evasion. Mutational signatures correlating with DNA replication and mitosis are significantly enriched in PCNSL. TERT gene expression is significantly higher in PCNSL compared to activated B-cell (ABC)-DLBCL. Transcriptome analysis clearly distinguishes PCNSL and systemic DLBCL into distinct molecular subtypes. Epstein-Barr virus (EBV)+ CNSL cases lack recurrent mutational hotspots apart from IG and HLA-DRB loci. We show that PCNSL can be clearly distinguished from DLBCL, having distinct expression profiles, IG expression and translocation patterns, as well as specific combinations of genetic alterations.
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Montesinos-Rongen M, Brunn A, Sanchez-Ruiz M, Küppers R, Siebert R, Deckert M. Impact of a Faulty Germinal Center Reaction on the Pathogenesis of Primary Diffuse Large B Cell Lymphoma of the Central Nervous System. Cancers (Basel) 2021; 13:cancers13246334. [PMID: 34944954 PMCID: PMC8699297 DOI: 10.3390/cancers13246334] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 01/12/2023] Open
Abstract
Simple Summary The pathogenetic mechanisms and peculiar tropism of primary CNS lymphoma (PCNSL) of the central nervous system (CNS) have been the subject of debate for decades. Hypothesis-driven targeted molecular studies have revealed that PCNSLs derived from self-/polyreactive B cells that have escaped developmental control mechanisms. The early acquisition of activating mutations targeting the B cell receptor pathway provides a survival advantage. The failure of the germinal center (GC) reaction and its checkpoints increases tumor B cell affinity for the CNS. During this faulty GC reaction, PCNSL tumor cells acquire further oncogenic alterations converging on the Toll-like receptor, B cell receptor, and NF-κB pathway. These activated pathways sustain proliferation. Concomitantly, cells become unable to complete terminal B cell differentiation, becoming trapped within the vicious cycle of the GC reaction as low-affinity IgM+ B cells related to memory cells. Abstract Primary lymphoma of the central nervous system (PCNSL, CNS) is a specific diffuse large B cell lymphoma (DLBCL) entity confined to the CNS. Key to its pathogenesis is a failure of B cell differentiation and a lack of appropriate control at differentiation stages before entrance and within the germinal center (GC). Self-/polyreactive B cells rescued from apoptosis by MYD88 and/or CD79B mutations accumulate a high load of somatic mutations in their rearranged immunoglobulin (IG) genes, with ongoing somatic hypermutation (SHM). Furthermore, the targeting of oncogenes by aberrant SHM (e.g., PIM1, PAX5, RHOH, MYC, BTG2, KLHL14, SUSD2), translocations of the IG and BCL6 genes, and genomic instability (e.g., gains of 18q21; losses of 9p21, 8q12, 6q21) occur in these cells in the course of their malignant transformation. Activated Toll-like receptor, B cell receptor (BCR), and NF-κB signaling pathways foster lymphoma cell proliferation. Hence, tumor cells are arrested in a late B cell differentiation stage, corresponding to late GC exit B cells, which are genetically related to IgM+ memory cells. Paradoxically, the GC reaction increases self-/polyreactivity, yielding increased tumor BCR reactivity for multiple CNS proteins, which likely contributes to CNS tropism of the lymphoma. The loss of MHC class I antigen expression supports tumor cell immune escape. Thus, specific and unique interactions of the tumor cells with resident CNS cells determine the hallmarks of PCNSL.
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Affiliation(s)
- Manuel Montesinos-Rongen
- Institute of Neuropathology, Faculty of Medicine, University Hospital Cologne, 50937 Cologne, Germany; (M.M.-R.); (A.B.); (M.S.-R.)
| | - Anna Brunn
- Institute of Neuropathology, Faculty of Medicine, University Hospital Cologne, 50937 Cologne, Germany; (M.M.-R.); (A.B.); (M.S.-R.)
| | - Monica Sanchez-Ruiz
- Institute of Neuropathology, Faculty of Medicine, University Hospital Cologne, 50937 Cologne, Germany; (M.M.-R.); (A.B.); (M.S.-R.)
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, 45122 Essen, Germany;
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081 Ulm, Germany;
| | - Martina Deckert
- Institute of Neuropathology, Faculty of Medicine, University Hospital Cologne, 50937 Cologne, Germany; (M.M.-R.); (A.B.); (M.S.-R.)
- Correspondence: ; Tel.: +49-221-478-5265; Fax: +49-221-478-3712
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You H, Wei L, Kaminska B. Emerging insights into origin and pathobiology of primary central nervous system lymphoma. Cancer Lett 2021; 509:121-129. [PMID: 33766752 DOI: 10.1016/j.canlet.2021.02.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/15/2021] [Accepted: 02/28/2021] [Indexed: 01/03/2023]
Abstract
Primary central nervous system lymphoma (PCNSL) is an aggressive cancer typically confined to the brain, eyes, leptomeninges and spinal cord, without evidence of systemic involvement. PCNSL remains a challenge for scientists and clinicians due to insufficient biological knowledge, a lack of appropriate animal models and validated diagnostic biomarkers. We summarize recent findings on genomic, transcriptomic and epigenetic alterations identified in PCNSL. These findings help to define pathobiology of the disease and delineate defects in B cell differentiation. Evidence from genomic and transcriptomic studies helps to separate PCNSL from other hematological malignancies, improves diagnostics and reveals new therapeutic targets for treatment. Discovery of the CNS lymphatic system may be instrumental in better understanding the origin of the disease. We critically assess the attempts to model PCNSL in rodents, and conclude that there is a lack of a genetic/transgenic model that adequately mimics pathogenesis of the disease. Contribution of the tumor microenvironment in tumorigenesis and aggressiveness of PCNSL remains understudied. Assessing heterogeneity of immune infiltrates, cytokine profiling and molecular markers, may improve diagnostics and put forward new therapeutic strategies.
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Affiliation(s)
- Hua You
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Li Wei
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Bozena Kaminska
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China; Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
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7
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Zhang Y, Ma L, Liu J, Zhu H, Lu L, Deng K, Ma W, Pan H, Wang R, Yao Y. Case Report: Identification of Potential Prognosis-Related TP53 Mutation and BCL6-LPP Fusion in Primary Pituitary Lymphoma by Next Generation Sequencing: Two Cases. Front Endocrinol (Lausanne) 2021; 12:673908. [PMID: 34381423 PMCID: PMC8350335 DOI: 10.3389/fendo.2021.673908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/20/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Primary pituitary lymphoma (PPL) is an extremely rare disease with poor prognosis. Although PPL has been shown to be different from classical primary central nervous system lymphoma because of the embryological origin of structures, individual and precise treatment of PPL remains unknown. METHODS A 61-year-old man and a 65-year-old woman both diagnosed with primary pituitary diffuse large B cell lymphoma underwent genetic analysis of cerebrospinal fluid and tumor tissue by next generation sequencing. RESULTS In the first case, partial remission was achieved following R²-MTX chemotherapy. In the other case with TP53 mutation and BCL6-LPP fusion, disease progressed although different chemotherapy regimens were given. CONCLUSION The gene mutation of TP53 and BCL6 may be identified as a marker responsible for prognostic difference in patients with PPL. Genetic analysis may provide a novel approach for precise management and prognosis prediction.
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Affiliation(s)
- Yi Zhang
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Liyuan Ma
- Department of Endocrinology, Peking Union Medical College Hospital, Beijing, China
| | - Jie Liu
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Huijuan Zhu
- Department of Endocrinology, Peking Union Medical College Hospital, Beijing, China
| | - Lin Lu
- Department of Endocrinology, Peking Union Medical College Hospital, Beijing, China
| | - Kan Deng
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Wenbin Ma
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Hui Pan
- Department of Endocrinology, Peking Union Medical College Hospital, Beijing, China
| | - Renzhi Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Yong Yao
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
- *Correspondence: Yong Yao,
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Molecular features of a large cohort of primary central nervous system lymphoma using tissue microarray. Blood Adv 2020; 3:3953-3961. [PMID: 31805190 DOI: 10.1182/bloodadvances.2019000989] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
The objective of this study was to evaluate the distribution and prognostic impact of a broad range of molecular attributes in a large cohort of immunocompetent patients with primary central nervous system lymphoma (PCNSL) by using tissue microarray. Patients diagnosed with PCNSL were initially identified in the BC Cancer Lymphoid Cancer clinical and pathology databases. Tissue microarrays were constructed by using archival formalin-fixed paraffin-embedded diagnostic biopsy tissue. Immunohistochemistry and fluorescent in situ hybridization studies were performed. A total of 115 patients with PCNSL with diffuse large B-cell lymphoma (DLBCL) histology were identified. The majority of cases (≥75%) had a non-germinal center B-cell phenotype according to immunohistochemistry algorithms, but cell of origin did not affect progression-free or overall survival. MYC (40%), BCL2 (75%), and programmed death-ligand 1 (29%) protein expression were common, but their corresponding gene rearrangements were rare (≤1% each), suggesting that alternate mechanisms were driving expression. There were no dual rearrangements involving MYC and BCL2. Only 22% of cases had membranous expression of major histocompatibility complex class II, suggesting a mechanism for escape from immune surveillance. Epstein-Barr virus-encoded RNA was positive in 1 immunocompetent patient. BCL6 protein expression (77%) and BCL6 rearrangements (31%) were frequent; the latter was the only factor associated with a poor prognosis in the overall cohort and in the subgroup of 52 patients treated with high-dose methotrexate-based regimens. This large population-based study shows that prominent molecular features of PCNSL are unique and different from those of systemic DLBCL. These results may better inform drug development in PCNSL.
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Pina-Oviedo S, Bellamy WT, Gokden M. Analysis of primary central nervous system large B-cell lymphoma in the era of high-grade B-cell lymphoma: Detection of two cases with MYC and BCL6 rearrangements in a cohort of 12 cases. Ann Diagn Pathol 2020; 48:151610. [PMID: 32889391 DOI: 10.1016/j.anndiagpath.2020.151610] [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: 05/11/2020] [Revised: 06/30/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
High-grade diffuse large B-cell lymphoma (HG-DLBCL) refers to DLBCL with MYC and BCL2 and/or BCL6 rearrangements (double-hit or triple-hit DLBCL) that exhibits poor prognosis. Double-expressor DLBCL (c-myc+/bcl-2+) has intermediate prognosis when compared to HG-DLBCL. Primary central nervous system lymphoma (PCNSL) has distinct pathophysiology (frequent non-germinal center-like subtype and double-expressor) and has worse prognosis than systemic DLBCL. By fluorescence in situ hybridization (FISH), 25-30% of PCNSLs harbor BCL6 abnormalities with rare alterations in MYC, BCL2, double-hit or triple-hit events. We describe the clinicopathologic features and status of MYC, BCL2 and BCL6 in 12 PCNSLs (7 women, 5 men; median age 63 years; range: 28-79). Six cases showed focal starry-sky pattern. Immunohistochemically, all (100%) were of non-germinal center-like subtype, and 8/10 (80%) cases were double-expressors. Ki-67 ranged from 70 to 100%. FISH was positive in 9/12 (75%) cases: 4 (33%) harbored a BCL6 rearrangement, 3 (25%) had a gain of BCL2, 2 (17%) cases each had a gain of BCL6 and gain of IGH, and gain of MYC and deletion of MYC were observed in 1 case each (8%). Two (16%) cases were MYC/BCL6 double-hit PCNSLs. No MYC/BCL2 or triple-hit cases were identified. Eleven (92%) patients received chemotherapy and one also received whole brain radiation. The median time of follow-up was 4.4 months (range, 0.3-40.3). Seven (58%) patients are alive, 4 (33%) have died, and 1 (8%) had no follow-up. Five alive patients are in remission, including one MYC/BCL6 double-hit PCNSL. Our results add two new cases of rare double-hit PCNSL to the literature.
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Affiliation(s)
- Sergio Pina-Oviedo
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - William T Bellamy
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America.
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Kim B, Kim E, Lee ST, Cheong JW, Lyu CJ, Min YH, Choi JR. Detection of recurrent, rare, and novel gene fusions in patients with acute leukemia using next-generation sequencing approaches. Hematol Oncol 2020; 38:82-88. [PMID: 31875988 DOI: 10.1002/hon.2709] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/08/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023]
Abstract
Identification of gene fusion is an essential part in the management of patients with acute leukemia, not only for diagnosis but also in predicting the treatment outcome and selecting appropriate treatment. Adopting next-generation sequencing (NGS) technology for identification of gene fusion in patients with acute leukemia can be a good alternative to conventional tests. In the present study, the NGS RNA fusion gene panel test was applied to diagnostic samples of patients with acute leukemia to identify fusion genes more efficiently. Among 134 patients with acute leukemia, 53 gene fusions were detected in 52 patients. In addition to the recurrent gene fusions specified in the WHO diagnostic criteria, 11 rare or novel gene fusions were identified. Of those, two were gene fusions associated with Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL), two were novel gene fusions, three were gene fusions with novel partner genes, and six were rare gene fusions from previous reports. We confirmed the clinical utility of the NGS test in identifying clinically significant gene fusions such as gene fusions involving KMT2A that has a large number of partners. Notably, Ph-like ALL-associated gene fusions could be easily identified despite the wide variety of genes involved. The results from the present study may contribute toward a better understanding of the genomic landscape of acute leukemia as well as patient management.
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Affiliation(s)
- Borahm Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Esl Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - June-Won Cheong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Chuhl Joo Lyu
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Yoo Hong Min
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
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11
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Zhang L, Dong X, Lee M, Maslov AY, Wang T, Vijg J. Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proc Natl Acad Sci U S A 2019; 116:9014-9019. [PMID: 30992375 PMCID: PMC6500118 DOI: 10.1073/pnas.1902510116] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell-specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.
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Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461;
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
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12
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Nosrati A, Monabati A, Sadeghipour A, Radmanesh F, Safaei A, Movahedinia S. MYC, BCL2, and BCL6 rearrangements in primary central nervous system lymphoma of large B cell type. Ann Hematol 2018; 98:169-173. [PMID: 30306208 DOI: 10.1007/s00277-018-3498-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 09/10/2018] [Indexed: 12/22/2022]
Abstract
Primary central nervous system lymphoma (PCNSL) is a rare specific subtype of non-Hodgkin lymphoma limited to the brain, leptomeninges, spinal cord, or eyes without any systemic presentation and relapse which mostly takes place in CNS. In more than 95% of patients, it is of diffuse large B cell lymphoma (DLBCL) type. Categorizing PCNSL to germinal center cell like or activated B cell like, as we usually do for DLBCL NOS, may not be applicable for predicting outcome. Possible prognostic significance of MYC, BCL2, and/or BCL6 rearrangements may be important given what we know about their impact in systemic DLBCL, but we have limited knowledge about the status of double or triple hit molecular changes in PCNSL. Here, we have investigated prevalence of these molecular alterations in PCNSL. Two independent tissue microarrays constructed from 78 formalin-fixed paraffin-embedded blocks of confirmed PCNSL were tested for rearrangement of MYC, BCL2, and BCL6 by interphase fluorescent in situ hybridization (FISH) using break apart dual color probes. BCL6 translocation was detected in 15 (12%) cases. Translocation involving MYC and BCL2 was identified in 3 cases (3.8%) and 1 case (1.3%) respectively. One double hit lymphoma was discovered with both MYC/BCL2 translocation (1.3%). To the best of our knowledge, few organized studies have been conducted for MYC, BCL2, and/or BCL6 rearrangement in PCNSL. This study is evaluating large number of PCNSL. Double or triple hit events which are rarely seen in PCNSL.
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Affiliation(s)
- Anahita Nosrati
- Hematopatholgy Service, Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Monabati
- Hematopatholgy Service, Department of Pathology and Hematology Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Alireza Sadeghipour
- Department of Pathology, Rasool-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Radmanesh
- Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Akbar Safaei
- Molecular Pathology and Cytogenetics, Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sajjadeh Movahedinia
- Pathology and Stem Cell Research Center, Afzalipour Medical School, Kerman University of Medical Sciences, Kerman, Iran.,Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
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Magnoli F, Bernasconi B, Vivian L, Proserpio I, Pinotti G, Campiotti L, Mazzucchelli L, Sessa F, Tibiletti MG, Uccella S. Primary extranodal diffuse large B-cell lymphomas: Many sites, many entities? Clinico-pathological, immunohistochemical and cytogenetic study of 106 cases. Cancer Genet 2018; 228-229:28-40. [PMID: 30553470 DOI: 10.1016/j.cancergen.2018.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/13/2018] [Accepted: 08/02/2018] [Indexed: 02/08/2023]
Abstract
We analyzed the clinicopathological, immunohistochemical and cytogenetic features of 106 extranodal (EN) diffuse large B-cell lymphomas (DLBCLs) from stomach (34 cases), intestine (10), cervico-cephalic region (11), central nervous system (13), testes (21), skin (8), and miscellaneous sites (9). Hans' algorithm and the immunohistochemical double expressor score (DES) for MYC and BCL2 were applied to all cases. A subset of fifty-eight cases were analyzed with fluorescent in situ hybridization (FISH) with specific break apart probes for BCL6, MYC, BCL2, CCND1, BCL10 and MALT1 genes. Clinical records were available for all patients. The immunohistochemical study showed that, in our series of EN-DLBCLs, the Hans' subgroup and the DES differed significantly according to the site of origin. At FISH analysis, BCL6 and BCL2 were the most commonly rearranged genes in non-GC and in GC cases, respectively. Gastrointestinal lymphomas displayed the highest rate of gene rearrangements, often with MYC involvement. One testicular DLBCL showed BCL2/MYC double hit. At survival analysis, cerebral and testicular origin was associated with poor prognosis. In addition, Hans' subgroup and other immunohistochemical markers influenced patients' outcome. In conclusion, our data suggest that immunophenotypic, genetic and survival characteristics of EN-DLBCL are related to the specific primary site of the disease.
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Affiliation(s)
- Francesca Magnoli
- Department Of Medicine and Surgery, Unit of Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy; Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Barbara Bernasconi
- Department of Obstetrics and Gynecology, ASST Sette Laghi, Varese, Italy
| | - Lisa Vivian
- Department Of Medicine and Surgery, Unit of Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | | | | | - Leonardo Campiotti
- Department of Medicine and Surgery, Unit of Internal Medicine, University of Insubria, Varese, Italy
| | | | - Fausto Sessa
- Department Of Medicine and Surgery, Unit of Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | | | - Silvia Uccella
- Department Of Medicine and Surgery, Unit of Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy.
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Abstract
Objective: Primary central nervous system lymphoma (PCNSL) is a specific type of non-Hodgkin lymphoma with poor prognosis. The rare incidence of this disease and difficulty to obtain sufficient tissue material impede deep research into PCNSL. However, application of modern molecular techniques makes it possible to find biological characteristics exclusive to PCNSL. Therefore, we systematically reviewed the latest research progress on biological characteristics and pathogenesis of PCNSL. Data Sources: The data analyzed in this review were from the articles listed in PubMed database. Study Selection: Articles focusing on the biology of PCNSL at the cytogenetic or molecular level were reviewed, including clinical, basic research, and review articles. Results: With respect to histopathology, perivascular growth pattern and reactive perivascular T-cell infiltration are regarded as typical histopathological manifestations of tumor cells in PCNSL. Moreover, tumor cells of PCNSL predominantly express an activated B-cell-like phenotype, including CD10− BCL-6+ MUM1+, CD10− BCL-6− MUM1+, and CD10− BCL-6− MUM1−. On the molecular level, some molecular and genetic alterations may contribute to malignant transformation, including mutations of proto-oncogenes and tumor suppressor genes, gains and losses of genetic material, as well as aberrant activation of some important signaling pathways, such as nuclear factor-κB and JAK/STAT pathway. Conclusions: The integrated molecular mechanisms involved in pathogenesis of PCNSL are not well understood. The important biomarkers indicating prognosis are not identified. Multicenter studies should be carried out to elucidate pathogenesis of PCNSL to find novel and effective therapeutic strategies.
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Affiliation(s)
- Xue-Liang Yang
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Yuan-Bo Liu
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
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Case Reports in Oncological Medicine Myoepithelioma: A New Rearrangement Involving the LPP Locus in a Case of Multiple Bone and Soft Tissue Lesions. Case Rep Oncol Med 2018; 2018:3512847. [PMID: 29992069 PMCID: PMC5848058 DOI: 10.1155/2018/3512847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/10/2017] [Indexed: 01/24/2023] Open
Abstract
We report a case of multiple myoepithelioma with synchronous bone and soft tissue tumors, associated with a new genomic alteration of the LPP locus. The lesions occurred in the foot by presenting one lump in the plantar soft tissue, and three lesions were detected in the calcaneus and in the navicular bone. All tumors showed the double immunophenotype of epithelial markers and S100 protein expression. No rearrangement of the EWSR1 and FUS loci was detected as reported in myoepitheliomas. However, molecular karyotyping detected an unbalanced rearrangement of the LPP locus, not involving the HMGA2 locus, which is the most frequent translocation partner observed in benign mesenchymal tumors such as lipomas (of soft tissue as well as parosteal) and pulmonary chondroid hamartoma.
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Kim H, Kim IS, Lee EY, Shin DH, Cho SH. First Case of Diffuse Large B-Cell Lymphoma Subtype of Monomorphic Post-Transplant Lymphoproliferative Disorder With 3q27 Translocation. Ann Lab Med 2016; 36:380-3. [PMID: 27139615 PMCID: PMC4855062 DOI: 10.3343/alm.2016.36.4.380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/14/2015] [Accepted: 02/12/2016] [Indexed: 12/03/2022] Open
Affiliation(s)
- Hyerim Kim
- Department of Laboratory Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - In Suk Kim
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.
| | - Eun Yup Lee
- Department of Laboratory Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Dong Hoon Shin
- Department of Pathology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Su Hee Cho
- Division of Hematology-Oncology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
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Yu X, Li Z, Shen J, Chan MTV, Wu WKK. Role of microRNAs in primary central nervous system lymphomas. Cell Prolif 2016; 49:147-53. [PMID: 26990358 DOI: 10.1111/cpr.12243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/16/2015] [Indexed: 12/11/2022] Open
Abstract
Primary central nervous system lymphomas (PCNSL) are extranodal non-Hodgkin lymphomas arising exclusively inside the CNS, and account for about 3% of primary intracranial tumours. This tumour lacks systemic manifestations and prognosis of patients with PCNSL remains poor despite recent advancement of chemoradiotherapy. MicroRNAs are small non-coding RNAs that post-transcriptionally downregulate gene expression by binding to target mRNAs, inducing their degradation or translational repression. MicroRNAs play significant roles in almost all malignancy-related biological processes, including cell proliferation, differentiation, apoptosis and metabolism. Many deregulated miRNAs has been identified in PCNSL but their biological significance remains to be fully elucidated. In this review, we summarize current evidence regarding the pathogenic role of PCNSL-associated microRNAs and their potential applications for diagnosis and prognostication of this deadly disease.
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Affiliation(s)
- Xin Yu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100042, China
| | - Zheng Li
- Department of Orthopedics Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100042, China
| | - Jianxiong Shen
- Department of Orthopedics Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100042, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, 999077, China.,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, 999077, China
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LIU JIA, LIU XUEQING, LIU YING, SUN YANAN, LI SI, LI CHUNMEI, LI JIE, TIAN WEI, SHANG XIAOMING, ZHOU YUNTAO. MicroRNA 28-5p regulates ATP-binding cassette transporter A1 via inhibiting extracellular signal-regulated kinase 2. Mol Med Rep 2015; 13:433-40. [DOI: 10.3892/mmr.2015.4563] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 07/29/2015] [Indexed: 11/05/2022] Open
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miR-28-5p Involved in LXR-ABCA1 Pathway is Increased in the Plasma of Unstable Angina Patients. Heart Lung Circ 2015; 24:724-30. [DOI: 10.1016/j.hlc.2014.12.160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 11/21/2022]
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Montesinos-Rongen M, Purschke F, Küppers R, Deckert M. Immunoglobulin Repertoire of Primary Lymphomas of the Central Nervous System. J Neuropathol Exp Neurol 2014; 73:1116-25. [DOI: 10.1097/nen.0000000000000133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Deckert M, Montesinos-Rongen M, Brunn A, Siebert R. Systems biology of primary CNS lymphoma: from genetic aberrations to modeling in mice. Acta Neuropathol 2014; 127:175-88. [PMID: 24240734 DOI: 10.1007/s00401-013-1202-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/21/2013] [Indexed: 12/15/2022]
Abstract
Primary lymphoma of the central nervous system (CNS, PCNSL) is a specific diffuse large B cell lymphoma entity arising in and confined to the CNS. Despite extensive research since many decades, the pathogenetic mechanisms underlying the remarkable tropism of this peculiar malignant hematopoietic tumor remain still to be elucidated. In the present review, we summarize the present knowledge on the genotypic and phenotypic characteristics of the tumor cells of PCNSL, give an overview over deregulated molecular pathways in PCNSL and present recent progress in the field of preclinical modeling of PCNSL in mice. With regard to the phenotype, PCNSL cells resemble late germinal center exit IgM+IgD+ B cells with blocked terminal B cell differentiation. They show continued BCL6 activity in line with ongoing activity of the germinal center program. This together with the pathways deregulated by genetic alterations may foster B cell activation and brisk proliferation, which correlated with the simultaneous MYC and BCL2 overexpression characteristic for PCNSL. On the genetic level, PCNSL are characterized by ongoing aberrant somatic hypermutation that, besides the IG locus, targets the PAX5, TTF, MYC, and PIM1 genes. Moreover, PCNSL cells show impaired IG class switch due to sμ region deletions, and PRDM1 mutations. Several important pathways, i.e., the B cell receptor (BCR), the toll-like receptor, and the nuclear factor-κB pathway, are activated frequently due to genetic changes affecting genes like CD79B, SHIP, CBL, BLNK, CARD11, MALT1, BCL2, and MYD88. These changes likely foster tumor cell survival. Nevertheless, many of these features are also present in subsets of systemic DLBLC and might not be the only reasons for the peculiar tropism of PCNSL. Here, preclinical animal models that closely mimic the clinical course and neuropathology of human PCNSL may provide further insight and we discuss recent advances in this field. Such models enable us to understand the pathogenetic interaction between the malignant B cells, resident cell populations of the CNS, and the associated inflammatory infiltrate. Indeed, the immunophenotype of the CNS as well as tumor cell characteristics and intracerebral interactions may create a micromilieu particularly conducive to PCNSL that may foster aggressiveness of tumor cells and accelerate the fatal course of disease. Suitable animal models may also serve as a well-defined preclinical system and may provide a useful tool for developing new specific therapeutic strategies.
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Rougemont AL, Bouron-Dal Soglio D, Patey-Mariaud de Serre N, Fetni R, Fan L, Barrette S, Fournet JC. A t(17;22)(q21;q12) with partial ETV4 deletion in a soft tissue Ewing sarcoma. Cancer Genet 2012; 205:55-60. [PMID: 22429598 DOI: 10.1016/j.cancergen.2012.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 01/13/2012] [Accepted: 01/16/2012] [Indexed: 11/17/2022]
Abstract
Cytogenetic analysis of a lumbar soft tissue Ewing sarcoma (ES) in a 7-month-old female child showed a t(17;22)(q21;q12), a rare translocation leading to an EWSR1-ETV4 chimeric transcript. These findings were confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) techniques. The breakpoints were characterized by direct sequencing of the chimeric fusion gene. Tumor genotyping using the Affymetrix Genome-Wide Human single nucleotide polymorphism (SNP) array 6.0 Genechip identified deletions of both chromosomal regions involved in the translocation, resulting in partial deletion of ETV4, but an uninvolved EWSR1 gene. The creation of a fusion between EWSR1 and an ETS family gene consecutive to a chromosomal translocation is characteristic of the Ewing family of tumors (EFT). This is the first report of a deletion involving the two breakpoints in an EWS-ETS translocation. To date, only two cases of t(17;22)(q21;q12) in Ewing sarcoma have been reported, with no associated deletion. Interestingly, both cases had also occurred in soft tissue tumors, which are less common than their bone-involving counterparts.
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Affiliation(s)
- Anne-Laure Rougemont
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada.
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Kim BY, Jin HJ, Kim JY. Genome-wide association analysis of Sasang constitution in the Korean population. J Altern Complement Med 2012; 18:262-9. [PMID: 22394158 DOI: 10.1089/acm.2010.0764] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Sasang constitutional medicine is a traditional Korean medicine in which an individual is classified into one of four types of constitution: Taeum (TE), Soeum (SE) Soyang (SY), and Taeyang (TY). These constitution types are determined with biologic and physiologic characteristics, so it has been assumed that genetic factors are associated with each constitution type. Identifying the genetic elements underlying each constitution is necessary for the elucidation of the molecular mechanism of Sasang constitutional medicine. DESIGN A total of 341,998 genetic loci across the whole genome were genotyped for 1222 subjects of defined constitution type. The genetic loci associated with each constitution type were identified and the functional connectivity of genes within these loci was analyzed using statistical text mining. RESULTS From the difference in allele frequencies between constitution types, significant genetic loci associated with each type were identified. Chromosomes 3q27.3 (rs10937331, p=2.71×10(-6)), 15q22.2 (rs7180547, p=1.58×10(-6)), and 14q22.3 (rs12431592, p=1.31×10(-6)) were most significantly associated with TE, SE, and SY constitution types, respectively. From the functional relationship analysis using all loci with a p-value≤10(-4), genes associated with each constitution type were identified. Fifteen (15) genes, including GPM6A, SYT4, and GRIK1, were significantly associated with the TE constitution type (p<0.05); 12 genes, including DRGX and AKAP11, were significantly associated with the SE constitution type (p<0.05); and 17 genes, including ZFP42, CDH22, ALDH1A2, OTX2, and EN2, were significantly associated with the SY constitution type (p<0.05). CONCLUSIONS Genetic loci and genes associated with Sasang constitution types were systematically identified from a genome-wide association study using a large number of subjects.
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Affiliation(s)
- Bu-Yeo Kim
- Division of Constitutional Medicine Research, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
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Cell Adhesion and Transcriptional Activity - Defining the Role of the Novel Protooncogene LPP. Transl Oncol 2011; 2:107-16. [PMID: 19701494 DOI: 10.1593/tlo.09112] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/20/2009] [Accepted: 02/25/2009] [Indexed: 12/13/2022] Open
Abstract
Integrating signals from the extracellular matrix through the cell surface into the nucleus is an essential feature of metazoan life. To date, many signal transducers known as shuttle proteins have been identified to act as both a cytoskeletal and a signaling protein. Among them, the most prominent representatives are zyxin and lipoma preferred (translocation) partner (LPP). These proteins belong to the LIM domain protein family and are associated with cell migration, proliferation, and transcription. LPP was first identified in benign human lipomas and was subsequently found to be overexpressed in human malignancies such as lung carcinoma, soft tissue sarcoma, and leukemia. This review portrays LPP in the context of human neoplasia based on a study of the literature to define its important role as a novel protooncogene in carcinogenesis.
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Preusser M, Woehrer A, Koperek O, Rottenfusser A, Dieckmann K, Gatterbauer B, Roessler K, Slavc I, Jaeger U, Streubel B, Hainfellner JA, Chott A. Primary central nervous system lymphoma: a clinicopathological study of 75 cases. Pathology 2011; 42:547-52. [PMID: 20854073 DOI: 10.3109/00313025.2010.508786] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AIMS Pathological and clinical data in a large series of immunocompetent patients with primary lymphoma of the central nervous system (PCNSL) were analysed. METHODS We immunostained tumour specimens of 75 patients for CD3, CD4, CD5, CD8, CD10, CD20, CD30, CD79a, Bcl-2, Bcl-6, CD138, MUM1, TDT, PAX5, FOXP1 and Ki-67 and performed in situ hybridisation for Epstein-Barr virus (EBV) RNA. Eleven cases were investigated for rearrangements of BCL6, immunoglobulin heavy chain (IGH) and FOXP1 genes using fluorescent in situ hybridisation (FISH). RESULTS Histologically, most cases were classified as diffuse large B-cell lymphoma (80.2%) predominantly of centroblastic type. Immunophenotypic profiling revealed that 96% and 4% of cases corresponded to non-germinal centre and germinal centre type, respectively. FISH analysis showed t(3;14)/IGH-BCL6 in 2/11 cases and trisomy 3 in 2/11 cases. FOXP1 rearrangements were not found. At survival analysis, Karnofsky index >80 and presence of Bcl-6 expression showed independent significant association with favourable patient outcome. CONCLUSIONS PCNSL represents a histologically and immunophenotypically very homogeneous lymphoma type, probably derived from germinal centre exit B cells. The frequent overexpression of FOXP1 appears not to be related to FOXP1 gene rearrangement. Survival analyses disclosed Bcl-6 expression and high Karnofsky performance score as independent prognostic parameters associated with favourable outcome.
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Schwindt H, Vater I, Kreuz M, Montesinos-Rongen M, Brunn A, Richter J, Gesk S, Ammerpohl O, Wiestler OD, Hasenclever D, Deckert M, Siebert R. Chromosomal imbalances and partial uniparental disomies in primary central nervous system lymphoma. Leukemia 2009; 23:1875-84. [PMID: 19494841 DOI: 10.1038/leu.2009.120] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
To determine the pattern of genetic alterations in primary central nervous system lymphomas (PCNSL), 19 PCNSL were studied by high-density single-nucleotide polymorphism arrays. Recurrent losses involved 6p21.32, 6q21, 8q12-12.2, 9p21.3, 3p14.2, 4q35.2, 10q23.21 and 12p13.2, whereas gains involved 18q21-23, 19q13.31, 19q13.43 and the entire chromosomes X and 12. Partial uniparental disomies (pUPDs) were identified in 6p and 9p21.3. These genomic alterations affected the HLA locus, the CDKN2A/p16, CDKN2B/p15 and MTAP, as well as the PRDM1, FAS, MALT1, and BCL2 genes. Increased methylation values of the CDKN2A/p16 promoter region were detected in 75% (6/8) PCNSL. Gene expression profiling showed 4/21 (20%) minimal common regions of imbalances to be associated with a differential mRNA expression affecting the FAS, STAT6, CD27, ARHGEF6 and SEPT6 genes. Collectively, this study unraveled novel genomic imbalances and pUPD with a high resolution in PCNSL and identified target genes of potential relevance in the pathogenesis of this lymphoma entity.
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Affiliation(s)
- H Schwindt
- Department of Neuropathology, University Hospital of Cologne, Cologne D-50924, Germany
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Schwaenen C, Viardot A, Berger H, Barth TFE, Bentink S, Döhner H, Enz M, Feller AC, Hansmann ML, Hummel M, Kestler HA, Klapper W, Kreuz M, Lenze D, Loeffler M, Möller P, Müller-Hermelink HK, Ott G, Rosolowski M, Rosenwald A, Ruf S, Siebert R, Spang R, Stein H, Truemper L, Lichter P, Bentz M, Wessendorf S. Microarray-based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status. Genes Chromosomes Cancer 2009; 48:39-54. [DOI: 10.1002/gcc.20617] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Epstein Barr virus-associated primary CNS lymphomas in elderly patients on immunosuppressive medications. J Neuropathol Exp Neurol 2008; 67:1103-11. [PMID: 18957891 DOI: 10.1097/nen.0b013e31818beaea] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Unlike primary central nervous system lymphomas (PCNSLs) in patients with AIDS or organ transplants, PCNSLs in the elderly are usually not considered to be mediated by Epstein Barr virus (EBV); hence, diagnostic studies for EBV are not routinely performed. We encountered 4 patients, 65 years or older, who developed EBV-associated PCNSLs and who had been treated with a variety of immunosuppressive drugs for different autoimmune/collagen vascular disorders, including autoimmune polyneuropathy (mycophenolate mofetil for 5 years), polymyositis (prednisone for 16 years with intermittent methotrexate, azathioprine, and cyclophosphamide), myasthenia gravis (azathioprine >10 years), and rheumatoid arthritis (methotrexate >10 years). All patients had multifocal, necrotic brain lesions typical of EBV-positive PCNSLs on neuroimaging. Withdrawing immunosuppressives lead to PCNSL regression in some patients. The patient who had received mycophenolate mofetil was treated successfully for his EBV-associated PCNSL with rituximab and methotrexate, but later developed fatal systemic malignant melanoma, which was likely immunosuppression related. The striking feature of these cases is the variety of underlying diseases-and hence accompanying medications-that can be associated with EBV-associated PCNSLs. They serve as a diagnostic alert for neuropathologists and suggest that increased testing of PCNSLs for EBV by immunohistochemistry or in situ hybridization may be warranted in any patient on any immunosuppressive medication, but particularly the elderly.
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Havelange V, Heaphy CEA, Garzon R. MicroRNAs in the diagnosis, prognosis and treatment of cancer. Oncol Rev 2008. [DOI: 10.1007/s12156-008-0076-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Recurrent inactivation of the PRDM1 gene in primary central nervous system lymphoma. J Neuropathol Exp Neurol 2008; 67:720-7. [PMID: 18596541 DOI: 10.1097/nen.0b013e31817dd02d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Primary lymphomas of the CNS (PCNSLs) show molecular features of the late germinal center exit B-cell phenotype and are impaired in their terminal differentiation as indicated by a lack of immunoglobulin class switching. Because the positive regulatory domain I protein with ZNF domain (PRDM1/BLIMP1) is a master regulator of terminal B-cell differentiation into plasma cells, we investigated a series of 21 PCNSLs for the presence of mutations in the PRDM1 gene and alterations in the expression pattern of the PRDM1 protein. Direct sequencing of all coding exons of the PRDM1 gene identified deleterious mutations associated with abrogation of PRDM1 protein expression in 4 of 21 (19%) PCNSLs. Thus, similar to systemic diffuse large B-cell lymphomas, PRDM1 may be a tumor suppressor in some PCNSL and contribute to lymphomagenesis by impairing terminal differentiation.
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Cady FM, O'Neill BP, Law ME, Decker PA, Kurtz DM, Giannini C, Porter AB, Kurtin PJ, Johnston PB, Dogan A, Remstein ED. Del(6)(q22) and BCL6 rearrangements in primary CNS lymphoma are indicators of an aggressive clinical course. J Clin Oncol 2008; 26:4814-9. [PMID: 18645192 DOI: 10.1200/jco.2008.16.1455] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Primary CNS lymphoma (PCNSL) is an aggressive lymphoma but clinically validated biologic markers that can predict natural history to tailor treatment according to risk are lacking. Several genetic changes including BCL6 rearrangements and deletion of 6q22, containing the putative tumor suppressor gene PTPRK, are potential risk predictors. Herein we determined the prevalence and survival impact of del(6)(q22) and BCL6, immunoglobulin heavy chain (IGH), and MYC gene rearrangements in a large PCNSL cohort treated in a single center. PATIENTS AND METHODS Interphase fluorescence in situ hybridization was performed using two-color probes for BCL6, MYC, IGH-BCL6, and del(6)(q22) on thin sections of 75 paraffin-embedded samples from 75 HIV-negative, immunocompetent patients newly diagnosed with PCNSL. Survival data were analyzed using Kaplan-Meier survival curves, log-rank tests, and proportional hazards regression adjusting for age, deep structure involvement, and high-dose methotrexate (HDMTX) treatment. RESULTS The prevalence of del(6)(q22) and BCL6, IGH, and MYC translocations was 45%,17%, 13%, and 3%, respectively. The presence of del(6)(q22) and/or a BCL6 translocation was associated with inferior overall survival (OS; P = .0097). The presence of either del(6)(q22) alone or a BCL6 translocation alone was also associated with inferior OS (P = .0087). Univariable results held after adjusting for age, deep structure involvement, and HDMTX. CONCLUSION Del (6)(q22) and BCL6 rearrangements are common in PCNSL and predict for decreased OS independent of deep structure involvement and HDMTX. Unlike systemic diffuse large B-cell lymphoma, del(6)(q22) is common and IGH translocations are infrequent and usually involve BCL6 rather than BCL2, suggesting a distinct pathogenesis.
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Affiliation(s)
- Francois M Cady
- Department of Pathology, CellNetix Pathology, Olympia, WA, USA
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Jais JP, Haioun C, Molina TJ, Rickman DS, de Reynies A, Berger F, Gisselbrecht C, Brière J, Reyes F, Gaulard P, Feugier P, Labouyrie E, Tilly H, Bastard C, Coiffier B, Salles G, Leroy K. The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab. Leukemia 2008; 22:1917-24. [PMID: 18615101 DOI: 10.1038/leu.2008.188] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gene expression profiles have been associated with clinical outcome in patients with diffuse large B-cell lymphoma (DLBCL) treated with anthracycline-containing chemotherapy. Using Affymetrix HU133A microarrays, we analyzed the lymphoma transcriptional profile of 30 patients treated with CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) and 23 patients treated with rituximab (R)-CHOP in the Groupe d'Etude des Lymphomes de l'Adulte clinical centers. We used this data set to select transcripts showing an association with progression-free survival in all patients or showing a differential effect in the two treatment groups. We performed real-time quantitative reverse transcription-PCR in the 23 R-CHOP samples of the screening set and an additional 44 R-CHOP samples set to evaluate the prognostic significance of these transcripts. In these 67 patients, the level of expression of 16 genes and the cell-of-origin classification were significantly associated with overall survival, independently of the International Prognostic Index. A multivariate model comprising four genes of the cell-of-origin signature (LMO2, MME, LPP and FOXP1) and two genes related to immune response, identified for their differential effects in R-CHOP patients (APOBEC3G and RAB33A), demonstrated a high predictive efficiency in this set of patients, suggesting that both features affect outcome in DLBCL patients receiving immunochemotherapy.
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Affiliation(s)
- J-P Jais
- Service de Biostatistique, AP-HP, hôpital Necker, Paris, France
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Calin GA, Croce CM. Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications. J Clin Invest 2007; 117:2059-66. [PMID: 17671640 PMCID: PMC1934569 DOI: 10.1172/jci32577] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is widespread aberrant expression of mature and/or precursor microRNAs in cancer cells, as microRNAs are deregulated consequent to chromosomal alterations and other genomic abnormalities. The identification of such abnormalities has a clear diagnostic and prognostic significance, and there are ever increasing examples of links between certain human cancers and modifications at microRNA loci.
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Affiliation(s)
- George A. Calin
- Department of Molecular Virology, Immunology and Medical Genetics, Colleges of Medicine and Public Health, and
Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Colleges of Medicine and Public Health, and
Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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Duquette ML, Huber MD, Maizels N. G-Rich Proto-Oncogenes Are Targeted for Genomic Instability in B-Cell Lymphomas. Cancer Res 2007; 67:2586-94. [PMID: 17363577 DOI: 10.1158/0008-5472.can-06-2419] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Diffuse large B-cell lymphoma is the most common lymphoid malignancy in adults. It is a heterogeneous disease with variability in outcome. Genomic instability of a subset of proto-oncogenes, including c-MYC, BCL6, RhoH, PIM1, and PAX5, can contribute to initial tumor development and has been correlated with poor prognosis and aggressive tumor growth. Lymphomas in which these proto-oncogenes are unstable derive from germinal center B cells that express activation-induced deaminase (AID), the B-cell-specific factor that deaminates DNA to initiate immunoglobulin gene diversification. Proto-oncogene instability is evident as both aberrant hypermutation and translocation, paralleling programmed instability which diversifies the immunoglobulin loci. We have asked if genomic sequence correlates with instability in AID-positive B-cell lymphomas. We show that instability does not correlate with enrichment of the WRC sequence motif that is the consensus for deamination by AID. Instability does correlate with G-richness, evident as multiple runs of the base guanine on the nontemplate DNA strand. Extending previous analysis of c-MYC, we show experimentally that transcription of BCL6 and RhoH induces formation of structures, G-loops, which contain single-stranded regions targeted by AID. We further show that G-richness does not characterize translocation breakpoints in AID-negative B- and T-cell malignancies. These results identify G-richness as one feature of genomic structure that can contribute to genomic instability in AID-positive B-cell malignancies.
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Affiliation(s)
- Michelle L Duquette
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98195, USA
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Hochberg FH, Baehring JM, Hochberg EP. Primary CNS lymphoma. ACTA ACUST UNITED AC 2007; 3:24-35. [PMID: 17205072 DOI: 10.1038/ncpneuro0395] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 11/16/2006] [Indexed: 02/07/2023]
Abstract
Non-Hodgkin's lymphoma invades the brain, the vitreous body and nerves of the eye, the meninges, and the nerve roots of brain and spine, leading to the development of a primary CNS lymphoma. The mechanism of involvement of these locations by malignant B lymphocytes is unknown, but it might involve molecular targeting of lymphoma cells generated at cryptic systemic sites. The diagnosis of primary CNS lymphoma has been facilitated by advances in imaging techniques and the discovery of molecular markers. Methotrexate-based regimens, even when radiation is deferred, prolong overall survival to over 5 years, but relapses eventually occur in most cases. Better tools for earlier diagnosis and monitoring of treatment response will emerge from molecular studies of therapeutic targets.
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