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Georges RO, Sepulveda H, Angel JC, Johnson E, Palomino S, Nowak RB, Desai A, López-Moyado IF, Rao A. Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3. Nat Commun 2022; 13:6230. [PMID: 36266342 PMCID: PMC9584922 DOI: 10.1038/s41467-022-33742-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
TET (Ten-Eleven Translocation) dioxygenases effect DNA demethylation through successive oxidation of the methyl group of 5-methylcytosine (5mC) in DNA. In humans and in mouse models, TET loss-of-function has been linked to DNA damage, genome instability and oncogenesis. Here we show that acute deletion of all three Tet genes, after brief exposure of triple-floxed, Cre-ERT2-expressing mouse embryonic stem cells (mESC) to 4-hydroxytamoxifen, results in chromosome mis-segregation and aneuploidy; moreover, embryos lacking all three TET proteins showed striking variation in blastomere numbers and nuclear morphology at the 8-cell stage. Transcriptional profiling revealed that mRNA encoding a KH-domain protein, Khdc3 (Filia), was downregulated in triple TET-deficient mESC, concomitantly with increased methylation of CpG dinucleotides in the vicinity of the Khdc3 gene. Restoring KHDC3 levels in triple Tet-deficient mESC prevented aneuploidy. Thus, TET proteins regulate Khdc3 gene expression, and TET deficiency results in mitotic infidelity and genome instability in mESC at least partly through decreased expression of KHDC3.
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Affiliation(s)
- Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Hugo Sepulveda
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - J Carlos Angel
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Eric Johnson
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Susan Palomino
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Roberta B Nowak
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Arshad Desai
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Isaac F López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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2
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Herek TA, Bouska A, Lone W, Sharma S, Amador C, Heavican TB, Li Y, Wei Q, Jochum D, Greiner TC, Smith L, Pileri S, Feldman AL, Rosenwald A, Ott G, Lim ST, Ong CK, Song J, Jaffe ES, Wang GG, Staudt L, Rimsza LM, Vose J, d'Amore F, Weisenburger DD, Chan WC, Iqbal J. DNMT3A mutations define a unique biological and prognostic subgroup associated with cytotoxic T cells in PTCL-NOS. Blood 2022; 140:1278-1290. [PMID: 35639959 PMCID: PMC9479030 DOI: 10.1182/blood.2021015019] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/08/2022] [Indexed: 11/20/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are heterogenous T-cell neoplasms often associated with epigenetic dysregulation. We investigated de novo DNA methyltransferase 3A (DNMT3A) mutations in common PTCL entities, including angioimmunoblastic T-cell lymphoma and novel molecular subtypes identified within PTCL-not otherwise specified (PTCL-NOS) designated as PTCL-GATA3 and PTCL-TBX21. DNMT3A-mutated PTCL-TBX21 cases showed inferior overall survival (OS), with DNMT3A-mutated residues skewed toward the methyltransferase domain and dimerization motif (S881-R887). Transcriptional profiling demonstrated significant enrichment of activated CD8+ T-cell cytotoxic gene signatures in the DNMT3A-mutant PTCL-TBX21 cases, which was further validated using immunohistochemistry. Genomewide methylation analysis of DNMT3A-mutant vs wild-type (WT) PTCL-TBX21 cases demonstrated hypomethylation in target genes regulating interferon-γ (IFN-γ), T-cell receptor signaling, and EOMES (eomesodermin), a master transcriptional regulator of cytotoxic effector cells. Similar findings were observed in a murine model of PTCL with Dnmt3a loss (in vivo) and further validated in vitro by ectopic expression of DNMT3A mutants (DNMT3A-R882, -Q886, and -V716, vs WT) in CD8+ T-cell line, resulting in T-cell activation and EOMES upregulation. Furthermore, stable, ectopic expression of the DNMT3A mutants in primary CD3+ T-cell cultures resulted in the preferential outgrowth of CD8+ T cells with DNMT3AR882H mutation. Single-cell RNA sequencing(RNA-seq) analysis of CD3+ T cells revealed differential CD8+ T-cell subset polarization, mirroring findings in DNMT3A-mutated PTCL-TBX21 and validating the cytotoxic and T-cell memory transcriptional programs associated with the DNMT3AR882H mutation. Our findings indicate that DNMT3A mutations define a cytotoxic subset in PTCL-TBX21 with prognostic significance and thus may further refine pathological heterogeneity in PTCL-NOS and suggest alternative treatment strategies for this subset.
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Affiliation(s)
- Tyler A Herek
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Alyssa Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Waseem Lone
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Sunandini Sharma
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Catalina Amador
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Tayla B Heavican
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Yuping Li
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Qi Wei
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Dylan Jochum
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Lynette Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE
| | - Stefano Pileri
- Division of Diagnostic Hematopathology, European Institute of Oncology-IEO IRCCS, Milan, Italy
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - 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 for Clinical Pharmacology, Stuttgart, Germany
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore/Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Choon Kiat Ong
- Division of Medical Oncology, National Cancer Centre Singapore/Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Joo Song
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Elaine S Jaffe
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center and
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Louis Staudt
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ
| | - Julie Vose
- Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE; and
| | - Francesco d'Amore
- Department of Haematology, Aarhus University Hospital, Aarhus N, Denmark
| | | | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
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3
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Biran A, Yin S, Kretzmer H, Ten Hacken E, Parvin S, Lucas F, Uduman M, Gutierrez C, Dangle N, Billington L, Regis FF, Rassenti LZ, Mohammad A, Hoffmann GB, Stevenson K, Zheng M, Witten E, Fernandes SM, Tausch E, Sun C, Stilgenbauer S, Brown JR, Kipps TJ, Aster JC, Gnirke A, Neuberg DS, Letai A, Wang L, Carrasco RD, Meissner A, Wu CJ. Activation of Notch and Myc Signaling via B-cell-Restricted Depletion of Dnmt3a Generates a Consistent Murine Model of Chronic Lymphocytic Leukemia. Cancer Res 2021; 81:6117-6130. [PMID: 34686499 PMCID: PMC8678341 DOI: 10.1158/0008-5472.can-21-1273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/18/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by disordered DNA methylation, suggesting these epigenetic changes might play a critical role in disease onset and progression. The methyltransferase DNMT3A is a key regulator of DNA methylation. Although DNMT3A somatic mutations in CLL are rare, we found that low DNMT3A expression is associated with more aggressive disease. A conditional knockout mouse model showed that homozygous depletion of Dnmt3a from B cells results in the development of CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yields a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haploinsufficient tumor suppressor. B1a cells were confirmed as the cell of origin of disease in this model, and Dnmt3a depletion resulted in focal hypomethylation and activation of Notch and Myc signaling. Amplification of chromosome 15 containing the Myc gene was detected in all CLL mice tested, and infiltration of high-Myc-expressing CLL cells in the spleen was observed. Notably, hyperactivation of Notch and Myc signaling was exclusively observed in the Dnmt3a CLL mice, but not in three other CLL mouse models tested (Sf3b1-Atm, Ikzf3, and MDR), and Dnmt3a-depleted CLL were sensitive to pharmacologic inhibition of Notch signaling in vitro and in vivo. Consistent with these findings, human CLL samples with lower DNMT3A expression were more sensitive to Notch inhibition than those with higher DNMT3A expression. Altogether, these results suggest that Dnmt3a depletion induces CLL that is highly dependent on activation of Notch and Myc signaling. SIGNIFICANCE: Loss of DNMT3A expression is a driving event in CLL and is associated with aggressive disease, activation of Notch and Myc signaling, and enhanced sensitivity to Notch inhibition.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Proliferation
- DNA Methyltransferase 3A/genetics
- DNA Methyltransferase 3A/metabolism
- DNA Methyltransferase 3A/physiology
- Daptomycin/pharmacology
- Disease Models, Animal
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Prognosis
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA-Seq
- Receptors, Notch/antagonists & inhibitors
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Salma Parvin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mohamed Uduman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nathan Dangle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Fara Faye Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - Arman Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Kristen Stevenson
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mei Zheng
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - John C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Ruben D Carrasco
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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4
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Angioimmunoblastic T-Cell Lymphoma and Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma: A Novel Form of Composite Lymphoma Potentially Mimicking Richter Syndrome. Am J Surg Pathol 2021; 45:773-786. [PMID: 33739791 DOI: 10.1097/pas.0000000000001646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) is an indolent small B-cell neoplasm that may transform into a clinically aggressive disease, namely Richter syndrome, usually as diffuse large B-cell lymphoma. Besides, CLL/SLL encompasses an increased risk of developing other secondary cancers, including a variety of T-cell lymphomas, often of the anaplastic large-cell type or with a cytotoxic phenotype. Here, we report a small series of patients with composite lymphomas consisting of CLL/SLL and angioimmunoblastic T-cell lymphoma (AITL), a hitherto unrecognized association. The 3 patients (1 male/2 females, 68 to 83 y) presented with high-grade-type symptoms. One patient was clinically suspicious for Richter syndrome, in the others CLL/SLL and AITL were concomitant de novo diagnoses. CLL/SLL and AITL were admixed in the same lymph nodes (3/3 cases) and in the bone marrow (1/2 cases). In all cases, the AITL comprised prominent clear cells with a strong T follicular helper immunophenotype and similar mutations consisting of TET2 or DNMT3A alterations, IDH2 R172K/M, and RHOA G17V. The 3 patients received chemotherapy. One died of early AITL relapse. The other 2 remained in complete remission of AITL, 1 died with recurrent CLL, and 1 of acute myeloid leukemia. These observations expand the spectrum of T-cell lymphoma entities that occur in association with CLL/SLL, adding AITL to the rare variants of aggressive neoplasms manifesting as Richter syndrome. Given that disturbances of T-cell homeostasis in CLL/SLL affect not only cytotoxic but also helper T-cell subsets, these may contribute to the emergence of neoplasms of T follicular helper derivation.
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5
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Mahajan VS, Mattoo H, Sun N, Viswanadham V, Yuen GJ, Allard-Chamard H, Ahmad M, Murphy SJH, Cariappa A, Tuncay Y, Pillai S. B1a and B2 cells are characterized by distinct CpG modification states at DNMT3A-maintained enhancers. Nat Commun 2021; 12:2208. [PMID: 33850140 PMCID: PMC8044213 DOI: 10.1038/s41467-021-22458-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 03/07/2021] [Indexed: 01/29/2023] Open
Abstract
The B1 and B2 lineages of B cells contribute to protection from pathogens in distinct ways. The role of the DNA CpG methylome in specifying these two B-cell fates is still unclear. Here we profile the CpG modifications and transcriptomes of peritoneal B1a and follicular B2 cells, as well as their respective proB cell precursors in the fetal liver and adult bone marrow from wild-type and CD19-Cre Dnmt3a floxed mice lacking DNMT3A in the B lineage. We show that an underlying foundational CpG methylome is stably established during B lineage commitment and is overlaid with a DNMT3A-maintained dynamic methylome that is sculpted in distinct ways in B1a and B2 cells. This dynamic DNMT3A-maintained methylome is composed of novel enhancers that are closely linked to lineage-specific genes. While DNMT3A maintains the methylation state of these enhancers in both B1a and B2 cells, the dynamic methylome undergoes a prominent programmed demethylation event during B1a but not B2 cell development. We propose that the methylation pattern of DNMT3A-maintained enhancers is determined by the coincident recruitment of DNMT3A and TET enzymes, which regulate the developmental expression of B1a and B2 lineage-specific genes.
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Affiliation(s)
- Vinay S Mahajan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Hamid Mattoo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Immunology and Inflammation Therapeutic Area, Sanofi, Cambridge, MA, USA
| | - Na Sun
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Vinayak Viswanadham
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Grace J Yuen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Maimuna Ahmad
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | - Yesim Tuncay
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Shiv Pillai
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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6
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Ye Y, Ding N, Mi L, Shi Y, Liu W, Song Y, Shu S, Zhu J. Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas. Exp Hematol Oncol 2021; 10:9. [PMID: 33546774 PMCID: PMC7866778 DOI: 10.1186/s40164-021-00200-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To explore the correlation of mutation landscape with clinical outcomes in patients with peripheral T-cell lymphoma (PTCL). METHODS We retrospectively analyzed the clinicopathological and prognosis data of 53 patients with PTCL from November 2011 to December 2017. Targeted next-generation sequencing of a 659-gene panel was performed for tissues from 53 patients with PTCLs. The correlation of mutation landscape with clinical outcomes was analyzed. RESULTS TET2 was the most frequently mutated gene (64%), followed by RHOA (43%), PCLO (23%), DNMT3A (19%), IDH2 (17%), PIEZO1 (17%) and TP53 (15%). When mutated genes were categorized into functional groups, the most common mutations were those involved in epigenetic/chromatin modification (75%), T-cell activation (74%), and the DNA repair/TP53 pathway (64%). TET2/TP53 mutations were significantly associated with positive B symptoms (P = 0.045), and elevated lactate dehydrogenase (LDH) level (P = 0.011). Moreover, TET2/TP53 mutation was a risk factor for PTCL patient survival (HR 3.574, 95% CI 1.069 - 11.941, P = 0.039). The occurrence of JAK/STAT pathway mutations in angioimmunoblastic T-cell lymphoma (AITL) patients conferred a worse progression-free survival (HR 2.366, 95% CI 0.9130-6.129, P = 0.0334). CONCLUSIONS Heterogeneous gene mutations occur in PTCL, some of which have a negative impact on the survival outcome.
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Affiliation(s)
- Yingying Ye
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Ning Ding
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Lan Mi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Yunfei Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Weiping Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Yuqin Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Shaokun Shu
- Department of Biomedical Engineering, Peking University, Beijing, 100871, China.
| | - Jun Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China.
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7
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Xanthopoulos C, Kostareli E. Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00178-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
Purpose of Review
The development and progression of chronic lymphocytic leukemia (CLL), a highly heterogenous B cell malignancy, are influenced by both genetic and environmental factors. Environmental factors, including pharmacological interventions, can affect the epigenetic landscape of CLL and thereby determine the CLL phenotype, clonal evolution, and clinical outcome. In this review, we critically present the latest advances in the field of CLL epigenomics/epigenetics in order to provide a systematic overview of to-date achievements and highlight the potential of epigenomics approaches in light of novel treatment therapies.
Recent Findings
Recent technological advances have enabled broad and precise mapping of the CLL epigenome. The identification of CLL-specific DNA methylation patterns has allowed for accurate CLL subtype definition, a better understanding of clonal origin and evolution, and the discovery of reliable biomarkers. More recently, studies have started to unravel the prognostic, predictive, and therapeutic potential of mapping chromatin dynamics and histone modifications in CLL. Finally, analysis of non-coding RNA expression has indicated their contribution to disease pathogenesis and helped to define prognostic subsets in CLL.
Summary
Overall, the potential of CLL epigenomics for predicting treatment response and resistance is mounting, especially with the advent of novel targeted CLL therapies.
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8
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Danlos FX, Papo M, Micol JB. L’hématopoïèse clonale : un concept émergent à la croisée des spécialités. Rev Med Interne 2019; 40:684-692. [DOI: 10.1016/j.revmed.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 12/17/2022]
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9
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B-cell tumor development in Tet2-deficient mice. Blood Adv 2019; 2:703-714. [PMID: 29581109 DOI: 10.1182/bloodadvances.2017014118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
The TET2 gene encodes an α-ketoglutarate-dependent dioxygenase able to oxidize 5-methylcytosine into 5-hydroxymethylcytosine, which is a step toward active DNA demethylation. TET2 is frequently mutated in myeloid malignancies but also in B- and T-cell malignancies. TET2 somatic mutations are also identified in healthy elderly individuals with clonal hematopoiesis. Tet2-deficient mouse models showed widespread hematological differentiation abnormalities, including myeloid, T-cell, and B-cell malignancies. We show here that, similar to what is observed with constitutive Tet2-deficient mice, B-cell-specific Tet2 knockout leads to abnormalities in the B1-cell subset and a development of B-cell malignancies after long latency. Aging Tet2-deficient mice accumulate clonal CD19+ B220low immunoglobulin M+ B-cell populations with transplantable ability showing similarities to human chronic lymphocytic leukemia, including CD5 expression and sensitivity to ibrutinib-mediated B-cell receptor (BCR) signaling inhibition. Exome sequencing of Tet2-/- malignant B cells reveals C-to-T and G-to-A mutations that lie within single-stranded DNA-specific activation-induced deaminase (AID)/APOBEC (apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide-like) cytidine deaminases targeted motif, as confirmed by the lack of a B-cell tumor in compound Tet2-Aicda-deficient mice. Finally, we show that Tet2 deficiency accelerates and exacerbates T-cell leukemia/lymphoma 1A-induced leukemogenesis. Together, our data establish that Tet2 deficiency predisposes to mature B-cell malignancies, which development might be attributed in part to AID-mediated accumulating mutations and BCR-mediated signaling.
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Molecular Insights Into Pathogenesis of Peripheral T Cell Lymphoma: a Review. Curr Hematol Malig Rep 2018; 13:318-328. [DOI: 10.1007/s11899-018-0460-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3-GENES GENOMES GENETICS 2018; 8:805-813. [PMID: 29326230 PMCID: PMC5844302 DOI: 10.1534/g3.117.300446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The DNA methyltransferase, Dnmt3a, is dynamically regulated throughout mammalian B cell development and upon activation by antigenic stimulation. Dnmt3a inactivation in hematopoietic stem cells has been shown to drive B cell-related malignancies, including chronic lymphocytic leukemia, and associates with specific DNA methylation patterns in transformed cells. However, while it is clear that inactivation of Dnmt3a in hematopoietic stem cells has profound functional effects, the consequences of Dnmt3a inactivation in cells of the B lineage are unclear. To assess whether loss of Dnmt3a at the earliest stages of B cell development lead to DNA methylation defects that might impair function, we selectively inactivated Dnmt3a early in mouse B cell development and then utilized whole genome bisulfite sequencing to generate base-resolution profiles of Dnmt3a+/+ and Dnmt3a−/− naïve splenic B cells. Overall, we find that global methylation patterns are largely consistent between Dnmt3a+/+ and Dnmt3a−/− naïve B cells, indicating a minimal functional effect of DNMT3A in mature B cells. However, loss of Dnmt3a induced 449 focal DNA methylation changes, dominated by loss-of-methylation events. Regions found to be hypomethylated in Dnmt3a−/− naïve splenic B cells were enriched in gene bodies of transcripts expressed in B cells, a fraction of which are implicated in B cell-related disease. Overall, the results from this study suggest that factors other than Dnmt3a are the major drivers for methylome maintenance in B cell development.
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Bagacean C, Le Dantec C, Berthou C, Tempescul A, Saad H, Bordron A, Zdrenghea M, Cristea V, Douet-Guilbert N, Renaudineau Y. Combining cytogenetic and epigenetic approaches in chronic lymphocytic leukemia improves prognosis prediction for patients with isolated 13q deletion. Clin Epigenetics 2017; 9:122. [PMID: 29209431 PMCID: PMC5704505 DOI: 10.1186/s13148-017-0422-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Both defective DNA methylation and active DNA demethylation processes are emerging as important risk factors in chronic lymphocytic leukemia (CLL). However, associations between 5-cytosine epigenetic markers and the most frequent chromosomal abnormalities detected in CLL remain to be established. Methods CLL patients were retrospectively classified into a cytogenetic low-risk group (isolated 13q deletion), an intermediate-risk group (normal karyotype or trisomy 12), and a high-risk group (11q deletion, 17p deletion, or complex karyotype [≥ 3 breakpoints]). The two 5-cytosine derivatives, 5-methylcytosine (5-mCyt) and 5-hydroxymethylcytosine (5-hmCyt), were tested by ELISA (n = 60), while real-time quantitative PCR was used for determining transcriptional expression levels of DNMT and TET (n = 24). Results By using global DNA methylation/demethylation levels, in the low-risk disease group, two subgroups with significantly different clinical outcomes have been identified (median treatment-free survival [TFS] 45 versus > 120 months for 5-mCyt, p = 0.0008, and 63 versus > 120 months for 5-hmCyt, p = 0.04). A defective 5-mCyt status was further associated with a higher percentage of 13q deleted nuclei (> 80%), thus suggesting an acquired process. When considering the cytogenetic intermediate/high-risk disease groups, an association of 5-mCyt status with lymphocytosis (p = 0.0008) and the lymphocyte doubling time (p = 0.04) but not with TFS was observed, as well as a reduction of DNMT3A, TET1, and TET2 transcripts. Conclusions Combining cytogenetic studies with 5-mCyt assessment adds accuracy to CLL patients’ prognoses and particularly for those with 13q deletion as a sole cytogenetic abnormality.
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Affiliation(s)
- Cristina Bagacean
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France.,"Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Christelle Le Dantec
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Christian Berthou
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Adrian Tempescul
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Anne Bordron
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Mihnea Zdrenghea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Yves Renaudineau
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France
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Bagacean C, Tempescul A, Le Dantec C, Bordron A, Mohr A, Saad H, Olivier V, Zdrenghea M, Cristea V, Cartron PF, Douet-Guilbert N, Berthou C, Renaudineau Y. Alterations in DNA methylation/demethylation intermediates predict clinical outcome in chronic lymphocytic leukemia. Oncotarget 2017; 8:65699-65716. [PMID: 29029465 PMCID: PMC5630365 DOI: 10.18632/oncotarget.20081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
Cytosine derivative dysregulations represent important epigenetic modifications whose impact on the clinical outcome in chronic lymphocytic leukemia (CLL) is incompletely understood. Hence, global levels of 5-methylcytosine (5-mCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-CaCyt) and 5-hydroxymethyluracil were tested in purified B cells from CLL patients (n = 55) and controls (n = 17). The DNA methylation 'writers' (DNA methyltransferases [DNMT1/3A/3B]), 'readers' (methyl-CpG-binding domain [MBD2/4]), 'editors' (ten-eleven translocation [TET1/2/3]) and 'modulators' (SAT1) were also evaluated. Accordingly, patients were stratified into three subgroups. First, a subgroup with a global deficit in cytosine derivatives characterized by hyperlymphocytosis, reduced median progression free survival (PFS = 52 months) and shorter treatment free survival (TFS = 112 months) was identified. In this subgroup, major epigenetic modifications were highlighted including a reduction of 5-mCyt, 5-hmCyt, 5-CaCyt associated with DNMT3A, MBD2/4 and TET1/2 downregulation. Second, the cytosine derivative analysis revealed a subgroup with a partial deficit (PFS = 84, TFS = 120 months), mainly affecting DNA demethylation (5-hmCyt reduction, SAT1 induction). Third, a subgroup epigenetically similar to controls was identified (PFS and TFS > 120 months). The prognostic impact of stratifying CLL patients within three epigenetic subgroups was confirmed in a validation cohort. In conclusion, our results suggest that dysregulations of cytosine derivative regulators represent major events acquired during CLL progression and are independent from IGHV mutational status.
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Affiliation(s)
- Cristina Bagacean
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adrian Tempescul
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Christelle Le Dantec
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Anne Bordron
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Audrey Mohr
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Valerie Olivier
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
| | - Mihnea Zdrenghea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, ‘Ion Chiricuta’ Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | | | - Christian Berthou
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Yves Renaudineau
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
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