1
|
Mazzarella L, Falvo P, Adinolfi M, Tini G, Gatti E, Piccioni R, Bonetti E, Gavilán E, Valli D, Gruszka A, Bodini M, Gallo B, Orecchioni S, de Michele G, Migliaccio E, Duso BA, Roerink S, Stratton M, Bertolini F, Alcalay M, Dellino GI, Pelicci PG. High-Fat Diet Promotes Acute Promyelocytic Leukemia through PPARδ-Enhanced Self-renewal of Preleukemic Progenitors. Cancer Prev Res (Phila) 2024; 17:59-75. [PMID: 37956420 DOI: 10.1158/1940-6207.capr-23-0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/04/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Risk and outcome of acute promyelocytic leukemia (APL) are particularly worsened in obese-overweight individuals, but the underlying molecular mechanism is unknown. In established mouse APL models (Ctsg-PML::RARA), we confirmed that obesity induced by high-fat diet (HFD) enhances leukemogenesis by increasing penetrance and shortening latency, providing an ideal model to investigate obesity-induced molecular events in the preleukemic phase. Surprisingly, despite increasing DNA damage in hematopoietic stem cells (HSC), HFD only minimally increased mutational load, with no relevant impact on known cancer-driving genes. HFD expanded and enhanced self-renewal of hematopoietic progenitor cells (HPC), with concomitant reduction in long-term HSCs. Importantly, linoleic acid, abundant in HFD, fully recapitulates the effect of HFD on the self-renewal of PML::RARA HPCs through activation of peroxisome proliferator-activated receptor delta, a central regulator of fatty acid metabolism. Our findings inform dietary/pharmacologic interventions to counteract obesity-associated cancers and suggest that nongenetic factors play a key role. PREVENTION RELEVANCE Our work informs interventions aimed at counteracting the cancer-promoting effect of obesity. On the basis of our study, individuals with a history of chronic obesity may still significantly reduce their risk by switching to a healthier lifestyle, a concept supported by evidence in solid tumors but not yet in hematologic malignancies. See related Spotlight, p. 47.
Collapse
Affiliation(s)
| | - Paolo Falvo
- IRCCS European Institute of Oncology, Milan, Italy
| | | | - Giulia Tini
- IRCCS European Institute of Oncology, Milan, Italy
| | - Elena Gatti
- IRCCS European Institute of Oncology, Milan, Italy
| | | | | | | | - Debora Valli
- IRCCS European Institute of Oncology, Milan, Italy
| | | | | | | | | | | | | | - Bruno A Duso
- IRCCS European Institute of Oncology, Milan, Italy
| | - Sophie Roerink
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Myriam Alcalay
- IRCCS European Institute of Oncology, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan
| | - Gaetano Ivan Dellino
- IRCCS European Institute of Oncology, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan
| | - Pier Giuseppe Pelicci
- IRCCS European Institute of Oncology, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan
| |
Collapse
|
2
|
Wu M, Zhou S. Harnessing tumor immunogenomics: Tumor neoantigens in ovarian cancer and beyond. Biochim Biophys Acta Rev Cancer 2023; 1878:189017. [PMID: 37935309 DOI: 10.1016/j.bbcan.2023.189017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Ovarian cancer is a major cause of death among gynecological cancers due to its highly aggressive nature. Immunotherapy has emerged as a promising avenue for ovarian cancer treatment, offering targeted approaches with reduced off-target effects. With the advent of next-generation sequencing, it has become possible to identify genomic alterations that can serve as potential targets for immunotherapy. Furthermore, immunogenomics research has revealed the importance of genetic alterations in shaping the cancer immune responses. However, the heterogeneity of immunogenicity and the low tumor mutation burden pose challenges for neoantigen-based immunotherapies. Further research is needed to identify neoantigen-specific tumor-infiltrating lymphocytes (TIL) and establish guidelines for patient inclusion criteria in TIL-based therapy. The study of neoantigens and their implications in ovarian cancer immunotherapy holds great promise, and efforts focused on personalized treatment strategies, refined neoantigen selection, and optimized therapeutic combinations will contribute to improving patient outcomes in the future.
Collapse
Affiliation(s)
- Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China.
| |
Collapse
|
3
|
Zhang Q, Li H, Chen X, Gu F, Zhang L, Zhang L, Chen T, Chen Q, Meng W, Wu Y, Chang H, Liu T, Chen C, Ma H, Liu Y. Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia. Blood 2023; 142:1494-1499. [PMID: 37624915 DOI: 10.1182/blood.2023020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Here we report a new fusion gene, STRN3-RARA, in acute promyelocytic leukemia (APL). It cooperates with UTX deficiency to drive full-blown APL in mice. Although STRN3-RARA leukemia quickly relapses after all-trans retinoic acid treatment, it can be restrained by cepharanthine.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - He Li
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelan Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fan Gu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lanxin Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lu Zhang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Tong Chen
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, China
| | - Qiang Chen
- Sichuan Neo-Life Stem Cell Biotech Inc, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Wentong Meng
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Chang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongbing Ma
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
4
|
Panni UY, Chen MY, Zhang F, Cullinan DR, Li L, James CA, Zhang X, Rogers S, Alarcon A, Baer JM, Zhang D, Gao F, Miller CA, Gong Q, Lim KH, DeNardo DG, Goedegebuure SP, Gillanders WE, Hawkins WG. Induction of cancer neoantigens facilitates development of clinically relevant models for the study of pancreatic cancer immunobiology. Cancer Immunol Immunother 2023; 72:2813-2827. [PMID: 37179276 PMCID: PMC10361914 DOI: 10.1007/s00262-023-03463-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Neoantigen burden and CD8 T cell infiltrate are associated with clinical outcome in pancreatic ductal adenocarcinoma (PDAC). A shortcoming of many genetic models of PDAC is the lack of neoantigen burden and limited T cell infiltrate. The goal of the present study was to develop clinically relevant models of PDAC by inducing cancer neoantigens in KP2, a cell line derived from the KPC model of PDAC. KP2 was treated with oxaliplatin and olaparib (OXPARPi), and a resistant cell line was subsequently cloned to generate multiple genetically distinct cell lines (KP2-OXPARPi clones). Clones A and E are sensitive to immune checkpoint inhibition (ICI), exhibit relatively high T cell infiltration, and have significant upregulation of genes involved in antigen presentation, T cell differentiation, and chemokine signaling pathways. Clone B is resistant to ICI and is similar to the parental KP2 cell line in terms of relatively low T cell infiltration and no upregulation of genes involved in the pathways noted above. Tumor/normal exome sequencing and in silico neoantigen prediction confirms successful generation of cancer neoantigens in the KP2-OXPARPi clones and the relative lack of cancer neoantigens in the parental KP2 cell line. Neoantigen vaccine experiments demonstrate that a subset of candidate neoantigens are immunogenic and neoantigen synthetic long peptide vaccines can restrain Clone E tumor growth. Compared to existing models, the KP2-OXPARPi clones better capture the diverse immunobiology of human PDAC and may serve as models for future investigations in cancer immunotherapies and strategies targeting cancer neoantigens in PDAC.
Collapse
Affiliation(s)
- Usman Y Panni
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Michael Y Chen
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Felicia Zhang
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Darren R Cullinan
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Lijin Li
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - C Alston James
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Xiuli Zhang
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - S Rogers
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - A Alarcon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John M Baer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daoxiang Zhang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - Feng Gao
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Christopher A Miller
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - Qingqing Gong
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Kian-Huat Lim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - William G Hawkins
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
5
|
Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
Collapse
Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| |
Collapse
|
6
|
Staehle HF, Pahl HL, Jutzi JS. The Cross Marks the Spot: The Emerging Role of JmjC Domain-Containing Proteins in Myeloid Malignancies. Biomolecules 2021; 11:biom11121911. [PMID: 34944554 PMCID: PMC8699298 DOI: 10.3390/biom11121911] [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] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Histone methylation tightly regulates chromatin accessibility, transcription, proliferation, and cell differentiation, and its perturbation contributes to oncogenic reprogramming of cells. In particular, many myeloid malignancies show evidence of epigenetic dysregulation. Jumonji C (JmjC) domain-containing proteins comprise a large and diverse group of histone demethylases (KDMs), which remove methyl groups from lysines in histone tails and other proteins. Cumulating evidence suggests an emerging role for these demethylases in myeloid malignancies, rendering them attractive targets for drug interventions. In this review, we summarize the known functions of Jumonji C (JmjC) domain-containing proteins in myeloid malignancies. We highlight challenges in understanding the context-dependent mechanisms of these proteins and explore potential future pharmacological targeting.
Collapse
Affiliation(s)
- Hans Felix Staehle
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Heike Luise Pahl
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Jonas Samuel Jutzi
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, MA, USA
- Correspondence:
| |
Collapse
|
7
|
Kdm6a deficiency restricted to mouse hematopoietic cells causes an age- and sex-dependent myelodysplastic syndrome-like phenotype. PLoS One 2021; 16:e0255706. [PMID: 34780480 PMCID: PMC8592440 DOI: 10.1371/journal.pone.0255706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Kdm6a/Utx, a gene on the X chromosome, encodes a histone H3K27me3 demethylase that has an orthologue on the Y chromosome (Uty) (Zheng et al. 2018). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2–15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6aflox/flox mice (with allele inactivation initiated by Vav1-Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a-knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a-WT and Kdm6a-KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis.
Collapse
|
8
|
di Martino O, Niu H, Hadwiger G, Ferris MA, Welch JS. Cytokine exposure mediates transcriptional activation of the orphan nuclear receptor Nur77 in hematopoietic cells. J Biol Chem 2021; 297:101240. [PMID: 34571009 PMCID: PMC8528724 DOI: 10.1016/j.jbc.2021.101240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
The orphan nuclear receptor Nur77 is an immediate-early response gene that based on tissue and cell context is implicated in a plethora of cellular processes, including proliferation, differentiation, apoptosis, metabolism, and inflammation. Nur77 has a ligand-binding pocket that is obstructed by hydrophobic side groups. Naturally occurring, cell-endogenous ligands have not been identified, and Nur77 transcriptional activity is thought to be regulated through posttranslational modification and modulation of protein levels. To determine whether Nur77 is transcriptionally active in hematopoietic cells in vivo, we used an upstream activating sequence (UAS)-GFP transgenic reporter. We found that Nur77 is transcriptionally inactive in vivo in hematopoietic cells under basal conditions, but that activation occurs following cytokine exposure by G-CSF or IL-3. We also identified a series of serine residues required for cytokine-dependent transactivation of Nur77. Moreover, a kinase inhibitor library screen and proximity labeling-based mass spectrometry identified overlapping kinase pathways that physically interacted with Nur77 and whose inhibition abrogated cytokine-induced activation of Nur77. We determined that transcriptional activation of Nur77 by G-CSF or IL-3 requires functional JAK and mTor signaling since their inhibition leads to Nur77 transcriptional inactivation. Thus, intracellular cytokine signaling networks appear to regulate Nur77 transcriptional activity in mouse hematopoietic cells.
Collapse
Affiliation(s)
- Orsola di Martino
- Department of Internal Medicine, Washington University, St Louis, Missouri, USA
| | - Haixia Niu
- Department of Internal Medicine, Washington University, St Louis, Missouri, USA; Division of Experimental Hematology and Cancer Biology, Cancer & Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University, St Louis, Missouri, USA
| | - Margaret A Ferris
- Department of Pediatrics, Washington University, St Louis, Missouri, USA
| | - John S Welch
- Department of Internal Medicine, Washington University, St Louis, Missouri, USA.
| |
Collapse
|
9
|
Tumor suppressor function of Gata2 in Acute Promyelocytic Leukemia. Blood 2021; 138:1148-1161. [PMID: 34125173 DOI: 10.1182/blood.2021011758] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Most patients with acute promyelocytic leukemia (APL) can be cured with combined All Trans Retinoic Acid (ATRA) and Arsenic Trioxide therapy, which induce the destruction of PML-RARA, the initiating fusion protein for this disease1. However, the underlying mechanisms by which PML-RARA initiates and maintains APL cells are still not clear. We therefore identified genes that are dysregulated by PML-RARA in mouse and human APL cells, and prioritized GATA2 for functional studies because 1) it is highly expressed in pre-leukemic cells expressing PML-RARA, 2) its high expression persists in transformed APL cells, and 3) spontaneous somatic mutations of GATA2 occur during APL progression in both mice and humans. These and other findings suggested that GATA2 may be upregulated to thwart the proliferative signal generated by PML-RARA, and that its inactivation by mutation (and/or epigenetic silencing) may accelerate disease progression in APL and other forms of AML. Indeed, biallelic knockout of Gata2 with CRISPR/Cas9-mediated gene editing increased the serial replating efficiency of PML-RARA-expressing myeloid progenitors (and also progenitors expressing RUNX1-RUNX1T1, or deficient for Cebpa), increased mouse APL penetrance, and decreased latency. Restoration of Gata2 expression suppressed PML-RARA-driven aberrant self-renewal and leukemogenesis. Conversely, addback of a mutant GATA2R362G protein associated with APL and AML minimally suppressed PML-RARA-induced aberrant self-renewal, suggesting that it is a loss-of-function mutation. These studies reveal a potential role for Gata2 as a tumor suppressor in AML, and suggest that restoration of its function (when inactivated) may provide benefit for AML patients.
Collapse
|
10
|
A novel fusion protein TBLR1-RARα acts as an oncogene to induce murine promyelocytic leukemia: identification and treatment strategies. Cell Death Dis 2021; 12:607. [PMID: 34117212 PMCID: PMC8196070 DOI: 10.1038/s41419-021-03889-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/04/2022]
Abstract
Acute promyelocytic leukemia (APL) is characterized by a specific chromosome translocation involving RARα and its fusion partners. For decades, the advent of all-trans retinoic acid (ATRA) synergized with arsenic trioxide (As2O3) has turned most APL from highly fatal to highly curable. TBLR1-RARα (TR) is the tenth fusion gene of APL identified in our previous study, with its oncogenic role in the pathogenesis of APL not wholly unraveled. In this study, we found the expression of TR in mouse hematopoietic progenitors induces blockade of differentiation with enhanced proliferative capacity in vitro. A novel murine transplantable leukemia model was then established by expressing TR fusion gene in lineage-negative bone marrow mononuclear cells. Characteristics of primary TR mice revealed a rapid onset of aggressive leukemia with bleeding diathesis, which recapitulates human APL more accurately than other models. Despite the in vitro sensitivity to ATRA-induced cell differentiation, neither ATRA monotherapy nor combination with As2O3 confers survival benefit to TR mice, consistent with poor clinical outcome of APL patients with TR fusion gene. Based on histone deacetylation phenotypes implied by bioinformatic analysis, HDAC inhibitors demonstrated significant survival superiority in the survival of TR mice, yielding insights into clinical efficacy against rare types of APL.
Collapse
|
11
|
Kirtonia A, Pandya G, Sethi G, Pandey AK, Das BC, Garg M. A comprehensive review of genetic alterations and molecular targeted therapies for the implementation of personalized medicine in acute myeloid leukemia. J Mol Med (Berl) 2020; 98:1069-1091. [PMID: 32620999 DOI: 10.1007/s00109-020-01944-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/18/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022]
Abstract
Acute myeloid leukemia (AML) is an extremely heterogeneous disease defined by the clonal growth of myeloblasts/promyelocytes not only in the bone marrow but also in peripheral blood and/or tissues. Gene mutations and chromosomal abnormalities are usually associated with aberrant proliferation and/or block in the normal differentiation of hematopoietic cells. So far, the combination of cytogenetic profiling and molecular and gene mutation analyses remains an essential tool for the classification, diagnosis, prognosis, and treatment for AML. This review gives an overview on how the development of novel innovative technologies has allowed us not only to detect the genetic alterations as early as possible but also to understand the molecular pathogenesis of AML to develop novel targeted therapies. We also discuss the remarkable advances made during the last decade to understand the AML genome both at primary and relapse diseases and how genetic alterations might influence the distinct biological groups as well as the clonal evolution of disease during the diagnosis and relapse. Also, the review focuses on how the persistence of epigenetic gene mutations during morphological remission is associated with relapse. It is suggested that along with the prognostic and therapeutic mutations, the novel molecular targeted therapies either approved by FDA or those under clinical trials including CART-cell therapy would be of immense importance in the effective management of AML.
Collapse
Affiliation(s)
- Anuradha Kirtonia
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Gouri Pandya
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology (AIB), Amity University, Gurgaon, Haryana, 122413, India
| | - Bhudev C Das
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, 201313, India.
| |
Collapse
|
12
|
Liquori A, Ibañez M, Sargas C, Sanz MÁ, Barragán E, Cervera J. Acute Promyelocytic Leukemia: A Constellation of Molecular Events around a Single PML-RARA Fusion Gene. Cancers (Basel) 2020; 12:cancers12030624. [PMID: 32182684 PMCID: PMC7139833 DOI: 10.3390/cancers12030624] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Although acute promyelocytic leukemia (APL) is one of the most characterized forms of acute myeloid leukemia (AML), the molecular mechanisms involved in the development and progression of this disease are still a matter of study. APL is defined by the PML-RARA rearrangement as a consequence of the translocation t(15;17)(q24;q21). However, this abnormality alone is not able to trigger the whole leukemic phenotype and secondary cooperating events might contribute to APL pathogenesis. Additional somatic mutations are known to occur recurrently in several genes, such as FLT3, WT1, NRAS and KRAS, whereas mutations in other common AML genes are rarely detected, resulting in a different molecular profile compared to other AML subtypes. How this mutational spectrum, including point mutations in the PML-RARA fusion gene, could contribute to the 10%–15% of relapsed or resistant APL patients is still unknown. Moreover, due to the uncertain impact of additional mutations on prognosis, the identification of the APL-specific genetic lesion is still the only method recommended in the routine evaluation/screening at diagnosis and for minimal residual disease (MRD) assessment. However, the gene expression profile of genes, such as ID1, BAALC, ERG, and KMT2E, once combined with the molecular events, might improve future prognostic models, allowing us to predict clinical outcomes and to categorize APL patients in different risk subsets, as recently reported. In this review, we will focus on the molecular characterization of APL patients at diagnosis, relapse and resistance, in both children and adults. We will also describe different standardized molecular approaches to study MRD, including those recently developed. Finally, we will discuss how novel molecular findings can improve the management of this disease.
Collapse
Affiliation(s)
- Alessandro Liquori
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Mariam Ibañez
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Claudia Sargas
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Miguel Ángel Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Eva Barragán
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - José Cervera
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence:
| |
Collapse
|
13
|
Hartmann L, Nadarajah N, Meggendorfer M, Höllein A, Vetro C, Kern W, Haferlach T, Haferlach C, Stengel A. Molecular characterization of a second myeloid neoplasm developing after treatment for acute myeloid leukemia. Leukemia 2019; 34:811-820. [PMID: 31719678 DOI: 10.1038/s41375-019-0633-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Therapy-related myeloid neoplasms (tMN) following successful treatment of acute myeloid leukemia (AML) are rare and poorly characterized. To evaluate the presence of a common ancestral clone, we performed whole-exome sequencing of 25 patients at AML diagnosis, tMN diagnosis (tMDS: 13; tAML: 12), and matched remission samples, identifying 607 mutations affecting 504 different genes (46 recurrently mutated). Number of mutations was higher in tAML vs. tMDS cases (median 19 vs 13 mutations, p = 0.05). Focusing on 24 genes commonly mutated in hematological malignancies, 19/25 (76%) patients were found to share mutations between AML and tMN, mostly affecting epigenetic modifiers (21/32; 66%), splicing factors (6/32; 19%), and chromatin modifiers (3/32; 9%). Analysis of remission samples identified 13 persisting mutations in 10/22 patients, affecting DNMT3A (n = 6), TET2 (n = 5), IDH1 and SRSF2 (n = 1, each). Comparison of cytogenetics revealed that 9/12 patients with a normal karyotype (NK) in AML harbored aberrations in tMN, four aberrant AML cases presented with NK in tMN, four other patients showed unrelated cytogenetic aberrations. Our study provides novel insights into the pathogenesis of tMN, hypothesizing the presence of a common ancestral clone in AML and tMN. Mutations mostly affected epigenetic modifiers, which have previously been linked to clonal hematopoiesis.
Collapse
Affiliation(s)
- Luise Hartmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Alexander Höllein
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Calogero Vetro
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
| |
Collapse
|
14
|
Noguera NI, Catalano G, Banella C, Divona M, Faraoni I, Ottone T, Arcese W, Voso MT. Acute Promyelocytic Leukemia: Update on the Mechanisms of Leukemogenesis, Resistance and on Innovative Treatment Strategies. Cancers (Basel) 2019; 11:cancers11101591. [PMID: 31635329 PMCID: PMC6826966 DOI: 10.3390/cancers11101591] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
This review highlights new findings that have deepened our understanding of the mechanisms of leukemogenesis, therapy and resistance in acute promyelocytic leukemia (APL). Promyelocytic leukemia-retinoic acid receptor α (PML-RARa) sets the cellular landscape of acute promyelocytic leukemia (APL) by repressing the transcription of RARa target genes and disrupting PML-NBs. The RAR receptors control the homeostasis of tissue growth, modeling and regeneration, and PML-NBs are involved in self-renewal of normal and cancer stem cells, DNA damage response, senescence and stress response. The additional somatic mutations in APL mainly involve FLT3, WT1, NRAS, KRAS, ARID1B and ARID1A genes. The treatment outcomes in patients with newly diagnosed APL improved dramatically since the advent of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO). ATRA activates the transcription of blocked genes and degrades PML-RARα, while ATO degrades PML-RARa by promoting apoptosis and has a pro-oxidant effect. The resistance to ATRA and ATO may derive from the mutations in the RARa ligand binding domain (LBD) and in the PML-B2 domain of PML-RARa, but such mutations cannot explain the majority of resistances experienced in the clinic, globally accounting for 5-10% of cases. Several studies are ongoing to unravel clonal evolution and resistance, suggesting the therapeutic potential of new retinoid molecules and combinatorial treatments of ATRA or ATO with different drugs acting through alternative mechanisms of action, which may lead to synergistic effects on growth control or the induction of apoptosis in APL cells.
Collapse
Affiliation(s)
- N I Noguera
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
- Santa Lucia Foundation, Unit of Neuro-Oncoematologia, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy.
| | - G Catalano
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
- Santa Lucia Foundation, Unit of Neuro-Oncoematologia, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy.
| | - C Banella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
- Santa Lucia Foundation, Unit of Neuro-Oncoematologia, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy.
| | - M Divona
- Policlinico Tor vergata, 00133 Rome, Italy.
| | - I Faraoni
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy.
| | - T Ottone
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
- Santa Lucia Foundation, Unit of Neuro-Oncoematologia, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy.
| | - W Arcese
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
| | - M T Voso
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
- Santa Lucia Foundation, Unit of Neuro-Oncoematologia, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy.
| |
Collapse
|
15
|
Wu B, Pan X, Chen X, Chen M, Shi K, Xu J, Zheng J, Niu T, Chen C, Shuai X, Liu Y. Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy. Signal Transduct Target Ther 2019; 4:11. [PMID: 31044091 PMCID: PMC6483994 DOI: 10.1038/s41392-019-0040-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 02/05/2023] Open
Abstract
UTX (also known as KDM6A), a histone 3 lysine 27 demethylase, is among the most frequently mutated epigenetic regulators in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Recent studies have suggested that UTX mutations promote MDS and AML by blocking the differentiation of hematopoietic stem and progenitor cells (HSPCs). Here, we performed an epigenetic drug library screening for small molecules able to release the differentiation block on HSPCs induced by UTX deficiency. We found that SP2509, a selective inhibitor of LSD1, specifically promoted the differentiation of Utx-null HSPCs while sparing wild-type HSPCs. Transcriptome profiling showed that Utx loss reduced the expression of differentiation-related and tumor suppressor genes, correlating with their potential roles in HSPC self-renewal and leukemogenesis. In contrast, SP2509 treatment reversed these changes in gene expression in Utx-null HSPCs. Accordingly, Utx loss decreased H3K4 methylation level probably through the COMPASS-like complex, while LSD1 inhibition by SP2509 partially reversed the reduction of H3K4 methylation in Utx-deficient HSPCs. Further, SP2509 promoted the differentiation of Utx-null AML cells in vitro and in vivo and, therefore, extended the survival of these leukemic mice. Thus, our study identified a novel strategy to specifically target both premalignant and malignant cells with Utx deficiency for differentiation therapy and provided insights into the molecular mechanisms underlying the role of Utx in regulating HSPCs and related diseases.
Collapse
Affiliation(s)
- Baohong Wu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiangyu Pan
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xuelan Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Mei Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Kaidou Shi
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jing Xu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jianan Zheng
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Ting Niu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chong Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiao Shuai
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Yu Liu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| |
Collapse
|
16
|
Hill KS, Roberts ER, Wang X, Marin E, Park TD, Son S, Ren Y, Fang B, Yoder S, Kim S, Wan L, Sarnaik AA, Koomen JM, Messina JL, Teer JK, Kim Y, Wu J, Chalfant CE, Kim M. PTPN11 Plays Oncogenic Roles and Is a Therapeutic Target for BRAF Wild-Type Melanomas. Mol Cancer Res 2018; 17:583-593. [PMID: 30355677 DOI: 10.1158/1541-7786.mcr-18-0777] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
Abstract
Melanoma is one of the most highly mutated cancer types. To identify functional drivers of melanoma, we searched for cross-species conserved mutations utilizing a mouse melanoma model driven by loss of PTEN and CDKN2A, and identified mutations in Kras, Erbb3, and Ptpn11. PTPN11 encodes the SHP2 protein tyrosine phosphatase that activates the RAS/RAF/MAPK pathway. Although PTPN11 is an oncogene in leukemia, lung, and breast cancers, its roles in melanoma are not clear. In this study, we found that PTPN11 is frequently activated in human melanoma specimens and cell lines and is required for full RAS/RAF/MAPK signaling activation in BRAF wild-type (either NRAS mutant or wild-type) melanoma cells. PTPN11 played oncogenic roles in melanoma by driving anchorage-independent colony formation and tumor growth. In Pten- and Cdkn2a-null mice, tet-inducible and melanocyte-specific PTPN11E76K expression significantly enhanced melanoma tumorigenesis. Melanoma cells derived from this mouse model showed doxycycline-dependent tumor growth in nude mice. Silencing PTPN11E76K expression by doxycycline withdrawal caused regression of established tumors by induction of apoptosis and senescence, and suppression of proliferation. Moreover, the PTPN11 inhibitor (SHP099) also caused regression of NRASQ61K -mutant melanoma. Using a quantitative tyrosine phosphoproteomics approach, we identified GSK3α/β as one of the key substrates that were differentially tyrosine-phosphorylated in these experiments modulating PTPN11. This study demonstrates that PTPN11 plays oncogenic roles in melanoma and regulates RAS and GSK3β signaling pathways. IMPLICATIONS: This study identifies PTPN11 as an oncogenic driver and a novel and actionable therapeutic target for BRAF wild-type melanoma.
Collapse
Affiliation(s)
- Kristen S Hill
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Evan R Roberts
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Xue Wang
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Ellen Marin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Taeeun D Park
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Sorany Son
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Yuan Ren
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Bin Fang
- Department of Proteomics, Moffitt Cancer Center, Tampa, Florida
| | - Sean Yoder
- Molecular Genomics Core, Moffitt Cancer Center, Tampa, Florida
| | - Sungjune Kim
- Department of Immunology, Moffitt Cancer Center, Tampa, Florida.,Department of Radiology, Moffitt Cancer Center, Tampa, Florida
| | - Lixin Wan
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Amod A Sarnaik
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Proteomics, Moffitt Cancer Center, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Pathology, Moffitt Cancer Center, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Jie Wu
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Charles E Chalfant
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida.,Department of Research Service, James A. Haley Veterans Hospital, Tampa, Florida
| | - Minjung Kim
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida. .,Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| |
Collapse
|
17
|
Dual origin of relapses in retinoic-acid resistant acute promyelocytic leukemia. Nat Commun 2018; 9:2047. [PMID: 29795382 PMCID: PMC5967331 DOI: 10.1038/s41467-018-04384-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 04/26/2018] [Indexed: 12/11/2022] Open
Abstract
Retinoic acid (RA) and arsenic target the t(15;17)(q24;q21) PML/RARA driver of acute promyelocytic leukemia (APL), their combination now curing over 95% patients. We report exome sequencing of 64 matched samples collected from patients at initial diagnosis, during remission, and following relapse after historical combined RA-chemotherapy treatments. A first subgroup presents a high incidence of additional oncogenic mutations disrupting key epigenetic or transcriptional regulators (primarily WT1) or activating MAPK signaling at diagnosis. Relapses retain these cooperating oncogenes and exhibit additional oncogenic alterations and/or mutations impeding therapy response (RARA, NT5C2). The second group primarily exhibits FLT3 activation at diagnosis, which is lost upon relapse together with most other passenger mutations, implying that these relapses derive from ancestral pre-leukemic PML/RARA-expressing cells that survived RA/chemotherapy. Accordingly, clonogenic activity of PML/RARA-immortalized progenitors ex vivo is only transiently affected by RA, but selectively abrogated by arsenic. Our studies stress the role of cooperating oncogenes in direct relapses and suggest that targeting pre-leukemic cells by arsenic contributes to its clinical efficacy. Historical acute promyelocytic leukemia patients treated with retinoic acid and chemotherapy sometimes did relapse. Here the authors performed exome sequencing on 64 patient's samples from diagnosis/relapse/remission and show relapse associates either with cooperating oncogenes at diagnosis, or with unexpected persistence of ancestral pre-leukemic clones.
Collapse
|
18
|
Voisset E, Moravcsik E, Stratford EW, Jaye A, Palgrave CJ, Hills RK, Salomoni P, Kogan SC, Solomon E, Grimwade D. Pml nuclear body disruption cooperates in APL pathogenesis and impairs DNA damage repair pathways in mice. Blood 2018; 131:636-648. [PMID: 29191918 PMCID: PMC5805489 DOI: 10.1182/blood-2017-07-794784] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/26/2017] [Indexed: 01/20/2023] Open
Abstract
A hallmark of acute promyelocytic leukemia (APL) is altered nuclear architecture, with disruption of promyelocytic leukemia (PML) nuclear bodies (NBs) mediated by the PML-retinoic acid receptor α (RARα) oncoprotein. To address whether this phenomenon plays a role in disease pathogenesis, we generated a knock-in mouse model with NB disruption mediated by 2 point mutations (C62A/C65A) in the Pml RING domain. Although no leukemias developed in PmlC62A/C65A mice, these transgenic mice also expressing RARα linked to a dimerization domain (p50-RARα model) exhibited a doubling in the rate of leukemia, with a reduced latency period. Additionally, we found that response to targeted therapy with all-trans retinoic acid in vivo was dependent on NB integrity. PML-RARα is recognized to be insufficient for development of APL, requiring acquisition of cooperating mutations. We therefore investigated whether NB disruption might be mutagenic. Compared with wild-type cells, primary PmlC62A/C65A cells exhibited increased sister-chromatid exchange and chromosome abnormalities. Moreover, functional assays showed impaired homologous recombination (HR) and nonhomologous end-joining (NHEJ) repair pathways, with defective localization of Brca1 and Rad51 to sites of DNA damage. These data directly demonstrate that Pml NBs are critical for DNA damage responses, and suggest that Pml NB disruption is a central contributor to APL pathogenesis.
Collapse
MESH Headings
- Animals
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- DNA Damage/genetics
- DNA End-Joining Repair/genetics
- DNA Repair/genetics
- Intranuclear Inclusion Bodies/genetics
- Intranuclear Inclusion Bodies/metabolism
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Mice
- Mice, Transgenic
- Mutagenesis/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promyelocytic Leukemia Protein/genetics
- Promyelocytic Leukemia Protein/physiology
- Signal Transduction/genetics
Collapse
Affiliation(s)
- Edwige Voisset
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Eva Moravcsik
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Eva W Stratford
- Department of Tumor Biology, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Amie Jaye
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | | | - Robert K Hills
- Centre for Trials Research, College of Biomedical & Life Sciences, Cardiff University, Cardiff, United Kingdom
| | | | - Scott C Kogan
- Helen Diller Family Comprehensive Cancer Center and
- Department of Laboratory Medicine, University of California, San Francisco, CA
| | - Ellen Solomon
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Grimwade
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| |
Collapse
|
19
|
Greif PA, Hartmann L, Vosberg S, Stief SM, Mattes R, Hellmann I, Metzeler KH, Herold T, Bamopoulos SA, Kerbs P, Jurinovic V, Schumacher D, Pastore F, Bräundl K, Zellmeier E, Ksienzyk B, Konstandin NP, Schneider S, Graf A, Krebs S, Blum H, Neumann M, Baldus CD, Bohlander SK, Wolf S, Görlich D, Berdel WE, Wörmann BJ, Hiddemann W, Spiekermann K. Evolution of Cytogenetically Normal Acute Myeloid Leukemia During Therapy and Relapse: An Exome Sequencing Study of 50 Patients. Clin Cancer Res 2018; 24:1716-1726. [PMID: 29330206 DOI: 10.1158/1078-0432.ccr-17-2344] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/03/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: To study mechanisms of therapy resistance and disease progression, we analyzed the evolution of cytogenetically normal acute myeloid leukemia (CN-AML) based on somatic alterations.Experimental Design: We performed exome sequencing of matched diagnosis, remission, and relapse samples from 50 CN-AML patients treated with intensive chemotherapy. Mutation patterns were correlated with clinical parameters.Results: Evolutionary patterns correlated with clinical outcome. Gain of mutations was associated with late relapse. Alterations of epigenetic regulators were frequently gained at relapse with recurring alterations of KDM6A constituting a mechanism of cytarabine resistance. Low KDM6A expression correlated with adverse clinical outcome, particularly in male patients. At complete remission, persistent mutations representing preleukemic lesions were observed in 48% of patients. The persistence of DNMT3A mutations correlated with shorter time to relapse.Conclusions: Chemotherapy resistance might be acquired through gain of mutations. Insights into the evolution during therapy and disease progression lay the foundation for tailored approaches to treat or prevent relapse of CN-AML. Clin Cancer Res; 24(7); 1716-26. ©2018 AACR.
Collapse
Affiliation(s)
- Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, München, Germany. .,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luise Hartmann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie M Stief
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Mattes
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, Martinsried, Germany
| | - Klaus H Metzeler
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vindi Jurinovic
- Institute for Medical Information Procesing, Biometry and Epidemiology (IBE), LMU Munich, München, Germany
| | - Daniela Schumacher
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friederike Pastore
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Bräundl
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelyn Zellmeier
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Bianka Ksienzyk
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Nikola P Konstandin
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Stephanie Schneider
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Martin Neumann
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Claudia D Baldus
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Stephan Wolf
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A -Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Bernhard J Wörmann
- Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Spiekermann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
20
|
Pan MR, Hsu MC, Chen LT, Hung WC. Orchestration of H3K27 methylation: mechanisms and therapeutic implication. Cell Mol Life Sci 2018; 75:209-223. [PMID: 28717873 PMCID: PMC5756243 DOI: 10.1007/s00018-017-2596-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Accepted: 07/13/2017] [Indexed: 01/08/2023]
Abstract
Histone proteins constitute the core component of the nucleosome, the basic unit of chromatin. Chemical modifications of histone proteins affect their interaction with genomic DNA, the accessibility of recognized proteins, and the recruitment of enzymatic complexes to activate or diminish specific transcriptional programs to modulate cellular response to extracellular stimuli or insults. Methylation of histone proteins was demonstrated 50 years ago; however, the biological significance of each methylated residue and the integration between these histone markers are still under intensive investigation. Methylation of histone H3 on lysine 27 (H3K27) is frequently found in the heterochromatin and conceives a repressive marker that is linked with gene silencing. The identification of enzymes that add or erase the methyl group of H3K27 provides novel insights as to how this histone marker is dynamically controlled under different circumstances. Here we summarize the methyltransferases and demethylases involved in the methylation of H3K27 and show the new evidence by which the H3K27 methylation can be established via an alternative mechanism. Finally, the progress of drug development targeting H3K27 methylation-modifying enzymes and their potential application in cancer therapy are discussed.
Collapse
Affiliation(s)
- Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, 704, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan.
| |
Collapse
|
21
|
Yang Z, Jia M, Liu G, Hao H, Chen L, Li G, Liu S, Li Y, Wu CI, Lu X, Wang S. Genomic sequencing identifies a few mutations driving the independent origin of primary liver tumors in a chronic hepatitis murine model. PLoS One 2017; 12:e0187551. [PMID: 29117265 PMCID: PMC5678715 DOI: 10.1371/journal.pone.0187551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/20/2017] [Indexed: 12/11/2022] Open
Abstract
With the development of high-throughput genomic analysis, sequencing a mouse primary cancer model provides a new opportunity to understand fundamental mechanisms of tumorigenesis and progression. Here, we characterized the genomic variations in a hepatitis-related primary hepatocellular carcinoma (HCC) mouse model. A total of 12 tumor sections and four adjacent non-tumor tissues from four mice were used for whole exome and/or whole genome sequencing and validation of genotyping. The functions of the mutated genes in tumorigenesis were studied by analyzing their mutation frequency and expression in clinical HCC samples. A total of 46 single nucleotide variations (SNVs) were detected within coding regions. All SNVs were only validated in the sequencing samples, except the Hras mutation, which was shared by three tumors in the M1 mouse. However, the mutated allele frequency varied from high (0.4) to low (0.1), and low frequency (0.1-0.2) mutations existed in almost every tumor. Together with a diploid karyotype and an equal distribution pattern of these SNVs within the tumor, these results suggest the existence of subclones within tumors. A total of 26 mutated genes were mapped to 17 terms describing different molecular and cellular functions. All 41 human homologs of the mutated genes were mutated in the clinical samples, and some mutations were associated with clinical outcomes, suggesting a high probability of cancer driver genes in the spontaneous tumors of the mouse model. Genomic sequencing shows that a few mutations can drive the independent origin of primary liver tumors and reveals high heterogeneity among tumors in the early stage of hepatitis-related primary hepatocellular carcinoma.
Collapse
Affiliation(s)
- Zuyu Yang
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mingming Jia
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China
| | - Guojing Liu
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Huaining Hao
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China
| | - Guanghao Li
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sixue Liu
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yawei Li
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chung-I Wu
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Xuemei Lu
- CAS Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (SW); (XL)
| | - Shengdian Wang
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (SW); (XL)
| |
Collapse
|
22
|
Wei L, Murphy BL, Wu G, Parker M, Easton J, Gilbertson RJ, Zhang J, Roussel MF. Exome sequencing analysis of murine medulloblastoma models identifies WDR11 as a potential tumor suppressor in Group 3 tumors. Oncotarget 2017; 8:64685-64697. [PMID: 29029386 PMCID: PMC5630286 DOI: 10.18632/oncotarget.19642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/09/2017] [Indexed: 01/11/2023] Open
Abstract
Mouse models of human cancers are widely used in cancer research, yet questions frequently arise regarding their faithfulness in recapitulating their human counterparts. To compare the somatic mutations of murine models with human medulloblastoma (MB), we performed whole-exome sequencing on 12 tumors representing three distinct medulloblastoma subgroups: Wnt, Sonic Hedgehog (Shh) and Group 3 (G3). In total, 64 somatic mutations were identified and validated, including 40 predicted to cause amino acid changes. After filtering and cross-species analysis with 366 human MBs from four independent studies, human orthologs for 16 of the 40 mouse genes were found to harbor non-silent mutations in human MB. Loss-of-function Kmt2d mutations detected in one mouse tumor was previously reported in 30 of 366 human MBs. In mice bearing G3 MB, one mouse succumbed to tumor burden at least 15 days earlier than other mice, raising the possibility that somatic mutations may have accelerated the tumorigenesis process. In this mouse tumor, four novel candidate genes harbored non-silent somatic mutations, Lrfn2, Smyd1, Ubn2 and Wdr11. Extended survival was found in mice harboring mouse G3 overexpressing WDR11 but not the other three genes. Genes in the KEGG WNT signaling pathway, including Ccnd1/2/3, Myc and Tcf7l1, were down-regulated in the transcriptome of G3 MB tumorspheres overexpressing WDR11, consistent with reduced tumor progression. In conclusion, we demonstrated that common spontaneous mutations were shared between human and murine models of MB suggesting similar molecular mechanisms of tumorigenesis, and identified WDR11 as a protein with tumor suppressive activity in G3 MB.
Collapse
Affiliation(s)
- Lei Wei
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Brian L. Murphy
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Genomics England, Queen Mary University of London, London, UK
| | - John Easton
- Pediatric Cancer Genome Project, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard J. Gilbertson
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Martine F. Roussel
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| |
Collapse
|
23
|
Molecular Profiling: A Case of ZBTB16-RARA Acute Promyelocytic Leukemia. Case Rep Hematol 2017; 2017:7657393. [PMID: 28529810 PMCID: PMC5424191 DOI: 10.1155/2017/7657393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/09/2017] [Indexed: 11/17/2022] Open
Abstract
Several variant RARA translocations have been reported in acute promyelocytic leukemia (APL) of which the t(11;17)(q23;q21), which results in a ZBTB16-RARA fusion, is the most widely identified and is largely resistant to therapy with all-trans retinoic acid (ATRA). The clinical course together with the cytogenetic and molecular characterization of a case of ATRA-unresponsive ZBTB16-RARA APL is described. Additional mutations potentially cooperating with the translocation fusion product in leukemogenesis have been hitherto unreported in ZBTB16-RARA APL and were sought by application of a next-generation sequencing approach to detect those recurrently found in myeloid malignancies. This technique identified a solitary, low level mutation in the CEBPA gene. Molecular profiling of additional mutations may provide a platform to individualise therapeutic management in patients with this rare form of APL.
Collapse
|
24
|
Goldberg L, Gough SM, Lee F, Dang C, Walker RL, Zhu YJ, Bilke S, Pineda M, Onozawa M, Jo Chung Y, Meltzer PS, Aplan PD. Somatic mutations in murine models of leukemia and lymphoma: Disease specificity and clinical relevance. Genes Chromosomes Cancer 2017; 56:472-483. [PMID: 28196408 DOI: 10.1002/gcc.22451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 12/17/2022] Open
Abstract
Malignant transformation is a multistep process that is dictated by the acquisition of multiple genomic aberrations that provide growth and survival advantage. During the post genomic era, high throughput genomic sequencing has advanced exponentially, leading to identification of countless cancer associated mutations with potential for targeted therapy. Mouse models of cancer serve as excellent tools to examine the functionality of gene mutations and their contribution to the malignant process. However, it remains unclear whether the genetic events that occur during transformation are similar in mice and humans. To address that, we chose several transgenic mouse models of hematopoietic malignancies and identified acquired mutations in these mice by means of targeted re-sequencing of known cancer-associated genes as well as whole exome sequencing. We found that mutations that are typically found in acute myeloid leukemia or T cell acute lymphoblastic leukemia patients are also common in mouse models of the respective disease. Moreover, we found that the most frequent mutations found in a mouse model of lymphoma occur in a set of epigenetic modifier genes, implicating this pathway in the generation of lymphoma. These results demonstrate that genetically engineered mouse models (GEMM) mimic the genetic evolution of human cancer and serve as excellent platforms for target discovery and validation.
Collapse
Affiliation(s)
- Liat Goldberg
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sheryl M Gough
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Fan Lee
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Christine Dang
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yuelin J Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sven Bilke
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Marbin Pineda
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Masahiro Onozawa
- Center for Medical Education/Department of hematology, Hokkaido University Graduate School of Medicine Hokkaido, Japan
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| |
Collapse
|
25
|
Araki R, Mizutani E, Hoki Y, Sunayama M, Wakayama S, Nagatomo H, Kasama Y, Nakamura M, Wakayama T, Abe M. The Number of Point Mutations in Induced Pluripotent Stem Cells and Nuclear Transfer Embryonic Stem Cells Depends on the Method and Somatic Cell Type Used for Their Generation. Stem Cells 2017; 35:1189-1196. [PMID: 28233378 DOI: 10.1002/stem.2601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/09/2017] [Accepted: 01/29/2017] [Indexed: 01/05/2023]
Abstract
Induced pluripotent stem cells hold great promise for regenerative medicine but point mutations have been identified in these cells and have raised serious concerns about their safe use. We generated nuclear transfer embryonic stem cells (ntESCs) from both mouse embryonic fibroblasts (MEFs) and tail-tip fibroblasts (TTFs) and by whole genome sequencing found fewer mutations compared with iPSCs generated by retroviral gene transduction. Furthermore, TTF-derived ntESCs showed only a very small number of point mutations, approximately 80% less than the number observed in iPSCs generated using retrovirus. Base substitution profile analysis confirmed this greatly reduced number of point mutations. The point mutations in iPSCs are therefore not a Yamanaka factor-specific phenomenon but are intrinsic to genome reprogramming. Moreover, the dramatic reduction in point mutations in ntESCs suggests that most are not essential for genome reprogramming. Our results suggest that it is feasible to reduce the point mutation frequency in iPSCs by optimizing various genome reprogramming conditions. We conducted whole genome sequencing of ntES cells derived from MEFs or TTFs. We thereby succeeded in establishing TTF-derived ntES cell lines with far fewer point mutations. Base substitution profile analysis of these clones also indicated a reduced point mutation frequency, moving from a transversion-predominance to a transition-predominance. Stem Cells 2017;35:1189-1196.
Collapse
Affiliation(s)
- Ryoko Araki
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Eiji Mizutani
- Department of Biotechnology, Faculty of Life and Environmental Science, University of Yamanashi, Kofu, Japan
| | - Yuko Hoki
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Misato Sunayama
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Sayaka Wakayama
- Department of Biotechnology, Faculty of Life and Environmental Science, University of Yamanashi, Kofu, Japan
| | - Hiroaki Nagatomo
- Department of Biotechnology, Faculty of Life and Environmental Science, University of Yamanashi, Kofu, Japan
| | - Yasuji Kasama
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Miki Nakamura
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Teruhiko Wakayama
- Department of Biotechnology, Faculty of Life and Environmental Science, University of Yamanashi, Kofu, Japan
| | - Masumi Abe
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| |
Collapse
|
26
|
Lefebure M, Tothill RW, Kruse E, Hawkins ED, Shortt J, Matthews GM, Gregory GP, Martin BP, Kelly MJ, Todorovski I, Doyle MA, Lupat R, Li J, Schroeder J, Wall M, Craig S, Poortinga G, Cameron D, Bywater M, Kats L, Gearhart MD, Bardwell VJ, Dickins RA, Hannan RD, Papenfuss AT, Johnstone RW. Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene. Nat Commun 2017; 8:14581. [PMID: 28262675 PMCID: PMC5343491 DOI: 10.1038/ncomms14581] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 01/12/2017] [Indexed: 01/05/2023] Open
Abstract
The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor. These findings challenge the assumed two-hit model of Eμ-Myc lymphoma and demonstrate a functional in vivo role for Bcor in suppressing tumorigenesis. The Eμ-Myc lymphoma mouse model has been invaluable in the study of this disease. Here, the authors use multiple sequencing strategies to analyse the tumours in these mice and find recurrent inactivating mutations in Bcor, suggesting that this gene has a negative role in Myc signalling.
Collapse
Affiliation(s)
- Marcus Lefebure
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Elizabeth Kruse
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Edwin D Hawkins
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Jake Shortt
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing &Health Sciences, Clayton, Victoria 3168, Australia
| | | | - Gareth P Gregory
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Benjamin P Martin
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Madison J Kelly
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Richard Lupat
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jan Schroeder
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia.,Department of Medicine, St Vincent's Hospital, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Stuart Craig
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Don Cameron
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Megan Bywater
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lev Kats
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Micah D Gearhart
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Vivian J Bardwell
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, AMREP Building, Commercial Road, The Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Ross D Hannan
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Cancer Biology and Therapeutics Department, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Anthony T Papenfuss
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| |
Collapse
|
27
|
Dang J, Nance S, Ma J, Cheng J, Walsh MP, Vogel P, Easton J, Song G, Rusch M, Gedman AL, Koss C, Downing JR, Gruber TA. AMKL chimeric transcription factors are potent inducers of leukemia. Leukemia 2017; 31:2228-2234. [PMID: 28174417 DOI: 10.1038/leu.2017.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 01/08/2023]
Abstract
Acute megakaryoblastic leukemia in patients without Down syndrome is a rare malignancy with a poor prognosis. RNA sequencing of fourteen pediatric cases previously identified novel fusion transcripts that are predicted to be pathological including CBFA2T3-GLIS2, GATA2-HOXA9, MN1-FLI and NIPBL-HOXB9. In contrast to CBFA2T3-GLIS2, which is insufficient to induce leukemia, we demonstrate that the introduction of GATA2-HOXA9, MN1-FLI1 or NIPBL-HOXB9 into murine bone marrow induces overt disease in syngeneic transplant models. With the exception of MN1, full penetrance was not achieved through the introduction of fusion partner genes alone, suggesting that the chimeric transcripts possess a unique gain-of-function phenotype. Leukemias were found to exhibit elements of the megakaryocyte erythroid progenitor gene expression program, as well as unique leukemia-specific signatures that contribute to transformation. Comprehensive genomic analyses of resultant murine tumors revealed few cooperating mutations confirming the strength of the fusion genes and their role as pathological drivers. These models are critical for both the understanding of the biology of disease as well as providing a tool for the identification of effective therapeutic agents in preclinical studies.
Collapse
Affiliation(s)
- J Dang
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Nance
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Ma
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Cheng
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M P Walsh
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - P Vogel
- Department of Veterinary Pathology Core, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J Easton
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - G Song
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - A L Gedman
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - C Koss
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - T A Gruber
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
28
|
Pan Q, Lou X, Zhang J, Zhu Y, Li F, Shan Q, Chen X, Xie Y, Su S, Wei H, Lin L, Wu L, Liu S. Genomic variants in mouse model induced by azoxymethane and dextran sodium sulfate improperly mimic human colorectal cancer. Sci Rep 2017; 7:25. [PMID: 28154415 PMCID: PMC5453956 DOI: 10.1038/s41598-017-00057-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/19/2016] [Indexed: 01/11/2023] Open
Abstract
Mouse model induced by azoxymethane (AOM) and dextran sodium sulfate (DSS) is generally accepted as an ideal object to study on the carcinogenesis mechanisms of human colorectal cancer (CRC). The genomic responses to the AOM/DSS treatment in mouse that possibly lead to elucidation of CRC pathological mechanism are still poorly understood. For the first time, we investigated the cancer genome landscape of AOM/DSS mouse model by exome sequencing, to testify its molecular faithfulness to human CRC. Of 14 neoplastic samples, 7575 somatic variants were identified, which resulted in 2507 mutant genes and exhibited a large diversity in both colorectal aberrant crypt foci (ACF) and tumors even those tissues that were gained from the similar morphology or same treatment period. Cross-species comparison of the somatic variants demonstrated the totally different patterns of variable sites, mutant genes and perturbed pathways between mouse and human CRC. We therefore come to a conclusion that the tumorigenesis at genomic level in AOM/DSS model may not be properly comparable with that in human CRC, and the molecular mechanism elicited from this animal model should be carefully evaluated.
Collapse
Affiliation(s)
- Qingfei Pan
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yinghui Zhu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | | | - Qiang Shan
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xianwei Chen
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yingying Xie
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Siyuan Su
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hanfu Wei
- Beijing Protein Innovation, Beijing, China
| | | | - Lin Wu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China. .,BGI-Shenzhen, Shenzhen, China.
| |
Collapse
|
29
|
PML nuclear body disruption impairs DNA double-strand break sensing and repair in APL. Cell Death Dis 2016; 7:e2308. [PMID: 27468685 PMCID: PMC4973339 DOI: 10.1038/cddis.2016.115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/28/2016] [Indexed: 12/12/2022]
Abstract
Proteins involved in DNA double-strand break (DSB) repair localize within the promyelocytic leukemia nuclear bodies (PML-NBs), whose disruption is at the root of the acute promyelocytic leukemia (APL) pathogenesis. All-trans-retinoic acid (RA) treatment induces PML-RARα degradation, restores PML-NB functions, and causes terminal cell differentiation of APL blasts. However, the precise role of the APL-associated PML-RARα oncoprotein and PML-NB integrity in the DSB response in APL leukemogenesis and tumor suppression is still lacking. Primary leukemia blasts isolated from APL patients showed high phosphorylation levels of H2AX (γ-H2AX), an initial DSBs sensor. By addressing the consequences of ionizing radiation (IR)-induced DSB response in primary APL blasts and RA-responsive and -resistant myeloid cell lines carrying endogenous or ectopically expressed PML-RARα, before and after treatment with RA, we found that the disruption of PML-NBs is associated with delayed DSB response, as revealed by the impaired kinetic of disappearance of γ-H2AX and 53BP1 foci and activation of ATM and of its substrates H2AX, NBN, and CHK2. The disruption of PML-NB integrity by PML-RARα also affects the IR-induced DSB response in a preleukemic mouse model of APL in vivo. We propose the oncoprotein-dependent PML-NB disruption and DDR impairment as relevant early events in APL tumorigenesis.
Collapse
|
30
|
Wartman LD. A case of me: clinical cancer sequencing and the future of precision medicine. Cold Spring Harb Mol Case Stud 2016; 1:a000349. [PMID: 27148564 PMCID: PMC4850894 DOI: 10.1101/mcs.a000349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In this invited Perspective, I detail how my own experience as a patient with acute lymphoblastic leukemia (ALL) exemplifies several key concepts central to the implementation of cancer sequencing and precision medicine into clinical practice.
Collapse
Affiliation(s)
- Lukas D Wartman
- Washington University School of Medicine, St. Louis, Missouri 63110, USA
| |
Collapse
|
31
|
Madan V, Shyamsunder P, Han L, Mayakonda A, Nagata Y, Sundaresan J, Kanojia D, Yoshida K, Ganesan S, Hattori N, Fulton N, Tan KT, Alpermann T, Kuo MC, Rostami S, Matthews J, Sanada M, Liu LZ, Shiraishi Y, Miyano S, Chendamarai E, Hou HA, Malnassy G, Ma T, Garg M, Ding LW, Sun QY, Chien W, Ikezoe T, Lill M, Biondi A, Larson RA, Powell BL, Lübbert M, Chng WJ, Tien HF, Heuser M, Ganser A, Koren-Michowitz M, Kornblau SM, Kantarjian HM, Nowak D, Hofmann WK, Yang H, Stock W, Ghavamzadeh A, Alimoghaddam K, Haferlach T, Ogawa S, Shih LY, Mathews V, Koeffler HP. Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia. Leukemia 2016; 30:1672-81. [PMID: 27063598 PMCID: PMC4972641 DOI: 10.1038/leu.2016.69] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/12/2016] [Accepted: 03/15/2016] [Indexed: 12/16/2022]
Abstract
Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17), leading to the formation of PML-RARA (promyelocytic leukemia-retinoic acid receptor alpha) fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations, which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, whereas mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large-scale activation of gene expression and reduced in vitro differentiation potential.
Collapse
Affiliation(s)
- V Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - P Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - L Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - A Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Y Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J Sundaresan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - D Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - K Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - S Ganesan
- Department of Haematology, Christian Medical College, Vellore, India
| | - N Hattori
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - N Fulton
- Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - K-T Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - T Alpermann
- Munich Leukemia Laboratory (MLL), Munich, Germany
| | - M-C Kuo
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - S Rostami
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - J Matthews
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - L-Z Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Y Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - E Chendamarai
- Department of Haematology, Christian Medical College, Vellore, India
| | - H-A Hou
- Department of Internal Medicine, National Taiwan University, Medical College and Hospital, Taipei, Taiwan
| | - G Malnassy
- Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - T Ma
- Division of Hematology, Oncology and Stem Cell Transplantation, Department of Internal Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - M Garg
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - L-W Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Q-Y Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - W Chien
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - T Ikezoe
- Department of Hematology and Respiratory Medicine, Kochi Medical School, Kochi University, Nankoku, Kochi, Japan
| | - M Lill
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA
| | - A Biondi
- Paediatric Haematology-Oncology Department and 'Tettamanti' Research Centre, Milano-Bicocca University, 'Fondazione MBBM', San Gerardo Hospital, Monza, Italy
| | - R A Larson
- Department of Medicine, University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - B L Powell
- Department of Internal Medicine, Section on Hematology and Oncology, Comprehensive Cancer Center of Wake Forest University, Winston-Salem, NC, USA
| | - M Lübbert
- Division of Hematology, Oncology and Stem Cell Transplantation, Department of Internal Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - W J Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Singapore
| | - H-F Tien
- Department of Internal Medicine, National Taiwan University, Medical College and Hospital, Taipei, Taiwan
| | - M Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - A Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - M Koren-Michowitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Division of Hematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Israel
| | - S M Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H M Kantarjian
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - W-K Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - H Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - W Stock
- Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - A Ghavamzadeh
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - K Alimoghaddam
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - T Haferlach
- Munich Leukemia Laboratory (MLL), Munich, Germany
| | - S Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - L-Y Shih
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - V Mathews
- Department of Haematology, Christian Medical College, Vellore, India
| | - H P Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Singapore
| |
Collapse
|
32
|
Jones KB, Barrott JJ, Xie M, Haldar M, Jin H, Zhu JF, Monument MJ, Mosbruger TL, Langer EM, Randall RL, Wilson RK, Cairns BR, Ding L, Capecchi MR. The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis. Oncogene 2016; 35:5021-32. [PMID: 26947017 PMCID: PMC5014712 DOI: 10.1038/onc.2016.38] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/14/2015] [Accepted: 01/11/2016] [Indexed: 02/07/2023]
Abstract
Synovial sarcomas are aggressive soft-tissue malignancies that express chromosomal translocation-generated fusion genes, SS18-SSX1 or SS18-SSX2 in most cases. Here, we report a mouse sarcoma model expressing SS18-SSX1, complementing our prior model expressing SS18-SSX2. Exome sequencing identified no recurrent secondary mutations in tumors of either genotype. Most of the few mutations identified in single tumors were present in genes that were minimally or not expressed in any of the tumors. Chromosome 6, either entirely or around the fusion gene expression locus, demonstrated a copy number gain in a majority of tumors of both genotypes. Thus, by fusion oncogene coding sequence alone, SS18-SSX1 and SS18-SSX2 can each drive comparable synovial sarcomagenesis, independent from other genetic drivers. SS18-SSX1 and SS18-SSX2 tumor transcriptomes demonstrated very few consistent differences overall. In direct tumorigenesis comparisons, SS18-SSX2 was slightly more sarcomagenic than SS18-SSX1, but equivalent in its generation of biphasic histologic features. Meta-analysis of human synovial sarcoma patient series identified two tumor-gentoype-phenotype correlations that were not modeled by the mice, namely a scarcity of male hosts and biphasic histologic features among SS18-SSX2 tumors. Re-analysis of human SS18-SSX1 and SS18-SSX2 tumor transcriptomes demonstrated very few consistent differences, but highlighted increased native SSX2 expression in SS18-SSX1 tumors. This suggests that the translocated locus may drive genotype-phenotype differences more than the coding sequence of the fusion gene created. Two possible roles for native SSX2 in synovial sarcomagenesis are explored. Thus, even specific partial failures of mouse genetic modeling can be instructive to human tumor biology.
Collapse
Affiliation(s)
- K B Jones
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - J J Barrott
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - M Xie
- Department of Medicine, Washington University, St Louis, MO, USA
| | - M Haldar
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - H Jin
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - J-F Zhu
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - M J Monument
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - T L Mosbruger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Bioinformatics, University of Utah, Salt Lake City, UT, USA
| | - E M Langer
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - R L Randall
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - R K Wilson
- Department of Medicine, Washington University, St Louis, MO, USA.,McDonnell Genome Institute, Washington University, St Louis, MO, USA.,Department of Genetics, Washington University, St Louis, MO, USA.,Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - B R Cairns
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - L Ding
- Department of Medicine, Washington University, St Louis, MO, USA.,McDonnell Genome Institute, Washington University, St Louis, MO, USA.,Department of Genetics, Washington University, St Louis, MO, USA.,Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - M R Capecchi
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
33
|
Niu H, Hadwiger G, Fujiwara H, Welch JS. Pathways of retinoid synthesis in mouse macrophages and bone marrow cells. J Leukoc Biol 2016; 99:797-810. [PMID: 26768478 DOI: 10.1189/jlb.2hi0415-146rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 12/18/2015] [Indexed: 12/31/2022] Open
Abstract
In vivo pathways of natural retinoid metabolism and elimination have not been well characterized in primary myeloid cells, even though retinoids and retinoid receptors have been strongly implicated in regulating myeloid maturation. With the use of a upstream activation sequence-GFP reporter transgene and retrovirally expressed Gal4-retinoic acid receptor α in primary mouse bone marrow cells, we identified 2 distinct enzymatic pathways used by mouse myeloid cells ex vivo to synthesize retinoic acid receptor α ligands from free vitamin A metabolites (retinyl acetate, retinol, and retinal). Bulk Kit(+) bone marrow progenitor cells use diethylaminobenzaldehyde-sensitive enzymes, whereas bone marrow-derived macrophages use diethylaminobenzaldehyde-insensitive enzymes to synthesize natural retinoic acid receptor α-activating retinoids (all-trans retinoic acid). Bone marrow-derived macrophages do not express the diethylaminobenzaldehyde-sensitive enzymes Aldh1a1, Aldh1a2, or Aldh1a3 but instead, express Aldh3b1, which we found is capable of diethylaminobenzaldehyde-insensitive synthesis of all trans-retinoic acid. However, under steady-state and stimulated conditions in vivo, diverse bone marrow cells and peritoneal macrophages showed no evidence of intracellular retinoic acid receptor α-activating retinoids, despite expression of these enzymes and a vitamin A-sufficient diet, suggesting that the enzymatic conversion of retinal is not the rate-limiting step in the synthesis of intracellular retinoic acid receptor α-activating retinoids in myeloid bone marrow cells and that retinoic acid receptor α remains in an unliganded configuration during adult hematopoiesis.
Collapse
Affiliation(s)
- Haixia Niu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Hideji Fujiwara
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John S Welch
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| |
Collapse
|
34
|
Hatlen MA, Arora K, Vacic V, Grabowska EA, Liao W, Riley-Gillis B, Oschwald DM, Wang L, Joergens JE, Shih AH, Rapaport F, Gu S, Voza F, Asai T, Neel BG, Kharas MG, Gonen M, Levine RL, Nimer SD. Integrative genetic analysis of mouse and human AML identifies cooperating disease alleles. J Exp Med 2015; 213:25-34. [PMID: 26666262 PMCID: PMC4710200 DOI: 10.1084/jem.20150524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 11/13/2015] [Indexed: 01/22/2023] Open
Abstract
Hatlen et al. provide an integrative analysis of the mutational landscape of mouse and human AML and identify functionally relevant cooperation between AML1-ETO and PTPN11 D61Y. Based on these findings, they generate a novel mouse model of t(8;21)+ AML. t(8;21) is one of the most frequent chromosomal abnormalities observed in acute myeloid leukemia (AML). However, expression of AML1-ETO is not sufficient to induce transformation in vivo. Consistent with this observation, patients with this translocation harbor additional genetic abnormalities, suggesting a requirement for cooperating mutations. To better define the genetic landscape in AML and distinguish driver from passenger mutations, we compared the mutational profiles of AML1-ETO–driven mouse models of leukemia with the mutational profiles of human AML patients. We identified TET2 and PTPN11 mutations in both mouse and human AML and then demonstrated the ability of Tet2 loss and PTPN11 D61Y to initiate leukemogenesis in concert with expression of AML1-ETO in vivo. This integrative genetic profiling approach allowed us to accurately predict cooperating events in t(8;21)+ AML in a robust and unbiased manner, while also revealing functional convergence in mouse and human AML.
Collapse
Affiliation(s)
- Megan A Hatlen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Weill Cornell Graduate School of Medical Sciences, New York, NY 10065
| | | | | | | | | | | | | | - Lan Wang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136 Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Jacob E Joergens
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Franck Rapaport
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Shengqing Gu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 2M9, Canada Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Francesca Voza
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Takashi Asai
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136 Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Benjamin G Neel
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 2M9, Canada Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Cellular Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Mithat Gonen
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Stephen D Nimer
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136 Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136 Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136
| |
Collapse
|
35
|
Gaillard C, Tokuyasu TA, Rosen G, Sotzen J, Vitaliano-Prunier A, Roy R, Passegué E, de Thé H, Figueroa ME, Kogan SC. Transcription and methylation analyses of preleukemic promyelocytes indicate a dual role for PML/RARA in leukemia initiation. Haematologica 2015; 100:1064-75. [PMID: 26088929 DOI: 10.3324/haematol.2014.123018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/06/2015] [Indexed: 12/15/2022] Open
Abstract
Acute promyelocytic leukemia is an aggressive malignancy characterized by the accumulation of promyelocytes in the bone marrow. PML/RARA is the primary abnormality implicated in this pathology, but the mechanisms by which this chimeric fusion protein initiates disease are incompletely understood. Identifying PML/RARA targets in vivo is critical for comprehending the road to pathogenesis. Utilizing a novel sorting strategy, we isolated highly purified promyelocyte populations from normal and young preleukemic animals, carried out microarray and methylation profiling analyses, and compared the results from the two groups of animals. Surprisingly, in the absence of secondary lesions, PML/RARA had an overall limited impact on both the transcriptome and methylome. Of interest, we did identify down-regulation of secondary and tertiary granule genes as the first step engaging the myeloid maturation block. Although initially not sufficient to arrest terminal granulopoiesis in vivo, such alterations set the stage for the later, complete differentiation block seen in leukemia. Further, gene set enrichment analysis revealed that PML/RARA promyelocytes exhibit a subtle increase in expression of cell cycle genes, and we show that this leads to both increased proliferation of these cells and expansion of the promyelocyte compartment. Importantly, this proliferation signature was absent from the poorly leukemogenic p50/RARA fusion model, implying a critical role for PML in the altered cell-cycle kinetics and ability to initiate leukemia. Thus, our findings challenge the predominant model in the field and we propose that PML/RARA initiates leukemia by subtly shifting cell fate decisions within the promyelocyte compartment.
Collapse
Affiliation(s)
- Coline Gaillard
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA Institut Universitaire d'Hématologie, Université Paris-Diderot UMR 944/7212, France
| | - Taku A Tokuyasu
- Computational Biology Core, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Galit Rosen
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, AZ, USA
| | - Jason Sotzen
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Ritu Roy
- Computational Biology Core, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Emmanuelle Passegué
- Department of Medicine, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Hugues de Thé
- Institut Universitaire d'Hématologie, Université Paris-Diderot UMR 944/7212, France
| | - Maria E Figueroa
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Scott C Kogan
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| |
Collapse
|
36
|
Francis JC, Melchor L, Campbell J, Kendrick H, Wei W, Armisen-Garrido J, Assiotis I, Chen L, Kozarewa I, Fenwick K, Swain A, Smalley MJ, Lord CJ, Ashworth A. Whole-exome DNA sequence analysis of Brca2- and Trp53-deficient mouse mammary gland tumours. J Pathol 2015; 236:186-200. [PMID: 25692405 DOI: 10.1002/path.4517] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 02/03/2015] [Accepted: 02/11/2015] [Indexed: 01/08/2023]
Abstract
Germline mutations in the tumour suppressor BRCA2 predispose to breast, ovarian and a number of other human cancers. Brca2-deficient mouse models are used for preclinical studies but the pattern of genomic alterations in these tumours has not yet been described in detail. We have performed whole-exome DNA sequencing analysis of mouse mammary tumours from Blg-Cre Brca2(f/f) Trp53(f/f) animals, a model of BRCA2-deficient human cancer. We also used the sequencing data to estimate DNA copy number alterations in these tumours and identified a recurrent copy number gain in Met, which has been found amplified in other mouse mammary cancer models. Through a comparative genomic analysis, we identified several mouse Blg-Cre Brca2(f/f) Trp53(f/f) mammary tumour somatic mutations in genes that are also mutated in human cancer, but few of these genes have been found frequently mutated in human breast cancer. A more detailed analysis of these somatic mutations revealed a set of genes that are mutated in human BRCA2 mutant breast and ovarian tumours and that are also mutated in mouse Brca2-null, Trp53-null mammary tumours. Finally, a DNA deletion surrounded by microhomology signature found in human BRCA1/2-deficient cancers was not common in the genome of these mouse tumours. Although a useful model, there are some differences in the genomic landscape of tumours arising in Blg-Cre Brca2(f/f) Trp53(f/f) mice compared to human BRCA-mutated breast cancers. Therefore, this needs to be taken into account in the use of this model.
Collapse
MESH Headings
- Animals
- Antigens, CD/genetics
- Breast Neoplasms/genetics
- Chromosomal Proteins, Non-Histone/genetics
- DNA Copy Number Variations/genetics
- DNA, Neoplasm/genetics
- Disease Models, Animal
- Female
- Gene Knockout Techniques
- Genes, BRCA2/physiology
- Germ-Line Mutation/genetics
- Humans
- Mammary Neoplasms, Experimental/genetics
- Mice, Transgenic
- Mutation, Missense/genetics
- Ovarian Neoplasms/genetics
- Protein Serine-Threonine Kinases/genetics
- Receptors, Immunologic/genetics
- Sequence Analysis, DNA
- Signaling Lymphocytic Activation Molecule Family
- Tumor Suppressor Protein p53/deficiency
Collapse
Affiliation(s)
- Jeffrey C Francis
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Lorenzo Melchor
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - James Campbell
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Howard Kendrick
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Wenbin Wei
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | | | | | - Lina Chen
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Iwanka Kozarewa
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Amanda Swain
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Matthew J Smalley
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| |
Collapse
|
37
|
Nebbioso A, Benedetti R, Conte M, Iside C, Altucci L. Genetic mutations in epigenetic modifiers as therapeutic targets in acute myeloid leukemia. Expert Opin Ther Targets 2015; 19:1187-202. [PMID: 26028314 DOI: 10.1517/14728222.2015.1051728] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Despite enormous insights into the molecular mechanisms of acute myeloid leukemia (AML) pathophysiology, this disease is still fatal in the majority of patients, highlighting the urgent need for novel biomarkers useful in AML prognosis and therapy. AREAS COVERED The advent of modern sequencing technologies has allowed the identification of genetic mutations in genes encoding for specific enzymes involved in the epigenetic regulation of gene expression. The authors review recent data demonstrating the involvement of mutations in genes encoding for epigenetic players and their complex combination with somatic genetic mutations in the pathogenesis of AML. They also discuss the prognostic and therapeutic implications of these findings. EXPERT OPINION Current clinical and preclinical studies are underscoring the importance of targeting epigenetic modifiers as new biomarkers for a better prognostic risk stratification and therapeutic evaluation of intermediate-risk patients. Combining data from traditional and modern methodologies will allow a definition of the complex networks of epigenetic changes and molecular interactions between candidate epitargets and key regulators of hematopoiesis. It will thus be possible to achieve an overview of potential aberrant mechanisms driving leukemogenesis in different classes of AML patients. Such an improved approach could pave the way towards 'personalized' therapies.
Collapse
Affiliation(s)
- Angela Nebbioso
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples , Via L. De Crecchio 7, 80138 Naples , Italy
| | | | | | | | | |
Collapse
|
38
|
Langabeer SE, Haslam K. Lack of myeloproliferative neoplasm-associated CALRmutations in acute promyelocytic leukemia. Leuk Lymphoma 2015; 56:1168-9. [DOI: 10.3109/10428194.2014.953156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
39
|
Chen J, Hackett CS, Zhang S, Song YK, Bell RJA, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. The genetics of splicing in neuroblastoma. Cancer Discov 2015; 5:380-95. [PMID: 25637275 PMCID: PMC4390477 DOI: 10.1158/2159-8290.cd-14-0892] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Regulation of mRNA splicing, a critical and tightly regulated cellular function, underlies the majority of proteomic diversity and is frequently disrupted in disease. Using an integrative genomics approach, we combined both genomic data and exon-level transcriptome data in two somatic tissues (cerebella and peripheral ganglia) from a transgenic mouse model of neuroblastoma, a tumor that arises from the peripheral neural crest. Here, we describe splicing quantitative trait loci associated with differential splicing across the genome that we use to identify genes with previously unknown functions within the splicing pathway and to define de novo intronic splicing motifs that influence splicing from hundreds of bases away. Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma. SIGNIFICANCE Somatic mutations with predictable downstream effects are largely relegated to coding regions, which comprise less than 2% of the human genome. Using an unbiased in vivo analysis of a mouse model of neuroblastoma, we have identified intronic splicing motifs that translate into sites for recurrent somatic mutations in human cancers.
Collapse
Affiliation(s)
- Justin Chen
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California. Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California
| | - Christopher S Hackett
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California
| | - Shile Zhang
- Program in Bioinformatics, Boston University, Boston, Massachusetts. Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Young K Song
- Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Robert J A Bell
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Annette M Molinaro
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California. Institute for Cancer Research, Oslo, Norway
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jun S Song
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California. Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, Illinois. Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Joseph F Costello
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - W Clay Gustafson
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Terry Van Dyke
- Mouse Cancer Genetics Program, Center for Advanced Preclinical Research, National Cancer Institute, Frederick, Maryland
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California. Department of Dermatology, University of California, San Francisco, San Francisco, California. Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California
| | - Javed Khan
- Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California. Department of Pediatrics, University of California, San Francisco, San Francisco, California.
| |
Collapse
|
40
|
Grove CS, Vassiliou GS. Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer? Dis Model Mech 2015; 7:941-51. [PMID: 25056697 PMCID: PMC4107323 DOI: 10.1242/dmm.015974] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acute myeloid leukaemia (AML) is an uncontrolled clonal proliferation of abnormal myeloid progenitor cells in the bone marrow and blood. Advances in cancer genomics have revealed the spectrum of somatic mutations that give rise to human AML and drawn our attention to its molecular evolution and clonal architecture. It is now evident that most AML genomes harbour small numbers of mutations, which are acquired in a stepwise manner. This characteristic, combined with our ability to identify mutations in individual leukaemic cells and our detailed understanding of normal human and murine haematopoiesis, makes AML an excellent model for understanding the principles of cancer evolution. Furthermore, a better understanding of how AML evolves can help us devise strategies to improve the therapy and prognosis of AML patients. Here, we draw from recent advances in genomics, clinical studies and experimental models to describe the current knowledge of the clonal evolution of AML and its implications for the biology and treatment of leukaemias and other cancers.
Collapse
Affiliation(s)
- Carolyn S Grove
- Haematological Cancer Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| |
Collapse
|
41
|
Enforced differentiation of Dnmt3a-null bone marrow leads to failure with c-Kit mutations driving leukemic transformation. Blood 2015; 125:619-28. [PMID: 25416276 DOI: 10.1182/blood-2014-08-594564] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Genome sequencing studies of patient samples have implicated the involvement of various components of the epigenetic machinery in myeloid diseases, including the de novo DNA methyltransferase DNMT3A. We have recently shown that Dnmt3a is essential for hematopoietic stem cell differentiation. Here, we investigated the effect of loss of Dnmt3a on hematopoietic transformation by forcing the normally quiescent hematopoietic stem cells to divide in vivo. Mice transplanted with Dnmt3a-null bone marrow in the absence of wildtype support cells succumbed to bone marrow failure (median survival, 328 days) characteristic of myelodysplastic syndromes with symptoms including anemia, neutropenia, bone marrow hypercellularity, and splenomegaly with myeloid infiltration. Two out of 25 mice developed myeloid leukemia with >20%blasts in the blood and bone marrow. Four out of 25 primary mice succumbed to myeloproliferative disorders, some of which progressed to secondary leukemia after long latency. Exome sequencing identified cooperating c-Kit mutations found only in the leukemic samples. Ectopic introduction of c-Kit variants into a Dnmt3a-deficient background produced acute leukemia with a short latency (median survival, 67 days). Our data highlight crucial roles of Dnmt3a in normal and malignant hematopoiesis and suggest that a major role for this enzyme is to facilitate developmental progression of progenitor cells at multiple decision checkpoints.
Collapse
|
42
|
Agarwal SK. Exploring the tumors of multiple endocrine neoplasia type 1 in mouse models for basic and preclinical studies. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2014; 1:153-161. [PMID: 25685317 DOI: 10.2217/ije.14.16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Most patients (70-90%) with the multiple endocrine neoplasia type 1 (MEN1) syndrome possess germline heterozygous mutations in MEN1 that predisposes to tumors of multiple endocrine and nonendocrine tissues. Some endocrine tumors of the kinds seen in MEN1 that occur sporadically in the general population also possess somatic mutations in MEN1. Interestingly, the endocrine tumors of MEN1 are recapitulated in mouse models of Men1 loss that serve as a valuable resource to understand the pathophysiology and molecular basis of tumorigenesis. Exploring these endocrine tumors in mouse models using in vivo, ex vivo and in vitro methods can help to follow the process of tumorigenesis, and can be useful for preclinical testing of therapeutics and understanding their mechanisms of action.
Collapse
Affiliation(s)
- Sunita K Agarwal
- National Institutes of Health, NIDDK, Metabolic Diseases Branch, Bldg 10, Room 8C-101, Bethesda, MD 20892, USA, Tel.: +1 301 402 7834
| |
Collapse
|
43
|
Choi J, Cooper ML, Alahmari B, Ritchey J, Collins L, Holt M, DiPersio JF. Pharmacologic blockade of JAK1/JAK2 reduces GvHD and preserves the graft-versus-leukemia effect. PLoS One 2014; 9:e109799. [PMID: 25289677 PMCID: PMC4188578 DOI: 10.1371/journal.pone.0109799] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 09/13/2014] [Indexed: 12/13/2022] Open
Abstract
We have recently reported that interferon gamma receptor deficient (IFNγR-/-) allogeneic donor T cells result in significantly less graft-versus-host disease (GvHD) than wild-type (WT) T cells, while maintaining an anti-leukemia or graft-versus-leukemia (GvL) effect after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We demonstrated that IFNγR signaling regulates alloreactive T cell trafficking to GvHD target organs through expression of the chemokine receptor CXCR3 in alloreactive T cells. Since IFNγR signaling is mediated via JAK1/JAK2, we tested the effect of JAK1/JAK2 inhibition on GvHD. While we demonstrated that pharmacologic blockade of JAK1/JAK2 in WT T cells using the JAK1/JAK2 inhibitor, INCB018424 (Ruxolitinib), resulted in a similar effect to IFNγR-/- T cells both in vitro (reduction of CXCR3 expression in T cells) and in vivo (mitigation of GvHD after allo-HSCT), it remains to be determined if in vivo administration of INCB018424 will result in preservation of GvL while reducing GvHD. Here, we report that INCB018424 reduces GvHD and preserves the beneficial GvL effect in two different murine MHC-mismatched allo-HSCT models and using two different murine leukemia models (lymphoid leukemia and myeloid leukemia). In addition, prolonged administration of INCB018424 further improves survival after allo-HSCT and is superior to other JAK1/JAK2 inhibitors, such as TG101348 or AZD1480. These data suggest that pharmacologic inhibition of JAK1/JAK2 might be a promising therapeutic approach to achieve the beneficial anti-leukemia effect and overcome HLA-barriers in allo-HSCT. It might also be exploited in other diseases besides GvHD, such as organ transplant rejection, chronic inflammatory diseases and autoimmune diseases.
Collapse
MESH Headings
- Animals
- Disease Models, Animal
- Gene Expression Regulation, Leukemic
- Graft vs Host Disease/enzymology
- Graft vs Host Disease/immunology
- Graft vs Host Disease/pathology
- Graft vs Host Disease/prevention & control
- Graft vs Leukemia Effect/drug effects
- Hematopoietic Stem Cell Transplantation
- Janus Kinase 1/antagonists & inhibitors
- Janus Kinase 1/genetics
- Janus Kinase 1/immunology
- Janus Kinase 2/antagonists & inhibitors
- Janus Kinase 2/genetics
- Janus Kinase 2/immunology
- Leukemia, Lymphoid/drug therapy
- Leukemia, Lymphoid/enzymology
- Leukemia, Lymphoid/immunology
- Leukemia, Lymphoid/pathology
- Leukemia, Myeloid/drug therapy
- Leukemia, Myeloid/enzymology
- Leukemia, Myeloid/immunology
- Leukemia, Myeloid/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Knockout
- Nitriles
- Protein Kinase Inhibitors/pharmacology
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Pyrrolidines/pharmacology
- Receptors, Interferon/deficiency
- Receptors, Interferon/genetics
- Receptors, Interferon/immunology
- Signal Transduction
- Sulfonamides/pharmacology
- T-Lymphocytes/drug effects
- T-Lymphocytes/enzymology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Transplantation, Homologous
- Whole-Body Irradiation
- Interferon gamma Receptor
Collapse
Affiliation(s)
- Jaebok Choi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Matthew L. Cooper
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bader Alahmari
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Julie Ritchey
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lynne Collins
- BRIGHT Institute, and Molecular Imaging Center, Mallinckrodt Institute of Radiology, and Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Matthew Holt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| |
Collapse
|
44
|
Mazzarella L, Riva L, Luzi L, Ronchini C, Pelicci PG. The Genomic and Epigenomic Landscapes of AML. Semin Hematol 2014; 51:259-72. [DOI: 10.1053/j.seminhematol.2014.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
45
|
Werner B, Gallagher RE, Paietta EM, Litzow MR, Tallman MS, Wiernik PH, Slack JL, Willman CL, Sun Z, Traulsen A, Dingli D. Dynamics of leukemia stem-like cell extinction in acute promyelocytic leukemia. Cancer Res 2014; 74:5386-96. [PMID: 25082816 PMCID: PMC4184925 DOI: 10.1158/0008-5472.can-14-1210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many tumors are believed to be maintained by a small number of cancer stem-like cells, where cure is thought to require eradication of this cell population. In this study, we investigated the dynamics of acute promyelocytic leukemia (APL) before and during therapy with regard to disease initiation, progression, and therapeutic response. This investigation used a mathematical model of hematopoiesis and a dataset derived from the North American Intergroup Study INT0129. The known phenotypic constraints of APL could be explained by a combination of differentiation blockade of PML-RARα-positive cells and suppression of normal hematopoiesis. All-trans retinoic acid (ATRA) neutralizes the differentiation block and decreases the proliferation rate of leukemic stem cells in vivo. Prolonged ATRA treatment after chemotherapy can cure patients with APL by eliminating the stem-like cell population over the course of approximately one year. To our knowledge, this study offers the first estimate of the average duration of therapy that is required to eliminate stem-like cancer cells from a human tumor, with the potential for the refinement of treatment strategies to better manage human malignancy.
Collapse
Affiliation(s)
- Benjamin Werner
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | | | - Mark R Litzow
- Division of Hematology and Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | | | | | - James L Slack
- Division of Hematology, Mayo Clinic Arizona, Scottsdale, Arizona
| | | | - Zhuoxin Sun
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David Dingli
- Division of Hematology and Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota. Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
46
|
Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O'Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA. The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol 2014; 14:R113. [PMID: 24148783 PMCID: PMC3983654 DOI: 10.1186/gb-2013-14-10-r113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022] Open
Abstract
Background Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even with germline mutated p53, these engineered melanomas present with variable onset and pathology, implicating additional somatic mutations in a multi-hit tumorigenic process. Results To decipher the genetics of these melanomas, we sequence the protein coding exons of 53 primary melanomas generated from several BRAFV600E or NRASQ61K driven transgenic zebrafish lines. We find that engineered zebrafish melanomas show an overall low mutation burden, which has a strong, inverse association with the number of initiating germline drivers. Although tumors reveal distinct mutation spectrums, they show mostly C > T transitions without UV light exposure, and enrichment of mutations in melanogenesis, p53 and MAPK signaling. Importantly, a recurrent amplification occurring with pre-configured drivers BRAFV600E and p53-/- suggests a novel path of BRAF cooperativity through the protein kinase A pathway. Conclusion This is the first analysis of a melanoma mutational landscape in the absence of UV light, where tumors manifest with remarkably low mutation burden and high heterogeneity. Genotype specific amplification of protein kinase A in cooperation with BRAF and p53 mutation suggests the involvement of melanogenesis in these tumors. This work is important for defining the spectrum of events in BRAF or NRAS driven melanoma in the absence of UV light, and for informed exploitation of models such as transgenic zebrafish to better understand mechanisms leading to human melanoma formation.
Collapse
|
47
|
Rice KL, de Thé H. The acute promyelocytic leukaemia success story: curing leukaemia through targeted therapies. J Intern Med 2014; 276:61-70. [PMID: 24635409 DOI: 10.1111/joim.12208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The recent finding that almost all patients with acute promyelocytic leukaemia (APL) may be cured using a combination of retinoic acid (RA) and arsenic trioxide (As(2)O(3)) (N Engl J Med, 369, 2013 and 111) highlights the progress made in our understanding of APL pathogenesis and therapeutic approaches over the past 25 years. The study of APL has revealed many important lessons related to transcriptional control, nuclear organization, epigenetics and the role of proteolysis in biological control. Even more important has been the clinical demonstration that molecularly targeted therapy can eradicate disease.
Collapse
Affiliation(s)
- K L Rice
- Université Paris Diderot, Sorbonne Paris Cité, Hôpital St. Louis, Paris Cedex, France; INSERM UMR 944, Equipe labellisée par la Ligue Nationale contre le Cancer, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex, France; CNRS UMR 7212, Hôpital St. Louis, Paris Cedex, France
| | | |
Collapse
|
48
|
McFadden DG, Papagiannakopoulos T, Taylor-Weiner A, Stewart C, Carter SL, Cibulskis K, Bhutkar A, McKenna A, Dooley A, Vernon A, Sougnez C, Malstrom S, Heimann M, Park J, Chen F, Farago AF, Dayton T, Shefler E, Gabriel S, Getz G, Jacks T. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell 2014; 156:1298-1311. [PMID: 24630729 DOI: 10.1016/j.cell.2014.02.031] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 11/27/2013] [Accepted: 02/12/2014] [Indexed: 12/14/2022]
Abstract
Small cell lung carcinoma (SCLC) is a highly lethal, smoking-associated cancer with few known targetable genetic alterations. Using genome sequencing, we characterized the somatic evolution of a genetically engineered mouse model (GEMM) of SCLC initiated by loss of Trp53 and Rb1. We identified alterations in DNA copy number and complex genomic rearrangements and demonstrated a low somatic point mutation frequency in the absence of tobacco mutagens. Alterations targeting the tumor suppressor Pten occurred in the majority of murine SCLC studied, and engineered Pten deletion accelerated murine SCLC and abrogated loss of Chr19 in Trp53; Rb1; Pten compound mutant tumors. Finally, we found evidence for polyclonal and sequential metastatic spread of murine SCLC by comparative sequencing of families of related primary tumors and metastases. We propose a temporal model of SCLC tumorigenesis with implications for human SCLC therapeutics and the nature of cancer-genome evolution in GEMMs.
Collapse
Affiliation(s)
- David G McFadden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Thales Papagiannakopoulos
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amaro Taylor-Weiner
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott L Carter
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristian Cibulskis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Arjun Bhutkar
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aaron McKenna
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alison Dooley
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amanda Vernon
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott Malstrom
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Megan Heimann
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jennifer Park
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Frances Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna F Farago
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Talya Dayton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Erica Shefler
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Gabriel
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
49
|
Robles-Espinoza CD, Adams DJ. Cross-species analysis of mouse and human cancer genomes. Cold Spring Harb Protoc 2014; 2014:350-8. [PMID: 24173316 DOI: 10.1101/pdb.top078824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fundamental advances in our understanding of the human cancer genome have been made over the last five years, driven largely by the development of next-generation sequencing (NGS) technologies. Here we will discuss the tools and technologies that have been used to profile human tumors, how they may be applied to the analysis of the mouse cancer genome, and the results thus far. In addition to mutations that disrupt cancer genes, NGS is also being applied to the analysis of the transcriptome of cancers, and, through the use of techniques such as ChIP-Seq, the protein-DNA landscape is also being revealed. Gaining a comprehensive picture of the mouse cancer genome, at the DNA level and through the analysis of the transcriptome and regulatory landscape, will allow us to "biofilter" for driver genes in more complex human cancers and represents a critical test to determine which mouse cancer models are faithful genetic surrogates of the human disease.
Collapse
|
50
|
Lo-Coco F, Hasan SK. Understanding the molecular pathogenesis of acute promyelocytic leukemia. Best Pract Res Clin Haematol 2014; 27:3-9. [DOI: 10.1016/j.beha.2014.04.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|