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Kimura S, Polonen P, Montefiori L, Park CS, Iacobucci I, Yeoh AE, Attarbaschi A, Moore AS, Brown A, Manabe A, Buldini B, Freeman BB, Chen C, Cheng C, Kean Hui C, Li CK, Pui CH, Qu C, Tomizawa D, Teachey DT, Varotto E, Paietta EM, Arnold ED, Locatelli F, Escherich G, Elisa Muhle H, Marquart HV, de Groot-Kruseman HA, Rowe JM, Stary J, Trka J, Choi JK, Meijerink JPP, Yang JJ, Takita J, Pawinska-Wasikowska K, Roberts KG, Han K, Caldwell KJ, Schmiegelow K, Crews KR, Eguchi M, Schrappe M, Zimmerman M, Takagi M, Maybury M, Svaton M, Reiterova M, Kicinski M, Prater MS, Kato M, Reyes N, Spinelli O, Thomas P, Mazilier P, Gao Q, Masetti R, Kotecha RS, Pieters R, Elitzur S, Luger SM, Mitchell S, Pruett-Miller SM, Shen S, Jeha S, Köhrer S, Kornblau SM, Skoczeń S, Miyamura T, Vincent TL, Imamura T, Conter V, Tang Y, Liu YC, Chang Y, Gu Z, Cheng Z, Yinmei Z, Inaba H, Mullighan CG. Biologic and clinical features of childhood gamma delta T-ALL: identification of STAG2/LMO2 γδ T-ALL as an extremely high risk leukemia in the very young. medRxiv 2023:2023.11.06.23298028. [PMID: 37986997 PMCID: PMC10659466 DOI: 10.1101/2023.11.06.23298028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
PURPOSE Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease. METHODS We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations. Therapeutic vulnerabilities were identified by high throughput drug screening of cell lines and xenografts. RESULTS γδ T-ALL in children under three was extremely high-risk with 5-year event-free survival (33% v. 70% [age 3-<10] and 73% [age ≥10], P =9.5 x 10 -5 ) and 5-year overall survival (49% v. 78% [age 3-<10] and 81% [age ≥10], P =0.002), differences not observed in non-γδ T-ALL. γδ T-ALL in this age group was enriched for genomic alterations activating LMO2 activation and inactivating STAG2 inactivation ( STAG2/LMO2 ). Mechanistically, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping resulting in deregulation of gene expression associated with T-cell differentiation. Drug screening showed resistance to prednisolone, consistent with clinical slow treatment response, but identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which was efficaciously targeted by Poly(ADP-ribose) polymerase (PARP) inhibition, with synergism with HDAC inhibitors. Ex-vivo drug screening on PDX cells validated the efficacy of PARP inhibitors as well as other potential targets including nelarabine. CONCLUSION γδ T-ALL in children under the age of three is extremely high-risk and enriched for STAG2/LMO2 ALL. STAG2 loss perturbs chromatin conformation and differentiation, and STAG2/LMO2 ALL is sensitive to PARP inhibition. These data provide a diagnostic and therapeutic framework for pediatric γδ T-ALL. SUPPORT The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children's Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick's Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children's Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173. DISCLAIMER The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies were not directly involved in the design of the study, gathering, analysis and interpretation of the data, writing of the manuscript, or decision to submit the manuscript for publication.
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Schwartz JR, Ma J, Kamens J, Westover T, Walsh MP, Brady SW, Robert Michael J, Chen X, Montefiori L, Song G, Wu G, Wu H, Branstetter C, Hiltenbrand R, Walsh MF, Nichols KE, Maciaszek JL, Liu Y, Kumar P, Easton J, Newman S, Rubnitz JE, Mullighan CG, Pounds S, Zhang J, Gruber T, Ma X, Klco JM. The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms. Nat Commun 2021; 12:985. [PMID: 33579957 PMCID: PMC7880998 DOI: 10.1038/s41467-021-21255-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Pediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n = 28, tAML: n = 56). Our data show that Ras/MAPK pathway mutations, alterations in RUNX1 or TP53, and KMT2A rearrangements are frequent somatic drivers, and we identify cases with aberrant MECOM expression secondary to enhancer hijacking. Unlike adults with tMN, we find no evidence of pre-existing minor tMN clones (including those with TP53 mutations), but rather the majority of cases are unrelated clones arising as a consequence of cytotoxic therapy. These studies also uncover rare cases of lineage switch disease rather than true secondary neoplasms. Paediatric therapy-related myeloid neoplasms (tMN) have a dismal prognosis and have not been comprehensively profiled. Here the authors characterise the molecular landscape of 84 paediatric tMN patients, and find that, unlike adult tMNs, these do not emerge from pre-existing clones and that MECOM dysregulation is frequent.
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Affiliation(s)
- Jason R Schwartz
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, US
| | - Jing Ma
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Jennifer Kamens
- Stanford University School of Medicine, Department of Pediatrics, Stanford, CA, US
| | - Tamara Westover
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Michael P Walsh
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Samuel W Brady
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - J Robert Michael
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Xiaolong Chen
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Lindsey Montefiori
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Guangchun Song
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Gang Wu
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Huiyun Wu
- St. Jude Children's Research Hospital, Department of Biostatistics, Memphis, TN, US
| | - Cristyn Branstetter
- Arkansas Children's Northwest Hospital, Department of Hematology/Oncology, Springdale, AR, US
| | - Ryan Hiltenbrand
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, Department of Pediatrics, New York, NY, US
| | - Kim E Nichols
- St. Jude Children's Research Hospital, Department of Oncology, Memphis, TN, US
| | - Jamie L Maciaszek
- St. Jude Children's Research Hospital, Department of Oncology, Memphis, TN, US
| | - Yanling Liu
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Priyadarshini Kumar
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - John Easton
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Scott Newman
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Jeffrey E Rubnitz
- St. Jude Children's Research Hospital, Department of Oncology, Memphis, TN, US
| | - Charles G Mullighan
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US
| | - Stanley Pounds
- St. Jude Children's Research Hospital, Department of Biostatistics, Memphis, TN, US
| | - Jinghui Zhang
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US
| | - Tanja Gruber
- Stanford University School of Medicine, Department of Pediatrics, Stanford, CA, US. .,Stanford University School of Medicine, Stanford Cancer Institute, Stanford, CA, US.
| | - Xiaotu Ma
- St. Jude Children's Research Hospital, Department of Computational Biology, Memphis, TN, US.
| | - Jeffery M Klco
- St. Jude Children's Research Hospital, Department of Pathology, Memphis, TN, US.
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Boogerd CJ, Zhu X, Aneas I, Sakabe N, Zhang L, Sobreira DR, Montefiori L, Bogomolovas J, Joslin AC, Zhou B, Chen J, Nobrega MA, Evans SM. Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development. Circ Res 2019; 123:428-442. [PMID: 29903739 PMCID: PMC6092109 DOI: 10.1161/circresaha.118.311339] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Supplemental Digital Content is available in the text. Rationale: Mutations in the transcription factor TBX20 (T-box 20) are associated with congenital heart disease. Germline ablation of Tbx20 results in abnormal heart development and embryonic lethality by embryonic day 9.5. Because Tbx20 is expressed in multiple cell lineages required for myocardial development, including pharyngeal endoderm, cardiogenic mesoderm, endocardium, and myocardium, the cell type–specific requirement for TBX20 in early myocardial development remains to be explored. Objective: Here, we investigated roles of TBX20 in midgestation cardiomyocytes for heart development. Methods and Results: Ablation of Tbx20 from developing cardiomyocytes using a doxycycline inducible cTnTCre transgene led to embryonic lethality. The circumference of developing ventricular and atrial chambers, and in particular that of prospective left atrium, was significantly reduced in Tbx20 conditional knockout mutants. Cell cycle analysis demonstrated reduced proliferation of Tbx20 mutant cardiomyocytes and their arrest at the G1-S phase transition. Genome-wide transcriptome analysis of mutant cardiomyocytes revealed differential expression of multiple genes critical for cell cycle regulation. Moreover, atrial and ventricular gene programs seemed to be aberrantly regulated. Putative direct TBX20 targets were identified using TBX20 ChIP-Seq (chromatin immunoprecipitation with high throughput sequencing) from embryonic heart and included key cell cycle genes and atrial and ventricular specific genes. Notably, TBX20 bound a conserved enhancer for a gene key to atrial development and identity, COUP-TFII/Nr2f2 (chicken ovalbumin upstream promoter transcription factor 2/nuclear receptor subfamily 2, group F, member 2). This enhancer interacted with the NR2F2 promoter in human cardiomyocytes and conferred atrial specific gene expression in a transgenic mouse in a TBX20-dependent manner. Conclusions: Myocardial TBX20 directly regulates a subset of genes required for fetal cardiomyocyte proliferation, including those required for the G1-S transition. TBX20 also directly downregulates progenitor-specific genes and, in addition to regulating genes that specify chamber versus nonchamber myocardium, directly activates genes required for establishment or maintenance of atrial and ventricular identity. TBX20 plays a previously unappreciated key role in atrial development through direct regulation of an evolutionarily conserved COUPT-FII enhancer.
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Affiliation(s)
- Cornelis J. Boogerd
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Xiaoming Zhu
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Ivy Aneas
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Noboru Sakabe
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lunfeng Zhang
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Debora R. Sobreira
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lindsey Montefiori
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Julius Bogomolovas
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (J.B.)
| | - Amelia C. Joslin
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Bin Zhou
- Department of Genetics, Medicine and Pediatrics, Albert Einstein College of Medicine of Yeshiva University, New York, NY (B.Z.)
| | - Ju Chen
- Department of Medicine (J.B., J.C., S.M.E.)
| | - Marcelo A. Nobrega
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Sylvia M. Evans
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Pharmacology (S.M.E.)
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Montefiori L, Wuerffel R, Roqueiro D, Lajoie B, Guo C, Gerasimova T, De S, Wood W, Becker KG, Dekker J, Liang J, Sen R, Kenter AL. Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. Cell Rep 2016; 14:896-906. [PMID: 26804913 DOI: 10.1016/j.celrep.2015.12.083] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/29/2015] [Accepted: 12/16/2015] [Indexed: 12/19/2022] Open
Abstract
Early B cell development is characterized by large-scale Igh locus contraction prior to V(D)J recombination to facilitate a highly diverse Ig repertoire. However, an understanding of the molecular architecture that mediates locus contraction remains unclear. We have combined high-resolution chromosome conformation capture (3C) techniques with 3D DNA FISH to identify three conserved topological subdomains. Each of these topological folds encompasses a major VH gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the VHJ558 gene family. In its absence, the J558 VH genes fail to associate with the proximal VH genes, thereby providing a plausible explanation for reduced VHJ558 gene rearrangements in Pax5-deficient pro-B cells. We propose that Igh locus contraction is the cumulative effect of several independently controlled chromatin subdomains that provide the structural infrastructure to coordinate optimal antigen receptor assembly.
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Affiliation(s)
- Lindsey Montefiori
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert Wuerffel
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA
| | - Damian Roqueiro
- Department of Bioengineering, University of Illinois College of Engineering and College of Medicine, Chicago, IL 60612-7344, USA
| | - Bryan Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Changying Guo
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - Tatiana Gerasimova
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Gene Expression and Genomics Unit, Laboratory of Genetics, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - William Wood
- Gene Expression and Genomics Unit, Laboratory of Genetics, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, Laboratory of Genetics, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois College of Engineering and College of Medicine, Chicago, IL 60612-7344, USA
| | - Ranjan Sen
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224, USA.
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612-7344, USA.
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