1
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Jann JC, Hergott CB, Winkler M, Liu Y, Braun B, Charles A, Copson KM, Barua S, Meggendorfer M, Nadarajah N, Shimony S, Winer ES, Wadleigh M, Stone RM, DeAngelo DJ, Garcia JS, Haferlach T, Lindsley RC, Luskin MR, Stahl M, Tothova Z. Subunit-specific analysis of cohesin-mutant myeloid malignancies reveals distinct ontogeny and outcomes. Leukemia 2024; 38:1992-2002. [PMID: 39033241 PMCID: PMC11347381 DOI: 10.1038/s41375-024-02347-y] [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: 02/21/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
Mutations in the cohesin complex components (STAG2, RAD21, SMC1A, SMC3, and PDS5B) are recurrent genetic drivers in myelodysplastic neoplasm (MDS) and acute myeloid leukemia (AML). Whether the different cohesin subunit mutations share clinical characteristics and prognostic significance is not known. We analyzed 790 cohesin-mutant patients from the Dana-Farber Cancer Institute (DFCI) and the Munich Leukemia Laboratory (MLL), 390 of which had available outcome data, and identified subunit-specific clinical, prognostic, and genetic characteristics suggestive of distinct ontogenies. We found that STAG2 mutations are acquired at MDS stage and are associated with secondary AML, adverse prognosis, and co-occurrence of secondary AML-type mutations. In contrast, mutations in RAD21, SMC1A and SMC3 share features with de novo AML with better prognosis, and co-occurrence with de novo AML-type lesions. The findings show the heterogeneous nature of cohesin complex mutations, and inform clinical and prognostic classification, as well as distinct biology of the cohesin complex.
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Affiliation(s)
- Johann-Christoph Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Cancer Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Christopher B Hergott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Marisa Winkler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Element Iowa City (JMI Laboratories), North Liberty, IA, 52317, USA
| | - Yiwen Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Anne Charles
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kevin M Copson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shougat Barua
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute, Cambridge, MA, 02142, USA.
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2
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Fischer A, Hernández-Rodríguez B, Mulet-Lazaro R, Nuetzel M, Hölzl F, van Herk S, Kavelaars FG, Stanewsky H, Ackermann U, Niang AH, Diaz N, Reuschel E, Strieder N, Hernández-López I, Valk PJM, Vaquerizas JM, Rehli M, Delwel R, Gebhard C. STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemia. Cell Rep 2024; 43:114498. [PMID: 39084219 DOI: 10.1016/j.celrep.2024.114498] [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: 12/11/2023] [Revised: 05/24/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2, but not its paralog STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression, and local chromatin activation, which were not compensated by the remaining STAG1-cohesin. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. Complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs) revealed effects resembling STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by the depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression, and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.
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MESH Headings
- Humans
- Cohesins
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Mutation/genetics
- Hematopoietic Stem Cells/metabolism
- Cell Differentiation/genetics
- Gene Expression Regulation, Leukemic
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/genetics
- Nuclear Proteins
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Affiliation(s)
- Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Hölzl
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Amadou H Niang
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Noelia Diaz
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | | | | | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany; Department of Developmental Epigenomics, MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
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3
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Hayatigolkhatmi K, Valzelli R, El Menna O, Minucci S. Epigenetic alterations in AML: Deregulated functions leading to new therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:27-75. [PMID: 39179348 DOI: 10.1016/bs.ircmb.2024.06.003] [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: 08/26/2024]
Abstract
Acute myeloid leukemia (AML) results in disruption of the hematopoietic differentiation process. Crucial progress has been made, and new therapeutic strategies for AML have been developed. Induction chemotherapy, however, remains the main option for the majority of AML patients. Epigenetic dysregulation plays a central role in AML pathogenesis, supporting leukemogenesis and maintenance of leukemic stem cells. Here, we provide an overview of the intricate interplay of altered epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling, in AML development. We explore the role of epigenetic regulators, such as DNMTs, HMTs, KDMs, and HDACs, in mediating gene expression patterns pushing towards leukemic cell transformation. Additionally, we discuss the impact of cytogenetic lesions on epigenomic remodeling and the potential of targeting epigenetic vulnerabilities as a therapeutic strategy. Understanding the epigenetic landscape of AML offers insights into novel therapeutic avenues, including epigenetic modifiers and particularly their use in combination therapies, to improve treatment outcomes and overcome drug resistance.
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Affiliation(s)
- Kourosh Hayatigolkhatmi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
| | - Riccardo Valzelli
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Oualid El Menna
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy; Department of Hemato-Oncology, Università Statale di Milano, Milan, Italy.
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4
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Lu Z, Wang Y, Assumpção ALFV, Liu P, Kopp A, Saka S, Mcilwain SJ, Viny AD, Brand M, Pan X. Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Adv 2024; 8:3076-3091. [PMID: 38531064 PMCID: PMC11222949 DOI: 10.1182/bloodadvances.2023011411] [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: 08/09/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
ABSTRACT Yin Yang 1 (YY1) and structural maintenance of chromosomes 3 (SMC3) are 2 critical chromatin structural factors that mediate long-distance enhancer-promoter interactions and promote developmentally regulated changes in chromatin architecture in hematopoietic stem/progenitor cells (HSPCs). Although YY1 has critical functions in promoting hematopoietic stem cell (HSC) self-renewal and maintaining HSC quiescence, SMC3 is required for proper myeloid lineage differentiation. However, many questions remain unanswered regarding how YY1 and SMC3 interact with each other and affect hematopoiesis. We found that YY1 physically interacts with SMC3 and cooccupies with SMC3 at a large cohort of promoters genome wide, and YY1 deficiency deregulates the genetic network governing cell metabolism. YY1 occupies the Smc3 promoter and represses SMC3 expression in HSPCs. Although deletion of 1 Smc3 allele partially restores HSC numbers and quiescence in YY1 knockout mice, Yy1-/-Smc3+/- HSCs fail to reconstitute blood after bone marrow transplant. YY1 regulates HSC metabolic pathways and maintains proper intracellular reactive oxygen species levels in HSCs, and this regulation is independent of the YY1-SMC3 axis. Our results establish a distinct YY1-SMC3 axis and its impact on HSC quiescence and metabolism.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Yinghua Wang
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Anna L. F. V. Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Audrey Kopp
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sahitya Saka
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Sean J. Mcilwain
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Aaron D. Viny
- Division of Hematology & Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY
| | - Marjorie Brand
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
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5
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Xu JJ, Viny AD. Chromatin organization in myelodysplastic syndrome. Exp Hematol 2024; 134:104216. [PMID: 38582293 DOI: 10.1016/j.exphem.2024.104216] [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: 01/10/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Disordered chromatin organization has emerged as a new aspect of the pathogenesis of myelodysplastic syndrome (MDS). Characterized by lineage dysplasia and a high transformation rate to acute myeloid leukemia (AML), the genetic determinant of MDS is thought to be the main driver of the disease's progression. Among the recurrently mutated pathways, alterations in chromatin organization, such as the cohesin complex, have a profound impact on hematopoietic stem cell (HSC) function and lineage commitment. The cohesin complex is a ring-like structure comprised of structural maintenance of chromosomes (SMC), RAD21, and STAG proteins that involve three-dimensional (3D) genome organization via loop extrusion in mammalian cells. The partial loss of the functional cohesin ring leads to altered chromatin accessibility specific to key hematopoietic transcription factors, which is thought to be the molecular mechanism of cohesin dysfunction. Currently, there are no specific targeting agents for cohesin mutant MDS/AML. Potential therapeutic strategies have been proposed based on the current understanding of cohesin mutant leukemogenesis. Here, we will review the recent advances in investigation and targeting approaches against cohesin mutant MDS/AML.
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Affiliation(s)
- Jane Jialu Xu
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York.
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6
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Hall T, Gurbuxani S, Crispino JD. Malignant progression of preleukemic disorders. Blood 2024; 143:2245-2255. [PMID: 38498034 PMCID: PMC11181356 DOI: 10.1182/blood.2023020817] [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: 09/27/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
ABSTRACT The spectrum of myeloid disorders ranges from aplastic bone marrow failure characterized by an empty bone marrow completely lacking in hematopoiesis to acute myeloid leukemia in which the marrow space is replaced by undifferentiated leukemic blasts. Recent advances in the capacity to sequence bulk tumor population as well as at a single-cell level has provided significant insight into the stepwise process of transformation to acute myeloid leukemia. Using models of progression in the context of germ line predisposition (trisomy 21, GATA2 deficiency, and SAMD9/9L syndrome), premalignant states (clonal hematopoiesis and clonal cytopenia of unknown significance), and myelodysplastic syndrome, we review the mechanisms of progression focusing on the hierarchy of clonal mutation and potential roles of transcription factor alterations, splicing factor mutations, and the bone marrow environment in progression to acute myeloid leukemia. Despite major advances in our understanding, preventing the progression of these disorders or treating them at the acute leukemia phase remains a major area of unmet medical need.
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Affiliation(s)
- Trent Hall
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Sandeep Gurbuxani
- Section of Hematopathology, Department of Pathology, University of Chicago, Chicago, IL
| | - John D. Crispino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
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7
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Barwe SP, Kolb EA, Gopalakrishnapillai A. Down syndrome and leukemia: An insight into the disease biology and current treatment options. Blood Rev 2024; 64:101154. [PMID: 38016838 DOI: 10.1016/j.blre.2023.101154] [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: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023]
Abstract
Children with Down syndrome (DS) have a 10- to 20-fold greater predisposition to develop acute leukemia compared to the general population, with a skew towards myeloid leukemia (ML-DS). While ML-DS is known to be a subtype with good outcome, patients who relapse face a dismal prognosis. Acute lymphocytic leukemia in DS (DS-ALL) is considered to have poor prognosis. The relapse rate is high in DS-ALL compared to their non-DS counterparts. We have a better understanding about the mutational spectrum of DS leukemia. Studies using animal, embryonic stem cell- and induced pluripotent stem cell-based models have shed light on the mechanism by which these mutations contribute to disease initiation and progression. In this review, we list the currently available treatment strategies for DS-leukemias along with their outcome with emphasis on challenges with chemotherapy-related toxicities in children with DS. We focus on the mechanisms of initiation and progression of leukemia in children with DS and highlight the novel molecular targets with greater success in preclinical trials that have the potential to progress to the clinic.
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Affiliation(s)
- Sonali P Barwe
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - E Anders Kolb
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - Anilkumar Gopalakrishnapillai
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA.
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8
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Pati D. Role of chromosomal cohesion and separation in aneuploidy and tumorigenesis. Cell Mol Life Sci 2024; 81:100. [PMID: 38388697 PMCID: PMC10884101 DOI: 10.1007/s00018-024-05122-5] [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: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Cell division is a crucial process, and one of its essential steps involves copying the genetic material, which is organized into structures called chromosomes. Before a cell can divide into two, it needs to ensure that each newly copied chromosome is paired tightly with its identical twin. This pairing is maintained by a protein complex known as cohesin, which is conserved in various organisms, from single-celled ones to humans. Cohesin essentially encircles the DNA, creating a ring-like structure to handcuff, to keep the newly synthesized sister chromosomes together in pairs. Therefore, chromosomal cohesion and separation are fundamental processes governing the attachment and segregation of sister chromatids during cell division. Metaphase-to-anaphase transition requires dissolution of cohesins by the enzyme Separase. The tight regulation of these processes is vital for safeguarding genomic stability. Dysregulation in chromosomal cohesion and separation resulting in aneuploidy, a condition characterized by an abnormal chromosome count in a cell, is strongly associated with cancer. Aneuploidy is a recurring hallmark in many cancer types, and abnormalities in chromosomal cohesion and separation have been identified as significant contributors to various cancers, such as acute myeloid leukemia, myelodysplastic syndrome, colorectal, bladder, and other solid cancers. Mutations within the cohesin complex have been associated with these cancers, as they interfere with chromosomal segregation, genome organization, and gene expression, promoting aneuploidy and contributing to the initiation of malignancy. In summary, chromosomal cohesion and separation processes play a pivotal role in preserving genomic stability, and aberrations in these mechanisms can lead to aneuploidy and cancer. Gaining a deeper understanding of the molecular intricacies of chromosomal cohesion and separation offers promising prospects for the development of innovative therapeutic approaches in the battle against cancer.
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Affiliation(s)
- Debananda Pati
- Texas Children's Cancer Center, Department of Pediatrics Hematology/Oncology, Molecular and Cellular Biology, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA.
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9
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Filipek-Gorzała J, Kwiecińska P, Szade A, Szade K. The dark side of stemness - the role of hematopoietic stem cells in development of blood malignancies. Front Oncol 2024; 14:1308709. [PMID: 38440231 PMCID: PMC10910019 DOI: 10.3389/fonc.2024.1308709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/02/2024] [Indexed: 03/06/2024] Open
Abstract
Hematopoietic stem cells (HSCs) produce all blood cells throughout the life of the organism. However, the high self-renewal and longevity of HSCs predispose them to accumulate mutations. The acquired mutations drive preleukemic clonal hematopoiesis, which is frequent among elderly people. The preleukemic state, although often asymptomatic, increases the risk of blood cancers. Nevertheless, the direct role of preleukemic HSCs is well-evidenced in adult myeloid leukemia (AML), while their contribution to other hematopoietic malignancies remains less understood. Here, we review the evidence supporting the role of preleukemic HSCs in different types of blood cancers, as well as present the alternative models of malignant evolution. Finally, we discuss the clinical importance of preleukemic HSCs in choosing the therapeutic strategies and provide the perspective on further studies on biology of preleukemic HSCs.
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Affiliation(s)
- Jadwiga Filipek-Gorzała
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Patrycja Kwiecińska
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Szade
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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10
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Meyer A, Stelloh C, Zhu N, Rao S. Cohesin loss and MLL-AF9 are not synthetic lethal in murine hematopoietic stem and progenitor cells. RESEARCH SQUARE 2024:rs.3.rs-3894962. [PMID: 38352423 PMCID: PMC10862952 DOI: 10.21203/rs.3.rs-3894962/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Objective As cohesin mutations are rarely found in MLL-rearranged acute myeloid leukemias, we investigated the potential synthetic lethality between cohesin mutations and MLL-AF9 using murine hematopoietic stem and progenitor cells. Results Contrary to our hypothesis, a complete loss of Stag2 or haploinsufficiency of Smc3 were well tolerated in MLL-AF9-expressing hematopoietic stem and progenitor cells. Minimal effect of cohesin subunit loss on the in vitro self-renewal of MLL-AF9-expressing cells was observed. Despite the differing mutational landscapes of cohesin-mutated and MLL fusion AMLs, previous studies showed that cohesin and MLL fusion mutations similarly drive abnormal self-renewal through HOXA gene upregulation. The utilization of a similar mechanism suggests that little selective pressure exists for the acquisition of cohesin mutations in AMLs expressing MLL fusions, explaining their lack of co-occurrence. Our results emphasize the importance of using genetic models to test suspected synthetic lethality and suggest that a lack of co-occurrence may instead point to a common mechanism of action between two mutations.
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11
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Wheeler EC, Martin BJE, Doyle WC, Neaher S, Conway CA, Pitton CN, Gorelov RA, Donahue M, Jann JC, Abdel-Wahab O, Taylor J, Seiler M, Buonamici S, Pikman Y, Garcia JS, Belizaire R, Adelman K, Tothova Z. Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS and AML. Sci Transl Med 2024; 16:eade2774. [PMID: 38170787 PMCID: PMC11222919 DOI: 10.1126/scitranslmed.ade2774] [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: 08/05/2022] [Accepted: 10/08/2023] [Indexed: 01/05/2024]
Abstract
Splicing modulation is a promising treatment strategy pursued to date only in splicing factor-mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we showed that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing factor 3B subunit 1 (SF3B1) H3B-8800 and E-7107. We identified drug-induced alterations in splicing, and corresponding reduced gene expression, of a number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We found that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators due to their long length and large number of exons per transcript. Furthermore, we demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators not only resulted in impaired DNA damage response and accumulation of DNA damage, but it sensitized cells to subsequent killing by poly(ADP-ribose) polymerase (PARP) inhibitors and chemotherapy and led to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML.
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Affiliation(s)
- Emily C. Wheeler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Benjamin J. E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William C. Doyle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Sofia Neaher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline A. Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline N. Pitton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Rebecca A. Gorelov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Melanie Donahue
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Johann C. Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael Seiler
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Silvia Buonamici
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02215 USA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karen Adelman
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
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12
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Bhattacharya SA, Dias E, Nieto-Aliseda A, Buschbeck M. The consequences of cohesin mutations in myeloid malignancies. Front Mol Biosci 2023; 10:1319804. [PMID: 38033389 PMCID: PMC10684907 DOI: 10.3389/fmolb.2023.1319804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Recurrent somatic mutations in the genes encoding the chromatin-regulatory cohesin complex and its modulators occur in a wide range of human malignancies including a high frequency in myeloid neoplasms. The cohesin complex has a ring-like structure which can enclose two strands of DNA. A first function for the complex was described in sister chromatid cohesion during metaphase avoiding defects in chromosome segregation. Later studies identified additional functions of the cohesin complex functions in DNA replication, DNA damage response, 3D genome organisation, and transcriptional regulation through chromatin looping. In this review, we will focus on STAG2 which is the most frequently mutated cohesin subunit in myeloid malignancies. STAG2 loss of function mutations are not associated with chromosomal aneuploidies or genomic instability. We hypothesize that this points to changes in gene expression as disease-promoting mechanism and summarize the current state of knowledge on affected genes and pathways. Finally, we discuss potential strategies for targeting cohesion-deficient disease cells.
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Affiliation(s)
- Shubhra Ashish Bhattacharya
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Eve Dias
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Andrea Nieto-Aliseda
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Marcus Buschbeck
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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13
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Pulver C, Grun D, Duc J, Sheppard S, Planet E, Coudray A, de Fondeville R, Pontis J, Trono D. Statistical learning quantifies transposable element-mediated cis-regulation. Genome Biol 2023; 24:258. [PMID: 37950299 PMCID: PMC10637000 DOI: 10.1186/s13059-023-03085-7] [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: 08/16/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs). RESULTS Here, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 500 kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks. CONCLUSION Our results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.
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Affiliation(s)
- Cyril Pulver
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Raphaël de Fondeville
- Swiss Data Science Center, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| | - Julien Pontis
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- SOPHiA GENETICS SA, La Pièce 12, CH-1180, Rolle, Switzerland.
| | - Didier Trono
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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14
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Fan AC, Nakauchi Y, Bai L, Azizi A, Nuno KA, Zhao F, Köhnke T, Karigane D, Cruz-Hernandez D, Reinisch A, Khatri P, Majeti R. RUNX1 loss renders hematopoietic and leukemic cells dependent on IL-3 and sensitive to JAK inhibition. J Clin Invest 2023; 133:e167053. [PMID: 37581927 PMCID: PMC10541186 DOI: 10.1172/jci167053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
Disease-initiating mutations in the transcription factor RUNX1 occur as germline and somatic events that cause leukemias with particularly poor prognosis. However, the role of RUNX1 in leukemogenesis is not fully understood, and effective therapies for RUNX1-mutant leukemias remain elusive. Here, we used primary patient samples and a RUNX1-KO model in primary human hematopoietic cells to investigate how RUNX1 loss contributes to leukemic progression and to identify targetable vulnerabilities. Surprisingly, we found that RUNX1 loss decreased proliferative capacity and stem cell function. However, RUNX1-deficient cells selectively upregulated the IL-3 receptor. Exposure to IL-3, but not other JAK/STAT cytokines, rescued RUNX1-KO proliferative and competitive defects. Further, we demonstrated that RUNX1 loss repressed JAK/STAT signaling and rendered RUNX1-deficient cells sensitive to JAK inhibitors. Our study identifies a dependency of RUNX1-mutant leukemias on IL-3/JAK/STAT signaling, which may enable targeting of these aggressive blood cancers with existing agents.
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Affiliation(s)
- Amy C. Fan
- Immunology Graduate Program
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Yusuke Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- University of California Irvine School of Medicine, Irvine, California, USA
| | - Kevin A. Nuno
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, California, USA
| | - Feifei Zhao
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Köhnke
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Daiki Karigane
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - David Cruz-Hernandez
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Medical Research Council (MRC) Molecular Haematology Unit and Oxford Centre for Haematology, University of Oxford, Oxford, United Kingdom
| | - Andreas Reinisch
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, and
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine
- Cancer Institute
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
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15
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Patel SA. Precision and strategic targeting of novel mutation-specific vulnerabilities in acute myeloid leukemia: the semi-centennial of 7 + 3. Leuk Lymphoma 2023; 64:1503-1513. [PMID: 37328939 PMCID: PMC10913147 DOI: 10.1080/10428194.2023.2224473] [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: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023]
Abstract
The year 2023 marks the semi-centennial of the introduction of classic '7 + 3' chemotherapy for acute myeloid leukemia (AML) in 1973. It also marks the decennial of the first comprehensive sequencing efforts from The Cancer Genome Atlas (TCGA), which revealed that dozens of unique genes are recurrently mutated in AML genomes. Although more than 30 distinct genes have been implicated in AML pathogenesis, the current therapeutic armamentarium that is commercially available only targets FLT3 and IDH1/2 mutations, with olutasidenib as the most recent addition. This focused review spotlights management approaches that exploit the exquisite molecular dependencies of specific subsets of AML, with an emphasis on emerging therapies in the pipeline, including agents targeting TP53-mutant cells. We summarize precision and strategic targeting of AML based on leveraging functional dependencies and explore how mechanisms involving critical gene products can inform rational therapeutic design in 2024.
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Affiliation(s)
- Shyam A Patel
- Department of Medicine, Division of Hematology/Oncology, UMass Memorial Medical Center, Center for Clinical & Translational Science, UMass Chan Medical School, Worcester, MA, USA
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16
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Wu J, Liu Y, Zhangding Z, Liu X, Ai C, Gan T, Liang H, Guo Y, Chen M, Liu Y, Yin J, Zhang W, Hu J. Cohesin maintains replication timing to suppress DNA damage on cancer genes. Nat Genet 2023; 55:1347-1358. [PMID: 37500731 DOI: 10.1038/s41588-023-01458-z] [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: 09/29/2022] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Cohesin loss-of-function mutations are frequently observed in tumors, but the mechanism underlying its role in tumorigenesis is unclear. Here, we found that depletion of RAD21, a core subunit of cohesin, leads to massive genome-wide DNA breaks and 147 translocation hotspot genes, co-mutated with cohesin in multiple cancers. Increased DNA damages are independent of RAD21-loss-induced transcription alteration and loop anchor disruption. However, damage-induced chromosomal translocations coincide with the asymmetrically distributed Okazaki fragments of DNA replication, suggesting that RAD21 depletion causes replication stresses evidenced by the slower replication speed and increased stalled forks. Mechanistically, approximately 30% of the human genome exhibits an earlier replication timing after RAD21 depletion, caused by the early initiation of >900 extra dormant origins. Correspondingly, most translocation hotspot genes lie in timing-altered regions. Therefore, we conclude that cohesin dysfunction causes replication stresses induced by excessive DNA replication initiation, resulting in gross DNA damages that may promote tumorigenesis.
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Affiliation(s)
- Jinchun Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Zhengrong Zhangding
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Xuhao Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Tingting Gan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Haoxin Liang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yuefeng Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Mohan Chen
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yiyang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China.
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17
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Bouligny IM, Maher KR, Grant S. Secondary-Type Mutations in Acute Myeloid Leukemia: Updates from ELN 2022. Cancers (Basel) 2023; 15:3292. [PMID: 37444402 DOI: 10.3390/cancers15133292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
The characterization of the molecular landscape and the advent of targeted therapies have defined a new era in the prognostication and treatment of acute myeloid leukemia. Recent revisions in the European LeukemiaNet 2022 guidelines have refined the molecular, cytogenetic, and treatment-related boundaries between myelodysplastic neoplasms (MDS) and AML. This review details the molecular mechanisms and cellular pathways of myeloid maturation aberrancies contributing to dysplasia and leukemogenesis, focusing on recent molecular categories introduced in ELN 2022. We provide insights into novel and rational therapeutic combination strategies that exploit mechanisms of leukemogenesis, highlighting the underpinnings of splicing factors, the cohesin complex, and chromatin remodeling. Areas of interest for future research are summarized, and we emphasize approaches designed to advance existing treatment strategies.
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Affiliation(s)
- Ian M Bouligny
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
| | - Keri R Maher
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
| | - Steven Grant
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
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18
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [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: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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19
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Horsfield JA. Full circle: a brief history of cohesin and the regulation of gene expression. FEBS J 2023; 290:1670-1687. [PMID: 35048511 DOI: 10.1111/febs.16362] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
The cohesin complex has a range of crucial functions in the cell. Cohesin is essential for mediating chromatid cohesion during mitosis, for repair of double-strand DNA breaks, and for control of gene transcription. This last function has been the subject of intense research ever since the discovery of cohesin's role in the long-range regulation of the cut gene in Drosophila. Subsequent research showed that the expression of some genes is exquisitely sensitive to cohesin depletion, while others remain relatively unperturbed. Sensitivity to cohesin depletion is also remarkably cell type- and/or condition-specific. The relatively recent discovery that cohesin is integral to forming chromatin loops via loop extrusion should explain much of cohesin's gene regulatory properties, but surprisingly, loop extrusion has failed to identify a 'one size fits all' mechanism for how cohesin controls gene expression. This review will illustrate how early examples of cohesin-dependent gene expression integrate with later work on cohesin's role in genome organization to explain mechanisms by which cohesin regulates gene expression.
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Affiliation(s)
- Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, New Zealand
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20
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Eckardt JN, Stasik S, Röllig C, Sauer T, Scholl S, Hochhaus A, Crysandt M, Brümmendorf TH, Naumann R, Steffen B, Kunzmann V, Einsele H, Schaich M, Burchert A, Neubauer A, Schäfer-Eckart K, Schliemann C, Krause SW, Herbst R, Hänel M, Hanoun M, Kaiser U, Kaufmann M, Rácil Z, Mayer J, Cerqueira T, Kroschinsky F, Berdel WE, Serve H, Müller-Tidow C, Platzbecker U, Baldus CD, Schetelig J, Siepmann T, Bornhäuser M, Middeke JM, Thiede C. Alterations of cohesin complex genes in acute myeloid leukemia: differential co-mutations, clinical presentation and impact on outcome. Blood Cancer J 2023; 13:18. [PMID: 36693840 PMCID: PMC9873811 DOI: 10.1038/s41408-023-00790-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
Functional perturbations of the cohesin complex with subsequent changes in chromatin structure and replication are reported in a multitude of cancers including acute myeloid leukemia (AML). Mutations of its STAG2 subunit may predict unfavorable risk as recognized by the 2022 European Leukemia Net recommendations, but the underlying evidence is limited by small sample sizes and conflicting observations regarding clinical outcomes, as well as scarce information on other cohesion complex subunits. We retrospectively analyzed data from a multi-center cohort of 1615 intensively treated AML patients and identified distinct co-mutational patters for mutations of STAG2, which were associated with normal karyotypes (NK) and concomitant mutations in IDH2, RUNX1, BCOR, ASXL1, and SRSF2. Mutated RAD21 was associated with NK, mutated EZH2, KRAS, CBL, and NPM1. Patients harboring mutated STAG2 were older and presented with decreased white blood cell, bone marrow and peripheral blood blast counts. Overall, neither mutated STAG2, RAD21, SMC1A nor SMC3 displayed any significant, independent effect on clinical outcomes defined as complete remission, event-free, relapse-free or overall survival. However, we found almost complete mutual exclusivity of genetic alterations of individual cohesin subunits. This mutual exclusivity may be the basis for therapeutic strategies via synthetic lethality in cohesin mutated AML.
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Affiliation(s)
- Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany. .,Division of Health Care Sciences, Dresden International University, Dresden, Germany.
| | - Sebastian Stasik
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Christoph Röllig
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Tim Sauer
- grid.5253.10000 0001 0328 4908German Cancer Research Center (DKFZ) and Medical Clinic V, University Hospital Heidelberg, Heidelberg, Germany
| | - Sebastian Scholl
- grid.275559.90000 0000 8517 6224Department of Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Andreas Hochhaus
- grid.275559.90000 0000 8517 6224Department of Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Martina Crysandt
- grid.412301.50000 0000 8653 1507Department of Hematology, Oncology, Hemostaseology, and Cell Therapy, University Hospital RWTH Aachen, Aachen, Germany
| | - Tim H. Brümmendorf
- grid.412301.50000 0000 8653 1507Department of Hematology, Oncology, Hemostaseology, and Cell Therapy, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralph Naumann
- Medical Clinic III, St. Marien-Hospital Siegen, Siegen, Germany
| | - Björn Steffen
- grid.411088.40000 0004 0578 8220Medical Clinic II, University Hospital Frankfurt, Frankfurt (Main), Germany
| | - Volker Kunzmann
- grid.411760.50000 0001 1378 7891Medical Clinic and Policlinic II, University Hospital Würzburg, Würzburg, Germany
| | - Hermann Einsele
- grid.411760.50000 0001 1378 7891Medical Clinic and Policlinic II, University Hospital Würzburg, Würzburg, Germany
| | - Markus Schaich
- grid.459932.0Department of Hematology, Oncology and Palliative Care, Rems-Murr-Hospital Winnenden, Winnenden, Germany
| | - Andreas Burchert
- grid.10253.350000 0004 1936 9756Department of Hematology, Oncology and Immunology, Philipps-University-Marburg, Marburg, Germany
| | - Andreas Neubauer
- grid.10253.350000 0004 1936 9756Department of Hematology, Oncology and Immunology, Philipps-University-Marburg, Marburg, Germany
| | - Kerstin Schäfer-Eckart
- grid.511981.5Department of Internal Medicine V, Paracelsus Medizinische Privatuniversität and University Hospital Nurnberg, Nurnberg, Germany
| | - Christoph Schliemann
- grid.16149.3b0000 0004 0551 4246Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Stefan W. Krause
- grid.411668.c0000 0000 9935 6525Medical Clinic V, University Hospital Erlangen, Erlangen, Germany
| | - Regina Herbst
- grid.459629.50000 0004 0389 4214Medical Clinic III, Chemnitz Hospital AG, Chemnitz, Germany
| | - Mathias Hänel
- grid.459629.50000 0004 0389 4214Medical Clinic III, Chemnitz Hospital AG, Chemnitz, Germany
| | - Maher Hanoun
- grid.410718.b0000 0001 0262 7331Department of Hematology, University Hospital Essen, Essen, Germany
| | - Ulrich Kaiser
- grid.460019.aMedical Clinic II, St. Bernward Hospital, Hildesheim, Germany
| | - Martin Kaufmann
- grid.416008.b0000 0004 0603 4965Department of Hematology, Oncology and Palliative Care, Robert-Bosch-Hospital, Stuttgart, Germany
| | - Zdenek Rácil
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, Brno, Czech Republic
| | - Jiri Mayer
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, Brno, Czech Republic
| | - Tiago Cerqueira
- grid.440925.e0000 0000 9874 1261Division of Health Care Sciences, Dresden International University, Dresden, Germany
| | - Frank Kroschinsky
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Wolfgang E. Berdel
- grid.16149.3b0000 0004 0551 4246Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Hubert Serve
- grid.411088.40000 0004 0578 8220Medical Clinic II, University Hospital Frankfurt, Frankfurt (Main), Germany
| | - Carsten Müller-Tidow
- grid.5253.10000 0001 0328 4908German Cancer Research Center (DKFZ) and Medical Clinic V, University Hospital Heidelberg, Heidelberg, Germany
| | - Uwe Platzbecker
- grid.411339.d0000 0000 8517 9062Medical Clinic I Hematology and Celltherapy, University Hospital Leipzig, Leipzig, Germany
| | - Claudia D. Baldus
- grid.412468.d0000 0004 0646 2097Department of Internal Medicine, University Hospital Kiel, Kiel, Germany
| | - Johannes Schetelig
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany ,DKMS Clinical Trials Unit, Dresden, Germany
| | - Timo Siepmann
- grid.440925.e0000 0000 9874 1261Division of Health Care Sciences, Dresden International University, Dresden, Germany ,grid.4488.00000 0001 2111 7257Department of Neurology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin Bornhäuser
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany ,grid.7497.d0000 0004 0492 0584German Consortium for Translational Cancer Research DKTK, Heidelberg, Germany ,National Center for Tumor Disease (NCT), Dresden, Germany
| | - Jan Moritz Middeke
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Christian Thiede
- grid.412282.f0000 0001 1091 2917Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
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21
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Wang H, Han Y, Qian P. Emerging Roles of Epigenetic Regulators in Maintaining Hematopoietic Stem Cell Homeostasis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:29-44. [PMID: 38228957 DOI: 10.1007/978-981-99-7471-9_3] [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: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) are adult stem cells with the ability of self-renewal and multilineage differentiation into functional blood cells, thus playing important roles in the homeostasis of hematopoiesis and the immune response. Continuous self-renewal of HSCs offers fresh supplies for the HSC pool, which differentiate into all kinds of mature blood cells, supporting the normal functioning of the entire blood system. Nevertheless, dysregulation of the homeostasis of hematopoiesis is often the cause of many blood diseases. Excessive self-renewal of HSCs leads to hematopoietic malignancies (e.g., leukemia), while deficiency in HSC regeneration results in pancytopenia (e.g., anemia). The regulation of hematopoietic homeostasis is finely tuned, and the rapid development of high-throughput sequencing technologies has greatly boosted research in this field. In this chapter, we will summarize the recent understanding of epigenetic regulators including DNA methylation, histone modification, chromosome remodeling, noncoding RNAs, and RNA modification that are involved in hematopoietic homeostasis, which provides fundamental basis for the development of therapeutic strategies against hematopoietic diseases.
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Affiliation(s)
- Hui Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Pengxu Qian
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.
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22
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Roy D, Kundu S, Mukherjee S. Development of Computational Correlations among Known Drug Scaffolds and their Target-Specific Non-Coding RNA Scaffolds of Alzheimer's Disease. Curr Alzheimer Res 2023; 20:539-556. [PMID: 37870052 DOI: 10.2174/0115672050261526231013095933] [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: 05/09/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND Alzheimer's disease is the most common neurodegenerative disorder. Recent development in sciences has also identified the pivotal role of microRNAs (miRNAs) in AD pathogenesis. OBJECTIVES We proposed a novel method to identify AD pathway-specific statistically significant miRNAs from the targets of known AD drugs. Moreover, microRNA scaffolds and corresponding drug scaffolds of different pathways were also discovered. MATERIAL AND METHODS A Wilcoxon signed-rank test was performed to identify pathway-specific significant miRNAs. We generated feed-forward loop regulations of microRNA-TF-gene-based networks, studied the minimum free energy structures of pre-microRNA sequences, and clustered those microRNAs with their corresponding structural motifs of robust transcription factors. Conservation analyses of significant microRNAs were done, and the phylogenetic trees were constructed. We identified 3'UTR binding sites and chromosome locations of these significant microRNAs. RESULTS In this study, hsa-miR-4261, hsa-miR-153-5p, hsa-miR-6766, and hsa-miR-4319 were identified as key miRNAs for the ACHE pathway and hsa-miR-326, hsa-miR-6133, hsa-miR-4251, hsa-miR-3148, hsa-miR-10527-5p, hsa-miR-527, and hsa-miR-518a were identified as regulatory miRNAs for the NMDA pathway. These miRNAs were regulated by several AD-specific TFs, namely RAD21, FOXA1, and ESR1. It has been observed that anisole and adamantane are important chemical scaffolds to regulate these significant miRNAs. CONCLUSION This is the first study that developed a detailed correlation between known AD drug scaffolds and their AD target-specific miRNA scaffolds. This study identified chromosomal locations of microRNAs and corresponding structural scaffolds of transcription factors that may be responsible for miRNA co-regulation for Alzheimer's disease. Our study provides hope for therapeutic improvements in the existing microRNAs by regulating pathways and targets.
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Affiliation(s)
- Debjani Roy
- Department of Biological Sciences Bose Institute, Unified Academic Campus. EN-80, Sector V, Bidhan Nagar, Kolkata- 700091, West Bengal, India
| | - Shymodip Kundu
- Department of Pharmaceutical Science and Technology, Maulana Abul Kalam Azad University of Technology, Nadia, Haringhata, 741249, India
| | - Swayambhik Mukherjee
- Department of Biotechnology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India
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23
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Tcf12 is required to sustain myogenic genes synergism with MyoD by remodelling the chromatin landscape. Commun Biol 2022; 5:1201. [DOI: 10.1038/s42003-022-04176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractMuscle stem cells (MuSCs) are essential for skeletal muscle development and regeneration, ensuring muscle integrity and normal function. The myogenic proliferation and differentiation of MuSCs are orchestrated by a cascade of transcription factors. In this study, we elucidate the specific role of transcription factor 12 (Tcf12) in muscle development and regeneration based on loss-of-function studies. Muscle-specific deletion of Tcf12 cause muscle weight loss owing to the reduction of myofiber size during development. Inducible deletion of Tcf12 specifically in adult MuSCs delayed muscle regeneration. The examination of MuSCs reveal that Tcf12 deletion resulted in cell-autonomous defects during myogenesis and Tcf12 is necessary for proper myogenic gene expression. Mechanistically, TCF12 and MYOD work together to stabilise chromatin conformation and sustain muscle cell fate commitment-related gene and chromatin architectural factor expressions. Altogether, our findings identify Tcf12 as a crucial regulator of MuSCs chromatin remodelling that regulates muscle cell determination and participates in skeletal muscle development and regeneration.
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24
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Kontandreopoulou CN, Kalopisis K, Viniou NA, Diamantopoulos P. The genetics of myelodysplastic syndromes and the opportunities for tailored treatments. Front Oncol 2022; 12:989483. [PMID: 36338673 PMCID: PMC9630842 DOI: 10.3389/fonc.2022.989483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic instability, microenvironmental aberrations, and somatic mutations contribute to the phenotype of myelodysplastic syndrome and the risk for transformation to AML. Genes involved in RNA splicing, DNA methylation, histone modification, the cohesin complex, transcription, DNA damage response pathway, signal transduction and other pathways constitute recurrent mutational targets in MDS. RNA-splicing and DNA methylation mutations seem to occur early and are reported as driver mutations in over 50% of MDS patients. The improved understanding of the molecular landscape of MDS has led to better disease and risk classification, leading to novel therapeutic opportunities. Based on these findings, novel agents are currently under preclinical and clinical development and expected to improve the clinical outcome of patients with MDS in the upcoming years. This review provides a comprehensive update of the normal gene function as well as the impact of mutations in the pathogenesis, deregulation, diagnosis, and prognosis of MDS, focuses on the most recent advances of the genetic basis of myelodysplastic syndromes and their clinical relevance, and the latest targeted therapeutic approaches including investigational and approved agents for MDS.
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25
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Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
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Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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26
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F. V, V. D. P, C. M, M. LI, C. D, G. P, D. C, A. T, M. G, S. DF, M. T, V. V, G. S. Targeting epigenetic alterations in cancer stem cells. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:1011882. [PMID: 39086963 PMCID: PMC11285701 DOI: 10.3389/fmmed.2022.1011882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/08/2022] [Indexed: 08/02/2024]
Abstract
Oncogenes or tumor suppressor genes are rarely mutated in several pediatric tumors and some early stage adult cancers. This suggests that an aberrant epigenetic reprogramming may crucially affect the tumorigenesis of these tumors. Compelling evidence support the hypothesis that cancer stem cells (CSCs), a cell subpopulation within the tumor bulk characterized by self-renewal capacity, metastatic potential and chemo-resistance, may derive from normal stem cells (NSCs) upon an epigenetic deregulation. Thus, a better understanding of the specific epigenetic alterations driving the transformation from NSCs into CSCs may help to identify efficacious treatments to target this aggressive subpopulation. Moreover, deepening the knowledge about these alterations may represent the framework to design novel therapeutic approaches also in the field of regenerative medicine in which bioengineering of NSCs has been evaluated. Here, we provide a broad overview about: 1) the role of aberrant epigenetic modifications contributing to CSC initiation, formation and maintenance, 2) the epigenetic inhibitors in clinical trial able to specifically target the CSC subpopulation, and 3) epigenetic drugs and stem cells used in regenerative medicine for cancer and diseases.
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Affiliation(s)
- Verona F.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Pantina V. D.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Modica C.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Lo Iacono M.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - D’Accardo C.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Porcelli G.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Cricchio D.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Turdo A.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Gaggianesi M.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Di Franco S.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Todaro M.
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Veschi V.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Stassi G.
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
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27
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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28
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Meyer AE, Stelloh C, Pulakanti K, Burns R, Fisher JB, Heimbruch KE, Tarima S, Furumo Q, Brennan J, Zheng Y, Viny AD, Vassiliou GS, Rao S. Combinatorial genetics reveals the Dock1-Rac2 axis as a potential target for the treatment of NPM1;Cohesin mutated AML. Leukemia 2022; 36:2032-2041. [PMID: 35778533 PMCID: PMC9357218 DOI: 10.1038/s41375-022-01632-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/03/2023]
Abstract
Acute myeloid leukemia (AML) is driven by mutations that occur in numerous combinations. A better understanding of how mutations interact with one another to cause disease is critical to developing targeted therapies. Approximately 50% of patients that harbor a common mutation in NPM1 (NPM1cA) also have a mutation in the cohesin complex. As cohesin and Npm1 are known to regulate gene expression, we sought to determine how cohesin mutation alters the transcriptome in the context of NPM1cA. We utilized inducible Npm1cAflox/+ and core cohesin subunit Smc3flox/+ mice to examine AML development. While Npm1cA/+;Smc3Δ/+ mice developed AML with a similar latency and penetrance as Npm1cA/+ mice, RNA-seq suggests that the Npm1cA/+; Smc3Δ/+ mutational combination uniquely alters the transcriptome. We found that the Rac1/2 nucleotide exchange factor Dock1 was specifically upregulated in Npm1cA/+;Smc3Δ/+ HSPCs. Knockdown of Dock1 resulted in decreased growth and adhesion and increased apoptosis only in Npm1cA/+;Smc3Δ/+ AML. Higher Rac activity was also observed in Npm1cA/+;Smc3Δ/+ vs. Npm1cA/+ AMLs. Importantly, the Dock1/Rac pathway is targetable in Npm1cA/+;Smc3Δ/+ AMLs. Our results suggest that Dock1/Rac represents a potential target for the treatment of patients harboring NPM1cA and cohesin mutations and supports the use of combinatorial genetics to identify novel precision oncology targets.
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Affiliation(s)
| | - Cary Stelloh
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | | | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Joseph B Fisher
- Department of Natural Sciences, Concordia University Wisconsin, Mequon, WI, USA
| | - Katelyn E Heimbruch
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sergey Tarima
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Quinlan Furumo
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - John Brennan
- Department of Pathology and Lab Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yongwei Zheng
- Guangzhou Bio-gene Technology Co., Ltd., Guangzhou, China
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.
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29
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Postmitotic differentiation of human monocytes requires cohesin-structured chromatin. Nat Commun 2022; 13:4301. [PMID: 35879286 PMCID: PMC9314343 DOI: 10.1038/s41467-022-31892-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Cohesin is a major structural component of mammalian genomes and is required to maintain loop structures. While acute depletion in short-term culture models suggests a limited importance of cohesin for steady-state transcriptional circuits, long-term studies are hampered by essential functions of cohesin during replication. Here, we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profile and compare epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome and detect numerous architectural changes, ranging from higher level compartments down to chromatin loops. Changes in loop structures correlate with cohesin-binding, as well as epigenetic and transcriptional changes during differentiation. Functional studies show that the siRNA-mediated depletion of cohesin (and to a lesser extent also CTCF) markedly disturbs loop structures and dysregulates genes and enhancers that are primarily regulated during normal MO differentiation. In addition, gene activation programs in cohesin-depleted MO-derived macrophages are disturbed. Our findings implicate an essential function of cohesin in controlling long-term, differentiation- and activation-associated gene expression programs. How chromatin structure and gene accessibility changes during monocyte differentiation is not clearly defined. Here the authors characterize the chromatin changes during macrophage or dendritic cell maturation from monocytes and the dependence of this upon cohesin and CTCF.
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30
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Arkoun B, Robert E, Boudia F, Mazzi S, Dufour V, Siret A, Mammasse Y, Aid Z, Vieira M, Imanci A, Aglave M, Cambot M, Petermann R, Souquere S, Rameau P, Catelain C, Diot R, Tachdjian G, Hermine O, Droin N, Debili N, Plo I, Malinge S, Soler E, Raslova H, Mercher T, Vainchenker W. Stepwise GATA1 and SMC3 mutations alter megakaryocyte differentiation in a Down syndrome leukemia model. J Clin Invest 2022; 132:156290. [PMID: 35587378 PMCID: PMC9282925 DOI: 10.1172/jci156290] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modeled the megakaryocyte differentiation defect through stepwise gene editing of GATA1s, SMC3+/–, and MPLW515K, providing 20 different T21 or disomy 21 (D21) induced pluripotent stem cell (iPSC) clones. GATA1s profoundly reshaped iPSC-derived hematopoietic architecture with gradual myeloid-to-megakaryocyte shift and megakaryocyte differentiation alteration upon addition of SMC3 and MPL mutations. Transcriptional, chromatin accessibility, and GATA1-binding data showed alteration of essential megakaryocyte differentiation genes, including NFE2 downregulation that was associated with loss of GATA1s binding and functionally involved in megakaryocyte differentiation blockage. T21 enhanced the proliferative phenotype, reproducing the cellular and molecular abnormalities of DS-AMKL. Our study provides an array of human cell–based models revealing individual contributions of different mutations to DS-AMKL differentiation blockage, a major determinant of leukemic progression.
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Affiliation(s)
- Brahim Arkoun
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Elie Robert
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
| | - Fabien Boudia
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
| | - Stefania Mazzi
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Virginie Dufour
- INSERM, UMR1287, Institut National de la Transfusion Sanguine, Villejuif, France
| | - Aurelie Siret
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
| | - Yasmine Mammasse
- Département d'Immunologie Plaquettaire, Institut National de la Transfusion Sanguine, Paris, France
| | - Zakia Aid
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
| | - Mathieu Vieira
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Aygun Imanci
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Marine Aglave
- Plateforme de Bioinformatique, Institut Gustave Roussy, Villejuif, France
| | - Marie Cambot
- Département d'Immunologie Plaquettaire, Institut National de la Transfusion Sanguine, Paris, France
| | - Rachel Petermann
- Département d'Immunologie Plaquettaire, Institut National de Transfusion Sanguine, Paris, France
| | - Sylvie Souquere
- Centre National de la Recherche Scientifique, UMR8122, Institut Gustave Roussy, Villejuif, France
| | - Philippe Rameau
- UMS AMMICA, INSERM US23, Institut Gustave Roussy, Villejuif, France
| | - Cyril Catelain
- UMS AMMICA, INSERM US23, Institut Gustave Roussy, Villejuif, France
| | - Romain Diot
- Service d'Histologie, Embryologie et Cytogénétique, Hôpital Antoine Béclère, Clamart, France
| | - Gerard Tachdjian
- Service d'Histologie, Embryologie et Cytogénétique, Hôpital Antoine Béclère, Clamart, France
| | | | - Nathalie Droin
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
| | - Najet Debili
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Isabelle Plo
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Sebastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Eric Soler
- IGMM, University of Montpellier, Montpellier, France
| | - Hana Raslova
- INSERM, UMR1287, Institut Gustave Roussy, Villejuif, France
| | - Thomas Mercher
- INSERM, UMR1170, Institut Gustave Roussy, Villejuif, France
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Nakauchi Y, Azizi A, Thomas D, Corces MR, Reinisch A, Sharma R, Cruz Hernandez D, Kohnke T, Karigane D, Fan A, Martinez-Krams D, Stafford M, Kaur S, Dutta R, Phan P, Ediriwickrema A, McCarthy E, Ning Y, Phillips T, Ellison CK, Guler GD, Bergamaschi A, Ku CJ, Levy S, Majeti R. The cell type specific 5hmC landscape and dynamics of healthy human hematopoiesis and TET2-mutant pre-leukemia. Blood Cancer Discov 2022; 3:346-367. [DOI: 10.1158/2643-3230.bcd-21-0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/07/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
The conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) is a key step in DNA demethylation that is mediated by ten-eleven-translocation (TET) enzymes, which require ascorbate/vitamin C. Here, we report the 5hmC landscape of normal hematopoiesis and identify cell type-specific 5hmC profiles associated with active transcription and chromatin accessibility of key hematopoietic regulators. We utilized CRISPR/Cas9 to model TET2 loss-of-function mutations in primary human HSPCs. Disrupted cells exhibited increased colonies in serial replating, defective erythroid/megakaryocytic differentiation, and in vivo competitive advantage and myeloid skewing coupled with reduction of 5hmC at erythroid-associated gene loci. Azacitidine and ascorbate restored 5hmC abundance and slowed or reverted the expansion of TET2-mutant clones in vivo. These results demonstrate the key role of 5hmC in normal hematopoiesis and TET2-mutant phenotypes and raise the possibility of utilizing these agents to further our understanding of pre-leukemia/clonal hematopoiesis.
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Affiliation(s)
- Yusuke Nakauchi
- Stanford University School of Medicine, Stanford, California, United States
| | - Armon Azizi
- Stanford University, Stanford, CA, United States
| | - Daniel Thomas
- University of Adelaide, Adelaide, South Australia, Australia
| | - M. Ryan Corces
- Gladstone Institute of Neurological Disease, San Fransisco, California, United States
| | - Andreas Reinisch
- Stanford University School of Medicine, Stanford, CA, United States
| | - Rajiv Sharma
- Stanford University School of Medicine, Stanford, California, United States
| | - David Cruz Hernandez
- MRC Molecular Haematology Unit and Oxford Centre for Haematology, Weatherall Institute of Molecular Medicine,, Oxford, United Kingdom
| | - Thomas Kohnke
- Stanford University School of Medicine, Stanford, California, United States
| | - Daiki Karigane
- Stanford University School of Medicine, Stanford, California, United States
| | - Amy Fan
- Stanford University, Palo Alto, United States
| | | | | | - Satinder Kaur
- Stanford University School of Medicine, Palo Alto, CA, United States
| | - Ritika Dutta
- Stanford University School of Medicine, Palo Alto, CA, United States
| | - Paul Phan
- Stanford University School of Medicine, Stanford, California, United States
| | | | | | - Yuhong Ning
- Bluestar Genomics Inc., San Diego, CA, United States
| | | | | | | | | | | | - Samuel Levy
- Bluestar Genomics, San Diego, California, United States
| | - Ravindra Majeti
- Stanford University School of Medicine, Palo Alto, CA, United States
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32
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Schedel A, Friedrich UA, Morcos MNF, Wagener R, Mehtonen J, Watrin T, Saitta C, Brozou T, Michler P, Walter C, Försti A, Baksi A, Menzel M, Horak P, Paramasivam N, Fazio G, Autry RJ, Fröhling S, Suttorp M, Gertzen C, Gohlke H, Bhatia S, Wadt K, Schmiegelow K, Dugas M, Richter D, Glimm H, Heinäniemi M, Jessberger R, Cazzaniga G, Borkhardt A, Hauer J, Auer F. Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma. Int J Mol Sci 2022; 23:ijms23095174. [PMID: 35563565 PMCID: PMC9106003 DOI: 10.3390/ijms23095174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Somatic loss of function mutations in cohesin genes are frequently associated with various cancer types, while cohesin disruption in the germline causes cohesinopathies such as Cornelia-de-Lange syndrome (CdLS). Here, we present the discovery of a recurrent heterozygous RAD21 germline aberration at amino acid position 298 (p.P298S/A) identified in three children with lymphoblastic leukemia or lymphoma in a total dataset of 482 pediatric cancer patients. While RAD21 p.P298S/A did not disrupt the formation of the cohesin complex, it altered RAD21 gene expression, DNA damage response and primary patient fibroblasts showed increased G2/M arrest after irradiation and Mitomycin-C treatment. Subsequent single-cell RNA-sequencing analysis of healthy human bone marrow confirmed the upregulation of distinct cohesin gene patterns during hematopoiesis, highlighting the importance of RAD21 expression within proliferating B- and T-cells. Our clinical and functional data therefore suggest that RAD21 germline variants can predispose to childhood lymphoblastic leukemia or lymphoma without displaying a CdLS phenotype.
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Affiliation(s)
- Anne Schedel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Ulrike Anne Friedrich
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Mina N. F. Morcos
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Titus Watrin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Claudia Saitta
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Pia Michler
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Carolin Walter
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany; (C.W.); (M.D.)
| | - Asta Försti
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.F.); (R.J.A.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Arka Baksi
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.B.); (R.J.)
| | - Maria Menzel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.H.); (S.F.)
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Grazia Fazio
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
| | - Robert J Autry
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.F.); (R.J.A.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.H.); (S.F.)
| | - Meinolf Suttorp
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Christoph Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (C.G.); (H.G.)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (C.G.); (H.G.)
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Karin Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Faculty of health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Martin Dugas
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany; (C.W.); (M.D.)
- Institute of Medical Informatics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Daniela Richter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, 01307 Dresden, Germany; (D.R.); (H.G.)
- German Cancer Consortium (DKTK), 01307 Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, 01307 Dresden, Germany; (D.R.); (H.G.)
- German Cancer Consortium (DKTK), 01307 Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.B.); (R.J.)
| | - Gianni Cazzaniga
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
- Medical Genetics, Department of Medicine and Surgery, University of Milan Bicocca, 20900 Monza, Italy
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Julia Hauer
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
- German Cancer Consortium (DKTK), 81675 Munich, Germany
- Correspondence: ; Tel.: +49-(89)-3068-3940
| | - Franziska Auer
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
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33
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Qin W, Chen X, Shen H, Wang Z, Cai X, Jiang N, Hua H. Comprehensive mutation profile in acute myeloid leukemia patients with RUNX1-RUNX1T1 or CBFB-MYH11 fusions. Turk J Haematol 2022; 39:84-93. [PMID: 35445594 PMCID: PMC9160702 DOI: 10.4274/tjh.galenos.2022.2021.0641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Objective: This study was undertaken with the aim of better understanding the genomic landscape of core-binding factor (CBF) acute myeloid leukemia (AML). Materials and Methods: We retrospectively analyzed 112 genes that were detected using next-generation sequencing in 134 patients with de novo CBF-AML. FLT3-ITD, NPM1, and CEBPA mutations were detected by DNA-PCR and Sanger sequencing. Results: In the whole cohort, the most commonly mutated genes were c-KIT (33.6%) and NRAS (33.6%), followed by FLT3 (18.7%), KRAS (13.4%), RELN (8.2%), and NOTCH1 (8.2%). The frequencies of mutated genes associated with epigenetic modification, such as IDH1, IDH2, DNMT3A, and TET2, were low, being present in 1.5%, 0.7%, 2.2%, and 7.5% of the total number of patients, respectively. Inv(16)/t(16;16) AML patients exhibited more mutations of NRAS and KRAS (p=0.001 and 0.0001, respectively) than t(8;21) AML patients. Functionally mutated genes involved in signaling pathways were observed more frequently in the inv(16)/t(16;16) AML group (p=0.016), while the mutations involved in cohesin were found more frequently in the t(8;21) AML group (p=0.011). Significantly higher white blood cell counts were found in inv(16)/t(16;16) AML patients with c-KIT (c-KITmut) or NRAS (NRASmut) mutations compared to the corresponding t(8;21) AML/c-KITmut and t(8;21) AML/NRASmut groups (p=0.001 and 0.009, respectively). Conclusion: The mutation profiles of t(8;21) AML patients showed evident differences from those of patients with inv(16)/t(16;16) AML. We have provided a comprehensive overview of the mutational landscape of CBF-AML.
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Affiliation(s)
- Wei Qin
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, China
| | - Xiayu Chen
- Department of Hematology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - HongJie Shen
- Department of Hematology,The First Affiliated Hospital of Soochow University, Soochow, China
| | - Zheng Wang
- Department of Hematology,The First Affiliated Hospital of Soochow University, Soochow, China.,SuZhou jsuniwell medical laboratory, Suzhou, China
| | - Xiaohui Cai
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, China
| | - Naike Jiang
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, China
| | - Haiying Hua
- Department of Hematology, Affiliated Hospital of Jiangnan University, Wuxi, China
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34
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Reilly A, Philip Creamer J, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, Doulatov S. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Cell Stem Cell 2022; 29:577-592.e8. [PMID: 35278369 PMCID: PMC9018112 DOI: 10.1016/j.stem.2022.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/05/2022] [Accepted: 02/15/2022] [Indexed: 11/19/2022]
Abstract
Abnormal nuclear morphology is a hallmark of malignant cells widely used in cancer diagnosis. Pelger-Huët anomaly (PHA) is a common abnormality of neutrophil nuclear morphology of unknown molecular etiology in myeloid neoplasms (MNs). We show that loss of nuclear lamin B1 (LMNB1) encoded on chromosome 5q, which is frequently deleted in MNs, induces defects in nuclear morphology and human hematopoietic stem cell (HSC) function associated with malignancy. LMNB1 deficiency alters genome organization inducing in vitro and in vivo expansion of HSCs, myeloid-biased differentiation with impaired lymphoid commitment, and genome instability due to defective DNA damage repair. Nuclear dysmorphology of neutrophils in patients with MNs is associated with 5q deletions spanning the LMNB1 locus, and lamin B1 loss is both necessary and sufficient to cause PHA in normal and 5q-deleted neutrophils. LMNB1 loss thus causes acquired PHA and links abnormal nuclear morphology with HSCs and progenitor cell fate determination via genome organization.
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Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - J Philip Creamer
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sintra Stewart
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Massiel C Stolla
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuchuan Wang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jing Du
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Stephanie Busch
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Elihu H Estey
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pamela S Becker
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Division of Hematology/Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92617, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Min Fang
- Department of Clinical Transplant Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Siobán B Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Janis L Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lorinda A Soma
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jian Ma
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
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35
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Qi M, Nayar U, Ludwig LS, Wagle N, Rheinbay E. cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries. BMC Bioinformatics 2021; 22:611. [PMID: 34952565 PMCID: PMC8709999 DOI: 10.1186/s12859-021-04529-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines. RESULTS We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls. CONCLUSIONS cDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis.
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Affiliation(s)
- Meifang Qi
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Utthara Nayar
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leif S Ludwig
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115, Berlin, Germany
| | - Nikhil Wagle
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Esther Rheinbay
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA.
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36
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Zou W, Xing J, Zou S, Jiang M, Chen X, Chen Q, Liu D, Zhang X, Fu X. HIV-1 LAI Nef blocks the development of hematopoietic stem/progenitor cells into myeloid-erythroid lineage cells. Biol Direct 2021; 16:27. [PMID: 34930406 PMCID: PMC8686389 DOI: 10.1186/s13062-021-00317-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/12/2021] [Indexed: 01/07/2023] Open
Abstract
Background A variety of hematopoietic abnormalities are commonly seen in human immunodeficiency virus-1 (HIV-1) infected individuals despite antiviral therapy, but the underlying mechanism remains elusive. Nef plays an important role in HIV-1 induced T cell loss and disease progression, but it is not known whether Nef participates in other hematopoietic abnormalities associated with infection. Results In the current study we investigated the influence of HIV-1LAI Nef (LAI Nef) on the development of hematopoietic stem/progenitor cells (HSPCs) into myeloid-erythroid lineage cells, and found that nef expression in HSPCs blocked their differentiation both in vitro and in humanized mice reconstituted with nef-expressing HSPCs. Conclusions Our novel findings demonstrate LAI Nef compromised the development of myeloid-erythroid lineage cells, and therapeutics targeting Nef would be promising in correcting HIV-1 associated hematopoietic abnormalities. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-021-00317-3.
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Affiliation(s)
- Wei Zou
- Department of Infectious Diseases, The 1St Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Juanjuan Xing
- Department of Burn, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Shijie Zou
- Department of Infectious Diseases, The 1St Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Mei Jiang
- Department of Experimental Medicine, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xinping Chen
- Department of Gynecology and Obstetrics, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Qi Chen
- Department of Gynecology and Obstetrics, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Daozheng Liu
- Department of Gynecology and Obstetrics, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiangcheng Zhang
- Department of Gynecology and Obstetrics, The 1st Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xin Fu
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, 330006, Jiangxi, China
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37
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Boucher AC, Caldwell KJ, Crispino JD, Flerlage JE. Clinical and biological aspects of myeloid leukemia in Down syndrome. Leukemia 2021; 35:3352-3360. [PMID: 34518645 PMCID: PMC8639661 DOI: 10.1038/s41375-021-01414-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023]
Abstract
Children with Down syndrome are at an elevated risk of leukemia, especially myeloid leukemia (ML-DS). This malignancy is frequently preceded by transient abnormal myelopoiesis (TAM), which is self-limited expansion of fetal liver-derived megakaryocyte progenitors. An array of international studies has led to consensus in treating ML-DS with reduced-intensity chemotherapy, leading to excellent outcomes. In addition, studies performed in the past 20 years have revealed many of the genetic and epigenetic features of the tumors, including GATA1 mutations that are arguably associated with all cases of both TAM and ML-DS. Despite these advances in understanding the clinical and biological aspects of ML-DS, little is known about the mechanisms of relapse. Upon relapse, patients face a poor outcome, and there is no consensus on treatment. Future studies need to be focused on this challenging aspect of leukemia in children with DS.
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Affiliation(s)
- Austin C Boucher
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kenneth J Caldwell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Jamie E Flerlage
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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38
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Zhang Z, Liu L, Shen Y, Meng Z, Chen M, Lu Z, Zhang X. Characterization of chromatin accessibility in psoriasis. Front Med 2021; 16:483-495. [PMID: 34669155 DOI: 10.1007/s11684-021-0872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022]
Abstract
The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
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Affiliation(s)
- Zheng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Yanyun Shen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ziyuan Meng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Min Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China.,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China
| | - Zhong Lu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Xuejun Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China. .,Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China. .,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China.
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39
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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40
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Rivas MA, Durmaz C, Kloetgen A, Chin CR, Chen Z, Bhinder B, Koren A, Viny AD, Scharer CD, Boss JM, Elemento O, Mason CE, Melnick AM. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol 2021; 12:688493. [PMID: 34621263 PMCID: PMC8490713 DOI: 10.3389/fimmu.2021.688493] [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: 03/30/2021] [Accepted: 08/24/2021] [Indexed: 01/10/2023] Open
Abstract
The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 haploinsufficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 haploinsufficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/immunology
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/immunology
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/immunology
- Chromosomal Proteins, Non-Histone/metabolism
- Coculture Techniques
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Databases, Genetic
- Dioxygenases/genetics
- Dioxygenases/metabolism
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Germinal Center/immunology
- Germinal Center/metabolism
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Phenotype
- Plasma Cells/immunology
- Plasma Cells/metabolism
- Transcription, Genetic
- Mice
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Affiliation(s)
- Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Ceyda Durmaz
- Graduate Program on Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, New York, NY, United States
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cristopher R. Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, United States
| | - Bhavneet Bhinder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Aaron D. Viny
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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41
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Patel SA, Lloyd MR, Cerny J, Shi Q, Simin K, Ediriwickrema A, Hutchinson L, Miron PM, Higgins AW, Ramanathan M, Gerber JM. Clinico-genomic profiling and clonal dynamic modeling of TP53-aberrant myelodysplastic syndrome and acute myeloid leukemia. Leuk Lymphoma 2021; 62:3348-3360. [PMID: 34496723 DOI: 10.1080/10428194.2021.1957869] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
TP53-aberrant myelodysplastic syndrome and acute myeloid leukemia have dismal outcomes. Here, we define the clinico-genomic landscape of TP53 disruptions in 40 patients and employ clonal dynamic modeling to map the mutational hierarchy against clinical outcomes. Most TP53 mutations (45.2%) localized to the L3 loop or LSH motif of the DNA-binding domain. TP53 disruptions had high co-occurrence with mutations in epigenetic regulators, spliceosome machinery, and cohesin complex and low co-occurrence with mutations in proliferative signaling genes. Ancestral and descendant TP53 mutations constituted measurable residual disease and fueled relapse. High mutant TP53 gene dosage predicted low durability of remission. The median overall survival (OS) was 280 days. Hypomethylating agent-based therapy served as an effective bridge to transplant, leading to improved median OS compared to patients who did not receive a transplant (14.7 vs. 5.1 months). OS was independent of the genomic location of TP53 disruption, which has implications for rational therapeutic design.
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Affiliation(s)
- Shyam A Patel
- Department of Medicine-Hematology & Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maxwell R Lloyd
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jan Cerny
- Department of Medicine-Hematology & Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qiming Shi
- Department of Medicine-Hematology & Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Population & Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Karl Simin
- Department of Molecular, Cell & Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Asiri Ediriwickrema
- Division of Hematology, Department of Medicine, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Lloyd Hutchinson
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Patricia M Miron
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anne W Higgins
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Muthalagu Ramanathan
- Department of Medicine-Hematology & Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan M Gerber
- Department of Medicine-Hematology & Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
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42
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Jann JC, Tothova Z. Cohesin mutations in myeloid malignancies. Blood 2021; 138:649-661. [PMID: 34157074 PMCID: PMC8394903 DOI: 10.1182/blood.2019004259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
Cohesin is a multisubunit protein complex that forms a ring-like structure around DNA. It is essential for sister chromatid cohesion, chromatin organization, transcriptional regulation, and DNA damage repair and plays a major role in dynamically shaping the genome architecture and maintaining DNA integrity. The core complex subunits STAG2, RAD21, SMC1, and SMC3, as well as its modulators PDS5A/B, WAPL, and NIPBL, have been found to be recurrently mutated in hematologic and solid malignancies. These mutations are found across the full spectrum of myeloid neoplasia, including pediatric Down syndrome-associated acute megakaryoblastic leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia, and de novo and secondary acute myeloid leukemias. The mechanisms by which cohesin mutations act as drivers of clonal expansion and disease progression are still poorly understood. Recent studies have described the impact of cohesin alterations on self-renewal and differentiation of hematopoietic stem and progenitor cells, which are associated with changes in chromatin and epigenetic state directing lineage commitment, as well as genomic integrity. Herein, we review the role of the cohesin complex in healthy and malignant hematopoiesis. We discuss clinical implications of cohesin mutations in myeloid malignancies and discuss opportunities for therapeutic targeting.
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Affiliation(s)
- Johann-Christoph Jann
- Department of Hematology and Oncology, University of Heidelberg, Mannheim, Germany; and
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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43
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de Castro CPM, Cadefau M, Cuartero S. The Mutational Landscape of Myeloid Leukaemia in Down Syndrome. Cancers (Basel) 2021; 13:4144. [PMID: 34439298 PMCID: PMC8394284 DOI: 10.3390/cancers13164144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Children with Down syndrome (DS) are particularly prone to haematopoietic disorders. Paediatric myeloid malignancies in DS occur at an unusually high frequency and generally follow a well-defined stepwise clinical evolution. First, the acquisition of mutations in the GATA1 transcription factor gives rise to a transient myeloproliferative disorder (TMD) in DS newborns. While this condition spontaneously resolves in most cases, some clones can acquire additional mutations, which trigger myeloid leukaemia of Down syndrome (ML-DS). These secondary mutations are predominantly found in chromatin and epigenetic regulators-such as cohesin, CTCF or EZH2-and in signalling mediators of the JAK/STAT and RAS pathways. Most of them are also found in non-DS myeloid malignancies, albeit at extremely different frequencies. Intriguingly, mutations in proteins involved in the three-dimensional organization of the genome are found in nearly 50% of cases. How the resulting mutant proteins cooperate with trisomy 21 and mutant GATA1 to promote ML-DS is not fully understood. In this review, we summarize and discuss current knowledge about the sequential acquisition of genomic alterations in ML-DS.
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Affiliation(s)
| | - Maria Cadefau
- Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain; (C.P.M.d.C); (M.C.)
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain; (C.P.M.d.C); (M.C.)
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
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44
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Antony J, Gimenez G, Taylor T, Khatoon U, Day R, Morison IM, Horsfield JA. BET inhibition prevents aberrant RUNX1 and ERG transcription in STAG2 mutant leukaemia cells. J Mol Cell Biol 2021; 12:397-399. [PMID: 31897485 PMCID: PMC7288737 DOI: 10.1093/jmcb/mjz114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/16/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Terry Taylor
- Southern Community Laboratories, Dunedin 9016, New Zealand
| | - Umaima Khatoon
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Robert Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Ian M Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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45
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Martín-Izquierdo M, Abáigar M, Hernández-Sánchez JM, Tamborero D, López-Cadenas F, Ramos F, Lumbreras E, Madinaveitia-Ochoa A, Megido M, Labrador J, Sánchez-Real J, Olivier C, Dávila J, Aguilar C, Rodríguez JN, Martín-Nuñez G, Santos-Mínguez S, Miguel-García C, Benito R, Díez-Campelo M, Hernández-Rivas JM. Co-occurrence of cohesin complex and Ras signaling mutations during progression from myelodysplastic syndromes to secondary acute myeloid leukemia. Haematologica 2021; 106:2215-2223. [PMID: 32675227 PMCID: PMC8327724 DOI: 10.3324/haematol.2020.248807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are hematological disorders at high risk of progression to secondary acute myeloid leukemia (sAML). However, the mutational dynamics and clonal evolution underlying disease progression are poorly understood at present. To elucidate the mutational dynamics of pathways and genes occurring during the evolution to sAML, next generation sequencing was performed on 84 serially paired samples of MDS patients who developed sAML (discovery cohort) and 14 paired samples from MDS patients who did not progress to sAML during follow-up (control cohort). Results were validated in an independent series of 388 MDS patients (validation cohort). We used an integrative analysis to identify how mutations, alone or in combination, contribute to leukemic transformation. The study showed that MDS progression to sAML is characterized by greater genomic instability and the presence of several types of mutational dynamics, highlighting increasing (STAG2) and newly-acquired (NRAS and FLT3) mutations. Moreover, we observed cooperation between genes involved in the cohesin and Ras pathways in 15-20% of MDS patients who evolved to sAML, as well as a high proportion of newly acquired or increasing mutations in the chromatin-modifier genes in MDS patients receiving a disease-modifying therapy before their progression to sAML.
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Affiliation(s)
- Marta Martín-Izquierdo
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Abáigar
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Jesús M Hernández-Sánchez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - David Tamborero
- Hospital del Mar Medical Research Institute (IMIM), Barcelona and Karolinska Institutet, Stockholm
| | - Félix López-Cadenas
- University of Salamanca, IBSAL, Hematology, Hospital Clinico Universitario, Salamanca, Spain
| | - Fernando Ramos
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | - Eva Lumbreras
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | | | - Marta Megido
- Hematology, Hospital del Bierzo, Ponferrada, León, Spain
| | - Jorge Labrador
- Hematology, Hospital Universitario de Burgos, Burgos, Spain
| | - Javier Sánchez-Real
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | | | - Julio Dávila
- Hematology, Hospital Nuestra Señora de Sónsoles, Ávila, Spain
| | | | | | | | - Sandra Santos-Mínguez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Cristina Miguel-García
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Rocío Benito
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Díez-Campelo
- University of Salamanca, IBSAL, Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Jesús M Hernández-Rivas
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
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46
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Liu S, Li D, Lyu C, Gontarz PM, Miao B, Madden PAF, Wang T, Zhang B. AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:641-651. [PMID: 34273560 PMCID: PMC9040017 DOI: 10.1016/j.gpb.2020.06.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/28/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022]
Abstract
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis. Several tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data; however, key quality control (QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data, including reads under peak ratio (RUPr), background (BG), promoter enrichment (ProEn), subsampling enrichment (SubEn), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package (AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity (20%–60%) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed qATACViewer for the user-friendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://github.com/Zhang-lab/ATAC-seq_QC_analysis.
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Affiliation(s)
- Shaopeng Liu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Daofeng Li
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Cheng Lyu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Paul M Gontarz
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Ting Wang
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA.
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47
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Antony J, Chin CV, Horsfield JA. Cohesin Mutations in Cancer: Emerging Therapeutic Targets. Int J Mol Sci 2021; 22:6788. [PMID: 34202641 PMCID: PMC8269296 DOI: 10.3390/ijms22136788] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex is crucial for mediating sister chromatid cohesion and for hierarchal three-dimensional organization of the genome. Mutations in cohesin genes are present in a range of cancers. Extensive research over the last few years has shown that cohesin mutations are key events that contribute to neoplastic transformation. Cohesin is involved in a range of cellular processes; therefore, the impact of cohesin mutations in cancer is complex and can be cell context dependent. Candidate targets with therapeutic potential in cohesin mutant cells are emerging from functional studies. Here, we review emerging targets and pharmacological agents that have therapeutic potential in cohesin mutant cells.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Chue Vin Chin
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
| | - Julia A. Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin 9016, New Zealand
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48
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Zhang TY, Dutta R, Benard B, Zhao F, Yin R, Majeti R. IL-6 blockade reverses bone marrow failure induced by human acute myeloid leukemia. Sci Transl Med 2021; 12:12/538/eaax5104. [PMID: 32269167 DOI: 10.1126/scitranslmed.aax5104] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 12/04/2019] [Accepted: 01/31/2020] [Indexed: 12/18/2022]
Abstract
Most patients with acute myeloid leukemia (AML) die from complications arising from cytopenias resulting from bone marrow (BM) failure. The common presumption among physicians is that AML-induced BM failure is primarily due to overcrowding, yet BM failure is observed even with low burden of disease. Here, we use large clinical datasets to show the lack of correlation between BM blast burden and degree of cytopenias at the time of diagnosis. We develop a splenectomized xenograft model to demonstrate that transplantation of human primary AML into immunocompromised mice recapitulates the human disease course by induction of BM failure via depletion of mouse hematopoietic stem and progenitor populations. Using unbiased approaches, we show that AML-elaborated IL-6 acts to block erythroid differentiation at the proerythroblast stage and that blocking antibodies against human IL-6 can improve AML-induced anemia and prolong overall survival, suggesting a potential therapeutic approach.
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Affiliation(s)
- Tian Yi Zhang
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.,Stanford School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ritika Dutta
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.,Stanford School of Medicine, Stanford, CA 94305, USA
| | - Brooks Benard
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Feifei Zhao
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.,Stanford School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Raymond Yin
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.,Stanford School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. .,Stanford School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
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49
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French R, Pauklin S. Epigenetic regulation of cancer stem cell formation and maintenance. Int J Cancer 2021; 148:2884-2897. [PMID: 33197277 PMCID: PMC8246550 DOI: 10.1002/ijc.33398] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/23/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Cancerous tumours contain a rare subset of cells with stem-like properties that are termed cancer stem cells (CSCs). CSCs are defined by their ability to divide both symmetrically and asymmetrically, to initiate new tumour growth and to tolerate the foreign niches required for metastatic dissemination. Accumulating evidence suggests that tumours arise from cells with stem-like properties, the generation of CSCs is therefore likely to be an initiatory event in carcinogenesis. Furthermore, CSCs in established tumours exist in a dynamic and plastic state, with nonstem tumour cells thought to be capable of de-differentiation to CSCs. The regulation of the CSC state both during tumour initiation and within established tumours is a desirable therapeutic target and is mediated by epigenetic factors. In this review, we will explore the epigenetic parallels between induced pluripotency and the generation of CSCs, and discuss how the epigenetic regulation of CSCs opens up novel opportunities for therapeutic intervention.
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Affiliation(s)
- Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesUniversity of OxfordOxfordUK
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50
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Abstract
OBJECTIVE Despite successful antiviral therapy, the recovery of CD4+ T cells may not be complete in certain HIV-1-infected individuals. In our previous work with humanized mice infected with CXCR4-tropic HIV-1LAI (LAI), viral protein Nef was found the major factor determining rapid loss of both CD4+ T cells and CD4+CD8+ thymocytes but its effect on early T-cell development is unknown. The objective of this study is to investigate the influence of LAI Nef on the development of hematopoietic stem/progenitor cells (HSPCs) into T lymphoid cells. DESIGN HSPC-OP9-DL1 cell co-culture and humanized mouse model was used to investigate the objective of our study in vitro and in vivo. RNA-seq was exploited to study the change of gene expression signature after nef expression in HSPCs. RESULTS Nef expression in HSPCs was found to block their development into T lymphoid cells both in vitro and in the mice reconstituted with nef-expressing HSPCs derived from human cord blood. More surprisingly, in humanized mice nef expression preferentially suppressed the production of CD4+ T cells. This developmental defect was not the result of CD34+ cell loss. RNA-seq analysis revealed that Nef affected the expression of 176 genes in HSPCs, including those involved in tumor necrosis factor, Toll-like receptor, and nucleotide-binding oligomerization domain-like receptor signaling pathways that are important for hematopoietic cell development. CONCLUSION Our results demonstrate that Nef compromises the development of HSPCs into T lymphoid cells, especially CD4+ T cells. This observation suggests that therapeutics targeting Nef may correct HIV-1-associated hematopoietic abnormalities, especially defects in T-cell development.
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