1
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Ros-Pardo D, Gómez-Puertas P, Marcos-Alcalde Í. STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion. Int J Biol Macromol 2024; 276:133822. [PMID: 39002918 DOI: 10.1016/j.ijbiomac.2024.133822] [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: 02/05/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
DNA loop extrusion plays a key role in the regulation of gene expression and the structural arrangement of chromatin. Most existing mechanistic models of loop extrusion depend on some type of ratchet mechanism, which should permit the elongation of loops while preventing their collapse, by enabling DNA to move in only one direction. STAG2 is already known to exert a role as DNA anchor, but the available structural data suggest a possible role in unidirectional DNA motion. In this work, a computational simulation framework was constructed to evaluate whether STAG2 could enforce such unidirectional displacement of a DNA double helix. The results reveal that STAG2 V-shape allows DNA sliding in one direction, but blocks opposite DNA movement via a linear ratchet mechanism. Furthermore, these results suggest that RAD21 binding to STAG2 controls its flexibility by narrowing the opening of its V-shape, which otherwise remains widely open in absence of RAD21. Therefore, in the proposed model, in addition to its already described role as a DNA anchor, the STAG2-RAD21 complex would be part of a ratchet mechanism capable of exerting directional selectivity on DNA sliding during loop extrusion. The identification of the molecular basis of the ratchet mechanism of loop extrusion is a critical step in unraveling new insights into a broad spectrum of chromatin activities and their implications for the mechanisms of chromatin-related diseases.
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Affiliation(s)
- David Ros-Pardo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Paulino Gómez-Puertas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain.
| | - Íñigo Marcos-Alcalde
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, CL Nicolás Cabrera, 1, 28049 Madrid, Spain
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2
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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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3
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Thatikonda V, Supper V, Wachter J, Kaya O, Kombara A, Bilgilier C, Ravichandran MC, Lipp JJ, Sharma R, Badertscher L, Boghossian AS, Rees MG, Ronan MM, Roth JA, Grosche S, Neumüller RA, Mair B, Mauri F, Popa A. Genetic dependencies associated with transcription factor activities in human cancer cell lines. Cell Rep 2024; 43:114175. [PMID: 38691456 DOI: 10.1016/j.celrep.2024.114175] [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: 03/14/2023] [Revised: 02/02/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024] Open
Abstract
Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focus on TF activity (TFa) as a biomarker for cell-line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss of function of a given gene (i.e., genetic dependencies [GDs]). Our linear-regression-based framework identifies 3,047 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which are then cross-examined for impact on survival in patient cohorts. One of the most prominent biomarkers is TEAD1 activity, whose associations with its predicted GDs are validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology.
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Affiliation(s)
- Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
| | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Johannes Wachter
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Onur Kaya
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ceren Bilgilier
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | | | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Rahul Sharma
- Myllia Biotechnology GmbH, Am Kanal 27, Vienna 1110, Austria
| | | | | | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Melissa M Ronan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Grosche
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Federico Mauri
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
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4
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Rittenhouse NL, Dowen JM. Cohesin regulation and roles in chromosome structure and function. Curr Opin Genet Dev 2024; 85:102159. [PMID: 38382406 PMCID: PMC10947815 DOI: 10.1016/j.gde.2024.102159] [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: 09/12/2023] [Revised: 01/22/2024] [Accepted: 01/27/2024] [Indexed: 02/23/2024]
Abstract
Chromosome structure regulates DNA-templated processes such as transcription of genes. Dynamic changes to chromosome structure occur during development and in disease contexts. The cohesin complex is a molecular motor that regulates chromosome structure by generating DNA loops that bring two distal genomic sites into close spatial proximity. There are many open questions regarding the formation and dissolution of DNA loops, as well as the role(s) of DNA loops in regulating transcription of the interphase genome. This review focuses on recent discoveries that provide molecular insights into the role of cohesin and chromosome structure in gene transcription during development and disease.
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Affiliation(s)
- Natalie L Rittenhouse
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jill M Dowen
- Department of Biophysics & Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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5
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Pallotta MM, Di Nardo M, Musio A. Synthetic Lethality between Cohesin and WNT Signaling Pathways in Diverse Cancer Contexts. Cells 2024; 13:608. [PMID: 38607047 PMCID: PMC11011321 DOI: 10.3390/cells13070608] [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: 02/27/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
Cohesin is a highly conserved ring-shaped complex involved in topologically embracing chromatids, gene expression regulation, genome compartmentalization, and genome stability maintenance. Genomic analyses have detected mutations in the cohesin complex in a wide array of human tumors. These findings have led to increased interest in cohesin as a potential target in cancer therapy. Synthetic lethality has been suggested as an approach to exploit genetic differences in cancer cells to influence their selective killing. In this study, we show that mutations in ESCO1, NIPBL, PDS5B, RAD21, SMC1A, SMC3, STAG2, and WAPL genes are synthetically lethal with stimulation of WNT signaling obtained following LY2090314 treatment, a GSK3 inhibitor, in several cancer cell lines. Moreover, treatment led to the stabilization of β-catenin and affected the expression of c-MYC, probably due to the occupancy decrease in cohesin at the c-MYC promoter. Finally, LY2090314 caused gene expression dysregulation mainly involving pathways related to transcription regulation, cell proliferation, and chromatin remodeling. For the first time, our work provides the underlying molecular basis for synthetic lethality due to cohesin mutations and suggests that targeting the WNT may be a promising therapeutic approach for tumors carrying mutated cohesin.
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Affiliation(s)
| | | | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), 56124 Pisa, Italy; (M.M.P.); (M.D.N.)
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6
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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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7
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Zhang Y, Liu Z, Hirschi M, Brodsky O, Johnson E, Won SJ, Nagata A, Petroski MD, Majmudar JD, Niessen S, VanArsdale T, Gilbert AM, Hayward MM, Stewart AE, Nager AR, Melillo B, Cravatt B. Expanding the ligandable proteome by paralog hopping with covalent probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576274. [PMID: 38293178 PMCID: PMC10827202 DOI: 10.1101/2024.01.18.576274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.
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Affiliation(s)
- Yuanjin Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Zhonglin Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Marsha Hirschi
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Oleg Brodsky
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Eric Johnson
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Asako Nagata
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | | | - Jaimeen D Majmudar
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Cambridge, MA 02139, USA
| | - Sherry Niessen
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Current address: Belharra Therapeutics, 3985 Sorrento Valley Blvd suite c, San Diego, CA 92121
| | - Todd VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
- Current address: Magnet Biomedicine, 321 Harrison Ave., Suite 600, Boston, MA 02118, USA
| | - Al E Stewart
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Andrew R Nager
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Benjamin Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
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8
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Hoffmann T, Hörmann A, Corcokovic M, Zmajkovic J, Hinterndorfer M, Salkanovic J, Spreitzer F, Köferle A, Gitschtaler K, Popa A, Oberndorfer S, Andersch F, Schaefer M, Fellner M, Budano N, Ruppert JG, Chetta P, Wurm M, Zuber J, Neumüller RA. Precision RNAi using synthetic shRNAmir target sites. eLife 2023; 12:RP84792. [PMID: 37552050 PMCID: PMC10409502 DOI: 10.7554/elife.84792] [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] [Indexed: 08/09/2023] Open
Abstract
Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.
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Affiliation(s)
- Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Jakub Zmajkovic
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | | | - Jasko Salkanovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Katrin Gitschtaler
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Florian Andersch
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Markus Schaefer
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Nicole Budano
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Jan G Ruppert
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Paolo Chetta
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Melanie Wurm
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
- Medical University of Vienna, Vienna BioCenterViennaAustria
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
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9
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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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10
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Xin Y, Zhang Y. Paralog-based synthetic lethality: rationales and applications. Front Oncol 2023; 13:1168143. [PMID: 37350942 PMCID: PMC10282757 DOI: 10.3389/fonc.2023.1168143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023] Open
Abstract
Tumor cells can result from gene mutations and over-expression. Synthetic lethality (SL) offers a desirable setting where cancer cells bearing one mutated gene of an SL gene pair can be specifically targeted by disrupting the function of the other genes, while leaving wide-type normal cells unharmed. Paralogs, a set of homologous genes that have diverged from each other as a consequence of gene duplication, make the concept of SL feasible as the loss of one gene does not affect the cell's survival. Furthermore, homozygous loss of paralogs in tumor cells is more frequent than singletons, making them ideal SL targets. Although high-throughput CRISPR-Cas9 screenings have uncovered numerous paralog-based SL pairs, the unclear mechanisms of targeting these gene pairs and the difficulty in finding specific inhibitors that exclusively target a single but not both paralogs hinder further clinical development. Here, we review the potential mechanisms of paralog-based SL given their function and genetic combination, and discuss the challenge and application prospects of paralog-based SL in cancer therapeutic discovery.
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11
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Ryan CJ, Mehta I, Kebabci N, Adams DJ. Targeting synthetic lethal paralogs in cancer. Trends Cancer 2023; 9:397-409. [PMID: 36890003 DOI: 10.1016/j.trecan.2023.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Synthetic lethal interactions, where mutation of one gene renders cells sensitive to inhibition of another gene, can be exploited for the development of targeted therapeutics in cancer. Pairs of duplicate genes (paralogs) often share common functionality and hence are a potentially rich source of synthetic lethal interactions. Because the majority of human genes have paralogs, exploiting such interactions could be a widely applicable approach for targeting gene loss in cancer. Moreover, existing small-molecule drugs may exploit synthetic lethal interactions by inhibiting multiple paralogs simultaneously. Consequently, the identification of synthetic lethal interactions between paralogs could be extremely informative for drug development. Here we review approaches to identify such interactions and discuss some of the challenges of exploiting them.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Systems Biology Ireland, University College Dublin, Dublin, Ireland.
| | - Ishan Mehta
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Narod Kebabci
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Science Foundation Ireland (SFI) Centre for Research Training in Genomics Data Science, University College Dublin, Dublin, Ireland
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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12
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Bäckström A, Yudovich D, Žemaitis K, Nilsén Falck L, Subramaniam A, Larsson J. Combinatorial gene targeting in primary human hematopoietic stem and progenitor cells. Sci Rep 2022; 12:18169. [PMID: 36307542 PMCID: PMC9616885 DOI: 10.1038/s41598-022-23118-8] [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] [Received: 03/31/2022] [Accepted: 10/25/2022] [Indexed: 12/31/2022] Open
Abstract
The CRISPR/Cas9 system offers enormous versatility for functional genomics but many applications have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, to establish a paradigm for multiplexed gene editing in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs), we used co-delivery of lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The fluorescent markers allow for tracking of either single- or double-edited cells, and we could achieve robust double knockout of the cell surface molecules CD45 and CD44 with an efficiency of ~ 70%. As a functional proof of concept, we demonstrate that this system can be used to model gene dependencies for cell survival, by simultaneously targeting the cohesin genes STAG1 and STAG2. Moreover, we show combinatorial effects with potential synergy for HSPC expansion by targeting the Aryl Hydrocarbon Receptor (AHR) in conjunction with members of the CoREST complex. Taken together, our traceable multiplexed CRISPR/Cas9 system enables studies of genetic dependencies and cooperation in primary HSPCs, and has important implications for modelling polygenic diseases, as well as investigation of the underlying mechanisms of gene interactions.
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Affiliation(s)
- Alexandra Bäckström
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - David Yudovich
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Kristijonas Žemaitis
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Ludvig Nilsén Falck
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Agatheeswaran Subramaniam
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
| | - Jonas Larsson
- grid.4514.40000 0001 0930 2361Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84 Lund, Sweden
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13
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Saitta C, Rebellato S, Bettini LR, Giudici G, Panini N, Erba E, Massa V, Auer F, Friedrich U, Hauer J, Biondi A, Fazio G, Cazzaniga G. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies. Blood Cancer J 2022; 12:88. [PMID: 35654786 PMCID: PMC9163173 DOI: 10.1038/s41408-022-00683-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
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14
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Characterization of transcriptome diversity and in vitro behavior of primary human high-risk breast cells. Sci Rep 2022; 12:6159. [PMID: 35459280 PMCID: PMC9033878 DOI: 10.1038/s41598-022-10246-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/01/2022] [Indexed: 11/09/2022] Open
Abstract
Biology and transcriptomes of non-cancerous human mammary epithelial cells at risk for breast cancer development were explored following primary isolation utilizing conditional reprogramming cell technology from mastectomy tissue ipsilateral to invasive breast cancer. Cultures demonstrated consistent categorizable behaviors. Relative viability and mammosphere formation differed between samples but were stable across three different mammary-specific media. E2F cell cycle target genes expression levels were positively correlated with viability and advancing age was inversely associated. Estrogen growth response was associated with Tissue necrosis factor signaling and Interferon alpha response gene enrichment. Neoadjuvant chemotherapy exposure significantly altered transcriptomes, shifting them towards expression of genes linked to mammary stem cell formation. Breast cancer prognostic signature sets include genes that in normal development are limited to specific stages of pregnancy or the menstrual cycle. Sample transcriptomes were queried for stage specific gene expression patterns. All cancer samples and a portion of high-risk samples showed overlapping stages reflective of abnormal gene expression patterns, while other high-risk samples exhibited more stage specific patterns. In conclusion, at-risk cells preserve behavioral and transcriptome diversity that could reflect different risk profiles. It is possible that prognostic platforms analogous to those used for breast cancer could be developed for high-risk mammary cells.
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15
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Gordon NS, Humayun-Zakaria N, Goel A, Abbotts B, Zeegers MP, Cheng K, James ND, Arnold R, Bryan RT, Ward DG. STAG2 Protein Expression in Non–muscle-invasive Bladder Cancer: Associations with Sex, Genomic and Transcriptomic Changes, and Clinical Outcomes. EUR UROL SUPPL 2022; 38:88-95. [PMID: 35495284 PMCID: PMC9051973 DOI: 10.1016/j.euros.2022.02.004] [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] [Accepted: 02/15/2022] [Indexed: 01/01/2023] Open
Abstract
Background Mutations in STAG2 cause complete loss of STAG2 protein in approximately one-third of non–muscle-invasive bladder cancers (NMIBCs). STAG2 protein expression is easily determined via immunohistochemistry (IHC) and published data suggest that loss of STAG2 expression is a good prognostic indicator in NMIBC. Objective To confirm the relationship between STAG2 protein expression and clinical outcomes and tumour characteristics in NMIBC. Design, setting, and participants IHC was used to determine STAG2 expression in 748 incident urothelial bladder cancers (UBCs) and recurrence-free, progression-free, and disease-specific survival were compared for patients with and without STAG2 loss. Exome and RNA sequencing were used to explore links between STAG2 loss and tumour molecular characteristics. Results and limitations STAG2 loss was observed in 19% of UBC patients and was 1.6-fold more common among female patients. Loss was frequent among grade 1 pTa tumours (40%), decreasing with stage and grade to only 5% among grade 3 pT2+ tumours. Loss was associated with fewer copy-number changes and less aggressive expression subtypes. In UBC, STAG2 loss was a highly significant prognostic indicator of better disease-free survival but was not independent of stage and grade. STAG2 loss was not a statistically significant predictor of NMIBC recurrence. STAG2 loss was significantly associated with better progression-free survival in NMIBC and appeared to be more prognostic for males than for females. Conclusions A simple IHC-based STAG2 test shows promise for identifying NMIBC patients at lower risk of progression to MIBC for whom more conservative treatments may be suitable. Patient summary A protein called STAG2 is frequently lost in early bladder cancers, most often in less aggressive tumours. STAG2 loss is easily measured and could be used as a biomarker to help guide treatment decisions.
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16
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Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [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: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
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Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
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17
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Park TY, Leiserson MD, Klau GW, Raphael BJ. SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. CELL GENOMICS 2022; 2. [PMID: 35382456 PMCID: PMC8979493 DOI: 10.1016/j.xgen.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent genome-wide CRISPR-Cas9 loss-of-function screens have identified genetic dependencies across many cancer cell lines. Associations between these dependencies and genomic alterations in the same cell lines reveal phenomena such as oncogene addiction and synthetic lethality. However, comprehensive identification of such associations is complicated by complex interactions between genes across genetically heterogeneous cancer types. We introduce and apply the algorithm SuperDendrix to CRISPR-Cas9 loss-of-function screens from 769 cancer cell lines, to identify differential dependencies across cell lines and to find associations between differential dependencies and combinations of genomic alterations and cell-type-specific markers. These associations respect the position and type of interactions within pathways: for example, we observe increased dependencies on downstream activators of pathways, such as NFE2L2, and decreased dependencies on upstream activators of pathways, such as CDK6. SuperDendrix also reveals dozens of dependencies on lineage-specific transcription factors, identifies cancer-type-specific correlations between dependencies, and enables annotation of individual mutated residues. Using SuperDendrix, Park et al. examine associations between genetic dependencies in 769 cancer cell lines. They report 127 genetic dependencies explained by combinations of mutually exclusive somatic mutations congregating into a few oncogenic pathways across cancer subtypes. These present a small number of prominent and highly specific genetic vulnerabilities in cancer. Graphical abstract
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18
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Gilbertson SR, Zhang N, Lin KF, Yang C, Peruski S, Pati D, Gilbertson SR. Synthesis and Evaluation of a Class of Compounds Inhibiting the Growth of Stromal Antigen 2 (STAG2)-Mutant Ewing Sarcoma Cells. ChemMedChem 2022; 17:e202100653. [PMID: 35018729 DOI: 10.1002/cmdc.202100653] [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: 10/08/2021] [Revised: 12/15/2021] [Indexed: 11/06/2022]
Abstract
STAG2 (SA2) is a critical component of the cohesin complex that regulates gene expression and the separation of sister chromatids in cells. Mutations in STAG2 have been identified in over thirty different types of cancers including non-small cell lung, bladder and Ewing sarcoma. Selectively inhibiting cancer cells lacking of STAG2 is an attractive approach for the cancer therapy. Here we report that a small molecule, StagX1, identified through a high-throughput screening, inhibits the growth of Ewing sarcoma cells possessing mutant STAG2 . A new synthetic route to the StagX1 scaffold and new versions of the molecule along with their activity in a cell viability assay are reported.
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Affiliation(s)
- Scott Richard Gilbertson
- University of Houston, Department of Chemistry, 136 Fleming Building, 77204-5003, Houston, UNITED STATES
| | - Nenggang Zhang
- Baylor College of Medicine, Pediatrics, 77030, Houston, UNITED STATES
| | - Keng-Fu Lin
- University of Houston, Chemistry, UNITED STATES
| | | | | | | | - Scott R Gilbertson
- University of Houston, Chemistry, 112 Fleming Building, Houston, 77204, Houston, UNITED STATES
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19
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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20
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Bailey ML, Tieu D, Habsid A, Tong AHY, Chan K, Moffat J, Hieter P. Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2. Life Sci Alliance 2021; 4:e202101083. [PMID: 34462321 PMCID: PMC8408347 DOI: 10.26508/lsa.202101083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.
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Affiliation(s)
- Melanie L Bailey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Canada
| | | | | | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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21
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Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Cell Syst 2021; 12:1144-1159.e6. [PMID: 34529928 DOI: 10.1016/j.cels.2021.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have an identifiable paralog, exploiting synthetic lethality between paralogs may be a broadly applicable approach for targeting gene loss in cancer. However, only a biased subset of human paralog pairs has been tested for synthetic lethality to date. Here, by analyzing genome-wide CRISPR screens and molecular profiles of over 700 cancer cell lines, we identify features predictive of synthetic lethality between paralogs, including shared protein-protein interactions and evolutionary conservation. We develop a machine-learning classifier based on these features to predict which paralog pairs are most likely to be synthetic lethal and to explain why. We show that our classifier accurately predicts the results of combinatorial CRISPR screens in cancer cell lines and furthermore can distinguish pairs that are synthetic lethal in multiple cell lines from those that are cell-line specific. A record of this paper's transparent peer review process is included in the supplemental information.
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22
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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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23
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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: 16] [Impact Index Per Article: 5.3] [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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24
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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: 21] [Impact Index Per Article: 7.0] [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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25
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Adane B, Alexe G, Seong BKA, Lu D, Hwang EE, Hnisz D, Lareau CA, Ross L, Lin S, Dela Cruz FS, Richardson M, Weintraub AS, Wang S, Iniguez AB, Dharia NV, Conway AS, Robichaud AL, Tanenbaum B, Krill-Burger JM, Vazquez F, Schenone M, Berman JN, Kung AL, Carr SA, Aryee MJ, Young RA, Crompton BD, Stegmaier K. STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell 2021; 39:827-844.e10. [PMID: 34129824 PMCID: PMC8378827 DOI: 10.1016/j.ccell.2021.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/28/2021] [Accepted: 05/13/2021] [Indexed: 02/08/2023]
Abstract
The core cohesin subunit STAG2 is recurrently mutated in Ewing sarcoma but its biological role is less clear. Here, we demonstrate that cohesin complexes containing STAG2 occupy enhancer and polycomb repressive complex (PRC2)-marked regulatory regions. Genetic suppression of STAG2 leads to a compensatory increase in cohesin-STAG1 complexes, but not in enhancer-rich regions, and results in reprogramming of cis-chromatin interactions. Strikingly, in STAG2 knockout cells the oncogenic genetic program driven by the fusion transcription factor EWS/FLI1 was highly perturbed, in part due to altered enhancer-promoter contacts. Moreover, loss of STAG2 also disrupted PRC2-mediated regulation of gene expression. Combined, these transcriptional changes converged to modulate EWS/FLI1, migratory, and neurodevelopmental programs. Finally, consistent with clinical observations, functional studies revealed that loss of STAG2 enhances the metastatic potential of Ewing sarcoma xenografts. Our findings demonstrate that STAG2 mutations can alter chromatin architecture and transcriptional programs to promote an aggressive cancer phenotype.
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Affiliation(s)
- Biniam Adane
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Bo Kyung A Seong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diana Lu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Elizabeth E Hwang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Linda Ross
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Shan Lin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sarah Wang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Saur Conway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Amanda L Robichaud
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Jason N Berman
- Department of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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26
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Surdez D, Zaidi S, Grossetête S, Laud-Duval K, Ferre AS, Mous L, Vourc'h T, Tirode F, Pierron G, Raynal V, Baulande S, Brunet E, Hill V, Delattre O. STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma. Cancer Cell 2021; 39:810-826.e9. [PMID: 33930311 DOI: 10.1016/j.ccell.2021.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/31/2020] [Accepted: 04/02/2021] [Indexed: 12/19/2022]
Abstract
STAG2, a cohesin family gene, is among the most recurrently mutated genes in cancer. STAG2 loss of function (LOF) is associated with aggressive behavior in Ewing sarcoma, a childhood cancer driven by aberrant transcription induced by the EWSR1-FLI1 fusion oncogene. Here, using isogenic Ewing cells, we show that, while STAG2 LOF profoundly changes the transcriptome, it does not significantly impact EWSR1-FLI1, CTCF/cohesin, or acetylated H3K27 DNA binding patterns. In contrast, it strongly alters the anchored dynamic loop extrusion process at boundary CTCF sites and dramatically decreases promoter-enhancer interactions, particularly affecting the expression of genes regulated by EWSR1-FLI1 at GGAA microsatellite neo-enhancers. Down-modulation of cis-mediated EWSR1-FLI1 activity, observed in STAG2-LOF conditions, is associated with enhanced migration and invasion properties of Ewing cells previously observed in EWSR1-FLI1low cells. Our study illuminates a process whereby STAG2-LOF fine-tunes the activity of an oncogenic transcription factor through altered CTCF-anchored loop extrusion and cis-mediated enhancer mechanisms.
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MESH Headings
- Bone Neoplasms/genetics
- Bone Neoplasms/mortality
- Bone Neoplasms/pathology
- CCCTC-Binding Factor/chemistry
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Movement/genetics
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/metabolism
- Enhancer Elements, Genetic
- Gene Expression Regulation, Neoplastic
- Histones/metabolism
- Humans
- Loss of Function Mutation
- Lysine/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/mortality
- Sarcoma, Ewing/pathology
- Cohesins
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Affiliation(s)
- Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France.
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Anna Sole Ferre
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Lieke Mous
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Thomas Vourc'h
- UMR 168, Biology Inspired Physics at Mesoscales, PSL Research University, Institut Curie Research Centre, 75005 Paris, France
| | - Franck Tirode
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Center of Lyon, 69008 Lyon, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France
| | - Virginie Raynal
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Université, Institut Curie Research Centre, 75005 Paris, France
| | - Erika Brunet
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Université de Paris, Imagine Institute, 75005 Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France; Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, 75005 Paris, France.
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27
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Zhang N, Coutinho LE, Pati D. PDS5A and PDS5B in Cohesin Function and Human Disease. Int J Mol Sci 2021; 22:ijms22115868. [PMID: 34070827 PMCID: PMC8198109 DOI: 10.3390/ijms22115868] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/02/2023] Open
Abstract
Precocious dissociation of sisters 5 (PDS5) is an associate protein of cohesin that is conserved from yeast to humans. It acts as a regulator of the cohesin complex and plays important roles in various cellular processes, such as sister chromatid cohesion, DNA damage repair, gene transcription, and DNA replication. Vertebrates have two paralogs of PDS5, PDS5A and PDS5B, which have redundant and unique roles in regulating cohesin functions. Herein, we discuss the molecular characteristics and functions of PDS5, as well as the effects of its mutations in the development of diseases and their relevance for novel therapeutic strategies.
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Affiliation(s)
| | | | - Debananda Pati
- Correspondence: ; Tel.: +1-832-824-4575; Fax: +1-832-825-4651
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28
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Han C, Gao X, Li Y, Zhang J, Yang E, Zhang L, Yu L. Characteristics of Cohesin Mutation in Acute Myeloid Leukemia and Its Clinical Significance. Front Oncol 2021; 11:579881. [PMID: 33928020 PMCID: PMC8076553 DOI: 10.3389/fonc.2021.579881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/18/2021] [Indexed: 12/18/2022] Open
Abstract
The occurrence of gene mutation is a major contributor to the initiation and propagation of acute myeloid leukemia (AML). Accumulating evidence suggests that genes encoding cohesin subunits have a high prevalence of mutations in AML, especially in the t(8;21) subtype. Therefore, it is important to understand how cohesin mutations contribute to leukemogenesis. However, the fundamental understanding of cohesin mutation in clonal expansion and myeloid transformation in hematopoietic cells remains ambiguous. Previous studies briefly introduced the cohesin mutation in AML; however, an in-depth summary of mutations in AML was not provided, and the correlation between cohesin and AML1-ETO in t (8;21) AML was also not analyzed. By summarizing the major findings regarding the cohesin mutation in AML, this review aims to define the characteristics of the cohesin complex mutation, identify its relationships with co-occurring gene mutations, assess its roles in clonal evolution, and discuss its potential for the prognosis of AML. In particular, we focus on the function of cohesin mutations in RUNX1-RUNX1T1 fusion.
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Affiliation(s)
- Caixia Han
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Xuefeng Gao
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Yonghui Li
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Juan Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Erna Yang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Li Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
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29
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Ochi Y, Ogawa S. Chromatin-Spliceosome Mutations in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13061232. [PMID: 33799787 PMCID: PMC7999050 DOI: 10.3390/cancers13061232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Recent genomic studies have identified chromatin-spliceosome (CS)-acute myeloid leukemia (AML) as a new subgroup of AML. CS-AML is defined by several mutations that perturb epigenetic regulation, such as those affecting splicing factors, cohesin components, transcription factors, and chromatin modifiers, which are also frequently mutated in other myeloid malignancies, such as myelodysplastic syndrome and secondary AML. Thus, these mutations identify myeloid neoplasms that lie on the boundaries of conventional differential diagnosis. CS-AML shares several clinical characteristics with secondary AML. Therefore, the presence of CS-mutations may help to better classify and manage patients with AML and related disorders. The aim of this review is to discuss the genetic and clinical characteristics of CS-AML and roles of driver mutations defining this unique genomic subgroup of AML. Abstract Recent genetic studies on large patient cohorts with acute myeloid leukemia (AML) have cataloged a comprehensive list of driver mutations, resulting in the classification of AML into distinct genomic subgroups. Among these subgroups, chromatin-spliceosome (CS)-AML is characterized by mutations in the spliceosome, cohesin complex, transcription factors, and chromatin modifiers. Class-defining mutations of CS-AML are also frequently identified in myelodysplastic syndrome (MDS) and secondary AML, indicating the molecular similarity among these diseases. CS-AML is associated with myelodysplasia-related changes in hematopoietic cells and poor prognosis, and, thus, can be treated using novel therapeutic strategies and allogeneic stem cell transplantation. Functional studies of CS-mutations in mice have revealed that CS-mutations typically cause MDS-like phenotypes by altering the epigenetic regulation of target genes. Moreover, multiple CS-mutations often synergistically induce more severe phenotypes, such as the development of lethal MDS/AML, suggesting that the accumulation of many CS-mutations plays a crucial role in the progression of MDS/AML. Indeed, the presence of multiple CS-mutations is a stronger indicator of CS-AML than a single mutation. This review summarizes the current understanding of the genetic and clinical features of CS-AML and the functional roles of driver mutations characterizing this unique category of AML.
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Affiliation(s)
- Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 171 77, Sweden
- Correspondence: ; Tel.: +81-75-753-9285
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30
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Heimbruch KE, Meyer AE, Agrawal P, Viny AD, Rao S. A cohesive look at leukemogenesis: The cohesin complex and other driving mutations in AML. Neoplasia 2021; 23:337-347. [PMID: 33621854 PMCID: PMC7905235 DOI: 10.1016/j.neo.2021.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukemia (AML) affects tens of thousands of patients a year, yet survival rates are as low as 25% in certain populations. This poor survival rate is partially due to the vast genetic diversity of the disease. Rarely do 2 patients with AML have the same mutational profile, which makes the development of targeted therapies particularly challenging. However, a set of recurrent mutations in chromatin modifiers have been identified in many patients, including mutations in the cohesin complex, which have been identified in up to 20% of cases. Interestingly, the canonical function of the cohesin complex in establishing sister chromatid cohesin during mitosis is unlikely to be the affected role in leukemogenesis. Instead, the cohesin complex's role in DNA looping and gene regulation likely facilitates disease. The epigenetic mechanisms by which cohesin complex mutations promote leukemia are not completely elucidated, but alterations of enhancer-promoter interactions and differential histone modifications have been shown to drive oncogenic gene expression changes. Such changes commonly include HoxA upregulation, which may represent a common pathway that could be therapeutically targeted. As cohesin mutations rarely occur alone, examining the impact of common co-occurring mutations, including those in NPM1, the core-binding factor complex, FLT3, and ASXL1, will yield additional insight. While further study of these mutational interactions is required, current research suggests that the use of combinatorial genetics could be the key to uncovering new targets, allowing for the treatment of AML patients based on their individual genetic profiles.
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Affiliation(s)
- Katelyn E Heimbruch
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Puja Agrawal
- Blood Research Institute, Versiti, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology, and Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - 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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31
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Tothova Z, Valton AL, Gorelov RA, Vallurupalli M, Krill-Burger JM, Holmes A, Landers CC, Haydu JE, Malolepsza E, Hartigan C, Donahue M, Popova KD, Koochaki S, Venev SV, Rivera J, Chen E, Lage K, Schenone M, D’Andrea AD, Carr SA, Morgan EA, Dekker J, Ebert BL. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight 2021; 6:142149. [PMID: 33351783 PMCID: PMC7934867 DOI: 10.1172/jci.insight.142149] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/16/2020] [Indexed: 12/26/2022] Open
Abstract
The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of stromal antigen 2-mutant (STAG2-mutant) AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to poly(ADP-ribose) polymerase (PARP) inhibition. We developed a mouse model of MDS in which Stag2 mutations arose as clonal secondary lesions in the background of clonal hematopoiesis driven by tet methylcytosine dioxygenase 2 (Tet2) mutations and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which was associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and replication protein A complex. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies.
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MESH Headings
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Damage
- DNA Repair/genetics
- Disease Models, Animal
- Female
- Humans
- K562 Cells
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Mutant Strains
- Mice, SCID
- Mice, Transgenic
- Mutation
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- Nuclear Proteins/genetics
- Phthalazines/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- U937 Cells
- Xenograft Model Antitumor Assays
- Cohesins
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Affiliation(s)
- Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Mounica Vallurupalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Amie Holmes
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - J. Erika Haydu
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | | | - Melanie Donahue
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Sebastian Koochaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sergey V. Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeanne Rivera
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Edwin Chen
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Kasper Lage
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Monica Schenone
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Steven A. Carr
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Elizabeth A. Morgan
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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32
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Chin CV, Antony J, Ketharnathan S, Labudina A, Gimenez G, Parsons KM, He J, George AJ, Pallotta MM, Musio A, Braithwaite A, Guilford P, Hannan RD, Horsfield JA. Cohesin mutations are synthetic lethal with stimulation of WNT signaling. eLife 2020; 9:e61405. [PMID: 33284104 PMCID: PMC7746233 DOI: 10.7554/elife.61405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding subunits of the cohesin complex are common in several cancers, but may also expose druggable vulnerabilities. We generated isogenic MCF10A cell lines with deletion mutations of genes encoding cohesin subunits SMC3, RAD21, and STAG2 and screened for synthetic lethality with 3009 FDA-approved compounds. The screen identified several compounds that interfere with transcription, DNA damage repair and the cell cycle. Unexpectedly, one of the top 'hits' was a GSK3 inhibitor, an agonist of Wnt signaling. We show that sensitivity to GSK3 inhibition is likely due to stabilization of β-catenin in cohesin-mutant cells, and that Wnt-responsive gene expression is highly sensitized in STAG2-mutant CMK leukemia cells. Moreover, Wnt activity is enhanced in zebrafish mutant for cohesin subunits stag2b and rad21. Our results suggest that cohesin mutations could progress oncogenesis by enhancing Wnt signaling, and that targeting the Wnt pathway may represent a novel therapeutic strategy for cohesin-mutant cancers.
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Affiliation(s)
- Chue Vin Chin
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Jisha Antony
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Sarada Ketharnathan
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Anastasia Labudina
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Gregory Gimenez
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Kate M Parsons
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Jinshu He
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Amee J George
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Maria Michela Pallotta
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antony Braithwaite
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
| | - Parry Guilford
- Department of Biochemistry, University of OtagoDunedinNew Zealand
| | - Ross D Hannan
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
- Department of Biochemistry and Molecular Biology, University of MelbourneParkvilleAustralia
- Sir Peter MacCallum Department of Oncology, University of MelbourneParkvilleAustralia
- School of Biomedical Sciences, University of QueenslandSt LuciaAustralia
| | - Julia A Horsfield
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
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33
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Abstract
Mutations of the cohesin complex in human cancer were first discovered ~10 years ago. Since then, researchers worldwide have demonstrated that cohesin is among the most commonly mutated protein complexes in cancer. Inactivating mutations in genes encoding cohesin subunits are common in bladder cancers, paediatric sarcomas, leukaemias, brain tumours and other cancer types. Also in those 10 years, the prevailing view of the functions of cohesin in cell biology has undergone a revolutionary transformation. Initially, the predominant view of cohesin was as a ring that encircled and cohered replicated chromosomes until its cleavage triggered the metaphase-to-anaphase transition. As such, early studies focused on the role of tumour-derived cohesin mutations in the fidelity of chromosome segregation and aneuploidy. However, over the past 5 years the cohesin field has shifted dramatically, and research now focuses on the primary role of cohesin in generating, maintaining and regulating the intra-chromosomal DNA looping events that modulate 3D genome organization and gene expression. This Review focuses on recent discoveries in the cohesin field that provide insight into the role of cohesin inactivation in cancer pathogenesis, and opportunities for exploiting these findings for the clinical benefit of patients with cohesin-mutant cancers.
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Affiliation(s)
- Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC, USA.
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34
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Arruda NL, Carico ZM, Justice M, Liu YF, Zhou J, Stefan HC, Dowen JM. Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells. Epigenetics Chromatin 2020; 13:32. [PMID: 32778134 PMCID: PMC7418333 DOI: 10.1186/s13072-020-00353-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The three-dimensional organization of the genome in the nucleus plays an integral role in many biological processes, including gene expression. The genome is folded into DNA loops that bring together distal regulatory elements and genes. Cohesin, a ring-shaped protein complex, is a major player in the formation of DNA loops. Cohesin is composed of a core trimer and one of two variant STAG subunits, STAG1 or STAG2. It is not understood whether variant STAG proteins give rise to cohesin complexes with distinct functions. Recent studies have begun to characterize the roles of STAG1 and STAG2, with partially contradictory results. RESULTS Here, we generate stable single-knockout embryonic stem cell lines to investigate the individual contributions of STAG1 and STAG2 in regulating cohesin chromosomal localization and function. We report both overlapping roles for STAG1 and STAG2 in cohesin localization and somewhat distinct roles in gene expression. STAG1 and STAG2 occupy the same sites across the genome, yet do not exist together in a higher order complex. Despite their shared localization, STAG1 and STAG2 have both distinct and redundant effects on gene expression. Loss of both STAG1 and STAG2 causes widespread transcriptome dysregulation, altered cohesin DNA occupancy, and reduced cell proliferation. CONCLUSIONS Together, this work reveals the requirement of at least one STAG protein for proper cohesin function. STAG1 and STAG2 have independent roles in cohesin localization and both overlapping and distinct roles in gene expression. The roles of STAG1 and STAG2 in mouse embryonic stem cells may be somewhat different than in other cell types, due to their relative expression levels. These results advance our understanding of the link between mammalian genome organization and gene expression during development and disease contexts.
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Affiliation(s)
- Nicole L Arruda
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Zachary M Carico
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Megan Justice
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ying Frances Liu
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Junjie Zhou
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Holden C Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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35
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van der Lelij P, Newman JA, Lieb S, Jude J, Katis V, Hoffmann T, Hinterndorfer M, Bader G, Kraut N, Pearson MA, Peters JM, Zuber J, Gileadi O, Petronczki M. STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers. Life Sci Alliance 2020; 3:e202000725. [PMID: 32467316 PMCID: PMC7266993 DOI: 10.26508/lsa.202000725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The cohesin subunit STAG2 has emerged as a recurrently inactivated tumor suppressor in human cancers. Using candidate approaches, recent studies have revealed a synthetic lethal interaction between STAG2 and its paralog STAG1 To systematically probe genetic vulnerabilities in the absence of STAG2, we have performed genome-wide CRISPR screens in isogenic cell lines and identified STAG1 as the most prominent and selective dependency of STAG2-deficient cells. Using an inducible degron system, we show that chemical genetic degradation of STAG1 protein results in the loss of sister chromatid cohesion and rapid cell death in STAG2-deficient cells, while sparing STAG2-wild-type cells. Biochemical assays and X-ray crystallography identify STAG1 regions that interact with the RAD21 subunit of the cohesin complex. STAG1 mutations that abrogate this interaction selectively compromise the viability of STAG2-deficient cells. Our work highlights the degradation of STAG1 and inhibition of its interaction with RAD21 as promising therapeutic strategies. These findings lay the groundwork for the development of STAG1-directed small molecules to exploit synthetic lethality in STAG2-mutated tumors.
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Grants
- Wellcome Trust
- 106169/ZZ14/Z Wellcome Trust
- European Research Council
- Human Frontier Science Program
- Wellcome
- Innovative Medicines Initiative (European Union-EU/European Federation of Pharmaceutical Industries and Associations-EFPIA)
- European Community’s Seventh Framework Programme
- Austrian Science Fund, FWF
- AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada
- Janssen, Merck KGaA Darmstadt Germany, MSD, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph A Newman
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Simone Lieb
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Vittorio Katis
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Mark A Pearson
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Mark Petronczki
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
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36
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Casa V, Moronta Gines M, Gade Gusmao E, Slotman JA, Zirkel A, Josipovic N, Oole E, van IJcken WFJ, Houtsmuller AB, Papantonis A, Wendt KS. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Genome Res 2020; 30:515-527. [PMID: 32253279 PMCID: PMC7197483 DOI: 10.1101/gr.253211.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/01/2020] [Indexed: 12/28/2022]
Abstract
Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A, and RAD21, cohesin in somatic cells contains one of two orthologous STAG subunits, STAG1 or STAG2. How these variable subunits affect the function of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either STAG1 or STAG2. Following rapid depletion of either subunit, we perform high-resolution Hi-C, gene expression, and sequential ChIP studies to show that STAG1 and STAG2 do not co-occupy individual binding sites and have distinct ways by which they affect looping and gene expression. These findings are further supported by single-molecule localizations via direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging. Since somatic and congenital mutations of the STAG subunits are associated with cancer (STAG2) and intellectual disability syndromes with congenital abnormalities (STAG1 and STAG2), we verified STAG1-/STAG2-dependencies using human neural stem cells, hence highlighting their importance in particular disease contexts.
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Affiliation(s)
- Valentina Casa
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | | | - Eduardo Gade Gusmao
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Johan A Slotman
- Optical Imaging Centre, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Natasa Josipovic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Edwin Oole
- Center for Biomics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
- Center for Biomics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | | | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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37
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Tirtei E, Cereda M, De Luna E, Quarello P, Asaftei SD, Fagioli F. Omic approaches to pediatric bone sarcomas. Pediatr Blood Cancer 2020; 67:e28072. [PMID: 31736201 DOI: 10.1002/pbc.28072] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022]
Abstract
Over the last decade, next-generation sequencing technologies have improved our ability to assess biological aspects, at genomic and transcriptomic levels, on a large scale- and have been increasingly used for the management of adult cancers. However, their efficacy and feasibility within pediatrics is still under investigation. "Omic" approaches represent an opportunity to understand the oncogenic mechanisms driving the onset and progression of bone sarcoma and improve the clinical management of young patients with bone sarcomas. This review focuses on the current genomic and transcriptomic characteristics of managing pediatric patients, affected by Ewing sarcoma and osteosarcoma.
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Affiliation(s)
- Elisa Tirtei
- Pediatric Oncology Department, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Matteo Cereda
- Cancer Genomics and Bioinformatics Unit, Italian Institute for Genomic Medicine, Torino, Italy.,Candiolo Cancer Institute, FPO, IRCCS, Turin, Italy
| | - Elvira De Luna
- Pediatric Oncology Department, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Paola Quarello
- Pediatric Oncology Department, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Sebastian Dorin Asaftei
- Pediatric Oncology Department, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Franca Fagioli
- Pediatric Oncology Department, Regina Margherita Children's Hospital, AOU Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
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38
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De Kegel B, Ryan CJ. Paralog buffering contributes to the variable essentiality of genes in cancer cell lines. PLoS Genet 2019; 15:e1008466. [PMID: 31652272 PMCID: PMC6834290 DOI: 10.1371/journal.pgen.1008466] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/06/2019] [Accepted: 10/08/2019] [Indexed: 12/26/2022] Open
Abstract
What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other's loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background. Here, using gene essentiality profiles of 558 genetically heterogeneous tumor cell lines, we analyze the contribution of paralogy to variable essentiality. We find that, compared to singleton genes, paralogs are less frequently essential and that this is more evident when considering genes with multiple paralogs or with highly sequence-similar paralogs. In addition, we find that paralogs derived from whole genome duplication exhibit more variable essentiality than those derived from small-scale duplications. We provide evidence that in 13–17% of cases the variable essentiality of paralogs can be attributed to buffering relationships between paralog pairs, as evidenced by synthetic lethality. Paralog pairs derived from whole genome duplication and pairs that function in protein complexes are significantly more likely to display such synthetic lethal relationships. Overall we find that many of the observations made using a single strain of budding yeast can be extended to understand patterns of essentiality in genetically heterogeneous cancer cell lines. Somewhat surprisingly, the majority of human genes can be mutated or deleted in individual cell lines without killing the cells. This observation raises a number of questions—which genes can be lost and why? Here we address these questions by analyzing data on which genes are essential for the growth of over 500 cancer cell lines. In general we find that paralog genes are essential in fewer cell lines than genes that are not paralogs. Paralogs are genes that have been duplicated at some point in evolutionary history, resulting in our genome having two copies of the same gene—a paralog pair. These paralog pairs are a potential source of redundancy, similar to a car having a spare tire. If this is the case, one might expect that losing one gene from a paralog pair could be tolerated by cells, due to the existence of a 'backup gene', but losing both members would cause cells to die. By analyzing the cancer cell lines we estimate this to be the case for 13–17% of paralog pairs, and that this provides an explanation for why some genes are essential in some cell lines but not others.
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Affiliation(s)
- Barbara De Kegel
- School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Colm J. Ryan
- School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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39
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Viny AD, Bowman RL, Liu Y, Lavallée VP, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, Baslan T, Ott CJ, Pe'er D, Dekker J, Koche R, Levine RL. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell 2019; 25:682-696.e8. [PMID: 31495782 DOI: 10.1016/j.stem.2019.08.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 06/19/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022]
Abstract
Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show that Stag2 deletion in hematopoietic stem and progenitor cells (HSPCs) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. Chromatin immunoprecipitation (ChIP) sequencing revealed that, although Stag2 and Stag1 bind a shared set of genomic loci, a component of Stag2 binding sites is unoccupied by Stag1, even in Stag2-deficient HSPCs. Although concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to increased self-renewal and reduced HSPC commitment to the B cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.
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Affiliation(s)
- Aaron D Viny
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert L Bowman
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Liu
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vincent-Philippe Lavallée
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shira E Eisman
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anastasia Navitski
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jane Park
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephanie Braunstein
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Besmira Alija
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Abdul Karzai
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Isabelle S Csete
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew Witkin
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Dana Pe'er
- Center for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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40
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Ehrenhöfer-Wölfer K, Puchner T, Schwarz C, Rippka J, Blaha-Ostermann S, Strobl U, Hörmann A, Bader G, Kornigg S, Zahn S, Sommergruber W, Schweifer N, Zichner T, Schlattl A, Neumüller RA, Shi J, Vakoc CR, Kögl M, Petronczki M, Kraut N, Pearson MA, Wöhrle S. SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines. Sci Rep 2019; 9:11661. [PMID: 31406271 PMCID: PMC6691015 DOI: 10.1038/s41598-019-48152-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
SMARCA4/BRG1 and SMARCA2/BRM, the two mutually exclusive catalytic subunits of the BAF complex, display a well-established synthetic lethal relationship in SMARCA4-deficient cancers. Using CRISPR-Cas9 screening, we identify SMARCA4 as a novel dependency in SMARCA2-deficient esophageal squamous cell carcinoma (ESCC) models, reciprocal to the known synthetic lethal interaction. Restoration of SMARCA2 expression alleviates the dependency on SMARCA4, while engineered loss of SMARCA2 renders ESCC models vulnerable to concomitant depletion of SMARCA4. Dependency on SMARCA4 is linked to its ATPase activity, but not to bromodomain function. We highlight the relevance of SMARCA4 as a drug target in esophageal cancer using an engineered ESCC cell model harboring a SMARCA4 allele amenable to targeted proteolysis and identify SMARCA4-dependent cell models with low or absent SMARCA2 expression from additional tumor types. These findings expand the concept of SMARCA2/SMARCA4 paralog dependency and suggest that pharmacological inhibition of SMARCA4 represents a novel therapeutic opportunity for SMARCA2-deficient cancers.
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Affiliation(s)
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | - Janine Rippka
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | - Ursula Strobl
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Stefan Kornigg
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Stephan Zahn
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | | | - Thomas Zichner
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | | | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Manfred Kögl
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Mark Petronczki
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Mark A Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria.
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41
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Romero-Pérez L, Surdez D, Brunet E, Delattre O, Grünewald TGP. STAG Mutations in Cancer. Trends Cancer 2019; 5:506-520. [PMID: 31421907 DOI: 10.1016/j.trecan.2019.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022]
Abstract
Stromal Antigen 1 and 2 (STAG1/2) are key subunits of the cohesin complex that mediate sister chromatid cohesion, DNA repair, transcriptional regulation, and genome topology. Genetic alterations comprising any of the 11 cohesin-associated genes possibly occur in up to 26% of patients included in The Cancer Genome Atlas (TCGA) studies. STAG2 shows the highest number of putative driver truncating mutations. We provide a comprehensive review of the function of STAG1/2 in human physiology and disease and an integrative analysis of available omics data on STAG alterations in a wide array of cancers, comprising 53 691 patients and 1067 cell lines. Lastly, we discuss opportunities for therapeutic intervention.
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Affiliation(s)
- Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, Munich, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisé LNCC "Genetics and Biology of Pediatric Cancers", fhna PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Erika Brunet
- Institut Imagine, INSERM UMR1163, Équipe Labellisé LNCC, Dynamics of the Genome and Immune System Lab, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisé LNCC "Genetics and Biology of Pediatric Cancers", fhna PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, Munich, Germany; Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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42
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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43
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Mintzas K, Heuser M. Emerging strategies to target the dysfunctional cohesin complex in cancer. Expert Opin Ther Targets 2019; 23:525-537. [PMID: 31020869 DOI: 10.1080/14728222.2019.1609943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Mutations in cohesin genes have been described in numerous solid cancers and hematologic malignancies; subsequent experimental evidence has linked these mutations with carcinogenesis. Areas covered: In this review, we present current information about the physiological role of the cohesin complex in normal and malignant cells and describe current therapeutic strategies that are being explored in cohesin-mutated cancers. We discuss a range of targets and strategies that should be explored to develop targeted therapies for patients with aberrant cohesin. Expert opinion: Targeting of the cohesin complex is an underexplored area of drug development. There is a high frequency of cohesin mutations in multiple cancers, hence specific targeting strategies should be explored. Cohesins play a crucial role in cellular organization; therefore, we expect a narrow therapeutic window of direct inhibitors of cohesin components. Exploiting experimental approaches that correct dysfunctional cohesins and coupling them with current therapeutic strategies can provide novel, innovative and more effective treatment regimens.
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Affiliation(s)
- Konstantinos Mintzas
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
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44
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Mondal G, Stevers M, Goode B, Ashworth A, Solomon DA. A requirement for STAG2 in replication fork progression creates a targetable synthetic lethality in cohesin-mutant cancers. Nat Commun 2019; 10:1686. [PMID: 30975996 PMCID: PMC6459917 DOI: 10.1038/s41467-019-09659-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Cohesin is a multiprotein ring that is responsible for cohesion of sister chromatids and formation of DNA loops to regulate gene expression. Genomic analyses have identified that the cohesin subunit STAG2 is frequently inactivated by mutations in cancer. However, the reason STAG2 mutations are selected during tumorigenesis and strategies for therapeutically targeting mutant cancer cells are largely unknown. Here we show that STAG2 is essential for DNA replication fork progression, whereby STAG2 inactivation in non-transformed cells leads to replication fork stalling and collapse with disruption of interaction between the cohesin ring and the replication machinery as well as failure to establish SMC3 acetylation. As a consequence, STAG2 mutation confers synthetic lethality with DNA double-strand break repair genes and increased sensitivity to select cytotoxic chemotherapeutic agents and PARP or ATR inhibitors. These studies identify a critical role for STAG2 in replication fork procession and elucidate a potential therapeutic strategy for cohesin-mutant cancers.
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Affiliation(s)
- Gourish Mondal
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Meredith Stevers
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Benjamin Goode
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, CA, 94143, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA.
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Lieb S, Blaha-Ostermann S, Kamper E, Rippka J, Schwarz C, Ehrenhöfer-Wölfer K, Schlattl A, Wernitznig A, Lipp JJ, Nagasaka K, van der Lelij P, Bader G, Koi M, Goel A, Neumüller RA, Peters JM, Kraut N, Pearson MA, Petronczki M, Wöhrle S. Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells. eLife 2019; 8:43333. [PMID: 30910006 PMCID: PMC6435321 DOI: 10.7554/elife.43333] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/14/2019] [Indexed: 12/31/2022] Open
Abstract
Targeted cancer therapy is based on exploiting selective dependencies of tumor cells. By leveraging recent functional screening data of cancer cell lines we identify Werner syndrome helicase (WRN) as a novel specific vulnerability of microsatellite instability-high (MSI-H) cancer cells. MSI, caused by defective mismatch repair (MMR), occurs frequently in colorectal, endometrial and gastric cancers. We demonstrate that WRN inactivation selectively impairs the viability of MSI-H but not microsatellite stable (MSS) colorectal and endometrial cancer cell lines. In MSI-H cells, WRN loss results in severe genome integrity defects. ATP-binding deficient variants of WRN fail to rescue the viability phenotype of WRN-depleted MSI-H cancer cells. Reconstitution and depletion studies indicate that WRN dependence is not attributable to acute loss of MMR gene function but might arise during sustained MMR-deficiency. Our study suggests that pharmacological inhibition of WRN helicase function represents an opportunity to develop a novel targeted therapy for MSI-H cancers.
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Affiliation(s)
- Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Janine Rippka
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Minoru Koi
- Division of Gastroenterology, Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan, Ann Arbor, United States
| | - Ajay Goel
- Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, United States
| | | | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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Liu Y, Xu H, Van der Jeught K, Li Y, Liu S, Zhang L, Fang Y, Zhang X, Radovich M, Schneider BP, He X, Huang C, Zhang C, Wan J, Ji G, Lu X. Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer. J Clin Invest 2018; 128:2951-2965. [PMID: 29649003 PMCID: PMC6025969 DOI: 10.1172/jci98727] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022] Open
Abstract
A synthetic lethality-based strategy has been developed to identify therapeutic targets in cancer harboring tumor-suppressor gene mutations, as exemplified by the effectiveness of poly ADP-ribose polymerase (PARP) inhibitors in BRCA1/2-mutated tumors. However, many synthetic lethal interactors are less reliable due to the fact that such genes usually do not perform fundamental or indispensable functions in the cell. Here, we developed an approach to identifying the "essential lethality" arising from these mutated/deleted essential genes, which are largely tolerated in cancer cells due to genetic redundancy. We uncovered the cohesion subunit SA1 as a putative synthetic-essential target in cancers carrying inactivating mutations of its paralog, SA2. In SA2-deficient Ewing sarcoma and bladder cancer, further depletion of SA1 profoundly and specifically suppressed cancer cell proliferation, survival, and tumorigenic potential. Mechanistically, inhibition of SA1 in the SA2-mutated cells led to premature chromatid separation, dramatic extension of mitotic duration, and consequently, lethal failure of cell division. More importantly, depletion of SA1 rendered those SA2-mutated cells more susceptible to DNA damage, especially double-strand breaks (DSBs), due to reduced functionality of DNA repair. Furthermore, inhibition of SA1 sensitized the SA2-deficient cancer cells to PARP inhibitors in vitro and in vivo, providing a potential therapeutic strategy for patients with SA2-deficient tumors.
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MESH Headings
- Animals
- Antigens, Nuclear/chemistry
- Antigens, Nuclear/genetics
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/genetics
- Cell Line, Tumor
- Chromosomal Proteins, Non-Histone/antagonists & inhibitors
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- DNA Breaks, Double-Stranded
- Female
- Gene Knockdown Techniques
- Genes, Essential
- Humans
- Mice
- Mice, Nude
- Mutation
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/pathology
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Phthalazines/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Protein Subunits/antagonists & inhibitors
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Sarcoma, Ewing/drug therapy
- Sarcoma, Ewing/genetics
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/genetics
- Xenograft Model Antitumor Assays
- Cohesins
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Affiliation(s)
- Yunhua Liu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Kevin Van der Jeught
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Yujing Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Sheng Liu
- Department of Medical and Molecular Genetics
| | - Lu Zhang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Yuanzhang Fang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Xinna Zhang
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
| | - Milan Radovich
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
- Department of Surgery, and
| | - Bryan P. Schneider
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Xiaoming He
- Department of Biomedical Engineering, Ohio State University, Columbus, Ohio, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
- Martha and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, USA
| | - Cheng Huang
- Drug Discovery Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chi Zhang
- Department of Medical and Molecular Genetics
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
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Abstract
PURPOSE OF REVIEW Disturbance of the delicate balance between self-renewal and differentiation in haematopoietic stem cells (HSCs) can lead to both leukaemia and bone marrow failure. The regulation of this balance in HSC biology has been intensely investigated in several model systems, and lately the importance of epigenetic modifications as well as the organization and architecture of chromatin has become increasingly recognized. In this review, we will focus on the role of the chromatin organizing protein complex cohesin in regulation of normal and malignant haematopoiesis. RECENT FINDINGS Several functional studies in both mouse and human systems have implicated cohesin as a critical regulator of self-renewal and differentiation in HSCs. Together with the discovery of recurrent mutations of cohesin genes in myeloid malignancies, this points towards a direct role of perturbed cohesin function in leukemogenesis. SUMMARY The work reviewed here provides new insights about the role of the cohesin complex and chromatin architecture in normal and malignant HSCs, and indicates how cohesin may be specifically targeted for therapeutic benefit in the future.
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Affiliation(s)
- Roman Galeev
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
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48
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Abstract
PURPOSE OF REVIEW Recurrent loss of function mutations within genes of the cohesin complex have been identified in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). STAG2 is the most commonly mutated cohesin member in AML as well as solid tumors. STAG2 is recurrently, mutated in Ewing's Sarcoma, bladder cancer, and glioblastoma, and is one of only ten genes known to be recurrently mutated in over four distinct tissue types of human cancer RECENT FINDINGS: The cohesin complex, a multiprotein ring, is canonically known to align and stabilize replicated chromosomes prior to cell division. Although initially thought to lead to unequal chromosomal separation in dividing cells, data in myeloid malignancies show this is not observed in cohesin mutant MDS/AML, either in large patient cohorts or mouse models. Mounting evidence supports a potential alternate mechanism whereby drivers of cell-type specific gene expression and hematopoietic development are impaired through alteration in three-dimensional nuclear organization and gene structure. SUMMARY Understanding the functional consequences of cohesin mutations in regulating lineage-specific and signal-dependent defects and in myeloid transformation will identify novel pathophysiologic mechanisms of disease and inform the development of novel therapeutic targets.
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MESH Headings
- Animals
- Antigens, Nuclear/genetics
- Antigens, Nuclear/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/metabolism
- Hematologic Neoplasms/pathology
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- Myelodysplastic Syndromes/pathology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Cohesins
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Affiliation(s)
- Aaron D Viny
- Human Oncology & Pathogenesis Program, Center for Hematologic Malignancies, and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
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49
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van der Lelij P, Lieb S, Jude J, Wutz G, Santos CP, Falkenberg K, Schlattl A, Ban J, Schwentner R, Hoffmann T, Kovar H, Real FX, Waldman T, Pearson MA, Kraut N, Peters JM, Zuber J, Petronczki M. Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts. eLife 2017; 6:e26980. [PMID: 28691904 PMCID: PMC5531830 DOI: 10.7554/elife.26980] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/03/2017] [Indexed: 11/13/2022] Open
Abstract
Recent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex, STAG2, displays a strong synthetic lethal interaction with its paralog STAG1. Mechanistically, STAG1 loss abrogates sister chromatid cohesion in STAG2 mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 support sister chromatid cohesion to redundantly ensure cell survival. STAG1 represents a vulnerability of cancer cells carrying mutations in the major emerging tumor suppressor STAG2 across different cancer contexts. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Catarina P Santos
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Katrina Falkenberg
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | | | - Jozef Ban
- Children’s Cancer Research Institute, Vienna, Austria
| | | | - Thomas Hoffmann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Heinrich Kovar
- Children’s Cancer Research Institute, Vienna, Austria
- Department for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Francisco X Real
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Department de Ciències Experimentals I de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington DC, United States
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
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