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Kundu M, Dey A, Maji PK, Mandal M. Targeting friend leukemia integration 1: A promising approach for prevention and treatment of solid tumors. Int J Biol Macromol 2025; 309:143080. [PMID: 40228766 DOI: 10.1016/j.ijbiomac.2025.143080] [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: 07/07/2024] [Revised: 04/08/2025] [Accepted: 04/09/2025] [Indexed: 04/16/2025]
Abstract
Friend leukemia integration 1 (FLI1) is an ETS transcription factor first identified in erythroleukemia. This protein contributes to various cellular functions such as cell growth and proliferation, apoptosis, angiogenesis, etc. FLI1 is also known to be involved in tumorigenesis. The role of this transcription factor as a proto-oncogene, promoting cancer progression, especially Ewing sarcoma, is well reported. Recent research has found the connection of FLI1 with other solid cancers, including breast cancer, prostate cancer, glioma, and lung cancer. The role of this protein in solid cancers is also controversial. FLI1 is found to promote and suppress cancer growth and progression, particularly in Ewing sarcoma and breast cancer. This review article aims to provide a detailed perception of the FLI1-associated mechanisms in various solid cancers for preventive and therapeutic implications. The result of bioinformatic analysis using the cBioportal database (https://www.cbioportal.org/) is also presented in this article to understand the effect of this protein on solid cancers. Moreover, the current status of FLI1 targeting agents for preventing and treating solid cancers has been focused. Several studies established the efficacy of FLI1 inhibitors in solid tumor therapy. A few reports are also available on the effect of FLI1 agonists on solid tumors. This article discussed different FLI1 targeting agents to provide insight into the FLI1 targeting mechanisms required for discovering more potent FLI1 targeting agents and better therapeutic outcomes.
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Affiliation(s)
- Moumita Kundu
- Department of Pharmaceutical Technology, Brainware University, Barasat, India; Center for Multidisciplinary Research & Innovations, Brainware University, Barasat, India.
| | - Ankita Dey
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pallab Kumar Maji
- Department of Pharmaceutical Technology, Brainware University, Barasat, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India.
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2
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Xu JJ, Scoca V, Chen Y, Zhan YA, Fisher A, Udoh EO, Fernando S, Alija B, Pantazi J, Sudunagunta V, Stewart E, Galang AMD, Williams M, Bhagat G, Gebhard C, Visconte V, Ondrejka S, Delwel R, Hu M, Koche R, Viny AD. Enhanced FLI1 accessibility mediates STAG2-mutant leukemogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.01.646632. [PMID: 40236115 PMCID: PMC11996548 DOI: 10.1101/2025.04.01.646632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Transcription factors (TFs) influencing cell fate can be dysregulated in cancer. FLI1 is crucial for hematopoietic stem/progenitor cell (HSPC) function, with STAG2 regulating FLI1 target accessibility. STAG2 depletion enhances HSPC self-renewal, but its role in leukemic transformation is unclear. We uncovered that STAG2 loss maintains FLI1 target accessibility in murine HSPCs and enhances FLI1 binding in NPM1c leukemia. In our Stag2/Npm1c/+ murine model, myeloid-biased HSPCs with increased FLI1 accessibility are reservoirs for transformation, leading to a fully penetrant leukemia. STAG2 deleted NPM1c cell lines exhibit increased chromatin accessibility and chromatin-looping of key stem and leukemia genes including FLI1-target genes CD34 and MEN1. Similarly, enrichment for a CD34+ immunophenotype was observed in co-mutant leukemia patients. STAG2 deficient cells show increased chromatin-bound MENIN and increased sensitivity to MENIN inhibition. Our findings demonstrate that altered chromatin architecture can co-opt oncogenic TF signaling, such as FLI1, as a hallmark of leukemogenesis. Key Findings Loss of STAG2 results in aberrant increased accessibility at FLI1 targets in mouse and human hematopoietic stem and progenitor cellsIncreased accessibility results in an increased fraction of chromatin-bound FLI1, which overlap with NPM1c targets in STAG2 NPM1c AML cellsStag2 Npm1c co-mutation leads to dysplastic murine AML phenotype arising from myeloid biased progenitors that exhibit increased Fli1 target accessibilityIn addition to higher chromatin-bound FLI1, co-mutant cells have higher chromatin-bound MENIN, including at the HOXA cluster, rendering cells highly sensitive to MENIN inhibition. Statement of Significance Here, we identify enhanced FLI1 chromatin accessibility as a driver of stemness and leukemic transformation in STAG2 mutant leukemia. Through comprehensive in vivo and in vitro modeling, we demonstrate that altered chromatin architecture can co-opt oncogenic TF activity, like FLI1, to drive divergent leukemia development and therapeutic response.
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3
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Amodeo ME, Eyler CE, Johnstone SE. Rewiring cancer: 3D genome determinants of cancer hallmarks. Curr Opin Genet Dev 2025; 91:102307. [PMID: 39862605 PMCID: PMC11867856 DOI: 10.1016/j.gde.2024.102307] [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: 09/09/2024] [Revised: 12/30/2024] [Accepted: 12/31/2024] [Indexed: 01/27/2025]
Abstract
In modern cancer biology, Hanahan and Weinberg's classic depiction of the Hallmarks of Cancer serves as a heuristic for understanding malignant phenotypes [1]. Genetic determinants of these phenotypes promote cancer induction and progression, and these mutations drive current approaches to understanding and treating cancer. Meanwhile, for over a century, pathologists have noted that profound alterations of nuclear structure accompany transformation, integrating these changes into diagnostic classifications (Figure 1). Nevertheless, the relationship of nuclear organization to malignant phenotypes has lagged. Recent advances yield profound insight into the 3D genome's relationship with cancer phenotypes, suggesting that spatial genome organization influences many, if not all, of these malignant features. Here, we highlight recent discoveries elucidating connections between 3D genome organization and cancer phenotypes.
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Affiliation(s)
- Maria E Amodeo
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Christine E Eyler
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, USA.
| | - Sarah E Johnstone
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA.
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4
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Chicón‐Bosch M, Sánchez‐Serra S, Rosàs‐Lapeña M, Costa‐Fraga N, Besalú‐Velázquez J, Illa‐Bernadí J, Mateo‐Lozano S, Cidre‐Aranaz F, Grünewald TG, Díaz‐Lagares Á, Lopez‐Alemany R, Tirado ÒM. Multi-omics profiling reveals key factors involved in Ewing sarcoma metastasis. Mol Oncol 2025; 19:1002-1028. [PMID: 39757762 PMCID: PMC11977646 DOI: 10.1002/1878-0261.13788] [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: 04/23/2024] [Revised: 08/28/2024] [Accepted: 11/14/2024] [Indexed: 01/07/2025] Open
Abstract
Ewing sarcoma (EWS) is the second most common bone tumor affecting children and young adults, with dismal outcomes for patients with metastasis at diagnosis. Mechanisms leading to metastasis remain poorly understood. To deepen our knowledge on EWS progression, we have profiled tumors and metastases from a spontaneous metastasis mouse model using a multi-omics approach. Combining transcriptomics, proteomics, and methylomics analyses, we identified signaling cascades and candidate genes enriched in metastases that could be modulating aggressiveness in EWS. Phenotypical validation of two of these candidates, cyclic AMP-responsive element-binding protein 1 (CREB1) and lipoxygenase homology domain-containing protein 1 (LOXHD1), showed an association with migration and clonogenic abilities. Moreover, previously described CREB1 downstream targets were present amongst the metastatic-enriched results. Combining the different omics datasets, we identified FYVE, RhoGEF, and PH domain-containing protein 4 (FGD4) as a CREB1 target interconnecting the different EWS biological layers (RNA, protein and methylation status) and whose high expression is associated with worse clinical outcome. Further studies will provide insight into EWS metastasis mechanisms and ultimately improve survival rates for EWS patients.
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Affiliation(s)
- Mariona Chicón‐Bosch
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Sara Sánchez‐Serra
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
- Universitat de Barcelona (UB)BarcelonaSpain
| | - Marta Rosàs‐Lapeña
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Nicolás Costa‐Fraga
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (ONCOMET), Health Research Institute of Santiago (IDIS)University Clinical Hospital of Santiago (CHUS/SERGAS)Santiago de CompostelaSpain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry SchoolUniversidade de Santiago de Compostela (USC)Spain
- Universidad de Santiago de Compostela (USC)Spain
- Department of Clinical AnalysisUniversity Hospital Complex of Santiago de Compostela (CHUS)Spain
| | - Judit Besalú‐Velázquez
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Janet Illa‐Bernadí
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Silvia Mateo‐Lozano
- Developmental Tumor Biology LaboratoryInstitut de Recerca Sant Joan de Déu, Hospital Sant Joan de DéuBarcelonaSpain
- Pediatric Cancer Center BarcelonaHospital Sant Joan de DéuBarcelonaSpain
| | - Florencia Cidre‐Aranaz
- Division of Translational Paediatric Sarcoma ResearchGerman Cancer Research Center (DKFZ), German Cancer Consortium (DKTK)HeidelbergGermany
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- National Center for Tumor Diseases (NCT)NCT Heidelberg, a partnership between DKFZ and Heidelberg University HospitalGermany
| | - Thomas G.P. Grünewald
- Division of Translational Paediatric Sarcoma ResearchGerman Cancer Research Center (DKFZ), German Cancer Consortium (DKTK)HeidelbergGermany
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- National Center for Tumor Diseases (NCT)NCT Heidelberg, a partnership between DKFZ and Heidelberg University HospitalGermany
- Institute of PathologyHeidelberg University HospitalHeidelbergGermany
| | - Ángel Díaz‐Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (ONCOMET), Health Research Institute of Santiago (IDIS)University Clinical Hospital of Santiago (CHUS/SERGAS)Santiago de CompostelaSpain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry SchoolUniversidade de Santiago de Compostela (USC)Spain
- Universidad de Santiago de Compostela (USC)Spain
- Department of Clinical AnalysisUniversity Hospital Complex of Santiago de Compostela (CHUS)Spain
- CIBERONCCarlos III Institute of Health (ISCIII)MadridSpain
| | - Roser Lopez‐Alemany
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
| | - Òscar M. Tirado
- Sarcoma Research GroupInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL), Oncobell, L'Hospitalet de LlobregatBarcelonaSpain
- CIBERONCCarlos III Institute of Health (ISCIII)MadridSpain
- Institut Català d'Oncologia (ICO)L'Hospitalet de LlobregatBarcelonaSpain
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5
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Athans SR, Withers H, Stablewski A, Gurova K, Ohm J, Woloszynska A. STAG2 expression imparts distinct therapeutic vulnerabilities in muscle-invasive bladder cancer cells. Oncogenesis 2025; 14:4. [PMID: 40025053 PMCID: PMC11873148 DOI: 10.1038/s41389-025-00548-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 01/14/2025] [Accepted: 02/14/2025] [Indexed: 03/04/2025] Open
Abstract
Expression of stromal antigen 2 (STAG2), a member of the cohesin complex, is associated with aggressive tumor characteristics and worse clinical outcomes in muscle invasive bladder cancer (MIBC) patients. The mechanism by which STAG2 acts in a pro-oncogenic manner in bladder cancer remains unknown. Due to this elusive role of STAG2, targetable vulnerabilities based on STAG2 expression have not yet been identified. In the current study, we sought to uncover therapeutic vulnerabilities of muscle invasive bladder cancer cells based on the expression of STAG2. Using CRISPR-Cas9, we generated isogenic STAG2 wild-type (WT) and knock out (KO) cell lines and treated each cell line with a panel of 312 anti-cancer compounds. We identified 100 total drug hits and found that STAG2 KO sensitized cells to treatment with PLK1 inhibitor rigosertib, whereas STAG2 KO protected cells from treatment with MEK inhibitor TAK-733 and PI3K inhibitor PI-103. After querying drug sensitivity data of over 4500 drugs in 24 bladder cancer cell lines from the DepMap database, we found that cells with less STAG2 mRNA expression are more sensitive to ATR and CHK inhibition. In dose-response studies, STAG2 KO cells are more sensitive to the ATR inhibitor berzosertib, whereas STAG2 WT cells are more sensitive to PI3K inhibitor PI-103. These results, in combination with RNA-seq analysis of STAG2-regulated genes, suggest a novel role of STAG2 in regulating PI3K signaling in bladder cancer cells. Finally, synergy experiments revealed that berzosertib exhibits significant synergistic cytotoxicity in combination with cisplatin against MIBC cells. Altogether, our study presents evidence that berzosertib, PI-103, and the combination of berzosertib with cisplatin may be novel opportunities to investigate as precision medicine approaches for MIBC patients based on STAG2 tumor expression.
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Affiliation(s)
- Sarah R Athans
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Henry Withers
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Aimee Stablewski
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Joyce Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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6
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Powell AM, Watson L, Luzietti L, Prekovic S, Young LS, Varešlija D. The epigenetic landscape of brain metastasis. Oncogene 2025:10.1038/s41388-025-03315-1. [PMID: 40016470 DOI: 10.1038/s41388-025-03315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 01/16/2025] [Accepted: 02/17/2025] [Indexed: 03/01/2025]
Abstract
Brain metastasis represents a significant challenge in oncology, driven by complex molecular and epigenetic mechanisms that distinguish it from primary tumors. While recent research has focused on identifying genomic mutation drivers with potential clinical utility, these strategies have not pinpointed specific genetic mutations responsible for site-specific metastasis to the brain. It is now clear that successful brain colonization by metastatic cancer cells requires intricate interactions with the brain tumor ecosystem and the acquisition of specialized molecular traits that facilitate their adaptation to this highly selective environment. This is best exemplified by widespread transcriptional adaptation during brain metastasis, resulting in aberrant gene programs that promote extravasation, seeding, and colonization of the brain. Increasing evidence suggests that epigenetic mechanisms play a significant role in shaping these pro-brain metastasis traits. This review explores dysregulated chromatin patterns driven by chromatin remodeling, histone modifications, DNA/RNA methylation, and other epigenetic regulators that underpin brain metastatic seeding, initiation, and outgrowth. We provide novel insights into how these epigenetic modifications arise within both the brain metastatic tumor and the surrounding brain metastatic tumor ecosystem. Finally, we discuss how the inherent plasticity and reversibility of the epigenomic landscape in brain metastases may offer new therapeutic opportunities.
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Affiliation(s)
- Aoibhín M Powell
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Louise Watson
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Lara Luzietti
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Stefan Prekovic
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonie S Young
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland.
| | - Damir Varešlija
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland.
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7
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Selivanovskiy AV, Molodova MN, Khrameeva EE, Ulianov SV, Razin SV. Liquid condensates: a new barrier to loop extrusion? Cell Mol Life Sci 2025; 82:80. [PMID: 39976773 PMCID: PMC11842697 DOI: 10.1007/s00018-024-05559-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 12/04/2024] [Accepted: 12/20/2024] [Indexed: 02/23/2025]
Abstract
Liquid-liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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Affiliation(s)
- Arseniy V Selivanovskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Maria N Molodova
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia.
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8
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Wang C, Leong MM, Ding W, Narita Y, Liu X, Wang H, Yiu SPT, Lee J, Zhao KRS, Cui A, Gewurz B, Hammerschmidt W, Teng M, Zhao B. Viral oncogene EBNALP regulates YY1 DNA binding and alters host 3D genome organization. EMBO Rep 2025; 26:810-835. [PMID: 39747661 PMCID: PMC11811279 DOI: 10.1038/s44319-024-00357-6] [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: 06/12/2024] [Revised: 12/04/2024] [Accepted: 12/13/2024] [Indexed: 01/04/2025] Open
Abstract
The Epstein-Barr virus (EBV) nuclear antigen leader protein (EBNALP) is essential for the immortalization of naive B lymphocytes (NBLs). However, the mechanisms remain elusive. To understand EBNALP's role in B-cell transformation, we compare NBLs infected with wild-type EBV and an EBNALP-null mutant EBV using multi-omics techniques. EBNALP inactivation alters enhancer-promoter interactions, resulting in decreased CCND2 and increased CASP1 and BCL2L11 expression. Mechanistically, EBNALP interacts with and colocalizes with the looping factor YY1. Depletion of EBNALP reduces YY1 DNA-binding and enhancer-promoter interactions, similar to effects observed with YY1 depletion. Furthermore, EBNALP colocalizes with DPF2, a protein that binds to H3K14ac and H4K16ac. CRISPR depletion of DPF2 reduces both EBNALP and YY1 DNA binding, suggesting that the DPF2/EBNALP complex may tether YY1 to DNA to increase enhancer-promoter interactions. EBNALP inactivation also increases enhancer-promoter interactions at the CASP1 and BCL2L11 loci, along with elevated DPF2 and YY1 binding and DNA accessibility. Our data suggest that EBNALP regulates YY1 to rewire the host genome, which might facilitate naive B-cell transformation.
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Affiliation(s)
- Chong Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Merrin Manlong Leong
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weiyue Ding
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yohei Narita
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiang Liu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Hongbo Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefanie P T Yiu
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica Lee
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katelyn R S Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy Cui
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research, Munich, Germany
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
| | - Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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9
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Scott JS, Al Ayadi L, Epeslidou E, van Scheppingen RH, Mukha A, Kaaij LJT, Lutz C, Prekovic S. Emerging roles of cohesin-STAG2 in cancer. Oncogene 2025; 44:277-287. [PMID: 39613934 DOI: 10.1038/s41388-024-03221-y] [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: 09/15/2024] [Revised: 10/30/2024] [Accepted: 11/04/2024] [Indexed: 12/01/2024]
Abstract
Cohesin, a crucial regulator of genome organisation, plays a fundamental role in maintaining chromatin architecture as well as gene expression. Among its subunits, STAG2 stands out because of its frequent deleterious mutations in various cancer types, such as bladder cancer and melanoma. Loss of STAG2 function leads to significant alterations in chromatin structure, disrupts transcriptional regulation, and impairs DNA repair pathways. In this review, we explore the molecular mechanisms underlying cohesin-STAG2 function, highlighting its roles in healthy cells and its contributions to cancer biology, showing how STAG2 dysfunction promotes tumourigenesis and presents opportunities for targeted therapeutic interventions.
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Affiliation(s)
- Julia S Scott
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Loubna Al Ayadi
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Anna Mukha
- Department of Medical BioSciences, RadboudUMC, Nijmegen, The Netherlands
| | - Lucas J T Kaaij
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Stefan Prekovic
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands.
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10
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Jia K, Cao L, Yu Y, Jing D, Wu W, Van Tine BA, Shao Z. Signaling pathways and targeted therapies in Ewing sarcoma. Pharmacol Ther 2025; 266:108765. [PMID: 39622389 DOI: 10.1016/j.pharmthera.2024.108765] [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: 06/04/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/08/2024]
Abstract
Ewing sarcoma, the second most prevalent malignant bone tumor with potential occurrence in soft tissues, exhibits a high level of aggressiveness, primarily afflicting children and adolescents. It is characterized by fusion proteins arising from chromosomal translocations. The fusion proteins induce aberrations in multiple signaling pathways and molecules, constituting a key event in oncogenic transformation. While diagnostic and therapeutic modalities have advanced in recent decades and multimodal treatments, including surgery, radiotherapy, and chemotherapy, have significantly improved survival of patients with localized tumors, patients with metastatic tumors continue to face poor prognoses. There persists a pressing need for novel alternative treatments, yet the translation of our understanding of Ewing sarcoma pathogenesis into improved clinical outcomes remains a critical challenge. Here, we provide a comprehensive review of Ewing sarcoma, including fusion proteins, various signaling pathways, pivotal pathogenetic molecules implicated in its development, and associated targeted therapies and immunotherapies. We summarize past endeavors, current advancements, and deliberate on limitations and future research directions. It is envisaged that this review will furnish novel insights into prospective treatment avenues for Ewing sarcoma.
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Affiliation(s)
- Ke Jia
- Department of Orthopaedics, Union hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Li Cao
- Department of Orthopaedics, Union hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Washington University School of Medicine, St Louis, MO, USA.
| | - Yihan Yu
- Department of Orthopaedics, Union hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Doudou Jing
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, China.
| | - Wei Wu
- Department of Orthopaedics, Union hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | | | - Zengwu Shao
- Department of Orthopaedics, Union hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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11
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Gillani R, Shulman DS, DelRocco NJ, Klega K, Han R, Krailo MD, Slack JC, Tanhaemami M, Ward A, Bainer V, Ricker C, Sparks J, Bailey KM, Reed DR, DuBois SG, Leavey P, Mascarenhas L, Grohar PJ, Church AJ, Crompton BD, Janeway KA. Molecular characterization informs prognosis in patients with localized Ewing sarcoma: A report from the Children's Oncology Group. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.20.25320840. [PMID: 39974064 PMCID: PMC11838998 DOI: 10.1101/2025.01.20.25320840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
PURPOSE Identification of discrete sub-groups associated with treatment response and resistance in localized Ewing sarcoma (EWS) remains a challenge. The primary objective of the Children's Oncology Group biology study AEWS18B1-Q was to perform molecular characterization of a large cohort of patients with localized Ewing sarcoma treated on prospective trials with modern standard of care therapy. METHODS We analyzed clinical and molecular features from patients with localized EWS enrolled on AEWS0031, AEWS1031, or INT-0154 frontline trials. All patients had available FFPE tissue, frozen tissue, or whole-genome amplified material. Sequencing was performed for identification of canonical fusions, recurrent copy number alterations (CNAs), and alterations in TP53 and STAG2. Where available, tissue was analyzed for loss of STAG2 protein expression. Molecular features were evaluated for their association with cumulative incidence of relapse in univariate and multivariable analyses. RESULTS Three hundred and fifty-one cases had sufficient tissue, which in most cases was extracted from two FFPE slides. EWS canonical fusions were identified in 282 cases (80.3%). Pathogenic mutations in TP53 and STAG2 were identified in 5.1% and 7.6% of cases, respectively and 63.1% of cases were found to have recurrent CNAs. In univariate analysis, there was an increased cumulative incidence of relapse in patients with TP53 mutation (5-year cumulative incidence of relapse 43%, CI [17%, 67%] vs. 22%, CI [17%, 27%]; Gray's test P = 0.039), STAG2 mutation (53%, CI [29%, 73%] vs. 21%, CI [16%, 26%]; P < 0.001), and recurrent CNAs (30%, CI [22%, 37%] vs. 16%, CI [9%, 24%]; P = 0.005). In a multivariable analysis, STAG2 mutation was the only molecular biomarker that remained prognostic. CONCLUSION This is a prospective validation of the molecular prognostic features of localized EWS receiving standard of care therapy on therapeutic clinical trials. Building on prior work, patients with STAG2 mutations were at high risk of relapse.
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Affiliation(s)
- Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - David S. Shulman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Natalie J. DelRocco
- Children’s Oncology Group, Monrovia, CA 91016
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032
| | - Kelly Klega
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Ruxu Han
- Children’s Oncology Group, Monrovia, CA 91016
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032
| | - Mark D. Krailo
- Children’s Oncology Group, Monrovia, CA 91016
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032
| | - Jonathan C. Slack
- Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195
| | - Mohammad Tanhaemami
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Abigail Ward
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Victoria Bainer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Cora Ricker
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Josee Sparks
- Biopathology Center, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205
| | - Kelly M. Bailey
- University of Pittsburgh School of Medicine, 4401 Penn Avenue, Pittsburgh, PA 15224
| | - Damon R. Reed
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Steven G. DuBois
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Patrick Leavey
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Children’s Medical Center, Dallas, TX 75235
| | | | - Patrick J. Grohar
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Michigan Medical School, CS Mott Children’s Hospital, Ann Arbor, MI 48109
| | - Alanna J. Church
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Katherine A. Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
- Boston Children’s Hospital, Boston, MA 02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142
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12
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He F, Xu J, Zeng F, Wang B, Yang Y, Xu J, Sun X, Ren T, Tang X. Integrative analysis of Ewing's sarcoma reveals that the MIF-CD74 axis is a target for immunotherapy. Cell Commun Signal 2025; 23:23. [PMID: 39800691 PMCID: PMC11727170 DOI: 10.1186/s12964-024-02020-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Accepted: 12/28/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Ewing's sarcoma (EwS), a common pediatric bone cancer, is associated with poor survival due to a lack of therapeutic targets for immunotherapy or targeted therapy. Therefore, more effective treatment options are urgently needed. METHODS Since novel immunotherapies may address this need, we performed an integrative analysis involving single-cell RNA sequencing, cell function experiments, and humanized models to dissect the immunoregulatory interactions in EwS and identify strategies for optimizing immunotherapeutic efficacy. RESULTS EwS is infiltrated by immunosuppressive myeloid populations, T and B lymphocytes, and natural killer cells. We found that SLC40A1 and C1QA macrophages were associated with a poor prognosis, whereas CD8+ T-cell infiltration was associated with a good prognosis. A comparative analysis of paired samples revealed that in tumors with a good chemotherapeutic response, macrophages presented increased antigen presentation and reduced release of protumor cytokines, whereas CD8+ T cells presented increased cytotoxicity and reduced exhaustion. An interaction analysis revealed a vast immunoregulatory network and identified MIF-CD74 as a crucial immunoregulatory target that can simultaneously promote M2 polarization of macrophages and inhibit CD8+ T-cell infiltration. Importantly, MIF blockade effectively reshaped the tumor immune microenvironment, turning cold tumors hot and inhibiting tumor growth. CONCLUSIONS Our integrative analysis revealed that the MIF/CD74 axis is a promising target for the treatment of Ewing sarcoma and provides a rationale for this novel immunotherapy.
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Affiliation(s)
- Fangzhou He
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China
| | - Jiuhui Xu
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China
| | - Fanwei Zeng
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China
| | - Boyang Wang
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China
| | - Yi Yang
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Jie Xu
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Xin Sun
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Tingting Ren
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China.
| | - Xiaodong Tang
- Department of Musculoskeletal Tumor, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
- Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, China.
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13
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Ashkin EL, Tang YJ, Xu H, Hung KL, Belk JA, Cai H, Lopez SS, Dolcen DN, Hebert JD, Li R, Ruiz PA, Keal T, Andrejka L, Chang HY, Petrov DA, Dixon JR, Xu Z, Winslow MM. A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis. J Exp Med 2025; 222:e20240765. [PMID: 39652422 PMCID: PMC11627241 DOI: 10.1084/jem.20240765] [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: 04/30/2024] [Revised: 09/16/2024] [Accepted: 10/30/2024] [Indexed: 12/12/2024] Open
Abstract
The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.
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Affiliation(s)
- Emily L. Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuning J. Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Haiqing Xu
- Department of Biology, Stanford University, Stanford, CA, USA
| | - King L. Hung
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A. Belk
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven S. Lopez
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deniz Nesli Dolcen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jess D. Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Paloma A. Ruiz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tula Keal
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A. Petrov
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jesse R. Dixon
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Zhichao Xu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Monte M. Winslow
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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14
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Sudunagunta VS, Viny AD. Untangling the loops of STAG2 mutations in myelodysplastic syndrome. Leuk Lymphoma 2025; 66:6-15. [PMID: 39264305 DOI: 10.1080/10428194.2024.2400210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/11/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024]
Abstract
Myelodysplastic syndrome (MDS) is a heterogeneous myeloid neoplasm that is hallmarked by the acquisition of genetic events that disrupt normal trilineage hematopoiesis and results in bone marrow dysfunction. Somatic genes involving transcriptional regulation, signal transduction, DNA methylation, and chromatin modification are often implicated in disease pathogenesis. The cohesin complex, composed of SMC1, SMC3, RAD21, and either STAG1 or STAG2, has been identified as a recurrent mutational target with STAG2 mutations accounting for more than half of all cohesin mutations in myeloid malignancies. In the last decade, STAG2 cohesin biology has been of great interest given its role in transcriptional activation, association with poorer prognosis, and lack of mutation-specific therapies. This review discusses the clinical landscape of cohesin mutant myeloid malignancies, particularly STAG2 mutant MDS, including molecular features of STAG2 mutations, clinical implications of cohesin mutant neoplasms, and the current understanding of the pathophysiological function of STAG2 mutations in MDS.
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Affiliation(s)
- Varun S Sudunagunta
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Department of Genetics and Development, New York, NY, USA
| | - Aaron D Viny
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Department of Genetics and Development, New York, NY, USA
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15
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Pan M, Zhou M, Xie L, Bui N, Ganjoo K. Recent advances in sarcoma therapy: new agents, strategies and predictive biomarkers. J Hematol Oncol 2024; 17:124. [PMID: 39696530 PMCID: PMC11656826 DOI: 10.1186/s13045-024-01650-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 12/05/2024] [Indexed: 12/20/2024] Open
Abstract
Soft tissue and bone sarcomas are a heterogenous group of uncommon mesenchymal tumors with high unmet needs for novel therapeutic and diagnostic strategies. Despite many challenges that persist, innovative therapeutics are emerging. Here we provide a review of the studies presented at the 2024 American Society of Clinical Oncology annual meeting that were focused on sarcoma. There were many outstanding studies that were reported at the meeting. We begin by discussing the clinical studies on soft tissue sarcoma (STS) that included multiple histology subtypes, followed by highlighting developments in cellular therapy, before delving into specific STS histologic subtypes followed by a section covering the studies that were focused on predictive biomarkers. We conclude by discussing the studies in bone sarcomas. Some of the studies discussed here are likely to be practice changing. Some of the early-phase clinical trials have shown encouraging results.
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Affiliation(s)
- Minggui Pan
- Department of Medicine Division of Oncology, Sarcoma Program, Stanford University School of Medicine, Stanford, Palo Alto, CA, 94305, USA.
| | - Maggie Zhou
- Department of Medicine Division of Oncology, Sarcoma Program, Stanford University School of Medicine, Stanford, Palo Alto, CA, 94305, USA
| | - Lu Xie
- Musculoskeletal Tumor Center, Peking University People's Hospital, Beijing, China
| | - Nam Bui
- Department of Medicine Division of Oncology, Sarcoma Program, Stanford University School of Medicine, Stanford, Palo Alto, CA, 94305, USA
| | - Kristen Ganjoo
- Department of Medicine Division of Oncology, Sarcoma Program, Stanford University School of Medicine, Stanford, Palo Alto, CA, 94305, USA
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16
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Giménez-Llorente D, Cuadrado A, Andreu MJ, Sanclemente-Alamán I, Solé-Ferran M, Rodríguez-Corsino M, Losada A. STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1. EMBO Rep 2024; 25:5537-5560. [PMID: 39487368 PMCID: PMC11624272 DOI: 10.1038/s44319-024-00303-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 09/20/2024] [Accepted: 10/10/2024] [Indexed: 11/04/2024] Open
Abstract
Cohesin complexes carrying STAG1 or STAG2 organize the genome into chromatin loops. STAG2 loss-of-function mutations promote metastasis in Ewing sarcoma, a pediatric cancer driven by the fusion transcription factor EWS::FLI1. We integrated transcriptomic data from patients and cellular models to identify a STAG2-dependent gene signature associated with worse prognosis. Subsequent genomic profiling and high-resolution chromatin interaction data from Capture Hi-C indicated that cohesin-STAG2 facilitates communication between EWS::FLI1-bound long GGAA repeats, presumably acting as neoenhancers, and their target promoters. Changes in CTCF-dependent chromatin contacts involving signature genes, unrelated to EWS::FLI1 binding, were also identified. STAG1 is unable to compensate for STAG2 loss and chromatin-bound cohesin is severely decreased, while levels of the processivity factor NIPBL remain unchanged, likely affecting DNA looping dynamics. These results illuminate how STAG2 loss modifies the chromatin interactome of Ewing sarcoma cells and provide a list of potential biomarkers and therapeutic targets.
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MESH Headings
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Humans
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Proto-Oncogene Protein c-fli-1/metabolism
- Proto-Oncogene Protein c-fli-1/genetics
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Promoter Regions, Genetic
- Enhancer Elements, Genetic
- Oncogene Proteins, Fusion/metabolism
- Oncogene Proteins, Fusion/genetics
- Gene Expression Regulation, Neoplastic
- Chromatin/metabolism
- Chromatin/genetics
- Cell Line, Tumor
- Cohesins
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/genetics
- Protein Binding
- Bone Neoplasms/genetics
- Bone Neoplasms/metabolism
- Bone Neoplasms/pathology
- Nuclear Proteins
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Affiliation(s)
- Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - María José Andreu
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Inmaculada Sanclemente-Alamán
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Maria Solé-Ferran
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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17
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Ryzhkova A, Maltseva E, Battulin N, Kabirova E. Loop Extrusion Machinery Impairments in Models and Disease. Cells 2024; 13:1896. [PMID: 39594644 PMCID: PMC11592926 DOI: 10.3390/cells13221896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 11/15/2024] [Accepted: 11/15/2024] [Indexed: 11/28/2024] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes play a crucial role in organizing the three-dimensional structure of chromatin, facilitating key processes such as gene regulation, DNA repair, and chromosome segregation. This review explores the molecular mechanisms and biological significance of SMC-mediated loop extrusion complexes, including cohesin, condensins, and SMC5/6, focusing on their structure, their dynamic function during the cell cycle, and their impact on chromatin architecture. We discuss the implications of impairments in loop extrusion machinery as observed in experimental models and human diseases. Mutations affecting these complexes are linked to various developmental disorders and cancer, highlighting their importance in genome stability and transcriptional regulation. Advances in model systems and genomic techniques have provided deeper insights into the pathological roles of SMC complex dysfunction, offering potential therapeutic avenues for associated diseases.
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Affiliation(s)
- Anastasiya Ryzhkova
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.R.); (N.B.)
| | - Ekaterina Maltseva
- Department of Genetics and Genetic Technologies, Sirius University of Science and Technology, 354340 Sirius, Russia;
| | - Nariman Battulin
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.R.); (N.B.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evelyn Kabirova
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.R.); (N.B.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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18
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Meyers PA, Federman N, Daw N, Anderson PM, Davis LE, Kim A, Macy ME, Pietrofeso A, Ratan R, Riedel RF, Trucco M, Breitmeyer JB, Toretsky JA, Ludwig JA. Open-Label, Multicenter, Phase I/II, First-in-Human Trial of TK216: A First-Generation EWS::FLI1 Fusion Protein Antagonist in Ewing Sarcoma. J Clin Oncol 2024; 42:3725-3734. [PMID: 38954782 PMCID: PMC11521759 DOI: 10.1200/jco.24.00020] [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: 01/03/2024] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 07/04/2024] Open
Abstract
PURPOSE Ewing Sarcoma (ES), a rare cancer with a pathognomonic translocation resulting in the Ewing sarcoma gene (EWS)::FLI1 oncoprotein, has a poor prognosis in the relapsed/refractory (R/R) setting. Tokalas (TK)216 was designed to bind EWS::FLI1 proteins directly, disrupt protein-protein interactions, and inhibit transcription factor function. TK216 plus vincristine showed synergistic activity in preclinical tumor models. To our knowledge, we report the results of a first-in-class, first-in-human phase I/II trial of TK216 in R/R ES. PATIENTS AND METHODS TK216 was administered intravenously as a continuous infusion to patients with R/R ES in 11 cohorts. The dosing duration of 7 days was later extended to 10, 14, and 28 days. Vincristine could be added on day 1 after cycle 2, per investigators' choice. The trial used a 3 + 3 design with an expansion cohort at the recommended phase II dose (RP2D). RESULTS A total of 85 patients with a median age of 27 years (range, 11-77) were enrolled. The maximum tolerated dose for the 14-day infusion of TK216, 200 mg/m2 once daily, was determined in cohort 9 and selected as the RP2D. The median previous number of systemic therapies regimens was three (range, 1-10). The most frequent-related adverse events in patients treated at the RP2D included neutropenia (44.7%), anemia (29.4%), leukopenia (29.4%), febrile neutropenia (15.3%), thrombocytopenia (11.8%), and infections (17.6%). In cohorts 9 and 10, two patients had a complete response, one had a partial response, and 14 had stable disease; the 6-month progression-free survival was 11.9%. There were no responses among the eight patients in cohort 11. CONCLUSION TK216 administered as 14-day continuous infusion with or without vincristine was well tolerated and showed limited activity at the RP2D in R/R ES.
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Affiliation(s)
- Paul A Meyers
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Noah Federman
- University of California Los Angeles, Los Angeles, CA
| | - Najat Daw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lara E Davis
- Oregon Health and Science University, Portland, OR
| | - AeRang Kim
- Children's National Hospital, Washington, DC
| | - Margaret E Macy
- University of Colorado School of Medicine and Children's Hospital Colorado, Denver, CO
| | | | - Ravin Ratan
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Joseph A Ludwig
- The University of Texas MD Anderson Cancer Center, Houston, TX
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19
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Boucher A, Murray J, Rao S. Cohesin mutations in acute myeloid leukemia. Leukemia 2024; 38:2318-2328. [PMID: 39251741 DOI: 10.1038/s41375-024-02406-4] [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: 07/12/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/11/2024]
Abstract
The cohesin complex, encoded by SMC3, SMC1A, RAD21, and STAG2, is a critical regulator of DNA-looping and gene expression. Over a decade has passed since recurrent mutations affecting cohesin subunits were first identified in myeloid malignancies such as Acute Myeloid Leukemia (AML). Since that time there has been tremendous progress in our understanding of chromatin structure and cohesin biology, but critical questions remain because of the multiple critical functions the cohesin complex is responsible for. Recent findings have been particularly noteworthy with the identification of crosstalk between DNA-looping and chromatin domains, a deeper understanding of how cohesin establishes sister chromatid cohesion, a renewed interest in cohesin's role for DNA damage response, and work demonstrating cohesin's importance for Polycomb repression. Despite these exciting findings, the role of cohesin in normal hematopoiesis, and the precise mechanisms by which cohesin mutations promote cancer, remain poorly understood. This review discusses what is known about the role of cohesin in normal hematopoiesis, and how recent findings could shed light on the mechanisms through which cohesin mutations promote leukemic transformation. Important unanswered questions in the field, such as whether cohesin plays a role in HSC heterogeneity, and the mechanisms by which it regulates gene expression at a molecular level, will also be discussed. Particular attention will be given to the potential therapeutic vulnerabilities of leukemic cells with cohesin subunit mutations.
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Affiliation(s)
- Austin Boucher
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Josiah Murray
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
- Versiti Blood Research Institute, Milwaukee, WI, USA.
- Department of Pediatrics, Division of Hematology/Oncology/Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.
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20
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Zhang C, Liu M, Luan L, Guo X, You Y, Wang Z, Li W, Lu N, Hou Y, Lu L, Lu W, Zhou Y. Establishment and characterization of a patient-derived metastatic extraskeletal Ewing sarcoma cell line ES-ZSS-1. Hum Cell 2024; 38:12. [PMID: 39475964 DOI: 10.1007/s13577-024-01133-3] [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: 07/10/2024] [Accepted: 10/04/2024] [Indexed: 01/30/2025]
Abstract
The methods available for treating metastatic Ewing sarcoma (ES) are inadequate; thus, innovative therapeutic approaches need to be developed. However, the lack of clinically relevant ES models has hindered the discovery of drugs for this disease. In this study, we established and characterized a patient-derived xenograft (PDX) cell line model, which was constructed using tumor tissue from a patient with metastatic extraskeletal ES. The cells were found to recapitulate the morphological and histopathological features of the patient tumor and were designated as ES-ZSS-1. The cells harbor the characteristic EWSR1-FLI1 infusion and underwent successive passages in vitro. By performing gene expression profiling, we found that the mutation in STAG2 was the most frequent. An increase in Twist1 and epithelial-to-mesenchymal transition (EMT) was recorded. These genetic features might be relevant to metastasis and resistance to chemotherapy. To summarize, the novel patient-derived ES cell line we developed closely mimics the phenotype and genotype of patient tumors, making it a reliable tool for research on metastatic ES.
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Affiliation(s)
- Chenlu Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Mengling Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Lijuan Luan
- Department of Pathology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Xi Guo
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yang You
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Zhiming Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Wei Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Nanhang Lu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Lili Lu
- Department of Biotherapy Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, China.
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21
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Schneider C, Spaink H, Alexe G, Dharia NV, Meyer A, Merickel LA, Khalid D, Scheich S, Häupl B, Staudt LM, Oellerich T, Stegmaier K. Targeting the Sodium-Potassium Pump as a Therapeutic Strategy in Acute Myeloid Leukemia. Cancer Res 2024; 84:3354-3370. [PMID: 39024560 PMCID: PMC11479832 DOI: 10.1158/0008-5472.can-23-3560] [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: 11/13/2023] [Revised: 05/08/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024]
Abstract
Tissue-specific differences in the expression of paralog genes, which are not essential in most cell types due to the buffering effect of the partner pair, can make for highly selective gene dependencies. To identify selective paralogous targets for acute myeloid leukemia (AML), we integrated the Cancer Dependency Map with numerous datasets characterizing protein-protein interactions, paralog relationships, and gene expression in cancer models. In this study, we identified ATP1B3 as a context-specific, paralog-related dependency in AML. ATP1B3, the β-subunit of the sodium-potassium pump (Na/K-ATP pump), interacts with the α-subunit ATP1A1 to form an essential complex for maintaining cellular homeostasis and membrane potential in all eukaryotic cells. When ATP1B3's paralog ATP1B1 is poorly expressed, elimination of ATP1B3 leads to the destabilization of the Na/K-ATP pump. ATP1B1 expression is regulated through epigenetic silencing in hematopoietic lineage cells through histone and DNA methylation in the promoter region. Loss of ATP1B3 in AML cells induced cell death in vitro and reduced leukemia burden in vivo, which could be rescued by stabilizing ATP1A1 through overexpression of ATP1B1. Thus, ATP1B3 is a potential therapeutic target for AML and other hematologic malignancies with low expression of ATP1B1. Significance: ATP1B3 is a lethal selective paralog dependency in acute myeloid leukemia that can be eliminated to destabilize the sodium-potassium pump, inducing cell death.
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Affiliation(s)
- Constanze Schneider
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Hermes Spaink
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Neekesh V. Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
| | - Ashleigh Meyer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lucy A. Merickel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sebastian Scheich
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
| | - Björn Häupl
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas Oellerich
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
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22
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Kimura S, Park CS, Montefiori LE, Iacobucci I, Polonen P, Gao Q, Arnold ED, Attarbaschi A, Brown A, Buldini B, Caldwell KJ, Chang Y, Chen C, Cheng C, Cheng Z, Choi J, Conter V, Crews KR, de Groot-Kruseman HA, Deguchi T, Eguchi M, Muhle HE, Elitzur S, Escherich G, Freeman BB, Gu Z, Han K, Horibe K, Imamura T, Jeha S, Kato M, Chiew KH, Khan T, Kicinski M, Köhrer S, Kornblau SM, Kotecha RS, Li CK, Liu YC, Locatelli F, Luger SM, Paietta EM, Manabe A, Marquart HV, Masetti R, Maybury M, Mazilier P, Meijerink JP, Mitchell S, Miyamura T, Moore AS, Oshima K, Pawinska-Wasikowska K, Pieters R, Prater MS, Pruett-Miller SM, Pui CH, Qu C, Reiterova M, Reyes N, Roberts KG, Rowe JM, Sato A, Schmiegelow K, Schrappe M, Shen S, Skoczeń S, Spinelli O, Stary J, Svaton M, Takagi M, Takita J, Tang Y, Teachey DT, Thomas PG, Tomizawa D, Trka J, Varotto E, Vincent TL, Yang JJ, Yeoh AEJ, Zhou Y, Zimmermann M, Inaba H, Mullighan CG. Biologic and Clinical Analysis of Childhood Gamma Delta T-ALL Identifies LMO2/STAG2 Rearrangements as Extremely High Risk. Cancer Discov 2024; 14:1838-1859. [PMID: 38916500 PMCID: PMC11452281 DOI: 10.1158/2159-8290.cd-23-1452] [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: 12/06/2023] [Revised: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Acute lymphoblastic leukemia expressing the gamma delta T-cell receptor (γδ T-ALL) is a poorly understood disease. We studied 200 children with γδ T-ALL from 13 clinical study groups to understand the clinical and genetic features of this disease. We found age and genetic drivers were significantly associated with outcome. γδ T-ALL diagnosed in children under 3 years of age was extremely high-risk and enriched for genetic alterations that result in both LMO2 activation and STAG2 inactivation. Mechanistically, using patient samples and isogenic cell lines, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping, resulting in deregulation of gene expression associated with T-cell differentiation. High-throughput drug screening identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which can be targeted by poly(ADP-ribose) polymerase inhibition. These data provide a diagnostic framework for classification and risk stratification of pediatric γδ T-ALL. Significance: Patients with acute lymphoblastic leukemia expressing the gamma delta T-cell receptor under 3 years old or measurable residual disease ≥1% at end of induction showed dismal outcomes and should be classified as having high-risk disease. The STAG2/LMO2 subtype was enriched in this very young age group. STAG2 inactivation may perturb chromatin conformation and cell differentiation and confer vulnerability to poly(ADP-ribose) polymerase inhibition.
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Affiliation(s)
- Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chun Shik Park
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth D. Arnold
- Department of Cell and Molecular Biology and Center for Advance Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Andishe Attarbaschi
- Department of Pediatric Hematology and Oncology, St. Anna Children’s Hospital, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Anthony Brown
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Barbara Buldini
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, Padova, Italy
- Pediatric Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, Istituto di Ricerca Pediatrica (IRP)-Città della Speranza, Padova, Italy
| | | | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chelsey Chen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Choi
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Valentino Conter
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Kristine R. Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Takao Deguchi
- Children's Cancer Center, National Center for Child Health and Development
| | - Mariko Eguchi
- Department of Pediatrics, Ehime University, Ehime, Japan
| | - Hannah Elisa Muhle
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Elitzur
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Burgess B. Freeman
- Preclinical Pharmacokinetic Shared Resource, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Departments of Computational and Quantitative Medicine, and Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Katie Han
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sima Jeha
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Motohiro Kato
- Department of Pediatrics, Tokyo University, Tokyo, Japan
| | - Kean Hui Chiew
- Department of Paediatrics, National University of Singapore, National University of Singapore, Singapore, Singapore
| | - Tanya Khan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Rishi S Kotecha
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Chi-Kong Li
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Franco Locatelli
- Department of Pediatric Hematology–Oncology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Catholic University of the Sacred Heart, Rome, Italy
| | - Selina M. Luger
- Abramson Cancer Center, Univeristy of Pennsylvania, Philadelphia, PA, USA
| | | | - Atsushi Manabe
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Riccardo Masetti
- Pediatric Hematology and Oncology, IRCCS Azienda Ospedaliero Universitaria di Bologna, University of Bologna, Bologna, Italy
| | - Mellissa Maybury
- Child Health Research Centre, the University of Queensland, Brisbane, QLD, Australia
| | - Pauline Mazilier
- Pediatric hemato-oncology and transplantation, HUB - HUDERF, Brussels, Belgium
| | | | - Sharnise Mitchell
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Takako Miyamura
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Andrew S. Moore
- Child Health Research Centre, the University of Queensland, Brisbane, QLD, Australia
- Oncology Service, Children’s Health Queensland Hospital and Health Service, Brisbane, QLD, Australia
| | - Koichi Oshima
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | | | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Mollie S. Prater
- Department of Cell and Molecular Biology and Center for Advance Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advance Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michaela Reiterova
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Noemi Reyes
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G. Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jacob M. Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, København, Denmark
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Berlin, Germany
| | - Shuhong Shen
- Department of Hematology/Oncology, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Szymon Skoczeń
- Department of Pediatric Oncology and Hematology, Jagiellonian University Medical College, Krakow, Poland
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, ASST-Papa Giovanni XXIII Hospital, Piazza OMS, Bergamo, Italy
| | - Jan Stary
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michael Svaton
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine Kyoto University, Kyoto, Japan
| | - Yanjing Tang
- Department of Hematology/Oncology, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - David T. Teachey
- Division of Oncology, Children's Hospital of Philadelphia, PA, USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Elena Varotto
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, Padova, Italy
| | | | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allen EJ Yeoh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yinmei Zhou
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Medical School Hannover, Hannover, Germany
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN, USA
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23
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Fischer A, Hernández-Rodríguez B, Mulet-Lazaro R, Nuetzel M, Hölzl F, van Herk S, Kavelaars FG, Stanewsky H, Ackermann U, Niang AH, Diaz N, Reuschel E, Strieder N, Hernández-López I, Valk PJM, Vaquerizas JM, Rehli M, Delwel R, Gebhard C. STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemia. Cell Rep 2024; 43:114498. [PMID: 39084219 DOI: 10.1016/j.celrep.2024.114498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/24/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2, but not its paralog STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression, and local chromatin activation, which were not compensated by the remaining STAG1-cohesin. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. Complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs) revealed effects resembling STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by the depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression, and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.
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MESH Headings
- Humans
- Cohesins
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Mutation/genetics
- Hematopoietic Stem Cells/metabolism
- Cell Differentiation/genetics
- Gene Expression Regulation, Leukemic
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/genetics
- Nuclear Proteins
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Affiliation(s)
- Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Hölzl
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Amadou H Niang
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Noelia Diaz
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | | | | | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany; Department of Developmental Epigenomics, MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
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24
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Giusti V, Miserocchi G, Sbanchi G, Pannella M, Hattinger CM, Cesari M, Fantoni L, Guerrieri AN, Bellotti C, De Vita A, Spadazzi C, Donati DM, Torsello M, Lucarelli E, Ibrahim T, Mercatali L. Xenografting Human Musculoskeletal Sarcomas in Mice, Chick Embryo, and Zebrafish: How to Boost Translational Research. Biomedicines 2024; 12:1921. [PMID: 39200384 PMCID: PMC11352184 DOI: 10.3390/biomedicines12081921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
Musculoskeletal sarcomas pose major challenges to researchers and clinicians due to their rarity and heterogeneity. Xenografting human cells or tumor fragments in rodents is a mainstay for the generation of cancer models and for the preclinical trial of novel drugs. Lately, though, technical, intrinsic and ethical concerns together with stricter regulations have significantly curbed the employment of murine patient-derived xenografts (mPDX). In alternatives to murine PDXs, researchers have focused on embryonal systems such as chorioallantoic membrane (CAM) and zebrafish embryos. These systems are time- and cost-effective hosts for tumor fragments and near-patient cells. The CAM of the chick embryo represents a unique vascularized environment to host xenografts with high engraftment rates, allowing for ease of visualization and molecular detection of metastatic cells. Thanks to the transparency of the larvae, zebrafish allow for the tracking of tumor development and metastatization, enabling high-throughput drug screening. This review will focus on xenograft models of musculoskeletal sarcomas to highlight the intrinsic and technically distinctive features of the different hosts, and how they can be exploited to elucidate biological mechanisms beneath the different phases of the tumor's natural history and in drug development. Ultimately, the review suggests the combination of different models as an advantageous approach to boost basic and translational research.
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Affiliation(s)
- Veronica Giusti
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Giacomo Miserocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.M.); (A.D.V.); (C.S.)
| | - Giulia Sbanchi
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Micaela Pannella
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Claudia Maria Hattinger
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Marilena Cesari
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Leonardo Fantoni
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ania Naila Guerrieri
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Chiara Bellotti
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Alessandro De Vita
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.M.); (A.D.V.); (C.S.)
| | - Chiara Spadazzi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.M.); (A.D.V.); (C.S.)
| | - Davide Maria Donati
- Orthopaedic Oncology Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy;
| | - Monica Torsello
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Enrico Lucarelli
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Toni Ibrahim
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
| | - Laura Mercatali
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (V.G.); (G.S.); (M.P.); (C.M.H.); (M.C.); (L.F.); (A.N.G.); (C.B.); (T.I.); (L.M.)
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25
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Green D, van Ewijk R, Tirtei E, Andreou D, Baecklund F, Baumhoer D, Bielack SS, Botchu R, Boye K, Brennan B, Capra M, Cottone L, Dirksen U, Fagioli F, Fernandez N, Flanagan AM, Gambarotti M, Gaspar N, Gelderblom H, Gerrand C, Gomez-Mascard A, Hardes J, Hecker-Nolting S, Kabickova E, Kager L, Kanerva J, Kester LA, Kuijjer ML, Laurence V, Lervat C, Marchais A, Marec-Berard P, Mendes C, Merks JH, Ory B, Palmerini E, Pantziarka P, Papakonstantinou E, Piperno-Neumann S, Raciborska A, Roundhill EA, Rutkauskaite V, Safwat A, Scotlandi K, Staals EL, Strauss SJ, Surdez D, Sys GM, Tabone MD, Toulmonde M, Valverde C, van de Sande MA, Wörtler K, Campbell-Hewson Q, McCabe MG, Nathrath M. Biological Sample Collection to Advance Research and Treatment: A Fight Osteosarcoma Through European Research and Euro Ewing Consortium Statement. Clin Cancer Res 2024; 30:3395-3406. [PMID: 38869831 PMCID: PMC11334773 DOI: 10.1158/1078-0432.ccr-24-0101] [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: 01/09/2024] [Revised: 03/27/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Osteosarcoma and Ewing sarcoma are bone tumors mostly diagnosed in children, adolescents, and young adults. Despite multimodal therapy, morbidity is high and survival rates remain low, especially in the metastatic disease setting. Trials investigating targeted therapies and immunotherapies have not been groundbreaking. Better understanding of biological subgroups, the role of the tumor immune microenvironment, factors that promote metastasis, and clinical biomarkers of prognosis and drug response are required to make progress. A prerequisite to achieve desired success is a thorough, systematic, and clinically linked biological analysis of patient samples, but disease rarity and tissue processing challenges such as logistics and infrastructure have contributed to a lack of relevant samples for clinical care and research. There is a need for a Europe-wide framework to be implemented for the adequate and minimal sampling, processing, storage, and analysis of patient samples. Two international panels of scientists, clinicians, and patient and parent advocates have formed the Fight Osteosarcoma Through European Research consortium and the Euro Ewing Consortium. The consortia shared their expertise and institutional practices to formulate new guidelines. We report new reference standards for adequate and minimally required sampling (time points, diagnostic samples, and liquid biopsy tubes), handling, and biobanking to enable advanced biological studies in bone sarcoma. We describe standards for analysis and annotation to drive collaboration and data harmonization with practical, legal, and ethical considerations. This position paper provides comprehensive guidelines that should become the new standards of care that will accelerate scientific progress, promote collaboration, and improve outcomes.
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Affiliation(s)
- Darrell Green
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom.
| | - Roelof van Ewijk
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Elisa Tirtei
- Pediatric Oncology, Regina Margherita Children’s Hospital, Turin, Italy.
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy.
| | - Dimosthenis Andreou
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria.
| | - Fredrik Baecklund
- Pediatric Oncology Unit, Karolinska University Hospital, Stockholm, Sweden.
| | - Daniel Baumhoer
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
| | - Stefan S. Bielack
- Center for Pediatric, Adolescent and Women’s Medicine, Klinikum Stuttgart—Olgahospital, Stuttgart Cancer Centre, Stuttgart, Germany.
| | - Rajesh Botchu
- Department of Musculoskeletal Radiology, Royal Orthopaedic Hospital NHS Foundation Trust, Birmingham, United Kingdom.
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway.
| | - Bernadette Brennan
- Paediatric Oncology, Royal Manchester Children’s Hospital, Central Manchester University Hospital NHS Foundation Trust, Manchester, United Kingdom.
| | - Michael Capra
- Haematology/Oncology, Children’s Health Ireland at Crumlin, Dublin, Ireland.
| | - Lucia Cottone
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom.
| | - Uta Dirksen
- Pediatrics III, West German Cancer Center, University Hospital Essen, German Cancer Consortium (DKTK) Site Essen, Cancer Research Center (NCT) Cologne-Essen, University of Duisburg-Essen, Essen, Germany.
| | - Franca Fagioli
- Pediatric Oncology, Regina Margherita Children’s Hospital, Turin, Italy.
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy.
| | - Natalia Fernandez
- Patient and Parent Advocacy Group, FOSTER, Washington, District of Columbia.
| | - Adrienne M. Flanagan
- Department of Pathology, UCL Cancer Institute, University College London, London, United Kingdom.
- Histopathology, The Royal National Orthopaedic Hospital NHS Trust, Stanmore, United Kingdom.
| | - Marco Gambarotti
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
- U1015, Université Paris-Saclay, Villejuif, France.
| | - Hans Gelderblom
- Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Craig Gerrand
- Orthopaedic Oncology, The Royal National Orthopaedic Hospital NHS Trust, Stanmore, United Kingdom.
| | - Anne Gomez-Mascard
- Department of Pathology, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France.
- EQ ONCOSARC, CRCT Inserm/UT3, ERL CNRS, Toulouse, France.
| | - Jendrik Hardes
- Tumour Orthopaedics, University Hospital Essen, German Cancer Consortium (DKTK) Site Essen, Cancer Research Center (NCT) Cologne-Essen, University of Duisburg-Essen, Essen, Germany.
| | - Stefanie Hecker-Nolting
- Center for Pediatric, Adolescent and Women’s Medicine, Klinikum Stuttgart—Olgahospital, Stuttgart Cancer Centre, Stuttgart, Germany.
| | - Edita Kabickova
- Paediatric Haematology and Oncology, University Hospital Motol, Prague, Czech Republic.
| | - Leo Kager
- Pediatrics, St Anna Children’s Hospital, Medical University Vienna, Vienna, Austria.
- St Anna Children’s Cancer Research Institute, Vienna, Austria.
| | - Jukka Kanerva
- Hematology-Oncology and Stem Cell Transplantation, HUS Helsinki University Hospital, New Children’s Hospital, Helsinki, Finland.
| | - Lennart A. Kester
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Marieke L. Kuijjer
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.
- Pathology, Leiden University Medical Center, Leiden, the Netherlands.
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands.
| | | | - Cyril Lervat
- Department of Pediatrics and AYA Oncology, Centre Oscar Lambret, Lille, France.
| | - Antonin Marchais
- Department of Oncology for Child and Adolescent, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
| | - Perrine Marec-Berard
- Institute of Hematology and Pediatric Oncology, Léon Bérard Center, Lyon, France.
| | - Cristina Mendes
- Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal.
| | - Johannes H.M. Merks
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Division of Imaging and Oncology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Benjamin Ory
- School of Medicine, Nantes Université, Nantes, France.
| | - Emanuela Palmerini
- Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Orthopedico Rizzoli, Bologna, Italy.
| | - Pan Pantziarka
- Patient and Parent Advocacy Group, FOSTER, Washington, District of Columbia.
- Anticancer Fund, Meise, Belgium.
- The George Pantziarka TP53 Trust, London, United Kingdom.
| | - Evgenia Papakonstantinou
- Pediatric Hematology-Oncology, Ippokratio General Hospital of Thessaloniki, Thessaloniki, Greece.
| | | | - Anna Raciborska
- Oncology and Surgical Oncology for Children and Youth, Institute of Mother and Child, Warsaw, Poland.
| | - Elizabeth A. Roundhill
- Children’s Cancer Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom.
| | - Vilma Rutkauskaite
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Akmal Safwat
- The Danish Centre for Particle Therapy, Aarhus University Hospital, Aarhus, Denmark.
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Eric L. Staals
- Orthopaedics and Trauma, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Sandra J. Strauss
- Department of Oncology, University College London Hospitals NHS Foundation Trust, UCL Cancer Institute, London, United Kingdom.
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland.
| | - Gwen M.L. Sys
- Department of Orthopaedic Surgery and Traumatology, Ghent University Hospital, Belgium.
| | - Marie-Dominique Tabone
- Department of Hematology and Oncology, A. Trousseau Hospital, Sorbonne University, APHP, Paris, France.
| | - Maud Toulmonde
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France.
| | - Claudia Valverde
- Medical Oncology, Vall d’Hebron University Hospital, Barcelona, Spain.
| | | | - Klaus Wörtler
- Musculoskeletal Radiology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.
| | - Quentin Campbell-Hewson
- Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
| | - Martin G. McCabe
- Division of Cancer Sciences, School of Medical Sciences, The University of Manchester, Manchester, United Kingdom.
- The Christie NHS Foundation Trust, Manchester, United Kingdom.
| | - Michaela Nathrath
- Children’s Cancer Research Center, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.
- Pediatric Oncology, Klinikum Kassel, Kassel, Germany.
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26
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Kim YR, Joo J, Lee HJ, Kim C, Park JC, Yu YS, Kim CR, Lee DH, Cha J, Kwon H, Hanssen KM, Grünewald TGP, Choi M, Han I, Bae S, Jung I, Shin Y, Baek SH. Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing's sarcoma. Nat Commun 2024; 15:6569. [PMID: 39095374 PMCID: PMC11297139 DOI: 10.1038/s41467-024-51050-0] [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: 04/09/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless organelles within cells, with implications in various biological processes and disease states. AT-rich interactive domain-containing protein 1A (ARID1A) is a chromatin remodeling factor frequently associated with cancer mutations, yet its functional mechanism remains largely unknown. Here, we find that ARID1A harbors a prion-like domain (PrLD), which facilitates the formation of liquid condensates through PrLD-mediated LLPS. The nuclear condensates formed by ARID1A LLPS are significantly elevated in Ewing's sarcoma patient specimen. Disruption of ARID1A LLPS results in diminished proliferative and invasive abilities in Ewing's sarcoma cells. Through genome-wide chromatin structure and transcription profiling, we identify that the ARID1A condensate localizes to EWS/FLI1 target enhancers and induces long-range chromatin architectural changes by forming functional chromatin remodeling hubs at oncogenic target genes. Collectively, our findings demonstrate that ARID1A promotes oncogenic potential through PrLD-mediated LLPS, offering a potential therapeutic approach for treating Ewing's sarcoma.
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Affiliation(s)
- Yong Ryoul Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jaegeon Joo
- Department of Biological Sciences, Korea Advanced Institute of Science & Technology, Daejeon, South Korea
| | - Hee Jung Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Ju-Chan Park
- Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Young Suk Yu
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Chang Rok Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Do Hui Lee
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Joowon Cha
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Hyemin Kwon
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Kimberley M Hanssen
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, (A Partnership) Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas G P Grünewald
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, (A Partnership) Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Ilkyu Han
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Sangsu Bae
- Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science & Technology, Daejeon, South Korea.
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea.
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea.
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul, South Korea.
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27
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Labudina AA, Meier M, Gimenez G, Tatarakis D, Ketharnathan S, Mackie B, Schilling TF, Antony J, Horsfield JA. Cohesin composition and dosage independently affect early development in zebrafish. Development 2024; 151:dev202593. [PMID: 38975838 DOI: 10.1242/dev.202593] [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: 12/07/2023] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed 'cohesinopathies' are characterized by germline variants of cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear whether mutations in individual cohesin subunits have independent developmental consequences. Here, we show that zebrafish rad21 or stag2b mutants independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2b mutants have narrower notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single-cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2b, but not rad21, mutants. Our results suggest that mutations altering the quantity versus composition of cohesin have independent developmental consequences, with implications for the understanding and management of cohesinopathies.
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Affiliation(s)
- Anastasia A Labudina
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Michael Meier
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - David Tatarakis
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Sarada Ketharnathan
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Bridget Mackie
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
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28
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Fan Z, Dong S, Wang N, Khawar MB, Wang J, Sun H. Unlocking epigenetics for precision treatment of Ewing's sarcoma. Chin J Cancer Res 2024; 36:322-340. [PMID: 38988487 PMCID: PMC11230886 DOI: 10.21147/j.issn.1000-9604.2024.03.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/16/2024] [Indexed: 07/12/2024] Open
Abstract
Ewing's sarcoma (EWS) is a highly aggressive malignant bone tumor primarily affecting adolescents and young adults. Despite the efficacy of chemoradiotherapy in some cases, the cure rate for patients with metastatic and recurrent disease remains low. Therefore, there is an urgent need for innovative therapeutic approaches to address the challenges associated with EWS treatment. Epigenetic regulation, a crucial factor in physiological processes, plays a significant role in controlling cell proliferation, maintaining gene integrity, and regulating transcription. Recent studies highlight the importance of abnormal epigenetic regulation in the initiation and progression of EWS. A comprehensive understanding of the intricate interactions between EWS and aberrant epigenetic regulation is essential for advancing clinical drug development. This review aims to provide a comprehensive overview of both epigenetic targets implicated in EWS, integrating various therapeutic modalities to offer innovative perspectives for the clinical diagnosis and treatment of EWS.
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Affiliation(s)
- Zhehao Fan
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou 225001, China
| | - Shuangshuang Dong
- Department of Pathology, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou 225001, China
| | - Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou 225001, China
| | - Muhammad Babar Khawar
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou 225001, China
| | - Jingcheng Wang
- Department of Orthopedics, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University, Yangzhou 225001, China
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou 225001, China
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29
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Yu L, Deng Y, Wang X, Santos C, Davis IJ, Earp HS, Liu P. Co-targeting JAK1/STAT6/GAS6/TAM signaling improves chemotherapy efficacy in Ewing sarcoma. Nat Commun 2024; 15:5292. [PMID: 38906855 PMCID: PMC11192891 DOI: 10.1038/s41467-024-49667-2] [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: 09/14/2023] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Ewing sarcoma is a pediatric bone and soft tissue tumor treated with chemotherapy, radiation, and surgery. Despite intensive multimodality therapy, ~50% patients eventually relapse and die of the disease due to chemoresistance. Here, using phospho-profiling, we find Ewing sarcoma cells treated with chemotherapeutic agents activate TAM (TYRO3, AXL, MERTK) kinases to augment Akt and ERK signaling facilitating chemoresistance. Mechanistically, chemotherapy-induced JAK1-SQ phosphorylation releases JAK1 pseudokinase domain inhibition allowing for JAK1 activation. This alternative JAK1 activation mechanism leads to STAT6 nuclear translocation triggering transcription and secretion of the TAM kinase ligand GAS6 with autocrine/paracrine consequences. Importantly, pharmacological inhibition of either JAK1 by filgotinib or TAM kinases by UNC2025 sensitizes Ewing sarcoma to chemotherapy in vitro and in vivo. Excitingly, the TAM kinase inhibitor MRX-2843 currently in human clinical trials to treat AML and advanced solid tumors, enhances chemotherapy efficacy to further suppress Ewing sarcoma tumor growth in vivo. Our findings reveal an Ewing sarcoma chemoresistance mechanism with an immediate translational value.
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Affiliation(s)
- Le Yu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yu Deng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaodong Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charlene Santos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Medicine and Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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30
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Stanton BZ, Pomella S. Epigenetic determinants of fusion-driven sarcomas: paradigms and challenges. Front Cell Dev Biol 2024; 12:1416946. [PMID: 38946804 PMCID: PMC11211607 DOI: 10.3389/fcell.2024.1416946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/14/2024] [Indexed: 07/02/2024] Open
Abstract
We describe exciting recent advances in fusion-driven sarcoma etiology, from an epigenetics perspective. By exploring the current state of the field, we identify and describe the central mechanisms that determine sarcomagenesis. Further, we discuss seminal studies in translational genomics, which enabled epigenetic characterization of fusion-driven sarcomas. Important context for epigenetic mechanisms include, but are not limited to, cell cycle and metabolism, core regulatory circuitry, 3-dimensional chromatin architectural dysregulation, integration with ATP-dependent chromatin remodeling, and translational animal modeling. Paradoxically, while the genetic requirements for oncogenic transformation are highly specific for the fusion partners, the epigenetic mechanisms we as a community have uncovered are categorically very broad. This dichotomy prompts the question of whether the investigation of rare disease epigenomics should prioritize studying individual cell populations, thereby examining whether the mechanisms of chromatin dysregulation are specific to a particular tumor. We review recent advances focusing on rhabdomyosarcoma, synovial sarcoma, alveolar soft part sarcoma, clear cell sarcoma, undifferentiated round cell sarcoma, Ewing sarcoma, myxoid/round liposarcoma, epithelioid hemangioendothelioma and desmoplastic round cell tumor. The growing number of groundbreaking discoveries in the field, motivated us to anticipate further exciting advances in the area of mechanistic epigenomics and direct targeting of fusion transcription factors in the years ahead.
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Affiliation(s)
- Benjamin Z. Stanton
- Nationwide Children’s Hospital, Center for Childhood Cancer Research, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Silvia Pomella
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
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Xu W, Kim JS, Yang T, Ya A, Sadzewicz L, Tallon L, Harris BT, Sarkaria J, Jin F, Waldman T. STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme. J Biol Chem 2024; 300:107341. [PMID: 38705393 PMCID: PMC11157269 DOI: 10.1016/j.jbc.2024.107341] [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: 02/14/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024] Open
Abstract
Inactivating mutations of genes encoding the cohesin complex are common in a wide range of human cancers. STAG2 is the most commonly mutated subunit. Here we report the impact of stable correction of endogenous, naturally occurring STAG2 mutations on gene expression, 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme (GBM). In two GBM cell lines, correction of their STAG2 mutations significantly altered the expression of ∼10% of all expressed genes. Virtually all the most highly regulated genes were negatively regulated by STAG2 (i.e., expressed higher in STAG2-mutant cells), and one of them-HEPH-was regulated by STAG2 in uncultured GBM tumors as well. While STAG2 correction had little effect on large-scale features of 3D genome organization (A/B compartments, TADs), STAG2 correction did alter thousands of individual chromatin loops, some of which controlled the expression of adjacent genes. Loops specific to STAG2-mutant cells, which were regulated by STAG1-containing cohesin complexes, were very large, supporting prior findings that STAG1-containing cohesin complexes have greater loop extrusion processivity than STAG2-containing cohesin complexes and suggesting that long loops may be a general feature of STAG2-mutant cancers. Finally, STAG2 mutation activated Polycomb activity leading to increased H3K27me3 marks, identifying Polycomb signaling as a potential target for therapeutic intervention in STAG2-mutant GBM tumors. Together, these findings illuminate the landscape of STAG2-regulated genes, A/B compartments, chromatin loops, and pathways in GBM, providing important clues into the largely still unknown mechanism of STAG2 tumor suppression.
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Affiliation(s)
- Wanying Xu
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, Ohio, USA; The Biomedical Sciences Training Program, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Tianyi Yang
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, Ohio, USA; The Biomedical Sciences Training Program, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alvin Ya
- MD/PhD Program, Georgetown University School of Medicine, Washington, District of Columbia, USA; Tumor Biology Training Program, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Brent T Harris
- Departments of Neurology and Pathology, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Jann Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve School of Medicine, Cleveland, Ohio, USA; Department of Computer and Data Sciences, Department of Population and Quantitative Health Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA.
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA.
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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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Sannigrahi MK, Cao AC, Rajagopalan P, Sun L, Brody RM, Raghav L, Gimotty PA, Basu D. A novel pipeline for prioritizing cancer type-specific therapeutic vulnerabilities using DepMap identifies PAK2 as a target in head and neck squamous cell carcinomas. Mol Oncol 2024; 18:336-349. [PMID: 37997254 PMCID: PMC10850805 DOI: 10.1002/1878-0261.13558] [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: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
There is limited guidance on exploiting the genome-wide loss-of-function CRISPR screens in cancer Dependency Map (DepMap) to identify new targets for individual cancer types. This study integrated multiple tools to filter these data in order to seek new therapeutic targets specific to head and neck squamous cell carcinoma (HNSCC). The resulting pipeline prioritized 143 targetable dependencies that represented both well-studied targets and emerging target classes like mitochondrial carriers and RNA-binding proteins. In total, 14 targets had clinical inhibitors used for other cancers or nonmalignant diseases that hold near-term potential to repurpose for HNSCC therapy. Comparing inhibitor response data that were publicly available for 13 prioritized targets between the cell lines with high vs. low dependency on each target uncovered novel therapeutic potential for the PAK2 serine/threonine kinase. PAK2 gene dependency was found to be associated with wild-type p53, low PAK2 mRNA, and diploid status of the 3q amplicon containing PAK2. These findings establish a generalizable pipeline to prioritize clinically relevant targets for individual cancer types using DepMap. Its application to HNSCC highlights novel relevance for PAK2 inhibition and identifies biomarkers of PAK2 inhibitor response.
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Affiliation(s)
- Malay K. Sannigrahi
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Austin C. Cao
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pavithra Rajagopalan
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lova Sun
- Department of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Robert M. Brody
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lovely Raghav
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Devraj Basu
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
- Ellen and Ronald Caplan Cancer CenterThe Wistar InstitutePhiladelphiaPAUSA
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De Feo A, Manfredi M, Mancarella C, Maqueda JJ, De Giorgis V, Pignochino Y, Sciandra M, Cristalli C, Donadelli M, Scotlandi K. CD99 Modulates the Proteomic Landscape of Ewing Sarcoma Cells and Related Extracellular Vesicles. Int J Mol Sci 2024; 25:1588. [PMID: 38338867 PMCID: PMC10855178 DOI: 10.3390/ijms25031588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Ewing sarcoma (EWS) is an aggressive pediatric bone tumor characterized by unmet clinical needs and an incompletely understood epigenetic heterogeneity. Here, we considered CD99, a major surface molecule hallmark of EWS malignancy. Fluctuations in CD99 expression strongly impair cell dissemination, differentiation, and death. CD99 is also loaded within extracellular vesicles (EVs), and the delivery of CD99-positive or CD99-negative EVs dynamically exerts oncogenic or oncosuppressive functions to recipient cells, respectively. We undertook mass spectrometry and functional annotation analysis to investigate the consequences of CD99 silencing on the proteomic landscape of EWS cells and related EVs. Our data demonstrate that (i) the decrease in CD99 leads to major changes in the proteomic profile of EWS cells and EVs; (ii) intracellular and extracellular compartments display two distinct signatures of differentially expressed proteins; (iii) proteomic changes converge to the modulation of cell migration and immune-modulation biological processes; and (iv) CD99-silenced cells and related EVs are characterized by a migration-suppressive, pro-immunostimulatory proteomic profile. Overall, our data provide a novel source of CD99-associated protein biomarkers to be considered for further validation as mediators of EWS malignancy and as EWS disease liquid biopsy markers.
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Affiliation(s)
- Alessandra De Feo
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.D.G.)
| | - Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
| | - Joaquín J. Maqueda
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
| | - Veronica De Giorgis
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.D.G.)
| | - Ymera Pignochino
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy;
- Sarcoma Unit, Candiolo Cancer Institute, FPO-IRCCS, 10060 Turin, Italy
| | - Marika Sciandra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
| | - Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134 Verona, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (A.D.F.); (C.M.); (J.J.M.); (M.S.); (C.C.)
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Wrenn ED, Apfelbaum AA, Rudzinski ER, Deng X, Jiang W, Sud S, Van Noord RA, Newman EA, Garcia NM, Miyaki A, Hoglund VJ, Bhise SS, Kanaan SB, Waltner OG, Furlan SN, Lawlor ER. Cancer-Associated Fibroblast-Like Tumor Cells Remodel the Ewing Sarcoma Tumor Microenvironment. Clin Cancer Res 2023; 29:5140-5154. [PMID: 37471463 PMCID: PMC10801911 DOI: 10.1158/1078-0432.ccr-23-1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. EXPERIMENTAL DESIGN Single-cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining. RESULTS We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAF), and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution was detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci. CONCLUSIONS EwS tumor cells can adopt CAF-like properties, and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment. See related commentary by Kuo and Amatruda, p. 5002.
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Affiliation(s)
- Emma D. Wrenn
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - April A. Apfelbaum
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, Michigan
| | - Erin R. Rudzinski
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Xuemei Deng
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Wei Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Sudha Sud
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | | | - Erika A. Newman
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Nicolas M. Garcia
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Aya Miyaki
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Virginia J. Hoglund
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Shruti S. Bhise
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sami B. Kanaan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Olivia G. Waltner
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Scott N. Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
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Zhou J, Nie R, He Z, Cai X, Chen J, Lin W, Yin Y, Xiang Z, Zhu T, Xie J, Zhang Y, Wang X, Lin P, Xie D, D'Andrea AD, Cai M. STAG2 Regulates Homologous Recombination Repair and Sensitivity to ATM Inhibition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302494. [PMID: 37985839 PMCID: PMC10754142 DOI: 10.1002/advs.202302494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Stromal antigen 2 (STAG2), a subunit of the cohesin complex, is recurrently mutated in various tumors. However, the role of STAG2 in DNA repair and its therapeutic implications are largely unknown. Here it is reported that knockout of STAG2 results in increased double-stranded breaks (DSBs) and chromosomal aberrations by reducing homologous recombination (HR) repair, and confers hypersensitivity to inhibitors of ataxia telangiectasia mutated (ATMi), Poly ADP Ribose Polymerase (PARPi), or the combination of both. Of note, the impaired HR by STAG2-deficiency is mainly attributed to the restored expression of KMT5A, which in turn methylates H4K20 (H4K20me0) to H4K20me1 and thereby decreases the recruitment of BRCA1-BARD1 to chromatin. Importantly, STAG2 expression correlates with poor prognosis of cancer patients. STAG2 is identified as an important regulator of HR and a potential therapeutic strategy for STAG2-mutant tumors is elucidated.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Guangxi International Travel Healthcare Centre (Port Clinic of Nanning Customs District)NanningGuangxi530021China
| | - Run‐Cong Nie
- Department of Gastric SurgeryState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Zhang‐Ping He
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xiao‐Xia Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jie‐Wei Chen
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Wen‐ping Lin
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yi‐Xin Yin
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Zhi‐Cheng Xiang
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Tian‐Chen Zhu
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Juan‐Juan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - You‐Cheng Zhang
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Peng Lin
- Department of Thoracic SurgeryState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Alan D D'Andrea
- Department of Radiation OncologyDana‐Farber Cancer InstituteBostonMA02215USA
- Center for DNA Damage and RepairDana‐Farber Cancer InstituteBostonMA02215USA
| | - Mu‐Yan Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
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Kimura S, Polonen P, Montefiori L, Park CS, Iacobucci I, Yeoh AE, Attarbaschi A, Moore AS, Brown A, Manabe A, Buldini B, Freeman BB, Chen C, Cheng C, Kean Hui C, Li CK, Pui CH, Qu C, Tomizawa D, Teachey DT, Varotto E, Paietta EM, Arnold ED, Locatelli F, Escherich G, Elisa Muhle H, Marquart HV, de Groot-Kruseman HA, Rowe JM, Stary J, Trka J, Choi JK, Meijerink JPP, Yang JJ, Takita J, Pawinska-Wasikowska K, Roberts KG, Han K, Caldwell KJ, Schmiegelow K, Crews KR, Eguchi M, Schrappe M, Zimmerman M, Takagi M, Maybury M, Svaton M, Reiterova M, Kicinski M, Prater MS, Kato M, Reyes N, Spinelli O, Thomas P, Mazilier P, Gao Q, Masetti R, Kotecha RS, Pieters R, Elitzur S, Luger SM, Mitchell S, Pruett-Miller SM, Shen S, Jeha S, Köhrer S, Kornblau SM, Skoczeń S, Miyamura T, Vincent TL, Imamura T, Conter V, Tang Y, Liu YC, Chang Y, Gu Z, Cheng Z, Yinmei Z, Inaba H, Mullighan CG. Biologic and clinical features of childhood gamma delta T-ALL: identification of STAG2/LMO2 γδ T-ALL as an extremely high risk leukemia in the very young. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.06.23298028. [PMID: 37986997 PMCID: PMC10659466 DOI: 10.1101/2023.11.06.23298028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
PURPOSE Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease. METHODS We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations. Therapeutic vulnerabilities were identified by high throughput drug screening of cell lines and xenografts. RESULTS γδ T-ALL in children under three was extremely high-risk with 5-year event-free survival (33% v. 70% [age 3-<10] and 73% [age ≥10], P =9.5 x 10 -5 ) and 5-year overall survival (49% v. 78% [age 3-<10] and 81% [age ≥10], P =0.002), differences not observed in non-γδ T-ALL. γδ T-ALL in this age group was enriched for genomic alterations activating LMO2 activation and inactivating STAG2 inactivation ( STAG2/LMO2 ). Mechanistically, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping resulting in deregulation of gene expression associated with T-cell differentiation. Drug screening showed resistance to prednisolone, consistent with clinical slow treatment response, but identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which was efficaciously targeted by Poly(ADP-ribose) polymerase (PARP) inhibition, with synergism with HDAC inhibitors. Ex-vivo drug screening on PDX cells validated the efficacy of PARP inhibitors as well as other potential targets including nelarabine. CONCLUSION γδ T-ALL in children under the age of three is extremely high-risk and enriched for STAG2/LMO2 ALL. STAG2 loss perturbs chromatin conformation and differentiation, and STAG2/LMO2 ALL is sensitive to PARP inhibition. These data provide a diagnostic and therapeutic framework for pediatric γδ T-ALL. SUPPORT The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children's Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick's Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children's Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173. DISCLAIMER The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies were not directly involved in the design of the study, gathering, analysis and interpretation of the data, writing of the manuscript, or decision to submit the manuscript for publication.
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Rock A, Uche A, Yoon J, Agulnik M, Chow W, Millis S. Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma. J Pers Med 2023; 13:1499. [PMID: 37888109 PMCID: PMC10608227 DOI: 10.3390/jpm13101499] [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: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.
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Affiliation(s)
- Adam Rock
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - An Uche
- Alameda Health System, 1411 E. 31st St., Oakland, CA 94602, USA;
| | - Janet Yoon
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Mark Agulnik
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Warren Chow
- UCI Health, 101 The City Drive, South Orange, CA 92868, USA;
| | - Sherri Millis
- Foundation Medicine, Inc., 150 Second St., Cambridge, MA 02141, USA;
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Yasir M, Park J, Chun W. EWS/FLI1 Characterization, Activation, Repression, Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Int J Mol Sci 2023; 24:15173. [PMID: 37894854 PMCID: PMC10607184 DOI: 10.3390/ijms242015173] [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: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Despite their clonal origins, tumors eventually develop into complex communities made up of phenotypically different cell subpopulations, according to mounting evidence. Tumor cell-intrinsic programming and signals from geographically and temporally changing microenvironments both contribute to this variability. Furthermore, the mutational load is typically lacking in childhood malignancies of adult cancers, and they still exhibit high cellular heterogeneity levels largely mediated by epigenetic mechanisms. Ewing sarcomas represent highly aggressive malignancies affecting both bone and soft tissue, primarily afflicting adolescents. Unfortunately, the outlook for patients facing relapsed or metastatic disease is grim. These tumors are primarily fueled by a distinctive fusion event involving an FET protein and an ETS family transcription factor, with the most prevalent fusion being EWS/FLI1. Despite originating from a common driver mutation, Ewing sarcoma cells display significant variations in transcriptional activity, both within and among tumors. Recent research has pinpointed distinct fusion protein activities as a principal source of this heterogeneity, resulting in markedly diverse cellular phenotypes. In this review, we aim to characterize the role of the EWS/FLI fusion protein in Ewing sarcoma by exploring its general mechanism of activation and elucidating its implications for tumor heterogeneity. Additionally, we delve into potential therapeutic opportunities to target this aberrant fusion protein in the context of Ewing sarcoma treatment.
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Affiliation(s)
| | | | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.)
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Marques Da Costa ME, Zaidi S, Scoazec JY, Droit R, Lim WC, Marchais A, Salmon J, Cherkaoui S, Morscher RJ, Laurent A, Malinge S, Mercher T, Tabone-Eglinger S, Goddard I, Pflumio F, Calvo J, Redini F, Entz-Werlé N, Soriano A, Villanueva A, Cairo S, Chastagner P, Moro M, Owens C, Casanova M, Hladun-Alvaro R, Berlanga P, Daudigeos-Dubus E, Dessen P, Zitvogel L, Lacroix L, Pierron G, Delattre O, Schleiermacher G, Surdez D, Geoerger B. A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors. Commun Biol 2023; 6:949. [PMID: 37723198 PMCID: PMC10507044 DOI: 10.1038/s42003-023-05320-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient's tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Pediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and treatments development in advanced pediatric malignancies.
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Grants
- This work was supported by grants from Fondation Gustave Roussy; Fédération Enfants Cancers et Santé, Société Française de lutte contre les Cancers et les leucémies de l’Enfant et l’adolescent (SFCE), Association AREMIG and Thibault BRIET; Parrainage médecin-chercheur of Gustave Roussy; INSERM; Canceropôle Ile-de-France; Ligue Nationale Contre le Cancer (Equipe labellisée); Fondation ARC for the European projects ERA-NET on Translational Cancer Research (TRANSCAN 2) Joint Transnational Call 2014 (JTC 2014) ‘Targeting Of Resistance in PEDiatric Oncology (TORPEDO)’, ERA-NET TRANSCAN JTC 2014 (TRAN201501238), and TRANSCAN JTC 2017 (TRANS201801292); Agence Nationale de la Recherche (ANR-10-EQPX-03, Institut Curie Génomique d’Excellence (ICGex); IMI ITCC-P4 ; The Child Cancer Research Foundation (CCRF), Cancer Council Western Australia (CCWA); PAIR-Pédiatrie/CONECT-AML (INCa-ARC-LIGUE_11905 and Association Laurette Fugain), Ligue contre le cancer (Equipe labellisée, since 2016), OPALE Carnot institute; Dell; Fondation Bristol-Myers Squibb; Association Imagine for Margo; Association Manon Hope; L’Etoile de Martin; La Course de l’Espoir; M la vie avec Lisa; ADAM; Couleur Jade; Dans les pas du Géant; Courir pour Mathieu; Marabout de Ficelle; Olivier Chape; Les Bagouz à Manon; Association Hubert Gouin Enfance et Cancer; Les Amis de Claire; Kurt-und Senta Hermann Stiftung; Holcim Stiftung Wissen; Gertrud-Hagmann-Stiftung für Malignom-Forschung; Heidi Ras Grant Forschungszentrum fürs Kind; Children’s Liver Tumour European Research Network (ChiLTERN) EU H2020 projet (668596); Fundación FERO and the Rotary Clubs Barcelona Eixample, Barcelona Diagonal, Santa Coloma de Gramanet, München-Blutenburg, Sassella-Stiftung, Berger-Janser Stiftung and Krebsliga Zürich, Deutschland Gemeindienst e.V. and others from Barcelona and province, and No Limits Contra el Cáncer Infantil Association.
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Affiliation(s)
- Maria Eugénia Marques Da Costa
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sakina Zaidi
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Robin Droit
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Sarah Cherkaoui
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Raphael J Morscher
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anouchka Laurent
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | - Sébastien Malinge
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
- Telethon Kids Institute - Cancer Centre, Perth Children's Hospital, Nedlands, WA, Australia
| | - Thomas Mercher
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | | | - Isabelle Goddard
- Small Animal Platform, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Claude Bernard Université Lyon 1, Lyon, France
| | - Francoise Pflumio
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | - Julien Calvo
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | | | - Natacha Entz-Werlé
- Pediatric Onco-Hematology Unit, University Hospital of Strasbourg, Strasbourg, UMR CNRS 7021, team tumoral signaling and therapeutic targets, University of Strasbourg, Faculty of Pharmacy, Illkirch, France
| | - Aroa Soriano
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Xenopat SL, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | | | - Pascal Chastagner
- Children University Hospital, Vandoeuvre‑lès‑Nancy, University of Nancy, Nancy, France
| | - Massimo Moro
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cormac Owens
- Paediatric Haematology/Oncology, Children's Health Ireland, Crumlin, Dublin, Republic of Ireland
| | | | - Raquel Hladun-Alvaro
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Philippe Dessen
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Ludovic Lacroix
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Didier Surdez
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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Tanaka M, Nakamura T. Targeting epigenetic aberrations of sarcoma in CRISPR era. Genes Chromosomes Cancer 2023; 62:510-525. [PMID: 36967299 DOI: 10.1002/gcc.23142] [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: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Sarcomas are rare malignancies that exhibit diverse biological, genetic, morphological, and clinical characteristics. Genetic alterations, such as gene fusions, mutations in transcriptional machinery components, histones, and DNA methylation regulatory molecules, play an essential role in sarcomagenesis. These mutations induce and/or cooperate with specific epigenetic aberrations required for the growth and maintenance of sarcomas. Appropriate mouse models have been developed to clarify the significance of genetic and epigenetic interactions in sarcomas. Studies using the mouse models for human sarcomas have demonstrated major advances in our understanding the developmental processes as well as tumor microenvironment of sarcomas. Recent technological progresses in epigenome editing will not only improve the studies using animal models but also provide a direct clue for epigenetic therapies. In this manuscript, we review important epigenetic aberrations in sarcomas and their representative mouse models, current methods of epigenetic editing using CRISPR/dCas9 systems, and potential applications in sarcoma studies and therapeutics.
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Affiliation(s)
- Miwa Tanaka
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Takuro Nakamura
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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Reed DR, Grohar P, Rubin E, Binitie O, Krailo M, Davis J, DuBois SG, Janeway KA. Children's Oncology Group's 2023 blueprint for research: Bone tumors. Pediatr Blood Cancer 2023; 70 Suppl 6:e30583. [PMID: 37501549 PMCID: PMC10499366 DOI: 10.1002/pbc.30583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/29/2023]
Abstract
The Children's Oncology Group (COG) Bone Tumor Committee is responsible for clinical trials and biological research on localized, metastatic, and recurrent osteosarcoma and Ewing sarcoma (EWS). Results of clinical trials in localized disease completed and published in the past 10 years have led to international standard-of-care chemotherapy for osteosarcoma and EWS. A recent focus on identifying disease subgroups has led to the identification of biological features associated with poor outcomes including the presence of circulating tumor DNA (ctDNA) at diagnosis, and specific genomic alterations-MYC amplification for osteosarcoma and STAG2 and TP53 mutation for EWS. Studies validating these potential biomarkers are under way. Clinical trials evaluating the addition of multitargeted kinase inhibitors, which are active in relapsed bone sarcomas, to standard chemotherapy are under way in osteosarcoma and planned in EWS. In addition, the Committee has data analyses and a clinical trial under way to evaluate approaches to local management of the primary tumor and metastatic sites. Given the rarity of bone sarcomas, we have prioritized international interactions and are in the process of forming an international data-sharing consortium to facilitate refinement of risk stratification and study of rare disease subtypes.
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Affiliation(s)
- Damon R Reed
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, Florida, USA
| | - Patrick Grohar
- Division of Oncology, Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elyssa Rubin
- Department of Oncology, Children's Hospital of Orange County, Orange, California, USA
| | - Odion Binitie
- Department of Sarcoma, Moffitt Cancer Center, Tampa, Florida, USA
| | - Mark Krailo
- Keck School of Medicine, University of Southern California and Children's Oncology Group, Monrovia, California, USA
| | - Jessica Davis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Steven G DuBois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
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Pietrobon A, Yockell‐Lelièvre J, Melong N, Smith LJ, Delaney SP, Azzam N, Xue C, Merwin N, Lian E, Camacho‐Magallanes A, Doré C, Musso G, Julian LM, Kristof AS, Tam RY, Berman JN, Shoichet MS, Stanford WL. Tissue-Engineered Disease Modeling of Lymphangioleiomyomatosis Exposes a Therapeutic Vulnerability to HDAC Inhibition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302611. [PMID: 37400371 PMCID: PMC10502849 DOI: 10.1002/advs.202302611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Indexed: 07/05/2023]
Abstract
Lymphangioleiomyomatosis (LAM) is a rare disease involving cystic lung destruction by invasive LAM cells. These cells harbor loss-of-function mutations in TSC2, conferring hyperactive mTORC1 signaling. Here, tissue engineering tools are employed to model LAM and identify new therapeutic candidates. Biomimetic hydrogel culture of LAM cells is found to recapitulate the molecular and phenotypic characteristics of human disease more faithfully than culture on plastic. A 3D drug screen is conducted, identifying histone deacetylase (HDAC) inhibitors as anti-invasive agents that are also selectively cytotoxic toward TSC2-/- cells. The anti-invasive effects of HDAC inhibitors are independent of genotype, while selective cell death is mTORC1-dependent and mediated by apoptosis. Genotype-selective cytotoxicity is seen exclusively in hydrogel culture due to potentiated differential mTORC1 signaling, a feature that is abrogated in cell culture on plastic. Importantly, HDAC inhibitors block invasion and selectively eradicate LAM cells in vivo in zebrafish xenografts. These findings demonstrate that tissue-engineered disease modeling exposes a physiologically relevant therapeutic vulnerability that would be otherwise missed by conventional culture on plastic. This work substantiates HDAC inhibitors as possible therapeutic candidates for the treatment of patients with LAM and requires further study.
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Affiliation(s)
- Adam Pietrobon
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
| | - Julien Yockell‐Lelièvre
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
| | - Nicole Melong
- Department of PediatricsCHEO Research InstituteOttawaK1H 5B2Canada
| | - Laura J. Smith
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoM5S 3E5Canada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoM5S 3G9Canada
- The Donnelly Centre for Cellular and Biomolecular ResearchTorontoM5S 3E1Canada
| | - Sean P. Delaney
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
| | - Nadine Azzam
- Department of PediatricsCHEO Research InstituteOttawaK1H 5B2Canada
| | - Chang Xue
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoM5S 3G9Canada
- The Donnelly Centre for Cellular and Biomolecular ResearchTorontoM5S 3E1Canada
| | | | - Eric Lian
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
| | - Alberto Camacho‐Magallanes
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
| | - Carole Doré
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
| | | | - Lisa M. Julian
- Centre for Cell BiologyDevelopmentand DiseaseDepartment of Biological SciencesSimon Fraser UniversityBurnabyV5A 1S6Canada
| | - Arnold S. Kristof
- Meakins‐Christie Laboratories and Translational Research in Respiratory Diseases ProgramResearch Institute of the McGill University Health CentreFaculty of MedicineDepartments of Medicine and Critical CareMontrealH4A 3J1Canada
| | - Roger Y. Tam
- Centre for Biologics EvaluationBiologic and Radiopharmaceutical Drugs DirectorateHealth CanadaOttawaK1Y 4X2Canada
| | - Jason N. Berman
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Department of PediatricsCHEO Research InstituteOttawaK1H 5B2Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoM5S 3E5Canada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoM5S 3G9Canada
- The Donnelly Centre for Cellular and Biomolecular ResearchTorontoM5S 3E1Canada
- Department of ChemistryUniversity of TorontoTorontoM5S 3H6Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell ResearchRegenerative Medicine ProgramOttawa Hospital Research InstituteOttawaK1Y 4E9Canada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaK1N 6N5Canada
- Ottawa Institute of Systems BiologyOttawaK1H 8M5Canada
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44
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Gong H, Xue B, Ru J, Pei G, Li Y. Targeted Therapy for EWS-FLI1 in Ewing Sarcoma. Cancers (Basel) 2023; 15:4035. [PMID: 37627063 PMCID: PMC10452796 DOI: 10.3390/cancers15164035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare and predominantly pediatric malignancy of bone and soft tissue in children and adolescents. Although international collaborations have greatly improved the prognosis of most EwS, the occurrence of macrometastases or relapse remains challenging. The prototypic oncogene EWS-FLI1 acts as an aberrant transcription factor that drives the cellular transformation of EwS. In addition to its involvement in RNA splicing and the DNA damage response, this chimeric protein directly binds to GGAA repeats, thereby modifying the transcriptional profile of EwS. Direct pharmacological targeting of EWS-FLI1 is difficult because of its intrinsically disordered structure. However, targeting the EWS-FLI1 protein complex or downstream pathways provides additional therapeutic options. This review describes the EWS-FLI1 protein partners and downstream pathways, as well as the related target therapies for the treatment of EwS.
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Affiliation(s)
- Helong Gong
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
| | - Busheng Xue
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Guoqing Pei
- Department of Orthopedics, Xijing Hospital, Air Force Medical University, Xi’an 710032, China;
| | - Yan Li
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
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45
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Vredevoogd DW, Peeper DS. Heterogeneity in functional genetic screens: friend or foe? Front Immunol 2023; 14:1162706. [PMID: 37398651 PMCID: PMC10312307 DOI: 10.3389/fimmu.2023.1162706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Functional genetic screens to uncover tumor-intrinsic nodes of immune resistance have uncovered numerous mechanisms by which tumors evade our immune system. However, due to technical limitations, tumor heterogeneity is imperfectly captured with many of these analyses. Here, we provide an overview of the nature and sources of heterogeneity that are relevant for tumor-immune interactions. We argue that this heterogeneity may actually contribute to the discovery of novel mechanisms of immune evasion, given a sufficiently large and heterogeneous set of input data. Taking advantage of tumor cell heterogeneity, we provide proof-of-concept analyses of mechanisms of TNF resistance. Thus, consideration of tumor heterogeneity is imperative to increase our understanding of immune resistance mechanisms.
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46
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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: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [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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47
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Wood GE, Graves LA, Rubin EM, Reed DR, Riedel RF, Strauss SJ. Bad to the Bone: Emerging Approaches to Aggressive Bone Sarcomas. Am Soc Clin Oncol Educ Book 2023; 43:e390306. [PMID: 37220319 DOI: 10.1200/edbk_390306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Bone sarcomas are rare heterogeneous tumors that affect patients of all ages including children, adolescent young adults, and older adults. They include many aggressive subtypes and patient groups with poor outcomes, poor access to clinical trials, and lack of defined standard therapeutic strategies. Conventional chondrosarcoma remains a surgical disease, with no defined role for cytotoxic therapy and no approved targeted systemic therapies. Here, we discuss promising novel targets and strategies undergoing evaluation in clinical trials. Multiagent chemotherapy has greatly improved outcomes for patients with Ewing sarcoma (ES) and osteosarcoma, but management of those with high-risk or recurrent disease remains challenging and controversial. We describe the impact of international collaborative trials, such as the rEECur study, that aim to define optimal treatment strategies for those with recurrent, refractory ES, and evidence for high-dose chemotherapy with stem-cell support. We also discuss current and emerging strategies for other small round cell sarcomas, such as CIC-rearranged, BCOR-rearranged tumors, and the evaluation of emerging novel therapeutics and trial designs that may offer a new paradigm to improve survival in these aggressive tumors with notoriously bad (to the bone) outcomes.
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Affiliation(s)
- Georgina E Wood
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
| | - Laurie A Graves
- Division of Hematology/Oncology, Department of Pediatrics, Duke University, Durham, NC
| | - Elyssa M Rubin
- Division of Oncology, Children's Hospital of Orange County, Orange, CA
| | - Damon R Reed
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL
| | - Richard F Riedel
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Durham, NC
| | - Sandra J Strauss
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
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48
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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49
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Wrenn ED, Apfelbaum AA, Rudzinski ER, Deng X, Jiang W, Sud S, Van Noord RA, Newman EA, Garcia NM, Hoglund VJ, Bhise SS, Kanaan SB, Waltner OG, Furlan SN, Lawlor ER. Carcinoma-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536619. [PMID: 37090655 PMCID: PMC10120623 DOI: 10.1101/2023.04.12.536619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Tumor heterogeneity is a major driver of cancer progression. In epithelial-derived malignancies, carcinoma-associated fibroblasts (CAFs) contribute to tumor heterogeneity by depositing extracellular matrix (ECM) proteins that dynamically remodel the tumor microenvironment (TME). Ewing sarcomas (EwS) are histologically monomorphous, mesenchyme-derived tumors that are devoid of CAFs. Here we identify a previously uncharacterized subpopulation of transcriptionally distinct EwS tumor cells that deposit pro-tumorigenic ECM. Single cell analyses revealed that these CAF-like cells differ from bulk EwS cells by their upregulation of a matrisome-rich gene signature that is normally repressed by EWS::FLI1, the oncogenic fusion transcription factor that underlies EwS pathogenesis. Further, our studies showed that ECM-depositing tumor cells express the cell surface marker CD73, allowing for their isolation ex vivo and detection in situ. Spatial profiling of tumor xenografts and patient biopsies demonstrated that CD73 + EwS cells and tumor cell-derived ECM are prevalent along tumor borders and invasive fronts. Importantly, despite loss of EWS::FLI1-mediated gene repression, CD73 + EwS cells retain expression of EWS::FLI1 and the fusion-activated gene signature, as well as tumorigenic and proliferative capacities. Thus, EwS tumor cells can be reprogrammed to adopt CAF-like properties and these transcriptionally and phenotypically distinct cell subpopulations contribute to tumor heterogeneity by remodeling the TME.
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50
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Horsfield JA. Full circle: a brief history of cohesin and the regulation of gene expression. FEBS J 2023; 290:1670-1687. [PMID: 35048511 DOI: 10.1111/febs.16362] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
The cohesin complex has a range of crucial functions in the cell. Cohesin is essential for mediating chromatid cohesion during mitosis, for repair of double-strand DNA breaks, and for control of gene transcription. This last function has been the subject of intense research ever since the discovery of cohesin's role in the long-range regulation of the cut gene in Drosophila. Subsequent research showed that the expression of some genes is exquisitely sensitive to cohesin depletion, while others remain relatively unperturbed. Sensitivity to cohesin depletion is also remarkably cell type- and/or condition-specific. The relatively recent discovery that cohesin is integral to forming chromatin loops via loop extrusion should explain much of cohesin's gene regulatory properties, but surprisingly, loop extrusion has failed to identify a 'one size fits all' mechanism for how cohesin controls gene expression. This review will illustrate how early examples of cohesin-dependent gene expression integrate with later work on cohesin's role in genome organization to explain mechanisms by which cohesin regulates gene expression.
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Affiliation(s)
- Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, New Zealand
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