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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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2
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Mathias KM, Liu Y, Wan L. Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions. Curr Opin Genet Dev 2024; 86:102203. [PMID: 38788489 PMCID: PMC11162900 DOI: 10.1016/j.gde.2024.102203] [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: 10/30/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Precise gene expression, crucial for normal development and health, depends on the co-ordinated assembly and function of various factors within the crowded nucleus. Recent evidence suggests that this process is in part regulated by mesoscale compartmentalization and concentration of transcriptional components within condensates, offering a new perspective on gene regulation. Dysregulation of transcriptional condensates is increasingly associated with diseases, indicating a potential role in pathogenesis. In this mini-review, we provide a concise overview of the current understanding of the formation and function of transcriptional condensates, with a specific focus on recent advances in their dysregulation and implications in diseases, notably cancer. We also address limitations in the field and highlight open questions for future research.
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Affiliation(s)
- Kaeli M Mathias
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiman Liu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liling Wan
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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He L, Cao Y, Sun L. NSD family proteins: Rising stars as therapeutic targets. CELL INSIGHT 2024; 3:100151. [PMID: 38371593 PMCID: PMC10869250 DOI: 10.1016/j.cellin.2024.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Epigenetic modifications, including DNA methylation and histone post-translational modifications, intricately regulate gene expression patterns by influencing DNA accessibility and chromatin structure in higher organisms. These modifications are heritable, are independent of primary DNA sequences, undergo dynamic changes during development and differentiation, and are frequently disrupted in human diseases. The reversibility of epigenetic modifications makes them promising targets for therapeutic intervention and drugs targeting epigenetic regulators (e.g., tazemetostat, targeting the H3K27 methyltransferase EZH2) have been applied in clinical therapy for multiple cancers. The NSD family of H3K36 methyltransferase enzymes-including NSD1 (KMT3B), NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1)-are now receiving drug development attention, with the exciting advent of an NSD2 inhibitor (KTX-1001) advancing to Phase I clinical trials for relapsed or refractory multiple myeloma. NSD proteins recognize and catalyze methylation of histone lysine marks, thereby regulating chromatin integrity and gene expression. Multiple studies have implicated NSD proteins in human disease, noting impacts from translocations, aberrant expression, and various dysfunctional somatic mutations. Here, we review the biological functions of NSD proteins, epigenetic cooperation related to NSD proteins, and the accumulating evidence linking these proteins to developmental disorders and tumorigenesis, while additionally considering prospects for the development of innovative epigenetic therapies.
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Affiliation(s)
- Lin He
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Yiping Cao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
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4
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Cai L, Wang GG. Through the lens of phase separation: intrinsically unstructured protein and chromatin looping. Nucleus 2023; 14:2179766. [PMID: 36821650 PMCID: PMC9980480 DOI: 10.1080/19491034.2023.2179766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
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Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
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5
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Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023; 14:6008. [PMID: 37770423 PMCID: PMC10539325 DOI: 10.1038/s41467-023-41655-2] [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: 11/10/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazheen K Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott D Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Arrakis Therapeutics, 830 Winter St, Waltham, MA, 02451, USA
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Rhodes College, Memphis, TN, USA
- Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Benjamin Lang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seyed Mohammad Hadi Hosseini
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brittany J Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilaria Iacobucci
- 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
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Bollinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, 451 D Street, Suite 104, Boston, MA, 02210, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, and Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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6
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Xu C, Kim A, Corbin JM, Wang GG. Onco-condensates: formation, multi-component organization, and biological functions. Trends Cancer 2023; 9:738-751. [PMID: 37349246 PMCID: PMC10524369 DOI: 10.1016/j.trecan.2023.05.006] [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: 03/28/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
Numerous cellular processes occur in the context of condensates, a type of large, membrane-less biomolecular assembly generated through phase separation. These condensates function as a hub of diversified cellular events by concentrating the required components. Cancer frequently coopts biomolecular condensation mechanisms to promote survival and/or proliferation. Onco-condensates, which refer to those that have causal roles or are critically involved in tumorigenicity, operate to abnormally elevate biological output of a proliferative process, or to suppress a tumor-suppressive pathway, thereby promoting oncogenesis. Here, we summarize advances regarding how multi-component onco-condensates are established and organized to promote oncogenesis, with those related to chromatin and transcription deregulation used as showcases. A better understanding should enable development of new means of targeting onco-condensates as potential therapeutics.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joshua M Corbin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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7
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Rasouli M, Blair H, Troester S, Szoltysek K, Cameron R, Ashtiani M, Krippner-Heidenreich A, Grebien F, McGeehan G, Zwaan CM, Heidenreich O. The MLL-Menin Interaction is a Therapeutic Vulnerability in NUP98-rearranged AML. Hemasphere 2023; 7:e935. [PMID: 37520776 PMCID: PMC10378738 DOI: 10.1097/hs9.0000000000000935] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Chromosomal translocations involving the NUP98 locus are among the most prevalent rearrangements in pediatric acute myeloid leukemia (AML). AML with NUP98 fusions is characterized by high expression of HOXA and MEIS1 genes and is associated with poor clinical outcome. NUP98 fusion proteins are recruited to their target genes by the mixed lineage leukemia (MLL) complex, which involves a direct interaction between MLL and Menin. Here, we show that therapeutic targeting of the Menin-MLL interaction inhibits the propagation of NUP98-rearrranged AML both ex vivo and in vivo. Treatment of primary AML cells with the Menin inhibitor revumenib (SNDX-5613) impairs proliferation and clonogenicity ex vivo in long-term coculture and drives myeloid differentiation. These phenotypic effects are associated with global gene expression changes in primary AML samples that involve the downregulation of many critical NUP98 fusion protein-target genes, such as MEIS1 and CDK6. In addition, Menin inhibition reduces the expression of both wild-type FLT3 and mutated FLT3-ITD, and in combination with FLT3 inhibitor, suppresses patient-derived NUP98-r AML cells in a synergistic manner. Revumenib treatment blocks leukemic engraftment and prevents leukemia-associated death of immunodeficient mice transplanted with NUP98::NSD1 FLT3-ITD-positive patient-derived AML cells. These results demonstrate that NUP98-rearranged AMLs are highly susceptible to inhibition of the MLL-Menin interaction and suggest the inclusion of AML patients harboring NUP98 fusions into the clinical evaluation of Menin inhibitors.
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Affiliation(s)
- Milad Rasouli
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Hematology/Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Selina Troester
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Katarzyna Szoltysek
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
- Maria Sklodowska-Curie Institute – Oncology Center, Gliwice Branch, Poland
| | - Rachel Cameron
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Minoo Ashtiani
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
| | | | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | | | - C. Michel Zwaan
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Hematology/Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Olaf Heidenreich
- Princess Maxima Center for pediatric Oncology, Utrecht, The Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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8
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Jevtic Z, Allram M, Grebien F, Schwaller J. Biomolecular Condensates in Myeloid Leukemia: What Do They Tell Us? Hemasphere 2023; 7:e923. [PMID: 37388925 PMCID: PMC10306439 DOI: 10.1097/hs9.0000000000000923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Recent studies have suggested that several oncogenic and tumor-suppressive proteins carry out their functions in the context of specific membrane-less cellular compartments. As these compartments, generally referred to as onco-condensates, are specific to tumor cells and are tightly linked to disease development, the mechanisms of their formation and maintenance have been intensively studied. Here we review the proposed leukemogenic and tumor-suppressive activities of nuclear biomolecular condensates in acute myeloid leukemia (AML). We focus on condensates formed by oncogenic fusion proteins including nucleoporin 98 (NUP98), mixed-lineage leukemia 1 (MLL1, also known as KMT2A), mutated nucleophosmin (NPM1c) and others. We also discuss how altered condensate formation contributes to malignant transformation of hematopoietic cells, as described for promyelocytic leukemia protein (PML) in PML::RARA-driven acute promyelocytic leukemia (APL) and other myeloid malignancies. Finally, we discuss potential strategies for interfering with the molecular mechanisms related to AML-associated biomolecular condensates, as well as current limitations of the field.
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Affiliation(s)
- Zivojin Jevtic
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
| | - Melanie Allram
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Juerg Schwaller
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
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9
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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10
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Berardi A, Botrugno OA, Quilici G, Manteiga JMG, Bachi A, Tonon G, Musco G. Nizp1 is a specific
NUP98
‐
NSD1
functional interactor that regulates
NUP98
‐
NSD1
‐dependent oncogenic programs. FEBS J 2022; 290:1782-1797. [PMID: 36271682 DOI: 10.1111/febs.16664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
NSD1, NSD2 and NSD3 proteins constitute a family of histone 3 lysine 36 (H3K36) methyltransferases with similar domain architecture, but diversified activities, in part, dependent on their non-enzymatic domains. These domains, despite their high sequence identity, recruit the hosting proteins to different chromatin regions through the recognition of diverse epigenetic marks and/or associations to distinct interactors. In this sense, the PHDvC5HCH finger tandem domain represents a paradigmatic example of functional divergence within the NSD family. In this work, we prove and give a structural rationale for the uniqueness of the PHDvC5HCH domain of NSD1 in recognizing the C2HR Zinc finger domain of Nizp1 (NSD1 interacting Zn finger protein). Importantly, we show that, in a leukaemogenic context, Nizp1 is pivotal in driving the unscheduled expression of HoxA genes and of genes involved in the type I IFN pathway, triggered by the expression of the fusion protein NUP98-NSD1. These data provide the first insight into the pathophysiological relevance of the Nizp1-NSD1 functional association. Targeting of this interaction might open new therapeutic windows to inhibit the NUP98-NSD1 oncogenic properties.
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Affiliation(s)
- Andrea Berardi
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
| | - Oronza A. Botrugno
- Functional Genomics of Cancer, Division of Experimental Oncology IRCCS Ospedale San Raffaele Milan Italy
| | - Giacomo Quilici
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
| | | | - Angela Bachi
- Functional Proteomics Group IFOM‐FIRC Institute of Molecular Oncology Milan Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer, Division of Experimental Oncology IRCCS Ospedale San Raffaele Milan Italy
| | - Giovanna Musco
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
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11
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Zhang FL, Li DQ. Targeting Chromatin-Remodeling Factors in Cancer Cells: Promising Molecules in Cancer Therapy. Int J Mol Sci 2022; 23:12815. [PMID: 36361605 PMCID: PMC9655648 DOI: 10.3390/ijms232112815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 03/28/2024] Open
Abstract
ATP-dependent chromatin-remodeling complexes can reorganize and remodel chromatin and thereby act as important regulator in various cellular processes. Based on considerable studies over the past two decades, it has been confirmed that the abnormal function of chromatin remodeling plays a pivotal role in genome reprogramming for oncogenesis in cancer development and/or resistance to cancer therapy. Recently, exciting progress has been made in the identification of genetic alteration in the genes encoding the chromatin-remodeling complexes associated with tumorigenesis, as well as in our understanding of chromatin-remodeling mechanisms in cancer biology. Here, we present preclinical evidence explaining the signaling mechanisms involving the chromatin-remodeling misregulation-induced cancer cellular processes, including DNA damage signaling, metastasis, angiogenesis, immune signaling, etc. However, even though the cumulative evidence in this field provides promising emerging molecules for therapeutic explorations in cancer, more research is needed to assess the clinical roles of these genetic cancer targets.
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Affiliation(s)
- Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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Kurtz KJ, Conneely SE, O'Keefe M, Wohlan K, Rau RE. Murine Models of Acute Myeloid Leukemia. Front Oncol 2022; 12:854973. [PMID: 35756660 PMCID: PMC9214208 DOI: 10.3389/fonc.2022.854973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023] Open
Abstract
Acute myeloid leukemia (AML) is a phenotypically and genetically heterogeneous hematologic malignancy. Extensive sequencing efforts have mapped the genomic landscape of adult and pediatric AML revealing a number of biologically and prognostically relevant driver lesions. Beyond identifying recurrent genetic aberrations, it is of critical importance to fully delineate the complex mechanisms by which they contribute to the initiation and evolution of disease to ultimately facilitate the development of targeted therapies. Towards these aims, murine models of AML are indispensable research tools. The rapid evolution of genetic engineering techniques over the past 20 years has greatly advanced the use of murine models to mirror specific genetic subtypes of human AML, define cell-intrinsic and extrinsic disease mechanisms, study the interaction between co-occurring genetic lesions, and test novel therapeutic approaches. This review summarizes the mouse model systems that have been developed to recapitulate the most common genomic subtypes of AML. We will discuss the strengths and weaknesses of varying modeling strategies, highlight major discoveries emanating from these model systems, and outline future opportunities to leverage emerging technologies for mechanistic and preclinical investigations.
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Affiliation(s)
- Kristen J Kurtz
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Shannon E Conneely
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Madeleine O'Keefe
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
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