1
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Şenbabaoğlu Y, Prabhakar V, Khormali A, Eastham J, Liu E, Warner E, Nabet B, Srivastava M, Ballinger M, Liu K. MOSBY enables multi-omic inference and spatial biomarker discovery from whole slide images. Sci Rep 2024; 14:18271. [PMID: 39107505 PMCID: PMC11303705 DOI: 10.1038/s41598-024-69198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
The utility of deep neural nets has been demonstrated for mapping hematoxylin-and-eosin (H&E) stained image features to expression of individual genes. However, these models have not been employed to discover clinically relevant spatial biomarkers. Here we develop MOSBY (Multi-Omic translation of whole slide images for Spatial Biomarker discoverY) that leverages contrastive self-supervised pretraining to extract improved H&E whole slide images features, learns a mapping between image and bulk omic profiles (RNA, DNA, and protein), and utilizes tile-level information to discover spatial biomarkers. We validate MOSBY gene and gene set predictions with spatial transcriptomic and serially-sectioned CD8 IHC image data. We demonstrate that MOSBY-inferred colocalization features have survival-predictive power orthogonal to gene expression, and enable concordance indices highly competitive with survival-trained multimodal networks. We identify and validate (1) an ER stress-associated colocalization feature as a chemotherapy-specific risk factor in lung adenocarcinoma, and (2) the colocalization of T effector cell vs cysteine signatures as a negative prognostic factor in multiple cancer indications. The discovery of clinically relevant biologically interpretable spatial biomarkers showcases the utility of the model in unraveling novel insights in cancer biology as well as informing clinical decision-making.
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Affiliation(s)
| | | | | | - Jeff Eastham
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Evan Liu
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Elisa Warner
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Barzin Nabet
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | | | | | - Kai Liu
- Genentech, Inc., South San Francisco, CA, 94080, USA.
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2
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Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Côté J, Nogales E. Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science 2024:eadl5816. [PMID: 39088653 DOI: 10.1126/science.adl5816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/25/2024] [Accepted: 06/25/2024] [Indexed: 08/03/2024]
Abstract
The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the EP400 subunit serves as a scaffold holding the different functional modules in specific positions, creating a unique arrangement of the ARP module. EP400 interacts with the TRRAP subunit using a footprint that overlaps with that of the SAGA acetyltransferase complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
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Affiliation(s)
- Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, USA
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Arul Banerjea
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Amélie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Endocrinology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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3
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Hedayati N, Mafi A, Farahani A, Hashemi M, Nabavi N, Alimohammadi M, Rahimzadeh P, Taheriazam A, Farahani N. The importance of the circRNA/Wnt axis in gliomas: Biological functions and clinical opportunities. Pathol Res Pract 2024; 261:155510. [PMID: 39116573 DOI: 10.1016/j.prp.2024.155510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Gliomas are among the most common cancers in the central nervous system, arising through various signaling pathways. One significant pathway is Wnt signaling, a tightly regulated process that plays a crucial role in gliomagenesis and development. The current study aims to explore the relationship between circular RNAs (circRNAs) and the Wnt/β-catenin signaling pathway in gliomas, considering the growing recognition of circRNAs in disease pathogenesis. A comprehensive review of recent research was conducted to investigate the roles of circRNAs in gliomas, focusing on their expression patterns and interactions with the Wnt signaling pathway. The analysis included studies examining circRNAs' function as microRNA sponges and their impact on glioma biology. The findings reveal that circRNAs are differentially expressed in gliomas and significantly influence the occurrence, growth, and metastasis of these tumors. Specifically, circRNAs interact with the Wnt signaling pathway, affecting glioma development and progression. This interaction highlights the importance of circRNAs in glioma pathophysiology. Understanding the regulatory network involving circRNAs and Wnt signaling offers valuable insights into glioma pathophysiology. CircRNAs hold promise as diagnostic and prognostic biomarkers and may serve as targets for novel therapeutic strategies in glioma treatment.
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Affiliation(s)
- Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Alireza Mafi
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Aryan Farahani
- Student Research Committee, Faculty of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Noushin Nabavi
- Independent Researcher, Victoria, British Columbia, Canada
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Payman Rahimzadeh
- Surgical Research Society (SRS), Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Najma Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.
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4
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Gayer FA, Klaus L, Reichardt SD, Fichtner A, Reichardt HM. Phenotype and gene signature of testicular tumors in 129.MOLF-Chr19 mice resemble human teratomas. Andrology 2024. [PMID: 39074032 DOI: 10.1111/andr.13717] [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: 02/27/2024] [Revised: 07/02/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Testicular germ cell tumor (TGCT) is the most common type of tumor in young men. Type II germ cell tumors including postpubertal-type teratomas are derived from the germ cell neoplasia in situ (GCNIS), whereas prepubertal-type teratomas arise independently of the GCNIS. The consomic mouse strain 129.MOLF-Chr19 (M19) is a suitable murine model of such tumors, but its characterization remains incomplete. OBJECTIVE Here, we interrogated the suitability of testicular tumors in M19 mice as a model of human TGCT by analyzing their histological features and gene expression signature. MATERIAL AND METHODS Testes collected from M19 mice of different ages were categorized by macroscopic appearance based on size and the degree of suspected tumorigenesis. Histological sections from selected tumors were stained with Hematoxylin and Eosin, and expression of genes associated with tumorigenesis was determined in frozen tissue samples from a large range of tumors of different subclasses using RT-qPCR and Fluidigm Dynamic Arrays. RESULTS Macroscopically, testicular specimens appeared very heterogeneous concerning size and signs indicating the presence of a tumor. Histological analysis confirmed the development of teratomas with areas of cells corresponding to all three germ cell layers. Gene expression analyses indicated upregulation of markers related to proliferation, vascular invasive potential and pluripotency, and revealed a strong correlation of gene expression with tumor size and a significant intercorrelation of individual genes. DISCUSSION AND CONCLUSION TGCT in M19 mice is reminiscent of human testicular teratomas presenting with areas of cells derived from all germ layers and showing a typical gene signature. We thus confirm that these mice can serve as a suitable murine model of pure teratomas for preclinical research.
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Affiliation(s)
- Fabian A Gayer
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
- Clinic of Urology, University Medical Center Göttingen, Göttingen, Germany
| | - Lucas Klaus
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
| | - Sybille D Reichardt
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
| | - Alexander Fichtner
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Holger M Reichardt
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
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5
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Maciejewski K, Giers M, Oleksiewicz U, Czerwinska P. The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors. Int J Mol Sci 2024; 25:7841. [PMID: 39063083 PMCID: PMC11277355 DOI: 10.3390/ijms25147841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/07/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Dysregulation of histone deacetylases (HDACs) is closely associated with cancer development and progression. Here, we comprehensively analyzed the association between all HDAC family members and several clinicopathological and molecular traits of solid tumors across 22 distinct tumor types, focusing primarily on cancer stemness and immunity. To this end, we used publicly available TCGA data and several bioinformatic tools (i.e., GEPIA2, TISIDB, GSCA, Enrichr, GSEA). Our analyses revealed that class I and class II HDAC proteins are associated with distinct cancer phenotypes. The transcriptomic profiling indicated that class I HDAC members, including HDAC2, are positively associated with cancer stemness, while class IIA HDAC proteins, represented by HDAC7, show a negative correlation to cancer stem cell-like phenotypes in solid tumors. In contrast to tumors with high amounts of HDAC7 proteins, the transcriptome signatures of HDAC2-overexpressing cancers are significantly enriched with biological terms previously determined as stemness-associated genes. Moreover, high HDAC2-expressing tumors are depleted with immune-related processes, and HDAC2 expression correlates with tumor immunosuppressive microenvironments. On the contrary, HDAC7 upregulation is significantly associated with enhanced immune responses, followed by enriched infiltration of CD4+ and CD8+ T cells. This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors.
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Affiliation(s)
- Kacper Maciejewski
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
| | - Marek Giers
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Patrycja Czerwinska
- Undergraduate Research Group “Biobase”, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (K.M.); (M.G.)
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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6
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Pan Z, Ke C, Zheng H, Guo X, Gao W, Huang X, Chen C, Xiong Y, Zheng S, Zheng F, Hu W. FERMT1 suppression induces anti-tumor effects and reduces stemness in glioma cancer cells. J Cancer Res Clin Oncol 2024; 150:338. [PMID: 38976072 PMCID: PMC11231014 DOI: 10.1007/s00432-024-05859-3] [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: 04/01/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
OBJECTIVE Glioma is a leading cause of mortality worldwide, its recurrence poses a major challenge in achieving effective treatment outcomes. Cancer stem cells (CSCs) have emerged as key contributors to tumor relapse and chemotherapy resistance, making them attractive targets for glioma cancer therapy. This study investigated the potential of FERMT1 as a prognostic biomarker and its role in regulating stemness through cell cycle in glioma. METHODS Using data from TCGA-GBM, GSE4290, GSE50161 and GSE147352 for analysis of FERMT1 expression in glioma tissues. Then, the effects of FERMT1 knockdown on cell cycle, proliferation, sphere formation ability, invasion and migration were investigated. The influences of FERMT1 on expression of glycolysis-related proteins and levels of ATP, glucose, lactate and G6PDH were also explored. Furthermore, the effects of FERMT1 knockdown on cellular metabolism were evidenced. RESULTS Significant upregulation of FERMT1 in glioma tissues was observed. Silencing FERMT1 not only affected the cell cycle but also led to a notable reduction in proliferation, invasion and migration. The expression of glycolysis-associated proteins including GLUT1, GLUT3, GLUT4, and SCO2 were reduced by FERMT1 knockdown, resulted in increased ATP and glucose as well as decreased lactic acid and G6PDH levels. FERMT1 knockdown also inhibited cellular metabolism. Moreover, FERMT1 knockdown significantly reduced sphere diameter, along with inhibiting the expression of transcription factors associated with stemness in glioma cells. CONCLUSION These findings demonstrated that FERMT1 could be an ideal target for the advancement of innovative strategies against glioma treatment via modulating cellular process involved in stemness regulation and metabolism.
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Affiliation(s)
- Zhigang Pan
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Chuhan Ke
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Hanlin Zheng
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Xiumei Guo
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Wen Gao
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Xinyue Huang
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Chunhui Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Yu Xiong
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Shuni Zheng
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China.
| | - Feng Zheng
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China.
| | - Weipeng Hu
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, 34# zhongshan North Road, Quanzhou, Fujian, 362000, China.
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7
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [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: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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8
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Zhou Y, Ray PS, Zhu J, Stein F, Rettel M, Sekaran T, Sahadevan S, Perez-Perri JI, Roth EK, Myklebost O, Meza-Zepeda LA, von Deimling A, Fu C, Brosig AN, Boye K, Nathrath M, Blattmann C, Lehner B, Hentze MW, Kulozik AE. Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma. Nat Commun 2024; 15:2810. [PMID: 38561347 PMCID: PMC10984982 DOI: 10.1038/s41467-024-47031-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: 01/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor with a strong tendency to metastasize, limiting the prognosis of affected patients. Genomic, epigenomic and transcriptomic analyses have demonstrated the exquisite molecular complexity of this tumor, but have not sufficiently defined the underlying mechanisms or identified promising therapeutic targets. To systematically explore RNA-protein interactions relevant to OS, we define the RNA interactomes together with the full proteome and the transcriptome of cells from five malignant bone tumors (four osteosarcomata and one malignant giant cell tumor of the bone) and from normal mesenchymal stem cells and osteoblasts. These analyses uncover both systematic changes of the RNA-binding activities of defined RNA-binding proteins common to all osteosarcomata and individual alterations that are observed in only a subset of tumors. Functional analyses reveal a particular vulnerability of these tumors to translation inhibition and a positive feedback loop involving the RBP IGF2BP3 and the transcription factor Myc which affects cellular translation and OS cell viability. Our results thus provide insight into potentially clinically relevant RNA-binding protein-dependent mechanisms of osteosarcoma.
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Affiliation(s)
- Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Partho Sarothi Ray
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jianguo Zhu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Eva K Roth
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ola Myklebost
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Chuli Fu
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika N Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University of Munich, School of Medicine, Munich, Germany
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Claudia Blattmann
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Burkhard Lehner
- Department of Orthopaedics, Trauma Surgery and Paraplegiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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9
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Wu T, Chen Y, You Q, Jiang Z, Chen X. Targeting bromodomian-containing protein 8 (BRD8): An advanced tool to interrogate BRD8. Eur J Med Chem 2024; 268:116271. [PMID: 38401187 DOI: 10.1016/j.ejmech.2024.116271] [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: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Epigenetic modifications play crucial roles in physiological processes, including cell differentiation, proliferation, and death. Bromodomain/Brd-containing proteins (BCPs) regulate abnormal gene expression in various diseases by recognizing the lysine-ε-N-acetylated residues (KAc) or by acting as transcriptional co-activators. Small molecule inhibitors targeting BCPs offer an attractive strategy for modulating aberrant gene expression. Besides the extensive research on the bromodomain and extra-terminal (BET) domain family proteins, the non-BET proteins have gained increasing attention. Bromodomain containing protein 8 (BRD8), a reader of KAc and co-activator of nuclear receptors (NRs), plays a key role in various cancers. This review provides a comprehensive analysis of the structure, disease-related functions, and inhibitor development of BRD8. Opportunities and challenges for future studies targeting BRD8 in disease treatment are discussed.
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Affiliation(s)
- Tingting Wu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yali Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xuetao Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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10
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Liu W, Liu X, Li L, Tai Z, Li G, Liu JX. EPC1/2 regulate hematopoietic stem and progenitor cell proliferation by modulating H3 acetylation and DLST. iScience 2024; 27:109263. [PMID: 38439957 PMCID: PMC10910311 DOI: 10.1016/j.isci.2024.109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/21/2023] [Accepted: 02/14/2024] [Indexed: 03/06/2024] Open
Abstract
Enhancers of polycomb 1 (EPC1) and 2 (EPC2) are involved in multiple biological processes as components of histone acetyltransferases/deacetylase complexes and transcriptional cofactors, and their dysfunction was associated with developmental defects and diseases. However, it remains unknown how their dysfunction induces hematopoietic stem and progenitor cell (HSPC) defects. Here, we show that depletion of EPC1/2 significantly reduced the number of hematopoietic stem and progenitor cells (HSPCs) in the aorta-gonad mesonephros and caudal hematopoietic tissue regions by impairing HSPC proliferation, and consistently downregulated the expression of HSPC genes in K562 cells. This study demonstrates the functions of EPC1/2 in regulating histone H3 acetylation, and in regulating DLST (dihydrolipoamide S-succinyltransferase) via H3 acetylation and cooperating with transcription factors serum response factor and FOXR2 together, and in the subsequent HSPC emergence and proliferation. Our results demonstrate the essential roles of EPC1/2 in regulating H3 acetylation, and DLST as a linkage between EPC1 and EPC2 with mitochondria metabolism, in HSPC emergence and proliferation.
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Affiliation(s)
- WenYe Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - LingYa Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - ZhiPeng Tai
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - GuoLiang Li
- College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing-Xia Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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11
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Kao YR, Chen J, Kumari R, Ng A, Zintiridou A, Tatiparthy M, Ma Y, Aivalioti MM, Moulik D, Sundaravel S, Sun D, Reisz JA, Grimm J, Martinez-Lopez N, Stransky S, Sidoli S, Steidl U, Singh R, D'Alessandro A, Will B. An iron rheostat controls hematopoietic stem cell fate. Cell Stem Cell 2024; 31:378-397.e12. [PMID: 38402617 PMCID: PMC10939794 DOI: 10.1016/j.stem.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.
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Affiliation(s)
- Yun-Ruei Kao
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anita Ng
- Karches Center for Oncology Research, the Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Madhuri Tatiparthy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Deeposree Moulik
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juliane Grimm
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Ulrich Steidl
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajat Singh
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Britta Will
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, USA.
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12
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Malla SB, Byrne RM, Lafarge MW, Corry SM, Fisher NC, Tsantoulis PK, Mills ML, Ridgway RA, Lannagan TRM, Najumudeen AK, Gilroy KL, Amirkhah R, Maguire SL, Mulholland EJ, Belnoue-Davis HL, Grassi E, Viviani M, Rogan E, Redmond KL, Sakhnevych S, McCooey AJ, Bull C, Hoey E, Sinevici N, Hall H, Ahmaderaghi B, Domingo E, Blake A, Richman SD, Isella C, Miller C, Bertotti A, Trusolino L, Loughrey MB, Kerr EM, Tejpar S, Maughan TS, Lawler M, Campbell AD, Leedham SJ, Koelzer VH, Sansom OJ, Dunne PD. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer. Nat Genet 2024; 56:458-472. [PMID: 38351382 PMCID: PMC10937375 DOI: 10.1038/s41588-024-01654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
Abstract
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1+ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers.
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Affiliation(s)
- Sudhir B Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Shania M Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | | | | | | | | | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sarah L Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Elena Grassi
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Courtney Bull
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Hoey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Nicoleta Sinevici
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Holly Hall
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Andrew Blake
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Claudio Isella
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Crispin Miller
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Maurice B Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Emma M Kerr
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Timothy S Maughan
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Owen J Sansom
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip D Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
- Cancer Research UK Scotland Institute, Glasgow, UK.
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13
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Huyghe A, Trajkova A, Lavial F. Cellular plasticity in reprogramming, rejuvenation and tumorigenesis: a pioneer TF perspective. Trends Cell Biol 2024; 34:255-267. [PMID: 37648593 DOI: 10.1016/j.tcb.2023.07.013] [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: 05/10/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
The multistep process of in vivo reprogramming, mediated by the transcription factors (TFs) Oct4, Sox2, Klf4, and c-Myc (OSKM), holds great promise for the development of rejuvenating and regenerative strategies. However, most of the approaches developed so far are accompanied by a persistent risk of tumorigenicity. Here, we review the groundbreaking effects of in vivo reprogramming with a particular focus on rejuvenation and regeneration. We discuss how the activity of pioneer TFs generates cellular plasticity that may be critical for inducing not only reprogramming and regeneration, but also cancer initiation. Finally, we highlight how a better understanding of the uncoupled control of cellular identity, plasticity, and aging during reprogramming might pave the way to the development of rejuvenating/regenerating strategies in a nontumorigenic manner.
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Affiliation(s)
- Aurélia Huyghe
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Aneta Trajkova
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Fabrice Lavial
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
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14
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Tanaka A, Ogawa M, Zhou Y, Namba K, Hendrickson RC, Miele MM, Li Z, Klimstra DS, Buckley PG, Gulcher J, Wang JY, Roehrl MHA. Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures. Cell Rep 2024; 43:113810. [PMID: 38377004 DOI: 10.1016/j.celrep.2024.113810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Metastatic progression of colorectal adenocarcinoma (CRC) remains poorly understood and poses significant challenges for treatment. To overcome these challenges, we performed multiomics analyses of primary CRC and liver metastases. Genomic alterations, such as structural variants or copy number alterations, were enriched in oncogenes and tumor suppressor genes and increased in metastases. Unsupervised mass spectrometry-based proteomics of 135 primary and 123 metastatic CRCs uncovered distinct proteomic subtypes, three each for primary and metastatic CRCs, respectively. Integrated analyses revealed that hypoxia, stemness, and immune signatures characterize these 6 subtypes. Hypoxic CRC harbors high epithelial-to-mesenchymal transition features and metabolic adaptation. CRC with a stemness signature shows high oncogenic pathway activation and alternative telomere lengthening (ALT) phenotype, especially in metastatic lesions. Tumor microenvironment analysis shows immune evasion via modulation of major histocompatibility complex (MHC) class I/II and antigen processing pathways. This study characterizes both primary and metastatic CRCs and provides a large proteogenomics dataset of metastatic progression.
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Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kei Namba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Ronald C Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew M Miele
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Paige.AI, New York, NY, USA
| | | | | | | | - Michael H A Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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15
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Villeneuve C, Hashmi A, Ylivinkka I, Lawson-Keister E, Miroshnikova YA, Pérez-González C, Myllymäki SM, Bertillot F, Yadav B, Zhang T, Matic Vignjevic D, Mikkola ML, Manning ML, Wickström SA. Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture. Nat Cell Biol 2024; 26:207-218. [PMID: 38302719 PMCID: PMC10866703 DOI: 10.1038/s41556-023-01332-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/08/2023] [Indexed: 02/03/2024]
Abstract
Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, which is initiated by the formation of an epithelial invagination-termed placode-that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions and physical compartmentalization of the placode are unknown. Here we identify a key role for coordinated mechanical forces stemming from contractile, proliferative and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which, in collaboration with polarized epithelial myosin activity, promote elongation and local tissue thickening. These mechanical stresses further enhance compartmentalization of Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodelling locally softens the basement membrane to facilitate a release of pressure on the placode, enabling localized cell divisions, tissue fluidification and epithelial invagination into the underlying mesenchyme. Together, our experiments and modelling identify dynamic cell shape transformations and tissue-scale mechanical cooperation as key factors for orchestrating organ formation.
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Affiliation(s)
- Clémentine Villeneuve
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ali Hashmi
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Irene Ylivinkka
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Yekaterina A Miroshnikova
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carlos Pérez-González
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS, Paris, France
| | - Satu-Marja Myllymäki
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Fabien Bertillot
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bhagwan Yadav
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tao Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | | | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - M Lisa Manning
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, NY, USA.
| | - Sara A Wickström
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
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16
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Yagita K. Emergence of the circadian clock oscillation during the developmental process in mammals. Curr Opin Genet Dev 2024; 84:102152. [PMID: 38266394 DOI: 10.1016/j.gde.2024.102152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024]
Abstract
The circadian clocks are cell-autonomous intrinsic oscillators existing throughout the body to coordinate intracellular and intercellular functions of each organ or tissue. The circadian clock oscillation gradually emerges during mid-to-late gestation in the mammalian developmental process. Recently, it has been revealed that the in vitro differentiation of mouse ES cells recapitulates the circadian clock development. Moreover, reprogramming of the cells results in the redisappearance of the clock, indicating that circadian clocks are tightly coupled with cellular differentiation. Interestingly, before the circadian clock develops, the embryo is governed under ultradian rhythms driven by the segmentation clock. This short review explores these observations, discussing the significance of the emergence of circadian clock oscillation during the mammalian developmental process.
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Affiliation(s)
- Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan.
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17
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Sung PJ, Selvam M, Riedel SS, Xie HM, Bryant K, Manning B, Wertheim GB, Kulej K, Pham L, Bowman RL, Peresie J, Nemeth MJ, Levine RL, Garcia BA, Meyer SE, Sidoli S, Bernt KM, Carroll M. FLT3 tyrosine kinase inhibition modulates PRC2 and promotes differentiation in acute myeloid leukemia. Leukemia 2024; 38:291-301. [PMID: 38182819 PMCID: PMC11141246 DOI: 10.1038/s41375-023-02131-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Internal tandem duplication mutations in fms-like tyrosine kinase 3 (FLT3-ITD) are recurrent in acute myeloid leukemia (AML) and increase the risk of relapse. Clinical responses to FLT3 inhibitors (FLT3i) include myeloid differentiation of the FLT3-ITD clone in nearly half of patients through an unknown mechanism. We identified enhancer of zeste homolog 2 (EZH2), a component of polycomb repressive complex 2 (PRC2), as a mediator of this effect using a proteomic-based screen. FLT3i downregulated EZH2 protein expression and PRC2 activity on H3K27me3. FLT3-ITD and loss-of-function mutations in EZH2 are mutually exclusive in human AML. We demonstrated that FLT3i increase myeloid maturation with reduced stem/progenitor cell populations in murine Flt3-ITD AML. Combining EZH1/2 inhibitors with FLT3i increased terminal maturation of leukemic cells and reduced leukemic burden. Our data suggest that reduced EZH2 activity following FLT3 inhibition promotes myeloid differentiation of FLT3-ITD leukemic cells, providing a mechanistic explanation for the clinical observations. These results demonstrate that in addition to its known cell survival and proliferation signaling, FLT3-ITD has a second, previously undefined function to maintain a myeloid stem/progenitor cell state through modulation of PRC2 activity. Our findings support exploring EZH1/2 inhibitors as therapy for FLT3-ITD AML.
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Affiliation(s)
- Pamela J Sung
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| | - Murugan Selvam
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Simone S Riedel
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katie Bryant
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bryan Manning
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Lucie Pham
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Robert L Bowman
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jennifer Peresie
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sara E Meyer
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Kathrin M Bernt
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Martin Carroll
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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18
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Scott MT, Liu W, Mitchell R, Clarke CJ, Kinstrie R, Warren F, Almasoudi H, Stevens T, Dunn K, Pritchard J, Drotar ME, Michie AM, Jørgensen HG, Higgins B, Copland M, Vetrie D. Activating p53 abolishes self-renewal of quiescent leukaemic stem cells in residual CML disease. Nat Commun 2024; 15:651. [PMID: 38246924 PMCID: PMC10800356 DOI: 10.1038/s41467-024-44771-9] [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: 10/24/2022] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Whilst it is recognised that targeting self-renewal is an effective way to functionally impair the quiescent leukaemic stem cells (LSC) that persist as residual disease in chronic myeloid leukaemia (CML), developing therapeutic strategies to achieve this have proved challenging. We demonstrate that the regulatory programmes of quiescent LSC in chronic phase CML are similar to that of embryonic stem cells, pointing to a role for wild type p53 in LSC self-renewal. In support of this, increasing p53 activity in primitive CML cells using an MDM2 inhibitor in combination with a tyrosine kinase inhibitor resulted in reduced CFC outputs and engraftment potential, followed by loss of multilineage priming potential and LSC exhaustion when combination treatment was discontinued. Our work provides evidence that targeting LSC self-renewal is exploitable in the clinic to irreversibly impair quiescent LSC function in CML residual disease - with the potential to enable more CML patients to discontinue therapy and remain in therapy-free remission.
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Affiliation(s)
- Mary T Scott
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wei Liu
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rebecca Mitchell
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cassie J Clarke
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ross Kinstrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Felix Warren
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Hassan Almasoudi
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Thomas Stevens
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Karen Dunn
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John Pritchard
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark E Drotar
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Michie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Heather G Jørgensen
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David Vetrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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19
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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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20
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Chandhasin C, Dang V, Perabo F, Del Rosario J, Chen YK, Filvaroff E, Stafford JA, Clarke M. TACH101, a first-in-class pan-inhibitor of KDM4 histone demethylase. Anticancer Drugs 2023; 34:1122-1131. [PMID: 37067993 PMCID: PMC10569680 DOI: 10.1097/cad.0000000000001514] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 04/18/2023]
Abstract
Histone lysine demethylase 4 (KDM4) is an epigenetic regulator that facilitates the transition between transcriptionally silent and active chromatin states by catalyzing the removal of methyl groups on histones H3K9, H3K36, and H1.4K26. KDM4 overamplification or dysregulation has been reported in various cancers and has been shown to drive key processes linked to tumorigenesis, such as replicative immortality, evasion of apoptosis, metastasis, DNA repair deficiency, and genomic instability. KDM4 also plays a role in epigenetic regulation of cancer stem cell renewal and has been linked to more aggressive disease and poorer clinical outcomes. The KDM4 family is composed of four main isoforms (KDM4A-D) that demonstrate functional redundancy and cross-activity; thus, selective inhibition of one isoform appears to be ineffective and pan-inhibition targeting multiple KDM4 isoforms is required. Here, we describe TACH101, a novel, small-molecule pan-inhibitor of KDM4 that selectively targets KDM4A-D with no effect on other KDM families. TACH101 demonstrated potent antiproliferative activity in cancer cell lines and organoid models derived from various histologies, including colorectal, esophageal, gastric, breast, pancreatic, and hematological malignancies. In vivo , potent inhibition of KDM4 led to efficient tumor growth inhibition and regression in several xenograft models. A reduction in the population of tumor-initiating cells was observed following TACH101 treatment. Overall, these observations demonstrate the broad applicability of TACH101 as a potential anticancer agent and support its advancement into clinical trials.
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21
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Fazilaty H, Basler K. Reactivation of embryonic genetic programs in tissue regeneration and disease. Nat Genet 2023; 55:1792-1806. [PMID: 37904052 DOI: 10.1038/s41588-023-01526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023]
Abstract
Embryonic genetic programs are reactivated in response to various types of tissue damage, providing cell plasticity for tissue regeneration or disease progression. In acute conditions, these programs remedy the damage and then halt to allow a return to homeostasis. In chronic situations, including inflammatory diseases, fibrosis and cancer, prolonged activation of embryonic programs leads to disease progression and tissue deterioration. Induction of progenitor identity and cell plasticity, for example, epithelial-mesenchymal plasticity, are critical outcomes of reactivated embryonic programs. In this Review, we describe molecular players governing reactivated embryonic genetic programs, their role during disease progression, their similarities and differences and lineage reversion in pathology and discuss associated therapeutics and drug-resistance mechanisms across many organs. We also discuss the diversity of reactivated programs in different disease contexts. A comprehensive overview of commonalities between development and disease will provide better understanding of the biology and therapeutic strategies.
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Affiliation(s)
- Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
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22
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Billingsley JL, Yevdokimova V, Ayoub K, Benoit YD. Colorectal Cancer Is Borrowing Blueprints from Intestinal Ontogenesis. Cancers (Basel) 2023; 15:4928. [PMID: 37894295 PMCID: PMC10604965 DOI: 10.3390/cancers15204928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Colorectal tumors are heterogenous cellular systems harboring small populations of self-renewing and highly tumorigenic cancer stem cells (CSCs). Understanding the mechanisms fundamental to the emergence of CSCs and colorectal tumor initiation is crucial for developing effective therapeutic strategies. Two recent studies have highlighted the importance of developmental gene expression programs as potential therapeutic targets to suppress pro-oncogenic stem cell populations in the colonic epithelium. Specifically, a subset of aberrant stem cells was identified in preneoplastic intestinal lesions sharing significant transcriptional similarities with fetal gut development. In such aberrant stem cells, Sox9 was shown as a cornerstone for altered cell plasticity, the maintenance of premalignant stemness, and subsequent colorectal tumor initiation. Independently, chemical genomics was used to identify FDA-approved drugs capable of suppressing neoplastic self-renewal based on the ontogenetic root of a target tumor and transcriptional programs embedded in pluripotency. Here, we discuss the joint conclusions from these two approaches, underscoring the importance of developmental networks in CSCs as a novel paradigm for identifying therapeutics targeting colorectal cancer stemness.
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Affiliation(s)
- Jacob L. Billingsley
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Veronika Yevdokimova
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Kristina Ayoub
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Yannick D. Benoit
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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23
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Mo J, Liu C, Li Z, Fan L, Wu S, Husain H, Zhong C, Zhang B. A bioinformatics analysis of potential cellular communication networks in non-alcoholic steatohepatitis and colorectal adenoma using scRNA-seq and bulk-seq. J Gastrointest Oncol 2023; 14:1770-1787. [PMID: 37720432 PMCID: PMC10502531 DOI: 10.21037/jgo-23-502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/27/2023] [Indexed: 09/19/2023] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is the global most common chronic liver disease. Non-alcoholic steatohepatitis (NASH), an inflammatory subtype of NAFLD, has been shown to significantly increase the risk of colorectal adenoma (CRA). Therefore, from the perspective of bioinformatics analysis, the potential mechanisms of NASH/NAFLD-CRA can be explored. Methods In this study, we screened the differentially expressed genes (DEGs) and core effect pathways between NASH and CRA by analyzing the single-cell data of CRA patients and the high-throughput sequencing data (GSE37364 and GSE89632) in the online database. We screened therapeutic targets and biomarkers through gene function classification, pathway enrichment analysis, and protein-protein interaction network analysis. In terms of single cell data, we screened the core effect pathway and specific signal pathway of cell communication through cell annotation and cell communication analyses. The purpose of the study was to find potential biomarkers, therapeutic targets, and related effect pathways of NASH-CRA. Results NASH-CRA comorbidities were concentrated in inflammatory regulation-related pathways, and the core genes of disease progression included IL1B, FOSL1, EGR1, MYC, PTGS2, and FOS. The results suggested the key pathway of NASH-CRA might be the WNT pathway. The main cell signal communication pathways included WNT2B - (FZD6 + LRP5) and WNT2B - (FZD6 + LRP6). The send-receive process occurred in embryonic stem cells. Conclusions The core genes of NASH-CRA (FOS, EGR1, MYC, PTGS2, FOSL1, and IL1B) may participate in inflammation and immune responses through up-regulation in the process of disease occurrence, interfering with the pathophysiological process of CRA and NASH. NASH-CRA produces cell signal communication in the WNT pathway sent by WNT2B and received by FZD6, LRP5, and LRP6 in embryonic stem cells. These findings may help formulate early diagnosis and treatment strategies for CRA in NAFLD/NASH patients, and further explore corresponding prognostic markers and potential approaches. The significance of scRNA-seq in exploring tumor heterogeneity lies in promoting our understanding of the expression program of tumor related genes in tumor development patterns. However, the biggest challenge is that this analysis may miss out on some biologically significant gene expression programs.
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Affiliation(s)
- Jiahao Mo
- The Second Clinical Medical College of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Chang Liu
- The Second Clinical Medical College of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Zhuolin Li
- The Second Clinical Medical College of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Longxiu Fan
- The Second Clinical Medical College of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Shaohua Wu
- The Second Clinical Medical College of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Hatim Husain
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Cailing Zhong
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Beiping Zhang
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
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24
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Biswas S, Kang K, Ng KP, Radivoyevitch T, Schalper K, Zhang H, Lindner DJ, Thomas A, MacPherson D, Gastman B, Schrump DS, Wong KK, Velcheti V, Saunthararajah Y. Neuroendocrine lineage commitment of small cell lung cancers can be leveraged into p53-independent non-cytotoxic therapy. Cell Rep 2023; 42:113016. [PMID: 37597186 PMCID: PMC10528072 DOI: 10.1016/j.celrep.2023.113016] [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: 02/22/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023] Open
Abstract
Small cell lung cancers (SCLCs) rapidly resist cytotoxic chemotherapy and immune checkpoint inhibitor (ICI) treatments. New, non-cross-resistant therapies are thus needed. SCLC cells are committed into neuroendocrine lineage then maturation arrested. Implicating DNA methyltransferase 1 (DNMT1) in the maturation arrests, we find (1) the repression mark methylated CpG, written by DNMT1, is retained at suppressed neuroendocrine-lineage genes, even as other repression marks are erased; (2) DNMT1 is recurrently amplified, whereas Ten-Eleven-Translocation 2 (TET2), which functionally opposes DNMT1, is deleted; (3) DNMT1 is recruited into neuroendocrine-lineage master transcription factor (ASCL1, NEUROD1) hubs in SCLC cells; and (4) DNMT1 knockdown activated ASCL1-target genes and released SCLC cell-cycling exits by terminal lineage maturation, which are cycling exits that do not require the p53/apoptosis pathway used by cytotoxic chemotherapy. Inhibiting DNMT1/corepressors with clinical compounds accordingly extended survival of mice with chemorefractory and ICI-refractory, p53-null, disseminated SCLC. Lineage commitment of SCLC cells can hence be leveraged into non-cytotoxic therapy able to treat chemo/ICI-refractory SCLC.
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Affiliation(s)
- Sudipta Biswas
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kai Kang
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kwok Peng Ng
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kurt Schalper
- Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Hua Zhang
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Daniel J Lindner
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anish Thomas
- Experimental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Brian Gastman
- Department of Plastic Surgery, Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kwok-Kin Wong
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Vamsidhar Velcheti
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA.
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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25
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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26
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Gao F, Zhou H, Huang X, Xie H, Zhou L, Chen J, Zheng S. WDR74 serves as a novel therapeutic target by its oncogenic role in hepatocellular carcinoma. Pathol Res Pract 2023; 248:154622. [PMID: 37331183 DOI: 10.1016/j.prp.2023.154622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most refractory human malignancies. WD repeat-containing protein 74 (WDR74) is involved in the tumorigenesis of various cancers, however, its clinical implications and biological function in HCC have yet to be clearly determined. METHODS Bioinformatics analysis was conducted using various databases, including The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and UALCAN. The expression of WDR74 was confirmed in HCC tumor samples and the corresponding adjacent nontumor samples by qRT-PCR, western blot and immunohistochemistry. Functional enrichment analysis was used for the biological function prediction. In vitro experiments were performed to determine the effects of WDR74 on HCC cell proliferation. RESULTS Our findings revealed that WDR74 was markedly upregulated in HCC tissues. Increased WDR74 expression had an unfavorable overall survival (OS). Multivariate Cox regression analysis demonstrated that WDR74 was an independent prognostic factor for OS in patients with HCC. Functional enrichment analysis suggested a significant correlation with cytokine-cytokine receptor interaction pathway in both TCGA-LIHC and GSE112790 datasets. Gene set enrichment analysis showed that WDR74 is probably involved in several pathways, such as MYC targets, ribosome, translation, and cell cycle. Finally, WDR74 knockdown reduced HCC cell proliferation by restraining the G1/S cell cycle transition and inducing apoptosis. CONCLUSIONS The current study demonstrates that elevated WDR74 expression is linked to an accelerated rate of tumor cell proliferation and is indicative of a poorer outcome in patients with HCC. Therefore, WDR74 could be used as a reliable prognostic biomarker and is a potential therapeutic target for HCC.
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Affiliation(s)
- Feng Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, China; NHC Key Laboratory of Combined Multi-organ Transplantation, China; Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), China; Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou 310003, China
| | - Hui Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaosong Huang
- Department of Pharmacy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Haiyang Xie
- NHC Key Laboratory of Combined Multi-organ Transplantation, China; Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), China; Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou 310003, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-organ Transplantation, China; Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), China; Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou 310003, China
| | - Junru Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, China; NHC Key Laboratory of Combined Multi-organ Transplantation, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, China; NHC Key Laboratory of Combined Multi-organ Transplantation, China; Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), China; Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province, Hangzhou 310003, China.
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27
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Aranda S, Alcaine-Colet A, Ballaré C, Blanco E, Mocavini I, Sparavier A, Vizán P, Borràs E, Sabidó E, Di Croce L. Thymine DNA glycosylase regulates cell-cycle-driven p53 transcriptional control in pluripotent cells. Mol Cell 2023:S1097-2765(23)00517-8. [PMID: 37506700 DOI: 10.1016/j.molcel.2023.07.003] [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: 01/31/2022] [Revised: 04/11/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Cell cycle progression is linked to transcriptome dynamics and variations in the response of pluripotent cells to differentiation cues, mostly through unknown determinants. Here, we characterized the cell-cycle-associated transcriptome and proteome of mouse embryonic stem cells (mESCs) in naive ground state. We found that the thymine DNA glycosylase (TDG) is a cell-cycle-regulated co-factor of the tumor suppressor p53. Furthermore, TDG and p53 co-bind ESC-specific cis-regulatory elements and thereby control transcription of p53-dependent genes during self-renewal. We determined that the dynamic expression of TDG is required to promote the cell-cycle-associated transcriptional heterogeneity. Moreover, we demonstrated that transient depletion of TDG influences cell fate decisions during the early differentiation of mESCs. Our findings reveal an unanticipated role of TDG in promoting molecular heterogeneity during the cell cycle and highlight the central role of protein dynamics for the temporal control of cell fate during development.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona 08025, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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28
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Andrieux G, Das T, Griffin M, Straehle J, Paine SML, Beck J, Boerries M, Heiland DH, Smith SJ, Rahman R, Chakraborty S. Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence. Genome Med 2023; 15:48. [PMID: 37434262 PMCID: PMC10337060 DOI: 10.1186/s13073-023-01207-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Spatiotemporal heterogeneity originating from genomic and transcriptional variation was found to contribute to subtype switching in isocitrate dehydrogenase-1 wild-type glioblastoma (GBM) prior to and upon recurrence. Fluorescence-guided neurosurgical resection utilizing 5-aminolevulinic acid (5ALA) enables intraoperative visualization of infiltrative tumors outside the magnetic resonance imaging contrast-enhanced regions. The cell population and functional status of tumor responsible for enhancing 5ALA-metabolism to fluorescence-active PpIX remain elusive. The close spatial proximity of 5ALA-metabolizing (5ALA +) cells to residual disease remaining post-surgery renders 5ALA + biology an early a priori proxy of GBM recurrence, which is poorly understood. METHODS We performed spatially resolved bulk RNA profiling (SPRP) analysis of unsorted Core, Rim, Invasive margin tissue, and FACS-isolated 5ALA + /5ALA - cells from the invasive margin across IDH-wt GBM patients (N = 10) coupled with histological, radiographic, and two-photon excitation fluorescence microscopic analyses. Deconvolution of SPRP followed by functional analyses was performed using CIBEROSRTx and UCell enrichment algorithms, respectively. We further investigated the spatial architecture of 5ALA + enriched regions by analyzing spatial transcriptomics from an independent IDH-wt GBM cohort (N = 16). Lastly, we performed survival analysis using Cox Proportinal-Hazards model on large GBM cohorts. RESULTS SPRP analysis integrated with single-cell and spatial transcriptomics uncovered that the GBM molecular subtype heterogeneity is likely to manifest regionally in a cell-type-specific manner. Infiltrative 5ALA + cell population(s) harboring transcriptionally concordant GBM and myeloid cells with mesenchymal subtype, -active wound response, and glycolytic metabolic signature, was shown to reside within the invasive margin spatially distinct from the tumor core. The spatial co-localization of the infiltrating MES GBM and myeloid cells within the 5ALA + region indicates PpIX fluorescence can effectively be utilized to resect the immune reactive zone beyond the tumor core. Finally, 5ALA + gene signatures were associated with poor survival and recurrence in GBM, signifying that the transition from primary to recurrent GBM is not discrete but rather a continuum whereby primary infiltrative 5ALA + remnant tumor cells more closely resemble the eventual recurrent GBM. CONCLUSIONS Elucidating the unique molecular and cellular features of the 5ALA + population within tumor invasive margin opens up unique possibilities to develop more effective treatments to delay or block GBM recurrence, and warrants commencement of such treatments as early as possible post-surgical resection of the primary neoplasm.
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Affiliation(s)
- Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tonmoy Das
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Systems Cell-Signaling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Michaela Griffin
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jakob Straehle
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Simon M L Paine
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stuart J Smith
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ruman Rahman
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Sajib Chakraborty
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Systems Cell-Signaling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
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29
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Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI. Cell state-dependent chromatin targeting in NUT carcinoma. Genetics 2023; 224:iyad083. [PMID: 37119804 PMCID: PMC10691748 DOI: 10.1093/genetics/iyad083] [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: 03/07/2023] [Revised: 03/07/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of 2 normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC, and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Disease Biology Department, Triana Biomedicine, Lexington, MA 02421, USA
| | - Barry M Zee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Proteomics Department, Cell Signaling Technology, Danvers, MA 01923, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica L Makofske
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Oncology Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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30
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Orlando L, Benoit YD, Reid JC, Nakanishi M, Boyd AL, García-Rodriguez JL, Tanasijevic B, Doyle MS, Luchman A, Restall IJ, Bergin CJ, Masibag AN, Aslostovar L, Di Lu J, Laronde S, Collins TJ, Weiss S, Bhatia M. Chemical genomics reveals targetable programs of human cancers rooted in pluripotency. Cell Chem Biol 2023:S2451-9456(23)00158-7. [PMID: 37379846 DOI: 10.1016/j.chembiol.2023.06.004] [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: 12/06/2022] [Revised: 04/04/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023]
Abstract
Overlapping principles of embryonic and tumor biology have been described, with recent multi-omics campaigns uncovering shared molecular profiles between human pluripotent stem cells (hPSCs) and adult tumors. Here, using a chemical genomic approach, we provide biological evidence that early germ layer fate decisions of hPSCs reveal targets of human cancers. Single-cell deconstruction of hPSCs-defined subsets that share transcriptional patterns with transformed adult tissues. Chemical screening using a unique germ layer specification assay for hPSCs identified drugs that enriched for compounds that selectively suppressed the growth of patient-derived tumors corresponding exclusively to their germ layer origin. Transcriptional response of hPSCs to germ layer inducing drugs could be used to identify targets capable of regulating hPSC specification as well as inhibiting adult tumors. Our study demonstrates properties of adult tumors converge with hPSCs drug induced differentiation in a germ layer specific manner, thereby expanding our understanding of cancer stemness and pluripotency.
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Affiliation(s)
- Luca Orlando
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Yannick D Benoit
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jennifer C Reid
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Mio Nakanishi
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Allison L Boyd
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | | | - Borko Tanasijevic
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Meaghan S Doyle
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Artee Luchman
- Arnie Charbonneau Cancer Institute & The Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Ian J Restall
- Arnie Charbonneau Cancer Institute & The Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Christopher J Bergin
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Angelique N Masibag
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lili Aslostovar
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Justin Di Lu
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Sarah Laronde
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Tony J Collins
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
| | - Samuel Weiss
- Arnie Charbonneau Cancer Institute & The Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Mickie Bhatia
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada.
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31
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Fritzke M, Chen K, Tang W, Stinson S, Pham T, Wang Y, Xu L, Chen EY. The MYC-YBX1 Circuit in Maintaining Stem-like Vincristine-Resistant Cells in Rhabdomyosarcoma. Cancers (Basel) 2023; 15:2788. [PMID: 37345125 DOI: 10.3390/cancers15102788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that causes significant devastation, with no effective therapy for relapsed disease. The mechanisms behind treatment failures are poorly understood. Our study showed that treatment of RMS cells with vincristine led to an increase in CD133-positive stem-like resistant cells. Single cell RNAseq analysis revealed that MYC and YBX1 were among the top-scoring transcription factors in CD133-high expressing cells. Targeting MYC and YBX1 using CRISPR/Cas9 reduced stem-like characteristics and viability of the vincristine-resistant cells. MYC and YBX1 showed mutual regulation, with MYC binding to the YBX1 promoter and YBX1 binding to MYC mRNA. The MYC inhibitor MYC361i synergized with vincristine to reduce tumor growth and stem-like cells in a zebrafish model of RMS. MYC and YBX expression showed a positive correlation in RMS patients, and high MYC expression correlated with poor survival. Targeting the MYC-YBX1 axis holds promise for improving survival in RMS patients.
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Affiliation(s)
- Madeline Fritzke
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weiliang Tang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Spencer Stinson
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Thao Pham
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
- Astellas US Technologies, Universal Cells, Inc., Seattle, WA 98121, USA
| | - Yadong Wang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eleanor Y Chen
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
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32
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Huang Y, Mo W, Ding X, Ding Y. Long non-coding RNAs in breast cancer stem cells. Med Oncol 2023; 40:177. [PMID: 37178429 DOI: 10.1007/s12032-023-02046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Breast cancer, one of the most commonly diagnosed cancers worldwide, is a heterogeneous disease with high rates of recurrence and metastasis that contribute to its high mortality rate. Breast cancer stem cells (BCSCs) are a small but significant subset of heterogeneous breast cancer cells that possess stem cell characteristics such as self-renewal and differentiation abilities that may drive metastasis and recurrence. Long non-coding RNAs (lncRNAs) are a class of RNAs that are longer than 200 nucleotides in length and do not possess protein-coding properties. An increasing number of studies have shown that some lncRNAs are abnormally expressed in BCSCs, and have great biological significance in the occurrence, progression, invasion, and metastasis of various cancers. However, the importance of lncRNAs, as well as the molecular mechanisms that regulate and promote the stemness of BCSCs, are still poorly understood. In the current review, we aim to summarize recent studies that highlight the role of lncRNAs in tumor occurrence and progression through BCSCs. In addition, the utility of lncRNAs as biomarkers of breast cancer progression, and their potential use as therapeutic targets for treatment of breast cancer, will be discussed.
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Affiliation(s)
- Yuting Huang
- Department of Oncology, Wenzhou Medical University, Wenzhou, 325035, China
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Wenju Mo
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Xiaowen Ding
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
| | - Yuqin Ding
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
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33
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Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI. Cell state-dependent chromatin targeting in NUT carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537367. [PMID: 37131839 PMCID: PMC10153199 DOI: 10.1101/2023.04.18.537367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of two normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC , and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
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Affiliation(s)
- Artyom A Alekseyenko
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Triana Biomedicine, Lexington, MA
| | - Barry M Zee
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Cell Signaling Technology, Danvers, MA
| | - Zuzer Dhoondia
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
| | - Hyuckjoon Kang
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
| | - Jessica L Makofske
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Mitzi I Kuroda
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
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34
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Uribe-Etxebarria V, Pineda JR, García-Gallastegi P, Agliano A, Unda F, Ibarretxe G. Notch and Wnt Signaling Modulation to Enhance DPSC Stemness and Therapeutic Potential. Int J Mol Sci 2023; 24:ijms24087389. [PMID: 37108549 PMCID: PMC10138690 DOI: 10.3390/ijms24087389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
The Dental Pulp of permanent human teeth is home to stem cells with remarkable multilineage differentiation ability: human Dental Pulp Stem Cells (DPSCs). These cells display a very notorious expression of pluripotency core factors, and the ability to give rise to mature cell lineages belonging to the three embryonic layers. For these reasons, several researchers in the field have long considered human DPSCs as pluripotent-like cells. Notably, some signaling pathways such as Notch and Wnt contribute to maintaining the stemness of these cells through a complex network involving metabolic and epigenetic regulatory mechanisms. The use of recombinant proteins and selective pharmacological modulators of Notch and Wnt pathways, together with serum-free media and appropriate scaffolds that allow the maintenance of the non-differentiated state of hDPSC cultures could be an interesting approach to optimize the potency of these stem cells, without a need for genetic modification. In this review, we describe and integrate findings that shed light on the mechanisms responsible for stemness maintenance of hDPSCs, and how these are regulated by Notch/Wnt activation, drawing some interesting parallelisms with pluripotent stem cells. We summarize previous work on the stem cell field that includes interactions between epigenetics, metabolic regulations, and pluripotency core factor expression in hDPSCs and other stem cell types.
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Affiliation(s)
| | - Jose Ramon Pineda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Achucarro Basque Center for Neuroscience Fundazioa Leioa, Sede Building, 3rd Floor, 48940 Leioa, Spain
| | - Patricia García-Gallastegi
- Physiology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Alice Agliano
- Division of Radiotherapy and Imaging, Cancer Research UK Cancer Imaging Centre, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London SW7 3RP, UK
- Department of Materials and Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Fernando Unda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Gaskon Ibarretxe
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
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35
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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Xie Y, Sahin M, Wakamatsu T, Inoue-Yamauchi A, Zhao W, Han S, Nargund AM, Yang S, Lyu Y, Hsieh JJ, Leslie CS, Cheng EH. SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis. JCI Insight 2023; 8:e154120. [PMID: 36810256 PMCID: PMC9977508 DOI: 10.1172/jci.insight.154120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
SETD2, a H3K36 trimethyltransferase, is the most frequently mutated epigenetic modifier in lung adenocarcinoma, with a mutation frequency of approximately 9%. However, how SETD2 loss of function promotes tumorigenesis remains unclear. Using conditional Setd2-KO mice, we demonstrated that Setd2 deficiency accelerated the initiation of KrasG12D-driven lung tumorigenesis, increased tumor burden, and significantly reduced mouse survival. An integrated chromatin accessibility and transcriptome analysis revealed a potentially novel tumor suppressor model of SETD2 in which SETD2 loss activates intronic enhancers to drive oncogenic transcriptional output, including the KRAS transcriptional signature and PRC2-repressed targets, through regulation of chromatin accessibility and histone chaperone recruitment. Importantly, SETD2 loss sensitized KRAS-mutant lung cancer to inhibition of histone chaperones, the FACT complex, or transcriptional elongation both in vitro and in vivo. Overall, our studies not only provide insight into how SETD2 loss shapes the epigenetic and transcriptional landscape to promote tumorigenesis, but they also identify potential therapeutic strategies for SETD2 mutant cancers.
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Affiliation(s)
- Yuchen Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Merve Sahin
- Computational and Systems Biology Program, MSKCC, New York, New York, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Toru Wakamatsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Akane Inoue-Yamauchi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Wanming Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Amrita M. Nargund
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Shaoyuan Yang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Yang Lyu
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - James J. Hsieh
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | | | - Emily H. Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Department of Pathology and Laboratory Medicine, MSKCC, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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von Eyben FE, Kristiansen K, Kapp DS, Hu R, Preda O, Nogales FF. Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis. Int J Mol Sci 2023; 24:ijms24044148. [PMID: 36835562 PMCID: PMC9966837 DOI: 10.3390/ijms24044148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
In testicular germ cell tumor type II (TGCT), a seminoma subtype expresses an induced pluripotent stem cell (iPSC) panel with four upregulated genes, OCT4/POU5F1, SOX17, KLF4, and MYC, and embryonal carcinoma (EC) has four upregulated genes, OCT4/POU5F1, SOX2, LIN28, and NANOG. The EC panel can reprogram cells into iPSC, and both iPSC and EC can differentiate into teratoma. This review summarizes the literature on epigenetic regulation of the genes. Epigenetic mechanisms, such as methylations of cytosines on the DNA string and methylations and acetylations of histone 3 lysines, regulate expression of these driver genes between the TGCT subtypes. In TGCT, the driver genes contribute to well-known clinical characteristics and the driver genes are also important for aggressive subtypes of many other malignancies. In conclusion, epigenetic regulation of the driver genes are important for TGCT and for oncology in general.
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Affiliation(s)
- Finn E. von Eyben
- Center for Tobacco Control Research, Birkevej 17, 5230 Odense, Denmark
- Correspondence: ; Tel.: +45-66145862
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, August Krogh Building Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
- BGI-Research, BGI-Shenzhen, Shenzhen 518120, China
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 166555, China
| | - Daniel S. Kapp
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Rong Hu
- Department of Pathology, Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, USA
| | - Ovidiu Preda
- Department of Pathology, San Cecilio University Hospital, 18071 Granada, CP, Spain
| | - Francisco F. Nogales
- Department of Pathology, School of Medicine, University Granada, 18071 Granada, CP, Spain
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Wang E, Pineda JMB, Kim WJ, Chen S, Bourcier J, Stahl M, Hogg SJ, Bewersdorf JP, Han C, Singer ME, Cui D, Erickson CE, Tittley SM, Penson AV, Knorr K, Stanley RF, Rahman J, Krishnamoorthy G, Fagin JA, Creger E, McMillan E, Mak CC, Jarvis M, Bossard C, Beaupre DM, Bradley RK, Abdel-Wahab O. Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia. Cancer Cell 2023; 41:164-180.e8. [PMID: 36563682 PMCID: PMC9839614 DOI: 10.1016/j.ccell.2022.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments.
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Affiliation(s)
- Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Won Jun Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sisi Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessie Bourcier
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Phillipp Bewersdorf
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael E Singer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Cui
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline E Erickson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven M Tittley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Knorr
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gnana Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | | | | | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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41
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Singh A, Rajeevan A, Gopalan V, Agrawal P, Day CP, Hannenhalli S. Broad misappropriation of developmental splicing profile by cancer in multiple organs. Nat Commun 2022; 13:7664. [PMID: 36509773 PMCID: PMC9744839 DOI: 10.1038/s41467-022-35322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with key oncogenic processes and predict proliferation rates in cancer cell lines as well as patient survival. Such events preferentially target nitrosylation and transmembrane-region domains, whose coordinated splicing in multiple genes respectively affect intracellular transport and N-linked glycosylation. We infer critical splicing factors potentially regulating embryonic splicing events and show that such factors are potential oncogenic drivers and are upregulated specifically in malignant cells. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of critical splicing factors in brain and liver. Our study provides a comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest anti-cancer targets including splicing events, and their upstream splicing and transcriptional regulators.
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Affiliation(s)
- Arashdeep Singh
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Arati Rajeevan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Vishaka Gopalan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Piyush Agrawal
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Chi-Ping Day
- grid.94365.3d0000 0001 2297 5165Laboratory of Cancer Biology and Genetics National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Sridhar Hannenhalli
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
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Wang L, Tan X, Chen L, Xu S, Huang W, Chen N, Wu Y, Wang C, Zhou D, Li M. Sall4 Guides p53-Mediated Enhancer Interference upon DNA Damage in Mouse Embryonic Stem Cells. Stem Cells 2022; 40:1008-1019. [PMID: 35977539 DOI: 10.1093/stmcls/sxac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022]
Abstract
p53 plays a pivotal role in maintaining the genomic stability of mouse embryonic stem cells (mESCs) through transcriptionally activating and repressing target genes. However, how p53 recognizes its repressed targets remains largely unknown. Herein, we demonstrate that Sall4 negatively regulates DNA damage induced apoptosis (DIA) of mESCs through mediating p53 recruitment to enhancers of ESC-associated genes repressed by p53 from promoters of p53-activated genes. Upon DNA damage, Sall4 is transcriptionally repressed by p53 and plays an anti-apoptotic role without altering p53 activation. Moreover, Sall4 is identified as a novel p53-interacting partner. Consistently, Sall4 exerts its anti-apoptotic function in a p53-dependent manner. Intriguingly, Sall4 depletion not only promotes the transcriptional activation of several p53-regulated pro-apoptotic genes but also compromises p53-mediated repression of ESC master transcription factors in response to DNA damage. Mechanistically, Sall4 balances p53-binding affinity between p53-activated and -repressed genes through tethering p53 to ESC enhancers. In light of our study, Sall4 may contribute to tumorigenesis by antagonizing p53-mediated apoptosis.
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Affiliation(s)
- Lei Wang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaojun Tan
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Lu Chen
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Sisi Xu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Weiping Huang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Nan Chen
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Yizhou Wu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Chunyan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Daqiang Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Mangmang Li
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
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Zatzman M, Fuligni F, Ripsman R, Suwal T, Comitani F, Edward LM, Denroche R, Jang GH, Notta F, Gallinger S, Selvanathan SP, Toretsky JA, Hellmann MD, Tabori U, Huang A, Shlien A. Widespread hypertranscription in aggressive human cancers. SCIENCE ADVANCES 2022; 8:eabn0238. [PMID: 36417526 PMCID: PMC9683723 DOI: 10.1126/sciadv.abn0238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 05/10/2023]
Abstract
Cancers are often defined by the dysregulation of specific transcriptional programs; however, the importance of global transcriptional changes is less understood. Hypertranscription is the genome-wide increase in RNA output. Hypertranscription's prevalence, underlying drivers, and prognostic significance are undefined in primary human cancer. This is due, in part, to limitations of expression profiling methods, which assume equal RNA output between samples. Here, we developed a computational method to directly measure hypertranscription in 7494 human tumors, spanning 31 cancer types. Hypertranscription is ubiquitous across cancer, especially in aggressive disease. It defines patient subgroups with worse survival, even within well-established subtypes. Our data suggest that loss of transcriptional suppression underpins the hypertranscriptional phenotype. Single-cell analysis reveals hypertranscriptional clones, which dominate transcript production regardless of their size. Last, patients with hypertranscribed mutations have improved response to immune checkpoint therapy. Our results provide fundamental insights into gene dysregulation across human cancers and may prove useful in identifying patients who would benefit from novel therapies.
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Affiliation(s)
- Matthew Zatzman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fabio Fuligni
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan Ripsman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tannu Suwal
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rob Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | | | - Jeffrey A. Toretsky
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Annie Huang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Adam Shlien
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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Kim M, Singh M, Lee BK, Hibbs M, Richardson K, Ellies L, Wintle L, Stuart LM, Wang JY, Voon DC, Blancafort P, Wang J, Kim J, Leedman PJ, Woo AJ. A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer. Oncogenesis 2022; 11:60. [PMID: 36207293 PMCID: PMC9546828 DOI: 10.1038/s41389-022-00435-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
The MYC proto-oncogene (MYC) is one of the most frequently overexpressed genes in breast cancer that drives cancer stem cell-like traits, resulting in aggressive disease progression and poor prognosis. In this study, we identified zinc finger transcription factor 148 (ZNF148, also called Zfp148 and ZBP-89) as a direct target of MYC. ZNF148 suppressed cell proliferation and migration and was transcriptionally repressed by MYC in breast cancer. Depletion of ZNF148 by short hairpin RNA (shRNA) and CRISPR/Cas9 increased triple-negative breast cancer (TNBC) cell proliferation and migration. Global transcriptome and chromatin occupancy analyses of ZNF148 revealed a central role in inhibiting cancer cell de-differentiation and migration. Mechanistically, we identified the Inhibitor of DNA binding 1 and 3 (ID1, ID3), drivers of cancer stemness and plasticity, as previously uncharacterized targets of transcriptional repression by ZNF148. Silencing of ZNF148 increased the stemness and tumorigenicity in TNBC cells. These findings uncover a previously unknown tumor suppressor role for ZNF148, and a transcriptional regulatory circuitry encompassing MYC, ZNF148, and ID1/3 in driving cancer stem cell traits in aggressive breast cancer.
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Affiliation(s)
- Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Manjot Singh
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Moira Hibbs
- RPH Research Centre, Royal Perth Hospital, Perth, WA, 6000, Australia
| | - Kirsty Richardson
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lesley Ellies
- Division of Pharmacology and Toxicology, School of Biomedical Sciences, The University of Western Australia, Perth, WA, 6000, Australia
| | - Larissa Wintle
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lisa M Stuart
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Jenny Y Wang
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Dominic C Voon
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, 920-1192, Japan
- Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6000, Australia
- The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
| | - Andrew J Woo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6000, Australia.
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Machida K. HCV and tumor-initiating stem-like cells. Front Physiol 2022; 13:903302. [PMID: 36187761 PMCID: PMC9520593 DOI: 10.3389/fphys.2022.903302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
Neoplasms contain tumor-initiating stem-like cells (TICs) that are characterized by increased drug resistance. The incidence of many cancer types have trended downward except for few cancer types, including hepatocellular carcinoma (HCC). Therefore mechanism of HCC development and therapy resistance needs to be understood. These multiple hits by hepatitis C virus (HCV) eventually promotes transformation and TIC genesis, leading to HCC development. This review article describes links between HCV-associated HCC and TICs. This review discusses 1) how HCV promotes genesis of TICs and HCC development; 2) how this process avails itself as a novel therapeutic target for HCC treatment; and 3) ten hall marks of TIC oncogenesis and HCC development as targets for novel therapeutic modalities.
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Mohapatra BC, Mirza S, Bele A, Gurumurthy CB, Raza M, Saleem I, Storck MD, Sarkar A, Kollala SS, Shukla SK, Southekal S, Wagner KU, Qiu F, Lele SM, Alsaleem MA, Rakha EA, Guda C, Singh PK, Cardiff RD, Band H, Band V. Ecdysoneless Overexpression Drives Mammary Tumorigenesis through Upregulation of C-MYC and Glucose Metabolism. Mol Cancer Res 2022; 20:1391-1404. [PMID: 35675041 PMCID: PMC9437571 DOI: 10.1158/1541-7786.mcr-22-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 01/09/2023]
Abstract
Ecdysoneless (ECD) protein is essential for embryogenesis, cell-cycle progression, and cellular stress mitigation with an emerging role in mRNA biogenesis. We have previously shown that ECD protein as well as its mRNA are overexpressed in breast cancer and ECD overexpression predicts shorter survival in patients with breast cancer. However, the genetic evidence for an oncogenic role of ECD has not been established. Here, we generated transgenic mice with mammary epithelium-targeted overexpression of an inducible human ECD transgene (ECDTg). Significantly, ECDTg mice develop mammary hyperplasia, preneoplastic lesions, and heterogeneous tumors with occasional lung metastasis. ECDTg tumors exhibit epithelial to mesenchymal transition and cancer stem cell characteristics. Organoid cultures of ECDTg tumors showed ECD dependency for in vitro oncogenic phenotype and in vivo growth when implanted in mice. RNA sequencing (RNA-seq) analysis of ECDTg tumors showed a c-MYC signature, and alterations in ECD levels regulated c-MYC mRNA and protein levels as well as glucose metabolism. ECD knockdown-induced decrease in glucose uptake was rescued by overexpression of mouse ECD as well as c-MYC. Publicly available expression data analyses showed a significant correlation of ECD and c-MYC overexpression in breast cancer, and ECD and c-MYC coexpression exhibits worse survival in patients with breast cancer. Taken together, we establish a novel role of overexpressed ECD as an oncogenesis driver in the mouse mammary gland through upregulation of c-MYC-mediated glucose metabolism. IMPLICATIONS We demonstrate ECD overexpression in the mammary gland of mice led to the development of a tumor progression model through upregulation of c-MYC signaling and glucose metabolism.
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Affiliation(s)
- Bhopal C. Mohapatra
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Aditya Bele
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Channabasavaiah B. Gurumurthy
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Mohsin Raza
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Irfana Saleem
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Matthew D. Storck
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Aniruddha Sarkar
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Surendra K. Shukla
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Kay-Uwe Wagner
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Fang Qiu
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska
| | - Subodh M. Lele
- Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Mansour A. Alsaleem
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Department of Applied Medical Sciences, Applied College, Qassim University, Qassim, Saudi Arabia
| | - Emad A. Rakha
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Chittibabu Guda
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Pankaj K. Singh
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Robert D. Cardiff
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Hamid Band
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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Yan J, Chen Y, Patel AJ, Warda S, Lee CJ, Nixon BG, Wong EW, Miranda-Román MA, Yang N, Wang Y, Pachai MR, Sher J, Giff E, Tang F, Khurana E, Singer S, Liu Y, Galbo PM, Maag JL, Koche RP, Zheng D, Antonescu CR, Deng L, Li MO, Chen Y, Chi P. Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. J Clin Invest 2022; 132:e153437. [PMID: 35852856 PMCID: PMC9433107 DOI: 10.1172/jci153437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Immune checkpoint blockade (ICB) has demonstrated clinical success in "inflamed" tumors with substantial T cell infiltrates, but tumors with an immune-desert tumor microenvironment (TME) fail to benefit. The tumor cell-intrinsic molecular mechanisms of the immune-desert phenotype remain poorly understood. Here, we demonstrated that inactivation of the polycomb-repressive complex 2 (PRC2) core components embryonic ectoderm development (EED) or suppressor of zeste 12 homolog (SUZ12), a prevalent genetic event in malignant peripheral nerve sheath tumors (MPNSTs) and sporadically in other cancers, drove a context-dependent immune-desert TME. PRC2 inactivation reprogramed the chromatin landscape that led to a cell-autonomous shift from primed baseline signaling-dependent cellular responses (e.g., IFN-γ signaling) to PRC2-regulated developmental and cellular differentiation transcriptional programs. Further, PRC2 inactivation led to diminished tumor immune infiltrates through reduced chemokine production and impaired antigen presentation and T cell priming, resulting in primary resistance to ICB. Intratumoral delivery of inactivated modified vaccinia virus Ankara (MVA) enhanced tumor immune infiltrates and sensitized PRC2-loss tumors to ICB. Our results identify molecular mechanisms of PRC2 inactivation-mediated, context-dependent epigenetic reprogramming that underline the immune-desert phenotype in cancer. Our studies also point to intratumoral delivery of immunogenic viruses as an initial therapeutic strategy to modulate the immune-desert TME and capitalize on the clinical benefit of ICB.
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Affiliation(s)
- Juan Yan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Yuedan Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Amish J. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Sarah Warda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Cindy J. Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Briana G. Nixon
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Immunology Program, Sloan Kettering Institute
| | - Elissa W.P. Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Miguel A. Miranda-Román
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, and
| | - Ning Yang
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Yi Wang
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Mohini R. Pachai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Jessica Sher
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Emily Giff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Fanying Tang
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Institute for Computational Biomedicine
- Meyer Cancer Center, and
| | - Ekta Khurana
- Institute for Computational Biomedicine
- Meyer Cancer Center, and
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Sam Singer
- Department of Surgery, MSK Cancer Center, New York, New York, USA
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Phillip M. Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jesper L.V. Maag
- Center for Epigenetics Research, MSK Cancer Center, New York, New York, USA
| | - Richard P. Koche
- Center for Epigenetics Research, MSK Cancer Center, New York, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Neurology, and
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Liang Deng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Ming O. Li
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Immunology Program, Sloan Kettering Institute
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, and
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
- Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
- Department of Medicine, MSK Cancer Center, New York, New York, USA
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49
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Lauko A, Lo A, Ahluwalia MS, Lathia JD. Cancer cell heterogeneity & plasticity in glioblastoma and brain tumors. Semin Cancer Biol 2022; 82:162-175. [PMID: 33640445 PMCID: PMC9618157 DOI: 10.1016/j.semcancer.2021.02.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Brain tumors remain one of the most difficult tumors to treat and, depending on the diagnosis, have a poor prognosis. Of brain tumors, glioblastoma (GBM) is the most common malignant glioma and has a dismal prognosis, with only about 5% of patients alive five years after diagnosis. While advances in targeted therapies and immunotherapies are rapidly improving outcomes in a variety of other cancers, the standard of care for GBM has largely remained unaltered since 2005. There are many well-studied challenges that are either unique to brain tumors (i.e., blood-brain barrier and immunosuppressive environment) or amplified within GBM (i.e., tumor heterogeneity at the cellular and molecular levels, plasticity, and cancer stem cells) that make this disease particularly difficult to treat. While we touch on all these concepts, the focus of this review is to discuss the immense inter- and intra-tumoral heterogeneity and advances in our understanding of tumor cell plasticity and epigenetics in GBM. With each improvement in technology, our understanding of the complexity of tumoral heterogeneity and plasticity improves and we gain more clarity on the causes underlying previous therapeutic failures. However, these advances are unlocking new therapeutic opportunities that scientists and physicians are currently exploiting and have the potential for new breakthroughs.
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Affiliation(s)
- Adam Lauko
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States; Medical Scientist Training Program, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Alice Lo
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Manmeet S Ahluwalia
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States
| | - Justin D Lathia
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States; Medical Scientist Training Program, Case Western Reserve University School of Medicine, Cleveland, OH, United States; Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
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50
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Dijkwel Y, Tremethick DJ. The Role of the Histone Variant H2A.Z in Metazoan Development. J Dev Biol 2022; 10:jdb10030028. [PMID: 35893123 PMCID: PMC9326617 DOI: 10.3390/jdb10030028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 12/10/2022] Open
Abstract
During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.
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