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Liu C, Wang Y, Shi M, Tao X, Man D, Zhang J, Han B. hnRNPA0 promotes MYB expression by interacting with enhancer lncRNA MY34UE-AS in human leukemia cells. Biochem Biophys Res Commun 2024; 724:150221. [PMID: 38865811 DOI: 10.1016/j.bbrc.2024.150221] [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: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
MYB is a key regulator of hematopoiesis and erythropoiesis, and dysregulation of MYB is closely involved in the development of leukemia, however the mechanism of MYB regulation remains still unclear so far. Our previous study identified a long noncoding RNA (lncRNA) derived from the -34 kb enhancer of the MYB locus, which can promote MYB expression, the proliferation and migration of human leukemia cells, and is therefore termed MY34UE-AS. Then the interacting partner proteins of MY34UE-AS were identified and studied in the present study. hnRNPA0 was identified as a binding partner of MY34UE-AS through RNA pulldown assay, which was further validated through RNA immunoprecipitation (RIP). hnRNPA0 interacted with MY34UE-AS mainly through its RRM2 domain. hnRNPA0 overexpression upregulated MYB and increased the proliferation and migration of K562 cells, whereas hnRNPA0 knockdown showed opposite effects. Rescue experiments showed MY34UE-AS was required for above mentioned functions of hnRNPA0. These results reveal that hnRNPA0 is involved in leukemia through upregulating MYB expression by interacting with MY34UE-AS, suggesting that the hnRNPA0/MY34UE-AS axis could serve as a potential target for leukemia treatment.
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Affiliation(s)
- Chao Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Yucheng Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Mengjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Xiaoxiao Tao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Da Man
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, 201306, China.
| | - Bingshe Han
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, 201306, China.
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2
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Klein Nulent TJW, van Es RJJ, Breimer GE, Valstar MH, Smit LA, Speksnijder CM, de Bree R, Willems SM. MYB immunohistochemistry as a predictor of MYB::NFIB fusion in the diagnosis of adenoid cystic carcinoma of the head and neck. Oral Surg Oral Med Oral Pathol Oral Radiol 2024:S2212-4403(24)00433-4. [PMID: 39218775 DOI: 10.1016/j.oooo.2024.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/02/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVES Diagnosing adenoid cystic carcinoma (AdCC) is challenging due to histopathological variability and similarities with other tumors. In AdCC pathogenesis, the cellular myeloblastosis gene (c-MYB) often exhibits a MYB::NFIB fusion from a reciprocal translocation. This study aimed to assess the predictive accuracy of MYB immunohistochemistry for detecting this translocation compared to fluorescence in situ hybridization (FISH). STUDY DESIGN This study included 110 AdCC patients (1999-2017) from two Dutch head and neck centers using tissue microarrays and full slides. Median MYB expression levels by immunohistochemistry were compared based on translocation status by FISH, and differences within clinicopathological parameters were examined. An immunohistochemical cut-off was established to estimate the translocation. RESULTS MYB immunohistochemistry was available in 90/110 patients, with a median expression of 27%. FISH was interpretable in 79/108 tumors, identifying MYB::NFIB fusion in 44 (56%). Among 62 patients with both MYB expression and translocation data, the fusion was present in 38 (61%). These tumors had higher MYB expression (30%) than nontranslocated tumors (6%); P = .02. A 60% MYB expression cut-off yielded 100% specificity for detecting the translocation but had no prognostic value. CONCLUSIONS Although MYB protein expression alone lacks diagnostic precision, protein expression >60% predicted the MYB::NFIB fusion in all tumors.
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Affiliation(s)
- Thomas J W Klein Nulent
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Oral and Maxillofacial Surgery, Haaglanden Medical Center, The Hague, The Netherlands; Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Robert J J van Es
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerben E Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Matthijs H Valstar
- Department of Head and Neck Oncology and Surgery, Netherlands Cancer Institute/Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Laura A Smit
- Department of Pathology, Netherlands Cancer Institute/Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Caroline M Speksnijder
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
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3
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Zhang Y, Zhang S. CRISPR perfect adaptation for robust control of cellular immune and apoptotic responses. Nucleic Acids Res 2024:gkae665. [PMID: 39087566 DOI: 10.1093/nar/gkae665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/26/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
A central challenge in the quest for precise gene regulation within mammalian cells is the development of regulatory networks that can achieve perfect adaptation-where outputs consistently return to a set baseline post-stimulus. Here, we present such a system that leverages the CRISPR activation (CRISPRa) and anti-CRISPR proteins as two antithetic elements to establish perfect adaptation in mammalian cells and dynamically regulate gene expression. We demonstrate that this system can maintain stable expression levels of target genes in the face of external perturbations, thus providing a robust platform for biological applications. The versatility of our system is further showcased through its integration with endogenous regulatory mechanisms in T cells, such as the NF-κB-mediated immune response, and its ability to program apoptosis responses for precise spatial and temporal control of cellular growth and death. This study not only advances our understanding of gene regulation in mammalian cells but also opens new avenues for therapeutic intervention, particularly in diseases characterized by dysregulated gene expression.
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Affiliation(s)
- Yichi Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuyi Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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4
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Sommer A, Gomez Perdiguero E. Extraembryonic hematopoietic lineages-to macrophages and beyond. Exp Hematol 2024; 136:104285. [PMID: 39053841 DOI: 10.1016/j.exphem.2024.104285] [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: 06/06/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The first blood and immune cells in vertebrates emerge in the extraembryonic yolk sac. Throughout the last century, it has become evident that this extraembryonic tissue gives rise to transient primitive and definitive hematopoiesis but not hematopoietic stem cells. More recently, studies have elucidated that yolk sac-derived blood and immune cells are present far longer than originally expected. These cells take over essential roles for the survival and proper organogenesis of the developing fetus up until birth. In this review, we discuss the most recent findings and views on extraembryonic hematopoiesis in mice and humans.
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Affiliation(s)
- Alina Sommer
- Macrophages and Endothelial Cells Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France; Sorbonne Université, Collège Doctoral, Paris, France
| | - Elisa Gomez Perdiguero
- Macrophages and Endothelial Cells Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France.
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5
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Corleone G, Sorino C, Caforio M, Di Giovenale S, De Nicola F, Goeman F, Bertaina V, Pitisci A, Cortile C, Locatelli F, Folgiero V, Fanciulli M. Enhancer engagement sustains oncogenic transformation and progression of B-cell precursor acute lymphoblastic leukemia. J Exp Clin Cancer Res 2024; 43:179. [PMID: 38926853 PMCID: PMC11210131 DOI: 10.1186/s13046-024-03075-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: 04/11/2024] [Accepted: 05/18/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Enhancer reprogramming plays a significant role in the heterogeneity of cancer. However, we have limited knowledge about the impact of chromatin remodeling in B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) patients, and how it affects tumorigenesis and drug response. Our research focuses on investigating the role of enhancers in sustaining oncogenic transformation in children with BCP-ALL. METHODS We used ATAC-seq to study the accessibility of chromatin in pediatric BCP-ALL at three different stages-onset, remission, and relapse. Using a combination of computational and experimental methods, we were able to analyze the accessibility landscape and focus on the most significant cis-regulatory sites. These sites were then functionally validated through the use of Promoter capture Hi-C in a primary cell line model called LAL-B, followed by RNA-seq and genomic deletion of target sites using CRISPR-Cas9 editing. RESULTS We found that enhancer activity changes during cancer progression and is mediated by the production of enhancer RNAs (eRNAs). CRISPR-Cas9-mediated validation of previously unknown eRNA productive enhancers demonstrated their capability to control the oncogenic activities of the MYB and DCTD genes. CONCLUSIONS Our findings directly support the notion that productive enhancer engagement is a crucial determinant of the BCP-ALL and highlight the potential of enhancers as therapeutic targets in pediatric BCP-ALL.
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Affiliation(s)
- Giacomo Corleone
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Cristina Sorino
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Matteo Caforio
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Stefano Di Giovenale
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
- Department of Computer, Control, and Management, Engineering Antonio Ruberti, Sapienza University of Rome, Rome, 00161, Italy
| | - Francesca De Nicola
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Frauke Goeman
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Valentina Bertaina
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Angela Pitisci
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Clelia Cortile
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Valentina Folgiero
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy.
| | - Maurizio Fanciulli
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy.
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6
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Lipsick J. A History of Cancer Research: Oncogenic Transcription Factors. Cold Spring Harb Perspect Biol 2024; 16:a035881. [PMID: 38830699 PMCID: PMC11146308 DOI: 10.1101/cshperspect.a035881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Transcription factors play crucial roles in cancer, and oncogenic counterparts of cellular transcription factors are present in a number of tumor viruses. It was studies in the early 1980s that first showed tumor viruses could encode nuclear as well as cytoplasmic oncoproteins. Subsequent work provided detailed insight into their mechanisms of action, as well as potential therapeutic avenues. In this excerpt from his forthcoming book on the history of cancer research, Joe Lipsick looks back at early work on nuclear oncogenes, including the discovery of MYC, MYB, FOS and JUN, Rel/NF-κB, and nuclear receptors such as the retinoic acid receptor and thyroid hormone receptor.
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Affiliation(s)
- Joseph Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, California 94305-5324, USA
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7
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Rep 2024; 43:114139. [PMID: 38652658 PMCID: PMC11199018 DOI: 10.1016/j.celrep.2024.114139] [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: 10/16/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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8
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Jiménez JM, Contreras-Riquelme JS, Vidal PM, Prado C, Bastías M, Meneses C, Martín AJM, Perez-Acle T, Pacheco R. Identification of master regulator genes controlling pathogenic CD4 + T cell fate in inflammatory bowel disease through transcriptional network analysis. Sci Rep 2024; 14:10553. [PMID: 38719901 PMCID: PMC11078927 DOI: 10.1038/s41598-024-61158-4] [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: 01/04/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions of the gastrointestinal tract associated with multiple pathogenic factors, including dysregulation of the immune response. Effector CD4+ T cells and regulatory CD4+ T cells (Treg) are central players in maintaining the balance between tolerance and inflammation. Interestingly, genetic modifications in these cells have been implicated in regulating the commitment of specific phenotypes and immune functions. However, the transcriptional program controlling the pathogenic behavior of T helper cells in IBD progression is still unknown. In this study, we aimed to find master transcription regulators controlling the pathogenic behavior of effector CD4+ T cells upon gut inflammation. To achieve this goal, we used an animal model of IBD induced by the transfer of naïve CD4+ T cells into recombination-activating gene 1 (Rag1) deficient mice, which are devoid of lymphocytes. As a control, a group of Rag1-/- mice received the transfer of the whole CD4+ T cells population, which includes both effector T cells and Treg. When gut inflammation progressed, we isolated CD4+ T cells from the colonic lamina propria and spleen tissue, and performed bulk RNA-seq. We identified differentially up- and down-regulated genes by comparing samples from both experimental groups. We found 532 differentially expressed genes (DEGs) in the colon and 30 DEGs in the spleen, mostly related to Th1 response, leukocyte migration, and response to cytokines in lamina propria T-cells. We integrated these data into Gene Regulatory Networks to identify Master Regulators, identifying four up-regulated master gene regulators (Lef1, Dnmt1, Mybl2, and Jup) and only one down-regulated master regulator (Foxo3). The altered expression of master regulators observed in the transcriptomic analysis was confirmed by qRT-PCR analysis and found an up-regulation of Lef1 and Mybl2, but without differences on Dnmt1, Jup, and Foxo3. These two master regulators have been involved in T cells function and cell cycle progression, respectively. We identified two master regulator genes associated with the pathogenic behavior of effector CD4+ T cells in an animal model of IBD. These findings provide two new potential molecular targets for treating IBD.
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Affiliation(s)
- José M Jiménez
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
| | | | - Pía M Vidal
- Biomedical Science Research Laboratory, Neuroimmunology and Regeneration of the Central Nervous System Unit, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Carolina Prado
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile
| | - Macarena Bastías
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Meneses
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto J M Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Tomás Perez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Rodrigo Pacheco
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile.
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile.
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Li X, Liu C, Li W, Dai Y, Gu C, Zhou W, Ciliberto VC, Liang J, Udhaya KS, Guan D, Hu Z, Zheng H, Chen H, Liu Z, Wan YW, Sun Z. Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592289. [PMID: 38746443 PMCID: PMC11092636 DOI: 10.1101/2024.05.02.592289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Physical exercise represents a primary defense against age-related cognitive decline and neurodegenerative disorders like Alzheimer's disease (AD). To impartially investigate the underlying mechanisms, we conducted single-nucleus transcriptomic and chromatin accessibility analyses (snRNA-seq and ATAC-seq) on the hippocampus of mice carrying AD-linked NL-G-F mutations in the amyloid precursor protein gene (APPNL-G-F) following prolonged voluntary wheel-running exercise. Our study reveals that exercise mitigates amyloid-induced changes in both transcriptomic expression and chromatin accessibility through cell type-specific transcriptional regulatory networks. These networks converge on the activation of growth factor signaling pathways, particularly the epidermal growth factor receptor (EGFR) and insulin signaling, correlating with an increased proportion of immature dentate granule cells and oligodendrocytes. Notably, the beneficial effects of exercise on neurocognitive functions can be blocked by pharmacological inhibition of EGFR and the downstream phosphoinositide 3-kinases (PI3K). Furthermore, exercise leads to elevated levels of heparin-binding EGF (HB-EGF) in the blood, and intranasal administration of HB-EGF enhances memory function in sedentary APPNL-G-F mice. These findings offer a panoramic delineation of cell type-specific hippocampal transcriptional networks activated by exercise and suggest EGF-related growth factor signaling as a druggable contributor to exercise-induced memory enhancement, thereby suggesting therapeutic avenues for combatting AD-related cognitive decline.
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Affiliation(s)
- Xin Li
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chaozhong Liu
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wenbo Li
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yanwan Dai
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chaohao Gu
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wenjun Zhou
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Veronica C. Ciliberto
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jing Liang
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Kumar. S Udhaya
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Dongyin Guan
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhaoyong Hu
- Department of Medicine – Nephrology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hui Zheng
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hu Chen
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhandong Liu
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ying-Wooi Wan
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zheng Sun
- Department of Medicine – Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas77030, USA
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10
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Parveen M, Karaosmanoglu B, Sucularli C, Uner A, Taskiran EZ, Esendagli G. Acquired immune resistance is associated with interferon signature and modulation of KLF6/c-MYB transcription factors in myeloid leukemia. Eur J Immunol 2024; 54:e2350717. [PMID: 38462943 DOI: 10.1002/eji.202350717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 03/12/2024]
Abstract
Resistance to immunity is associated with the selection of cancer cells with superior capacities to survive inflammatory reactions. Here, we tailored an ex vivo immune selection model for acute myeloid leukemia (AML) and isolated the residual subpopulations as "immune-experienced" AML (ieAML) cells. We confirmed that upon surviving the immune reactions, the malignant blasts frequently decelerated proliferation, displayed features of myeloid differentiation and activation, and lost immunogenicity. Transcriptomic analyses revealed a limited number of commonly altered pathways and differentially expressed genes in all ieAML cells derived from distinct parental cell lines. Molecular signatures predominantly associated with interferon and inflammatory cytokine signaling were enriched in the AML cells resisting the T-cell-mediated immune reactions. Moreover, the expression and nuclear localization of the transcription factors c-MYB and KLF6 were noted as the putative markers for immune resistance and identified in subpopulations of AML blasts in the patients' bone marrow aspirates. The immune modulatory capacities of ieAML cells lasted for a restricted period when the immune selection pressure was omitted. In conclusion, myeloid leukemia cells harbor subpopulations that can adapt to the harsh conditions established by immune reactions, and a previous "immune experience" is marked with IFN signature and may pave the way for susceptibility to immune intervention therapies.
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Affiliation(s)
- Mubaida Parveen
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Türkiye
| | - Beren Karaosmanoglu
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
| | - Ceren Sucularli
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Türkiye
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
| | - Ekim Z Taskiran
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
| | - Gunes Esendagli
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Türkiye
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11
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Veerappa A, Guda C. Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis. Front Neurosci 2024; 18:1332419. [PMID: 38660223 PMCID: PMC11041639 DOI: 10.3389/fnins.2024.1332419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Determining the key genetic variants is a crucial step to comprehensively understand substance use disorders (SUDs). In this study, utilizing whole exome sequences of five multi-generational pedigrees with SUDs, we used an integrative omics-based approach to uncover candidate genetic variants that impart susceptibility to SUDs and influence addition traits. We identified several SNPs and rare, protein-function altering variants in genes, GRIA3, NCOR1, and SHANK1; compound heterozygous variants in LNPEP, LRP1, and TBX2, that play a significant role in the neurotransmitter-neuropeptide axis, specifically in the dopaminergic circuits. We also noted a greater frequency of heterozygous and recessive variants in genes involved in the structural and functional integrity of synapse receptors, CHRNA4, CNR2, GABBR1, DRD4, NPAS4, ADH1B, ADH1C, OPRM1, and GABBR2. Variant analysis in upstream promoter regions revealed regulatory variants in NEK9, PRRX1, PRPF4B, CELA2A, RABGEF1, and CRBN, crucial for dopamine regulation. Using family-and pedigree-based data, we identified heterozygous recessive alleles in LNPEP, LRP1 (4 frameshift deletions), and TBX2 (2 frameshift deletions) linked to SUDs. GWAS overlap identified several SNPs associated with SUD susceptibility, including rs324420 and rs1229984. Furthermore, miRNA variant analysis revealed notable variants in mir-548 U and mir-532. Pathway studies identified the presence of extensive coordination among these genetic variants to impart substance use susceptibility and pathogenesis. This study identified variants that were found to be overrepresented among genes of dopaminergic circuits participating in the neurotransmitter-neuropeptide axis, suggesting pleiotropic influences in the development and sustenance of chronic substance use. The presence of a diverse set of haploinsufficient variants in varying frequencies demonstrates the existence of extraordinary coordination among them in attributing risk and modulating severity to SUDs.
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Affiliation(s)
- Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
- Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE, United States
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12
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Huang J, Fehr A, Jäwert F, Nilsson JA, Morris LGT, Stenman G, Andersson MK. MYB alternative promoter activity is increased in adenoid cystic carcinoma metastases and is associated with a specific gene expression signature. Oral Oncol 2024; 151:106763. [PMID: 38493544 DOI: 10.1016/j.oraloncology.2024.106763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVE Adenoid cystic carcinoma (ACC) is a head and neck cancer with a poor long-term prognosis that shows frequent local recurrences and distant metastases. The tumors are characterized by MYB oncogene activation and are notoriously unresponsive to systemic therapies. The biological underpinnings behind therapy resistance of disseminated ACC are largely unknown. Here, we have studied the molecular and clinical significance of MYB alternative promoter (TSS2) usage in ACC metastases. MATERIALS AND METHODS MYB TSS2 activity was investigated in primary tumors and metastases from 26 ACC patients using RNA-sequencing and quantitative real-time PCR analysis. Differences in global gene expression between MYB TSS2 high and low cases were studied, and pathway analyses were performed. RESULTS MYB TSS2 activity was significantly higher in ACC metastases than in primary tumors (median activity 15.1 vs 3.0, P = 0.0003). MYB TSS2 high ACC metastases showed a specific gene expression signature, including increased expression of multi-drug resistance genes and canonical MYB target genes, and suppression of the p53 and NOTCH pathways. CONCLUSIONS Collectively, our findings indicate that elevated MYB TSS2 activity is associated with metastases, potential drug resistance, and augmented MYB-driven gene expression in ACC. Our study advocates the need for new therapies that specifically target MYB and drug resistance mechanisms in disseminated ACC.
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Affiliation(s)
- Junchi Huang
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - André Fehr
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Jäwert
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Jonas A Nilsson
- Harry Perkins Institute of Medical Research, University of Western Australia, Perth, Australia; Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Göran Stenman
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Mattias K Andersson
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden.
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13
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Malta TM, Sabedot TS, Morosini NS, Datta I, Garofano L, Vallentgoed W, Varn FS, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan JS, Gan HK, Hasanain M, Hau AC, Johnson KC, Cazacu S, deCarvalho AC, Khasraw M, Kocakavuk E, Kouwenhoven MC, Migliozzi S, Niclou SP, Niers JM, Ormond DR, Paek SH, Reifenberger G, Sillevis Smitt PA, Smits M, Stead LF, van den Bent MJ, Van Meir EG, Walenkamp A, Weiss T, Weller M, Westerman BA, Ylstra B, Wesseling P, Lasorella A, French PJ, Poisson LM, Verhaak RG, Iavarone A, Noushmehr H. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen. Cancer Res 2024; 84:741-756. [PMID: 38117484 PMCID: PMC10911804 DOI: 10.1158/0008-5472.can-23-2093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype. SIGNIFICANCE Standard treatments are related to loss of DNA methylation in IDHmut glioma, resulting in epigenetic activation of genes associated with tumor progression and alterations in the microenvironment that resemble treatment-naïve IDHwt glioma.
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Affiliation(s)
- Tathiane M. Malta
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais S. Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Indrani Datta
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Wies Vallentgoed
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Hui K. Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Heidelberg, Melbourne, Australia
| | - Mohammad Hasanain
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Kevin C. Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Simona Cazacu
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Ana C. deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Emre Kocakavuk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mathilde C.M. Kouwenhoven
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Johanna M. Niers
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - D. Ryan Ormond
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, Colorado
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea (South)
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Dusseldorf, Germany
| | - Peter A. Sillevis Smitt
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Lucy F. Stead
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Martin J. van den Bent
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Erwin G. Van Meir
- Department of Neurosurgery and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Tobias Weiss
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Bart A. Westerman
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Pim J. French
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Laila M. Poisson
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Roel G.W. Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
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14
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Almeida A, T'Sas S, Pagliaro L, Fijalkowski I, Sleeckx W, Van Steenberge H, Zamponi R, Lintermans B, Van Loocke W, Palhais B, Reekmans A, Bardelli V, Demoen L, Reunes L, Deforce D, Van Nieuwerburgh F, Kentsis A, Ntziachristos P, Van Roy N, De Moerloose B, Mecucci C, La Starza R, Roti G, Goossens S, Van Vlierberghe P, Pieters T. Myb overexpression synergizes with the loss of Pten and is a dependency factor and therapeutic target in T-cell lymphoblastic leukemia. Hemasphere 2024; 8:e51. [PMID: 38463444 PMCID: PMC10924755 DOI: 10.1002/hem3.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/28/2024] [Indexed: 03/12/2024] Open
Abstract
T-lineage acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that accounts for 10%-15% of pediatric and 25% of adult ALL cases. Although the prognosis of T-ALL has improved over time, the outcome of T-ALL patients with primary resistant or relapsed leukemia remains poor. Therefore, further progress in the treatment of T-ALL requires a better understanding of its biology and the development of more effective precision oncologic therapies. The proto-oncogene MYB is highly expressed in diverse hematologic malignancies, including T-ALLs with genomic aberrations that further potentiate its expression and activity. Previous studies have associated MYB with a malignant role in the pathogenesis of several cancers. However, its role in the induction and maintenance of T-ALL remains relatively poorly understood. In this study, we found that an increased copy number of MYB is associated with higher MYB expression levels, and might be associated with inferior event-free survival of pediatric T-ALL patients. Using our previously described conditional Myb overexpression mice, we generated two distinct MYB-driven T-ALL mouse models. We demonstrated that the overexpression of Myb synergizes with Pten deletion but not with the overexpression of Lmo2 to accelerate the development of T-cell lymphoblastic leukemias. We also showed that MYB is a dependency factor in T-ALL since RNA interference of Myb blocked cell cycle progression and induced apoptosis in both human and murine T-ALL cell lines. Finally, we provide preclinical evidence that targeting the transcriptional activity of MYB can be a useful therapeutic strategy for the treatment of T-ALL.
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Affiliation(s)
- André Almeida
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Sara T'Sas
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Luca Pagliaro
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Igor Fijalkowski
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Wouter Sleeckx
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Hannah Van Steenberge
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | - Béatrice Lintermans
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Wouter Van Loocke
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Bruno Palhais
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Alexandra Reekmans
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Valentina Bardelli
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Lisa Demoen
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Lindy Reunes
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | | | - Alex Kentsis
- Tow Center for Developmental Oncology, Sloan Kettering Institute and Department of PediatricsMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Panagiotis Ntziachristos
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Nadine Van Roy
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Lab for Translational Oncogenomics and Bioinformatics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Pediatric Precision Oncology Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Department of Pediatric Hematology‐OncologyGhent University HospitalGhentBelgium
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Roberta La Starza
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Giovanni Roti
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Pieter Van Vlierberghe
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Tim Pieters
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
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15
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Anand S, Vikramdeo KS, Sudan SK, Sharma A, Acharya S, Khan MA, Singh S, Singh AP. From modulation of cellular plasticity to potentiation of therapeutic resistance: new and emerging roles of MYB transcription factors in human malignancies. Cancer Metastasis Rev 2024; 43:409-421. [PMID: 37950087 PMCID: PMC11015973 DOI: 10.1007/s10555-023-10153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
MYB transcription factors are encoded by a large family of highly conserved genes from plants to vertebrates. There are three members of the MYB gene family in human, namely, MYB, MYBL1, and MYBL2 that encode MYB/c-MYB, MYBL1/A-MYB, and MYBL2/B-MYB, respectively. MYB was the first member to be identified as a cellular homolog of the v-myb oncogene carried by the avian myeloblastosis virus (AMV) causing leukemia in chickens. Under the normal scenario, MYB is predominantly expressed in hematopoietic tissues, colonic crypts, and neural stem cells and plays a role in maintaining the undifferentiated state of the cells. Over the years, aberrant expression of MYB genes has been reported in several malignancies and recent years have witnessed tremendous progress in understanding of their roles in processes associated with cancer development. Here, we review various MYB alterations reported in cancer along with the roles of MYB family proteins in tumor cell plasticity, therapy resistance, and other hallmarks of cancer. We also discuss studies that provide mechanistic insights into the oncogenic functions of MYB transcription factors to identify potential therapeutic vulnerabilities.
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Affiliation(s)
- Shashi Anand
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Kunwar Somesh Vikramdeo
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Sarabjeet Kour Sudan
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Amod Sharma
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Srijan Acharya
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Mohammad Aslam Khan
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Seema Singh
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Biochemistry and Molecular Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Ajay Pratap Singh
- Department of Pathology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36617, USA.
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Biochemistry and Molecular Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, 36688, USA.
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16
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Kosasih HJ, Healey G, Brennan MS, Bjelosevic S, Sadras T, Jalud FB, Ibnat T, Ng AP, Mayoh C, Mao J, Tax G, Ludlow LEA, Johnstone RW, Herold MJ, Khaw SL, de Bock CE, Ekert PG. A novel MYB::PAIP1 oncogenic fusion in pediatric blastic plasmacytoid dendritic cell neoplasm (BPDCN) is dependent on BCL2 expression and is sensitive to venetoclax. Hemasphere 2024; 8:e1. [PMID: 38435422 PMCID: PMC10878182 DOI: 10.1002/hem3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/05/2024] Open
Affiliation(s)
- Hansen J. Kosasih
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
| | - Gerry Healey
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
| | - Margs S. Brennan
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medicine Huddinge, Centre for Haematology and Regenerative MedicineKarolinska InstitutetStockholmSweden
| | - Stefan Bjelosevic
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Teresa Sadras
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | | | - Tasnia Ibnat
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
| | - Ashley P. Ng
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of BiologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
| | - Jie Mao
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
| | - Gabor Tax
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
- School of Clinical Medicine, UNSW Medicine & HealthUNSW SydneySydneyNew South WalesAustralia
| | - Louise E. A. Ludlow
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneParkvilleVictoriaAustralia
| | - Ricky W. Johnstone
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Marco J. Herold
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityHeidelbergVictoriaAustralia
| | - Seong L. Khaw
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Charles E. de Bock
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
- School of Women's and Children's HealthUNSW SydneyKensingtonNew South WalesAustralia
| | - Paul G. Ekert
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneyKensingtonNew South WalesAustralia
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
- School of Clinical Medicine, UNSW Medicine & HealthUNSW SydneySydneyNew South WalesAustralia
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17
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Ferrarotto R, Swiecicki PL, Zandberg DP, Baiocchi RA, Wesolowski R, Rodriguez CP, McKean M, Kang H, Monga V, Nath R, Palmisiano N, Babbar N, Sun W, Hanna GJ. PRT543, a protein arginine methyltransferase 5 inhibitor, in patients with advanced adenoid cystic carcinoma: An open-label, phase I dose-expansion study. Oral Oncol 2024; 149:106634. [PMID: 38118249 DOI: 10.1016/j.oraloncology.2023.106634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 12/22/2023]
Abstract
OBJECTIVES Currently, no systemic treatments are approved for patients with recurrent and/or metastatic (R/M) adenoid cystic carcinoma (ACC). PRT543, a protein arginine methyltransferase 5 inhibitor that downregulates NOTCH1 and MYB signalling in tumours, is a potential candidate for R/M ACC treatment. We report the safety, tolerability and preliminary efficacy of PRT543 in a dose-expansion cohort of patients with R/M ACC. MATERIALS AND METHODS This phase I multicentre, open-label, sequential-cohort, dose-escalation and dose-expansion study (NCT03886831) enrolled patients with advanced solid tumours and select haematologic malignancies. Dose-escalation study design and results were reported previously. In the dose expansion, patients with R/M ACC received recommended phase II doses of 35 or 45 mg PRT543 orally on days 1-5 of each week. Primary objectives were to establish the safety and tolerability of PRT543. Secondary objectives included efficacy. RESULTS Between February 2019 and May 2022, 56 patients with ACC were enrolled across 23 US sites and received either 35 mg (n = 28) or 45 mg (n = 28) of PRT543. Overall, 23% of patients experienced a grade 3 treatment-related adverse event, most commonly anaemia (16%) and thrombocytopaenia (9%). No grade 4/5 treatment-emergent adverse events were reported. Median progression-free survival was 5.9 months (95% CI: 3.8-8.3). The clinical benefit rate was 57% (95% CI: 43-70). Overall response rate (per Response Evaluation Criteria in Solid Tumours v1.1) was 2%, with 70% of patients having stable disease. CONCLUSION In this analysis, PRT543 was tolerable, and the observed efficacy was limited in patients with R/M ACC.
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Affiliation(s)
- Renata Ferrarotto
- Department of Thoracic/Head and Neck Medical, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
| | - Paul L Swiecicki
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Dan P Zandberg
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert A Baiocchi
- Department of Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Robert Wesolowski
- Department of Medicine, Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Meredith McKean
- Sarah Cannon Research Institute, Tennessee Oncology, Nashville, TN, USA
| | - Hyunseok Kang
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Varun Monga
- Department of Medicine, Division of Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Neil Palmisiano
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Naveen Babbar
- Prelude Therapeutics, Research and Development, Wilmington, DE, USA
| | - William Sun
- Prelude Therapeutics, Research and Development, Wilmington, DE, USA
| | - Glenn J Hanna
- Center for Head and Neck Oncology, Center for Salivary and Rare Head and Neck Cancers, Dana-Farber Cancer Institute, Boston, MA, USA
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18
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Lemma RB, Fuglerud BM, Frampton J, Gabrielsen OS. MYB: A Key Transcription Factor in the Hematopoietic System Subject to Many Levels of Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:3-29. [PMID: 39017837 DOI: 10.1007/978-3-031-62731-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
MYB is a master regulator and pioneer factor highly expressed in hematopoietic progenitor cells (HPCs) where it contributes to the reprogramming processes operating during hematopoietic development. MYB plays a complex role being involved in several lineages of the hematopoietic system. At the molecular level, the MYB gene is subject to intricate regulation at many levels through several enhancer and promoter elements, through transcriptional elongation control, as well as post-transcriptional regulation. The protein is modulated by post-translational modifications (PTMs) such as SUMOylation restricting the expression of its downstream targets. Together with a range of interaction partners, cooperating transcription factors (TFs) and epigenetic regulators, MYB orchestrates a fine-tuned symphony of genes expressed during various stages of haematopoiesis. At the same time, the complex MYB system is vulnerable, being a target for unbalanced control and cancer development.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | | | - Jon Frampton
- Department of Cancer & Genomic Sciences, College of Medicine & Health, University of Birmingham, Edgbaston, Birmingham, UK
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19
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Swid MA, Li L, Drahnak EM, Idom H, Quinones W. Updated Salivary Gland Immunohistochemistry: A Review. Arch Pathol Lab Med 2023; 147:1383-1389. [PMID: 37074867 DOI: 10.5858/arpa.2022-0461-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 04/20/2023]
Abstract
CONTEXT.— Salivary gland neoplasms are rare lesions in the head and neck (H&N) pathology realm. There are more than 20 malignant and 15 benign salivary gland neoplasms in the 5th edition of the World Health Organization classification of H&N tumors. These neoplasms consist of heterogeneous groups of uncommon diseases that make diagnosis and treatment challenging for the clinical team. Using an algorithmic immunohistochemical approach-defined tumor origin and type has proven to be effective and advantageous. Immunohistochemistry may be used as sort of a "diagnostic looking glass," not as a positive or negative type tool, but as an indispensable complement to a hematoxylin-eosin morphologic pattern-based approach. Furthermore, the understanding of the novel discoveries of the salivary gland gene fusions and the molecular aspects of these tumors makes the process easier and improve the diagnosis as well as treatment aspects. This review reflects our experience with more recent diagnostic antibodies, which include MYB RNA, Pan-TRK, PLAG1, LEF1, and NR4A3. Each of these is linked with a specific type of neoplasm; for example, gene fusions involving the PLAG1 and HMGA2 oncogenes are specific for benign pleomorphic adenomas, and MYB is associated with adenoid cystic carcinoma. OBJECTIVE.— To review these more recent antibodies, which highly enhance salivary gland neoplasm diagnosis. DATA SOURCES.— The study sources involved literature PubMed searches, including multiple review articles, case reports, selected book chapters, and Geisinger Medical Center cases. CONCLUSIONS.— Salivary gland tumors are a rare, varied group of lesions in H&N pathology. We need to have continuous readings and revisions of the molecular consequences of these fusion oncoproteins and their subsequent targets, which will eventually lead to the identification of novel driver genes in salivary gland neoplasms.
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Affiliation(s)
- Mohammed Amer Swid
- From Laboratory Medicine and Pathology, Geisinger Medical Center, Danville, Pennsylvania (Swid, Li, Quinones)
| | - Liping Li
- From Laboratory Medicine and Pathology, Geisinger Medical Center, Danville, Pennsylvania (Swid, Li, Quinones)
| | | | - Hayden Idom
- Fordham University, New York, New York (Idom)
| | - William Quinones
- From Laboratory Medicine and Pathology, Geisinger Medical Center, Danville, Pennsylvania (Swid, Li, Quinones)
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20
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Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [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: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
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Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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21
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Pulver C, Grun D, Duc J, Sheppard S, Planet E, Coudray A, de Fondeville R, Pontis J, Trono D. Statistical learning quantifies transposable element-mediated cis-regulation. Genome Biol 2023; 24:258. [PMID: 37950299 PMCID: PMC10637000 DOI: 10.1186/s13059-023-03085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs). RESULTS Here, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 500 kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks. CONCLUSION Our results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.
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Affiliation(s)
- Cyril Pulver
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Raphaël de Fondeville
- Swiss Data Science Center, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| | - Julien Pontis
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- SOPHiA GENETICS SA, La Pièce 12, CH-1180, Rolle, Switzerland.
| | - Didier Trono
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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22
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Tan M, Pan Q, Gong H, Zhai X, Wan Z, Ge M, Gu J, Zhang D, Chen X, Xu D. Super-enhancer-associated SNHG15 cooperating with FOSL1 contributes to bladder cancer progression through the WNT pathway. Pharmacol Res 2023; 197:106940. [PMID: 37758102 DOI: 10.1016/j.phrs.2023.106940] [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: 02/03/2023] [Revised: 09/11/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Small nucleolar RNA host gene 15 (SNHG15) plays an oncogenic role in many cancers. However, the role of SNHG15 in bladder cancer (BLCA) remains unclear. In this study, the regulation of SNHG15 on the activities of BLCA cells (T24 and RT112) was investigated. In detail, super-enhancers (SEs), differentially expressed genes, and functional enrichment were detected by bioinformatic analyses. Mutant cell lines lacking SNHG15-SEs were established using CRISPR-Cas9. Relative gene expression was detected by quantitative polymerase chain reaction (qPCR), western blot, in situ hybridization, and immunohistochemistry assays. Cell senescence, apoptosis, viability, and proliferation were measured. Chromatin immunoprecipitation (ChIP)-qPCR and luciferase reporter gene assays were conducted to analyze the interactions between genes. A novel super-enhancer of SNHG15 (SNHG15-SEs) was discovered in several BLCA datasets. The deletion of SNHG15-SEs resulted in a significant downregulation of SNHG15. Mechanistically, the core active region of SNHG15-SEs recruited the transcription factor FOSL1 to facilitate the SNHG15 transcription, thereby inducing the proliferation and metastasis of BLCA cells. Deletion of SNHG15-SEs inhibited the growth and metastasis of T24 and RT112 cells by inactivating the WNT/CTNNB1 pathway activation. Overexpression of FOSL1 in SNHG15-SEs restored the cell proliferation and metastasis. Next, a xenograft mouse model showed that SNHG15-SEs deletion inhibited the proliferation and metastasis of BLCA cells in vivo. Collectively, our data indicate that SNHG15-SEs recruit FOSL1 to promote the expression of SNHG15 which interacts with CTNNB1 in the nucleus to activate the transcription of ADAM12, leading to the malignance of BLCA cells.
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Affiliation(s)
- Mingyue Tan
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qi Pan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hua Gong
- Department of Urology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
| | - Xinyu Zhai
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhong Wan
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Minyao Ge
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianyi Gu
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dingguo Zhang
- Department of Urology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, China.
| | - Xia Chen
- Department of Endocrinology, Gongli Hospital of Shanghai Pudong New Area, Shanghai 200135, China.
| | - Dongliang Xu
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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23
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Lei T, Shi Y, Da W, Xia C, Wang H. A novel EWSR1-MYB fusion in an aggressive advanced breast adenoid cystic carcinoma with mixed classical and solid-basaloid components. Virchows Arch 2023; 483:717-722. [PMID: 36719454 DOI: 10.1007/s00428-023-03500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 02/01/2023]
Abstract
Breast adenoid cystic carcinoma (AdCC) with a solid-basaloid component is rare. The solid-basaloid component is usually characterized by solid nests composed of basal-like cells with marked nuclear atypia, high mitotic activity, and necrosis. Given the rarity of such tumors, information on their clinicopathological and genomic characteristics is limited. Herein, we report a case of advanced breast cancer with a poor prognosis with histological and immunohistochemical characteristics of AdCC with a solid-basaloid component. For the solid-basaloid component, fluorescence in situ hybridization (FISH) analysis revealed rearrangement of the EWSR1 and MYB genes, and immunohistochemical staining indicated MYB positivity. Next-generation sequencing-based technology revealed a novel EWSR1-MYB fusion. To our knowledge, this is the first report of an EWSR1-MYB fusion in AdCC with a solid-basaloid component and a poor prognosis. Our findings may extend the genetic understanding of AdCC and aid in the clinical diagnosis of AdCC.
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Affiliation(s)
- Ting Lei
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Ju Qian Street 185, Changzhou, 213003, Jiangsu, China
| | - Yongqiang Shi
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Ju Qian Street 185, Changzhou, 213003, Jiangsu, China
| | - Wenyue Da
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Ju Qian Street 185, Changzhou, 213003, Jiangsu, China
| | - Cunyan Xia
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Ju Qian Street 185, Changzhou, 213003, Jiangsu, China
| | - Hui Wang
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Ju Qian Street 185, Changzhou, 213003, Jiangsu, China.
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24
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van Gogh M, Glaus Garzon JF, Sahin D, Knopfova L, Benes P, Boyman O, Jurisica I, Borsig L. Tumor Cell-Intrinsic c-Myb Upregulation Stimulates Antitumor Immunity in a Murine Colorectal Cancer Model. Cancer Immunol Res 2023; 11:1432-1444. [PMID: 37478172 PMCID: PMC10548106 DOI: 10.1158/2326-6066.cir-22-0912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023]
Abstract
The transcription factor c-Myb is overexpressed in many different types of solid tumors, including colorectal cancer. However, its exact role in tumorigenesis is unclear. In this study, we show that tumor-intrinsic c-Myb expression in mouse models of colon cancer and melanoma suppresses tumor growth. Although no differences in proliferation, apoptosis, and angiogenesis of tumors were evident in tumors with distinct levels of c-Myb expression, we observed changes in intratumoral immune cell infiltrates. MC38 tumors with upregulated c-Myb expression showed increased numbers of CD103+ dendritic cells and eosinophils, but decreased tumor-associated macrophages (TAM). Concomitantly, an increase in the number of activated cytotoxic CD8+ T cells upon c-Myb upregulation was observed, which correlated with a pro-inflammatory tumor microenvironment and increased numbers of M1 polarized TAMs. Mechanistically, c-Myb upregulation in immunogenic MC38 colon cancer cells resulted in enhanced expression of immunomodulatory genes, including those encoding β2-microglobulin and IFNβ, and decreased expression of the gene encoding the chemokine receptor CCR2. The increased numbers of activated cytotoxic CD8+ T cells contributed to tumor growth attenuation. In poorly immunogenic CT26, LLC, and B16-BL6 tumor cells, c-Myb upregulation did not affect the immunomodulatory gene expression. Despite this, c-Myb upregulation led to reduced B16-BL6 tumor growth but it did not affect tumor growth of CT26 and LLC tumors. Altogether, we postulate that c-Myb functions as a tumor suppressor in a tumor cell-type specific manner and modulates antitumor immunity.
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Affiliation(s)
- Merel van Gogh
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Dilara Sahin
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Lucia Knopfova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Petr Benes
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and, Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital (UHN), Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University Hospital of Zurich, Zurich, Switzerland
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25
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Ueda K, Murase T, Kawakita D, Nagao T, Kusafuka K, Nakaguro M, Urano M, Yamamoto H, Taguchi KI, Kano S, Tada Y, Tsukahara K, Okami K, Onitsuka T, Fujimoto Y, Sakurai K, Hanai N, Nagao T, Kawata R, Hato N, Nibu KI, Inagaki H. The Landscape of MYB/MYBL1- and Peri-MYB/MYBL1-Associated Rearrangements in Adenoid Cystic Carcinoma. Mod Pathol 2023; 36:100274. [PMID: 37423587 DOI: 10.1016/j.modpat.2023.100274] [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: 04/11/2023] [Revised: 06/03/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Approximately 60% of adenoid cystic carcinoma (AdCC) cases are positive for MYB::NFIB or MYBL1::NFIB, whereas MYB/MYBL1 oncoprotein, a key driver of AdCC, is overexpressed in most cases. Juxtaposition of superenhancer regions in NFIB and other genes into the MYB/MYBL1 locus is an attractive oncogenic hypothesis for AdCC cases, either negative or positive for MYB/MYBL1::NFIB. However, evidence supporting this hypothesis is insufficient. We examined 160 salivary AdCC cases for rearrangements in MYB/MYBL1 loci and peri-MYB/MYBL1 areas (centromeric and telomeric areas of 10 Mb each) using formalin-fixed, paraffin-embedded tumor sections. For the detection of the rearrangements, we employed conventional fluorescence in situ hybridization split and fusion assays and a 5 Mb fluorescence in situ hybridization split assay. The latter is a novel assay that enabled us to detect any possible splits within a 5 Mb distance of a chromosome. We found MYB/MYBL1- and peri-MYB/MYBL1-associated rearrangements in 149/160 patients (93%). AdCC cases positive for rearrangements in MYB, MYBL1, the peri-MYB area, and the peri-MYBL1 area numbered 105 (66%), 20 (13%), 19 (12%), and 5 (3%), respectively. In 24 peri-MYB/MYBL1 rearrangement-positive cases, 14 (58%) were found to have a juxtaposition of the NFIB or RAD51B locus into the MYB/MYBL1 loci. On comparing with a tumor group positive for MYB::NFIB, a hallmark of AdCC, other genetically classified tumor groups had similar features of overexpression of the MYB transcript and MYB oncoprotein as detected by semiquantitative RT-qPCR and immunohistochemistry, respectively. In addition, clinicopathological and prognostic features were similar among these groups. Our study suggests that peri-MYB/MYBL1 rearrangements may be a frequent event in AdCC and may result in biological and clinicopathological consequences comparable to MYB/MYBL1 rearrangements. The landscape of MYB/MYBL1 and peri-MYB/MYBL1 rearrangements shown here strongly suggests that juxtaposition of superenhancers into MYB/MYBL1 or peri-MYB/MYBL1 loci is an alteration that acts as a key driver for AdCC oncogenesis and may unify MYB/MYBL1 rearrangement-positive and negative cases.
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Affiliation(s)
- Kaori Ueda
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan; Department of Maxillofacial Surgery, School of Dentistry, Aichi-Gakuin University, Nagoya, Japan
| | - Takayuki Murase
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Daisuke Kawakita
- Department of Otorhinolaryngology, Head and Neck Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Toshitaka Nagao
- Department of Anatomic Pathology, Tokyo Medical University, Tokyo, Japan
| | | | - Masato Nakaguro
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Makoto Urano
- Department of Diagnostic Pathology, Bantane Hospital, Fujita Health University School of Medicine, Nagoya, Japan
| | - Hidetaka Yamamoto
- Department of Anatomic Pathology, Graduate of School of Medical Science, Kyushu University, Fukuoka, Japan
| | - Ken-Ichi Taguchi
- Department of Pathology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Satoshi Kano
- Department of Otolaryngology-Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yuichiro Tada
- Department of Head and Neck Oncology and Surgery, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Kiyoaki Tsukahara
- Department of Otorhinolaryngology, Head and Neck Surgery, Tokyo Medical University, Tokyo, Japan
| | - Kenji Okami
- Department of Otolaryngology-Head and Neck Surgery, Tokai University School of Medicine, Isehara, Japan
| | - Tetsuro Onitsuka
- Division of Head and Neck Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yasushi Fujimoto
- Department of Otorhinolaryngology, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Otolaryngology-Head and Neck Surgery, Aichi Medical University, Nagakute, Japan
| | - Kazuo Sakurai
- Department of Otorhinolaryngology, Fujita Health University, Okazaki Medical Center, Okazaki, Japan
| | - Nobuhiro Hanai
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Toru Nagao
- Department of Maxillofacial Surgery, School of Dentistry, Aichi-Gakuin University, Nagoya, Japan
| | - Ryo Kawata
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Naohito Hato
- Department of Otolaryngology, Ehime University School of Medicine, Toon, Japan
| | - Ken-Ichi Nibu
- Department of Otolaryngology-Head and Neck Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Inagaki
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
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26
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Fehr A, Arvidsson G, Nordlund J, Lönnerholm G, Stenman G, Andersson MK. Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia. Genes Chromosomes Cancer 2023; 62:597-606. [PMID: 37218648 DOI: 10.1002/gcc.23151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Therapy-resistant disease is a major cause of death in patients with acute lymphoblastic leukemia (ALL). Activation of the MYB oncogene is associated with ALL and leads to uncontrolled neoplastic cell proliferation and blocked differentiation. Here, we used RNA-seq to study the clinical significance of MYB expression and MYB alternative promoter (TSS2) usage in 133 pediatric ALLs. RNA-seq revealed that all cases analyzed overexpressed MYB and demonstrated MYB TSS2 activity. qPCR analyses confirmed the expression of the alternative MYB promoter also in seven ALL cell lines. Notably, high MYB TSS2 activity was significantly associated with relapse (p = 0.007). Moreover, cases with high MYB TSS2 usage showed evidence of therapy-resistant disease with increased expression of ABC multidrug resistance transporter genes (e.g., ABCA2, ABCB5, and ABCC10) and enzymes catalyzing drug degradation (e.g., CYP1A2, CYP2C9, and CYP3A5). Elevated MYB TSS2 activity was further associated with augmented KRAS signaling (p < 0.05) and decreased methylation of the conventional MYB promoter (p < 0.01). Taken together, our results suggest that MYB alternative promoter usage is a novel potential prognostic biomarker for relapse and therapy resistance in pediatric ALL.
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Affiliation(s)
- André Fehr
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Gustav Arvidsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Göran Stenman
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Mattias K Andersson
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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Weng J, Yang S, Shen J, Liu H, Xu Y, Hao D, Wang S. Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter. J Zhejiang Univ Sci B 2023; 24:883-895. [PMID: 37752090 PMCID: PMC10522569 DOI: 10.1631/jzus.b2200634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/07/2023] [Indexed: 09/28/2023]
Abstract
This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation. Therefore, we chose the chicken myeloid gene, mitochondrial import protein 1 (mim-1), as a target to study the binding specificity between potential dual-Myb-binding sites. The c-Myb-binding site in mim-1 is a pseudo-palindromic sequence AACGGTT, which contains two AACNG consensuses. Simulation studies in different biological scenarios revealed that c-Myb binding with mim-1 in the forward strand (complex F) ismore stable than that inthereverse strand (complex R). The principal component analysis (PCA) dynamics trajectory analyses suggested an opening motion of the recognition helices of R2 and R3 (R2R3), resulting in the dissociation of DNA from c-Myb in complex R at 330 K, triggered by the reduced electrostatic potential on the surface of R2R3. Furthermore, the DNA confirmation and hydrogen-bond interaction analyses indicated that the major groove width of DNA increased in complex R, which affected on the hydrogen-bond formation ability between R2R3 and DNA, and directly resulted in the dissociation of DNA from R2R3. The steered molecular dynamics (SMD) simulation studies also suggested that the electrostatic potential, major groove width, and hydrogen bonds made major contribution to the DNA-specific recognition. In vitro trials confirmed the simulation results that c-Myb specifically bound to mim-1 in the forward strand. This study indicates that the three-dimensional (3D) structure features play an important role in the DNA-specific recognition mechanism by c-Myb besides the AACNG consensuses, which is beneficial to understanding the cell early differentiation and proliferation regulated by c-Myb, as well as the prediction of novel c-Myb-binding motifs in tumorigenesis.
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Affiliation(s)
- Jinru Weng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130021, China
| | - Jinkang Shen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China
| | - Hongsen Liu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China
| | - Yuzi Xu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China
| | - Dongyun Hao
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (JAAS), Changchun 130033, China.
| | - Shan Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China.
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28
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Deleuze V, Garcia L, Rouaisnel B, Salma M, Kinoo A, Andrieu-Soler C, Soler E. Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions. iScience 2023; 26:107641. [PMID: 37670779 PMCID: PMC10475484 DOI: 10.1016/j.isci.2023.107641] [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: 03/27/2023] [Revised: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in (KI), remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein KI efficiency in low expressed transcription factor (TF) genes (e.g., Myb or Zeb1). We further show the ability to target two independent loci in individual cells, exemplified by MYB-GFP and NuMA-Cherry double KI, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our KI tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.
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Affiliation(s)
| | - Leonor Garcia
- IGMM, University Montpellier, CNRS, Montpellier, France
| | | | - Mohammad Salma
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Alexia Kinoo
- IGMM, University Montpellier, CNRS, Montpellier, France
| | - Charlotte Andrieu-Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Eric Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
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29
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557001. [PMID: 37745469 PMCID: PMC10515771 DOI: 10.1101/2023.09.09.557001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target because of its dual roles in proliferation and invasion. The clinical utility of KIF11 inhibitors has been limited by drug resistance, which has mainly been studied in animal models. We used multiplexed lineage tracing barcodes and scRNA-seq to analyze drug resistance time courses for patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lost their neural lineage identity and transitioned to a mesenchymal phenotype, which is associated with poor prognosis. In contrast, cells subjected to long-term ispinesib treatment exhibited a proneural phenotype. We generated patient-derived xenografts to show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Finally, we used lineage barcodes to nominate drug combination targets by retrospective analysis of ispinesib-resistant clones in the drug-naïve setting and identified drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
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30
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Lemma RB, Ledsaak M, Fuglerud BM, Rodríguez-Castañeda F, Eskeland R, Gabrielsen OS. MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape. J Biol Chem 2023; 299:105062. [PMID: 37468105 PMCID: PMC10463205 DOI: 10.1016/j.jbc.2023.105062] [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: 11/18/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
SUMOylation is a post-translational modification frequently found on nuclear proteins, including transcription factors (TFs) and coactivators. By controlling the activity of several TFs, SUMOylation may have far-reaching effects. MYB is an example of a developmental TF subjected to SUMO-mediated regulation, through both SUMO conjugation and SUMO binding. How SUMO affects MYB target genes is unknown. Here, we explored the global effect of reduced SUMOylation of MYB on its downstream gene programs. RNA-Seq in K562 cells after MYB knockdown and rescue with mutants having an altered SUMO status revealed a number of differentially regulated genes and distinct gene ontology term enrichments. Clearly, the SUMO status of MYB both quantitatively and qualitatively affects its regulome. The transcriptome data further revealed that MYB upregulates the SUMO protease SENP1, a key enzyme that removes SUMO conjugation from SUMOylated proteins. Given this role of SENP1 in the MYB regulome, we expanded the analysis, mapped interaction partners of SENP1, and identified UXT as a novel player affecting the SUMO system by acting as a repressor of SENP1. MYB inhibits the expression of UXT suggesting that MYB is able not only to control a specific gene program directly but also indirectly by affecting the SUMO landscape through SENP1 and UXT. These findings suggest an autoactivation loop whereby MYB, through enhancing SENP1 and reducing UXT, is itself being activated by a reduced level of repressive SUMOylation. We propose that overexpressed MYB, seen in multiple cancers, may drive this autoactivation loop and contribute to oncogenic activation of MYB.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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31
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Eckelt K, Hinterreiter A, Adelberger P, Walchshofer C, Dhanoa V, Humer C, Heckmann M, Steinparz C, Streit M. Visual Exploration of Relationships and Structure in Low-Dimensional Embeddings. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:3312-3326. [PMID: 35254984 DOI: 10.1109/tvcg.2022.3156760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work, we propose an interactive visual approach for the exploration and formation of structural relationships in embeddings of high-dimensional data. These structural relationships, such as item sequences, associations of items with groups, and hierarchies between groups of items, are defining properties of many real-world datasets. Nevertheless, most existing methods for the visual exploration of embeddings treat these structures as second-class citizens or do not take them into account at all. In our proposed analysis workflow, users explore enriched scatterplots of the embedding, in which relationships between items and/or groups are visually highlighted. The original high-dimensional data for single items, groups of items, or differences between connected items and groups are accessible through additional summary visualizations. We carefully tailored these summary and difference visualizations to the various data types and semantic contexts. During their exploratory analysis, users can externalize their insights by setting up additional groups and relationships between items and/or groups. We demonstrate the utility and potential impact of our approach by means of two use cases and multiple examples from various domains.
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32
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Hoch CC, Stögbauer F, Wollenberg B. Unraveling the Role of Epithelial-Mesenchymal Transition in Adenoid Cystic Carcinoma of the Salivary Glands: A Comprehensive Review. Cancers (Basel) 2023; 15:cancers15112886. [PMID: 37296849 DOI: 10.3390/cancers15112886] [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: 04/15/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Salivary adenoid cystic carcinoma (SACC) is considered a challenging malignancy; it is characterized by a slow-growing nature, yet a high risk of recurrence and distant metastasis, presenting significant hurdles in its treatment and management. At present, there are no approved targeted agents available for the management of SACC and systemic chemotherapy protocols that have demonstrated efficacy remain to be elucidated. Epithelial-mesenchymal transition (EMT) is a complex process that is closely associated with tumor progression and metastasis, enabling epithelial cells to acquire mesenchymal properties, including increased mobility and invasiveness. Several molecular signaling pathways have been implicated in the regulation of EMT in SACC, and understanding these mechanisms is crucial to identifying new therapeutic targets and developing more effective treatment approaches. This manuscript aims to provide a comprehensive overview of the latest research on the role of EMT in SACC, including the molecular pathways and biomarkers involved in EMT regulation. By highlighting the most recent findings, this review offers insights into potential new therapeutic strategies that could improve the management of SACC patients, especially those with recurrent or metastatic disease.
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Affiliation(s)
- Cosima C Hoch
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Barbara Wollenberg
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
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33
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Gonda TJ. MYB deficiency leads to myeloid neoplasia too. Blood 2023; 141:1786-1787. [PMID: 37052943 DOI: 10.1182/blood.2022019533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
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Clarke ML, Lemma RB, Walton DS, Volpe G, Noyvert B, Gabrielsen OS, Frampton J. MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia. Blood 2023; 141:1858-1870. [PMID: 36603185 PMCID: PMC10646772 DOI: 10.1182/blood.2022019138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of leukemias, although inherited noncoding variants of the MYB gene are a susceptibility factor for many hematological conditions, including myeloproliferative neoplasms (MPN). The mechanisms that connect variations in MYB levels to disease predisposition, especially concerning age dependency in disease initiation, are completely unknown. Here, we describe a model of Myb insufficiency in mice that leads to MPN, myelodysplasia, and leukemia in later life, mirroring the age profile of equivalent human diseases. We show that this age dependency is intrinsic to HSC, involving a combination of an initial defective cellular state resulting from small effects on the expression of multiple genes and a progressive accumulation of further subtle changes. Similar to previous studies showing the importance of proteostasis in HSC maintenance, we observed altered proteasomal activity and elevated proliferation indicators, followed by elevated ribosome activity in young Myb-insufficient mice. We propose that these alterations combine to cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation.
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Affiliation(s)
- Mary L. Clarke
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roza B. Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - David S. Walton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Giacomo Volpe
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Boris Noyvert
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | | | - Jon Frampton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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35
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Harada T, Perez MW, Kalfon J, Braes FD, Batley R, Eagle K, Nabet B, Leifer B, Kruell J, Paralkar VR, Stegmaier K, Koehler AN, Orkin SH, Pimkin M. Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536032. [PMID: 37066194 PMCID: PMC10104119 DOI: 10.1101/2023.04.07.536032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Attenuating aberrant transcriptional circuits holds great promise for the treatment of numerous diseases, including cancer. However, development of transcriptional inhibitors is hampered by the lack of a generally accepted functional cellular readout to characterize their target specificity and on-target activity. We benchmarked the direct gene-regulatory signatures of six agents reported as inhibitors of the oncogenic transcription factor MYB against targeted MYB degradation in a nascent transcriptomics assay. The inhibitors demonstrated partial specificity for MYB target genes but displayed significant off-target activity. Unexpectedly, the inhibitors displayed bimodal on-target effects, acting as mixed agonists-antagonists. Our data uncover unforeseen agonist effects of small molecules originally developed as TF inhibitors and argue that rapid-kinetics benchmarking against degron models should be used for functional characterization of transcriptional modulators.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Flora Dievenich Braes
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Rashad Batley
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Ken Eagle Consulting, Houston, TX, 77494, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Becky Leifer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jasmin Kruell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Angela N. Koehler
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
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Tejera Nevado P, Tešan Tomić T, Atefyekta A, Fehr A, Stenman G, Andersson MK. Synthetic oleanane triterpenoids suppress MYB oncogene activity and sensitize T-cell acute lymphoblastic leukemia cells to chemotherapy. Front Oncol 2023; 13:1126354. [PMID: 37077825 PMCID: PMC10106619 DOI: 10.3389/fonc.2023.1126354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with poor prognosis. The MYB oncogene encodes a master transcription factor that is activated in the majority of human T-ALLs. In the present study, we have performed a large-scale screening with small-molecule drugs to find clinically useful inhibitors of MYB gene expression in T-ALL. We identified several pharmacological agents that potentially could be used to treat MYB-driven malignancies. In particular, treatment with the synthetic oleanane triterpenoids (OTs) bardoxolone methyl and omaveloxolone decreased MYB gene activity and expression of MYB downstream target genes in T-ALL cells with constitutive MYB gene activation. Notably, treatment with bardoxolone methyl and omaveloxolone led to a dose-dependent reduction in cell viability and induction of apoptosis at low nanomolar concentrations. In contrast, normal bone marrow-derived cells were unaffected at these concentrations. Bardoxolone methyl and omaveloxolone treatment downregulated the expression of DNA repair genes and sensitized T-ALL cells to doxorubicin, a drug that is part of the standard therapy of T-ALL. OT treatment may thus potentiate DNA-damaging chemotherapy through attenuation of DNA repair. Taken together, our results indicate that synthetic OTs may be useful in the treatment of T-ALL and potentially also in other MYB-driven malignancies.
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Tadi S, Ka-Yan Cheung V, Lee CS, Nguyen K, Luk PP, Low THH, Palme C, Clark J, Gupta R. MYB RNA detection by in situ hybridisation has high sensitivity and specificity for the diagnosis of adenoid cystic carcinoma. Pathology 2023; 55:456-465. [PMID: 37055331 DOI: 10.1016/j.pathol.2023.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/11/2022] [Accepted: 01/20/2023] [Indexed: 04/15/2023]
Abstract
Adenoid cystic carcinoma (ACC) is one of the most common primary salivary gland cancers. ACC has several benign and malignant mimics amongst salivary gland neoplasms. An accurate diagnosis of ACC is essential for optimal management of the patients and their follow-up. Upregulation of MYB has been described in 85-90% of ACC, but not in other salivary gland neoplasms. In ACC, MYB upregulation can occur as a result of a genetic rearrangement t(6;9) (q22-23;p23-24), MYB copy number variation (CNV), or enhancer hijacking of MYB. All mechanisms of MYB upregulation result in increased RNA transcription that can be detected using RNA in situ hybridisation (ISH) methods. In this study, utilising 138 primary salivary gland neoplasms including 78 ACC, we evaluate the diagnostic utility of MYB RNA ISH for distinguishing ACC from other primary salivary gland neoplasms with a prominent cribriform architecture including pleomorphic adenoma, basal cell adenoma, basal cell adenocarcinoma, epithelial myoepithelial carcinoma, and polymorphous adenocarcinoma. Fluorescent in situ hybridisation and next generation sequencing were also performed to evaluate the sensitivity and specificity of RNA ISH for detecting increased MYB RNA when MYB gene alterations were present. Detection of MYB RNA has 92.3% sensitivity and 98.2% specificity for a diagnosis of ACC amongst salivary gland neoplasms. The sensitivity of MYB RNA detection by ISH (92.3%) is significantly higher than that of the FISH MYB break-apart probe (42%) for ACC. Next generation sequencing did not demonstrate MYB alterations in cases that lacked MYB RNA overexpression indicating high sensitivity of MYB RNA ISH for detecting MYB gene alterations. The possibility that the sensitivity may be higher in clinical practice with contemporary samples as compared with older retrospective tissue samples with RNA degradation is not entirely excluded. In addition to the high sensitivity and specificity, MYB RNA testing can be performed using standard IHC platforms and protocols and evaluated using brightfield microscopy making it a time and cost-efficient diagnostic tool in routine clinical practice.
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Affiliation(s)
- Sahithi Tadi
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Veronica Ka-Yan Cheung
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - C Soon Lee
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Discipline of Pathology, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia; Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia; Cancer Pathology Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; CONCERT Biobank, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW, Australia
| | - Kevin Nguyen
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia; Department of Otolaryngology - Head and Neck Surgery, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Peter P Luk
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Tsu-Hui Hubert Low
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Otolaryngology - Head and Neck Surgery, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Carsten Palme
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Jonathan Clark
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
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Klempnauer KH. C/EBPβ cooperates with MYB to maintain the oncogenic program of AML cells. Oncotarget 2023; 14:174-177. [PMID: 36913305 PMCID: PMC10010626 DOI: 10.18632/oncotarget.28377] [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: 02/10/2023] [Indexed: 03/13/2023] Open
Abstract
Studies on the role of transcription factor MYB in acute myeloid leukemia (AML) have identified MYB as a key regulator of a transcriptional program for self-renewal of AML cells. Recent work summarized here has now highlighted the CCAAT-box/enhancer binding protein beta (C/EBPβ) as an essential factor and potential therapeutic target that cooperates with MYB and coactivator p300 in the maintenance of the leukemic cells.
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Affiliation(s)
- Karl-Heinz Klempnauer
- Correspondence to:Karl-Heinz Klempnauer, Institute for Biochemistry, Westfälische-Wilhelms-Universität, Muenster D-48149, Germany email
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Jones M, Grosche P, Floersheimer A, André J, Gattlen R, Oser D, Tinchant J, Wille R, Chie-Leon B, Gerspacher M, Ertl P, Ostermann N, Altmann E, Manchado E, Vorherr T, Chène P. Design and Biochemical Characterization of Peptidic Inhibitors of the Myb/p300 Interaction. Biochemistry 2023; 62:1321-1329. [PMID: 36883372 DOI: 10.1021/acs.biochem.2c00690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The Myb transcription factor is involved in the proliferation of hematopoietic cells, and deregulation of its expression can lead to cancers such as leukemia. Myb interacts with various proteins, including the histone acetyltransferases p300 and CBP. Myb binds to a small domain of p300, the KIX domain (p300KIX), and inhibiting this interaction is a potential new drug discovery strategy in oncology. The available structures show that Myb binds to a very shallow pocket of the KIX domain, indicating that it might be challenging to identify inhibitors of this interaction. Here, we report the design of Myb-derived peptides which interact with p300KIX. We show that by mutating only two Myb residues that bind in or near a hotspot at the surface of p300KIX, it is possible to obtain single-digit nanomolar peptidic inhibitors of the Myb/p300KIX interaction that bind 400-fold tighter to p300KIX than wildtype Myb. These findings suggest that it might also be possible to design potent low molecular-weight compounds to disrupt the Myb/p300KIX interaction.
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Affiliation(s)
- Matthew Jones
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Philipp Grosche
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Andreas Floersheimer
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Jérome André
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Raphael Gattlen
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Dieter Oser
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Juliette Tinchant
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Roman Wille
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Barbara Chie-Leon
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Marc Gerspacher
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Peter Ertl
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Nils Ostermann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Eva Altmann
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Eusebio Manchado
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Thomas Vorherr
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Patrick Chène
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
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Zhou MJ, Yang JJ, Ma TY, Feng GX, Wang XL, Wang LY, Ge YZ, Gao R, Liu HL, Shan L, Kong L, Chen XH. Increased retinoic acid signaling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway. Exp Mol Med 2023; 55:597-611. [PMID: 36879115 PMCID: PMC10073150 DOI: 10.1038/s12276-023-00957-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 03/08/2023] Open
Abstract
MYB-NFIB fusion and NOTCH1 mutation are common hallmark genetic events in salivary gland adenoid cystic carcinoma (SACC). However, abnormal expression of MYB and NOTCH1 is also observed in patients without MYB-NFIB fusion and NOTCH1 mutation. Here, we explore in-depth the molecular mechanisms of lung metastasis through single-cell RNA sequencing (scRNA-seq) and exome target capture sequencing in two SACC patients without MYB-NFIB fusion and NOTCH1 mutation. Twenty-five types of cells in primary and metastatic tissues were identified via Seurat clustering and categorized into four main stages ranging from near-normal to cancer-based on the abundance of each cell cluster in normal tissue. In this context, we identified the Notch signaling pathway enrichment in almost all cancer cells; RNA velocity, trajectory, and sub-clustering analyses were performed to deeply investigate cancer progenitor-like cell clusters in primary tumor-associated lung metastases, and signature genes of progenitor-like cells were enriched in the "MYC_TARGETS_V2" gene set. In vitro, we detected the NICD1-MYB-MYC complex by co-immunoprecipitation (Co-IP) and incidentally identified retinoic acid (RA) as an endogenous antagonist of genes in the "MYC_TARGETS_V2" gene set. Following this, we confirmed that all-trans retinoic acid (ATRA) suppresses the lung metastasis of SACC by correcting erroneous cell differentiation mainly caused by aberrant NOTCH1 or MYB expression. Bioinformatic, RNA-seq, and immunohistochemical (IHC) analyses of primary tissues and metastatic lung tissues from patients with SACC suggested that RA system insufficiency partially promotes lung metastasis. These findings imply the value of the RA system in diagnosis and treatment.
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Affiliation(s)
- Meng-Jiao Zhou
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, 100021, China
| | - Jia-Jie Yang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China
| | - Ting-Yao Ma
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Ge-Xuan Feng
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China
| | - Xue-Lian Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Li-Yong Wang
- The Central Laboratory for Molecular Biology, Capital Medical University, Beijing, 100069, China
| | - Yu-Ze Ge
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China
| | - Ran Gao
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, 100021, China
| | - Hong-Liang Liu
- SHANDONG Longfine PHARMACEUTICAL CO., LTD, Shandong, 272622, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China
| | - Lu Kong
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China.
| | - Xiao-Hong Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
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Zheng C, Wei Y, Zhang P, Xu L, Zhang Z, Lin K, Hou J, Lv X, Ding Y, Chiu Y, Jain A, Islam N, Malovannaya A, Wu Y, Ding F, Xu H, Sun M, Chen X, Chen Y. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. J Clin Invest 2023; 133:e159940. [PMID: 36856111 PMCID: PMC9974104 DOI: 10.1172/jci159940] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/19/2023] [Indexed: 03/02/2023] Open
Abstract
Emerging evidence suggests that cryptic translation within long noncoding RNAs (lncRNAs) may produce novel proteins with important developmental/physiological functions. However, the role of this cryptic translation in complex diseases (e.g., cancer) remains elusive. Here, we applied an integrative strategy combining ribosome profiling and CRISPR/Cas9 screening with large-scale analysis of molecular/clinical data for breast cancer (BC) and identified estrogen receptor α-positive (ER+) BC dependency on the cryptic ORFs encoded by lncRNA genes that were upregulated in luminal tumors. We confirmed the in vivo tumor-promoting function of an unannotated protein, GATA3-interacting cryptic protein (GT3-INCP) encoded by LINC00992, the expression of which was associated with poor prognosis in luminal tumors. GTE-INCP was upregulated by estrogen/ER and regulated estrogen-dependent cell growth. Mechanistically, GT3-INCP interacted with GATA3, a master transcription factor key to mammary gland development/BC cell proliferation, and coregulated a gene expression program that involved many BC susceptibility/risk genes and impacted estrogen response/cell proliferation. GT3-INCP/GATA3 bound to common cis regulatory elements and upregulated the expression of the tumor-promoting and estrogen-regulated BC susceptibility/risk genes MYB and PDZK1. Our study indicates that cryptic lncRNA-encoded proteins can be an important integrated component of the master transcriptional regulatory network driving aberrant transcription in cancer, and suggests that the "hidden" lncRNA-encoded proteome might be a new space for therapeutic target discovery.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Longyong Xu
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Kangyu Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yao Ding
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Anna Malovannaya
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Mass Spectrometry Proteomics Core and
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center
- Genetics and Epigenetics Program, and
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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42
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Acharya S, Anand S, Khan MA, Zubair H, Srivastava SK, Singh S, Singh AP. Biphasic transcriptional and posttranscriptional regulation of MYB by androgen signaling mediates its growth control in prostate cancer. J Biol Chem 2022; 299:102725. [PMID: 36410437 PMCID: PMC9791434 DOI: 10.1016/j.jbc.2022.102725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022] Open
Abstract
MYB, a proto-oncogene, is overexpressed in prostate cancer (PCa) and promotes its growth, aggressiveness, and resistance to androgen-deprivation therapy. Here, we examined the effect of androgen signaling on MYB expression and delineated the underlying molecular mechanisms. Paralleling a dichotomous effect on growth, low-dose androgen induced MYB expression at both transcript and protein levels, whereas it was suppressed in high-dose androgen-treated PCa cells. Interestingly, treatment with both low- and high-dose androgen transcriptionally upregulated MYB by increasing the binding of androgen receptor to the MYB promoter. In a time-course assay, androgen induced MYB expression at early time points followed by a sharp decline in high-dose androgen-treated cells due to decreased stability of MYB mRNA. Additionally, profiling of MYB-targeted miRNAs demonstrated significant induction of miR-150 in high-dose androgen-treated PCa cells. We observed a differential binding of androgen receptor on miR-150 promoter with significantly greater occupancy recorded in high-dose androgen-treated cells than those treated with low-dose androgen. Functional inhibition of miR-150 relieved MYB suppression by high-dose androgen, while miR-150 mimic abolished MYB induction by low-dose androgen. Furthermore, MYB-silencing or miR-150 mimic transfection suppressed PCa cell growth induced by low-dose androgen, whereas miR-150 inhibition rescued PCa cells from growth repression by high-dose androgen. Similarly, we observed that MYB silencing suppressed the expression of androgen-responsive, cell cycle-related genes in low-dose androgen-treated cells, while miR-150 inhibition increased their expression in cells treated with high-dose androgen. Overall, these findings reveal novel androgen-mediated mechanisms of MYB regulation that support its biphasic growth control in PCa cells.
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Affiliation(s)
- Srijan Acharya
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Shashi Anand
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Mohammad Aslam Khan
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Haseeb Zubair
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Sanjeev Kumar Srivastava
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Seema Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA; Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.
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43
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Matsumura T, Totani H, Gunji Y, Fukuda M, Yokomori R, Deng J, Rethnam M, Yang C, Tan TK, Karasawa T, Kario K, Takahashi M, Osato M, Sanda T, Suda T. A Myb enhancer-guided analysis of basophil and mast cell differentiation. Nat Commun 2022; 13:7064. [PMID: 36400777 PMCID: PMC9674656 DOI: 10.1038/s41467-022-34906-1] [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: 03/03/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb -68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb -68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
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Affiliation(s)
- Takayoshi Matsumura
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan ,grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Haruhito Totani
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yoshitaka Gunji
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Masahiro Fukuda
- grid.428397.30000 0004 0385 0924Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rui Yokomori
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianwen Deng
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Malini Rethnam
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tze King Tan
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tadayoshi Karasawa
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Kazuomi Kario
- grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Masafumi Takahashi
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Motomi Osato
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toshio Suda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Chen W, Zhu L, Wang L, Zeng J, Wen M, Xu X, Zou L, Huang F, Huang Q, Qin D, Mei Q, Yang J, Wang Q, Wu J. A Novel Antithrombocytopenia Agent, Rhizoma cibotii, Promotes Megakaryopoiesis and Thrombopoiesis through the PI3K/AKT, MEK/ERK, and JAK2/STAT3 Signaling Pathways. Int J Mol Sci 2022; 23:ijms232214060. [PMID: 36430539 PMCID: PMC9694118 DOI: 10.3390/ijms232214060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Cibotii rhizoma (CR) is a famous traditional Chinese medicine (TCM) used to treat bleeding, rheumatism, lumbago, etc. However, its therapeutic effects and mechanism against thrombocytopenia are still unknown so far. In the study, we investigated the effects of aqueous extracts of Cibotii rhizoma (AECRs) against thrombocytopenia and its molecular mechanism. METHODS Giemsa staining, phalloidin staining, and flow cytometry were performed to measure the effect of AECRs on the megakaryocyte differentiation in K562 and Meg-01 cells. A radiation-induced thrombocytopenia mouse model was constructed to assess the therapeutic actions of AECRs on thrombocytopenia. Network pharmacology and experimental verification were carried out to clarify its mechanism against thrombocytopenia. RESULTS AECRs promoted megakaryocyte differentiation in K562 and Meg-01 cells and accelerated platelet recovery and megakaryopoiesis with no systemic toxicity in radiation-induced thrombocytopenia mice. The PI3K/AKT, MEK/ERK, and JAK2/STAT3 signaling pathways contributed to AECR-induced megakaryocyte differentiation. The suppression of the above signaling pathways by their inhibitors blocked AERC-induced megakaryocyte differentiation. CONCLUSIONS AECRs can promote megakaryopoiesis and thrombopoiesis through activating PI3K/AKT, MEK/ERK, and JAK2/STAT3 signaling pathways, which has the potential to treat radiation-induced thrombocytopenia in the clinic.
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Affiliation(s)
- Wang Chen
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Linjie Zhu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Long Wang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jing Zeng
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Min Wen
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Xiyan Xu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - LiLe Zou
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Feihong Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Qianqian Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Dalian Qin
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Education Ministry Key Laboratory of Medical Electrophysiology, Southwest Medical University, Luzhou 646000, China
| | - Qibing Mei
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Education Ministry Key Laboratory of Medical Electrophysiology, Southwest Medical University, Luzhou 646000, China
| | - Jing Yang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Education Ministry Key Laboratory of Medical Electrophysiology, Southwest Medical University, Luzhou 646000, China
| | - Qiaozhi Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
- Correspondence: (Q.W.); (J.W.); Tel.: 86-18015728611 (Q.W.); 86-13982416641 (J.W.)
| | - Jianming Wu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
- Education Ministry Key Laboratory of Medical Electrophysiology, Southwest Medical University, Luzhou 646000, China
- Correspondence: (Q.W.); (J.W.); Tel.: 86-18015728611 (Q.W.); 86-13982416641 (J.W.)
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45
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Köhler LF, Reich S, Yusenko M, Klempnauer KH, Shaikh AH, Ahmed K, Begemann G, Schobert R, Biersack B. A New Naphthopyran Derivative Combines c-Myb Inhibition, Microtubule-Targeting Effects, and Antiangiogenic Properties. ACS Med Chem Lett 2022; 13:1783-1790. [PMID: 36385941 PMCID: PMC9661705 DOI: 10.1021/acsmedchemlett.2c00403] [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: 08/25/2022] [Accepted: 10/28/2022] [Indexed: 11/28/2022] Open
Abstract
Based on the promising c-Myb inhibitor 1b, a series of 2-amino-4-aryl-4H-naphtho[1,2-b]pyran-3-carbonitriles (1a, 2a-q, 3a-g) were repurposed or newly synthesized via a three-component reaction of 1-naphthol, and various aryl aldehydes and malononitrile and screened for their c-Myb inhibitory activities. 1b also served as a lead compound for seven new naphthopyran derivatives (3a-f), which were cytotoxic with nanomolar IC50 values, to inhibit the polymerization of tubulin, and to destabilize microtubules in living cells. Especially, the alkyne 3f, originally made for intracellular localization studies using click chemistry, showed an overall high activity in all assays performed. A strong G2/M cell cycle arrest was detected, which resulted in a distinct increase in sub-G1 cells through the induction of effector caspases 3 and 7. Inhibition of angiogenesis was confirmed in vitro and in vivo. In summary, 3f was found to be a pleiotropic compound with high selectivity for cancer cells, combining c-Myb inhibitory, microtubule destabilizing, and antiangiogenic effects.
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Affiliation(s)
- Leonhard
H. F. Köhler
- Organic
Chemistry Laboratory, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Sebastian Reich
- Organic
Chemistry Laboratory, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Maria Yusenko
- Institute
for Biochemistry, Westfälische-Wilhelms-Universität, Wilhelm-Klemm-Strasse 2, 48149 Münster, Germany
| | - Karl-Heinz Klempnauer
- Institute
for Biochemistry, Westfälische-Wilhelms-Universität, Wilhelm-Klemm-Strasse 2, 48149 Münster, Germany
| | - Amin H. Shaikh
- Department
of Chemistry & Post Graduate Research Center, Abeda Inamdar Senior College, Camp, Pune 411001, India
| | - Khursheed Ahmed
- Department
of Chemistry & Post Graduate Research Center, Abeda Inamdar Senior College, Camp, Pune 411001, India
| | - Gerrit Begemann
- Developmental
Biology, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Rainer Schobert
- Organic
Chemistry Laboratory, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Bernhard Biersack
- Organic
Chemistry Laboratory, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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46
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Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Rep 2022; 41:111630. [PMID: 36351387 PMCID: PMC9687083 DOI: 10.1016/j.celrep.2022.111630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
A scarcity of functionally validated enhancers in the human genome presents a significant hurdle to understanding how these cis-regulatory elements contribute to human diseases. We carry out highly multiplexed CRISPR-based perturbation and sequencing to identify enhancers required for cell proliferation and fitness in 10 human cancer cell lines. Our results suggest that the cell fitness enhancers, unlike their target genes, display high cell-type specificity of chromatin features. They typically adopt a modular structure, comprised of activating elements enriched for motifs of oncogenic transcription factors, surrounded by repressive elements enriched for motifs recognized by transcription factors with tumor suppressor functions. We further identify cell fitness enhancers that are selectively accessible in clinical tumor samples, and the levels of chromatin accessibility are associated with patient survival. These results reveal functional enhancers across multiple cancer cell lines, characterize their context-dependent chromatin organization, and yield insights into altered transcription programs in cancer cells.
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Affiliation(s)
- Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Singapore
| | - Patrick C Fiaux
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shan Jiang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Emma Rooholfada
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Mengchi Wang
- Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Bioinformatics and System Biology Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paul S Mischel
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genome Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, San Diego, La Jolla, CA 92093, USA.
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47
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Vasileva AN, Aleshina OA, Biderman BV, Sudarikov AB. Molecular genetic abnormalities in patients with T-cell acute lymphoblastic leukemia: a literature review. ONCOHEMATOLOGY 2022. [DOI: 10.17650/1818-8346-2022-17-4-166-176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
T-cell acute lymphoblastic leukemia/lymphoma (T-ALL) is an aggressive hematological disease. Modern polychemotherapy protocols allow achieving a 5-year overall survival of 60–90 % in different age groups, however, relapses and refractory forms of T-ALL remain incurable. Over the past decades, the pathogenesis of this variant of leukemia has been studied in many trials, and it has been found that various signaling pathways are involved in the multi-step process of leukemogenesis. This opens the way for targeted therapy.In this review, we provide an update on the pathogenesis of T-ALL, opportunities for introducing targeted therapies, and issues that remain to be addressed.
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Affiliation(s)
- A. N. Vasileva
- National Research Center for Hematology, Ministry of Health of Russia
| | - O. A. Aleshina
- National Research Center for Hematology, Ministry of Health of Russia
| | - B. V. Biderman
- National Research Center for Hematology, Ministry of Health of Russia
| | - A. B. Sudarikov
- National Research Center for Hematology, Ministry of Health of Russia
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48
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Evaluation of the Synergistic Potential of Simultaneous Pan- or Isoform-Specific BET and SYK Inhibition in B-Cell Lymphoma: An In Vitro Approach. Cancers (Basel) 2022; 14:cancers14194691. [PMID: 36230614 PMCID: PMC9564024 DOI: 10.3390/cancers14194691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary B-cell lymphomas represent the majority of non-Hodgkin lymphomas and are the most common lymphoid malignancies in the Western world. Genetic alterations or epigenetic modulations can lead to tumor initiation and tumor progression. Aside from standard care, targeted, individualized therapies can be highly effective. Here, we evaluated the impact of simultaneous specific inhibition of two key regulators involved in B lymphoid tumor progression. Spleen tyrosine kinase (SYK) is a B-cell receptor-associated kinase acting as a proto-oncogene in B-cell malignancies, while bromodomain and extra-terminal domain (BET) proteins are epigenetic reader proteins involved in histone recognition and transcription regulation. The simultaneous inhibition of SYK and BET showed enhanced anti-proliferative effects, as well as inducing a distinct combination-specific gene expression profile, suggesting SYK and BET inhibition as a promising combination in the treatment of B-cell lymphoma. Abstract Background: Both bromodomain and extra-terminal domain (BET) proteins and spleen tyrosine kinase (SYK) represent promising targets in diffuse large B-cell (DLBCL) and Burkitt’s lymphoma (BL). We evaluated the anti-lymphoma activity of the isoform-specific bivalent BET inhibitor AZD5153 (AZD) and the pan-BET inhibitor I-BET151 (I-BET) as single agents and in combination with SYK inhibitor Entospletinib (Ento) in vitro. Methods: The effect of the single agents on cell proliferation and metabolic activity was evaluated in two DLBCL and two BL cell lines. Proliferation, metabolic activity, apoptosis, cell cycle and morphology were further investigated after a combined treatment of AZD or I-BET and Ento. RNAseq profiling of combined AZD+Ento treatment was performed in SU-DHL-4 cells. Results: Both BET inhibitors reduced cell proliferation and metabolic activity in a dose- and time-dependent manner. Combined BET and SYK inhibition enhanced the anti-proliferative effect and induced a G0/G1 cell cycle arrest. SU-DHL-4 demonstrated a pronounced modulation of gene expression by AZD, which was markedly increased by additional SYK inhibition. Functional enrichment analyses identified combination-specific GO terms related to DNA replication and cell division. Genes such as ADGRA2, MYB, TNFRSF11A, S100A10, PLEKHH3, DHRS2 and FOXP1-AS1 were identified as possible key regulators. Conclusion: Simultaneous inhibition of BET and SYK enhanced the anti-proliferative effects, and induced a combination-specific gene expression signature.
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Eagle K, Harada T, Kalfon J, Perez MW, Heshmati Y, Ewers J, Koren JV, Dempster JM, Kugener G, Paralkar VR, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Transcriptional Plasticity Drives Leukemia Immune Escape. Blood Cancer Discov 2022; 3:394-409. [PMID: 35709529 PMCID: PMC9897290 DOI: 10.1158/2643-3230.bcd-21-0207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
Relapse of acute myeloid leukemia (AML) after allogeneic bone marrow transplantation has been linked to immune evasion due to reduced expression of major histocompatibility complex class II (MHCII) genes through unknown mechanisms. In this work, we developed CORENODE, a computational algorithm for genome-wide transcription network decomposition that identified a transcription factor (TF) tetrad consisting of IRF8, MYB, MEF2C, and MEIS1, regulating MHCII expression in AML cells. We show that reduced MHCII expression at relapse is transcriptionally driven by combinatorial changes in the expression of these TFs, where MYB and IRF8 play major opposing roles, acting independently of the IFNγ/CIITA pathway. Beyond the MHCII genes, MYB and IRF8 antagonistically regulate a broad genetic program responsible for cytokine signaling and T-cell stimulation that displays reduced expression at relapse. A small number of cells with altered TF abundance and silenced MHCII expression are present at the time of initial leukemia diagnosis, likely contributing to eventual relapse. SIGNIFICANCE Our findings point to an adaptive transcriptional mechanism of AML evolution after allogeneic transplantation whereby combinatorial fluctuations of TF expression under immune pressure result in the selection of cells with a silenced T-cell stimulation program. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Ken Eagle Consulting, Houston, Texas
| | - Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jérémie Kalfon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jošt Vrabič Koren
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | | | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Neekesh V. Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston, Massachusetts
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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50
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Epigenetic Alterations in Sports-Related Injuries. Genes (Basel) 2022; 13:genes13081471. [PMID: 36011382 PMCID: PMC9408207 DOI: 10.3390/genes13081471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports activities, it is important to maintain proper levels of training, without encountering frequent injuries. The bodily responses to physical stress and intensive physical activity are detected on many levels. Epigenetic modifications, including DNA methylation, histone protein methylation, acetylation, and miRNA expression occur in response to environmental changes and play fundamental roles in the regulation of cellular activities. In the current review, we summarise the available knowledge on epigenetic alterations present in tissues and organs (e.g., muscles, the brain, tendons, and bones) as a consequence of sports-related injuries. Epigenetic mechanism observations have the potential to become useful tools in sports medicine, as predictors of approaching pathophysiological alterations and injury biomarkers that have already taken place.
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