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Herwig A, Osterhof C, Keppner A, Maric D, Koay TW, Mbemba-Nsungi A, Hoogewijs D. Ectopic MYBL2-Mediated Regulation of Androglobin Gene Expression. Cells 2024; 13:826. [PMID: 38786048 PMCID: PMC11119863 DOI: 10.3390/cells13100826] [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: 08/29/2023] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Androglobin (ADGB) is a highly conserved and recently identified member of the globin superfamily. Although previous studies revealed a link to ciliogenesis and an involvement in murine spermatogenesis, its physiological function remains mostly unknown. Apart from FOXJ1-dependent regulation, the transcriptional landscape of the ADGB gene remains unexplored. We, therefore, aimed to obtain further insights into regulatory mechanisms governing ADGB expression. To this end, changes in ADGB promoter activity were examined using luciferase reporter gene assays in the presence of a set of more than 475 different exogenous transcription factors. MYBL2 and PITX2 resulted in the most pronounced increase in ADGB promoter-dependent luciferase activity. Subsequent truncation strategies of the ADGB promoter fragment narrowed down the potential MYBL2 and PITX2 binding sites within the proximal ADGB promoter. Furthermore, MYBL2 binding sites on the ADGB promoter were further validated via a guide RNA-mediated interference strategy using reporter assays. Chromatin immunoprecipitation (ChIP)-qPCR experiments illustrated enrichment of the endogenous ADGB promoter region upon MYBL2 and PITX2 overexpression. Consistently, ectopic MYBL2 expression induced endogenous ADGB mRNA levels. Collectively, our data indicate that ADGB is strongly regulated at the transcriptional level and might have functions beyond ciliogenesis.
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Affiliation(s)
| | | | | | | | | | | | - David Hoogewijs
- Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, 1700 Fribourg, Switzerland; (A.H.); (C.O.); (A.K.); (D.M.); (T.W.K.); (A.M.-N.)
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2
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Gao W, Zhou J, Huang J, Zhang Z, Chen W, Zhang R, Kang T, Liao D, Zhong L. Up-regulation of RAN by MYBL2 maintains osteosarcoma cancer stem-like cells population during heterogeneous tumor generation. Cancer Lett 2024; 586:216708. [PMID: 38336287 DOI: 10.1016/j.canlet.2024.216708] [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: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Intratumor heterogeneity is one of the major features of cancers, leading to aggressive disease and treatment failure. Cancer stem-like cells (CSCs) are believed to give rise to the heterogeneous cell types within tumors. Hence, understanding the regulatory mechanism underlying the recurrence process of heterogeneous tumor by CSCs could facilitate the development of CSC-targeted therapies. Here, utilizing single-cell transcriptomics, we present the molecular profile of osteosarcoma CSCs-derived heterogeneous tumors consisting of CSC clusters, osteoprogenitor and differentiated cell types, such as pre-osteoblasts, osteoblasts and chondroblasts. Furthermore, by constructing the comprehensive map of modulated genes during CSCs self-renewal and differentiation, we identify RAN exhibiting specific peak expression in osteosarcoma CSCs clusters which is transcriptionally up-regulated by MYBL2. Functionality, MYBL2-RAN pathway promotes the CSCs self-renewal by enhancing the nuclear accumulation of MYC protein, which in turn boosts the overexpression of RAN as a positive feedback. Importantly, blockage of MYBL2-RAN pathway sensitizes CSCs to cisplatin treatment and synergistically enhanced the cisplatin-induced cytotoxicity. Both MYBL2 and RAN are highly expressed in clinical osteosarcoma tissues which indicate poor prognosis. Collectively, our study provides advanced insights into the regeneration process of heterogeneous tumor originating from CSCs and highlights the MYBL2-RAN pathway as a promising target for CSC-based therapy in osteosarcoma.
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Affiliation(s)
- Weijie Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, PR China
| | - Jing Zhou
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, School of Medicine, Hubei Polytechnic University, Huangshi, PR China
| | - Jintao Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Zhiguang Zhang
- Sun Yat-sen University School of Medicine, Shenzhen, PR China
| | - Wanqi Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Li Zhong
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China.
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Chen Y, Deng X, Li Y, Han Y, Peng Y, Wu W, Wang X, Ma J, Hu E, Zhou X, Shen E, Zeng S, Cai C, Qin Y, Shen H. Comprehensive molecular classification predicted microenvironment profiles and therapy response for HCC. Hepatology 2024:01515467-990000000-00822. [PMID: 38537130 DOI: 10.1097/hep.0000000000000869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/07/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND AND AIMS Tumor microenvironment (TME) heterogeneity leads to a discrepancy in survival prognosis and clinical treatment response for patients with HCC. The clinical applications of documented molecular subtypes are constrained by several issues. APPROACH AND RESULTS We integrated 3 single-cell data sets to describe the TME landscape and identified 6 prognosis-related cell subclusters. Unsupervised clustering of subcluster-specific markers was performed to generate transcriptomic subtypes. The predictive value of these molecular subtypes for prognosis and treatment response was explored in multiple external HCC cohorts and the Xiangya HCC cohort. TME features were estimated using single-cell immune repertoire sequencing, mass cytometry, and multiplex immunofluorescence. The prognosis-related score was constructed based on a machine-learning algorithm. Comprehensive single-cell analysis described TME heterogeneity in HCC. The 5 transcriptomic subtypes possessed different clinical prognoses, stemness characteristics, immune landscapes, and therapeutic responses. Class 1 exhibited an inflamed phenotype with better clinical outcomes, while classes 2 and 4 were characterized by a lack of T-cell infiltration. Classes 5 and 3 indicated an inhibitory tumor immune microenvironment. Analysis of multiple therapeutic cohorts suggested that classes 5 and 3 were sensitive to immune checkpoint blockade and targeted therapy, whereas classes 1 and 2 were more responsive to transcatheter arterial chemoembolization treatment. Class 4 displayed resistance to all conventional HCC therapies. Four potential therapeutic agents and 4 targets were further identified for high prognosis-related score patients with HCC. CONCLUSIONS Our study generated a clinically valid molecular classification to guide precision medicine in patients with HCC.
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Affiliation(s)
- Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangying Deng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinwen Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiayao Ma
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Erya Hu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Edward Shen
- Department of Life Science, McMaster University, Hamilton, Ontario, Canada
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiming Qin
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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4
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Domingo J, Minaeva M, Morris JA, Ziosi M, Sanjana NE, Lappalainen T. Non-linear transcriptional responses to gradual modulation of transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582837. [PMID: 38464330 PMCID: PMC10925300 DOI: 10.1101/2024.03.01.582837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene. However, our understanding of how gradual changes in gene dosage affect molecular, cellular, and organismal traits is currently limited. To address this gap, we induced gradual changes in gene expression of four genes using CRISPR activation and inactivation. Downstream transcriptional consequences of dosage modulation of three master trans-regulators associated with blood cell traits (GFI1B, NFE2, and MYB) were examined using targeted single-cell multimodal sequencing. We showed that guide tiling around the TSS is the most effective way to modulate cis gene expression across a wide range of fold-changes, with further effects from chromatin accessibility and histone marks that differ between the inhibition and activation systems. Our single-cell data allowed us to precisely detect subtle to large gene expression changes in dozens of trans genes, revealing that many responses to dosage changes of these three TFs are non-linear, including non-monotonic behaviours, even when constraining the fold-changes of the master regulators to a copy number gain or loss. We found that the dosage properties are linked to gene constraint and that some of these non-linear responses are enriched for disease and GWAS genes. Overall, our study provides a straightforward and scalable method to precisely modulate gene expression and gain insights into its downstream consequences at high resolution.
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Affiliation(s)
| | - Mariia Minaeva
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John A Morris
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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5
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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6
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Zaunz S, De Smedt J, Lauwereins L, Cleuren L, Laffeber C, Bajaj M, Lebbink JHG, Marteijn JA, De Keersmaecker K, Verfaillie C. APEX1 Nuclease and Redox Functions are Both Essential for Adult Mouse Hematopoietic Stem and Progenitor Cells. Stem Cell Rev Rep 2023:10.1007/s12015-023-10550-0. [PMID: 37266894 PMCID: PMC10390635 DOI: 10.1007/s12015-023-10550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) are carefully controlled by extrinsic and intrinsic factors, to ensure the lifelong process of hematopoiesis. Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein implicated in DNA repair and transcriptional regulation. Although previous studies have emphasized the necessity of studying APEX1 in a lineage-specific context and its role in progenitor differentiation, no studies have assessed the role of APEX1, nor its two enzymatic domains, in supporting adult HSPC function. In this study, we demonstrated that complete loss of APEX1 from murine bone marrow HSPCs (induced by CRISPR/Cas9) caused severe hematopoietic failure following transplantation, as well as a HSPC expansion defect in culture conditions maintaining in vivo HSC functionality. Using specific inhibitors against either the nuclease or redox domains of APEX1 in combination with single cell transcriptomics (CITE-seq), we found that both APEX1 nuclease and redox domains are regulating mouse HSPCs, but through distinct underlying transcriptional changes. Inhibition of the APEX1 nuclease function resulted in loss of HSPCs accompanied by early activation of differentiation programs and enhanced lineage commitment. By contrast, inhibition of the APEX1 redox function significantly downregulated interferon-stimulated genes and regulons in expanding HSPCs and their progeny, resulting in dysfunctional megakaryocyte-biased HSPCs, as well as loss of monocytes and lymphoid progenitor cells. In conclusion, we demonstrate that APEX1 is a key regulator for adult regenerative hematopoiesis, and that the APEX1 nuclease and redox domains differently impact proliferating HSPCs.
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Affiliation(s)
- Samantha Zaunz
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium.
| | - Jonathan De Smedt
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
- GlaxoSmithKline Biologicals SA, 1300, Wavre, Belgium
| | - Lukas Lauwereins
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Lana Cleuren
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Charlie Laffeber
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Manmohan Bajaj
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
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7
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Xia Y, Inoue K, Du Y, Baker SJ, Reddy EP, Greenblatt MB, Zhao B. TGFβ reprograms TNF stimulation of macrophages towards a non-canonical pathway driving inflammatory osteoclastogenesis. Nat Commun 2022; 13:3920. [PMID: 35798734 PMCID: PMC9263175 DOI: 10.1038/s41467-022-31475-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/20/2022] [Indexed: 01/12/2023] Open
Abstract
It is well-established that receptor activator of NF-κB ligand (RANKL) is the inducer of physiological osteoclast differentiation. However, the specific drivers and mechanisms driving inflammatory osteoclast differentiation under pathological conditions remain obscure. This is especially true given that inflammatory cytokines such as tumor necrosis factor (TNF) demonstrate little to no ability to directly drive osteoclast differentiation. Here, we found that transforming growth factor β (TGFβ) priming enables TNF to effectively induce osteoclastogenesis, independently of the canonical RANKL pathway. Lack of TGFβ signaling in macrophages suppresses inflammatory, but not basal, osteoclastogenesis and bone resorption in vivo. Mechanistically, TGFβ priming reprograms the macrophage response to TNF by remodeling chromatin accessibility and histone modifications, and enables TNF to induce a previously unrecognized non-canonical osteoclastogenic program, which includes suppression of the TNF-induced IRF1-IFNβ-IFN-stimulated-gene axis, IRF8 degradation and B-Myb induction. These mechanisms are active in rheumatoid arthritis, in which TGFβ level is elevated and correlates with osteoclast activity. Our findings identify a TGFβ/TNF-driven inflammatory osteoclastogenic program, and may lead to development of selective treatments for inflammatory osteolysis.
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Affiliation(s)
- Yuhan Xia
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kazuki Inoue
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yong Du
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Stacey J Baker
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E Premkumar Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew B Greenblatt
- Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Graduate Program in Cell and Development Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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8
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Huang D, Zhao Q, Zhang M, Weng Q, Zhang Q, Wang K, Dong F, Cheng H, Hu F, Wang J. Hoxb5 reprogrammes murine multipotent blood progenitors into haematopoietic stem cell-like cells. Cell Prolif 2022; 55:e13235. [PMID: 35582777 PMCID: PMC9201374 DOI: 10.1111/cpr.13235] [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: 01/26/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives The expression of transcription factor Hoxb5 specifically marks the functional haematopoietic stem cells (HSC) in mice. However, our recent work demonstrated that ectopic expression of Hoxb5 exerted little effect on HSC but could convert B‐cell progenitors into functional T cells in vivo. Thus, cell type‐ and development stage‐specific roles of Hoxb5 in haematopoietic hierarchy await more extensive exploration. In this study, we aim to investigate the effect of Hoxb5 expression in multipotent blood progenitor cells. Materials and Methods A Mx1cre/RosaLSL‐Hoxb5‐EGFP/+ mouse model was used to evaluate the effect of Hoxb5 expression in blood multipotent progenitor cells (MPP). Golden standard serial transplantation experiments were used to test the long‐term haematopoiesis potential of Hoxb5‐expressing MPP. Single‐cell RNA‐seq analysis was used to characterize the gained molecular features of Hoxb5‐expressing MPP and to compare with the global transcriptome features of natural adult HSC and fetal liver HSC (FL HSC). Results Here, with a mouse strain engineered with conditional expression of Hoxb5, we unveiled that induced expression of Hoxb5 in MPP led to the generation of a de novo Sca1+c‐kit+CD11b+CD48+ (CD11b+CD48+SK) cell type, which can repopulate long‐term multilineage haematopoiesis in serial transplantations. RNA‐seq analysis showed that CD11b+CD48+SK cells exhibited acquired features of DNA replication and cell division. Conclusions Our current study uncovers that Hoxb5 can empower MPP with self‐renewal ability and indicates an alternative approach for generating HSC‐like cells in vivo from blood lineage cells.
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Affiliation(s)
- Dehao Huang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qianhao Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, China
| | - Mengyun Zhang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qitong Weng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaitao Wang
- School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Fangxiao Hu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinyong Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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9
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Srivastava SK, Khan MA, Anand S, Zubair H, Deshmukh SK, Patel GK, Singh S, Andrews J, Wang B, Carter JE, Singh AP. MYB interacts with androgen receptor, sustains its ligand-independent activation and promotes castration resistance in prostate cancer. Br J Cancer 2022; 126:1205-1214. [PMID: 34837075 PMCID: PMC9023474 DOI: 10.1038/s41416-021-01641-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Aberrant activation of androgen receptor signalling following castration therapy is a common clinical observation in prostate cancer (PCa). Earlier, we demonstrated the role of MYB overexpression in androgen-depletion resistance and PCa aggressiveness. Here, we investigated MYB-androgen receptor (AR) crosstalk and its functional significance. METHODS Interaction and co-localization of MYB and AR were examined by co-immunoprecipitation and immunofluorescence analyses, respectively. Protein levels were measured by immunoblot analysis and enzyme-linked immunosorbent assay. The role of MYB in ligand-independent AR transcriptional activity and combinatorial gene regulation was studied by promoter-reporter and chromatin immunoprecipitation assays. The functional significance of MYB in castration resistance was determined using an orthotopic mouse model. RESULTS MYB and AR interact and co-localize in the PCa cells. MYB-overexpressing PCa cells retain AR in the nucleus even when cultured under androgen-deprived conditions. AR transcriptional activity is also sustained in MYB-overexpressing cells in the absence of androgens. MYB binds and promotes AR occupancy to the KLK3 promoter. MYB-overexpressing PCa cells exhibit greater tumorigenicity when implanted orthotopically and quickly regain growth following castration leading to shorter mice survival, compared to those carrying low-MYB-expressing prostate tumours. CONCLUSIONS Our findings reveal a novel MYB-AR crosstalk in PCa and establish its role in castration resistance.
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Affiliation(s)
- Sanjeev Kumar Srivastava
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Mohammad Aslam Khan
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Shashi Anand
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Haseeb Zubair
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Sachin Kumar Deshmukh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Girijesh Kumar Patel
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Seema Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Joel Andrews
- Bioimaging Core Facility, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Bin Wang
- Department of Mathematics and Statistics, University of South Alabama, Mobile, AL, 36688, USA
| | - James Elliot Carter
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL, 36617, USA.
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA.
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10
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Mann Z, Sengar M, Verma YK, Rajalingam R, Raghav PK. Hematopoietic Stem Cell Factors: Their Functional Role in Self-Renewal and Clinical Aspects. Front Cell Dev Biol 2022; 10:664261. [PMID: 35399522 PMCID: PMC8987924 DOI: 10.3389/fcell.2022.664261] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/14/2022] [Indexed: 01/29/2023] Open
Abstract
Hematopoietic stem cells (HSCs) possess two important properties such as self-renewal and differentiation. These properties of HSCs are maintained through hematopoiesis. This process gives rise to two subpopulations, long-term and short-term HSCs, which have become a popular convention for treating various hematological disorders. The clinical application of HSCs is bone marrow transplant in patients with aplastic anemia, congenital neutropenia, sickle cell anemia, thalassemia, or replacement of damaged bone marrow in case of chemotherapy. The self-renewal attribute of HSCs ensures long-term hematopoiesis post-transplantation. However, HSCs need to be infused in large numbers to reach their target site and meet the demands since they lose their self-renewal capacity after a few passages. Therefore, a more in-depth understanding of ex vivo HSCs expansion needs to be developed to delineate ways to enhance the self-renewability of isolated HSCs. The multifaceted self-renewal process is regulated by factors, including transcription factors, miRNAs, and the bone marrow niche. A developed classical hierarchical model that outlines the hematopoiesis in a lineage-specific manner through in vivo fate mapping, barcoding, and determination of self-renewal regulatory factors are still to be explored in more detail. Thus, an in-depth study of the self-renewal property of HSCs is essentially required to be utilized for ex vivo expansion. This review primarily focuses on the Hematopoietic stem cell self-renewal pathway and evaluates the regulatory molecular factors involved in considering a targeted clinical approach in numerous malignancies and outlining gaps in the current knowledge.
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Affiliation(s)
- Zoya Mann
- Independent Researcher, New Delhi, India
| | - Manisha Sengar
- Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Yogesh Kumar Verma
- Stem Cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, United States
- *Correspondence: Pawan Kumar Raghav, ,
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11
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Hu D, Shao W, Liu L, Wang Y, Yuan S, Liu Z, Liu J, Zhang J. Intricate crosstalk between MYB and noncoding RNAs in cancer. Cancer Cell Int 2021; 21:653. [PMID: 34876130 PMCID: PMC8650324 DOI: 10.1186/s12935-021-02362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
MYB is often overexpressed in malignant tumors and plays a carcinogenic role in the initiation and development of cancer. Deletion of the MYB regulatory C-terminal domain may be a driving mutation leading to tumorigenesis, therefore, different tumor mechanisms produce similar MYB proteins. As MYB is a transcription factor, priority has been given to identifying the genes that it regulates. All previous attention has been focused on protein-coding genes. However, an increasing number of studies have suggested that MYB can affect the complexity of cancer progression by regulating tumor-associated noncoding RNAs (ncRNAs), such as microRNAs, long-non-coding RNAs and circular RNAs. ncRNAs can regulate the expression of numerous downstream genes at the transcription, RNA processing and translation levels, thereby having various biological functions. Additionally, ncRNAs play important roles in regulating MYB expression. This review focuses on the intricate crosstalk between oncogenic MYB and ncRNAs, which play a pivotal role in tumorigenesis, including proliferation, apoptosis, angiogenesis, metastasis, senescence and drug resistance. In addition, we discuss therapeutic strategies for crosstalk between MYB and ncRNAs to prevent the occurrence and development of cancer.
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Affiliation(s)
- Dingyu Hu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Wenjun Shao
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Li Liu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Yanyan Wang
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Shunling Yuan
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Zhaoping Liu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jing Liu
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
| | - Ji Zhang
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China. .,Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, Guangdong, China.
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12
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Guo H, Li N, Sun Y, Wu C, Deng H, Xu L, Yang X. MYBL2 Gene Polymorphism Is Associated With Acute Lymphoblastic Leukemia Susceptibility in Children. Front Oncol 2021; 11:734588. [PMID: 34568071 PMCID: PMC8456030 DOI: 10.3389/fonc.2021.734588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose Although MYBL2 had been validated to participate in multiple cancers including leukemia, the role of MYBL2 polymorphisms in acute lymphoblastic leukemia (ALL) was still not clear. In this study, we aimed to evaluate the association between MYBL2 single nucleotide polymorphisms (SNPs) and ALL risk in children. Methods A total of 687 pediatric ALL cases and 971 cancer-free controls from two hospitals in South China were recruited. A case-control study by genotyping three SNPs in the MYBL2 gene (rs285162 C>T, rs285207 A>C, and rs2070235 A>G) was conducted. The associations were assessed by odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Subgroup and stratification analyses were conducted to explore the association of rs285207 with ALL risk in terms of age, sex, immunophenotype, risk level, and other clinical characteristics. The false-positive report probability (FPRP) analysis was performed to verify each significant finding. Functional analysis in silico was used to evaluate the probability that rs285207 might influence the regulation of MYBL2 . Results Our study demonstrated that rs285207 was related to a decreased ALL risk (adjusted OR = 0.78; 95% CI = 0.63-0.97, P = 0.022) in the dominant model. The associations of rs285207 with ALL risk appeared stronger in patients with pre B ALL (adjusted OR=0.56; 95% CI=0.38-0.84, P=0.004), with normal diploid (adjusted OR=0.73; 95% CI=0.57-0.95, P=0.017), with low risk (adjusted OR=0.68; 95% CI=0.49-0.94, P=0.021), with lower WBC (adjusted OR=0.62; 95% CI=0.43-0.87, P=0.007) or lower platelet level (adjusted OR=0.76; 95% CI=0.59-0.96, P=0.023). With FPRP analysis, the significant association between the rs285207 polymorphism and decreased ALL risk was still noteworthy (FPRP=0.128). Functional analysis showed that IKZF1 bound to DNA motif overlapping rs285207 and had a higher preference for the risk allele A. As for rs285162 C>T and rs2070235 A>G, no significant was found between them and ALL risk. Conclusion In this study, we revealed that rs285207 polymorphism decreased the ALL risk in children, and rs285207 might alter the binding to IKZF1, which indicated that the MYBL2 gene polymorphism might be a potential biomarker of childhood ALL.
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Affiliation(s)
- Haixia Guo
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Na Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yaping Sun
- Institute of Systems Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Cuiling Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huixia Deng
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ling Xu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xu Yang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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13
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Lu RJ, Taylor S, Contrepois K, Kim M, Bravo JI, Ellenberger M, Sampathkumar NK, Benayoun BA. Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation. NATURE AGING 2021; 1:715-733. [PMID: 34514433 PMCID: PMC8425468 DOI: 10.1038/s43587-021-00086-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 06/10/2021] [Indexed: 12/18/2022]
Abstract
Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.
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Affiliation(s)
- Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Shalina Taylor
- Departments of Pediatrics and of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Nirmal K. Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Present Address: UK-Dementia Research Institute, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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14
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Kaur A, Lim JYS, Sepramaniam S, Patnaik S, Harmston N, Lee MA, Petretto E, Virshup DM, Madan B. WNT inhibition creates a BRCA-like state in Wnt-addicted cancer. EMBO Mol Med 2021; 13:e13349. [PMID: 33660437 PMCID: PMC8033517 DOI: 10.15252/emmm.202013349] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Wnt signaling maintains diverse adult stem cell compartments and is implicated in chemotherapy resistance in cancer. PORCN inhibitors that block Wnt secretion have proven effective in Wnt-addicted preclinical cancer models and are in clinical trials. In a survey for potential combination therapies, we found that Wnt inhibition synergizes with the PARP inhibitor olaparib in Wnt-addicted cancers. Mechanistically, we find that multiple genes in the homologous recombination and Fanconi anemia repair pathways, including BRCA1, FANCD2, and RAD51, are dependent on Wnt/β-catenin signaling in Wnt-high cancers, and treatment with a PORCN inhibitor creates a BRCA-like state. This coherent regulation of DNA repair genes occurs in part via a Wnt/β-catenin/MYBL2 axis. Importantly, this pathway also functions in intestinal crypts, where high expression of BRCA and Fanconi anemia genes is seen in intestinal stem cells, with further upregulation in Wnt-high APCmin mutant polyps. Our findings suggest a general paradigm that Wnt/β-catenin signaling enhances DNA repair in stem cells and cancers to maintain genomic integrity. Conversely, interventions that block Wnt signaling may sensitize cancers to radiation and other DNA damaging agents.
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Affiliation(s)
- Amanpreet Kaur
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | - Jun Yi Stanley Lim
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | | | - Siddhi Patnaik
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
- Science DivisionYale‐NUS CollegeSingaporeSingapore
| | - May Ann Lee
- Experimental Drug Development CentreA*StarSingaporeSingapore
| | - Enrico Petretto
- Center for Computational Biology and Program in Cardiovascular and Metabolic DisordersDuke‐NUS Medical SchoolSingaporeSingapore
| | - David M Virshup
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
- Department of PediatricsDuke University School of MedicineDurhamNCUSA
| | - Babita Madan
- Program in Cancer and Stem Cell BiologyDuke‐NUS Medical SchoolSingaporeSingapore
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15
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Lal A, Chiang ZD, Yakovenko N, Duarte FM, Israeli J, Buenrostro JD. Deep learning-based enhancement of epigenomics data with AtacWorks. Nat Commun 2021; 12:1507. [PMID: 33686069 PMCID: PMC7940635 DOI: 10.1038/s41467-021-21765-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks, a deep learning toolkit to denoise sequencing coverage and identify regulatory peaks at base-pair resolution from low cell count, low-coverage, or low-quality ATAC-seq data. Models trained by AtacWorks can detect peaks from cell types not seen in the training data, and are generalizable across diverse sample preparations and experimental platforms. We demonstrate that AtacWorks enhances the sensitivity of single-cell experiments by producing results on par with those of conventional methods using ~10 times as many cells, and further show that this framework can be adapted to enable cross-modality inference of protein-DNA interactions. Finally, we establish that AtacWorks can enable new biological discoveries by identifying active regulatory regions associated with lineage priming in rare subpopulations of hematopoietic stem cells. ATAC-seq measures chromatin accessibility as a proxy for the activity of DNA regulatory regions across the genome. Here the authors present AtacWorks, a deep learning tool to denoise and identify accessible chromatin regions from low cell count, low-coverage, or low-quality ATAC-seq data.
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Affiliation(s)
| | - Zachary D Chiang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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16
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Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Rep 2020; 33:108474. [PMID: 33296649 DOI: 10.1016/j.celrep.2020.108474] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/25/2020] [Accepted: 11/12/2020] [Indexed: 01/03/2023] Open
Abstract
Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming.
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Affiliation(s)
- Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentina Schiavone
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiaochuan Tu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jordan Kesner
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Neus Romo
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Prem Subramaniam
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, J.P. Sulzberger Columbia Genome Center, Department of Biomedical Informatics, Department of Biochemistry and Molecular Biophysics, Department of Medicine, Columbia University, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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17
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Machine learning uncovers cell identity regulator by histone code. Nat Commun 2020; 11:2696. [PMID: 32483223 PMCID: PMC7264183 DOI: 10.1038/s41467-020-16539-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/09/2020] [Indexed: 01/13/2023] Open
Abstract
Conversion between cell types, e.g., by induced expression of master transcription factors, holds great promise for cellular therapy. Our ability to manipulate cell identity is constrained by incomplete information on cell identity genes (CIGs) and their expression regulation. Here, we develop CEFCIG, an artificial intelligent framework to uncover CIGs and further define their master regulators. On the basis of machine learning, CEFCIG reveals unique histone codes for transcriptional regulation of reported CIGs, and utilizes these codes to predict CIGs and their master regulators with high accuracy. Applying CEFCIG to 1,005 epigenetic profiles, our analysis uncovers the landscape of regulation network for identity genes in individual cell or tissue types. Together, this work provides insights into cell identity regulation, and delivers a powerful technique to facilitate regenerative medicine.
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18
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Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Rep 2019; 29:3147-3159.e12. [DOI: 10.1016/j.celrep.2019.10.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 09/20/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022] Open
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19
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Lin S, Guo J, Chen S. Transcriptome and DNA Methylome Signatures Associated With Retinal Müller Glia Development, Injury Response, and Aging. ACTA ACUST UNITED AC 2019; 60:4436-4450. [DOI: 10.1167/iovs.19-27361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Siyuan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jingyi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuyi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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20
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Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing. Cell Res 2019; 29:881-894. [PMID: 31501518 PMCID: PMC6888893 DOI: 10.1038/s41422-019-0228-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/13/2019] [Indexed: 12/20/2022] Open
Abstract
Tracing the emergence of the first hematopoietic stem cells (HSCs) in human embryos, particularly the scarce and transient precursors thereof, is so far challenging, largely due to the technical limitations and the material rarity. Here, using single-cell RNA sequencing, we constructed the first genome-scale gene expression landscape covering the entire course of endothelial-to-HSC transition during human embryogenesis. The transcriptomically defined HSC-primed hemogenic endothelial cells (HECs) were captured at Carnegie stage (CS) 12–14 in an unbiased way, showing an unambiguous feature of arterial endothelial cells (ECs) with the up-regulation of RUNX1, MYB and ANGPT1. Importantly, subcategorizing CD34+CD45− ECs into a CD44+ population strikingly enriched HECs by over 10-fold. We further mapped the developmental path from arterial ECs via HSC-primed HECs to hematopoietic stem progenitor cells, and revealed a distinct expression pattern of genes that were transiently over-represented upon the hemogenic fate choice of arterial ECs, including EMCN, PROCR and RUNX1T1. We also uncovered another temporally and molecularly distinct intra-embryonic HEC population, which was detected mainly at earlier CS 10 and lacked the arterial feature. Finally, we revealed the cellular components of the putative aortic niche and potential cellular interactions acting on the HSC-primed HECs. The cellular and molecular programs that underlie the generation of the first HSCs from HECs in human embryos, together with the ability to distinguish the HSC-primed HECs from others, will shed light on the strategies for the production of clinically useful HSCs from pluripotent stem cells.
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21
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Hematopoietic stem and progenitor cell proliferation and differentiation requires the trithorax protein Ash2l. Sci Rep 2019; 9:8262. [PMID: 31164666 PMCID: PMC6547667 DOI: 10.1038/s41598-019-44720-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Post-translational modifications of core histones participate in controlling the expression of genes. Methylation of lysine 4 of histone H3 (H3K4), together with acetylation of H3K27, is closely associated with open chromatin and gene transcription. H3K4 methylation is catalyzed by KMT2 lysine methyltransferases that include the mixed-lineage leukemia 1–4 (MLL1-4) and SET1A and B enzymes. For efficient catalysis, all six require a core complex of four proteins, WDR5, RBBP5, ASH2L, and DPY30. We report that targeted disruption of Ash2l in the murine hematopoietic system results in the death of the mice due to a rapid loss of mature hematopoietic cells. However, lin−Sca1+Kit+ (LSK) cells, which are highly enriched in hematopoietic stem and multi-potent progenitor cells, accumulated in the bone marrow. The loss of Ash2l resulted in global reduction of H3K4 methylation and deregulated gene expression, including down-regulation of many mitosis-associated genes. As a consequence, LSK cells accumulated in the G2-phase of the cell cycle and were unable to proliferate and differentiate. In conclusion, Ash2l is essential for balanced gene expression and for hematopoietic stem and multi-potent progenitor cell physiology.
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22
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Baker SJ, Cosenza SC, Ramana Reddy MV, Premkumar Reddy E. Rigosertib ameliorates the effects of oncogenic KRAS signaling in a murine model of myeloproliferative neoplasia. Oncotarget 2019; 10:1932-1942. [PMID: 30956775 PMCID: PMC6443005 DOI: 10.18632/oncotarget.26735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Aberrant signaling triggered by oncogenic or hyperactive RAS proteins contributes to the malignant phenotypes in a significant percentage of myeloid malignancies. Of these, juvenile myelomonocytic leukemia (JMML), an aggressive childhood cancer, is largely driven by mutations in RAS genes and those that encode regulators of these proteins. The Mx1-cre kras+/G12D mouse model mirrors several key features of this disease and has been used extensively to determine the utility and mechanism of small molecule therapeutics in the context of RAS-driven myeloproliferative disorders. Treatment of disease-bearing KRASG12D mice with rigosertib (RGS), a small molecule RAS mimetic that is in phase II and III clinical trials for MDS and AML, decreased the severity of leukocytosis and splenomegaly and extended their survival. RGS also increased the frequency of HSCs and rebalanced the ratios of myeloid progenitors. Further analysis of KRASG12D HSPCs in vitro revealed that RGS suppressed hyperproliferation in response to GM-CSF and inhibited the phosphorylation of key RAS effectors. Together, these data suggest that RGS might be of clinical benefit in RAS-driven myeloid disorders.
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Affiliation(s)
- Stacey J Baker
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen C Cosenza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M V Ramana Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - E Premkumar Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. SCIENCE ADVANCES 2018; 4:eaav8550. [PMID: 30555922 PMCID: PMC6292713 DOI: 10.1126/sciadv.aav8550] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/16/2018] [Indexed: 05/20/2023]
Abstract
As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.
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Affiliation(s)
- Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Armoskus
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fides D. Lay
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adrian Camarena
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Valeria N. Spitsyna
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin P. Berman
- Department of Biomedical Sciences, Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Oleg V. Evgrafov
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - James A. Knowles
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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24
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de Smith AJ, Walsh KM, Francis SS, Zhang C, Hansen HM, Smirnov I, Morimoto L, Whitehead TP, Kang A, Shao X, Barcellos LF, McKean-Cowdin R, Zhang L, Fu C, Wang R, Yu H, Hoh J, Dewan AT, Metayer C, Ma X, Wiemels JL. BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia. Int J Cancer 2018; 143:2647-2658. [PMID: 29923177 PMCID: PMC6235695 DOI: 10.1002/ijc.31622] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/07/2023]
Abstract
Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latino white ALL cases and controls from two independent California childhood leukemia studies, and additional Genetic Epidemiology Research on Aging study controls. Ethnicity-stratified association analyses were performed using logistic regression, with meta-analysis including 3,133 cases (1,949 Latino, 1,184 non-Latino white) and 12,135 controls (8,584 Latino, 3,551 non-Latino white). SNP associations were identified at both BMI1 and PIP4K2A. After adjusting for the lead PIP4K2A SNP, genome-wide significant associations remained at BMI1, and vice-versa (pmeta < 10-10 ), supporting independent effects. Lead SNPs differed by ethnicity at both peaks. We sought functional variants in tight linkage disequilibrium with both the lead Latino SNP among Admixed Americans and lead non-Latino white SNP among Europeans. This pinpointed rs11591377 (pmeta = 2.1 x 10-10 ) upstream of BMI1, residing within a hematopoietic stem cell enhancer of BMI1, and which showed significant preferential binding of the risk allele to MYBL2 (p = 1.73 x 10-5 ) and p300 (p = 1.55 x 10-3 ) transcription factors using binomial tests on ChIP-Seq data from a SNP heterozygote. At PIP4K2A, we identified rs4748812 (pmeta = 1.3 x 10-15 ), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.
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Affiliation(s)
- Adam J. de Smith
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
| | - Kyle M. Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Department of Neurosurgery, Duke University, Durham, NC 27710
| | - Stephen S. Francis
- Department of Epidemiology, School of Community Health Sciences, University of Nevada Reno, Reno, NV 89557
| | - Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Helen M. Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Todd P. Whitehead
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Alice Kang
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Xiaorong Shao
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Lisa F. Barcellos
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Roberta McKean-Cowdin
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
| | - Luoping Zhang
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Cecilia Fu
- Children’s Hospital of Los Angeles, Los Angeles, CA 90027
| | - Rong Wang
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Herbert Yu
- University of Hawaii Cancer Center, Honolulu, HI 96813
| | - Josephine Hoh
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Andrew T. Dewan
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Joseph L. Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
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25
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Demethylzeylasteral inhibits glioma growth by regulating the miR-30e-5p/MYBL2 axis. Cell Death Dis 2018; 9:1035. [PMID: 30305611 PMCID: PMC6180101 DOI: 10.1038/s41419-018-1086-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 01/25/2023]
Abstract
Glioma is the most common and malignant form of primary brain tumour, and is characterised by high proliferation and extensive invasion and neurological destruction. Demethylzeylasteral (T-96), which is extracted from Tripterygium wilfordii, is considered to have immunosuppressive, anti-inflammatory and anti-angiogenic effects. Here, the anti-tumour effect of T-96 on glioma was evaluated. Our results demonstrated that T-96 significantly inhibited glioma cell growth and induced cell cycle arrest in G1 phase but did not induce apoptosis. Cell invasion and migration were dramatically suppressed after treatment with T-96. Almost all genes related to cell cycle and DNA replication were downregulated after treatment with T-96. Our results showed that miR-30e-5p was noticeably upregulated after T-96 treatment, and MYBL2, which is involved in cell cycle progression and is a target gene of miR-30e-5p, was significantly reduced in synchrony. Overexpression of MYBL2 partially rescued the T-96-induced inhibition of cell growth and proliferation. Moreover, a miR-30e-5p antagomir significantly reduced the upregulation of miR-30e-5p expression induced by T-96, leading to recovery of MYBL2 expression, and partially rescued the T-96-induced inhibition of cell growth and proliferation. More important, T-96 effectively upregulated miR-30e-5p expression and downregulated MYBL2 expression, thus inhibiting LN-229 cell tumour growth in a mouse model. These results indicated that T-96 might inhibit glioma cell growth by regulating the miR-30e-5p/MYBL2 axis. Our study demonstrated that T-96 might act as a promising agent for malignant glioma therapy.
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26
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Distinguishing features of microglia- and monocyte-derived macrophages after stroke. Acta Neuropathol 2018; 135:551-568. [PMID: 29249001 DOI: 10.1007/s00401-017-1795-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 01/19/2023]
Abstract
After stroke, macrophages in the ischemic brain may be derived from either resident microglia or infiltrating monocytes. Using bone marrow (BM)-chimerism and dual-reporter transgenic fate mapping, we here set out to delimit the responses of either cell type to mild brain ischemia in a mouse model of 30 min transient middle cerebral artery occlusion (MCAo). A discriminatory analysis of gene expression at 7 days post-event yielded 472 transcripts predominantly or exclusively expressed in blood-derived macrophages as well as 970 transcripts for microglia. The differentially regulated genes were further collated with oligodendrocyte, astrocyte, and neuron transcriptomes, resulting in a dataset of microglia- and monocyte-specific genes in the ischemic brain. Functional categories significantly enriched in monocytes included migration, proliferation, and calcium signaling, indicative of strong activation. Whole-cell patch-clamp analysis further confirmed this highly activated state by demonstrating delayed outward K+ currents selectively in invading cells. Although both cell types displayed a mixture of known phenotypes pointing to the significance of 'intermediate states' in vivo, blood-derived macrophages were generally more skewed toward an M2 neuroprotective phenotype. Finally, we found that decreased engraftment of blood-borne cells in the ischemic brain of chimeras reconstituted with BM from Selplg-/- mice resulted in increased lesions at 7 days and worse post-stroke sensorimotor performance. In aggregate, our study establishes crucial differences in activation state between resident microglia and invading macrophages after stroke and identifies unique genomic signatures for either cell type.
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27
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Behdani E, Bakhtiarizadeh MR. Construction of an integrated gene regulatory network link to stress-related immune system in cattle. Genetica 2017; 145:441-454. [PMID: 28825201 DOI: 10.1007/s10709-017-9980-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023]
Abstract
The immune system is an important biological system that is negatively impacted by stress. This study constructed an integrated regulatory network to enhance our understanding of the regulatory gene network used in the stress-related immune system. Module inference was used to construct modules of co-expressed genes with bovine leukocyte RNA-Seq data. Transcription factors (TFs) were then assigned to these modules using Lemon-Tree algorithms. In addition, the TFs assigned to each module were confirmed using the promoter analysis and protein-protein interactions data. Therefore, our integrated method identified three TFs which include one TF that is previously known to be involved in immune response (MYBL2) and two TFs (E2F8 and FOXS1) that had not been recognized previously and were identified for the first time in this study as novel regulatory candidates in immune response. This study provides valuable insights on the regulatory programs of genes involved in the stress-related immune system.
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Affiliation(s)
- Elham Behdani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Ramin University, Khozestan, Iran
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28
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MYBL2 (B-Myb): a central regulator of cell proliferation, cell survival and differentiation involved in tumorigenesis. Cell Death Dis 2017. [PMID: 28640249 PMCID: PMC5520903 DOI: 10.1038/cddis.2017.244] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Limitless cell proliferation, evasion from apoptosis, dedifferentiation, metastatic spread and therapy resistance: all these properties of a cancer cell contribute to its malignant phenotype and affect patient outcome. MYBL2 (alias B-Myb) is a transcription factor of the MYB transcription factor family and a physiological regulator of cell cycle progression, cell survival and cell differentiation. When deregulated in cancer cells, MYBL2 mediates the deregulation of these properties. In fact, MYBL2 is overexpressed and associated with poor patient outcome in numerous cancer entities. MYBL2 and players of its downstream transcriptional network can be used as prognostic and/or predictive biomarkers as well as potential therapeutic targets to offer less toxic and more specific anti-cancer therapies in future. In this review, we summarize current knowledge on the physiological roles of MYBL2 and highlight the impact of its deregulation on cancer initiation and progression.
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29
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Zhou Z, Yin Y, Chang Q, Sun G, Lin J, Dai Y. Downregulation of B-myb promotes senescence via the ROS-mediated p53/p21 pathway, in vascular endothelial cells. Cell Prolif 2016; 50. [PMID: 27878894 DOI: 10.1111/cpr.12319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES To reveal whether B-myb is involved in preventing senescence of vascular endothelial cells, and if so, to identify possible mechanisms for it. MATERIALS AND METHODS C57/BL6 male mice and primary human aortic endothelial cells (HAECs) were used. Bleomycin was applied to induce stress-related premature senescence. B-myb knockdown was achieved using an siRNA technique and cell senescence was assessed using the senescence-associated β-galactosidase (SA-β-gal) assay. Intracellular reactive oxygen species (ROS) production was analysed using an ROS assay kit and cell proliferation was evaluated using KFluor488 EdU kit. Capillary tube network formation was determined by Matrigel assay. Expressions of mRNA and protein levels were detected by real-time PCR and western blotting. RESULTS B-myb expression significantly decreased, while p53 and p21 expressions increased in the aortas of aged mice. This expression pattern was also found in replicative senescent HAECs and senescent HAECs induced by bleomycin. B-myb knockdown resulted in upregulation of p22phox , ROS accumulation and cell senescence of HAECs. Downregulation of B-myb significantly inhibited cell proliferation and capillary tube network formation and activated the p53/p21 signalling pathway. Blocking ROS production or inhibiting p53 activation remarkably attenuated SA-β-gal activity and delayed cell senescence induced by B-myb-silencing. CONCLUSION Downregulation of B-myb induced senescence by upregulation of p22phox and activation of the ROS/p53/p21 pathway, in our vascular endothelial cells, suggesting that B-myb may be a novel candidate for regulating cell senescence to protect against endothelial senescence-related cardiovascular diseases.
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Affiliation(s)
- Zhihui Zhou
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
| | - Yanlin Yin
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
| | - Qun Chang
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
| | - Guanqun Sun
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
| | - Jiahui Lin
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
| | - Yalei Dai
- Department of Cardiology, Shanghai East Hospital and Immunology Department, Tongji University School of Medicine, Shanghai, China
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30
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Yang Z, Shah K, Khodadadi-Jamayran A, Jiang H. Dpy30 is critical for maintaining the identity and function of adult hematopoietic stem cells. J Exp Med 2016; 213:2349-2364. [PMID: 27647347 PMCID: PMC5068233 DOI: 10.1084/jem.20160185] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
As the major histone H3K4 methyltransferases in mammals, the Set1/Mll complexes play important roles in animal development and are associated with many diseases, including hematological malignancies. However, the role of the H3K4 methylation activity of these complexes in fate determination of hematopoietic stem and progenitor cells (HSCs and HPCs) remains elusive. Here, we address this question by generating a conditional knockout mouse for Dpy30, which is a common core subunit of all Set1/Mll complexes and facilitates genome-wide H3K4 methylation in cells. Dpy30 loss in the adult hematopoietic system results in severe pancytopenia but striking accumulation of HSCs and early HPCs that are defective in multilineage reconstitution, suggesting a differentiation block. In mixed bone marrow chimeras, Dpy30-deficient HSCs cannot differentiate or efficiently up-regulate lineage-regulatory genes, and eventually fail to sustain for long term with significant loss of HSC signature gene expression. Our molecular analyses reveal that Dpy30 directly and preferentially controls H3K4 methylation and expression of many hematopoietic development-associated genes including several key transcriptional and chromatin regulators involved in HSC function. Collectively, our results establish a critical and selective role of Dpy30 and the H3K4 methylation activity of the Set1/Mll complexes for maintaining the identity and function of adult HSCs.
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Affiliation(s)
- Zhenhua Yang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama School of Medicine, Birmingham, AL 35210
| | - Kushani Shah
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama School of Medicine, Birmingham, AL 35210
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama School of Medicine, Birmingham, AL 35210
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama School of Medicine, Birmingham, AL 35210
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31
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Inactivation of 3-hydroxybutyrate dehydrogenase 2 delays zebrafish erythroid maturation by conferring premature mitophagy. Proc Natl Acad Sci U S A 2016; 113:E1460-9. [PMID: 26929344 DOI: 10.1073/pnas.1600077113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mitochondria are the site of iron utilization, wherein imported iron is incorporated into heme or iron-sulfur clusters. Previously, we showed that a cytosolic siderophore, which resembles a bacterial siderophore, facilitates mitochondrial iron import in eukaryotes, including zebrafish. An evolutionarily conserved 3-hydroxy butyrate dehydrogenase, 3-hydroxy butyrate dehydrogenase 2 (Bdh2), catalyzes a rate-limiting step in the biogenesis of the eukaryotic siderophore. We found that inactivation of bdh2 in developing zebrafish embryo results in heme deficiency and delays erythroid maturation. The basis for this erythroid maturation defect is not known. Here we show that bdh2 inactivation results in mitochondrial dysfunction and triggers their degradation by mitophagy. Thus, mitochondria are prematurely lost in bdh2-inactivated erythrocytes. Interestingly, bdh2-inactivated erythroid cells also exhibit genomic alterations as indicated by transcriptome analysis. Reestablishment of bdh2 restores mitochondrial function, prevents premature mitochondrial degradation, promotes erythroid development, and reverses altered gene expression. Thus, mitochondrial communication with the nucleus is critical for erythroid development.
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32
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Bar-Or D, Thomas GW, Rael LT, Gersch ED, Rubinstein P, Brody E. Low Molecular Weight Fraction of Commercial Human Serum Albumin Induces Morphologic and Transcriptional Changes of Bone Marrow-Derived Mesenchymal Stem Cells. Stem Cells Transl Med 2015; 4:945-55. [PMID: 26041739 DOI: 10.5966/sctm.2014-0293] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/13/2015] [Indexed: 12/27/2022] Open
Abstract
Osteoarthritis (OA) is the most common chronic disease of the joint; however, the therapeutic options for severe OA are limited. The low molecular weight fraction of commercial 5% human serum albumin (LMWF5A) has been shown to have anti-inflammatory properties that are mediated, in part, by a diketopiperazine that is present in the albumin preparation and that was demonstrated to be safe and effective in reducing pain and improving function when administered intra-articularly in a phase III clinical trial. In the present study, bone marrow-derived mesenchymal stem cells (BMMSCs) exposed to LMWF5A exhibited an elongated phenotype with diffuse intracellular F-actin, pronounced migratory leading edges, and filopodia-like projections. In addition, LMWF5A promoted chondrogenic condensation in "micromass" culture, concurrent with the upregulation of collagen 2α1 mRNA. Furthermore, the transcription of the CXCR4-CXCL12 axis was significantly regulated in a manner conducive to migration and homing. Several transcription factors involved in stem cell differentiation were also found to bind oligonucleotide response element probes following exposure to LMWF5A. Finally, a rapid increase in PRAS40 phosphorylation was observed following treatment, potentially resulting in the activation mTORC1. Proteomic analysis of synovial fluid taken from a preliminary set of patients indicated that at 12 weeks following administration of LMWF5A, a microenvironment exists in the knee conducive to stem cell infiltration, self-renewal, and differentiation, in addition to indications of remodeling with a reduction in inflammation. Taken together, these findings imply that LMWF5A treatment may prime stem cells for both mobilization and chondrogenic differentiation, potentially explaining some of the beneficial effects achieved in clinical trials.
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Affiliation(s)
- David Bar-Or
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
| | - Gregory W Thomas
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
| | - Leonard T Rael
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
| | - Elizabeth D Gersch
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
| | - Pablo Rubinstein
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
| | - Edward Brody
- Swedish Medical Center, Trauma Research Department, Englewood, Colorado, USA; St. Anthony Hospital, Trauma Research Department, Lakewood, Colorado, USA; Medical Center of Plano, Trauma Research Department, Plano, Texas, USA; Ampio Pharmaceuticals Inc., Englewood, Colorado, USA; New York Blood Center, New York, New York, USA; SomaLogic Inc., Boulder, Colorado, USA
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33
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Ren F, Wang L, Shen X, Xiao X, Liu Z, Wei P, Wang Y, Qi P, Shen C, Sheng W, Du X. MYBL2 is an independent prognostic marker that has tumor-promoting functions in colorectal cancer. Am J Cancer Res 2015; 5:1542-1552. [PMID: 26101717 PMCID: PMC4473330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023] Open
Abstract
The MYBL2 gene plays an important role in the genesis and progression of tumors; however, few studies to date have defined the role of this gene in colorectal cancer (CRC). The aim of this study was to determine the relationship between MYBL2 and the prognosis of patients with CRC and to determine the possible effect of MYBL2 on colorectal carcinogenesis. Solid CRC tissues (n=180) preserved with RNAlater were collected to examine the mRNA levels of MYBL2 by real-time quantitative PCR (RT-qPCR). Formalin-fixed, paraffin-embedded (FFPE) blocks of CRC tissues (n=97) and adjacent noncancerous tissues (ANCTs, n=104) were obtained to detect MYBL2 protein levels by immunohistochemistry (IHC). siRNA was used to downregulate MYBL2 expression in the SW480 cell line to detect changes in proliferation, cell cycle progression, apoptosis, migration and invasion. The protein levels of MYBL2 were significantly higher in CRC tissues compared with ANCTs (P<0.05). Kaplan-Meier survival curves indicated that disease-free survival (DFS) was significantly worse in CRC patients in whom MYBL2 was overexpressed (at both the mRNA and protein levels) compared with patients not overexpressing MYBL2. Cox multivariate analysis revealed MYBL2 overexpression as an independent prognostic factor for poor patient survival. In addition, siRNA downregulation of MYBL2 suppressed SW480 cell proliferation, delayed cell cycle progression and induced apoptosis; however, changes in cell migration were minor. Western blot analysis demonstrated an association between MYBL2 expression and that of MMP9, Vimentin, and E-cadherin. MYBL2 is overexpressed in CRC and may therefore play an important role in tumourigenesis.
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Affiliation(s)
- Fei Ren
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Lisha Wang
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Xiaohan Shen
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Xiuying Xiao
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiaotong UniversityShanghai 200127, China
| | - Zebing Liu
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Ping Wei
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Yiqin Wang
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Peng Qi
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Chen Shen
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Weiqi Sheng
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
| | - Xiang Du
- Department of Pathology, Fudan University Shanghai Cancer CenterShanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, China
- Institute of Pathology, Fudan UniversityShanghai 200032, China
- Institutes of Biomedical Sciences, Fudan UniversityShanghai 200032, China
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Eirin A, Riester SM, Zhu XY, Tang H, Evans JM, O'Brien D, van Wijnen AJ, Lerman LO. MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells. Gene 2014; 551:55-64. [PMID: 25158130 DOI: 10.1016/j.gene.2014.08.041] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022]
Abstract
Mesenchymal stromal/stem cells (MSCs) are clinically useful for cell-based therapy, but concerns regarding their ability to replicate limit their human application. MSCs release extracellular vesicles (EVs) that mediate at least in part the paracrine effects of the parental cells. To understand the molecular basis of their biological properties, we characterized the RNA cargo of EVs from porcine adipose-tissue derived MSCs. Comprehensive characterization of mRNA and miRNA gene expression using high-throughput RNA sequencing (RNA-seq) revealed that EVs are selectively enriched for distinct classes of RNAs. For example, EVs preferentially express mRNA for transcription factors (e.g. MDFIC, POU3F1, NRIP1) and genes involved in angiogenesis (e.g. HGF, HES1, TCF4) and adipogenesis (e.g. CEBPA, KLF7). EVs also express Golgi apparatus genes (ARRB1, GOLGA4) and genes involved in TGF-β signaling. In contrast, mitochondrial, calcium signaling, and cytoskeleton genes are selectively excluded from EVs, possibly because these genes remain sequestered in organelles or intracellular compartments. RNA-seq generated reads for at least 386 annotated miRNAs, but only miR148a, miR532-5p, miR378, and let-7f were enriched in EVs compared to MSCs. Gene ontology analysis indicates that these miRNAs target transcription factors and genes that participate in several cellular pathways, including angiogenesis, cellular transport, apoptosis, and proteolysis. Our data suggest that EVs transport gene regulatory information to modulate angiogenesis, adipogenesis, and other cell pathways in recipient cells. These observations may contribute to development of regenerative strategies using EVs to overcome potential complications of cell-based therapy.
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Scott M Riester
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Jared M Evans
- Health Sciences Research & Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Daniel O'Brien
- Health Sciences Research & Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States.
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