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Gao Y, Huang X, Liu Y, Lv H, Yin X, Li W, Chu Z. Transcriptome analysis of large yellow croaker (Larimichthys crocea) at different growth rates. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1745-1757. [PMID: 38842792 DOI: 10.1007/s10695-024-01367-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
The unsynchronized growth of the large yellow croaker (Larimichthys crocea), which impacts growth efficiency, poses a challenge for aquaculture practitioners. In our study, juvenile stocks of large yellow croaker were sorted by size after being cultured in offshore cages for 4 months. Subsequently, individuals from both the fast-growing (FG) and slow-growing (SG) groups were sampled for analysis. High-throughput RNA-Seq was employed to identify genes and pathways that are differentially expressed during varying growth rates, which could suggest potential physiological mechanisms that influence growth rate. Our transcriptome analysis identified 382 differentially expressed genes (DEGs), comprising 145 upregulated and 237 downregulated genes in comparison to the SG group. GO and KEGG enrichment analyses indicated that these DEGs are predominantly involved in signal transduction and biochemical metabolic pathways. Quantitative PCR (qPCR) results demonstrated that cat, fasn, idh1, pgd, fgf19, igf2, and fads2 exhibited higher expression levels, whereas gadd45b and gadd45g showed lower expression compared to the slow-growing group. In conclusion, the differential growth rates of large yellow croaker are intricately associated with cellular proliferation, metabolic rates of the organism, and immune regulation. These findings offer novel insights into the molecular mechanisms and regulatory aspects of growth in large yellow croaker and enhance our understanding of growth-related genes.
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Affiliation(s)
- Yang Gao
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China.
| | - Xuming Huang
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Yanli Liu
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Huirong Lv
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Xiaolong Yin
- Zhoushan Fisheries Research Institute, Zhoushan, China
| | - Weiye Li
- Zhoushan Fisheries Research Institute, Zhoushan, China
| | - Zhangjie Chu
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
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2
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McLeod JJ, Rothschild SC, Francescatto L, Kim H, Tombes RM. Specific CaMKIIs mediate convergent extension cell movements in early zebrafish development. Dev Dyn 2024; 253:390-403. [PMID: 37860955 DOI: 10.1002/dvdy.665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Noncanonical Wnts are morphogens that can elevate intracellular Ca2+, activate the Ca2+/calmodulin-dependent protein kinase, CaMKII, and promote cell movements during vertebrate gastrulation. RESULTS Zebrafish express seven CaMKII genes during embryogenesis; two of these, camk2b1 and camk2g1, are necessary for convergent extension (CE) cell movements. CaMKII morphant phenotypes were observed as early as epiboly. At the 1-3 somite stage, neuroectoderm and paraxial cells remained unconverged in both morphants. Later, somites lacked their stereotypical shape and were wider, more closely spaced, and body gap angles increased. At 24hpf, somite compression and notochord undulation coincided with a shorter and broader body axis. A camk2b1 crispant was generated which phenocopied the camk2b1 morphant. The levels of cell proliferation, apoptosis and paraxial and neuroectodermal markers were unchanged in morphants. Hyperactivation of CaMKII during gastrulation by transient pharmacological intervention (thapsigargin) also caused CE defects. Mosaically expressed dominant-negative CaMKII recapitulated these phenotypes and showed significant midline bifurcation. Finally, the introduction of CaMKII partially rescued Wnt11 morphant phenotypes. CONCLUSIONS Overall, these data support a model whereby cyclically activated CaMKII encoded from two genes enables cell migration during the process of CE.
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Affiliation(s)
- Jamie J McLeod
- Department of Biology and VCU Life Sciences, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sarah C Rothschild
- Department of Biology and VCU Life Sciences, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Haerin Kim
- Department of Biology and VCU Life Sciences, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Robert M Tombes
- Department of Biology and VCU Life Sciences, Virginia Commonwealth University, Richmond, Virginia, USA
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3
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Muniz Seif EJ, Icimoto MY, da Silva Junior PI. In silico bioprospecting of receptors for Doderlin: an antimicrobial peptide isolated from Lactobacillus acidophilus. In Silico Pharmacol 2023; 11:11. [PMID: 37113323 PMCID: PMC10126193 DOI: 10.1007/s40203-023-00149-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The emergence of resistant bacteria strains against traditional antibiotics and treatments increases each year. Doderlin is a cationic and amphiphilic peptide active against gram-positive, negative and yeast stains. The aim of the present work was prospect potentials receptors associated of antimicrobial activity of Doderlin using in silico bioinformatics tools. To search for potential targets of Doderlin, PharmMapper software was used. Molecular docking between Doderlin and the receptor was performed by PatchDock. Additional interaction and ligand site prediction for each receptor was performed by I-TASSER software. Those PDB Id, 1XDJ (score: 11,746), 1JMH (score: 11,046), 1YR3 (score: 10,578), 1NG3 (score: 10,082) showed highest dock score. Doderlin was found to predicted/real sites co-localize with 1XDJ and 1JMH, enzymes accountable for nitrogenic bases synthesis. The resulting receptor bioprospecting is highly correlated and suggests that Doderlin might act by interfering with DNA metabolism/production of bacteria, altering microorganism homeostasis and growth impairment. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00149-1.
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Affiliation(s)
- Elias Jorge Muniz Seif
- Postgraduate Program in Molecular Biology, Federal University of São Paulo, São Paulo, Brazil
- Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CETICS/CEPID), Butantan Institute, São Paulo, Brazil
| | | | - Pedro Ismael da Silva Junior
- Postgraduate Program in Molecular Biology, Federal University of São Paulo, São Paulo, Brazil
- Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CETICS/CEPID), Butantan Institute, São Paulo, Brazil
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4
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Linehan JB, Zepeda JL, Mitchell TA, LeClair EE. Follow that cell: leukocyte migration in L-plastin mutant zebrafish. Cytoskeleton (Hoboken) 2022; 79:26-37. [PMID: 35811499 DOI: 10.1002/cm.21717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/21/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Actin assemblies are important in motile cells such as leukocytes which form dynamic plasma membrane extensions or podia. L-plastin (LCP1) is a leukocyte-specific calcium-dependent actin-bundling protein that, in mammals, is known to affect immune cell migration. Previously, we generated CRISPR/Cas9 engineered zebrafish lacking L-plastin (lcp1-/-) and reported that they had reduced survival to adulthood, suggesting that lack of this actin-bundler might negatively affect the immune system. To test this hypothesis, we examined the distribution and migration of neutrophils and macrophages in the transparent tail of early zebrafish larvae using cell-specific markers and an established wound-migration assay. Knockout larvae were similar to their heterozygous siblings in having equal body sizes and comparable numbers of neutrophils in caudal hematopoietic tissue at two days post-fertilization, indicating no gross defect in neutrophil production or developmental migration. When stimulated by a tail wound, all genotypes of neutrophils were equally migratory in a two-hour window. However for macrophages we observed both migration defects and morphological differences. L-plastin knockout macrophages (lcp1 -/-) still homed to wounds but were slower, less directional and had a star-like morphology with many leading and trailing projections. In contrast, heterozygous macrophages lcp1 (+/-) were faster, more directional, and had a streamlined, slug-like morphology. Overall, these findings show that in larval zebrafish L-plastin knockout primarily affects the macrophage response with possible consequences for organismal immunity. Consistent with our observations, we propose a model in which cytoplasmic L-plastin negatively regulates macrophage integrin adhesion by holding these transmembrane heterodimers in a 'clasped', inactive form and is a necessary part of establishing macrophage polarity during chemokine-induced motility. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- J B Linehan
- Department of Biological Sciences, DePaul University, USA
| | - J L Zepeda
- Department of Biological Sciences, DePaul University, USA
| | - T A Mitchell
- Department of Biological Sciences, DePaul University, USA
| | - E E LeClair
- Department of Biological Sciences, DePaul University, USA
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5
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Zeng S, Peng Y, Ma J, Ge Y, Huang Y, Xie S, Yuan W, Lu C, Zhang H, Luo Q, Liao X, Lu H. Hematopoietic stem cell and immunotoxicity in zebrafish embryos induced by exposure to Metalaxyl-M. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152102. [PMID: 34863748 DOI: 10.1016/j.scitotenv.2021.152102] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/13/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Metalaxyl-M (MM), a protective and therapeutic fungicide, has been shown to be a promising candidate, but its toxicity toward aquatic organisms is unknown. In this study, we evaluated for the first time the immunotoxicity of MM in zebrafish embryos. Phenotypes (heart rate, body length, and yolk area) and the number of neutrophils, macrophages, and T cells in the thymus were analyzed in zebrafish embryo after exposure to MM. Our results showed that zebrafish embryos exposed to MM showed a concentration-dependent increase in the yolk area and a significant decrease in the number of neutrophils, macrophages, and thymus T cells. We detected upregulated expression of related immune signaling genes, such as tnfa, nfkb3, cxcl-c1c, il6, mmp9, and tgfb1. Additionally, we observed a significant decrease in HSCs in zebrafish larvae after exposure to MM. IWR-1 could restore the number of neutrophils and macrophages after exposure to MM. The results indicated that MM exerted developmental toxicity and immunotoxicity to zebrafish embryos, and these phenomena may be caused by MM's regulation of WNT signaling pathway.
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Affiliation(s)
- Suwen Zeng
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yuyang Peng
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Jinze Ma
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yurui Ge
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yong Huang
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Shuling Xie
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Wei Yuan
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Chen Lu
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Hua Zhang
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Qiang Luo
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Xinjun Liao
- Jiangxi Engineering Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases, Jiangxi Key Laboratory of Developmental Biology of Organs, Affiliated Hospital of Jinggangshan University, Ji'an 343009, China
| | - Huiqiang Lu
- Ganzhou Cancer Hospital-Gannan Normal School Joint Research Center for Cancer Prevention and Treatment, Ganzhou Key Laboratory for Drug Screening and Discovery, Gannan Normal University, Ganzhou, 341000, Jiangxi, China; Jiangxi Engineering Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases, Jiangxi Key Laboratory of Developmental Biology of Organs, Affiliated Hospital of Jinggangshan University, Ji'an 343009, China.
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6
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Kabir AU, Subramanian M, Lee DH, Wang X, Krchma K, Wu J, Naismith T, Halabi CM, Kim JY, Pulous FE, Petrich BG, Kim S, Park HC, Hanson PI, Pan H, Wickline SA, Fremont DH, Park C, Choi K. Dual role of endothelial Myct1 in tumor angiogenesis and tumor immunity. Sci Transl Med 2021; 13:13/583/eabb6731. [PMID: 33658356 DOI: 10.1126/scitranslmed.abb6731] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
The cross-talk between angiogenesis and immunity within the tumor microenvironment (TME) is critical for tumor prognosis. While pro-angiogenic and immunosuppressive TME promote tumor growth, anti-angiogenic and immune stimulatory TME inhibit tumor progression. Therefore, there is a great interest in achieving vascular normalization to improve drug delivery and enhance antitumor immunity. However, anti-vascular endothelial growth factor (VEGF) mechanisms to normalize tumor vessels have offered limited therapeutic efficacies for patients with cancer. Here, we report that Myct1, a direct target of ETV2, was nearly exclusively expressed in endothelial cells. In preclinical mouse tumor models, Myct1 deficiency reduced angiogenesis, enhanced high endothelial venule formation, and promoted antitumor immunity, leading to restricted tumor progression. Analysis of The Cancer Genome Atlas (TCGA) datasets revealed a significant (P < 0.05) correlation between MYCT1 expression, angiogenesis, and antitumor immunity in human cancers, as suggested by decreased FOXP3 expression and increased antitumor macrophages in patients with low MYCT1 expression. Mechanistically, MYCT1 interacted with tight junction protein Zona Occludens 1 and regulated Rho GTPase-mediated actin cytoskeleton dynamics, thereby promoting endothelial motility in the angiogenic environment. Myct1-deficient endothelial cells facilitated trans-endothelial migration of cytotoxic T lymphocytes and polarization of M1 macrophages. Myct1 targeting combined with anti-PD1 treatment significantly (P < 0.05) increased complete tumor regression and long-term survival in anti-PD1-responsive and -refractory tumor models in mice. Our data collectively support a critical role for Myct1 in controlling tumor angiogenesis and reprogramming tumor immunity. Myct1-targeted vascular control, in combination with immunotherapy, may become an exciting therapeutic strategy.
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Affiliation(s)
- Ashraf Ul Kabir
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.,Molecular and Cell Biology Program, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Madhav Subramanian
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Dong Hun Lee
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Teri Naismith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Carmen M Halabi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Ju Young Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Fadi E Pulous
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Brian G Petrich
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Suhyun Kim
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan 15335, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan 15335, Republic of Korea
| | - Phyllis I Hanson
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-5624, USA
| | - Hua Pan
- Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Samuel A Wickline
- Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Changwon Park
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA. .,Department of Molecular and Cellular Physiology, Louisiana State University Health Science Center, Shreveport, LA 71103, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA. .,Molecular and Cell Biology Program, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.,Graduate School of Biotechnology, Kyung Hee University, Yong In 17104, Republic of Korea
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7
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Ferreira FJ, Carvalho L, Logarinho E, Bessa J. foxm1 Modulates Cell Non-Autonomous Response in Zebrafish Skeletal Muscle Homeostasis. Cells 2021; 10:cells10051241. [PMID: 34070077 PMCID: PMC8158134 DOI: 10.3390/cells10051241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/01/2021] [Accepted: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
foxm1 is a master regulator of the cell cycle, contributing to cell proliferation. Recent data have shown that this transcription factor also modulates gene networks associated with other cellular mechanisms, suggesting non-proliferative functions that remain largely unexplored. In this study, we used CRISPR/Cas9 to disrupt foxm1 in the zebrafish terminally differentiated fast-twitching muscle cells. foxm1 genomic disruption increased myofiber death and clearance. Interestingly, this contributed to non-autonomous satellite cell activation and proliferation. Moreover, we observed that Cas9 expression alone was strongly deleterious to muscle cells. Our report shows that foxm1 modulates a muscle non-autonomous response to myofiber death and highlights underreported toxicity to high expression of Cas9 in vivo.
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Affiliation(s)
- Fábio J. Ferreira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (F.J.F.); (L.C.)
- Vertebrate Development and Regeneration Group, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- Aging and Aneuploidy Group, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Leonor Carvalho
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (F.J.F.); (L.C.)
- Vertebrate Development and Regeneration Group, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Elsa Logarinho
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (F.J.F.); (L.C.)
- Aging and Aneuploidy Group, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: (E.L.); (J.B.)
| | - José Bessa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (F.J.F.); (L.C.)
- Vertebrate Development and Regeneration Group, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: (E.L.); (J.B.)
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8
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Somasagara RR, Huang X, Xu C, Haider J, Serody JS, Armistead PM, Leung T. Targeted therapy of human leukemia xenografts in immunodeficient zebrafish. Sci Rep 2021; 11:5715. [PMID: 33707624 PMCID: PMC7952715 DOI: 10.1038/s41598-021-85141-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/25/2021] [Indexed: 01/05/2023] Open
Abstract
Personalized medicine holds tremendous promise for improving safety and efficacy of drug therapies by optimizing treatment regimens. Rapidly developed patient-derived xenografts (pdx) could be a helpful tool for analyzing the effect of drugs against an individual's tumor by growing the tumor in an immunodeficient animal. Severe combined immunodeficiency (SCID) mice enable efficient in vivo expansion of vital tumor cells and generation of personalized xenografts. However, they are not amenable to large-scale rapid screening, which is critical in identifying new compounds from large compound libraries. The development of a zebrafish model suitable for pdx could facilitate large-scale screening of drugs targeted against specific malignancies. Here, we describe a novel strategy for establishing a zebrafish model for drug testing in leukemia xenografts. We used chronic myelogenous leukemia and acute myeloid leukemia for xenotransplantation into SCID zebrafish to evaluate drug screening protocols. We showed the in vivo efficacy of the ABL inhibitor imatinib, MEK inhibitor U0126, cytarabine, azacitidine and arsenic trioxide. We performed corresponding in vitro studies, demonstrating that combination of MEK- and FLT3-inhibitors exhibit an enhanced effect in vitro. We further evaluated the feasibility of zebrafish for transplantation of primary human hematopoietic cells that can survive at 15 day-post-fertilization. Our results provide critical insights to guide development of high-throughput platforms for evaluating leukemia.
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Affiliation(s)
- Ranganatha R Somasagara
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Xiaoyan Huang
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Chunyu Xu
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Jamil Haider
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Jonathan S Serody
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Paul M Armistead
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - TinChung Leung
- The Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC, 28081, USA. .,Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC, 27707, USA.
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9
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Dong Z, Haines S, Coates D. Proteomic Profiling of Stem Cell Tissues during Regeneration of Deer Antler: A Model of Mammalian Organ Regeneration. J Proteome Res 2020; 19:1760-1775. [DOI: 10.1021/acs.jproteome.0c00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Stephen Haines
- Proteins & Metabolites, AgResearch Lincoln Research Centre, Lincoln, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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10
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Deobald D, Hanna R, Shahryari S, Layer G, Adrian L. Identification and characterization of a bacterial core methionine synthase. Sci Rep 2020; 10:2100. [PMID: 32034217 PMCID: PMC7005905 DOI: 10.1038/s41598-020-58873-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/20/2020] [Indexed: 11/18/2022] Open
Abstract
Methionine synthases are essential enzymes for amino acid and methyl group metabolism in all domains of life. Here, we describe a putatively anciently derived type of methionine synthase yet unknown in bacteria, here referred to as core-MetE. The enzyme appears to represent a minimal MetE form and transfers methyl groups from methylcobalamin instead of methyl-tetrahydrofolate to homocysteine. Accordingly, it does not possess the tetrahydrofolate binding domain described for canonical bacterial MetE proteins. In Dehalococcoides mccartyi strain CBDB1, an obligate anaerobic, mesophilic, slowly growing organohalide-respiring bacterium, it is encoded by the locus cbdbA481. In line with the observation to not accept methyl groups from methyl-tetrahydrofolate, all known genomes of bacteria of the class Dehalococcoidia lack metF encoding for methylene-tetrahydrofolate reductase synthesizing methyl-tetrahydrofolate, but all contain a core-metE gene. We heterologously expressed core-MetECBDB in E. coli and purified the 38 kDa protein. Core-MetECBDB exhibited Michaelis-Menten kinetics with respect to methylcob(III)alamin (KM ≈ 240 µM) and L-homocysteine (KM ≈ 50 µM). Only methylcob(III)alamin was found to be active as methyl donor with a kcat ≈ 60 s-1. Core-MetECBDB did not functionally complement metE-deficient E. coli strain DH5α (ΔmetE::kan) suggesting that core-MetECBDB and the canonical MetE enzyme from E. coli have different enzymatic specificities also in vivo. Core-MetE appears to be similar to a MetE-ancestor evolved before LUCA (last universal common ancestor) using methylated cobalamins as methyl donor whereas the canonical MetE consists of a tandem repeat and might have evolved by duplication of the core-MetE and diversification of the N-terminal part to a tetrahydrofolate-binding domain.
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Affiliation(s)
- Darja Deobald
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Rafael Hanna
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Shahab Shahryari
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Gunhild Layer
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany.
- Technische Universität Berlin, Chair of Geobiotechnology, Ackerstraße 76, 13355, Berlin, Germany.
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11
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Guo HZ, Niu LT, Qiang WT, Chen J, Wang J, Yang H, Zhang W, Zhu J, Yu SH. Leukemic IL-17RB signaling regulates leukemic survival and chemoresistance. FASEB J 2019; 33:9565-9576. [PMID: 31136196 DOI: 10.1096/fj.201900099r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Secreted proteins provide crucial signals that have been implicated in the development of acute myeloid leukemia (AML) in the bone marrow microenvironment. Here we identify aberrant expressions of inflammatory IL-17B and its receptor (IL-17RB) in human and mouse mixed lineage leukemia-rearranged AML cells, which were further increased after exposure to chemotherapy. Interestingly, silencing of IL-17B or IL-17RB led to significant suppression of leukemic cell survival and disease progression in vivo. Moreover, the IL-17B-IL-17RB axis protected leukemic cells from chemotherapeutic agent-induced apoptotic effects. Mechanistic studies revealed that IL-17B promoted AML cell survival by enhancing ERK, NF-κB phosphorylation, and the expression of antiapoptotic protein B-cell lymphoma 2, which were reversed by small-molecule inhibitors. Thus, the inhibition of the IL-17B-IL-17RB axis may be a valid strategy to enhance sensitivity and therapeutic benefit of AML chemotherapy.-Guo, H.-Z., Niu, L.-T., Qiang, W.-T., Chen, J., Wang, J., Yang, H., Zhang, W., Zhu, J., Yu, S.-H. Leukemic IL-17RB signaling regulates leukemic survival and chemoresistance.
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Affiliation(s)
- He-Zhou Guo
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Li-Ting Niu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Wan-Ting Qiang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Juan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Juan Wang
- Bioinformatics and Genomics Program, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Hui Yang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Wu Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Jiang Zhu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Shan-He Yu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
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12
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Langevin C, Boudinot P, Collet B. IFN Signaling in Inflammation and Viral Infections: New Insights from Fish Models. Viruses 2019; 11:v11030302. [PMID: 30917538 PMCID: PMC6466407 DOI: 10.3390/v11030302] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
The overarching structure of the type I interferon (IFN) system is conserved across vertebrates. However, the variable numbers of whole genome duplication events during fish evolution offer opportunities for the expansion, diversification, and new functionalization of the genes that are involved in antiviral immunity. In this review, we examine how fish models provide new insights about the implication of virus-driven inflammation in immunity and hematopoiesis. Mechanisms that have been discovered in fish, such as the strong adjuvant effect of type I IFN that is used with DNA vaccination, constitute good models to understand how virus-induced inflammatory mechanisms can interfere with adaptive responses. We also comment on new discoveries regarding the role of pathogen-induced inflammation in the development and guidance of hematopoietic stem cells in zebrafish. These findings raise issues about the potential interferences of viral infections with the establishment of the immune system. Finally, the recent development of genome editing provides new opportunities to dissect the roles of the key players involved in the antiviral response in fish, hence enhancing the power of comparative approaches.
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Affiliation(s)
- Christelle Langevin
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
| | - Pierre Boudinot
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
| | - Bertrand Collet
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
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13
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Bhoyar RC, Jadhao AG, Sabharwal A, Ranjan G, Sivasubbu S, Pinelli C. Knockdown of calcium-binding calb2a and calb2b genes indicates the key regulator of the early development of the zebrafish, Danio rerio. Brain Struct Funct 2018; 224:627-642. [DOI: 10.1007/s00429-018-1797-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
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14
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Hersh TA, Dimond AL, Ruth BA, Lupica NV, Bruce JC, Kelley JM, King BL, Lutton BV. A role for the CXCR4-CXCL12 axis in the little skate, Leucoraja erinacea. Am J Physiol Regul Integr Comp Physiol 2018; 315:R218-R229. [PMID: 29641231 PMCID: PMC6139610 DOI: 10.1152/ajpregu.00322.2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The interaction between C-X-C chemokine receptor type 4 (CXCR4) and its cognate ligand C-X-C motif chemokine ligand 12 (CXCL12) plays a critical role in regulating hematopoietic stem cell activation and subsequent cellular mobilization. Extensive studies of these genes have been conducted in mammals, but much less is known about the expression and function of CXCR4 and CXCL12 in non-mammalian vertebrates. In the present study, we identify simultaneous expression of CXCR4 and CXCL12 orthologs in the epigonal organ (the primary hematopoietic tissue) of the little skate, Leucoraja erinacea. Genetic and phylogenetic analyses were functionally supported by significant mobilization of leukocytes following administration of Plerixafor, a CXCR4 antagonist and clinically important drug. Our results provide evidence that, as in humans, Plerixafor disrupts CXCR4/CXCL12 binding in the little skate, facilitating release of leukocytes into the bloodstream. Our study illustrates the value of the little skate as a model organism, particularly in studies of hematopoiesis and potentially for preclinical research on hematological and vascular disorders.
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Affiliation(s)
- Taylor A Hersh
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Alexandria L Dimond
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
| | - Brittany A Ruth
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
| | - Noah V Lupica
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Jacob C Bruce
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - John M Kelley
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
- Beth Israel Deaconess Medical Center, Program in Placebo Studies, Harvard Medical School , Boston, Massachusetts
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, Maine
| | - Bram V Lutton
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
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15
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Louie KW, Saera-Vila A, Kish PE, Colacino JA, Kahana A. Temporally distinct transcriptional regulation of myocyte dedifferentiation and Myofiber growth during muscle regeneration. BMC Genomics 2017; 18:854. [PMID: 29121865 PMCID: PMC5680785 DOI: 10.1186/s12864-017-4236-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tissue regeneration requires a series of steps, beginning with generation of the necessary cell mass, followed by cell migration into damaged area, and ending with differentiation and integration with surrounding tissues. Temporal regulation of these steps lies at the heart of the regenerative process, yet its basis is not well understood. The ability of zebrafish to dedifferentiate mature "post-mitotic" myocytes into proliferating myoblasts that in turn regenerate lost muscle tissue provides an opportunity to probe the molecular mechanisms of regeneration. RESULTS Following subtotal excision of adult zebrafish lateral rectus muscle, dedifferentiating residual myocytes were collected at two time points prior to cell cycle reentry and compared to uninjured muscles using RNA-seq. Functional annotation (GAGE or K-means clustering followed by GO enrichment) revealed a coordinated response encompassing epigenetic regulation of transcription, RNA processing, and DNA replication and repair, along with protein degradation and translation that would rewire the cellular proteome and metabolome. Selected candidate genes were phenotypically validated in vivo by morpholino knockdown. Rapidly induced gene products, such as the Polycomb group factors Ezh2 and Suz12a, were necessary for both efficient dedifferentiation (i.e. cell reprogramming leading to cell cycle reentry) and complete anatomic regeneration. In contrast, the late activated gene fibronectin was important for efficient anatomic muscle regeneration but not for the early step of myocyte cell cycle reentry. CONCLUSIONS Reprogramming of a "post-mitotic" myocyte into a dedifferentiated myoblast requires a complex coordinated effort that reshapes the cellular proteome and rewires metabolic pathways mediated by heritable yet nuanced epigenetic alterations and molecular switches, including transcription factors and non-coding RNAs. Our studies show that temporal regulation of gene expression is programmatically linked to distinct steps in the regeneration process, with immediate early expression driving dedifferentiation and reprogramming, and later expression facilitating anatomical regeneration.
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Affiliation(s)
- Ke'ale W Louie
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, 1011 N. University, Ann Arbor, MI, 48109, USA
| | - Alfonso Saera-Vila
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA.
| | - Phillip E Kish
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
- University of Michigan Comprehensive Cancer Center, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Alon Kahana
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA.
- University of Michigan Comprehensive Cancer Center, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, USA.
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16
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Xue Y, Lv J, Zhang C, Wang L, Ma D, Liu F. The Vascular Niche Regulates Hematopoietic Stem and Progenitor Cell Lodgment and Expansion via klf6a-ccl25b. Dev Cell 2017; 42:349-362.e4. [DOI: 10.1016/j.devcel.2017.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/06/2017] [Accepted: 07/14/2017] [Indexed: 01/07/2023]
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17
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Elagib KE, Lu CH, Mosoyan G, Khalil S, Zasadzińska E, Foltz DR, Balogh P, Gru AA, Fuchs DA, Rimsza LM, Verhoeyen E, Sansó M, Fisher RP, Iancu-Rubin C, Goldfarb AN. Neonatal expression of RNA-binding protein IGF2BP3 regulates the human fetal-adult megakaryocyte transition. J Clin Invest 2017; 127:2365-2377. [PMID: 28481226 DOI: 10.1172/jci88936] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 03/16/2017] [Indexed: 12/31/2022] Open
Abstract
Hematopoietic transitions that accompany fetal development, such as erythroid globin chain switching, play important roles in normal physiology and disease development. In the megakaryocyte lineage, human fetal progenitors do not execute the adult morphogenesis program of enlargement, polyploidization, and proplatelet formation. Although these defects decline with gestational stage, they remain sufficiently severe at birth to predispose newborns to thrombocytopenia. These defects may also contribute to inferior platelet recovery after cord blood stem cell transplantation and may underlie inefficient platelet production by megakaryocytes derived from pluripotent stem cells. In this study, comparison of neonatal versus adult human progenitors has identified a blockade in the specialized positive transcription elongation factor b (P-TEFb) activation mechanism that is known to drive adult megakaryocyte morphogenesis. This blockade resulted from neonatal-specific expression of an oncofetal RNA-binding protein, IGF2BP3, which prevented the destabilization of the nuclear RNA 7SK, a process normally associated with adult megakaryocytic P-TEFb activation. Knockdown of IGF2BP3 sufficed to confer both phenotypic and molecular features of adult-type cells on neonatal megakaryocytes. Pharmacologic inhibition of IGF2BP3 expression via bromodomain and extraterminal domain (BET) inhibition also elicited adult features in neonatal megakaryocytes. These results identify IGF2BP3 as a human ontogenic master switch that restricts megakaryocyte development by modulating a lineage-specific P-TEFb activation mechanism, revealing potential strategies toward enhancing platelet production.
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Affiliation(s)
- Kamaleldin E Elagib
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Chih-Huan Lu
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Goar Mosoyan
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shadi Khalil
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ewelina Zasadzińska
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Peter Balogh
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Alejandro A Gru
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Deborah A Fuchs
- Department of Pathology, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Els Verhoeyen
- Centre International de Recherche en Infectiologie (CIRI), Team EVIR, Inserm, U1111, Ecole Normale Supériere de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Camelia Iancu-Rubin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adam N Goldfarb
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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18
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Manesia JK, Franch M, Tabas-Madrid D, Nogales-Cadenas R, Vanwelden T, Van Den Bosch E, Xu Z, Pascual-Montano A, Khurana S, Verfaillie CM. Distinct Molecular Signature of Murine Fetal Liver and Adult Hematopoietic Stem Cells Identify Novel Regulators of Hematopoietic Stem Cell Function. Stem Cells Dev 2017; 26:573-584. [PMID: 27958775 DOI: 10.1089/scd.2016.0294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
During ontogeny, fetal liver (FL) acts as a major site for hematopoietic stem cell (HSC) maturation and expansion, whereas HSCs in the adult bone marrow (ABM) are largely quiescent. HSCs in the FL possess faster repopulation capacity as compared with ABM HSCs. However, the molecular mechanism regulating the greater self-renewal potential of FL HSCs has not yet extensively been assessed. Recently, we published RNA sequencing-based gene expression analysis on FL HSCs from 14.5-day mouse embryo (E14.5) in comparison to the ABM HSCs. We reanalyzed these data to identify key transcriptional regulators that play important roles in the expansion of HSCs during development. The comparison of FL E14.5 with ABM HSCs identified more than 1,400 differentially expressed genes. More than 200 genes were shortlisted based on the gene ontology (GO) annotation term "transcription." By morpholino-based knockdown studies in zebrafish, we assessed the function of 18 of these regulators, previously not associated with HSC proliferation. Our studies identified a previously unknown role for tdg, uhrf1, uchl5, and ncoa1 in the emergence of definitive hematopoiesis in zebrafish. In conclusion, we demonstrate that identification of genes involved in transcriptional regulation differentially expressed between expanding FL HSCs and quiescent ABM HSCs, uncovers novel regulators of HSC function.
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Affiliation(s)
- Javed K Manesia
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium
| | - Monica Franch
- 3 Functional Bioinformatics Group, National Center for Biotechnology-CSIC , Madrid, Spain
| | - Daniel Tabas-Madrid
- 3 Functional Bioinformatics Group, National Center for Biotechnology-CSIC , Madrid, Spain
| | - Ruben Nogales-Cadenas
- 3 Functional Bioinformatics Group, National Center for Biotechnology-CSIC , Madrid, Spain
| | - Thomas Vanwelden
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium
| | - Elisa Van Den Bosch
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium
| | - Zhuofei Xu
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium
| | | | - Satish Khurana
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium .,4 Indian Institute of Science Education and Research , Thiruvananthapuram, India
| | - Catherine M Verfaillie
- 1 Inter-Departmental Stem Cell Institute, KU Leuven , Leuven, Belgium .,2 Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven , Leuven, Belgium
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19
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Youn M, Wang N, LaVasseur C, Bibikova E, Kam S, Glader B, Sakamoto KM, Narla A. Loss of Forkhead box M1 promotes erythropoiesis through increased proliferation of erythroid progenitors. Haematologica 2017; 102:826-834. [PMID: 28154085 PMCID: PMC5477601 DOI: 10.3324/haematol.2016.156257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/24/2017] [Indexed: 01/02/2023] Open
Abstract
Forkhead box M1 (FOXM1) belongs to the forkhead/winged-helix family of transcription factors and regulates a network of proliferation-associated genes. Its abnormal upregulation has been shown to be a key driver of cancer progression and an initiating factor in oncogenesis. FOXM1 is also highly expressed in stem/progenitor cells and inhibits their differentiation, suggesting that FOXM1 plays a role in the maintenance of multipotency. However, the exact molecular mechanisms by which FOXM1 regulates human stem/progenitor cells are still uncharacterized. To understand the role of FOXM1 in normal hematopoiesis, human cord blood CD34+ cells were transduced with FOXM1 short hairpin ribonucleic acid (shRNA) lentivirus. Knockdown of FOXM1 resulted in a 2-fold increase in erythroid cells compared to myeloid cells. Additionally, knockdown of FOXM1 increased bromodeoxyuridine (BrdU) incorporation in erythroid cells, suggesting greater proliferation of erythroid progenitors. We also observed that the defective phosphorylation of FOXM1 by checkpoint kinase 2 (CHK2) or cyclin-dependent kinases 1/2 (CDK1/2) increased the erythroid population in a manner similar to knockdown of FOXM1. Finally, we found that an inhibitor of FOXM1, forkhead domain inhibitor-6 (FDI-6), increased red blood cell numbers through increased proliferation of erythroid precursors. Overall, our data suggest a novel function of FOXM1 in normal human hematopoiesis.
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Affiliation(s)
- Minyoung Youn
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | - Nan Wang
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | - Corinne LaVasseur
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | - Elena Bibikova
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | - Sharon Kam
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | - Bertil Glader
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
| | | | - Anupama Narla
- Department of Pediatrics, Stanford University School of Medicine, CA, USA
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20
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Niwa O, Barcellos-Hoff MH, Globus RK, Harrison JD, Hendry JH, Jacob P, Martin MT, Seed TM, Shay JW, Story MD, Suzuki K, Yamashita S. ICRP Publication 131: Stem Cell Biology with Respect to Carcinogenesis Aspects of Radiological Protection. Ann ICRP 2016; 44:7-357. [PMID: 26637346 DOI: 10.1177/0146645315595585] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This report provides a review of stem cells/progenitor cells and their responses to ionising radiation in relation to issues relevant to stochastic effects of radiation that form a major part of the International Commission on Radiological Protection's system of radiological protection. Current information on stem cell characteristics, maintenance and renewal, evolution with age, location in stem cell 'niches', and radiosensitivity to acute and protracted exposures is presented in a series of substantial reviews as annexes concerning haematopoietic tissue, mammary gland, thyroid, digestive tract, lung, skin, and bone. This foundation of knowledge of stem cells is used in the main text of the report to provide a biological insight into issues such as the linear-no-threshold (LNT) model, cancer risk among tissues, dose-rate effects, and changes in the risk of radiation carcinogenesis by age at exposure and attained age. Knowledge of the biology and associated radiation biology of stem cells and progenitor cells is more developed in tissues that renew fairly rapidly, such as haematopoietic tissue, intestinal mucosa, and epidermis, although all the tissues considered here possess stem cell populations. Important features of stem cell maintenance, renewal, and response are the microenvironmental signals operating in the niche residence, for which a well-defined spatial location has been identified in some tissues. The identity of the target cell for carcinogenesis continues to point to the more primitive stem cell population that is mostly quiescent, and hence able to accumulate the protracted sequence of mutations necessary to result in malignancy. In addition, there is some potential for daughter progenitor cells to be target cells in particular cases, such as in haematopoietic tissue and in skin. Several biological processes could contribute to protecting stem cells from mutation accumulation: (a) accurate DNA repair; (b) rapidly induced death of injured stem cells; (c) retention of the DNA parental template strand during divisions in some tissue systems, so that mutations are passed to the daughter differentiating cells and not retained in the parental cell; and (d) stem cell competition, whereby undamaged stem cells outcompete damaged stem cells for residence in the niche. DNA repair mainly occurs within a few days of irradiation, while stem cell competition requires weeks or many months depending on the tissue type. The aforementioned processes may contribute to the differences in carcinogenic radiation risk values between tissues, and may help to explain why a rapidly replicating tissue such as small intestine is less prone to such risk. The processes also provide a mechanistic insight relevant to the LNT model, and the relative and absolute risk models. The radiobiological knowledge also provides a scientific insight into discussions of the dose and dose-rate effectiveness factor currently used in radiological protection guidelines. In addition, the biological information contributes potential reasons for the age-dependent sensitivity to radiation carcinogenesis, including the effects of in-utero exposure.
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Abstract
The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines.
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Affiliation(s)
- Gloria R Garcia
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Pamela D Noyes
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Robert L Tanguay
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA.
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22
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Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli. Biochem J 2015; 473:277-84. [PMID: 26564203 DOI: 10.1042/bj20150980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/12/2015] [Indexed: 01/11/2023]
Abstract
Homocysteine S-methyltransferases (HMTs, EC 2.1.1.0) catalyse the conversion of homocysteine to methionine using S-methylmethionine or S-adenosylmethionine as the methyl donor. HMTs play an important role in methionine biosynthesis and are widely distributed among micro-organisms, plants and animals. Additionally, HMTs play a role in metabolite repair of S-adenosylmethionine by removing an inactive diastereomer from the pool. The mmuM gene product from Escherichia coli is an archetypal HMT family protein and contains a predicted zinc-binding motif in the enzyme active site. In the present study, we demonstrate X-ray structures for MmuM in oxidized, apo and metallated forms, representing the first such structures for any member of the HMT family. The structures reveal a metal/substrate-binding pocket distinct from those in related enzymes. The presented structure analysis and modelling of co-substrate interactions provide valuable insight into the function of MmuM in both methionine biosynthesis and cofactor repair.
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A distinct gene expression signature characterizes human neuroblastoma cancer stem cells. Stem Cell Res 2015; 15:419-26. [PMID: 26342562 DOI: 10.1016/j.scr.2015.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/14/2015] [Accepted: 08/13/2015] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma, a malignancy of multipotent embryonic neural crest cells, is the most common extracranial solid cancer in childhood and most common cancer in infancy. Cellular phenotype has been shown to be an important determinant of the malignant potential in human neuroblastoma cells and tumors. Whereas neuroblastic (N-type) are moderately malignant and nonneuronal (S-type) cells are nonmalignant, I-type stem cells are highly tumorigenic, irrespective of N-myc amplification status. In the present study, we sought to determine which genes were overexpressed in the I-type cells which might characterize and maintain the stem cell state and/or malignancy of human neuroblastoma cancer stem cells. We used a microarray platform to compare the steady-state expression levels of mRNAs from 13 human neuroblastoma cell lines representing the three cellular phenotypes. Using qRT-PCR and Western blot analyses, we identified seven genes whose expression is consistently elevated exclusively in neuroblastoma cancer stem cells: CD133, KIT, NOTCH1, GPRC5C, PIGF2, TRKB, and LNGFR. Moreover, we show that the genes are phenotype specific, as differentiation of I-type BE(2)-C cells to either an N- or S-type morphology results in significantly reduced mRNA expression. Finally, we show that NOTCH1 plays an important role in maintaining the stem cell phenotype. The identification and characterization of these genes, elevated in highly malignant neuroblastoma stem cells, could provide the basis for developing novel therapies for treatment of this lethal childhood cancer.
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In Silico Analysis of Sequence-Structure-Function Relationship of the Escherichia coli Methionine Synthase. Interdiscip Sci 2015. [PMID: 26223547 DOI: 10.1007/s12539-015-0271-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The molecular evolution of various metabolic pathways in the organisms can be employed for scrutinizing the molecular aspects behind origin of life. In the present study, we chiefly concerned about the sequence-structure-function relationship between the Escherichia coli methionine synthase and their respective animal homologs by in silico approach. Using homology prediction technique, it was observed that only 79 animal species showed similarity with the E. coli methionine synthase. Also, multiple sequence alignment depicted only 25 conserved patterns between the E. coli methionine synthase and their respective animal homologs. Based on that, Pfam analysis identified the protein families of 22 conserved patterns among the attained 25 conserved patterns. Furthermore, the 3D structure was generated by HHpred and evaluated by corresponding Ramachandran plot specifying 93% of the ϕ and ψ residues angles in the most ideal regions. Hence, the designed structure was established as a good quality model for the full length of E. coli methionine synthase.
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Seiler C, Gebhart N, Zhang Y, Shinton SA, Li YS, Ross NL, Liu X, Li Q, Bilbee AN, Varshney GK, LaFave MC, Burgess SM, Balciuniene J, Balciunas D, Hardy RR, Kappes DJ, Wiest DL, Rhodes J. Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish. PLoS One 2015; 10:e0131908. [PMID: 26161877 PMCID: PMC4498767 DOI: 10.1371/journal.pone.0131908] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 06/08/2015] [Indexed: 11/19/2022] Open
Abstract
Genetic screens are a powerful tool to discover genes that are important in immune cell development and function. The evolutionarily conserved development of lymphoid cells paired with the genetic tractability of zebrafish make this a powerful model system for this purpose. We used a Tol2-based gene-breaking transposon to induce mutations in the zebrafish (Danio rerio, AB strain) genome, which served the dual purpose of fluorescently tagging cells and tissues that express the disrupted gene and provided a means of identifying the disrupted gene. We identified 12 lines in which hematopoietic tissues expressed green fluorescent protein (GFP) during embryonic development, as detected by microscopy. Subsequent analysis of young adult fish, using a novel approach in which single cell suspensions of whole fish were analyzed by flow cytometry, revealed that 8 of these lines also exhibited GFP expression in young adult cells. An additional 15 lines that did not have embryonic GFP+ hematopoietic tissue by microscopy, nevertheless exhibited GFP+ cells in young adults. RT-PCR analysis of purified GFP+ populations for expression of T and B cell-specific markers identified 18 lines in which T and/or B cells were fluorescently tagged at 6 weeks of age. As transposon insertion is expected to cause gene disruption, these lines can be used to assess the requirement for the disrupted genes in immune cell development. Focusing on the lines with embryonic GFP+ hematopoietic tissue, we identified three lines in which homozygous mutants exhibited impaired T cell development at 6 days of age. In two of the lines we identified the disrupted genes, agtpbp1 and eps15L1. Morpholino-mediated knockdown of these genes mimicked the T cell defects in the corresponding mutant embryos, demonstrating the previously unrecognized, essential roles of agtpbp1 and eps15L1 in T cell development.
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Affiliation(s)
- Christoph Seiler
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Nichole Gebhart
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Susan A. Shinton
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Yue-sheng Li
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Nicola L. Ross
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Xingjun Liu
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Qin Li
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Alison N. Bilbee
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Gaurav K. Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Matthew C. LaFave
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jorune Balciuniene
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Richard R. Hardy
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Dietmar J. Kappes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
| | - Jennifer Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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26
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Weigele J, Franz‐Odendaal TA, Hilbig R. Expression of SPARC and the osteopontin‐like protein during skeletal development in the cichlid fish
Oreochromis mossambicus. Dev Dyn 2015; 244:955-72. [DOI: 10.1002/dvdy.24293] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/13/2015] [Accepted: 05/16/2015] [Indexed: 12/29/2022] Open
Affiliation(s)
- Jochen Weigele
- Zoological InstituteUniversity of Stuttgart‐HohenheimStuttgart Germany
- Department of BiologyMount Saint Vincent UniversityHalifax Nova Scotia Canada
| | | | - Reinhard Hilbig
- Zoological InstituteUniversity of Stuttgart‐HohenheimStuttgart Germany
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Raghavachari N. Gene expression profiling of hematopoietic stem cells (HSCs). Methods Mol Biol 2015; 1185:91-119. [PMID: 25062624 DOI: 10.1007/978-1-4939-1133-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Transcriptomic analysis to decipher the molecular phenotype of hematopoietic stem cells, regulatory mechanisms directing their life cycle, and the molecular signals mediating proliferation, mobilization, migration, and differentiation is believed to unravel disease-specific disturbances in hematological diseases and assist in the development of novel cell-based clinical therapies in this era of genomic medicine. The recent advent in genomic tools and technologies is now enabling the study of such comprehensive transcriptional characterization of cell types in a robust and successful manner. This chapter describes detailed protocols for isolating RNA from purified population of hematopoietic cells and gene expression profiling of those purified cells using both microarrays (Affymetrix) and RNA-Seq technology (Illumina Platform).
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Affiliation(s)
- Nalini Raghavachari
- Division of Geriatrics and Clinical Gerontology, National Institute on Aging, Gateway Building, Suite 3C307, 7201 Wisconsin Avenue, Bethesda, MD, 20892-9205, USA,
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Olena AF, Rao MB, Thatcher EJ, Wu SY, Patton JG. miR-216a regulates snx5, a novel notch signaling pathway component, during zebrafish retinal development. Dev Biol 2015; 400:72-81. [PMID: 25645681 DOI: 10.1016/j.ydbio.2015.01.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 01/14/2015] [Accepted: 01/17/2015] [Indexed: 01/13/2023]
Abstract
Precise regulation of Notch signaling is essential for normal vertebrate development. Mind bomb (Mib) is a ubiquitin ligase that is required for activation of Notch by Notch׳s ligand, Delta. Sorting Nexin 5 (SNX5) co-localizes with Mib and Delta complexes and has been shown to directly bind to Mib. We show that microRNA-216a (miR-216a) is expressed in the retina during early development and regulates snx5 to precisely regulate Notch signaling. miR-216a and snx5 have complementary expression patterns. Knocking down miR-216a and/or overexpression of snx5 resulted in increased Notch activation. Conversely, knocking down snx5 and/or miR-216a overexpression caused a decrease in Notch activation. We propose a model in which SNX5, precisely controlled by miR-216a, is a vital partner of Mib in promoting endocytosis of Delta and subsequent activation of Notch signaling.
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Affiliation(s)
- Abigail F Olena
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | - Mahesh B Rao
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | | | - Shu-Yu Wu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
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29
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Helliwell KE, Collins S, Kazamia E, Purton S, Wheeler GL, Smith AG. Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution. ISME JOURNAL 2014; 9:1446-55. [PMID: 25526368 DOI: 10.1038/ismej.2014.230] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/26/2014] [Accepted: 10/30/2014] [Indexed: 11/09/2022]
Abstract
A widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. Vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. Moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic demand for these important micronutrients has significant implications in terms of nutrient acquisition and, in microbial organisms, can affect community composition and metabolic exchange between coexisting species. Here we investigate the origins of vitamin dependence, using an experimental evolution approach with the vitamin B(12)-independent model green alga Chlamydomonas reinhardtii. In fewer than 500 generations of growth in the presence of vitamin B(12), we observe the evolution of a B(12)-dependent clone that rapidly displaces its ancestor. Genetic characterization of this line reveals a type-II Gulliver-related transposable element integrated into the B(12)-independent methionine synthase gene (METE), knocking out gene function and fundamentally altering the physiology of the alga.
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Affiliation(s)
| | - Sinéad Collins
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Saul Purton
- Institute of Structural and Molecular Biology, UCL, London, UK
| | - Glen L Wheeler
- 1] Plymouth Marine Laboratory, Plymouth, UK [2] Marine Biological Association of UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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30
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Abstract
Innate immune signalling has an essential role in inflammation, and the dysregulation of signalling components of this pathway is increasingly being recognised as an important mediator in cancer initiation and progression. In some malignancies, dysregulation of inflammatory toll-like receptor (TLR) and interleukin-1 receptor (IL1R) signalling is typified by increased NF-κB activity, and it occurs through somatic mutations, chromosomal deletions, and/or transcriptional deregulation. Interleukin-1 receptor-associated kinase (IRAK) family members are mediators of TLR/IL1R superfamily signalling, and mounting evidence implicates these kinases as viable cancer targets. Although there have been previous efforts aimed at the development of IRAK kinase inhibitors, this is currently an area of renewed interest for cancer drug development.
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Li J, Kurasawa Y, Wang Y, Clise-Dwyer K, Klumpp SA, Liang H, Tailor RC, Raymond AC, Estrov Z, Brandt SJ, Davis RE, Zweidler-McKay P, Amin HM, Nagarajan L. Requirement for ssbp2 in hematopoietic stem cell maintenance and stress response. THE JOURNAL OF IMMUNOLOGY 2014; 193:4654-62. [PMID: 25238756 DOI: 10.4049/jimmunol.1300337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Transcriptional mechanisms governing hematopoietic stem cell (HSC) quiescence, self-renewal, and differentiation are not fully understood. Sequence-specific ssDNA-binding protein 2 (SSBP2) is a candidate acute myelogenous leukemia (AML) suppressor gene located at chromosome 5q14. SSBP2 binds the transcriptional adaptor protein Lim domain-binding protein 1 (LDB1) and enhances LDB1 stability to regulate gene expression. Notably, Ldb1 is essential for HSC specification during early development and maintenance in adults. We previously reported shortened lifespan and greater susceptibility to B cell lymphomas and carcinomas in Ssbp2(-/-) mice. However, whether Ssbp2 plays a regulatory role in normal HSC function and leukemogenesis is unknown. In this study, we provide several lines of evidence to demonstrate a requirement for Ssbp2 in the function and transcriptional program of hematopoietic stem and progenitor cells (HSPCs) in vivo. We found that hematopoietic tissues were hypoplastic in Ssbp2(-/-) mice, and the frequency of lymphoid-primed multipotent progenitor cells in bone marrow was reduced. Other significant features of these mice were delayed recovery from 5-fluorouracil treatment and diminished multilineage reconstitution in lethally irradiated bone marrow recipients. Dramatic reduction of Notch1 transcripts and increased expression of transcripts encoding the transcription factor E2a and its downstream target Cdkn1a also distinguished Ssbp2(-/-) HSPCs from wild-type HSPCs. Finally, a tendency toward coordinated expression of SSBP2 and the AML suppressor NOTCH1 in a subset of the Cancer Genome Atlas AML cases suggested a role for SSBP2 in AML pathogenesis. Collectively, our results uncovered a critical regulatory function for SSBP2 in HSPC gene expression and function.
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Affiliation(s)
- June Li
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Yasuhiro Kurasawa
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Yang Wang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Sherry A Klumpp
- Department of Veterinary Medicine and Surgery, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Hong Liang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Ramesh C Tailor
- Department of Radiation Physics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Aaron C Raymond
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Genes and Development, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Zeev Estrov
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Stephen J Brandt
- Department of Medicine, Vanderbilt University, Nashville, TN 37232; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232; Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232
| | - Richard E Davis
- Department of Lymphoma and Myeloma, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Patrick Zweidler-McKay
- Division of Pediatrics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Hesham M Amin
- Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; and
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Genes and Development, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Human Molecular Genetics, Center for Stem Cell and Developmental Biology, and Center for Cancer Genetics and Genomics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
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Pickart MA, Klee EW. Zebrafish approaches enhance the translational research tackle box. Transl Res 2014; 163:65-78. [PMID: 24269745 DOI: 10.1016/j.trsl.2013.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 01/08/2023]
Abstract
During the past few decades, zebrafish (Danio rerio) have been a workhorse for developmental biology and genetics. Concurrently, zebrafish have proved highly accessible and effective for translational research by providing a vertebrate animal model useful for gene discovery, disease modeling, chemical genetic screening, and other medically relevant studies. Key resources such as an annotated and complete genome sequence, and diverse tools for genetic manipulation continue to spur broad use of zebrafish. Thus, the purpose of this introductory review is to provide a window into the unique characteristics and diverse uses of zebrafish and to highlight in particular the increasing relevance of zebrafish as a translational animal model. This is accomplished by reviewing broad considerations of anatomic and physiological conservation, approaches for disease modeling and creation, general laboratory methods, genetic tools, genome conservation, and diverse opportunities for functional validation. Additional commentary throughout the review also guides the reader to the 4 new reviews found elsewhere in this special issue that showcase the many unique ways the zebrafish is improving understanding of renal regeneration, mitochondrial disease, dyslipidemia, and aging, for example. With many other possible approaches and a rapidly increasing number of medically relevant reports, zebrafish approaches enhance significantly the tools available for translational research and are actively improving the understanding of human disease.
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Affiliation(s)
| | - Eric W Klee
- Mayo Clinic, College of Medicine, Rochester, Minn
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Connective tissue growth factor regulates adipocyte differentiation of mesenchymal stromal cells and facilitates leukemia bone marrow engraftment. Blood 2013; 122:357-66. [PMID: 23741006 DOI: 10.1182/blood-2012-06-437988] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mesenchymal stromal cells (MSCs) are a major component of the leukemia bone marrow (BM) microenvironment. Connective tissue growth factor (CTGF) is highly expressed in MSCs, but its role in the BM stroma is unknown. Therefore, we knocked down (KD) CTGF expression in human BM-derived MSCs by CTGF short hairpin RNA. CTGF KD MSCs exhibited fivefold lower proliferation compared with control MSCs and had markedly fewer S-phase cells. CTGF KD MSCs differentiated into adipocytes at a sixfold higher rate than controls in vitro and in vivo. To study the effect of CTGF on engraftment of leukemia cells into BM, an in vivo model of humanized extramedullary BM (EXM-BM) was developed in NOD/SCID/IL-2rg(null) mice. Transplanted Nalm-6 or Molm-13 human leukemia cells engrafted at a threefold higher rate in adipocyte-rich CTGF KD MSC-derived EXM-BM than in control EXM-BM. Leptin was found to be highly expressed in CTGF KD EXM-BM and in BM samples of patients with acute myeloid and acute lymphoblastic leukemia, whereas it was not expressed in normal controls. Given the established role of the leptin receptor in leukemia cells, the data suggest an important role of CTGF in MSC differentiation into adipocytes and of leptin in homing and progression of leukemia.
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Chen WH, Tseng WF, Lin GH, Schreiner A, Chen HR, M. Voigt M, Yuh CH, Wu JL, Huang SS, Huang JS. The Ortholog of LYVE-1 Is Required for Thoracic Duct Formation in Zebrafish*. Cell 2013. [DOI: 10.4236/cellbio.2013.24026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ceinos RM, Torres-Nuñez E, Chamorro R, Novoa B, Figueras A, Ruane NM, Rotllant J. Critical Role of the Matricellular Protein SPARC in Mediating Erythroid Progenitor Cell Development in Zebrafish. Cells Tissues Organs 2012. [DOI: 10.1159/000343291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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36
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Bagger FO, Rapin N, Theilgaard-Mönch K, Kaczkowski B, Thoren LA, Jendholm J, Winther O, Porse BT. HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis. Nucleic Acids Res 2012; 41:D1034-9. [PMID: 23143109 PMCID: PMC3531225 DOI: 10.1093/nar/gks1021] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The HemaExplorer (http://servers.binf.ku.dk/hemaexplorer) is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and progenitor cells as well as from more differentiated cell types. Moreover, data from distinct subtypes of human acute myeloid leukemia is included in the database allowing researchers to directly compare gene expression of leukemic cells with those of their closest normal counterpart. Normalization and batch correction lead to full integrity of the data in the database. The HemaExplorer has comprehensive visualization interface that can make it useful as a daily tool for biologists and cancer researchers to assess the expression patterns of genes encountered in research or literature. HemaExplorer is relevant for all research within the fields of leukemia, immunology, cell differentiation and the biology of the haematopoietic system.
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Affiliation(s)
- Frederik Otzen Bagger
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Denmark
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Auvray C, Delahaye A, Pflumio F, Haddad R, Amsellem S, Miri-Nezhad A, Broix L, Yacia A, Bulle F, Fichelson S, Vigon I. HOXC4 homeoprotein efficiently expands human hematopoietic stem cells and triggers similar molecular alterations as HOXB4. Haematologica 2012; 97:168-78. [PMID: 22298821 DOI: 10.3324/haematol.2011.051235] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Expansion of hematopoietic stem cells represents an important objective for improving cell and gene therapy protocols. Retroviral transduction of the HoxB4 homeogene in mouse and human hematopoietic stem cells and hematopoietic progenitors is known to promote the cells' expansion. A safer approach consists in transferring homeobox proteins into hematopoietic stem cells taking advantage of the natural ability of homeoproteins to cross cell membranes. Thus, HOXB4 protein transfer is operative for expanding human hematopoietic cells, but such expansion needs to be improved. DESIGN AND METHODS To that aim, we evaluated the effects of HOXC4, a protein encoded by a HOXB4 paralog gene, by co-culturing HOXC4-producing stromal cells with human CD34(+) hematopoietic cells. Numbers of progenitors and stem cells were assessed by in vitro cloning assays and injection into immuno-deficient mice, respectively. We also looked for activation or inhibition of target downstream gene expression. RESULTS We show that the HOXC4 homeoprotein expands human hematopoietic immature cells by 3 to 6 times ex vivo and significantly improves the level of in vivo engraftment. Comparative transcriptome analysis of CD34(+) cells subjected or not to HOXB4 or HOXC4 demonstrated that both homeoproteins regulate the same set of genes, some of which encode key hematopoietic factors and signaling molecules. Certain molecules identified herein are factors reported to be involved in stem cell fate or expansion in other models, such as MEF2C, EZH2, DBF4, DHX9, YPEL5 and Pumilio. CONCLUSIONS The present study may help to identify new HOX downstream key factors potentially involved in hematopoietic stem cell expansion or in leukemogenesis.
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Lim JP, Teasdale RD, Gleeson PA. SNX5 is essential for efficient macropinocytosis and antigen processing in primary macrophages. Biol Open 2012; 1:904-14. [PMID: 23213485 PMCID: PMC3507233 DOI: 10.1242/bio.20122204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 06/19/2012] [Indexed: 12/14/2022] Open
Abstract
Macropinocytosis mediates the bulk endocytosis of solute molecules, nutrients and antigens. As this endocytic pathway is considered important in functions associated with immune responses, the molecular mechanisms regulating this pathway in immune cells is of particular significance. However, the regulators of macropinocytosis in primary cells remain poorly defined. Members of the sorting nexin (SNX) family have been implicated in macropinosome biogenesis in cultured cells and here we have analyzed the role of two SNX family members, SNX1 and its binding partner SNX5, in macropinocytosis of mouse primary macrophages. We show that endogenous SNX1 and SNX5 are localised to newly-formed macropinosomes in primary mouse macrophages and, moreover, demonstrate that SNX5 plays an essential role in macropinosome biogenesis. Depletion of SNX5 in bone marrow-derived macrophages dramatically decreased both the number and size of macropinosomes. Depletion of SNX5 also resulted in dramatic reduction in uptake and processing of soluble ovalbumin in macrophages, indicating that the majority of antigen uptake and delivery to late endosomes is via macropinocytosis. By contrast, the absence of SNX1 had no effect on endogenous SNX5 localisation and macropinosome biogenesis using macrophages from SNX1 knockout mice. Therefore, SNX5 can function independently of SNX1 and is a modulator of macropinocytosis that influences the uptake and processing of soluble antigen in primary mouse macrophages.
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Affiliation(s)
- Jet Phey Lim
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Victoria 3010 , Australia
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HemaExplorer: a Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis. Blood 2012; 119:6394-5. [PMID: 22745298 DOI: 10.1182/blood-2012-05-427310] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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Abstract
Sprouty proteins are established modifiers of receptor tyrosine kinase (RTK) signaling and play important roles in vasculogenesis, bone morphogenesis, and renal uteric branching. Little is understood, however, concerning possible roles for these molecular adaptors during hematopoiesis. Within erythroid lineage, Spry1 was observed to be selectively and highly expressed at CFU-e to erythroblast stages. In analyses of possible functional roles, an Mx1-Cre approach was applied to conditionally delete Spry1. At steady state, Spry1 deletion selectively perturbed erythroid development and led to reticulocytosis plus heightened splenic erythropoiesis. When challenged by hemolysis, Spry1-null mice exhibited worsened anemia and delayed recovery. During short-term marrow transplantation, Spry1-null donor marrow also failed to efficiently rescue the erythron. In each anemia model, however, hyperexpansion of erythroid progenitors was observed. Spry function depends on phosphorylation of a conserved N-terminal PY motif. Through an LC-MS/MS approach, Spry1 was discovered to be regulated via the erythropoietin receptor (EPOR), with marked EPO-induced Spry1-PY53 phosphorylation observed. When EPOR signaling pathways were analyzed within Spry1-deficient erythroid progenitors, hyperactivation of not only Erk1,2 but also Jak2 was observed. Studies implicate Spry1 as a novel regulator of erythropoiesis during anemia, transducer of EPOR signals, and candidate suppressor of Jak2 activity.
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SPARC is dispensable for murine hematopoiesis, despite its suspected pathophysiological role in 5q-myelodysplastic syndrome. Leukemia 2012; 26:2416-9. [DOI: 10.1038/leu.2012.97] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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42
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The Fat1 cadherin is overexpressed and an independent prognostic factor for survival in paired diagnosis–relapse samples of precursor B-cell acute lymphoblastic leukemia. Leukemia 2011; 26:918-26. [DOI: 10.1038/leu.2011.319] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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Lawson ND, Wolfe SA. Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev Cell 2011; 21:48-64. [PMID: 21763608 DOI: 10.1016/j.devcel.2011.06.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of facile forward and reverse genetic approaches has propelled the deconvolution of gene function in biology. While the origins of these techniques reside in the study of single-cell or invertebrate organisms, in many cases these approaches have been applied to vertebrate model systems to gain powerful insights into gene function during embryonic development. This perspective provides a summary of the major forward and reverse genetic approaches that have contributed to the study of vertebrate gene function in zebrafish, which has become an established model for the study of animal development.
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Affiliation(s)
- Nathan D Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Helliwell KE, Wheeler GL, Leptos KC, Goldstein RE, Smith AG. Insights into the evolution of vitamin B12 auxotrophy from sequenced algal genomes. Mol Biol Evol 2011; 28:2921-33. [PMID: 21551270 DOI: 10.1093/molbev/msr124] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-independent methionine synthase (METE). Within the algal kingdom, approximately half of all microalgal species need the vitamin as a growth supplement, but there is no phylogenetic relationship between these species, suggesting that the auxotrophy arose multiple times through evolution. We set out to determine the underlying cellular mechanisms for this observation by investigating elements of B(12) metabolism in the sequenced genomes of 15 different algal species, with representatives of the red, green, and brown algae, diatoms, and coccolithophores, including both macro- and microalgae, and from marine and freshwater environments. From this analysis, together with growth assays, we found a strong correlation between the absence of a functional METE gene and B(12) auxotrophy. The presence of a METE unitary pseudogene in the B(12)-dependent green algae Volvox carteri and Gonium pectorale, relatives of the B(12)-independent Chlamydomonas reinhardtii, suggest that B(12) dependence evolved recently in these lineages. In both C. reinhardtii and the diatom Phaeodactylum tricornutum, growth in the presence of cobalamin leads to repression of METE transcription, providing a mechanism for gene loss. Thus varying environmental conditions are likely to have been the reason for the multiple independent origins of B(12) auxotrophy in these organisms. Because the ultimate source of cobalamin is from prokaryotes, the selective loss of METE in different algal lineages will have had important physiological and ecological consequences for these organisms in terms of their dependence on bacteria.
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Bedell VM, Westcot SE, Ekker SC. Lessons from morpholino-based screening in zebrafish. Brief Funct Genomics 2011; 10:181-8. [PMID: 21746693 PMCID: PMC3144740 DOI: 10.1093/bfgp/elr021] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Morpholino oligonucleotides (MOs) are an effective, gene-specific antisense knockdown technology used in many model systems. Here we describe the application of MOs in zebrafish (Danio rerio) for in vivo functional characterization of gene activity. We summarize our screening experience beginning with gene target selection. We then discuss screening parameter considerations and data and database management. Finally, we emphasize the importance of off-target effect management and thorough downstream phenotypic validation. We discuss current morpholino limitations, including reduced stability when stored in aqueous solution. Advances in MO technology now provide a measure of spatiotemporal control over MO activity, presenting the opportunity for incorporating more finely tuned analyses into MO-based screening. Therefore, with careful management, MOs remain a valuable tool for discovery screening as well as individual gene knockdown analysis.
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Zhou L, Opalinska J, Sohal D, Yu Y, Mo Y, Bhagat T, Abdel-Wahab O, Fazzari M, Figueroa M, Alencar C, Zhang J, Kambhampati S, Parmar S, Nischal S, Hueck C, Suzuki M, Freidman E, Pellagatti A, Boultwood J, Steidl U, Sauthararajah Y, Yajnik V, McMahon C, Gore SD, Platanias LC, Levine R, Melnick A, Wickrema A, Greally JM, Verma A. Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q. J Biol Chem 2011; 286:25211-23. [PMID: 21532034 DOI: 10.1074/jbc.m111.235028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are characterized by abnormal and dysplastic maturation of all blood lineages. Even though epigenetic alterations have been seen in MDS marrow progenitors, very little is known about the molecular alterations in dysplastic peripheral blood cells. We analyzed the methylome of MDS leukocytes by the HELP assay and determined that it was globally distinct from age-matched controls and was characterized by numerous novel, aberrant hypermethylated marks that were located mainly outside of CpG islands and preferentially affected GTPase regulators and other cancer-related pathways. Additionally, array comparative genomic hybridization revealed that novel as well as previously characterized deletions and amplifications could also be visualized in peripheral blood leukocytes, thus potentially reducing the need for bone marrow samples for future studies. Using integrative analysis, potentially pathogenic genes silenced by genetic deletions and aberrant hypermethylation in different patients were identified. DOCK4, a GTPase regulator located in the commonly deleted 7q31 region, was identified by this unbiased approach. Significant hypermethylation and reduced expression of DOCK4 in MDS bone marrow stem cells was observed in two large independent datasets, providing further validation of our findings. Finally, DOCK4 knockdown in primary marrow CD34(+) stem cells led to decreased erythroid colony formation and increased apoptosis, thus recapitulating the bone marrow failure seen in MDS. These findings reveal widespread novel epigenetic alterations in myelodysplastic leukocytes and implicate DOCK4 as a pathogenic gene located on the 7q chromosomal region.
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Affiliation(s)
- Li Zhou
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Yang X, Gong Y, Friesel R. Spry1 is expressed in hemangioblasts and negatively regulates primitive hematopoiesis and endothelial cell function. PLoS One 2011; 6:e18374. [PMID: 21483770 PMCID: PMC3069969 DOI: 10.1371/journal.pone.0018374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Development of the hematopoietic and endothelial lineages derives from a common mesodermal precursor, the Flk1(+) hemangioblast. However, the signaling pathways that regulate the development of hematopoietic and endothelial cells from this common progenitor cell remains incompletely understood. Using mouse models with a conditional Spry1 transgene, and a Spry1 knockout mouse, we investigated the role of Spry1 in the development of the endothelial and hematopoietic lineages during development. METHODOLOGY/PRINCIPAL FINDINGS Quantitative RT-PCR analysis demonstrates that Spry1, Spry2, and Spry4 are expressed in Flk1(+) hemangioblasts in vivo, and decline significantly in c-Kit(+) and CD41(+) hematopoietic progenitors, while expression is maintained in developing endothelial cells. Tie2-Cre-mediated over-expression of Spry1 results in embryonic lethality. At E9.5 Spry1;Tie2-Cre embryos show near normal endothelial cell development and vessel patterning but have reduced hematopoiesis. FACS analysis shows a reduction of primitive hematopoietic progenitors and erythroblastic cells in Spry1;Tie2-Cre embryos compared to controls. Colony forming assays confirm the hematopoietic defects in Spry1;Tie2-Cre transgenic embryos. Immunostaining shows a significant reduction of CD41 or CD71 and dpERK co-stained cells in Spry1;Tie2-Cre embryos compared to controls, whereas the number of VEC(+) and dpERK co-stained cells is comparable. Compared to controls, Spry1;Tie2-Cre embryos also show a decrease in proliferation and an increase in apoptosis. Furthermore, loss of Spry1 results in an increase of CD41(+) and CD71(+) cells at E9.5 compared with controls. CONCLUSIONS/SIGNIFICANCE These data indicate that primitive hematopoietic cells derive from Tie2-expressing hemangioblasts and that Spry1 over expression inhibits primitive hematopoietic progenitor and erythroblastic cell development and expansion while having no obvious effect on endothelial cell development.
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Affiliation(s)
- Xuehui Yang
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine, United States of America
| | - Yan Gong
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine, United States of America
| | - Robert Friesel
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine, United States of America
- * E-mail:
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Complex interactions in EML cell stimulation by stem cell factor and IL-3. Proc Natl Acad Sci U S A 2011; 108:4882-7. [PMID: 21383156 DOI: 10.1073/pnas.1018002108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Erythroid myeloid lymphoid (EML) cells are an established multipotent hematopoietic precursor cell line that can be maintained in medium including stem cell factor (SCF). EML cultures contain a heterogeneous mixture of cells, including a lineage-negative, CD34+ subset of cells that propagate rapidly in SCF and can clonally regenerate the mixed population. A second major subset of EML cells consists of lineage-negative. CD34- cells that can be propagated in IL-3 but grow slowly, if at all, in SCF, although they express the SCF receptor (c-kit). The response of these cells to IL-3 is stimulated synergistically by SCF, and we present evidence that both the synergy and the inhibition of c-kit responses may be mediated by direct interaction with IL-3 receptor. Further, the relative level of tyrosine phosphorylation of various substrates by either cytokine alone differs from that produced by the combination of the two cytokines, suggesting that cell signaling by the combination of the two cytokines differs from that produced by either alone.
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Underhill-Day N, Hill V, Latif F. N-terminal RASSF family: RASSF7-RASSF10. Epigenetics 2011; 6:284-92. [PMID: 21116130 DOI: 10.4161/epi.6.3.14108] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Epigenetic inactivation of tumor suppressor genes is a hallmark of cancer development. RASSF1A (Ras Association Domain Family 1 isoform A) tumor suppressor gene is one of the most frequently epigenetically inactivated genes in a wide range of adult and children's cancers and could be a useful molecular marker for cancer diagnosis and prognosis. RASSF1A has been shown to play a role in several biological pathways, including cell cycle control, apoptosis and microtubule dynamics. RASSF2, RASSF4, RASSF5 and RASSF6 are also epigenetically inactivated in cancer but have not been analysed in as wide a range of malignancies as RASSF1A. Recently four new members of the RASSF family were identified these are termed N-Terminal RASSF genes (RASSF7-RASSF10). Molecular and biological analysis of these newer members has just begun. This review highlights what we currently know in respects to structural, functional and molecular properties of the N-Terminal RASSFs.
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Affiliation(s)
- Nicholas Underhill-Day
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, UK
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MOUZANNAR R, MCCAFFERTY J, BENEDETTO G, RICHARDSON C. TRANSCRIPTIONAL AND PHOSPHO-PROTEOMIC SCREENS REVEAL STEM CELL ACTIVATION OF INSULIN-RESISTANCE AND TRANSFORMATION PATHWAYS FOLLOWING A SINGLE MINIMALLY TOXIC EPISODE OF ROS. INTERNATIONAL JOURNAL OF GENOMICS AND PROTEOMICS 2011; 2:34-49. [PMID: 21743783 PMCID: PMC3131088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Elevated reactive oxidative species (ROS) are cytotoxic, and chronic elevated levels of ROS have been implicated in multiple diseases as well as cellular transformation and tumor progression. However, the potential for a transient and minimally toxic episode of ROS exposure, or a minimal threshold dose of ROS, to initiate disease or cellular transformation is unclear. We examined both transcriptional and phospho-proteomic responses of murine embryonic stem (ES) cells to a single brief exposure of minimally toxic hydrogen peroxide (H(2)O(2)). The cellular response was distinct from those induced by either an acute exposure to H(2)O(2) or the topoisomerase II poison etoposide. Analysis of tumorigenesis-related transcripts revealed a significant up-regulation of oncogenes and down-regulation of tumor suppressors. Analysis of the phospho-proteomic response demonstrated insulin-signaling induction, including insulin receptor Y972 hypophosphorylation, similar to insulin-resistance mouse models and observed in diabetic patients. In addition, ES cells were more resistant to ROS than differentiated cells, and retained their transcriptional self-renewal signature, suggesting stem cells have a higher potential for ROS-mediated mutagenesis and proliferation in vivo. These results are a direct demonstration that even brief and non-toxic exposures to ROS may induce transduction of insulin resistance and transformation signaling in stem cells leading to diabetes and cancer.
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Affiliation(s)
- R. MOUZANNAR
- UNC-Charlotte, Department of Biology and Bioinformatics Research Center, Charlotte, NC 28223
| | - J. MCCAFFERTY
- UNC-Charlotte, Department of Bioinformatics and Genomics, Charlotte, NC 28223
| | - G. BENEDETTO
- UNC-Charlotte, Department of Biology and Bioinformatics Research Center, Charlotte, NC 28223
| | - C. RICHARDSON
- UNC-Charlotte, Department of Biology and Bioinformatics Research Center, Charlotte, NC 28223
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