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Guo R, Ma X, Xu H, Ma Y, Zhang R, Liu X, Lu B, Zhang J, Han Y. In silico prediction and a systematic toxicology-based in vivo investigation uncovering the mechanism of aquatic toxicity caused by beta-lactam antibiotics. CHEMOSPHERE 2024; 349:140884. [PMID: 38065262 DOI: 10.1016/j.chemosphere.2023.140884] [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: 08/24/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Recently, beta-lactam antibiotics have gained attention as significant contributors to public health and environmental issues due to their potential toxicity. Our study employed machine learning to develop a model for assessing the aquatic toxicity of beta-lactam antibiotics on zebrafish. Notably, aztreonam (AZT), a synthetic monobactam and a subclass of beta-lactam antibiotics, demonstrated developmental effects in zebrafish embryos comparable to cephalosporins, indicating a potential for toxicity. Using a systems toxicology-based approach, we identified apoptosis and metabolic disorders as the primary pathways affected by AZT and its impurity F exposure. During the administration of monobactams, we noted that ctsbb, nos2a, and dgat2, genes associated with apoptosis and the metabolic pathway, exhibited significant differential expression. Molecular docking studies were conducted to ascertain the binding affinity between monobactam compounds and their potential targets-Ctsbb, Nos2a, and Dgat2. Furthermore, our research revealed that monobactams influence pre-mRNA alternative splicing, resulting in disruptions in the expression of genes involved in hair cells, brain, spinal cord, and fin regeneration (e.g., krt4, krt5, krt17, cyt1). Notably, we observed a correlation between the levels of rpl3 and rps7 genes, both important ribosomal proteins, and the detected alternative splicing events. Overall, this study enhances our understanding of the toxicity of beta-lactam antibiotics in zebrafish by demonstrating the developmental effects of monobactams and uncovering the underlying mechanisms at the molecular level. It also identifies potential targets for further investigation into the mechanisms of toxicity and provides valuable insights for early assessment of biological toxicity associated with antibiotic pollutants.
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Affiliation(s)
- Ruixian Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Xinyan Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; School of Pharmacy, Minzu University of China, Beijing, 100081, China
| | - Huibo Xu
- University of Science and Technology of China, Hefei, 230031, China
| | - Yuanyuan Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rui Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xinyan Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Binan Lu
- School of Pharmacy, Minzu University of China, Beijing, 100081, China
| | - Jingpu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Ying Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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Shakeel M, Yoon M. Heat stress and stallion fertility. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:683-697. [PMID: 37970501 PMCID: PMC10640949 DOI: 10.5187/jast.2023.e29] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 11/17/2023]
Abstract
The threat posed by increased surface temperatures worldwide has attracted the attention of researchers to the reaction of animals to heat stress. Spermatogenesis in animals such as stallions is a temperature-dependent process, ideally occurring at temperatures slightly below the core body temperature. Thus, proper thermoregulation is essential, especially because stallion spermatogenesis and the resulting spermatozoa are negatively affected by increased testicular temperature. Consequently, the failure of thermoregulation resulting in heat stress may diminish sperm quality and increase the likelihood of stallion infertility. In this review, we emphasize upon the impact of heat stress on spermatogenesis and the somatic and germ cells and describe the subsequent testicular alterations. In addition, we explore the functions and molecular responses of heat shock proteins, including HSP60, HSP70, HSP90, and HSP105, in heat-induced stress conditions. Finally, we discuss the use of various therapies to alleviate heat stress-induced reproductive harm by modulating distinct signaling pathways.
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Affiliation(s)
- Muhammad Shakeel
- Department of Animal Science and
Biotechnology, Kyungpook National University, Sangju 37224,
Korea
- Department of Clinical Studies, Faculty of
Veterinary and Animal Sciences, Pir Mehr Ali Shah, Arid Agriculture
University, Rawalpindi 44000, Pakistan
| | - Minjung Yoon
- Department of Animal Science and
Biotechnology, Kyungpook National University, Sangju 37224,
Korea
- Department of Horse, Companion and Wild
Animal Science, Kyungpook National University, Sangju 37224,
Korea
- Reseach Center for Horse Industry,
Kyungpook National University, Sangju 37224, Korea
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3
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Lv Y, Mou Y, Su J, Liu S, Ding X, Yuan Y, Li G, Li G. The inhibitory effect and mechanism of Resina Draconis on the proliferation of MCF-7 breast cancer cells: a network pharmacology-based analysis. Sci Rep 2023; 13:3816. [PMID: 36882618 PMCID: PMC9992681 DOI: 10.1038/s41598-023-30585-0] [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: 11/09/2022] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Resina Draconis (RD) is known as the "holy medicine for promoting blood circulation" and possesses antitumor properties against various types of cancer, including breast cancer (BC); however, the underlying mechanism is not well understood. To explore the potential mechanism of RD against BC using network pharmacology and experimental validation, data on bioactive compounds, potential targets of RD, and related genes of BC were obtained from multiple public databases. Gene Ontology (GO) and KEGG pathway analyses were performed via the DAVID database. Protein interactions were downloaded from the STRING database. The mRNA and protein expression levels and survival analysis of the hub targets were analyzed using the UALCAN, HPA, Kaplan‒Meier mapper, and cBioPortal databases. Subsequently, molecular docking was used to verify the selected key ingredients and hub targets. Finally, the predicted results of network pharmacology methods were verified by cell experiments. In total, 160 active ingredients were obtained, and 148 RD target genes for the treatment of BC were identified. KEGG pathway analysis indicated that RD exerted its therapeutic effects on BC by regulating multiple pathways. Of these, the PI3K-AKT pathway was indicated to play an important role. In addition, RD treatment of BC seemed to involve the regulation of hub targets that were identified based on PPI interaction network analysis. Validation in different databases showed that AKT1, ESR1, HSP90AA1, CASP3, SRC and MDM2 may be involved in the carcinogenesis and progression of BC and that ESR1, IGF1 and HSP90AA1 were correlated with worse overall survival (OS) in BC patients. Molecular docking results showed that 103 active compounds have good binding activity with the hub targets, among which flavonoid compounds were the most important active components. Therefore, the sanguis draconis flavones (SDF) were selected for subsequent cell experiments. The experimental results showed that SDF significantly inhibited the cell cycle and cell proliferation of MCF-7 cells through the PI3K/AKT pathway and induced MCF-7 cell apoptosis. This study has preliminarily reported on the active ingredients, potential targets, and molecular mechanism of RD against BC, and RD was shown to exert its therapeutic effects on BC by regulating the PI3K/AKT pathway and related gene targets. Importantly, our work could provide a theoretical basis for further study of the complex anti-BC mechanism of RD.
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Affiliation(s)
- Yana Lv
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China.,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China
| | - Yan Mou
- Yuxi Normal University, Yuxi, 653100, China
| | - Jing Su
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China.,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China
| | - Shifang Liu
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China.,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China
| | - Xuan Ding
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China.,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China
| | - Yin Yuan
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China.,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China
| | - Ge Li
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China. .,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China.
| | - Guang Li
- Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 666100, China. .,Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong, 666100, China.
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4
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Jamieson-Lucy AH, Kobayashi M, James Aykit Y, Elkouby YM, Escobar-Aguirre M, Vejnar CE, Giraldez AJ, Mullins MC. A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb. Dev Biol 2022; 484:1-11. [PMID: 35065906 PMCID: PMC8967276 DOI: 10.1016/j.ydbio.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/17/2023]
Abstract
The Balbiani body (Bb) is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects, fish, amphibians, and mammals. During early zebrafish oogenesis, the Bb assembles as a transient aggregate of mRNA, proteins, and membrane-bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops, the Bb appears to grow slowly, until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs, this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable, solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity, little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles, translocates, and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample, including known Bb proteins and novel RNA-binding proteins. In particular, we identified Cirbpa and Cirbpb, which have both an RNA-binding domain and a predicted self-aggregation domain. In stage I oocytes, Cirbpa and Cirbpb localize to the Bb rather than the nucleus (as in somatic cells), indicating that they may have a specialized function in the germ line. Both the RNA-binding domain and the self-aggregation domain are sufficient to localize to the Bb, suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb, our proteomics dataset presents many candidates for further study, making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level.
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Affiliation(s)
- Allison H Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Y James Aykit
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yaniv M Elkouby
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matias Escobar-Aguirre
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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Rengaraj D, Cha DG, Lee HJ, Lee KY, Choi YH, Jung KM, Kim YM, Choi HJ, Choi HJ, Yoo E, Woo SJ, Park JS, Park KJ, Kim JK, Han JY. Dissecting chicken germ cell dynamics by combining a germ cell tracing transgenic chicken model with single-cell RNA sequencing. Comput Struct Biotechnol J 2022; 20:1654-1669. [PMID: 35465157 PMCID: PMC9010679 DOI: 10.1016/j.csbj.2022.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/02/2023] Open
Abstract
Avian germ cells can be distinguished by certain characteristics during development. On the basis of these characteristics, germ cells can be used for germline transmission. However, the dynamic transcriptional landscape of avian germ cells during development is unknown. Here, we used a novel germ-cell-tracing method to monitor and isolate chicken germ cells at different stages of development. We targeted the deleted in azoospermia like (DAZL) gene, a germ-cell-specific marker, to integrate a green fluorescent protein (GFP) reporter gene without affecting endogenous DAZL expression. The resulting transgenic chickens (DAZL::GFP) were used to uncover the dynamic transcriptional landscape of avian germ cells. Single-cell RNA sequencing of 4,752 male and 13,028 female DAZL::GFP germ cells isolated from embryonic day E2.5 to 1 week post-hatch identified sex-specific developmental stages (4 stages in male and 5 stages in female) and trajectories (apoptosis and meiosis paths in female) of chicken germ cells. The male and female trajectories were characterized by a gradual acquisition of stage-specific transcription factor activities. We also identified evolutionary conserved and species-specific gene expression programs during both chicken and human germ-cell development. Collectively, these novel analyses provide mechanistic insights into chicken germ-cell development.
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Affiliation(s)
- Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Dong Gon Cha
- Department of New Biology, DGIST, Daegu 42988, South Korea
| | - Hong Jo Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyung Youn Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Ha Choi
- Department of New Biology, DGIST, Daegu 42988, South Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Kyung Min Jung
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Young Min Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hyeon Jeong Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Eunhui Yoo
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seung Je Woo
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jin Se Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyung Je Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu 42988, South Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
- Corresponding authors at: POSTECH, 77 Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, South Korea (J.K. Kim). Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea (J.Y. Han).
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
- Corresponding authors at: POSTECH, 77 Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, South Korea (J.K. Kim). Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea (J.Y. Han).
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Aalto A, Olguin-Olguin A, Raz E. Zebrafish Primordial Germ Cell Migration. Front Cell Dev Biol 2021; 9:684460. [PMID: 34249937 PMCID: PMC8260996 DOI: 10.3389/fcell.2021.684460] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/17/2021] [Indexed: 01/03/2023] Open
Abstract
Similar to many other organisms, zebrafish primordial germ cells (PGCs) are specified at a location distinct from that of gonadal somatic cells. Guided by chemotactic cues, PGCs migrate through embryonic tissues toward the region where the gonad develops. In this process, PGCs employ a bleb-driven amoeboid migration mode, characterized by low adhesion and high actomyosin contractility, a strategy used by other migrating cells, such as leukocytes and certain types of cancer cells. The mechanisms underlying the motility and the directed migration of PGCs should be robust to ensure arrival at the target, thereby contributing to the fertility of the organism. These features make PGCs an excellent model for studying guided single-cell migration in vivo. In this review, we present recent findings regarding the establishment and maintenance of cell polarity that are essential for motility and discuss the mechanisms by which cell polarization and directed migration are controlled by chemical and physical cues.
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Affiliation(s)
- Anne Aalto
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Adan Olguin-Olguin
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
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Da Silveira Cavalcante L, Tessier SN. Zebrafish as a New Tool in Heart Preservation Research. J Cardiovasc Dev Dis 2021; 8:39. [PMID: 33917701 PMCID: PMC8068018 DOI: 10.3390/jcdd8040039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/25/2022] Open
Abstract
Heart transplantation became a reality at the end of the 1960s as a life-saving option for patients with end-stage heart failure. Static cold storage (SCS) at 4-6 °C has remained the standard for heart preservation for decades. However, SCS only allows for short-term storage that precludes optimal matching programs, requires emergency surgeries, and results in the unnecessary discard of organs. Among the alternatives seeking to extend ex vivo lifespan and mitigate the shortage of organs are sub-zero or machine perfusion modalities. Sub-zero approaches aim to prolong cold ischemia tolerance by deepening metabolic stasis, while machine perfusion aims to support metabolism through the continuous delivery of oxygen and nutrients. Each of these approaches hold promise; however, complex barriers must be overcome before their potential can be fully realized. We suggest that one barrier facing all experimental efforts to extend ex vivo lifespan are limited research tools. Mammalian models are usually the first choice due to translational aspects, yet experimentation can be restricted by expertise, time, and resources. Instead, there are instances when smaller vertebrate models, like the zebrafish, could fill critical experimental gaps in the field. Taken together, this review provides a summary of the current gold standard for heart preservation as well as new technologies in ex vivo lifespan extension. Furthermore, we describe how existing tools in zebrafish research, including isolated organ, cell specific and functional assays, as well as molecular tools, could complement and elevate heart preservation research.
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Affiliation(s)
- Luciana Da Silveira Cavalcante
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 2114, USA;
- Shriners Hospitals for Children, Boston, MA 2114, USA
| | - Shannon N. Tessier
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 2114, USA;
- Shriners Hospitals for Children, Boston, MA 2114, USA
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Chen X, Gu J, Neuwald AF, Hilakivi-Clarke L, Clarke R, Xuan J. Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence. Sci Rep 2021; 11:385. [PMID: 33432018 PMCID: PMC7801429 DOI: 10.1038/s41598-020-79603-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/18/2020] [Indexed: 11/09/2022] Open
Abstract
Exploring complex modularization of intracellular signal transduction pathways is critical to understanding aberrant cellular responses during disease development and drug treatment. IMPALA (Inferred Modularization of PAthway LAndscapes) integrates information from high throughput gene expression experiments and genome-scale knowledge databases to identify aberrant pathway modules, thereby providing a powerful sampling strategy to reconstruct and explore pathway landscapes. Here IMPALA identifies pathway modules associated with breast cancer recurrence and Tamoxifen resistance. Focusing on estrogen-receptor (ER) signaling, IMPALA identifies alternative pathways from gene expression data of Tamoxifen treated ER positive breast cancer patient samples. These pathways were often interconnected through cytoplasmic genes such as IRS1/2, JAK1, YWHAZ, CSNK2A1, MAPK1 and HSP90AA1 and significantly enriched with ErbB, MAPK, and JAK-STAT signaling components. Characterization of the pathway landscape revealed key modules associated with ER signaling and with cell cycle and apoptosis signaling. We validated IMPALA-identified pathway modules using data from four different breast cancer cell lines including sensitive and resistant models to Tamoxifen. Results showed that a majority of genes in cell cycle/apoptosis modules that were up-regulated in breast cancer patients with short survivals (< 5 years) were also over-expressed in drug resistant cell lines, whereas the transcription factors JUN, FOS, and STAT3 were down-regulated in both patient and drug resistant cell lines. Hence, IMPALA identified pathways were associated with Tamoxifen resistance and an increased risk of breast cancer recurrence. The IMPALA package is available at https://dlrl.ece.vt.edu/software/ .
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Affiliation(s)
- Xi Chen
- grid.438526.e0000 0001 0694 4940Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203 USA ,grid.430264.7Center for Computational Biology, Flatiron Institute, Simons Foundation, 162 Fifth Avenue, New York, NY 10010 USA
| | - Jinghua Gu
- grid.438526.e0000 0001 0694 4940Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203 USA
| | - Andrew F. Neuwald
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences and Department Biochemistry and Molecular Biology, University of Maryland School of Medicine, 670 W. Baltimore Street, Baltimore, MD 21201 USA
| | - Leena Hilakivi-Clarke
- grid.17635.360000000419368657Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912 USA
| | - Robert Clarke
- grid.17635.360000000419368657Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912 USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA, 22203, USA.
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Effects of HSP90 inhibition on primordial germ cells migration: A study in the gonad of the chick embryo. Morphologie 2020; 104:228-236. [PMID: 32896470 DOI: 10.1016/j.morpho.2020.07.002] [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: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Primordial Germ Cells (PGCs) differentiate into spermatozoa or oocytes. They appear early during embryonic development before migrating to the gonadal ridges. Because of their long migration, PGCs have been proposed as a valuable model to study long distance cell migration. Some species also present a vascular phase in the migration of the germline and could therefore be compared to metastatic migration. HSP90 is a heat shock protein involved in the stabilization of several client-proteins, including oncoproteins. HSP90 inhibition has been proved to decrease PGCs migration in mouse and zebrafish. MATERIAL AND METHODS We investigated the effect of geldanamycin on PGCs migration in a species with a vascular phase, the chicken. Geldanamycin was injected in the egg at 48h of incubation, PGC's were detected in blood using of blood smears, and in the embryo by immunohistochemistry using anti-HSP90 antibody. RESULTS The effects of the treatment were similar to those observed in mouse and zebrafish. We show the presence of ectopic germs cells in the vasculature and in the dorsal mesentery, and some deformities of the gonads. CONCLUSION Inhibition of HSP90 decreases the migration of PGCs and proposed the migration of PGCs in the chick embryo as an interesting model to study metastatic invasion.
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Li J, Ge W. Zebrafish as a model for studying ovarian development: Recent advances from targeted gene knockout studies. Mol Cell Endocrinol 2020; 507:110778. [PMID: 32142861 DOI: 10.1016/j.mce.2020.110778] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022]
Abstract
Ovarian development is a complex process controlled by precise coordination of multiple factors. The targeted gene knockout technique is a powerful tool to study the functions of these factors. The successful application of this technique in mice in the past three decades has significantly enhanced our understanding on the molecular mechanism of ovarian development. Recently, with the advent of genome editing techniques, targeted gene knockout research can be carried out in many species. Zebrafish has emerged as an excellent model system to study the control of ovarian development. Dozens of genes related to ovarian development have been knocked out in zebrafish in recent years. Much new information and perspectives on the molecular mechanism of ovarian development have been obtained from these mutant zebrafish. Some findings have challenged conventional views. Several genes have been identified for the first time in vertebrates to control ovarian development. Focusing on ovarian development, the purpose of this review is to briefly summarize recent findings using these gene knockout zebrafish models, and compare these findings with mammalian models. These established mutants and rapid development of gene knockout techniques have prompted zebrafish as an ideal animal model for studying ovarian development.
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Affiliation(s)
- Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China, 730070.
| | - Wei Ge
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China.
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11
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Lejong M, Vanmuylder N, Choa-Duterre M, Louryan S. A reviewed chronology of primordial germ cells migration in the chick embryo. Morphologie 2020; 104:64-69. [PMID: 31519429 DOI: 10.1016/j.morpho.2019.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/31/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Primordial Germ Cells (PGCs) are present in all sexually reproducing animals. They differentiate into spermatozoa or oocytes and are therefore responsible for the transmission of genetic and epigenetic information across generations. In birds, PGCs are first observed in the center of the blastodisc at stage Eyal-Giladi X. With the formation of the primitive streak, germ cells are translocated anteriorly to the germinal crescent. At stage Hamburger- Hamilton 10-12, they enter the vasculature before migrating through the dorsal mesentery towards the genital ridges. MATERIAL AND METHODS Embryos from stages Hamburger-Hamilton (HH) 16 to 22 were collected. Blood samples were taken from the dorsal aorta and from the heart in order to perform blood smears and PAS staining. Embryos were dissected and fixed in Serra's medium. Sections were placed on slides for PAS staining. A sample of each embryo was collected for DNA extraction and PCR in order to determine the sex of the embryos. RESULTS PGCs were observed in blood circulation until stage HH 20 on blood smears and until stage HH 19 on histological sections. The first PGCs arrived in the genital ridges were observed from stage HH 17. A few germ cells were still migrating in the dorsal mesentery at stage HH 22. The aim of this study was to review the chronology of the migration of PGCs in chick embryos.
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Affiliation(s)
- M Lejong
- Laboratoire d'Anatomie, Biomécanique et Organogenèse, faculté de médecine, université libre de Bruxelles, 1070 Brussels, Belgium
| | - N Vanmuylder
- Laboratoire d'Anatomie, Biomécanique et Organogenèse, faculté de médecine, université libre de Bruxelles, 1070 Brussels, Belgium
| | - M Choa-Duterre
- Laboratoire d'Anatomie, Biomécanique et Organogenèse, faculté de médecine, université libre de Bruxelles, 1070 Brussels, Belgium
| | - S Louryan
- Laboratoire d'Anatomie, Biomécanique et Organogenèse, faculté de médecine, université libre de Bruxelles, 1070 Brussels, Belgium.
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Grimaldi C, Raz E. Germ cell migration-Evolutionary issues and current understanding. Semin Cell Dev Biol 2019; 100:152-159. [PMID: 31864795 DOI: 10.1016/j.semcdb.2019.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 11/19/2022]
Abstract
In many organisms, primordial germ cells (PGCs) are specified at a different location than where the gonad forms, meaning that PGCs must migrate toward the gonad within the early developing embryo. Following species-specific paths, PGCs can be passively carried by surrounding tissues and also perform active migration. When PGCs actively migrate through and along a variety of embryonic structures in different organisms, they adopt an ancestral robust migration mode termed "amoeboid motility", which allows cells to migrate within diverse environments. In this review, we discuss the possible significance of the PGC migration process in facilitating the evolution of animal body shape. In addition, we summarize the latest findings relevant for the molecular and cellular mechanisms controlling the movement and the directed migration of PGCs in different species.
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Affiliation(s)
- Cecilia Grimaldi
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany.
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Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O. Retention of paternal DNA methylome in the developing zebrafish germline. Nat Commun 2019; 10:3054. [PMID: 31296860 PMCID: PMC6624265 DOI: 10.1038/s41467-019-10895-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterise the DNA methylomes of zebrafish PGCs at four developmental stages and identify retention of paternal epigenetic memory, in stark contrast to the findings in mammals. Gene expression profiling of zebrafish PGCs at the same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are independent of DNA methylation-mediated regulation. We identified promoters that are specifically targeted by DNA methylation in somatic and germline tissues during vertebrate embryogenesis and that are frequently misregulated in human cancers. Together, these detailed methylome and transcriptome maps of the zebrafish germline provide insight into vertebrate DNA methylation reprogramming and enhance our understanding of the relationships between germline fate acquisition and oncogenesis.
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Affiliation(s)
- Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Katsiaryna Tarbashevich
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max-Planck-Institute for Molecular Biomedicine, Roentgenstraße 20, 48149, Münster, Germany
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Molecular Medicine Division, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08002, Spain
- ICREA, Barcelona, 08010, Spain
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2010, Australia.
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