scholarly journals Zebrafish Cancer Predisposition Models

2021 ◽  
Vol 9 ◽  
Author(s):  
Kim Kobar ◽  
Keon Collett ◽  
Sergey V. Prykhozhij ◽  
Jason N. Berman
Keyword(s):  
Large Scale ◽  
Genetic Manipulation ◽  
Bone Marrow Failure ◽  
Cancer Predisposition ◽  
Potential Candidate ◽  
Cancer Evolution ◽  
High Fecundity ◽  
Cancer Models ◽  
The Impact

Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5–10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.

DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development

2021 ◽  
Author(s):  
Alissa D Marchione ◽  
Zanshé Thompson ◽  
Katie L Kathrein
Keyword(s):  
Stem Cell ◽  
Epigenetic Regulation ◽  
Chromatin Structure ◽  
Large Scale ◽  
Genetic Manipulation ◽  
Critical Role ◽  
External Fertilization ◽  
High Fecundity ◽  
Zebrafish Development

AbstractThe complex processes necessary for embryogenesis require a gene regulatory network that is complex and systematic. Gene expression regulates development and organogenesis, but this process is altered and fine-tuned by epigenetic regulators that facilitate changes in the chromatin landscape. Epigenetic regulation of embryogenesis adjusts the chromatin structure by modifying both DNA through methylation and nucleosomes through posttranslational modifications of histone tails. The zebrafish is a well-characterized model organism that is a quintessential tool for studying developmental biology. With external fertilization, low cost and high fecundity, the zebrafish are an efficient tool for studying early developmental stages. Genetic manipulation can be performed in vivo resulting in quick identification of gene function. Large-scale genome analyses including RNA sequencing, chromatin immunoprecipitation and chromatin structure all are feasible in the zebrafish. In this review, we highlight the key events in zebrafish development where epigenetic regulation plays a critical role from the early stem cell stages through differentiation and organogenesis.

scholarly journals Proteomics and metabolomics in cow fertility: a systematic review

Reproduction ◽  
2020 ◽  
Vol 160 (5) ◽  
pp. 639-658
Author(s):  
Nicolas Aranciaga ◽  
James D Morton ◽  
Debra K Berg ◽  
Jessica L Gathercole
Keyword(s):  
Oxidative Stress ◽  
Systematic Review ◽  
Large Scale ◽  
Reproductive Tract ◽  
Early Embryo ◽  
Female Reproductive Tract ◽  
Full Potential ◽  
Technical Standards ◽  
The Impact

Cow subfertility is a multi-factorial problem in many countries which is only starting to be unravelled. Molecular biology can provide a substantial source of insight into its causes and potential solutions, particularly through large scale, untargeted omics approaches. In this systematic review, we set out to compile, assess and integrate the latest proteomic and metabolomic research on cow reproduction, specifically that on the female reproductive tract and early embryo. We herein report a general improvement in technical standards throughout the temporal span examined; however, significant methodological limitations are also identified. We propose easily actionable avenues for ameliorating these shortcomings and enhancing the reach of this field. Text mining and pathway analysis corroborate the relevance of proteins and metabolites related to the triad oxidative stress-inflammation-disease on reproductive function. We envisage a breakthrough in cattle reproductive molecular research within the next few years as in vivo sample techniques are improved, omics analysis equipment becomes more affordable and widespread, and software tools for single- and multi-omics data processing are further developed. Additional investigation of the impact of local oxidative stress and inflammation on fertility, both at the local and systemic levels, is key towards realising the full potential of this field.

scholarly journals Exposure to airborne gold nanoparticles: a review of current toxicological data on the respiratory tract

2020 ◽  
Vol 22 (8) ◽  
Author(s):  
Barbara De Berardis ◽  
Magda Marchetti ◽  
Anna Risuglia ◽  
Federica Ietto ◽  
Carla Fanizza ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Human Health ◽  
Large Scale ◽  
Current Knowledge ◽  
Engineered Nanoparticles ◽  
In Vivo Studies ◽  
Field Exposure ◽  
The Impact

AbstractIn recent years, the introduction of innovative low-cost and large-scale processes for the synthesis of engineered nanoparticles with at least one dimension less than 100 nm has led to countless useful and extensive applications. In this context, gold nanoparticles stimulated a growing interest, due to their peculiar characteristics such as ease of synthesis, chemical stability and optical properties. This stirred the development of numerous applications especially in the biomedical field. Exposure of manufacturers and consumers to industrial products containing nanoparticles poses a potential risk to human health and the environment. Despite this, the precise mechanisms of nanomaterial toxicity have not yet been fully elucidated. It is well known that the three main routes of exposure to nanomaterials are by inhalation, ingestion and through the skin, with inhalation being the most common route of exposure to NPs in the workplace. To provide a complete picture of the impact of inhaled gold nanoparticles on human health, in this article, we review the current knowledge about the physico-chemical characteristics of this nanomaterial, in the size range of 1–100 nm, and its toxicity for pulmonary structures both in vitro and in vivo. Studies comparing the toxic effect of NPs larger than 100 nm (up to 250 nm) are also discussed.

scholarly journals DAPK1 loss triggers tumor invasion in colorectal tumor cells

2019 ◽  
Vol 10 (12) ◽  
Author(s):  
Sara Steinmann ◽  
Philipp Kunze ◽  
Chuanpit Hampel ◽  
Markus Eckstein ◽  
Jesper Bertram Bramsen ◽  
...  
Keyword(s):  
Chorioallantoic Membrane ◽  
Gene Expression Signature ◽  
Predictive Biomarker ◽  
Cancer Type ◽  
Potential Candidate ◽  
Metastatic Progression ◽  
Death Associated Protein Kinase ◽  
The Impact

AbstractColorectal cancer (CRC) is one of the leading cancer-related causes of death worldwide. Despite the improvement of surgical and chemotherapeutic treatments, as of yet, the disease has not been overcome due to metastasis to distant organs. Hence, it is of great relevance to understand the mechanisms responsible for metastasis initiation and progression and to identify novel metastatic markers for a higher chance of preventing the metastatic disease. The Death-associated protein kinase 1 (DAPK1), recently, has been shown to be a potential candidate for regulating metastasis in CRC. Hence, the aim of the study was to investigate the impact of DAPK1 protein on CRC aggressiveness. Using CRISPR/Cas9 technology, we generated DAPK1-deficient HCT116 monoclonal cell lines and characterized their knockout phenotype in vitro and in vivo. We show that loss of DAPK1 implemented changes in growth pattern and enhanced tumor budding in vivo in the chorioallantoic membrane (CAM) model. Further, we observed more tumor cell dissemination into chicken embryo organs and increased invasion capacity using rat brain 3D in vitro model. The novel identified DAPK1-loss gene expression signature showed a stroma typical pattern and was associated with a gained ability for remodeling the extracellular matrix. Finally, we suggest the DAPK1-ERK1 signaling axis being involved in metastatic progression of CRC. Our results highlight DAPK1 as an anti-metastatic player in CRC and suggest DAPK1 as a potential predictive biomarker for this cancer type.

scholarly journals iTRAQ-based proteomic profiling reveals protein alterations after traumatic brain injury and supports thyroxine as a potential treatment

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhongxiang Zhang ◽  
Jiangtao Yu ◽  
Pengcheng Wang ◽  
Lian Lin ◽  
Ruining Liu ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Large Scale ◽  
Transcriptional Level ◽  
Proteomic Profiling ◽  
Severity Scores ◽  
Itraq Proteomics ◽  
Protein Alterations ◽  
The Impact

AbstractTraumatic brain injury (TBI) is a primary cause of disability and death across the world. Previously, RNA analysis was widely used to study the pathophysiological mechanisms underlying TBI; however, the relatively low correlation between the transcriptome and proteome revealed that RNA transcription abundance does not reliably predict protein abundance, which led to the emergence of proteomic research. In this study, an iTRAQ proteomics approach was applied to detect protein alterations after TBI on a large scale. A total of 3937 proteins were identified, and 146 proteins were significantly changed after TBI. Moreover, 23 upregulated proteins were verified by parallel reaction monitoring (PRM), and fold changes in 16 proteins were consistent with iTRAQ outcomes. Transthyretin (Ttr) upregulation has been demonstrated at the transcriptional level, and this study further confirmed this at the protein level. After treatment with thyroxine (T4), which is transported by Ttr, the effects of T4 on neuronal histopathology and behavioral performance were determined in vivo (TBI + T4 group). Brain edema was alleviated, and the integrity of the blood brain barrier (BBB) improved. Escape latency in the Morris water maze (MWM) declined significantly compared with the group without T4 treatment. Modified neurological severity scores (mNSS) of the TBI + T4 group decreased from day 1 to day 7 post-TBI compared with the TBI + saline group. These results indicate that T4 treatment has potential to alleviate pathologic and behavioral abnormalities post-TBI. Protein alterations after T4 treatment were also detected by iTRAQ proteomics. Upregulation of proteins like Lgals3, Gfap and Apoe after TBI were reversed by T4 treatment. GO enrichment showed T4 mainly affected intermediate filament organization, cholesterol transportation and axonal regeneration. In summary, iTRAQ proteomics provides information about the impact of TBI on protein alterations and yields insight into underlying mechanisms and pathways involved in TBI and T4 treatment. Finally, Ttr and other proteins identified by iTRAQ may become potential novel treatment targets post-TBI.

scholarly journals Through the Looking Glass: Visualizing Leukemia Growth, Migration, and Engraftment Using Fluorescent Transgenic Zebrafish

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Finola E. Moore ◽  
David M. Langenau
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Genetic Manipulation ◽  
Fluorescent Proteins ◽  
Leukemia Cells ◽  
Transgenic Zebrafish ◽  
Cell Frequency ◽  
Response To Chemotherapy ◽  
Looking Glass

Zebrafish have emerged as a powerful model of development and cancer. Human, mouse, and zebrafish malignancies exhibit striking histopathologic and molecular similarities, underscoring the remarkable conservation of genetic pathways required to induce cancer. Zebrafish are uniquely suited for large-scale studies in which hundreds of animals can be used to investigate cancer processes. Moreover, zebrafish are small in size, optically clear during development, and amenable to genetic manipulation. Facile transgenic approaches and new technologies in gene inactivation have provided much needed genomic resources to interrogate the function of specific oncogenic and tumor suppressor pathways in cancer. This manuscript focuses on the unique attribute of labeling leukemia cells with fluorescent proteins and directly visualizing cancer processesin vivoincluding tumor growth, dissemination, and intravasation into the vasculature. We will also discuss the use of fluorescent transgenic approaches and cell transplantation to assess leukemia-propagating cell frequency and response to chemotherapy.

scholarly journals A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids

2017 ◽  
Vol 4 (5) ◽  
pp. 170095 ◽  
Author(s):  
Tom Beneke ◽  
Ross Madden ◽  
Laura Makin ◽  
Jessica Valli ◽  
Jack Sunter ◽  
...  
Keyword(s):  
Genome Editing ◽  
High Throughput ◽  
Large Scale ◽  
Leishmania Major ◽  
Fluorescent Protein ◽  
Genetic Manipulation ◽  
Gene Knockout ◽  
Guide Rna ◽  
Functional Studies

Clustered regularly interspaced short palindromic repeats (CRISPR), CRISPR-associated gene 9 (Cas9) genome editing is set to revolutionize genetic manipulation of pathogens, including kinetoplastids. CRISPR technology provides the opportunity to develop scalable methods for high-throughput production of mutant phenotypes. Here, we report development of a CRISPR-Cas9 toolkit that allows rapid tagging and gene knockout in diverse kinetoplastid species without requiring the user to perform any DNA cloning. We developed a new protocol for single-guide RNA (sgRNA) delivery using PCR-generated DNA templates which are transcribed in vivo by T7 RNA polymerase and an online resource (LeishGEdit.net) for automated primer design. We produced a set of plasmids that allows easy and scalable generation of DNA constructs for transfections in just a few hours. We show how these tools allow knock-in of fluorescent protein tags, modified biotin ligase BirA*, luciferase, HaloTag and small epitope tags, which can be fused to proteins at the N- or C-terminus, for functional studies of proteins and localization screening. These tools enabled generation of null mutants in a single round of transfection in promastigote form Leishmania major , Leishmania mexicana and bloodstream form Trypanosoma brucei ; deleted genes were undetectable in non-clonal populations, enabling for the first time rapid and large-scale knockout screens.

scholarly journals Measurement of the Absolute Immature Platelet Number Reflects Marrow Production and Is Not Impacted by Platelet Transfusion

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3425-3425
Author(s):  
Taha Bat ◽  
Susan F. Leitman ◽  
Katherine R Calvo ◽  
Donna Chauvet ◽  
Cynthia E. Dunbar
Keyword(s):  
Bone Marrow ◽  
Platelet Transfusion ◽  
Conflicts Of Interest ◽  
Bone Marrow Failure ◽  
High Dose Chemotherapy ◽  
High Dose ◽  
Immature Platelet Fraction ◽  
Platelet Number ◽  
The Impact

Abstract Abstract 3425 Background The ability to distinguish increased platelet destruction from platelet hypo-production is important in the care of patients with bone marrow failure syndromes and patients receiving high dose chemotherapy. The measurement of immature circulating platelets based on RNA content using an automated counter is now feasible. This study evaluated the impact of recent platelet transfusion on measurement of immature platelet parameters. Study Design and Methods The immature platelet fraction (IPF) and absolute immature platelet number (AIPN) were measured using the Sysmex XE-5000 analyzer prior to and following platelet transfusion in 9 transfusion-dependent patients with marrow failure secondary to aplastic anemia, myelodysplasia or transplantation conditioning. IPF and AIPN were also measured serially over 5 days of storage in 3 plateletpheresis components collected from normal donors. Results Platelet transfusion did not significantly change the mean AIPN in transfused patients. In contrast, IPF decreased significantly from 6.6 ±4.6% at day -1 to 2.3 ±1.4% at day 0 before returning to 4.3 ±2.3% at day +1. In the platelet component, AIPN and IPF% increased significantly over 5 days of storage, most likely due to an artifact of the staining and detection process for stored platelets, no longer detected in vivo once the platelets were transfused. Conclusion Platelet transfusion decreases the IPF due to the resultant increase in circulating platelet count. However, platelet transfusion does not change the circulating absolute immature platelet number (AIPN), validating this assay as a reflection of ongoing platelet production by the bone marrow in various clinical settings, regardless of proximity to platelet transfusion. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shitao Zhao ◽  
Michiaki Hamada
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Binding Sites ◽  
Prediction Accuracy ◽  
Large Scale ◽  
Rna Binding ◽  
Binding Prediction ◽  
Binding Preference ◽  
The Impact

Abstract Background Protein-RNA interactions play key roles in many processes regulating gene expression. To understand the underlying binding preference, ultraviolet cross-linking and immunoprecipitation (CLIP)-based methods have been used to identify the binding sites for hundreds of RNA-binding proteins (RBPs) in vivo. Using these large-scale experimental data to infer RNA binding preference and predict missing binding sites has become a great challenge. Some existing deep-learning models have demonstrated high prediction accuracy for individual RBPs. However, it remains difficult to avoid significant bias due to the experimental protocol. The DeepRiPe method was recently developed to solve this problem via introducing multi-task or multi-label learning into this field. However, this method has not reached an ideal level of prediction power due to the weak neural network architecture. Results Compared to the DeepRiPe approach, our Multi-resBind method demonstrated substantial improvements using the same large-scale PAR-CLIP dataset with respect to an increase in the area under the receiver operating characteristic curve and average precision. We conducted extensive experiments to evaluate the impact of various types of input data on the final prediction accuracy. The same approach was used to evaluate the effect of loss functions. Finally, a modified integrated gradient was employed to generate attribution maps. The patterns disentangled from relative contributions according to context offer biological insights into the underlying mechanism of protein-RNA interactions. Conclusions Here, we propose Multi-resBind as a new multi-label deep-learning approach to infer protein-RNA binding preferences and predict novel interactions. The results clearly demonstrate that Multi-resBind is a promising tool to predict unknown binding sites in vivo and gain biology insights into why the neural network makes a given prediction.

scholarly journals Zebrafish as a model to investigate the effects of exercise in cancer

2018 ◽  
Author(s):  
Alexandra Yin ◽  
Nathaniel R. Campbell ◽  
Lee W. Jones ◽  
Richard M. White
Keyword(s):  
Endurance Exercise ◽  
Large Scale ◽  
Flow Chamber ◽  
Model Systems ◽  
Zebrafish Model ◽  
Cancer Pathogenesis ◽  
Cancer Models ◽  
Key Aspects ◽  
Response To Exercise

AbstractEmerging data indicates that exercise may regulate cancer pathogenesis, but the mechanisms underpinning how it regulates the tumor as well as surrounding microenvironment are poorly understood. Dissecting this complex, highly integrated physiology requires model systems which accurately recapitulate key aspects of human response to exercise, yet permit rapid and unbiased genetic interrogation of relevant pathways. The zebrafish has emerged as a new model for cancer due to its high resolution in vivo imaging and capacity for large-scale, unbiased screening approaches. Here, we have developed a set of tools to study the effects of exercise in a zebrafish model of melanoma. Using a flow chamber, we studied the effects of endurance exercise bouts (3-6 hour/d, 5d/wk for 1 to 3 wks) in both larval and adult zebrafish. The regimen was well tolerated, with no unexpected toxicities or changes in survival. When the zebrafish were transplanted with ZMEL1-GFP melanoma cells, we found that endurance exercise over a 2-week period led to a significant decrease in cancer growth in the larval zebrafish. As zebrafish cancer models show strong conservation in human disease, our findings have direct application to understanding the human exercise/cancer relationship.

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