scholarly journals High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica

2021 ◽  
Author(s):  
Christian Südfeld ◽  
Michal Hubáček ◽  
Daniel Rodrigues Figueiredo ◽  
Mihris I.S. Naduthodi ◽  
John van der Oost ◽  
...  
Keyword(s):  
High Throughput ◽  
Lipid Accumulation ◽  
Insertional Mutagenesis ◽  
Nannochloropsis Oceanica ◽  
Novel Targets

scholarly journals Development of a Zebrafish Model for Studies of the Interaction of Methylenetetrahydrofolate Reductase Deficiency and Dietary Folates on Metabolic Regulation

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 947-947
Author(s):  
Emanuela Pannia ◽  
Rebecca Simonian ◽  
Rola Hammoud ◽  
Xiucheng Cui ◽  
Ruslan Kubant ◽  
...  
Keyword(s):  
High Throughput ◽  
Lipid Accumulation ◽  
Metabolic Regulation ◽  
Methylenetetrahydrofolate Reductase ◽  
Transcriptional Start Site ◽  
Whole Body ◽  
High Cholesterol Diet ◽  
Zebrafish Model ◽  
Metabolic Dysregulation ◽  
Mthfr Deficiency

Abstract Objectives Methylenetetrahydrofolate reductase (MTHFR) is required for 5-methyltetrahydrofolate (5MTHF) synthesis, and common variants reduces its efficiency and associate with metabolic disorders. High folic acid (FA) intakes, commonly consumed by pregnant women in North America, may further inhibit MTHFR enzyme; programming long-term metabolic dysregulation in offspring. The zebrafish (Danio rerio) is a valuable model for study of embryonic development and high-throughput nutrient × gene interactions. The objective of this study was to characterize a zebrafish model of mthfr deficiency and assess the interaction between mthfr and FA intakes on early-life metabolic dysregulation. Methods Zebrafish were co-injected with a set of 4 guide RNAs (gRNAs) or cas9 protein alone and F0 embryos were assayed for a high-throughput phenotypic screen. Germline F1 knock-out homozygous mutants (mthfr −/−) were made by co-injecting cas9 mRNA with 2 gRNAs targeting the transcriptional start site of the mthfr gene. Embryos were raised up to 5 days post-fertilization (dpf) and folate and 1-carbon metabolites measured by LC-MS/MS. Lipid accumulation was assessed at 5dpf and after feeding a high cholesterol diet (HDC) with cholesteryl-ester (CE)-BoDipy-C12® from 5–15dpf. A subset of embryos were exposed to no (0µM) or high (100µM) FA from 0–5dpf and whole-body lipids measured. Results mthfr disruption in zebrafish reduced (80%) mthfr mRNA and 5MTHF levels (90%) compared to controls (P < 0.0001). They had lower 1-carbon metabolites including betaine, methionine, s-adenosylmethionine, and higher choline, s-adenosylhomocysteine, cystathionine and homocysteine (P < 0.01). As well, neutral lipid accumulation was higher in liver, heart and vasculature at 5 and 15 dpf along with higher CE altered cholesterol transport/metabolism. High FA exposure ameliorated lipid accumulation in mthfr mutants at 5 dpf (P = 0.06), but increased lipids accumulation in controls compared to no exposure (P = 0.03). Conclusions The zebrafish mthfr deficient model exhibits a similar alteration to 1-carbon metabolites as in humans with severe MTHFR deficiency. This zebrafish model has potential for understanding the interaction of mthfr deficiency and dietary folates on metabolism. Funding Sources CIHR-INMD, EP by NSERC-CGS

Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae

2007 ◽  
Vol 44 (10) ◽  
pp. 1035-1049 ◽  
Author(s):  
Melania F. Betts ◽  
Sara L. Tucker ◽  
Natalia Galadima ◽  
Yan Meng ◽  
Gayatri Patel ◽  
...  
Keyword(s):  
High Throughput ◽  
Magnaporthe Oryzae ◽  
Insertional Mutagenesis ◽  
Transformation System

Bioinformatics of High-Throughput Insertional Mutagenesis

2010 ◽  
pp. 167-188
Author(s):  
Keiko Akagi ◽  
Ming Yi ◽  
Jean Roayaei ◽  
Robert M. Stephens
Keyword(s):  
High Throughput ◽  
Insertional Mutagenesis

scholarly journals TheMETGene Is a Common Integration Target in Avian Leukosis Virus Subgroup J-Induced Chicken Hemangiomas

2015 ◽  
Vol 89 (9) ◽  
pp. 4712-4719 ◽  
Author(s):  
James Justice ◽  
Sanandan Malhotra ◽  
Miguel Ruano ◽  
Yingying Li ◽  
Guillermo Zavala ◽  
...  
Keyword(s):  
High Throughput ◽  
Insertional Mutagenesis ◽  
High Throughput Sequencing ◽  
Avian Leukosis Virus ◽  
Economic Problem ◽  
Proviral Integration ◽  
Integration Sites ◽  
Myeloid Leukosis ◽  
Subgroup J ◽  
Avian Leukosis Virus Subgroup

ABSTRACTAvian leukosis virus subgroup J (ALV-J) is a simple retrovirus that can cause hemangiomas and myeloid tumors in chickens and is currently a major economic problem in Asia. Here we characterize ALV-J strain PDRC-59831, a newly studied U.S. isolate of ALV-J. Five-day-old chicken embryos were infected with this virus, and the chickens developed myeloid leukosis and hemangiomas within 2 months after hatching. To investigate the mechanism of pathogenesis, we employed high-throughput sequencing to analyze proviral integration sites in these tumors. We found expanded clones with integrations in theMETgene in two of the five hemangiomas studied. This integration locus was not seen in previous work characterizing ALV-J-induced myeloid leukosis.METis a known proto-oncogene that acts through a diverse set of signaling pathways and is involved in many neoplasms. We show that tumors harboringMETintegrations exhibit strong overexpression ofMETmRNA.IMPORTANCEThese data suggest that ALV-J induces oncogenesis by insertional mutagenesis, and integrations in theMEToncogene can drive the overexpression ofMETand contribute to the development of hemangiomas.

scholarly journals Cancer LncRNA Census 2 (CLC2): an enhanced resource reveals clinical features of cancer lncRNAs

NAR Cancer ◽  
2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Adrienne Vancura ◽  
Andrés Lanzós ◽  
Núria Bosch-Guiteras ◽  
Mònica Torres Esteban ◽  
Alejandro H Gutierrez ◽  
...  
Keyword(s):  
High Throughput ◽  
Insertional Mutagenesis ◽  
Somatic Mutations ◽  
Annotation Scheme ◽  
Genomic Features ◽  
Gene Sets ◽  
Therapeutic Development ◽  
Non Coding Rnas ◽  
Clinical Genomic ◽  
Suppressor Analysis

Abstract Long non-coding RNAs (lncRNAs) play key roles in cancer and are at the vanguard of precision therapeutic development. These efforts depend on large and high-confidence collections of cancer lncRNAs. Here, we present the Cancer LncRNA Census 2 (CLC2). With 492 cancer lncRNAs, CLC2 is 4-fold greater in size than its predecessor, without compromising on strict criteria of confident functional/genetic roles and inclusion in the GENCODE annotation scheme. This increase was enabled by leveraging high-throughput transposon insertional mutagenesis screening data, yielding 92 novel cancer lncRNAs. CLC2 makes a valuable addition to existing collections: it is amongst the largest, contains numerous unique genes (not found in other databases) and carries functional labels (oncogene/tumour suppressor). Analysis of this dataset reveals that cancer lncRNAs are impacted by germline variants, somatic mutations and changes in expression consistent with inferred disease functions. Furthermore, we show how clinical/genomic features can be used to vet prospective gene sets from high-throughput sources. The combination of size and quality makes CLC2 a foundation for precision medicine, demonstrating cancer lncRNAs’ evolutionary and clinical significance.

scholarly journals Identification of candidate therapeutics and signaling pathways for multiple myeloma

2021 ◽  
Author(s):  
Hanming Gu
Keyword(s):  
Multiple Myeloma ◽  
Cell Proliferation ◽  
Signaling Pathways ◽  
Plasma Cell ◽  
High Throughput ◽  
Biological Pathways ◽  
Transcription Activator ◽  
Number Of Factors ◽  
Novel Targets ◽  
Cell Malignancy

Multiple myeloma (MM), a plasma cell malignancy, is related to critical morbidity due to end-organ destruction. A number of factors affect the MM cell proliferation and functions. Though MM is not curable, novel targets and inhibitors have shown great effects on MM patients. Here, we aim to identify significant genes and signaling pathways of MM with SI2 treatment using a bioinformatics method. The GSE156871 dataset was originally produced by using the high-throughput BGISEQ-500. The KEGG and GO results suggested that biological pathways such as "the complement and coagulation cascades" and "the transcription activator activity" are mostly affected in the SI2 treatment of MM cells. Moreover, we identified several genes including SRC, KNG1, and PI3KCG were involved in the treatment of MM cells. Therefore, our study provides further insights into the treatment of MM.

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