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Functional Genomics - Europe PMC

Summarized by Plex Scholar
Last Updated: 17 June 2022

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Functional genomics screening identifies aspartyl-tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers.

"Recent developments in high-throughput nucleic acid synthesis techniques as well as next-generation sequencing platforms have made it possible to perform functional genomics testing using large-scale pooled lentiviral libraries aimed at finding novel cancer therapeutic targets. " Patients with high expression levels of DARS protein in combination with public records showed that patients with high expression levels of GC demonstrated more advanced clinicopathological characteristics and a worse prognosis, particularly among diffuse-type GC patients. Both in vitro and in vivo experiments showed that DARS inhibition resulted in significant growth suppression of GC cells. In addition, RNA-sequencing of GC cell lines in the aftermath of a shRNA-mediated DARS knockdown indicated that DARS inhibition has a direct effect on the activation of multiple p-ERK pathways. This MAPK-related growth inhibition by DARS inhibition would also be applicable to other cancers; as a result, it is necessary to investigate the clinical and clinical significance of DARS in a wide range of malignancies.

Source link: https://europepmc.org/article/MED/35696251


COVID-MVP: an interactive visualization for tracking SARS-CoV-2 mutations, variants, and prevalence, enabled by curated functional annotations and portable genomics workflow

"The SARS-CoV-2 pandemic has reiterated the importance of genomic epidemiology in monitoring the evolution of the virus, epidemiology, geographical origins, and emerging variants. " Pokay's COVID-MVP interactive visualization software summarizes the mutations and their prevalence in SARS-CoV-2 viral lineages and provides functional annotations from the literature curated in an ongoing effort, providing interactive visualization software. Users can interactively browse data and download summarized surveillance reports from COVID-MVP. COVID-MVP source code is available at https://github. com/cidgoh/COVID-MVP, and an instance is hosted at https://covidmvp. cidgoh. ca. "COVID-MVP source code is also available at https://github. com/cidgoh/COVID-MVP; COVID-MVP source code is also hosted at https://covidmvp. cidgoh. ca. ca github.

Source link: https://europepmc.org/article/PPR/PPR503509


ATRT-19. Functional genomics reveal distinct modulators of response to CDK4/6 inhibitors in ATRTs

"Abstract Brain tumors are the leading cause of cancer-related deaths in children, and atypical teratoid tumors are among the most common pediatric brain tumors. " CDK4/6 inhibitors, one of the most promising drugs in our review with direct translational potential, are capable of inhibiting tumor formation due to mutual exclusive dependence of ATRTs on either CDK4 or CDK6. While ATRT cell lines have published some well-known resistance mechanisms, such as loss of RB1 or FBXW7, we have also identified modulators of response to CDK4/6 inhibition, which have adverse effects across ATRT cell lines. The response of ATRTs to CDK4/6 inhibitors, which are one of the most promising class of therapeutic agents for ATRT treatment, is therefore more informative. ".

Source link: https://europepmc.org/article/MED/PMC9164964


PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions.

"Integrative prioritization supports translational use of disease genetic findings in target discovery. " The combinatory facility automates genetics-driven and network-based integrative prioritization for genetic targets at the gene level and across the crosstalk level by chaining together elementary tasks. Together with a tutorial-like booklet explaining how to use, the PiER facilities fulfill multi-tasking needs to accelerate computational translational medicine that uses human disease genetics and genomics for early-stage target discovery and drug repurposing. ".

Source link: https://europepmc.org/article/MED/35610036


A Functional Genomics Pipeline to Identify High-Value CpG Dinucleotides Related to Allergy or Asthma in the Human Methylome

"DNA methylation of cytosines at CpG dinucleotides is a common epigenetic marker that is responsive to environmental exposures and associated with a variety of human pathologies. " We developed a pipeline to find high-value asthma- and allergy-related CpGs among the more than 30 million CpG sites in the human genome to fill this need. To fill this void, we developed a pipeline to find high-value asthma- and allergy-associated CpGs. We used whole-genome bisulfite sequencing in these cells from children with and without allergic asthma, as well as in silico evidence of functionality to identify high-value CpGs for a custom DNA methylation array. Compared to commercial arrays, the Asthma&Allergy Custom array was more suitable for CpGs with intermediate methylation levels, which are more likely to be related to the expression of their nearest or target genes and associated with allergic sensitization in children of various ancestries, relative to commercial array CpGs. Our analysis revealed signature characteristics of functional CpGs and revealed a wealth of DNA methylation variations at functional CpG sites that are otherwise unhearded by current high-throughput arrays, indicating that inter-individual variation in DNA methylation may be more to disease risk than previously thought. Significance Statement DNA methylation at CpG dinucleotides is a common epigenetic hallmark associated with both exposures and diseases, as well as gene expression in particular cell types. To build a custom Asthma&Allergy DNA methylation array, we performed whole-genome bisulfite sequencing in airway epithelial cells from children with and without allergic asthma, as well as functional annotations of gene regulatory elements.

Source link: https://europepmc.org/article/PPR/PPR496783

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions