??LTA Chromothripsis in Osteosarcoma??, Ageing and Caloric Restriction in Muscle Wasting ??, Funmap: mapping causal variants ???
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 69 | Date: 17 January 2025
?? Welcome to the Bioinformer Weekly Roundup!
In this newsletter, we curate and bring you the most captivating stories, developments, and breakthroughs from the world of bioinformatics. Whether you are a seasoned researcher, a student, or simply curious about the intersection of biology and data science, we have got you covered. Subscribe now to stay ahead in the exciting realm of Bioinformatics!
?? Featured Research
In this study, researchers tested long-read sequencing (LRS) to improve the detection of disease-associated variants in complex genome regions. They sequenced 100 samples with 145 known clinically relevant germline variants, including pathogenic variants. LRS identified 93% of these challenging variants, such as 90% of structural variants, SNVs/indels, and short tandem repeat expansions. The study suggests that LRS could be a cost-effective, first-tier test for diagnosing rare diseases.?
In this study, researchers employed multi-region whole-genome sequencing to examine osteosarcoma. They discovered that chromothripsis, a mutational process, is present in 74% of osteosarcomas, contributing to tumor diversity. They also identified a new mechanism called loss-translocation-amplification (LTA) chromothripsis, which leads to TP53 inactivation and oncogene amplification, particularly common in osteosarcoma. Additionally, they found that genome-wide loss of heterozygosity is a strong prognostic indicator for high-grade osteosarcoma.?
In this study, researchers explored why some patients with metastatic clear cell renal cell carcinoma (mccRCC) respond exceptionally well to immunotherapy. They found that higher clonal neoantigen load was linked to exceptional responses in patients treated with PD1/PDL1 and CTLA-4 inhibitors. In patients treated with PD1/PDL1 and VEGF receptor inhibitors, exceptional responses were associated with enriched B cell receptor signaling pathways and tertiary lymphoid structures. The study suggests that strong T cell and B cell antitumor immunity may drive these exceptional responses.?
This study created long-term organoids from circulating tumor cells (CTCs) in metastatic breast cancer. They found that NRG1–HER3 signaling is vital for CTC survival and growth, while FGFR1 signaling compensates when NRG1 is deficient. Blocking both pathways impaired CTC growth, revealing potential treatment strategies. The organoid platform helps identify patient-specific vulnerabilities for precision medicine.?
In this study, researchers aimed to examine the effects of ageing and caloric restriction (CR) on gene expression in rat skeletal muscle. They found 442 genes upregulated and 377 downregulated with ageing. CR suppressed 69.7% of the upregulated genes and rescued 57.8% of the downregulated genes. Key genes affected included Gc, Plg, Irf7, and Blm. The study highlights potential therapeutic targets for combating sarcopenia, which is the loss of muscle tissue as a natural part of the aging process.?
This study introduces a neural mass network model that includes astrocytes, capturing their interactions with neurons. The model shows astrocytes influence brain activity and connectivity through fast-slow fluctuations and phase-amplitude processes. This research highlights glial-neuronal collaboration in health and disease.?
This study examined CD4+ and CD8+ regulatory T cells in human tonsil-derived immune organoids. Using CRISPR–Cas9, researchers reduced FOXP3 in CD4+ regulatory T cells and GZMB in CD8+ regulatory T cells by 90–95%. FOXP3 knockout led to autoantibody production and increased influenza-specific antibody affinity. GZMB knockout increased follicular helper T cells and expanded autoreactive CD8+ and CD4+ T cells. The findings highlight the distinct roles of these regulatory T cells in preventing autoimmunity.?
This study examined 688,808 individuals with major depression (MD) and 4,364,225 controls, uncovering 697 associations at 635 loci, including 293 novel ones. Researchers identified 308 high-confidence gene associations, enriched in postsynaptic density and receptor clustering. Neural cell-type analysis highlighted various neurons, including those in the amygdala. The results indicate potential repurposing opportunities for antidepressant targets.
??? Latest Tools
CompàreGenome is a command-line tool designed for estimating genomic diversity in both prokaryotes and eukaryotes. It identifies and annotates conserved and divergent genes, providing insights into biological processes, molecular functions, and cellular components. The tool is particularly useful in the early stages of comparative genomic studies, offering detailed genetic distance quantification and functional annotation.
The source code is available here.
Solu is a cloud-based platform designed for real-time genomic pathogen surveillance. It integrates genomic data into a privacy-focused system, offering automated bioinformatics pipelines for species identification, antimicrobial resistance gene detection, and phylogenetic analysis. Solu’s cloud infrastructure is suitable for continuous genomic surveillance in healthcare settings.
Tool is available here.
DTI-MHAPR is a framework for predicting drug-target interactions. It utilizes a PCA-enhanced multi-layer heterogeneous graph attention network to improve feature extraction and reduce redundancy. The framework integrates various similarity metrics and employs a random forest algorithm for final predictions.
Code is available here.
EnrichRBP is a computational platform for predicting and analyzing RNA-binding protein (RBP) interactions. It supports 70 deep learning algorithms for feature representation, model training, and evaluation. The platform provides comprehensive visualizations and functional annotations.
Code is available here.
Funmap is a method for integrating high-dimensional functional annotations to improve fine-mapping of causal variants in complex traits. It uses a random effects model to relate annotations to causal probabilities, reducing false positives. Funmap’s fast algorithm allows scalable integration of numerous annotations, enabling the identification of replicable variants in genome-wide association studies (GWAS).
The Code is available here.
The article introduces BenchAMRking, a Galaxy-based platform designed to address issues in antimicrobial resistance (AMR) gene prediction workflows. It highlights the variability in results from different workflows and the lack of standardization in naming AMR genes. The platform allows users to compare different workflows using their own datasets, aiming to identify and resolve AMR gene-calling problems. BenchAMRking facilitates the understanding and benchmarking of AMR gene prediction from microbial whole genome sequencing data.
Platform is available here.
领英推荐
The article introduces ProPr54, a web server for predicting σ54 promoters and regulons using a hybrid convolutional and recurrent deep neural network. It addresses the lack of comprehensive tools for identifying σ54 promoters in bacterial genomes. The model was trained on validated σ54 binding sites from 33 bacterial species and tested for robustness across various bacterial genomes. ProPr54 offers a reliable tool for predicting σ54 binding sites.
Server is accessible here.
The article introduces vClean, a tool for detecting virus sequence contamination in viral genomes. It uses machine learning to identify contaminations by analyzing nucleotide sequence features and gene patterns. The tool was evaluated using simulated datasets and public ocean metagenomic data, identifying contamination in 34.2% of the genomes tested. vClean aims to improve the quality control of environmental viral genomes.
Tool is available here.
?? Community News
Researchers have discovered that?a drug can protect the brain and reverse initial cognitive damage caused by dementia. The drug activates the cannabinoid neurotransmitter system, which in turn stimulates the cholinergic system, improving memory and learning.?
A study has found that saliva contains special vesicles that trigger rapid blood coagulation in patients with Hemophilia A. This discovery helps explain why mucosal bleeding in the mouth is rare and stops quickly in these patients.?
Researchers have developed an AI model that analyzes CT scans to predict the risk of heart failure and other cardiovascular events. This model aims to improve personalized healthcare by identifying high-risk individuals with greater accuracy.
?? Upcoming Events
This webinar will introduce the new Ensembl browser platform and demonstrate how to navigate the website to retrieve genomic data. The webinar will highlight the improvements in the new platform and how these enhancements can significantly aid in genomic research.
This symposium explores on latest work on the biological mechanisms that mediate drug resistance and tolerance across the species barriers.?
?? Educational Corner
This post delves into the use of non-API entry points in R's data.table package, highlighting their importance and the need for careful use to ensure code stability and performance.
This article explains the differences between Machine Learning and Data Science, highlighting their unique methodologies and applications. It also covers their intersection and real-world uses in fields like healthcare, finance, retail, and transportation.
This blog post explains a method to identify data gaps using R by comparing required data with available data. It uses a case study on Tanzania, employing packages like wbstats, tidyverse, and kableExtra to highlight gaps in data quality, quantity, and granularity.
This blog post guides you through setting up a Kubernetes cluster on Docker Desktop in three steps: downloading Docker Desktop, installing it on your OS, and enabling Kubernetes in the settings. It highlights the benefits of using Docker Desktop for local development and testing of Kubernetes-based applications.
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