Articles tagged with Transcriptomics
Researchers have developed a new system to map gene expression across whole mouse bodies, providing a toolkit for studying molecular and cellular processes. The technique allows for the analysis of inflammation in every cell type and organ tissue, paving the way for a 'virtual mouse' model that could be used for research.
Researchers find that rare stromal cells are responsible for maintaining immune cell organization in healthy lymph nodes. However, in aggressive lymphomas, this process breaks down due to a self-reinforcing inflammatory cycle, leading to tissue collapse and poorer outcomes.
Researchers at DZNE identified five particularly affected cell types in the motor cortex, which are equally susceptible to ALS and FTD. The study used molecular fingerprinting to analyze human tissue samples and found that excitatory cells are primarily affected by the disease.
New research reveals that tumor cells in supratentorial ependymomas cluster into distinct neighborhoods, each with a specific role, such as proliferating or invading. Understanding these cell subtypes could help predict treatment response and inform targeted therapies for this aggressive childhood brain cancer.
Researchers developed an integrative analysis of single-cell sequencing and spatial mapping to reveal novel mechanisms driving breast cancer metastasis. The study identifies key drivers of metastasis, including early disseminated cancer cells with enhanced invasive capabilities.
The development of spatial transcriptomics has advanced gene expression understanding, but selecting suitable analytical approaches is challenging. A database curated SpatialToolDB addresses this by classifying over 600 ST analytical tools and providing access to processed datasets.
Rice bioengineer Jerzy Szablowski has been awarded a Sloan Research Fellowship for his innovative work on noninvasive methods to communicate with the brain. He aims to develop versatile platform technologies to obtain new types of research data and treat multiple diseases.
A study by RIKEN researchers identifies a MYCN-driven biomarker that predicts the risk of liver cancer. The biomarker, known as the MYCN niche score, uses machine learning to analyze gene expression patterns and indicates whether a tumor-free liver is at high risk for developing tumors.
A new study found that shingles vaccination is associated with lower inflammation, slower epigenetic aging, and overall slower biological aging in older adults. Vaccination showed benefits even four years after the initial dose.
A new study maps the impact of stressors during pregnancy on the developing fetal brain, revealing a cell atlas and identifying key immune pathways. The research sheds light on how maternal gut-immune disruptions can shape neurodevelopmental disorders in children.
A deep learning framework called PRTS accurately predicts single-cell-resolution spatial transcriptomics from H&E-stained histology images. The model identifies 21 cell subtypes in mouse brain and maintains prediction accuracy in human breast and lung cancer tissues.
A recent study published in Cell Reports found that the vagus nerve's right branch is responsible for sensing nutritional information and reinforcing dietary behaviors. This research has implications for improving treatments of obesity, metabolic diseases, depression, and substance abuse.
Researchers at University of Texas M. D. Anderson Cancer Center discover that inflammation is responsible for driving the earliest stages of lung cancer, identifying potential targets for early intervention and suggesting a promising approach to intercepting lung cancer development.
Researchers created a comprehensive single-nucleus transcriptomic atlas of the pig intestine, identifying 19 major cell types and 58 cellular subtypes. This study provides valuable insights into the mechanisms by which neurons regulate inflammatory responses and the molecular basis for stronger immune functions in wild boars.
HTGAnalyzer is an automated tool simplifying complex transcriptomic workflows, enabling clinicians without bioinformatics expertise to perform essential analyses in precision medicine. The tool has been validated using multiple datasets and identified differentially expressed genes linked to cancer diagnosis, treatment, and prognosis.
Researchers developed TraMA, an RNA-based measure of biological aging that predicts health risks and mortality. It captures distinct aspects of aging and health decline, including inflammation, immune function, and kidney and brain health.
The Northwestern University-developed SOAR platform helps researchers understand diseases and find potential treatments by analyzing gene activity across various tissues. This tool enables prioritization of drugs to be sent to clinical studies, reducing development time.
Researchers at IGTP reveal a clear separation between lesional and non-lesional tissue, with high expression of pro-inflammatory genes in lesions. The study identifies 17 differential transcriptomic modules and associates molecular profiles with clinical indicators from the same patients.
Researchers at the University of Würzburg have developed a new, efficient method for recording gene activity in bacteria. The MATQ-seq protocol achieves a high cell retention rate of 95% and detects the activity of 300 to 600 genes per bacterial cell.
Researchers mapped a lung tumor's cellular neighborhoods in 3D using single-cell spatial technologies, identifying 18 cell types and potential targets for personalized cancer therapy. The study reveals new insights into how tumor cells interact with their surroundings and how to reverse immune suppression mechanisms.
Recent research reveals that avapritinib, a PDGFRA inhibitor, demonstrates potent activity against pediatric high-grade glioma tumors with PDGFRA alterations. Clinical trials in patients showed an initial clinical response and improved survival rates, suggesting the potential for avapritinib as a therapeutic option.
Researchers have developed a computational tool, Spotiphy, that uses generative AI to enhance the resolution of sequencing-based spatial transcriptomics without sacrificing gene coverage. This breakthrough enables single-cell resolution in tissue imaging while maintaining full transcriptome coverage.
A new technique called cycleHCR uses DNA barcodes to track hundreds of RNA and protein molecules in single cells within thick biological samples. This allows researchers to decipher how genes function in different parts of an organism, how they enable development, and how they might be altered in diseases.
A new Northwestern University study found that enhancing the brain's immune cells can clear Alzheimer's plaques and restore a healthier brain environment in immunized patient brains. The findings could reshape the future of Alzheimer's treatments by shifting the focus from removing plaques to harnessing the brain's natural defenses.
A new study finds that dexamethasone, a commonly prescribed anti-swelling drug, can significantly reduce the body's immune response to brain cancer for weeks after its last dose. This effect is stronger with higher dosages and may impact immunotherapy treatments.
A new method combines traditional histopathology with spatial transcriptomics data to improve understanding of chronic kidney disease lesions at the cellular and molecular levels. This approach has the potential to identify new biomarkers and therapeutic strategies for patients.
A new study combines genomic-scale microscopy with a technical innovation to capture genes bacteria turn on in different situations and environments. This technology promises to take the study of bacteria to the next level by providing powerful new insights into bacterial behavior, including gene expression and interactions.
Researchers at La Jolla Institute for Immunology discovered that tissue-resident memory CD8 T cells rise up to fight infections in the small intestine, using spatial transcriptomics technology. These immune cells are split between villi and crypts, with progenitor-like cells replenishing effector T cells.
A zebrafish protein, Hmga1, has been found to unlock dormant genes for heart repair in mice. The discovery could lead to regenerative therapies to prevent heart failure in humans.
Scientists at the Allen Institute have identified specific cell types in the brain that undergo major changes with age, which could lead to new treatments for age-related brain diseases. The study provides a detailed map of brain cells affected by aging and highlights potential connections between diet, inflammation, and brain health.
Researchers found that neural stem cells have a rejuvenating effect on nearby brain cells, while T cells promote stress and damage. The study opens new avenues for research into slowing or reversing brain aging.
The InSTAnT Toolkit allows scientists to investigate cellular processes by identifying proximal pairs of RNA transcripts, revealing sets of molecules that work together. This technology provides accurate and reproducible findings, shedding light on the complex interactions within cells.
Ewing sarcoma, a rare childhood cancer, is made more aggressive by the absence of STAG2 protein. This discovery provides potential biomarkers and therapeutic targets for treatment.
Researchers found that genetic collisions between transcription and DNA replication lead to large tandem duplications in cancer cells, which can be identified through dosage imbalance. These duplicates are associated with poor patient survival and high correlation with mutations in genes TP53, CDK12, and SPOP.
Researchers have identified a genetic signature that can predict neonatal sepsis in newborns before symptoms appear, allowing for earlier recognition and life-saving treatment. The discovery has the potential to improve healthcare outcomes in lower- and middle-income countries where neonatal sepsis is most prevalent.
Researchers have created a comprehensive atlas of zebrafish development, combining time-lapse videos and gene expression data to map the behavior of individual cells. This breakthrough tool offers new insights into how lifeforms develop from single cells to complex organisms.
A new study by Bar-Ilan University researchers found a significant link between the gut microbiome and aggression in mice, with reduced diversity in gut bacteria causing increased aggression. The study also identified key brain regions and biochemical mechanisms underlying these behavioral changes.
Researchers discovered faulty immune processes responsible for lingering lung issues after COVID-19, which can be disrupted by existing drugs. The study also identified molecules responsible for the issue and potential therapeutic options for patients with ongoing lung damage.
Scientists have mapped the global repertoire of genes that determine the male or female sexual fates in Plasmodium falciparum malaria parasites. This study reveals key regulators of gene expression during development and identifies novel candidate 'driver' genes, shedding light on the complex biology of malaria transmission.
Researchers have created the first spatial map of malaria infection in the mouse liver using Spatial Transcriptomics and single-cell RNA-sequencing. This discovery sheds light on the parasite's lifecycle, revealing changes in host cell gene expression near infected areas.
A new open-source platform, Nova-ST, is transforming gene expression profiling in tissue samples by offering affordable and high-resolution spatial analysis. This approach allows scientists to map gene expression across a tissue section with a spatial context, enabling the study of complex biological processes.
Researchers developed more resilient varieties of cotton by analyzing its genes and physical traits. They found two key regulatory genes that help cotton plants manage water stress while maintaining fiber production.
Researchers have developed ENGRAM, a method that records cell signals and biological states as they occur inside living cells. This approach offers a novel way to capture biological information in living systems, potentially helping answer questions about cellular pasts and futures.
Researchers found that the frequency of activated TREG cells remained elevated during treatment and continued to be high even after the virus was eliminated. Inflammatory features, such as increased TNF signaling, were sustained in TREG cells, indicating long-term immune system changes induced by the chronic infection.
A team of researchers has completed the diploid genome assembly of the Malbec grapevine, revealing the genetic factors that contribute to its exceptional wine quality. The study identifies polymorphic regions and gene expression differences among clones, shedding light on the molecular mechanisms driving clonal variation.
A recent study found that oleacein increases BDNF expression in human neuronal cells and reduces depressive behavior in mouse models. Gene expression analysis reveals the activation of cell cycle and neurogenesis processes, as well as a decrease in inflammatory response.
A platform called Open-ST enables scientists to reconstruct gene expression in cells within a tissue in three dimensions, capturing molecular and (sub)cellular structures. The platform was used to study cell types at subcellular resolution in tissues from mice brains, tumor tissue, and healthy lymph nodes, providing insights into cance...
A study by researchers at the Center for Genomic Regulation found that changes in mRNA content between germline and somatic cells are the primary source of variation in lifespan. Knocking down specific genes increased life expectancy, suggesting randomness in gene activity affects ageing.
A new atlas provides a detailed map of how cells and tissues age in roundworms, shedding light on the aging process and potential treatments. The study reveals unique aging features of different tissues and identifies key mechanisms underlying cellular aging.
Researchers used machine learning to integrate high-throughput transcriptomic, proteomic, metabolomic, and lipidomic profiles to identify four distinct molecular profiles of Alzheimer's Disease. These profiles were associated with varying levels of cognitive function and neuropathological features.
Researchers from Tokyo Medical and Dental University used long-read RNA sequencing to decode genetic intricacies and disease links. The study identified novel isoforms, cell-type-specific splicing patterns, and disease-linked transcripts associated with immune-related diseases.
A comprehensive, user-friendly repository has been created to help study Alzheimer's disease. The ssREAD database encompasses 277 integrated datasets from 67 scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells, and includes interactive visualizations for comprehensive analysis interpretations.
A research team has successfully assembled a nearly gap-free, telomere-to-telomere genome of P. ussuriensis, filling gaps present in the P. trichocarpa genome. The assembly's high collinearity with P. trichocarpa facilitates comparative genomics, epigenetic research, and reproductive biology studies.
A comprehensive study by McLean Hospital researchers reveals both shared and unique molecular changes across brain regions, genomic layers, cell types, and blood in individuals with posttraumatic stress disorder (PTSD) and major depressive disorder (MDD). The findings provide potential avenues for novel therapeutics and biomarkers.
Researchers analyzed genome of Oikopleura dioica, finding it has wildly different languages despite identical physical characteristics. The 'scrambling' phenomenon suggests genes are regulated differently, challenging assumptions about species identity.
Researchers have developed a modular epigenome editing platform to study the impact of chromatin modifications on transcription. The system allows for precise programming of nine biologically important chromatin marks, enabling the discovery of causal relationships between chromatin marks and gene regulation.
Researchers found associations between inflammatory and metabolic biomarkers and accelerated aging, with GlycA and GrimAge showing robust correlations. The study provides insight into the relationship between aging and cardiometabolic health, potentially informing vulnerable populations.
Researchers at Karolinska Institutet developed a Single Cell Atlas (SCA) platform to profile human biology through multi-omics technologies. The extensive collection of data provides unique insights into individual cell properties and tissue interactions.
Researchers have found that genetic mutations are not essential for cancer onset, and instead, epigenetic dysregulation plays a crucial role. Epigenetic changes can cause gene expression to be altered, leading to tumour formation even after the signal has been restored.
A consortium of scientists, including Brazilians, has successfully sequenced the reference genome of Arabica coffee. The study identified genes responsible for resistance to rust and other diseases, as well as those related to the aroma of Arabica coffee. By comparing a dihaploid-derived genome with a common tetraploid variety, researc...