When regulatory T cells go bad
Researchers at La Jolla Institute for Immunology and Augusta University have identified a link between
SourceLa Jolla Institute for Immunology·JournalNature Immunology·TypeExperimental study·DateAug 10, 2023
Rna Sequencing
Articles tagged with Rna Sequencing
Researchers at Leipzig University visualize activity of CRISPR genetic scissors
Researchers at Leipzig University have developed a new method to visualize the activity of CRISPR-Cas protein complexes, allowing for precise observation of gene recognition. The study reveals that base pairing with RNA is not energetically advantageous, but becomes stable only after the entire sequence is recognized.
SourceUniversität Leipzig·JournalNature Structural & Molecular Biology·TypeExperimental study·DateJul 12, 2023
Now, every biologist can use machine learning
BioAutoMATED is an all-in-one AutoML platform designed for biologists, enabling easy analysis and interpretation of biological sequences. The platform uses three existing AutoML tools to generate models that can predict biological functions from sequence information.
SourceWyss Institute for Biologically Inspired Engineering at Harvard·JournalCell Systems·TypeData/statistical analysis·DateJun 21, 2023
New method reveals bacterial reaction to antibiotics in five minutes
A new method called 5PSeq has been developed to quickly assess bacterial response to antibiotics, with potential implications for treating antibiotic-resistant infections. The method measures mRNA translation and decay, revealing how bacteria interact with environmental factors and stressors.
New computational tool identifies novel targets for cancer immunotherapy
Researchers developed a computational platform called IRIS to discover tumor antigens from alternative RNA splicing, expanding cancer immunotherapy targets. Hundreds of predicted TCR targets were found to be presented by human leukocyte antigen molecules.
SourceChildren's Hospital of Philadelphia·JournalProceedings of the National Academy of Sciences·DateMay 17, 2023
Single-cell transcriptomic analysis uncovers diverse and dynamic senescent cell populations
Researchers have identified distinct senescence subpopulations and dynamic changes in the transcriptome of human cells undergoing senescence. The study provides new understanding of the heterogeneous nature of senescence and its impact on aging diseases.
Improving wheat regeneration with novel DOF family transcription factors
Researchers have identified two novel DOF family transcription factors that enhance wheat regeneration and genetic transformation. These findings provide new insights into the transcriptional regulatory network involved in boosting wheat regeneration, offering opportunities for improving crop improvement.
SourceChinese Academy of Sciences Headquarters·JournalNature Plants·TypeExperimental study·DateMay 9, 2023
New RNA-seq, metabolomics protocol offers more efficient extraction that maintains data integrity
Researchers have developed a new extraction protocol for RNA-seq and metabolomic analysis, reducing variation and improving efficiency. The protocol preserves data fidelity and maximizes use of precious biospecimens, enabling the study of metabolic phenotypes in a unique way.
Hidden RNA repair mechanism discovered in humans
Researchers have identified a new human RNA ligase protein that plays a protective role against cellular stress and oxidative damage. The enzyme, C12orf29, links the ends of RNA strands in three characteristic steps and protects cells from menadione-induced oxidative stress.
First-in-Canada clinical RNA sequencing platform may improve rare disease diagnostics in pediatrics
A new clinical RNA sequencing platform at SickKids is helping researchers understand complex genetic conditions and improve diagnosis for patients with rare diseases. The platform has been validated to be used in the clinical space, providing valuable diagnostic information that complements genome sequencing.
Knockout of AMD-associated gene POLDIP2 reduces mitochondrial superoxide in retinal cells
Researchers generated a POLDIP2 knockout ARPE-19 cell line and found reduced mitochondrial superoxide levels, consistent with upregulated SOD2. The study demonstrates a potential role of POLDIP2 in regulating oxidative stress in AMD.
tRNA biomarkers for cancer diagnosis and prognosis enabled by new method
Researchers have developed a new method called Nano-tRNAseq to measure both the abundance and modification of tRNA molecules in a single step. This technology has significant advantages over conventional techniques, offering rapid, cost-effective, and high-throughput analysis with single-molecule resolution.
SourceCenter for Genomic Regulation·JournalNature Biotechnology·TypeExperimental study·DateApr 6, 2023
The ‘long read’ for cancer
Researchers used long-read sequencing to identify novel mutational patterns and complex genomic rearrangements in cancer genomes, including those associated with liposarcoma. This approach offers a more comprehensive understanding of DNA mutations and their impact on cell function.
Lipid nanoparticles highly effective in gene therapy
Gene therapy using CRISPR-Cas9 lipid nanoparticles has been shown to be highly effective in reducing target protein expression in mice. The new delivery system increases the efficiency of in vivo gene therapy, paving the way for safe and effective treatment.
SourceHokkaido University·JournalJournal of Controlled Release·TypeExperimental study·DateMar 1, 2023
RNA modification ‘pivotal’ for protein linked to neurodegeneration in ALS
A study found that RNA methylation plays a pivotal role in TDP-43-related neurodegeneration in ALS. The researchers observed highly abundant RNA methylation in the end-stage tissues of patients with ALS. This discovery opens up new avenues for research into the disease, which is linked to environmental exposure.
SourceMichigan Medicine - University of Michigan·JournalMolecular Cell·TypeExperimental study·DateFeb 27, 2023
Discovery of a circovirus involved in human hepatitis
Researchers identified HCirV-1 in a patient with unexplained chronic hepatitis, demonstrating its role in liver damage. After treatment, the patient's liver enzymes returned to normal levels, indicating the end of hepatic cytolysis.
How Huntington’s disease affects different neurons
Researchers identify vulnerable cell populations in the striatum, which contributes to loss of motor control and early mood disorders. Damage to striosomes may be responsible for mood disorders, while degeneration of matrix neurons likely contributes to motor decline.
CHOP researchers develop new, more accurate computational tool for long-read RNA sequencing
Researchers at Children's Hospital of Philadelphia developed ESPRESSO, a new computational tool that can accurately discover and quantify RNA molecules from error-prone long-read RNA sequencing data. This will enable better diagnosis of rare genetic diseases and discovery of potential therapeutic targets in cancer.
Poly(A)-tail-mediated remodeling of maternal mRNA controls start of life
Researchers discovered poly(A)-tail-mediated remodeling of maternal mRNA during the oocyte-to-embryo transition, involving partial degradation and re-polyadenylation. This process is essential for human embryo development, as blocked re-polyadenylation leads to failed first embryo cleavage.
SourceChinese Academy of Sciences Headquarters·JournalNature Structural & Molecular Biology·TypeMeta-analysis·DateJan 18, 2023
Researchers produce first-ever toolkit for RNA sequencing analysis using a ‘pantranscriptome’
A new toolkit enables researchers to map individual RNA data to a more diverse 'pantranscriptome', addressing reference bias and increasing the accuracy of gene expression mapping. This approach builds on pangenomics, allowing for the comparison of an individual's genome to genetically diverse cohorts of reference sequences.
Immune system B-cells can help predict HER2-positive breast cancer treatment response
A new study found that measuring activation of immune-system B cells may be better than measuring either T-cell activation or total number of immune cells in and around a tumor. The findings suggest that six signatures of immune cell gene activation from B cells were associated with higher elimination rates and better survival outcomes.
SourceUNC Lineberger Comprehensive Cancer Center·JournalJAMA Oncology·TypeRandomized controlled/clinical trial·DateJan 5, 2023
Study discovers triple immunotherapy combination as possible treatment for pancreatic cancer
Researchers at MD Anderson Cancer Center have discovered a novel triple immunotherapy combination targeting checkpoints in T cells and myeloid suppressor cells, improving anti-tumor responses and survival rates in preclinical models of pancreatic cancer. The study found that neutralizing specific immunosuppressive mechanisms dramatical...
Aging | Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence
A study published in Aging-US reveals changes in gene expression associated with age-related muscle loss and frailty. Researchers identified unique cellular subpopulations in aged and sarcopenic skeletal muscle, which may facilitate the development of new treatments for age-related frailty.
New immune culprit discovered in Alzheimer’s disease
A Northwestern University study found that as people age, their cerebrospinal fluid immune system becomes dysregulated, leading to cognitive impairment and neurodegeneration. The discovery provides a new clue to the process of neurodegeneration and may potentially be used to treat inflammation of the brain.
Meta-analysis reveals how crowds may change gene expression in some insects
A meta-analysis of transcriptome data from aphids and locusts reveals that DNA replication, metabolic processes, and the mitotic cell cycle are enriched in response to crowded conditions. The study also identifies discrepancies with previous research findings, suggesting alternative explanations for gene expression patterns.
Oncotarget | Treasures from trash in cancer research
A new study explores the value of 'trash data' from cancer genome sequencing, identifying new strategies to uncover previously unexplored information. The researchers found that genomic and transcriptomic data contain relevant information that can help elucidate carcinogenesis and discover putative biomarkers with clinical applications.
Key to the erroneous activation of the immune system
Researchers investigated Aicardi-Goutières syndrome and found that viral RNA recognition drives uncontrolled interferon production. The immune system mistakenly attacks healthy cells due to the failure of safety mechanisms to distinguish between viral and host genetic material.
Unique genetic signature found by research in different types of cancer
A research study led by Mabel Vidal identified a common genetic signature among infiltrating T cells of different cancer types. The study used AI to analyze data from public repositories and confirmed the results through proteomics experiments.
SourceMELISA Institute·JournalInternational Journal of Molecular Sciences·TypeComputational simulation/modeling·DateNov 2, 2022
RNA-sensing system controls protein expression in cells based on specific cell states
A new technology called RADARS allows scientists to detect and target specific cell types and states, opening up potential applications in diagnostics and therapeutics. The platform detects a particular RNA sequence in live cells and produces a protein of interest in response.
SourceBroad Institute of MIT and Harvard·JournalNature Biotechnology·TypeExperimental study·DateOct 27, 2022
Climate change could make High Arctic fertile ground for emerging pandemics: uOttawa study
A novel genetic analysis by University of Ottawa researchers reveals that climate change could lead to an increased risk of viral spillover in the High Arctic. This increased risk may result in new viruses infecting previously uninfected hosts, potentially leading to emerging pandemics.
SourceUniversity of Ottawa·JournalProceedings of the Royal Society B Biological Sciences·TypeComputational simulation/modeling·DateOct 19, 2022
Gene activity in a test tube
Researchers at the University of Würzburg have developed a new method called INRI-seq, which allows for detailed analysis of gene activity in individual cells. This technique can help identify new targets for targeted therapies and improve our understanding of protein synthesis.
Turning the spotlight on cells in tissues so RNA can tell their story
Researchers have developed a new DNA nanotechnology-driven method called Light-Seq that enables the analysis of gene expression patterns in hard-to-access cells within intact tissues. This approach overcomes limitations of existing spatial transcriptomics methods, allowing for deeper understanding of disease mechanisms and biology.
SourceWyss Institute for Biologically Inspired Engineering at Harvard·JournalNature Methods·TypeExperimental study·DateOct 10, 2022
Scientists chart how exercise affects the body
A new study in mice has mapped the cells, genes, and pathways that respond to exercise and diet, offering potential targets for drugs that mimic exercise's benefits. Exercise was found to push these systems in the opposite direction of high-fat diets.
Finding an RNA target and tool to fight premature aging
Scientists have identified long interspersed nuclear element-1 (L1) RNA as a promising new target for treating progeroid syndromes. Increased L1 RNA expression in cells from patients with these disorders led to deactivation of an enzyme, causing cell aging.
SourceKing Abdullah University of Science & Technology (KAUST)·JournalScience Translational Medicine·DateOct 4, 2022
Mayo Clinic researchers identify drug resistance factors for advanced prostate cancer
Mayo Clinic researchers identified critical genomic changes associated with abiraterone acetate/prednisone resistance in advanced prostate cancer. An 11-gene drug panel predicted a worse prognosis for a subset of patients, and whole-exome sequencing data revealed mechanisms of acquired resistance.
Tracking a network of 100,000 mutants
Researchers at OIST Graduate University have experimentally shown the concept of a neutral network, vital for increasing diversity, by designing and testing over 120,000 RNA variants. They found a large number of accessible pathways between two variants, challenging previous theoretical predictions.
SourceOkinawa Institute of Science and Technology (OIST) Graduate University·JournalNature Communications·TypeExperimental study·DateSep 20, 2022
COVID-19 mutations accelerated by virus-fighting enzyme in human cells, according to new research
Researchers at USC discovered that the COVID-19 virus uses a human enzyme to accelerate its mutations, allowing it to evade vaccines and spread quickly. By understanding this mechanism, scientists can predict new variants and develop more effective vaccines.
SourceUniversity of Southern California·JournalScientific Reports·TypeExperimental study·DateSep 13, 2022
Keck Foundation awards $1.2M to KU, University of Chicago to transform understanding of RNA splicing
KU and UChicago researchers are working on identifying human gene sequences that respond to drug therapies through RNA splicing. They hope to overcome the 'undruggable proteome' problem, where approximately 70% of proteins cannot be targeted by drugs.
Whole blood RNA profiling of severe COVID-19 cases
A study by Osaka University researchers comprehensively analyzed mRNA and microRNA expression patterns in the blood of patients with severe COVID-19, revealing specific mRNAs and microRNAs associated with the immune response pathway. The findings suggest that interferon-β plays a crucial role in COVID-19 severity.
SourceOsaka University·JournalMolecular Therapy — Nucleic Acids·TypeObservational study·DateAug 24, 2022
Reading RNA modifications more precisely
Scientists at Kyoto University developed two methods to identify RNA modifications impacting gene regulation and disease. Their approach uses probability algorithms with high-throughput sequencing technology, distinguishing pseudouridine substitutions from other base changes.
Live-seq: sequencing a cell without killing it
Scientists have developed Live-seq, an innovative approach that keeps cells alive during RNA extraction for further study. This technique uses FluidFM to manipulate tiny volumes of fluids in a sample under the microscope, allowing for the insertion and extraction of mRNA from single cells without killing them.
Genetic findings offer opportunity for personalized heart failure treatment
Researchers discovered distinct genetic mutations in heart failure patients, identifying potential targets for personalized treatment and improving patient care. The study's findings hold enormous potential for rethinking how to treat heart failure by understanding its root causes and the mutations that lead to changes in heart function.
Hallmark cancer gene regulates RNA ‘dark matter’
Researchers at UC Santa Cruz discovered that a key genetic mutation in the KRAS gene alters RNA 'dark matter', leading to the release of previously unknown RNA biomarkers. These biomarkers could be detected in the blood through a liquid biopsy, offering a promising step in cancer early detection.
Tadpoles undergo surprising number of vision changes when becoming frogs
Researchers found that the eyes of tadpoles undergo significant changes in gene expression and photoreceptor cell sensitivity to adapt to life on land. The study reveals that 42% of genes involved in vision changed between tadpole and juvenile frog stages, enabling better adaptation to a bluer light environment.
Novel, sensitive, and robust single-cell RNA sequencing technique outperforms competition
A novel single-cell RNA sequencing technique, TAS-Seq, has been developed to provide higher-precision data than current methods. The new method detects more genes and identifies highly variable genes, making it a sensitive high-throughput scRNA method.
SourceTokyo University of Science·JournalCommunications Biology·TypeExperimental study·DateJun 27, 2022
Can a parasitic wasp save your fruit crops?
Researchers at the University of Tsukuba have created a genetic toolkit to investigate the molecular mechanisms of a parasitic wasp, Asobara japonica. By analyzing its genome and using RNA interference, they identified key genes involved in venom production and found that suppressing these genes can lead to phenotypic changes.
How protists crack the walls of algae
A team of researchers from the University of Cologne identified a possible key enzyme that enables algae-eating protists to dissolve algal cell walls. The study, published in Current Biology, reveals new insights into the molecular toolkit used by these organisms to interact with their prey.
New database to "SpUR" on cancer research
A new interactive web portal, SpUR, catalogues over 1,000 splicing events found in cancers, highlighting their role in tumor development and progression. The database provides a platform for researchers to study RNA dysregulations in cancer and develop RNA-based anti-cancer drugs.
SourceKing Abdullah University of Science & Technology (KAUST)·JournalNature Cell Biology·DateMay 26, 2022
New gene identified in arrhythmogenic cardiomyopathy
Researchers discovered a new gene, ZBTB11, that drives heart muscle cell degeneration in arrhythmogenic cardiomyopathy. The gene's activity induces damage to neighboring heart cells, a key process in the disease.
How fat could help in tailoring cancer treatment plans
A study by Osaka University found that fat accumulation in liver tumors can predict patient response to immunotherapy. The researchers identified a unique tumor immune microenvironment, known as steatotic HCC, which is associated with high infiltration of immune cells but exhaustion of nearby T cells.
Single cell RNA sequencing uncovers new mechanisms of heart disease
Researchers applied scRNA-seq to study hypertrophic cardiomyopathy, identifying novel regulatory interactions and genes driving disease-related swelling. This knowledge can be used to develop new drugs that target underlying causes, reducing disease progression.
New tool integrates microbiome and host genetic sequencing analysis
Researchers developed a new software tool, called 'meta-transcriptome detector,' that integrates genetic sequencing analysis of hosts and their microbiomes. The tool enables analysis of gene expression activity in both microbes and hosts simultaneously, allowing researchers to spot relationships between them.
Revealing the individual immune cells inside the plaque that causes life-threatening heart attacks
A study by Kobe University researchers has illuminated the characteristics of Myeloid immune cells in coronary plaque, a major contributor to acute coronary syndrome. The findings suggest that macrophages and monocytes accumulate in the plaques of patients with acute coronary syndrome, leading to increased inflammation.
Rethinking congenital hydrocephalus
A new study suggests that up to 1 in 4 cases of congenital hydrocephalus may be linked to genetic mutations affecting neural stem cell growth, leading to underdeveloped brains and enlarged ventricles. This paradigm shift could lead to targeted therapies such as gene editing or drugs to optimize neurodevelopment.
A key brain region for substance use disorders now has a searchable atlas of distinct cell populations
Scientists have created a searchable atlas of distinct cell populations in the ventral tegmental area, a key brain region involved in reward-directed behavior and substance use disorders. The study identified 16 cell populations, including classic dopaminergic neurons, glutamatergic neurons, and GABAergic neurons.
SourceUniversity of Alabama at Birmingham·JournalCell Reports·TypeExperimental study·DateApr 15, 2022
Ocean water samples yield treasure trove of RNA virus data
An international team of researchers has identified 5,500 new RNA virus species that represent all five known RNA virus phyla. The study suggests there are at least five new RNA virus phyla needed to capture them and highlights the importance of marine microbes in ocean adaptation to climate change.
Study describes new method for probing the bewildering diversity of the microbiom
A new technique called Operational Genomic Units (OGU) allows for improved resolution and simplicity in analyzing microbiome samples. By using individual genomes as basic units, researchers can pinpoint biologically relevant characteristics such as age and sex with greater accuracy.
Computational approach enables spatial mapping of single-cell data within tissues
Researchers developed a computational approach called CellTrek to combine parallel gene-expression profiling methods, creating spatial maps at single-cell resolution. The tool provides detailed information on individual cell types' location within tissues, enabling unique biological insights.
Researchers put a spotlight on aggressive cancer cells
Researchers Miao-Ping Chien and Daan Brinks have developed a method to detect aggressive cancer cells, which can help identify the genetic profile of individual cells and develop targeted medicines. This breakthrough has the potential to improve treatment outcomes for patients with cancer.
Revealing the function of Mkx in periodontal ligament homeostasis
A study published at Tokyo Medical and Dental University found that Mkx regulates cellular heterogeneity and gene expression in the PDL, revealing its importance in homeostasis. The results showed that a deficiency of Mkx promotes ossification in the PDL and suggests a compensatory mechanism via Scx to maintain homeostasis.
SourceTokyo Medical and Dental University·JournalFrontiers in Cell and Developmental Biology·DateFeb 24, 2022