Articles tagged with Transcriptomics
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...
A new study identifies the mechanism underlying N6-methyladenosine (m6A) RNA modification in mammals, revealing its role in regulating gene expression and promoting genome stability. The study found that DDX21 and METTL3 work together to facilitate m6A deposition co-transcriptionally.
Researchers have discovered a way to enhance the functionality of CD34-negative hematopoietic stem cells, which could lead to better treatments for blood-related diseases. The treated cells showed improved homing abilities and increased gene activity, suggesting they could be more effective as a treatment option.
Researchers have deciphered trabectedin's precise mechanism of action, revealing its ability to induce persistent DNA breaks in cancer cells. This disruption of the transcription-coupled nucleotide excision repair (TC-NER) pathway leads to long-lasting DNA breaks that ultimately kill cancer cells.
A recent study by Pusan National University scientists discovered the crucial role of PKM gene and EPHA2 pathway in HNSCC development. The research highlights the importance of HPV infection status in shaping the tumor microenvironment, enabling precision medicine for targeted treatment.
Scientists used new techniques to analyze gene activities during mouse prenatal development, revealing hundreds of cell types and their formation. The study showed that massive transcriptional changes occur at birth, potentially necessary for survival outside the womb.
A new study unveiled over a thousand protein-protein interactions during early embryonic development, highlighting the role of transcription factors like paired-like homeobox (PRDL) family. This research paves the way for understanding embryonic genome activation and advancing treatments for developmental disorders.
A new study reveals a larger number of transposable elements in the human genome than previously known, shedding light on their potential role in human diseases. The 'genomic time machine' approach allowed researchers to identify degenerate TEs that were missed in previous studies.
A new statistical model developed by UChicago researchers accurately identifies causal genes and variants for a disease. The tool reduces false positives and takes into account multiple genes and variants, leading to the discovery of 35 putative causal genes for LDL cholesterol levels.
Researchers mapped dental pulp and periodontal ligament stem cells' genomes, revealing significant differences in their differentiation potential. The study identifies the genetic composition and mechanisms of differentiation, paving the way for targeted regenerative therapies.
Researchers identified RBM5 as a key regulator of HOXA9 expression in leukemia cells, revealing its dual function in DNA and RNA handling. Removing RBM5 from cells significantly reduced HOXA9 mRNA levels, suggesting its potential as a therapeutic target for acute myeloid leukemia treatment.
Researchers discovered a previously unreported neuron type with vulnerability in Parkinson's disease, shedding light on the complexity of the disease and potential therapeutic targets. The study identified distinct transcriptomic signatures of this neuron type and found reduced RIT2 expression in Parkinson's disease patients.
Researchers created a single-cell atlas of the human placenta, revealing changes in gene expression patterns among cell types. The study found that cells most affected by labor were in chorioamniotic membranes and generated inflammatory signaling.
A multidisciplinary study has elucidated the structure of the machinery responsible for writing much of our 'dark genome', a 98% unknown biological function. This discovery may lead to novel treatments for autoimmune diseases, cancer and neurodegeneration.
The study maps over 32 million cells in the mouse brain, describing their type, location, and molecular information. This atlas paves the way for a greater understanding of the human brain and development of precision therapeutics for mental and neurological disorders.
Spatial transcriptomics reveals cellular heterogeneity, organizational patterns, and molecular communications foundational to tissue structure and dynamics. The technique has enhanced throughput and resolution, offering a synthesized perspective of biological entities across various levels of detail.
A team has successfully assembled the telomere-to-telomere gap-free reference genome of Vaccinium duclouxii, revealing insights into sugar and acid accumulation, anthocyanin biosynthesis and genetic improvement. The study provides a foundation for understanding the evolution of the Vaccinium genus.
Researchers discuss a new approach integrating genomic, epigenomic, transcriptomic, and machine learning methods to identify functional genetic variants and characterize their mode of action in regulating target genes. This method aims to improve understanding of disease etiology and prioritize causative inherited genetic variants.
Researchers created a comprehensive chromatin map to understand gene regulatory networks contributing to differences between pediatric acute lymphoblastic leukemia subtypes. The study identified key transcription factor footprints and chromatin accessibility patterns, which can predict leukemia subtype with 89% accuracy.
Researchers identified a promising dual-purpose target, KDM1A, using AI analysis of transcriptomic data from 16,740 healthy samples and 11,303 tumors. KDM1A was found to significantly extend lifespan in Caenorhabditis elegans and has anti-cancer activities established in preclinical and clinical studies.
Researchers characterized changes in cognitive behaviors, neuronal morphology and gene expression in a tauopathy mouse model. The study found significant decreases in dendritic arborization and synaptic gene upregulation over time.
Researchers discovered BMAL1 is significantly upregulated in senescent cells and modulates the senescence program through AP-1. The study highlights a previously unappreciated role of BMAL1 in regulating cellular senescence and circadian clock components.
Researchers at Memorial Sloan Kettering Cancer Center developed an open-source computational method, Spectra, to analyze single-cell transcriptomic data. The algorithm identifies functionally relevant gene expression programs and is well-suited for studying large patient cohorts.
The study aims to identify genetic and molecular factors associated with susceptibility and progression of liver disease in Hispanics/Latinos. Researchers will collect data from 300 participants, including those with metabolic-associated fatty liver disease and healthy controls.
Researchers analyzed over 2 million cells from 400 postmortem brain samples to identify cellular pathways that could become new drug targets for Alzheimer's treatments. They found impairments in mitochondrial function, synaptic signaling, and protein complexes, as well as disrupted lipid metabolism.
The Keck School of Medicine of USC has launched a five-year, $50.3 million multi-omics study to better understand the causes and prevention of various diseases, including NAFLD, in underrepresented racial and ethnic groups.
Researchers identified four novel receptors potentially linking endometrial cancer with polycystic ovary syndrome, highlighting a major pathway involved in the increased EC risk in PCOS. The PI3K-AKT signaling pathway is consistent with a link between PCOS and EC.
Research finds that immune cells in older adults are similar to those in newborns and children, but less effective at recognizing infected cells. The study, published in Nature Immunology, suggests that tailored vaccines and therapies could be developed for different age groups based on the unique characteristics of killer T cells.
A study published in eBioMedicine identified 9 sets of biomarkers, both metagenomic and transcriptomic, associated with 30-day mortality in patients with severe community-acquired pneumonia. The biomarkers were validated with an accuracy of 85%, significantly higher than existing clinical prediction models.
SARS-CoV-2's nucleocapsid protein (N) uses human body temperature to replicate, binding to RNA motifs at specific spatial folds. The study reveals new functions and potential targets for antiviral drugs.
Researchers have identified a neoplastic fusion transcript RAD51AP1-DYRK4 in luminal B breast cancer, associated with higher ki67 expression and aggressive clinical characteristics. MEK inhibitor trametinib may be effective in blocking the MEK-ERK signaling driven by this fusion.
Researchers at Carnegie Mellon University have developed a new AI method that uses transformer models to analyze images of human cells. The technology, called subcellular spatial transcriptomics cell segmentation (SCS), accurately identifies individual cells and their constituent parts, revealing critical information about cellular org...
A team of scientists at Harvard Medical School has identified six chemical cocktails that can restore cellular aging and rejuvenate human cells. The study builds upon the discovery of Yamanaka factors, which can convert adult cells into induced pluripotent stem cells, raising hopes for treating age-related diseases and injuries. The im...
Researchers at Nara Institute of Science and Technology identified the WOX13 gene as a key negative regulator of shoot regeneration in plants. The study found that WOX13 inhibits a subset of shoot meristem regulators while directly activating cell wall modifier genes involved in cell expansion and differentiation.
A new study by CNIC researchers reveals that low-grade systemic inflammation triggered by subclinical atherosclerosis accelerates epigenetic aging in otherwise healthy young individuals. The study found a strong association between atherosclerosis progression and accelerated biological age, with potential reversibility through lifestyl...
Researchers developed Precious1GPT, a multimodal transformer-based approach for aging clock development and feature importance analysis. The model utilizes methylation and transcriptomic data to predict biological age and identify disease-related genes, providing a pathway for therapeutic drug discovery.
Researchers developed a non-invasive diagnostic method that analyzes sebum for biomarkers of early-onset atopic dermatitis in infants. The study revealed distinct gene expression profiles associated with AD, allowing for early detection and potential treatment monitoring.
Researchers at USC Norris Comprehensive Cancer Center have identified a biomarker, CX3CR1, that can predict which patients with non-small cell lung cancer will respond well to chemoimmunotherapy. Elevated levels of the biomarker in T-cells after six to nine weeks of treatment indicate long-term benefits from the combination therapy.
Coral reef fish larvae undergo significant physiological changes as they transition from open ocean swimming to settling on the reef floor. The study found that gene activity changes play a crucial role in adapting to hypoxic environments at night, allowing the fish to survive and thrive.
SpaceMarkers, a new machine learning software, can identify molecular interactions among distinct cell types in and around tumors. By analyzing spatial transcriptomics data, it reveals genes overexpressed due to cell-to-cell interactions, providing new avenues for understanding cancer progression and treatment responses.
A new computer-modeling system, scDesign3, has been developed to generate realistic synthetic data for analyzing genetic makeup of cells. The system can help researchers evaluate and validate computational methods for tasks such as gene expression analysis and cell trajectory modeling.
Researchers from the ALFA Score Consortium explore how nutrition and physical exercise can positively impact the aging process by modifying epigenetic changes. They find that healthy aging is associated with more tightly condensed chromatin, fewer histone post-translational modifications, and greater regulation by non-coding RNAs.
West Virginia University is leading a $20 million project to elevate neuroscience research, diversify the workforce, and enhance education. The initiative aims to study synaptic plasticity, expand data science education, and promote participation from underrepresented groups.
Researchers developed NetBID2 to analyze multi-omics data and find hidden druggable targets in cancer. The tool successfully identified previously unappreciated roles for genes like MYC and NOTCH1 in adult lung cancer and pediatric leukemia, highlighting its potential for accelerating clinical trials.
Researchers identified over 1,000 genes with age-related methylation changes in human sperm. These changes are associated with increased offspring disease susceptibility for neurodevelopmental disorders. The study found no correlation between paternal BMI or semen quality and age-related methylation changes.
Researchers estimate transcription error rates in human cells and identify genetic and epigenetic factors responsible for inaccuracies. Inaccurate transcription produces truncated or altered proteins, leading to disease.
Researchers found 270 distinct differentially methylated regions (DMRs) in AD brains compared to normal controls, validating their key findings using an independent cohort. The study offers a novel approach to investigating the relationship between DNA methylation and gene/protein expression.
A study published in Genome Biology and Evolution found a core genetic toolkit for reproductive division of labor in rudimentary insect societies. The authors identified common genes associated with fundamental social divisions in bees and wasps, suggesting a universal molecular 'theme' for cooperation across species.
Researchers at RIKEN Center for Integrative Medical Sciences discover genes and individual variations associated with atrial fibrillation, predicting stroke and mortality risk. They also uncover a potential treatment target, ERRg, involved in the pathogenesis of atrial fibrillation.
Researchers found that mice exposed to WTCPM dust exhibit impaired spatial recognition and memory, as well as changes in genes related to immune-inflammatory responses. The study suggests a peripheral-brain immune inflammatory 'cross-talking' mechanism that may increase cognitive decline risk.
Researchers identified 17 clusters of single cells in peripheral blood, showing upregulation of antigen processing and presentation pathways and downregulation of genes involved in ribosome pathways with age. The study also found senescent T cells resistant to apoptosis, potentially targeted for treatment.
A research team at Carnegie Mellon University has developed a machine learning method called SPICEMIX to analyze spatial transcriptomics data. The tool helps identify and understand gene expression patterns in cells, revealing new insights into brain cell types.
A new study has identified distinct patterns of circular RNA expression in human ALS muscle tissue, which display disease-specific gradients and could inform about neuromuscular molecular programs in ALS. The research reveals that specific circRNAs are elevated in ALS muscle biopsies but reduced in spinal cord samples from ALS patients.
UCSF researchers identified glioma's cellular source of recurrent disease, finding cells shift to mesenchymal, radiation-resistant phenotype in response to standard therapy. Paracrine signals from tumor microenvironment drive this transition through AP1 pathway, leading to therapy resistance and tumor recurrence.
A recent study has unveiled how nucleotide excision repair (NER) is controlled at the molecular level, shedding light on its role in cancer treatment. The research revealed that TFIIH uses XPG to stimulate motor activity and locate damaged DNA, licensing XPG nuclease activity to excise it.
A study using spatial single-cell transcriptomics reveals the spatial organization of cancer cells in patient tissues across ages and locations. The research highlights age- and location-dependent differences in tumor biology, suggesting that kids and adults with diffuse midline gliomas may need different treatments.
A new study suggests that a transcriptomic technique can help distinguish between infections and non-infectious causes of complications following knee and hip replacement surgery. The technique uses RNA sequencing to determine which genes are expressed and identifies specific immune cell types involved in the response to infection.
Researchers identify INPP5D as a key player in the inflammation process contributing to Alzheimer's disease, which may offer new potential targets for therapies. The study found that mice with inactivated INPP5D gene had more plaques covered by microglia, suggesting unexpected results when modulating inflammation genes.
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.
Researchers have characterized the functional significance of DDX41 in molecular processes underlying cancer. The study reveals that DDX41 serves crucial functions in transcriptional processes, RNA splicing, and genomic integrity maintenance, which may hold significance in treating hematopoietic malignancies.