From novel laboratory research that enables scientists to define pancreatic cancer cells better to innovative clinical approaches that help patients recover from surgery more quickly, Dana-Farber Brigham Cancer Center (DFBCC) is steadily advancing the diagnosis and management of pancreatic cancers. Reversible Fixation Overcomes Challenges of Single-Cell Profiling Sahar Nissim, MD, PhD, of the Brigham’s Division of Genetics and Division of Gastroenterology, Hepatology and Endoscopy is an award-winning physician-scientist. His team studies the earliest events that cause a no ..read more

Understanding the distinct gene sets and subpopulations within heterogeneous cell populations is essential for unraveling the complexities of biological systems. Recent advancements in computational pipelines have revolutionized the analysis of single-cell RNA and ATAC sequencing data, providing researchers with powerful tools to dissect cellular heterogeneity. Researchers at Duke University have developed SifiNet, is a robust and accurate computational pipeline designed to identify gene sets, extract cellular subpopulations, and elucidate intrinsic relationships among these subpopulations. W ..read more

For medical diagnostics and biomarker discovery, the ability to analyze gene expression from peripheral blood RNA holds immense potential. This technique offers valuable insights into systemic changes in gene expression and immune responses, aiding in the diagnosis and monitoring of various diseases. However, traditional methods for extracting RNA from frozen blood samples collected in EDTA tubes have posed significant challenges due to the degradation of RNA quality. In a new study, researchers from the University of Sydney have unveiled a novel protocol designed to overcome these obstacles ..read more

New research led by Qingyun Liu, PhD, assistant professor in the UNC Department of Genetics, has uncovered a genetic feature known as “transcriptional plasticity,” which plays a pivotal role in governing the transcriptional response of Mycobacteria to stressful conditions. Bacterial cells must swiftly modulate the expression of their genes to cope with abrupt changes in the external environment. However, the extent to which certain genes can alter their expression in response to environmental shifts, as opposed to maintaining stable expression levels, has long puzzled scientists. Understandin ..read more

The SARS-CoV-2 virus that causes COVID has the unsettling ability of often generating variants of itself. Other viruses also mutate, but as SARS-CoV-2 quickly spread throughout the entire human population during the pandemic, killing millions, the virus’ dynamic evolution posed a serious problem: it repeatedly challenged our bodies’ immune response fighting the virus and hindered the process of getting updated vaccines ready. Understanding the genetic mechanism fueling SARS-CoV-2’s ability to generate variants can go a long way in keeping COVID at bay. In this study published in Nature M ..read more

In genomics, understanding how genes are expressed in different cell types within their spatial context is a fundamental goal. With the advent of SPADE (SPAtial DEconvolution), a revolutionary method, researchers at the University of Arizona now have a powerful tool to unravel these spatial patterns and gain deeper insights into complex biological systems. SPADE takes a multi-faceted approach by integrating spatial information into the analysis of cell type composition. Leveraging single-cell RNA sequencing, spatial transcriptomics, and histological data, SPADE accurately estimates the propor ..read more

Understanding the function of rare non-coding variants has long been a daunting task. These elusive variants, residing in regions of the genome that do not code for proteins, play a crucial role in regulating gene expression post-transcriptionally. Now, a groundbreaking study by researchers at the University of California, Los Angeles utilizing a screening method called MapUTR has shed light on the function of these rare variants, particularly those found in the 3′ untranslated regions (UTRs) of messenger RNA (mRNA). MapUTR captures functional 3′ UTR variants in known functional motifs a&nb ..read more

Unraveling the mysteries of RNA has always been a challenging task, but recent advancements in technology have opened up new possibilities, allowing scientists to delve deeper into the secrets of RNA molecules. Direct RNA sequencing is a cutting-edge technique that offers a unique advantage: the ability to simultaneously identify both the canonical bases and epitranscriptomic modifications present in each individual RNA molecule. This means that researchers can now explore not only the genetic code encoded in RNA but also the chemical modifications that adorn it. However, despite the potentia ..read more

In a proof-of-concept study, researchers at the National Institutes of Health (NIH) have developed an artificial intelligence (AI) tool that uses data from individual cells inside tumors to predict whether a person’s cancer will respond to a specific drug. Researchers at the National Cancer Institute (NCI), part of NIH, published their work on April 18, 2024, in Nature Cancer, and suggest that such single-cell RNA sequencing data could one day be used to help doctors more precisely match cancer patients with drugs that will be effective for their cancer. Current approaches to matching pa ..read more

The technology used to sequence SARS-CoV-2 at record speed early in the COVID-19 pandemic has been successfully tested as a technique to monitor arboviruses and diseases transmitted mainly by mosquitoes. In an article published in the journal Microbiology Society, researchers affiliated with Pasteur Institute in São Paulo, Brazil, and the University of São Paulo (USP), in collaboration with colleagues at the University of Birmingham in the United Kingdom, describe the use of the technology to sequence viral RNA and DNA from blood-engorged mosquitoes collected in São P ..read more