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In a #WhyIScience Q&A, computer scientist and machine learning expert Juan Caicedo speaks about what excites him in machine learning, the challenges of putting together and leading a new team remotely during a pandemic, how he navigates imposter syndrome, and his passion for diversity and equity in the research community:
“Thirty-six years ago, as a genetics fellow, I was assigned a patient with progeria — a disease about which almost nothing was known. And I thought, ‘Boy, we really ought to figure this out — what is the cause and what could we do for it — because I didn't have a whole lot to offer my young patient.’” Francis Collins, director of the National Institutes of Health (NIH), tells this story to set the stage for describing a new study on treating progeria in an animal model. A team from the Broad Institute, the National Institutes of Health (NIH), and Vanderbilt University Medical Center has now used base editing, a recently developed form of gene editing, to rescue disease symptoms and lifespan in mice that have Hutchinson-Gilford progeria syndrome.
Few genome sequencing methods allow scientists to see how DNA is packaged within its cellular home. A new in situ sequencing method by Broad, McGovern Institute for Brain Research, and Harvard SCRB scientists lets researchers study sequence and cellular organization of the genome all at once.
The nervous and immune systems have long been thought to be separate entities in the body, but new research has uncovered a direct cellular interaction between the two. Scientists have found that pain-sensing neurons surround lymph nodes in mice, and modulate the activity of these small organs, which are key parts of the immune system. The new research, published in Cell, reveals the cells that mediate the crosstalk between the nervous and immune systems. It also paves the way for more research on how the nervous system regulates the immune response, for example, during an infection.
The vast majority of cancer deaths are attributed to metastasis — the spread of tumors from one organ to another. A team led by Broad researchers identified genetic and clinical factors associated with metastasis for 500 human cancer cell lines, and pulled those features together to create the Metastasis Map, or MetMap, the first ever map of how different cancers spread.
A three-month stint as a research assistant studying microbes in Antarctica was the perfect combination of swashbuckling adventure and science for Grace Tiao. It was her first job out of college, and also her first exposure to computational biology—a field where she would come to dedicate the next decade of her career. She’s now an associate director for computational genomics at Broad. Learn more about her story and career path in a #WhyIScience Q&A.
The rates at which mutations in important genes like EGFR and KRAS arise in lung cancer vary in different populations. A new study of lung cancer in patients from Latin America suggests that ancestry and germline genetics may play a bigger role than environment.
Perturb-Seq combines CRISPR with single cell RNA sequencing into a powerful tool that can genetically perturb cells and measure the effects on the activity of other genes. Researchers have now used the technology to learn the function of 35 autism risk genes in the brain of a developing animal.
The first ever study to sequence single cells infected with a BSL-4 level pathogen has revealed new details of how the Ebola virus alters the host immune response for its own benefit during infection. Researchers adapted a portable, low-cost single cell RNA sequencing approach called Seq-Well for use in a BSL-4 lab, and identified antiviral defence genes that the virus suppresses as well as pro-viral genes the virus activates. The findings could potentially help researchers find more precise ways to target the immune system as a therapeutic strategy for infections.
Disease prediction is complicated. In a new Nature Communications study, researchers from the Broad, IBM Research, and Color find that a person?s genetic background influences the risk of familial hypercholesterolemia, breast cancer, and colorectal cancer in individuals carrying high-risk single-gene variants that predispose them to these diseases. The findings help explain why some genetically predisposed individuals do not develop disease, and suggest ways to more accurately interpret patients? genetic risk of disease?eventually, guiding more informed genetic counseling in clinical practice.
