Cas9 conjugates, face mask models, pruning prion levels, and more
By Broad Communications
Credit: Erik Jacobs
Welcome to the August 14, 2020 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.
Souped-up Cas9 makes precise edits
Postdoctoral fellow Donghyun Lim, Chemical Biology and Therapeutics Science Program associate member Amit Choudhary, and colleagues have developed a way to fuse a wide variety of molecules to specific sites in Cas9's terminal and internal regions by using a short oligonucleotide handle ‘adaptor’ as an anchor. Using this platform, the researchers hybridized long single-stranded oligonucleotide donors (ssODNs) to Cas9, and showed that Cas9:ssODN conjugates could make precise edits at multiple genomic sites and in multiple cell types. The team also engineered insulin-producing beta cells to secrete an immunomodulatory protein, without incorporating any sequences other than that of the secreted molecule. Read more in Nature Communications, a Choudhary lab tweetorial, and a blog post on the Nature Research bioengineering community page.
Genetic variants in voltage-gated sodium and calcium channels are associated with disease, but experiments to determine the variants’ functional effects are laborious and narrowly focused. A team led by postdoctoral scholar Henrike Heyne and institute member Mark Daly in the Program in Medical and Population Genetics (MPG) developed a tool to predict the variants’ functional impact using machine learning. They trained their model using missense variants with known or probable effects, and validated it against experimentally tested variants and in patient cohorts. Described in Science Translational Medicine and in Henrike’s tweetorial, their model is a valuable clinical and research tool that can classify variants as loss- or gain-of-function, or as neutral or pathogenic.
Face mask use can mitigate spread of COVID-19
Months after COVID-19's global onset, there is still limited consensus on the use and
distribution of face masks among the general public. Colin Worby from Broad's Infectious Disease and Microbiome Program and Genomic Center for Infectious Diseases and Hsiao-Han Chang (National Tsing Hua University, Taiwan) used epidemic models to examine face masks' role in mitigating the spread of COVID-19 in the general population. They found that prioritized distribution of medical grade masks to vulnerable and infected individuals, together with widespread use of cloth face coverings, provided optimal reductions in morbidity and mortality. Read more in Nature Communication.
Polygenic scoring gets a little more worldly
Polygenic scores could be powerful tools for assessing individuals' genetic risk for several chronic diseases. But because they're largely developed using data from European populations, they have limited utility for people of other ancestries. Using data from UK Biobank and studies in India and Bangladesh, Minxian Wang, MPG associate member Amit Khera, and colleagues have developed and benchmarked a polygenic score for cardiovascular disease for people of South Asian descent. Their scoring system, reported in the Journal of the American College of Cardiology, provides a generalizable framework for developing ancestry-specific polygenic scores. Learn more in a Khera lab tweetorial.
Closer, cellular view of mitochondrial DNA mutations
Cells from patients with mitochondrial diseases often have both mutant and nonmutant mitochondrial DNA (mtDNA) –– a condition called heteroplasmy. In the past, single-cell analysis of heteroplasmy was limited in terms of scope. Caleb Lareau, Leif Ludwig, associate member Vijay Sankaran, core institute member Aviv Regev, and colleagues developed a high-throughput single-cell mitochondrial genomics assay to profile mtDNA mutations in thousands of individual cells that can further help to establish cells' ancestral relationships. In Nature Biotechnology the researchers use this methodology to clonally trace thousands of cancer cells and study cellular population dynamics in human hematopoiesis. Together with Melissa Walker and institute member and Metabolism Program co-director Vamsi Mootha, they further applied the technology to samples from mitochondrial disease patients. In the New England Journal of Medicine they report evidence for selection against pathogenic mtDNA in T cells.
A path forward against prion disease
Lowering prion protein (PrP) expression in the brain is a promising route to treat or prevent the onset of genetic prion disease. In Nucleic Acids Research, a team led by associated scientists Sonia Vallabh and Eric Minikel of the Stanley Center for Psychiatric Research and colleagues describes preclinical studies exploring this strategy — testing an antisense oligonucleotide (ASO) therapy against prion disease in an animal model. The researchers varied the dosing regimen, prion strain, and treatment timepoints, and examined symptomatic, survival, and biomarker readouts. Reducing prion protein levels in the affected animals significantly extended survival, even after symptoms appeared, supporting the potential of PrP-lowering therapeutics. Read more in the journal's press release and a short Twitter thread from Eric.