Precise DNA cleavage using CRISPR-SpRYgests
Precise DNA cleavage using CRISPR-SpRYgests
The ability to precisely cleave DNA at specifiable bases is critical for many applications in life science research, including for molecular biology and cloning, genome editing, DNA sequencing, protein engineering, and a wide variety of other methods. Until now, no enzyme or method existed that permitted efficient cleavage of any position of a DNA substrate. Current workflows typically rely on restriction enzymes (REs) that are beholden to constraining 6-8 bp binding motifs, and yet despite a diverse catalog of REs, collectively they can only target a small fraction of all DNA sequences. To solve this key challenge, CGM Investigator Ben Kleinstiver and colleagues optimized our recently engineered RNA-programmed PAMless Cas9 enzyme, named SpRY, as a highly precise DNA cleavage tool. The use of SpRY for DNA digests (SpRYgests) enables precise manipulation of nucleic acids in ways not possible with REs or other nucleases. The applications of SpRYgests are vast and hold promise to expedite and improve a range of biomedical research endeavors.
A Genomic Risk Score Identifies Individuals at High Risk for Intracerebral Hemorrhage
A Genomic Risk Score Identifies Individuals at High Risk for Intracerebral Hemorrhage
Intracerebral hemorrhage (ICH) is the most devastating type of stroke, being responsible for almost 50% of stroke-related morbidity and mortality. Given its severity, primary and secondary prevention is of critical importance. In this study, the authors, led by CGM Investigators Chris Anderson and Jonathan Rosand, developed and validated an ICH meta-genomic risk score (metaGRS) of 2.6 million variants, combining GWAS data from 21 ICH risk factors and related traits and tested its ability to predict ICH risk in relation to traditional clinical ICH predictors. ICH metaGRS was associated with 31% higher odds of ICH per standard deviation, and identified individuals with almost 5-fold higher odds of ICH in the top score percentile. In models incorporating both the metaGRS as well as a collection of traditional clinical predictors, the metaGRS showed comparable predictive performance to the most potent clinical predictor, hypertension, and, importantly, it improved the predictive performance on top of established risk factors. In an external validation in the UK Biobank, the metaGRS was associated with higher risk of incident ICH both in a relatively high-risk population of antithrombotic medications users, as well as among a relatively low-risk population with a good control of vascular risk factors and no use of anticoagulants. Overall, the results demonstrate that the incorporation of genomic information in clinical prediction models for ICH could enhance predictive performance and lay the groundwork for future analyses in larger genetic datasets for ICH to optimally combine genomic information to maximize predictive benefit.
Read more in Stroke
Oxygen restriction’s effects on lifespan
Oxygen restriction’s effects on lifespan
Oxygen restriction has been linked to longer lifespan in some organisms, but its effects on aging in mammals have been unclear. A team led by CGM faculty member, Vamsi Mootha, and Robert Rogers explored the effects of oxygen restriction on mammalian lifespan using a mouse model of accelerated aging. The researchers discovered that the mice living in an oxygen-restricted environment lived about 50 percent longer compared to those exposed to standard levels of oxygen, with delayed onset of aging-associated neurological deficits.
Read more in news releases from PLOS and Harvard Medical School, and coverage in The Daily Beast and Medical News Today.
Development of an oral treatment that rescues gait ataxia and retinal degeneration in a phenotypic mouse model of familial dysautonomia.
Development of an oral treatment that rescues gait ataxia and retinal degeneration in a phenotypic mouse model of familial dysautonomia.
Familial dysautonomia (FD) is a rare neurodegenerative disease caused by a mutation in the gene encoding for the Elongator complex protein 1 (ELP1). This mutation leads to a reduction of ELP1 protein, mainly in the nervous system. Due to the crucial function of ELP1 in neuronal development and survival, FD patients exhibit many neurological symptoms, including retinal degeneration and inability to coordinate movements. In our recently published study, the Slaugenhaupt and Morini lab describes the optimization of an oral treatment for FD that restores the expression of functional ELP1 protein in every tissue, including brain, and rescues retinal degeneration and motor coordination in a mouse model of FD.
Association of Soluble ST2 With Functional Outcome, Perihematomal Edema, and Immune Response After Intraparenchymal Hemorrhage
Association of Soluble ST2 With Functional Outcome, Perihematomal Edema, and Immune Response After Intraparenchymal Hemorrhage
This manuscript builds on the Kimberly Lab’s work that highlights the role of the interleukin-33/ST2 pathway and its link to post-stroke inflammation and brain edema. The lab had previously shown that this inflammatory signaling cascade is associated with brain edema and activation of innate immunity after ischemic stroke and subarachnoid hemorrhage. This paper extends previous work to show a similarly damaging activation after intracerebral hemorrhage. Collectively, this work highlights that modulation of the IL-33/ST2 pathway is a candidate target to reduce the severity of edema and inflammation after all major forms of acute brain injury.
Read more in Neurology
Uridine and RNA as energy
Uridine and RNA as energy
To identify genes and pathways that cells can use to survive when glucose — an important source of energy and carbon — is limited, Vamsi Mootha, and colleagues performed genome-wide genetic screens and a PRISM growth assay. They found that cells ranging from healthy immune cells to cancer cells can use uridine, a component of RNA, as an energy source when glucose is unavailable. Targeting the biochemical pathway that cells use to break down uridine-derived sugar could help treat cancers and metabolic disorders and tune the immune response.
Read more in Nature Metabolism, a Broad news story, and a tweetorial by Alexis Jourdain.
Clonal haematopoiesis and risk of chronic liver disease.
Clonal haematopoiesis and risk of chronic liver disease.
Through advances in population-based genomic sequencing an analysis, the Natarajan lab and others showed that ‘clonal hematopoiesis of indeterminate potential’ (CHIP) is a surprisingly common feature as we age. They also showed that CHIP plays a role in coronary artery disease, the leading contributor to death in the US and now globally. As inflammation appeared to be a principal driver, the Natarajan lab has since then attempted to understand whether CHIP plays a role in other conditions where inflammation has been invoked as a key driver. This study focused on chronic liver disease because, which has become increasingly common with the rising prevalence of obesity and metabolic syndrome. However, therapeutic options for chronic liver disease have remained limited for decades except for hepatitis C. Fatty liver disease is increasingly recognized but the reasons by inflammation and downstream liver disease occur remain limited. They therefore hypothesized that CHIP could play a role. It was found that CHIP offered to confer a relatively large risk for chronic liver disease, sometimes larger than currently recognized risk factors. And causal inference approaches, such as Mendelian randomization, supported a potential causal relationship. Liver MRIs and liver biopsies were consistent with greater steatohepatitis and not greater steatosis. Murine models similarly showed greater steatohepatitis without greater steatosis, and also greater fibrosis when followed for longer periods of time. Genetic deficiency of the NLRP3 inflammasome appeared to ameliorate this phenotype in the mice. This inflammatory pathway has also been invoked in CHIP-associated coronary artery disease. The relationship between CHIP and liver disease was previously unknown. These observations highlight a new potential precision medicine paradigm for chronic liver disease prevention. The findings support the scientific premise that, particularly for TET2 CHIP, inhibition of the NLRP3 inflammasome may reduce the risk of chronic liver disease.
Read more in Nature.
Read more in Nature.
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies
Meta-analysis of whole genome sequencing/whole exome sequencing (WGS/WES) studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare variants associated with complex phenotypes. Existing rare variant meta-analysis approaches are not scalable to biobank-scale WGS data. In this work in Nature Genetics by CGM Investigator Pradeep Natarajan and colleagues, a new, powerful and resource-efficient rare variant meta-analysis framework for large-scale WGS/WES studies is developed, which they name MetaSTAAR. The group puts MetaSTAAR to work by ananlyzing four lipid traits in 30,138 ancestrally diverse samples from 14 studies of the Trans Omics for Precision Medicine (TOPMed) Program, proving that it performs comparable to using pooled data, and in the process identifying several conditionally significant rare variant associations with lipid traits. MetaSTAAR is scalable to biobank-scale cohorts and lays the groundwork for very large (100K+) sample size analyses through TOPMed WGS data, UK Biobank WES data, and additional resources as they come online.
Read more in Nature Genetics.
Mono- and biallelic variant effects on disease at biobank scale
Mono- and biallelic variant effects on disease at biobank scale
Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance. In this work published in Nature by CGM Investigators Mark Daly, Aarno Palotie, Heidi Rehm, and colleagues, the richness of FinnGen was leveraged to examine homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. They found associations for homozygous genotypes across a broad spectrum of phenotypes, including recessive disease associations that would have been missed by the additive model that is typically used in genome-wide association studies. Importantly, the group also found variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects, and presumed benign variants with disease effects. This work powerfully illuminates how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.
Read more in Nature
The Center for Genomic Medicine (CGM) comprises one of the largest and most vibrant hubs of genomic medicine research in the world. The CGM includes 46 faculty collaborating to define the ‘genomic medicine cycle’ – which envisages a genomics community seeking to advance research from basic genomics research to ultimately using genome information for diagnostics and targeted therapeutics. All of our investigators are faculty at Harvard Medical School, and many members of our community are also investigators at the Broad Institute of Harvard and MIT.
