Research Roundup: January 17, 2020

An engineered enzyme for redox rebalancing, lncRNA links in cancer, base editors broken for delivery, and more.

Erik Jacobs
Credit: Erik Jacobs

Welcome to the January 17, 2020 installment of Research Roundup, a recurring snapshot of recent studies published by scientists at the Broad Institute and their collaborators.

An engineered enzyme with therapeutic potential

Intracellular redox imbalance can stall cellular metabolism and cell proliferation, contributing to the pathology of rare mitochondrial diseases as well as neurological disease. Intracellular redox imbalance tends to be in equilibrium with extracellular lactate. A research team led by postdoctoral scholar Anupam Patgiri and institute member and Metabolism Program  co-director Vamsi Mootha hypothesized that intracellular redox imbalance can be alleviated by directly targeting and oxidizing extracellular lactate to pyruvate. They engineered LOXCAT, a synthetic fusion of two bacterial enzymes, and tested its effect both in mice and in cultured human cells. Extracellular LOXCAT was able to restore intracellular redox imbalance and holds potential as an injectable therapeutic. Learn more in Nature Biotechnology.

New lncs between RNAs, proteins, and cancer

Long non-coding RNAs (lncRNAs) regulate many physiological processes and diseases. However, their mechanisms and interactions with their protein partners are poorly understood. In Cell Reports, a team led by postdoctoral fellows Karyn Schmidt of Dana-Farber Cancer Institute (DFCI) and Chase Weidmann of University of North Carolina at Chapel Hill, and Cancer Program associate member Carl Novina of DFCI, characterizes the interaction between the lncRNA SLNCR1 and the androgen receptor (AR) protein. Mutating individual nucleotides in SLNCR1 prevents AR binding and inhibits melanoma invasion. Oligonucleotides that block the SLNCR1-AR interaction also inhibit melanoma invasion. According to the authors, the work demonstrates how characterizing lncRNA structure and protein interactions can help identify novel functions and support design of lncRNA-targeting therapeutics.

Fast, highly sensitive ubiquitylome profiling in cells and tissue 

Cancer researchers are enormously interested in the processes cells use to label proteins with a molecular tag called ubiquitin, but need a high-throughput and comprehensive way of profiling proteins' ubiquitin attachment (ubiquitylation) sites using as few cells or as little tissue as possible. In Nature Communications, Namrata Udeshi, Deepak Mani, and institute scientist Steven Carr of the Broad Proteomics Platform, together with colleagues from the Cancer Program, present a new technique called UbiFast. As a proof-of-concept, they show that UbiFast can identify more than 10,000 ubiquitylation sites on breast cancer xenograft-derived peptides with as little as half a milligram of starting material, and in less than a third the instrument time of other methods.

Calculated risk

It’s unclear how much de novo (i.e., not inherited) mutations (DNMs) contribute to risk for schizophrenia. A team led by associated scientist Daniel Howrigan, institute member Benjamin Neale, and others in the Stanley Center for Psychiatric Research analyzed DNMs from exome sequencing of more than 2,700 parent-child trios in which the child had schizophrenia. Reporting in Nature Neuroscience, they found that affected children had a modest excess of DNMs in protein-coding genes above expectation, but tended to be in genes expressed in the brain or identified in other neurodevelopmental disorders. While DNMs explain a small fraction of schizophrenia risk, additional studies will soon identify individual risk genes.

Base editors break up and get back together

Base editors are large molecular machines that are hard to get into cells in vivo, largely because full-length base editors are too big to fit into adeno-associated viruses (AAVs) — the only FDA-approved gene therapy vector. To get around this, Jonathan Levy, Wei-Hsi Yeh, core institute member and Merkin Institute of Transformative Technologies director David Liu, and colleagues divided each cytosine or adenine base editor into two halves, fused each half to half of a split intein, and then packaged each in an AAV particle. The team used dual AAVs to deliver both base editor halves into cells, where protein splicing reconstitutes the full base editors. The base editors worked at therapeutically relevant efficiencies and dosages in mouse organs including the brain and liver, and also corrected a mutation that causes Niemann-Pick disease type C in mouse brain tissue, with partial phenotypic rescue. Read more in Nature Biomedical Engineering.

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