New Study Finds No Evidence for Genome Editing with NgAgo

Khin, C, N., et. al. (2017) PLOSOne, 12(6):e0178768. https://www.ncbi.nlm.nih.gov/pubmed/28609472

A new study in PLOSOne has found no evidence of gene editing activity with Natronobacterium gregoryi Argonaute (NgAgo).  Previously NgAgo had been described as a DNA targeting, DNA guided endonuclease similar to the CRISPR/Cas system. However, since its first report few labs have been able to duplicate the results.  In this report researchers injected over 100 mouse zygotes with the NgAgo plasmid supplied by AddGene and found no evidence of successful gene editing.

Genome Editing as Therapy for Muscular Dystrophies

Pini, V., et. al. (2017) Current Stem Cell Reports. 3:137-148. https://www.ncbi.nlm.nih.gov/pubmed/28616376

Muscular Dystrophy is one of the many diseases scientists are evaluating for treatment with CRISPR/Cas systems with many labs reporting new findings.  This review provides a survey of current findings and the impact they may have on Muscular Dystrophy treatments.

Genome Editing in Mammals

Fernandez, A., et. al. (2017) Mammalian Genome. https://www.ncbi.nlm.nih.gov/pubmed/28589393

Genome editing began in mammals with the development of Zinc Finger Nucleases and has since become an invaluable tool with the discovery of the CRISPR/Cas9 system.  This review article covers how gene editing technology has been applied to mammals and how far the technology has evolved.

Optimizing sgRNA Design

Kuan, P.F. et. al. (2017) BMC Bioinformatics, 18:297 https://www.ncbi.nlm.nih.gov/pubmed/28587596

Design of sgRNAs can prove challenging due to the tendency of RNA to form complex secondary structures and different sequences imparting different thermodynamic properties.  By using a machine learning approach and previous oligonucleotide design and models, Kuan et al. analyzed CRISPR datasets to create an R package, predictSGRNA, to help with sgRNA design.

Cloud-Based Deconvolution Software for CRISPR Pooled Screens

Jeong, H.H. et. al. (2017) Bioinformatics, btx335. https://www.ncbi.nlm.nih.gov/pubmed/28541456

Analyzing next generation sequencing data from pooled screening experiments can be a difficult and time-consuming process, with few programs providing a user-friendly interface and presentation of data.  Researchers from the Texas Children’s Hospital have developed a cloud based system for analysis, deconvolution, and presentation of sequencing data – allowing researchers to quickly determine the frequency and types of mutations.

CRISPR Off-Target Affects May be Greater than Previously Assumed

EurekAlert, Columbia University Medical Center Press Release, 29 May 2017, https://www.eurekalert.org/pub_releases/2017-05/cumc-cge052617.php

Since its discovery, the CRISPR/Cas9 system has been on an unprecedented pace towards clinical use, though a new Nature Letter may slow down this process.  In the letter, Unexpected mutations after CRISPR-Cas9 editing in vivo (https://www.ncbi.nlm.nih.gov/pubmed/28557981), researchers completed whole genome sequencing of CRISPR edited mice and discovered 1,500 single nucleotide mutations and greater than 100 larger deletions and insertions with none of the off-target mutations predicted by computer algorithms.  While this study could change the way CRISPR therapies progress, further researcher is needed to confirm the results.

Proximal Targeting With dCas Alters Chromatin Structure Allowing Genome Editing

Chen, Fuqiang, et. a. (2017) Nature Communications. 8:14958. https://www.nature.com/articles/ncomms14958

Many different Cas variants have been discovered, each with slightly different activities.  Francisella novicida Cas9 (FnCas9) is one such Cas variant. It is frequently inhibited at genomic loci, presumably due to chromatin formation.  By using dead SpCas9 to target proximally, FnCas9 could cleave at the target site, presumably due to chromatin rearrangements.

Could Casposons Have Given Rise to CRISPR?

Krupovic, M. et. al. (2017) Current Opinion in Microbiology 38:36-43. https://www.ncbi.nlm.nih.gov/pubmed/28472712

Casposons are a superfamily of self-synthesizing transposons found in prokaryotes.  One identified casposon is homologous to the Cas1 endonuclease and could have evolved into the adaption module of the CRISPR/Cas system and the CRISPR repeats.  This opinion publication covers how the casposon system is similar and different from that of CRISPR/Cas and the evidence supporting its evolution into the CRISPR system.

Induced Pluripotent Stem Cells Used to Study Chlamydia Pathogenesis

Yeung, A.T.Y., et. al. (2017) Nature Communications 8:15013. https://www.ncbi.nlm.nih.gov/pubmed/28440293

Chlamydia is a leading sexually transmitted disease and cause of preventable blindness. Cell based systems to study the interactions between Chlamydia and human macrophages remain limited.  Yeung et al. have developed human induced pluripotent stem cell-derived macrophages that are readily modifiable using CRISPR/Cas9 to study the interactions between Chlamydia and human macrophages.

Human ALS iPSCs Corrected Through CRISPR/Cas9 Treatment

Wang, L. et. al. (2017) Protein Cell. https://www.ncbi.nlm.nih.gov/pubmed/28401346

ALS is a neurodegenerative disease, with mutations in SOD1 and FUS associated with familial ALS.  Using CRISPR/Cas9 Wang et al. corrected human iPSCs generated from fibroblasts of familial ALS patients containing SOD1 and FUS mutations.  These regenerated cells were used for transcriptome comparison studies to the mutated cells with close to 900 aberrant transcripts identified.  Use of this system could lead to potential therapies for ALS patients with SOD1 and FUS mutations.