Zika field test uses CRISPR/Cas9 to distinguish between Zika strains

Pardee, K. et. al., Cell (2016), http://dx.doi.org/10.1016/j.cell.2016.04.059, http://www.ncbi.nlm.nih.gov/pubmed/27160350

Zika has proven challenging due to its close relation to other viruses such as Dengue. Pardee et al have developed a low cost field test that couples isothermal RNA amplification with toehold switch RNA sensors to detect Zika.  The assay provides a quick readout using a colorimetric change of the sensor.  By adding in a CRISPR/Cas9 component the researchers were able to provide an assay that can even distinguish between strains of Zika with single-base resolution.  Development of these types of tools should help researchers efficiently determine how quickly the Zika virus is spreading.

Science journalist Jennifer Kahn presents the benefits and problems of gene drives

Jennifer Kahn, TED, February 2016 http://www.ted.com/talks/jennifer_kahn_gene_editing_can_now_change_an_entire_species_forever?language=en#t-371494

Jennifer Kahn presented at TED 2016 on CRISPR gene drives.  Kahn covers the theory behind CRISPR gene drives and how they could be used to manage diseases such as malaria as well as invasive species like the Asian Carp.  By asking the question, “are we now gods?” she examines the ethics of gene drives as well as their risks and benefits. Ultimately Kahn makes the case that when confronted with diseases like malaria inaction could be worse.

Washington Grapples with a Thorny Question: What Is a GMO Anyway?

Mike Orcutt, May 26, 2016, MIT Technology Review https://www.technologyreview.com/s/601538/washington-grapples-with-a-thorny-question-what-is-a-gmo-anyway/

Gene editing technologies, such as CRISPR, have made it increasingly difficult to distinguish between traditionally bred and genetically modified crops leading to the need for new regulatory guidelines.  The National Academies of Science recently released a report providing guidelines for a new regulatory framework that judges the novelty of a crop and not the process under which it was created.  This is especially important as the USDA has recently stated that CRISPR edited crops will not be regulated like traditional GMOs.

Adaptation of CRISPR for use in neural tissue

25Emma Yasinki, GEN, May 25, 2016 http://www.genengnews.com/insight-and-intelligence/crispr-crossing-new-barriers/77900666/

CRISPR gene editing has now been used extensively to knock-in novel DNA sequences. However, as this mechanism relies in part on the cells native homologous recombination machinery, cells that don’t divide rapidly, such as neurons, have been difficult to modify.  Researchers have now developed a new technique coined SLENDR that uses CRISPR/Cas9 and in utero electroporation allowing transformation of prenatal models when the neural cells are still dividing thus allowing homology directed repair of double stranded breaks.

CRISPR/Cas9 has been adapted to aid in mapping of unknown genes

Catherine Offord, 5 May 2016,The Scientist, http://www.the-scientist.com/?articles.view/articleNo/46029/title/Mapping-Traits-to-Genes-with-CRISPR/

Traditional gene mapping follows phenotypic traits through multiple generations and homologous recombination events.  Using the cells natural meiotic processes researchers are able to determine regions of the genome responsible for certain traits, however this process is limited since crossing over is a rare event and it is impossible to control where the event occurs.  Researchers have now used CRISPR/Cas9 to induce crossing over through HDR  to control where crossing over occurs.  Coupled with a GFP marker, the researchers were able to quickly identify a SNP in yeast responsible for manganese sensitivity.  Additional research is needed to adapt this technique to more complex systems such as human cell lines.

CRISPR/Cas9 outperforms both CRISPRi and traditional shRNA in a genome wide knockout screen to identify essential genes

Evers, B., et. al. Nature Biotechnology (2016) https://www.ncbi.nlm.nih.gov/pubmed/27111720

High-throughput knockout screens have become an important tool in identifying essential genes.  Traditionally this process used shRNA to target genes with both CRISPR/Cas9 and CRISPRi currently emerging as alternatives.  To determine which type of screen produces the most reliable results with fewer off-target effects and low noise Evers et al compared the three technologies in RT-112 cells.  CRISPR/Cas9 was found to perform better than its inactive CRISPRi counterpart and traditional shRNA screens.

CRISPR based gene therapies may still be years away

Jocelyn Kaiser, Science


While gene editing techniques such as CRISPR/Cas9 have changed the way basic research is being conducted, widespread use of the technology in medical treatments could be years away.  As with previous promising gene therapies the largest obstacle is delivery of the required proteins into the organs of interest.    The repair of the mutations behind genetic disorders often necessitates the use of HDR, however as HDR has very low efficiencies most of the treated cells may end up being repaired by NHEJ, presenting a challenging obstacle to researchers.  While many gene therapists are excited for the potential of CRISPR/Cas9 technology, years of research are needed before it sees clinical application.

WBUR Boston sits down with Eric Lander to discuss CRISPR/Cas9

Radio Boston, WBUR Boston’s NPR News Station, 25 April 2016 http://radioboston.wbur.org/2016/04/25/eric-lander-crispr

WBUR Boston sits down with the Broad Institute’s Eric Lander to discuss how CRISPR/Cas9 technology works and the numerous potential applications.  He also responds to the controversy over his recent review article in Cell on the history of CRISPR and how the article could impact the patent fight between the Broad Institute and UC-Berkeley.

Researchers solve the crystal structure of Cpf1 in complex with CRISPR RNA

Dong, D., et. al. Nature (2016) 532:522-526 http://www.ncbi.nlm.nih.gov/pubmed/27096363

Researchers elucidated the crystal structure of the Cas9 functional analog Cpf1 in complex with crRNA at a 2.38Å resolution.  Cpf1 was isolated from Lachnospiraceae bacterium ND2006 and found to have a triangular  shape with a positively charged central channel.  Extensive intramolecular forces and Mg(H20)62+ stabilize  the Cpf1-crRNA structure.  The determination of this crystal structure will facilitate engineering of Cpf1 in order to improve its specificity and decrease off-target effects.