What more do we know since last year?
As more and more papers are published using models generated by CRISPR/Cas9 editing, and new and exciting applications for the CRISPR/Cas system continue to be invented, the potential for off-target editing continues to be discussed. We published an article on our blog a year ago which explains the potential for off-target editing with CRISPR/Cas9 and summarised some of the literature on this topic, and thought this was a good time for an update.
...are defined as genes that are critical for the survival of an organism. These are considered to be genes that are absolutely required for the cell to grown, proliferate and survive. Deletion of an essential gene from a cell eventually leads to the death of this cell or a severe proliferation defect. As a consequence, it is impossible to generate cells with a knock-out or deletion of essential genes.
In a breakthrough study, Blomen et al. (Science, 2015) used extensive mutagenesis to describe the complete set of essential genes in the human haploid cell line Hap1.
Mutations were generated by the random introduction of a gene-trap cassette that interferes with correct splicing.
A revolution is under way in functional genomics which is spearheaded by the CRISPR-Cas9 system and its application to pooled genetic screening. Remarkable new tools, made possible by dCas9, are coming to fruition that will allow for a new kind of interrogation of gene function, allowing us to ask more sophisticated questions about the biology of drug targets.
January 2013 was marked by a major breakthrough in genome engineering. Four labs simultaneously engineered the bacterial and archaeal CRISPR-Cas9 system to induce precise cleavage at mammalian genomic loci1–4. Within a year’s time, two back-to-back papers documented the application of CRISPR-Cas9 knockout technology to forward genetic screening5,6. These studies showed not just proof of concept of a new technology, but a spectacular jump in what is possible within functional genomics. Many studies have since capitalised on these discoveries and several publications, including from Horizon7, have demonstrated screening platforms with even greater precision and performance.
The dilemma of when to invest in new technology
Researchers in the life sciences community are constantly walking a fine line in assay development. On one side is the accuracy, specificity and reproducibility borne from use of a well-established tool; i.e., a tool that has been on the market for a long time. Put another way, there is a level of comfort in using the same products for many years - in science as in the rest of life.
On the other side is the importance of finding the most efficient, cost-effective methods to carry out experiments. Doing so often means taking a chance on a new product, running it alongside existing methods to compare. Of course, it’s not just cost-effectiveness that necessitates making changes; simply keeping up can mean bringing in a new product that incorporates new advances. The outcome, hopefully, is better results faster, at lower cost.
And yet, inertia is a challenging force to overcome, and there is always a tendency to maintain the status quo. Particularly, as noted above, when so much rides on maintaining consistent protocols.
Here at Horizon, our scientists have built a remarkable new tool in the HAP1 cell line to facilitate researcher's access to CRISPR technology. These knockout cell lines allow researchers to quickly validate their gene or target of interest, without having to invest time and resource in developing in-house CRISPR technology.
HAP1 and HAP1 cells gene-edited to knockout SLC30A6 (HAP1_SLC30A6, catalogue number: HZGHC002784c010) with the HPA antibody HPA057328 targeting SLC30A6 demonstarting the specificity of this antibody. The samples were prepared in parallel using the same antibody dilutions and reagents, and both images are acquired with the exact same settings. Images curtesy of Dr Emma Lundberg, Cell Profiling facility. KTH Royal Institute of Technology.
We believe that, for its designated applications, HAP1 cells are more than worth adding into a lab’s toolbox. However, our opinion only takes things so far. So we set out to ask a few scientists who have published using the HAP1 cells about their work, and how the cells played a role in their investigations.
Research conducted by Jian-Hua Luo, M.D., Ph.D. of the Pittsburgh School of Medicine is the first time gene editing has been used to specifically target cancer fusion genes, which are hybrid genes discovered in a wide array of solid tumors1.
These hybrid genes, formed from two previously separate genes, produce abnormal proteins that can be a catalyst to faster and/or further cancer growth. In patients this causes far more invasive cancers, reducing life expectancy and survival chances.
Read our blog on how new methods increase precision in protein visualization
Here we describe some of the great solutions that are coming out of recent advances using CRISPR CAS technology that give more precise and physiological results for protein visualization. In our previous blog (see link at end of article), we discussed the some of the difficulties with traditional methods for protein tracking and localization. One of the main causes of variability and wasted resources is the lack of standards for antibody quality.
To be useful, an antibody must:
Have a high signal to noise ratio
Be validated for the assay at hand
Efforts to reduced non-specific antibodies in both industry and academia
From an industry standpoint, numerous organizations and commercial suppliers have created (or are creating) programs to ensure that the above criteria are met for each new antibody brought to market.
Can I use the HAP1 cell line for my research?
The HAP1 cell line has been applied across a wide range of biological processes, such as DNA damage repair pathway and stress responses, as well as in disease modeling. These selected articles show the broad applicability of the HAP1 cell line, and provide characterization data to help your research. If you would like to know more, please follow these links to our ready made cell lines and cell line engineering services.
- Measurement of nanoscale DNA translocation by uracil DNA glycosylase in human cells
- CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions
- TrapSeq: An RNA Sequencing-based pipeline for the identification of genetrap insertions in mammalian cells
- Biallelic mutations in the ubiquitin ligase RFWD3 cause Fanconi anemia
- RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination
- eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs
- Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
- FBXO25 regulates MAPKsignaling pathway through inhibition of ERK1/2 phosphorylation
- Persistence of the mitochondrial permeability transition in the absence of subunit c of human ATP synthase
- Translation of Sindbis Subgenomic mRNA is Independent of eIF2, eIF2A and eIF2DJ
- Stress-specific differences in assembly and composition of stress granules and related foci
- Comparative genetic screens in human cells reveal new regulatory mechanisms in WNT signaling
- Recycling of Apolipoprotein(a) After PlgRKT-Mediated Endocytosis of Lipoprotein(a)
- The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay
- The Selenocysteine-Specific Elongation Factor Contains Unique Sequences That Are Required for Both Nuclear Export and Selenocysteine Incorporation
- Dual loss of succinate dehydrogenase (SDH) and complex I activity is necessary to recapitulate the metabolic phenotype of SDH mutant tumors
- Parallel reverse genetic screening in mutant human cells using transcriptomics
Sensitivity and resistance to DNA Damage Response Pathways identified with gene-edited cell lines and wildtype controls
The cellular DNA damage response (DDR) is an essential safeguard against cancer. Upon activation, the DDR can limit tumour progression at the early stages by inducing senescence or cell death. When this defence fails tumors are able to develop. However, with time, tumors accumulate more mutations in DNA repair proteins as cancers progress. The efficiency of DDR plays an essential role in the effectivity of cytotoxic treatments. Currently much research is focussed on identifying the DDR mechanisms involved in cancers and how these dysfunctional processes can be utilized against tumor growth.
When I have read articles just like this one early on in my career, I would laugh and categorize it with blogs regarding Bigfoot and the Loch Ness Monster. However, much has changed in the past 10 years. New technologies have been developed and milestones have been reached that should have Cancer a little worried. These 3 steps might be viewed to some as obvious, but I argue that it’s how the researchers have utilized the technology wisely that has made the difference. I have identified some papers that have carved a successful path to Cancer's possible demise.