Highlights from the 2017 AgBio Innovation Showcase Held by UC Davis

  • An Inconvenient Truth About Unsustainable Global Food Supply
  • Agricultural Biotechnology (AgBio) is Providing Transformative Solutions
  • Highlights from the Inaugural AgBio Innovation Showcase

Taken from the journal.ie

With expected global population to reach 8.3 billion in 2030, it’s clear that excessive exploitation of food resources is no longer sustainable and the problem will simply worsen with environmental problems and effects of climate change. This ominous outlook by food experts is reminiscent of former Vice President Al Gore’s dire vision for global warming in an award winning documentary film in 2016 titled An Inconvenient Truth.

This very real challenge of achieving adequate and sustainable food supplies—globally, not just for developed countries—has been, and continues to be, addressed by nucleic acid-based agricultural biotechnology (aka AgBio). At the forefront of this battle is development of genetically modified foods (aka genetically engineered foods or bioengineered foods), which are foods produced from organisms that have had changes introduced into their DNA using the methods of genetic engineering. Genetic engineering techniques allow for the introduction of new traits, as well as greater control over traits than was possible with previous methods such as selective breeding and mutation breeding.

Taken from intelligencesquaredus.org

Last year, I published a blog about genetically modified organisms (GMOs) in which I made fairly general comments about complex government regulatory issues related to “science vs. semantics” and varying degrees of country/consumer acceptance and rejection. This blog is somewhat of a follow-up to that post, and I will share specifics from the 2017 AgBio Innovation Showcase held by the University of California Davis at its World Food Center, which include GMO and non-GMO technologies. The Center was founded in 2013 as an institute aimed at “bridging agriculture, food science, nutrition, veterinary medicine, public health and policy in new and transformational ways.”

2017 AgBio Innovation Showcase

Taken from agshowcase.com

This inaugural event was held on May 8-9 and featured the most promising AgBio and AgTech startups and research projects. The showcase featured solutions in high-value, nutritious agriculture and food from across the globe. The four major showcase themes were Automation & Robotics, Boosting Nutrition & Sensory Value, Innovation in the Livestock & Dairy Sectors, and Water Management. I’ve selected several highlights that are summarized below. Takeaways from panel discussions about the future of agriculture can be read elsewhere.

Ag Biotech

  • Afingen – This biotech start-up was spun out of Lawrence Berkeley National Laboratory (LBNL) in 2014 and features technology based on proprietary cisgenesis. Cisgenesis involves modification of a recipient plant with a natural gene from a crossable plant. Importantly, cisgenic plants can harbor one or more cisgenes, but they do not contain any transgenes and therefore yield new, improved plant varieties that are classified non-GMO.
  • Taken from whattsupwiththat.com

    Bee Vectoring Technology – How this Canadian company cleverly turns bees into delivery agents that deposit biological products on crops for pest management is best understood by watching this video (details for which may be read in a patent). In brief, powder-form biologics to be delivered are placed in commercially-reared bee. The biologics stick to the bees’ feet and are released when the bee collects pollen from the targeted crop.

    Taken from saipanhydroponics.com

  • MiraculeX – A unique West African plant protein called miraculin (named for its “miracle” ability to transform sour foods into sweet treats), makes it possible to bite into a lemon and taste nothing but sweet lemonade. MiraculeX reportedly inserts the protein’s DNA into the genetic code of ordinary lettuce, which is grown hydroponically and in less than a week is ready to be harvested for processing.
  • Trace Genomics – This startup service in San Francisco provides advice to growers based on analysis of their soil. Growers simply provide a soil sample, from which TraceGenomics extracts DNA from the organisms in the soil and prepares a sequencing library to analyze the soil microbial community. Interpreted results are provided along with information about soil health, nutritional status, and corresponding recommendations for how to improve crop yield and quality.

Diagnostics

  • AstRoNa Biotechnologies – This UC Davis startup aims to commercialize an easy-to-use, hand-held pathogen detection device to quickly monitor food contamination by bacteria, viruses, and fungi. It’s basically “farm-to-table” analysis. The team reportedly developed a disposable test kit to capture and amplify RNA of pathogens, focusing on coli O157:H7. A fully automated handheld instrument is under development and will feature sample multiplexing, quantitative detection, and software to create a traceable record of safety—recording time, location, user, and results in real time.
  • SnapDNA – This startup has an R&D agreement with the US Department of Agriculture to develop rapid, highly specific tests for foodborne pathogens, including Salmonella enterica and human noroviruses (the latter of which is featured in an earlier blog). I was unable to find many details, but a board member states that SnapDNA is “a semiconductor-based bio-chip and multiplexed DNA detection platform.” Adding that “[a]major differentiator of SnapDNA is the specificity to detect DNA at the level of microbial strains in a fast, low cost test, major pain points in current systems.”

Food Science & Animal Health

  • Taken from Wikipedia.org

    Bonumose – This startup in Virginia is scaling up enzymatic production of tagatose (pictured below), which—unlike sucrose and high fructose corn syrup—does not raise blood sugar levels, is low-calorie, and does not cause tooth decay. Beyond not being harmful to health, tagatose provides positive health benefits: it is an effective prebiotic (good for gut health), blocks adsorption of sucrose and starch, is clinically-proven to reduce blood sugar levels in diabetics, contributes to a feeling of satiety, and breaks up dental biofilm. Even better, tagatose is nearly indistinguishable from sucrose in terms of taste and food functionality. And it blends very well with high intensity sweeteners such as stevia. I want some asap!

  • Resilient Biotics – This El Cerrito, California startup utilizes deep sequencing to characterize host genotypes, commensal microbial communities, and pathogen strain variants for microbiome resolution to rapidly identify important genetic elements and key microbial strains that influence states of health and disease. Heuristic search methods can rapidly pinpoint diagnostic biomarkers for pathogen identification and risk prediction. Resilient Biotics is actively developing live biotherapeutics to address major infectious diseases of the respiratory tract in production animal systems.

AgBio Meets CRISPR

As if the 2017 AgBio Innovation Showcase wasn’t stimulating enough, I was thrilled to discover another upcoming meeting that combines two of my favorite topics: agbio and CRISPR. Devoted readers of my blogs will recall numerous past postings on CRISPR for gene editing and other useful manipulations of genomic DNA. My search of Google Scholar indicated no AgBio CRISPR publications to date, but that will likely change, as evidenced by the upcoming conference.

Interested readers can register at the link above and download a detailed agenda and list of confirmed speakers. In doing so, it is apparent that this conference will comprehensively cover the newest topics and the regulatory status related to CRISPR/Cas9 technology.

I look forward to reading about these developments, and posting comments in a future blog titled AgBio Meets CRISPR. If you happen to be attending this conference, please share details about what you learned in the comments section below.

As usual, your comments are welcomed.

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Advances in Aptamer Applications – Part 2

  • Top Cited Aptamer Publications Over the Past Three Years
  • Jerry’s Picks for Top 3 Aptamer Publications So Far This Year
  • TriLink Products Cited in Numerous Aptamer Publications

Aptamers are highly structured nucleic acids that bind to a specific target molecule. RNA or DNA aptamers are usually selected from a very large pool (aka library) of random sequences, and can be comprised of either natural and/or chemically modified nucleotides. My first blog on aptamers was titled Aptamers: Chemistry Bests Mother Nature’s Antibodies. This purposefully provocative claim was intended to emphasize the growing body of evidence that collectively indicates aptamers can perform better than antibodies in many applications.

NMR-derived structures of aptamers binding to either a large protein or small molecule. Taken from genelink .com

Because it has been nearly four years since that boastful blog in 2013, I thought it was time to survey aptamer applications published since then to comment on what has been trending or is otherwise notable. I found more than 1,500 articles in PubMed for 2014 through 2017 (estimate) that have the search term “aptamer” in the title or abstract. Given this huge number of publications, I used Google Scholar citation frequency as a numerical indicator of interest, importance and/or impact for these publications in each year. I also decided to focus on original publications that, by definition, excludes review articles. 

Top 3 Cited Publications in 2014

  1. Activatable fluorescence/MRI bimodal platform for tumor cell imaging via MnO2 nanosheet–aptamer nanoprobe (109 citations)

This Chinese team of researchers led by uber-prolific Weihong Tan, about whom I’ve previously blogged, designed a novel methodology for imaging tumor cells using quenched-fluorescent aptamers. In the presence of target cells, the binding of these “dark” aptamers to cell surface markers weakens the adsorption of aptamers on MnO2 nanosheets causing partial fluorescence recovery (i.e., unquenching), thus illuminating the target cells, as well as facilitating endocytosis into target cells. After endocytosis, reduction of MnO2 nanosheets by glutathione further activates the fluorescence signals and generates large amounts of Mn2+ ions as a contrast agent for magnetic resonance imaging (MRI).

Taken from pubs.rsc.org

  1. A phase II trial of the nucleolin-targeted DNA aptamer AS1411 in metastatic refractory renal cell carcinoma (88 citations)

Taken from mct.aacr.org

The anticancer mechanism of action for DNA aptamer AS1411, which has multiple G-quadruplex moieties that disrupt cancer cell replication following nucleolin-mediated uptake, is depicted below and detailed elsewhere. In this clinical study, it was found that AS1411 appears to have limited activity in patients with metastatic renal cell carcinoma. However, rare, dramatic and durable responses can be observed and toxicity is low. Further studies with AS1411 and other nucleolin-targeted compounds may benefit from efforts to discover predictive biomarkers for response.

  1. An aptamer-based dipstick assay for the rapid and simple detection of aflatoxin B1 (61 citations)

Aflatoxin B₁ structure. Taken from wikipedia.org

Aflatoxin B₁ (AFB1) produced by Aspergillus flavus and A. parasiticus is considered the most toxic aflatoxin and it is highly implicated in hepatocellular carcinoma in humans. In this work by Korean researchers, a rapid and simple dipstick assay based on an aptamer has been developed for determination of AFB1 contamination in food. The dipstick assay format was based on a competitive reaction of a biotin-modified aptamer specific to AFB1 between target and Cy5-modified DNA probes. Streptavidin and anti-Cy5 antibody as capture reagents were immobilized at test and control lines on a membrane of the dipstick assay. The method was confirmed to be specific to AFB1, and the entire process of the assay can be completed within 30 min.

Top 3 Cited Publications in 2015

  1. Aptamer-conjugated silver nanoparticles for electrochemical dual-aptamer-based sandwich detection of staphylococcus aureus (63 citations)

Taken from sciencedirect .com

Staphylococcus aureus (S. aureus) is one of the most important human pathogens and causes numerous illnesses. This report by Iranian researchers describes a sensitive and highly selective dual-aptamer-based sandwich immunosensor for the detection of S. aureus. As depicted below, a biotinylated primary anti-S.aureus aptamer was immobilized on streptavidin coated magnetic beads (MB), which serves as a capture probe. A secondary anti-S.aureus aptamer was conjugated to silver (Ag) nanoparticles such that, in the presence of target bacterium, a sandwich complex is formed on the MB surface and the electrochemical signal of Ag is measured by anodic stripping voltammetry.

  1. Aptamer-based fluorescence biosensor for chloramphenicol determination using upconversion nanoparticles (59 citations)

Chloramphenicol. Taken from Wikipedia .com

Chloramphenicol (CAP) shown below is a naturally occurring antibiotic that is artificially manufactured for use in veterinary and human medicine. Due to its adverse effects in humans, use of the antibiotic is restricted and, in Europe, ‘zero tolerance’ for CAP in food products has been legislated. In this report by Chinese researchers, detection of CAP uses aptamer-conjugated magnetic nanoparticles for both recognition and concentration, together with upconversion nanoparticles for detection. The method was validated for measurement of CAP in milk vs. a commercially available enzyme-linked immunosorbent assay (ELISA) method.

  1. A new aptamer/graphene interdigitated gold electrode piezoelectric sensor for rapid and specific detection of Staphylococcus aureus (48 citations)

Taken from mdpi .com

This work by Chinese investigators describes a novel aptamer/graphene interdigitated gold electrode piezoelectric sensor for detecting S. aureus by binding to the aptamer, which is immobilized on the graphene via the π–π stacking of DNA bases, as depicted below. When S. aureus is present, aptamer dissociates from the graphene and thus leads to change of oscillator frequency of the piezoelectric sensor.

Top 3 Cited Publications in 2016

  1. Aptamer–MIP hybrid receptor for highly sensitive electrochemical detection of prostate specific antigen (38 citations)

This study in the UK uses a thiolated DNA aptamer for prostate specific antigen (PSA) immobilized on the surface of a gold electrode. Controlled electropolymerization of dopamine around the complex served to create an imprint of the complex following removal of PSA. This molecularly imprinted polymer (MIP) cavity was found to act synergistically with the embedded aptamer to provide recognition properties superior to that of aptamer alone. A generalized depiction for producing a MIP is shown below.

Taken from sigmaaldrich .com

  1. Aptamer-functionalized nanoparticles for surface immobilization-free electrochemical detection of cortisol in a microfluidic device (34 citations)

Taken from wikipedia.org

Monitoring the periodic diurnal variations in cortisol (aka hydrocortisone, show below) from small volume samples of serum or saliva is of great interest, due to the regulatory role of cortisol within various physiological functions and stress symptoms. This publication from China reports use of aptamer-functionalized gold nanoparticles pre-bound with electro-active triamcinolone for detection of cortisol based on its competitive binding to the aptamer by monitoring a signal from the displaced triamcinolone using square wave voltammetry at graphene-modified electrodes. The assay was benchmarked vs. ELISA and radioimmunoassays.

  1. Multifunctional aptamer-based nanoparticles for targeted drug delivery to circumvent cancer resistance (32 citations)

Taken from Liu et al. Biomaterials (2016)

In yet another publication from China, Liu et al. report use of a G-quadruplex nanostructure to target cancer cells by binding with nucleolin, in a manner analogous to that mentioned above. A second component is double-stranded DNA (dsDNA), which is rich in GC base pairs that can be applied for self-assembly with doxorubicin (Dox) for delivery to resistant cancer cells. These nanoparticles were found to effectively inhibit tumor growth with less cardiotoxicity.

Jerry’s Top 3 Publication Picks for 2017-to-Date

Here are my Top 3 “fav” aptamer articles published during the first half of 2017, and my reasons for these aptamer selections—pun intended. Interested readers can consult the original publication for technical details.

  1. Targeted delivery of CRISPR/Cas9 to prostate cancer by modified gRNA using a flexible aptamer-cationic liposome

CRISPR/Cas9 is unquestionably—in my opinion—the hottest topic in nucleic acid-based R&D these days, as I have previously blogged about. Off-target effects of CRISPR/Cas9 can be problematic, so using targeted delivery to cells of interest is an important approach for mitigating this problem. In this study, an aptamer-liposome-CRISPR/Cas9 chimera was designed to combine efficient delivery with adaptability to other situations. The chimera incorporated an RNA aptamer that specifically binds prostate cancer cells expressing the prostate-specific membrane antigen as a ligand, and the approach “provides a universal means of cell type-specific CRISPR/Cas9 delivery, which is a critical goal for the widespread therapeutic applicability of CRISPR/Cas9 or other nucleic acid drugs.”

  1. A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva

This report claims the first ever development of a split aptamer that achieves enhanced target-binding affinity through cooperative binding. In this instance, a split cocaine-binding aptamer incorporates two binding domains, such that target binding at one domain greatly increases the affinity of the second domain. This system afforded specific, ultra-sensitive, one-step fluorescence detection of cocaine in saliva without signal amplification. This limit of detection meets the standards recommended by the European Union’s Driving under the Influence of Drugs, Alcohol and Medicines program.

  1. Detection of organophosphorus pesticide–Malathion in environmental samples using peptide and aptamer based nanoprobes

Environmental contamination with pesticide residues has necessitated the development of rapid, easy and highly sensitive approaches for the detection of pesticides such as malathion, a toxic organophosphorus pesticide, widely used in agricultural fields. These Indian investigators employed an aptamer, cationic peptide and unmodified gold nanoparticles. The peptide, when linked to the aptamer renders the gold nanoparticles free and therefore, red in color. When the aptamer is associated with malathion, however, the peptide remains available to cause the aggregation of the nanoparticles and turn the suspension blue. The sensitivity was tested in real samples and the results implied the high practicability of the method.

Aptamer Publications in 2014-Present Citing TriLink Products

I was pleasantly surprised to find more than 250 publications on aptamers in Google Scholar citing the use of TriLink products since 2014. This volume of literature is way too large to summarize succinctly, so I decided to do a quick scan to select the following items that provide an indication of the broad diversity of applications partially enabled by TriLink products:

2’-F-UTP. Taken from trilinkbiotech .com

In closing, I should first mention that, while scanning the aptamer/TriLink publications mentioned above, it was evident that the most frequently cited TriLink products were 2’-F-CTP and 2’-F-UTP, which are incorporated into aptamers to impart nuclease resistance, as discussed on a TriLink webpage.

My second and last comment is that, as you may have noticed, there seems to be a high proportion of aptamer publications coming out of China and/or coauthored by Chinese investigators collaborating with researchers in other countries. This despite the fact that Chinese publications in Life Sciences are ~6-times fewer that those from the US, according to reliable statistics. I have no idea why this is so, but thought it’s an intriguing factoid.

As usual, your comments are welcomed.

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CRISPR-C2c2 Update: Powerful New Diagnostic Method Using CRISPR

  • CRISPR Craze Continues Led in Part by Wunderkind Feng Zhang
  • Nonspecific CRISPR-C2c2 “Collateral” Cutting Channeled into Diagnostics
  • Turning Biochemical “Lemons to Lemonade”

This blog post is about a new and powerful diagnostic approach based on CRISPR, which I’ll get to below. But first I’d like to point out several reasons why this is an especially interesting development:

  • Taken from spyhollywood.com

    Any new method using CRISPR is more “sizzle” for this “super-hot” technology

  • Feng Zhang, the 32-year-old author of this publication, is regarded as a wunderkind
  • My past blog post on CRISPR-C2c2 “collateral” cutting noted possibilities for turning “lemons into lemonade”
  • Such “lemonade” has emerged as a diagnostic cleverly acronymized as SHERLOCK

So, without further ado, here’s a brief recap of CRISPR-C2c2 as an intro to SHERLOCK (think Holmes), followed by why this acronym is apropos for a diagnostic method that magnifies detection, in this case Zika virus, about which I’ve previously commented. 

What’s CRISPR-C2c2?

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (CRISPR-Cas) adaptive immune systems in microbes contain endonucleases that can be leveraged for CRISPR-based gene editing using targeted CRISPR RNAs (crRNAs), as I’ve outlined in a previous blog post. While such Cas enzymes target DNA, others target RNA and function as RNA-guided RNases, which was reported by Feng Zhang and collaborators in Science last year in an article titled C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.

My blog post about that C2c2 publication provides more information, but the main point related to the present blog post about diagnostics is that after recognition of its RNA target, activated C2c2 engages in nonspecific (aka “collateral”) cleavage of nearby non-targeted RNAs. This post-cleavage non-specificity can be transformed, if you will, from something “bad” to something “good” in terms of mechanisms, which I described as being akin to converting ‘lemons into lemonade’. You’ll now see how SHERLOCK is such ‘lemonade’ concocted by Zhang and coworkers.

What is SHERLOCK?

Taken from US 20140199245 A1

Before answering this question, and not to confuse you, I need to first mention that the nuclease originally called C2c2 was renamed Cas13a to be more systematic, and will be referred to herein as such. Having said that, Cas13a can be reprogrammed with crRNAs to provide a platform for specific RNA sensing. Molecular recognition of an intended RNA target by crRNA in vitro serves as a sequence-specific “trigger” to activate Cas13a’s nonspecific, “collateral” cleavage of labeled RNA reporters. Cleavage of these fluorescently labeled, internally quenched RNAs leads to unquenching and fluorescent light emission for detection, as depicted below for a generic RNase.

Now that you have a sense of how CRISPR-Cas13a can generate a signal, you’re probably asking ‘What is SHERLOCK?’ It’s an acronym coined by a large team lead by CRISPR genome-editing pioneer Feng Zhang and bioengineer James Collins, both from the Broad Institute. SHERLOCK stands for High-sensitivity Enzymatic Reporter UnLOCKing, which is a recently published new method for sequence-specific detection of DNA or RNA in any sample of interest. This general utility represents a major advance in CRISPR-based diagnostics.

Feng Zhang. Taken from be.mit.edu // James Collins. Taken from achetron.com

As depicted below, sample prep workflows allow for input of either double-stranded DNA (dsDNA) or RNA, which are first amplified by recombinase polymerase amplification (RPA) directly or as cDNA, after reverse transcription (RT-RPA), respectively. In either case, further amplification utilizes T7 transcription into RNA (blue = target RNA; yellow = non-target RNA). Following cleavage of target RNA by Cas13a-crRNA, a commercially available “cleavage reporter” (i.e. internally quenched) RNA undergoes “collateral” cleavage to generate a reporter signal (i.e. fluorescence; pictured below) for real-time detection of the target.

Taken from Feng Zhang, Collins & coworkers Science (2017)

An advantage of RPA is that it is performed isothermally, which allows simplification of the detection device by eliminating the need for a thermal cycler, thus lending to incorporation into small, portable point-of-care (POC) systems (about which I previously commented several times). The abovementioned RPA/T7 sample prep methodology was shown to have attomolar (aM, 10−18 mol/L) sensitivity in model systems, and was next investigated for sensitivity and specificity of virus detection, as well as simplification of reagent format.

Zhang, Collins & coworkers constructed lentiviruses harboring genome fragments of either Zika virus (ZIKV) or the related flavivirus Dengue (DENV), and showed that SHERLOCK detected viral particles down to 2 aM could discriminate between ZIKV and DENV. To explore the potential for POC use of SHERLOCK with paper-spotting and lyophilization (aka freeze-drying), they first demonstrated that Cas13a-crRNA complexes lyophilized and subsequently rehydrated could detect 20 femtomolar (fM, 10−15 mol/L) non-amplified RNA, and that target detection was also possible on glass fiber paper.

The other components of SHERLOCK, namely the RPA reagents and T7 polymerase, were already known to be amenable to freeze-drying and storage at ambient temperatures. In combination, freeze-drying and paper-spotting the Cas13a detection reaction resulted in comparable levels of sensitive detection of RNA as aqueous reactions. Although paper-spotting and lyophilization slightly reduced the absolute signal of the readout, SHERLOCK could readily detect mock ZIKV virus at concentrations as low as 20 aM. Most importantly, SHERLOCK detected ZIKV in clinical isolates (ZIKV RNA extracted from patient serum or urine samples and reverse transcribed into cDNA) could be detected at concentrations down to 1.25 × 103 copies/mL (2.1 aM), as verified by qPCR.

Concluding Comments

If you reflect upon the schematic for SHERLOCK, you’ll note that the input can be either DNA or RNA, which get amplified to produce many copies of RNA that serve as substrates for cleavage by Cas13a-crRNA, thus inducing collateral cleavage of reporter RNA to produce a detectable signal. Lest you think SHERLOCK is too costly to be practical, its developers provide a detailed cost accounting that estimates $0.61 per test, which you’re welcome to compare with your cost of conventional qPCR. I’m quite sure that will lead you to concur with me that $0.61 per test is relatively inexpensive.

If you’re questioning whether SHERLOCK is generally applicable, I urge you to read Zhang, Collins & coworkers in its entirety to learn more about SHERLOCK’s proven ability to detect and distinguish (1) various bacterial pathogens, (2) single-base cancer mutations in cell-free DNA, and (3) health-related single-nucleotide polymorphisms (SNPs) benchmarked against 23andMe genotyping data as the gold standard of these SNPs.

In an article in Science about SHERLOCK, Harvard University’s George Church (who I’ve proclaimed is The Most Interesting Scientist in the World and is the co-founded of a CRISPR therapeutics company), sums up his reaction in one word: ‘Wow.’ I agree!

The article concludes with Collins saying the Broad is now ‘aggressively exploring’ how to commercialize SHERLOCK and may launch a startup company. But before a diagnostic comes to market, it must pass muster at regulatory agencies such as the U.S. Food and Drug Administration. I’m betting is does.

I welcome your sharing any thoughts or comments about this new CRISPR-based diagnostic method.

CRISPR-Mediated Interference (CRISPRi) of Long Non-Coding RNA (lncRNA)

  • More Methodology from CRISPR Mania
  • lncRNA Function Blocked by CRISPRi
  • Mysteries of lncRNA Can Now be Deciphered by CRISPRi

This blog is about yet another example of a powerful new methodology spawned by intense scientific interest in using CRISPR-related technologies. This near mania for all things CRISPR is reflected by there being ~5,000 (!) publications already in PubMed only ~5 years after seminal papers appeared.

I chose the present blog topic because it involves use of CRISPR for genome-wide identification of functional long non-coding RNA (lncRNA) in human cells. In an earlier blog about lncRNA, which are now recognized to be regulators of gene expression encoded by what was originally defined as “junk” DNA, it was pointed out that it is inherently difficult to experimentally identify such regulation by lncRNA. Thanks to CRISPR this task is now much less daunting as you’ll learn below, following a couple of introductory sections to set the stage.

Repurposing CRISPR/Cas9 Using “Dead” Cas9

Qi et al. very cleverly—at least to me—recognized that the CRISPR/Cas9 system could be repurposed as an RNA-guided platform for sequence-specific control of gene expression by finding a catalytically inactive mutant Cas9 protein that lacked exonuclease (i.e. cutting) activity of wild-type Cas9, and instead blocked transcription by RNA polymerase (RNAP), as depicted below. These researchers coined the overall process as “CRISPR interference” (CRISPRi) and loosely referred to such a mutant Cas9 as “dead” Cas9 (dCas9).

Taken from Qi et al.

Interested readers are encouraged to consult this publication by Qi et al. to fully appreciate the extensive amount of work that went into translating the above concept into practice, and supporting the proposed mechanism of action. In my opinion, it’s a tour de force example of applying hypothesis-driven, state-of-the art molecular biology to devise a new method—in this case specifically blocking transcription of a DNA region using CRISPRi in conjunction with target-specific short guide RNA (sgRNA).

Adding Functionality to Down-Regulate Transcription

Just as organic chemists can design and synthesize small molecules having desired functional properties, molecular biologists can design and produce complex macromolecules having desired functional elements. The latter is nicely exemplified by Gilbert et el., who demonstrated that fusion of dCas9 to transcription factor effector domains having repressive regulatory functions enables efficient transcriptional repression in human (or yeast) cells via sgRNA that target genes of interest.

Taken from Liu et al. (2017)

As depicted below, Gilbert et al. used dCas9 fused to the Krüppel associated box (KRAB) domain, which is a transcriptional repression domain, and Green Fluorescent Protein (GFP) as a reporter gene targeted by sgRNA. They employed RNA-sequencing to quantify the transcriptome of GFP-positive HEK293 cells expressing dCas9-KRAB or a negative control construct. It was shown that CRISPRi is highly specific, as GFP was the only gene that was significantly suppressed by GFP-targeting sgRNA. Averaged data from two independent biological replicates indicated that no gene other than GFP changes by >1.5-fold.

Genome-Scale CRISPRi to Identify Human lncRNA

According to Liu et al., it has not been possible to predict which lncRNA loci are functional or what function they perform. Consequently, there is a need for large-scale, systematic approaches to interrogating the functional contribution of lncRNA loci. This sizeable team of collaborators from various institutions in the San Francisco Bay area, therefore, developed a genome-scale screening platform using CRISPRi with dCas9-KRAB and a library of sgRNA.

Taken from Liu et al. (2017)

As depicted below for the overall approach, they first designed a CRISPRi Non-Coding Library, which targets 16,401 lncRNA genes each with 10 sgRNAs per transcription start site. The required 170,262 sgRNAs were not synthesized chemically, but rather produced intracellularly by first using array-based sgDNA synthesis followed by clonal (i.e. individual sgDNA sequence) incorporation into lentivirus, which in turn were transfected into seven types of cells for screening. More detail on such lentiviral libraries is given in a Footnote at the end of this blog.

As indicated pictorially above, they applied this pooled screening approach to identify lncRNA genes that modify robust cell growth for induced pluripotent stem cells (iPSC) and six well-known, transformed human cell lines (K562, U87, etc.). This led to identification of 499 lncRNA loci that modified cell growth upon CRISPRi targeting.

Interestingly—at least to me—372 (~75%) and 299 (~60%) of these 499 growth-modifying lncRNA loci were distal to a protein coding gene (PCG) or mapped enhancer, respectively. The diagram below, taken from a review by Vance & Ponting, depicts “distal” effects of lncRNA away from PCG between two chromosomes (chr). What “triggers” transcription of the lncRNA from chr A and how it “finds” its cognate PCG on chr B are open and indeed intriguing questions.

Taken from Vance & Ponting (2014)

In addition to these high percentages of distal effects, Liu et al. found the following surprising results with regard to cell-type specificity of lncRNA function:

“Remarkably, 89% of the lncRNA gene hits modified growth in just one of the cell lines tested, and no hits were common to all seven cell lines. Although nearly all of the hit genes were expressed in the cell line in which they exhibited a growth phenotype, expression alone was insufficient to explain the cell type specificity of their function.”

“[Thus,] in contrast to recent studies that found that essential protein-coding genes typically are required across a broad range of cell types, we show that lncRNA function is highly cell type-specific, a finding that has important implications for their involvement in both normal biology and disease.”

Following are some of the major unanswered questions about lncRNA posed in a review I recommend reading for more background on lncRNA:

  • How does the manner in which lncRNAs are transcribed, processed, and regulated differ from that of other RNAs?
  • Are lncRNAs evolutionarily conserved, both in terms of their primary sequences and secondary structures?
  • Are all lncRNAs functional? Which ones have detectable biological functions in cells or in the whole organism?
  • Does the pervasive transcription that generates the lncRNA transcripts play a regulatory role distinct from the steady-state accumulation of the lncRNAs?
  • Can lncRNAs be exploited for clinical applications and therapeutics?

After reading this review, I thought to myself that there are many open questions about lncRNA but no comprehensive answers yet deciphered. When I then checked Google Scholar for items with both “deciphered” and “lncRNA” as terms, I found there were over 1,800 such items. Evidently, there are quite a few authors who, like me, view unknown functions of lncRNA as a cipher. I suspect that much of the now mysterious lncRNA function will eventually be deciphered thanks, in part, to the power of CRISPRi.

Your comments are welcomed.

Footnote

Readers interested in lentiviral sgRNA library construction and use for screening target cells can find general information at this website from which the following self-explanatory schematic provides a high-level overview of the workflow.

Taken from cellecta.com

New CRISPR System Reported for Targeting RNA Instead of DNA

  • Current “CRISPR Craze” for DNA Editing is Catalyzing Creativity
  • Early CRISPR Innovator Feng Zhang Now Reports Targeting RNA
  • This New “C2c2” System has Specificity Issues But is Nevertheless Promising

Just when you thought that the “CRISPR craze” would soon transition from the fundamental discovery phase to the improvements phase, something entirely new for CRISPR has come along. That something, recently published by Feng Zhang and others in venerable Science magazine, targets RNA instead of DNA. Consequently, this may lead to transient vs. permanent editing, as well as other RNA- vs. DNA-based applications.

Before further commenting on this exciting new RNA-targeting approach using CRISPR, here are a few snippets about the original DNA version of CRISPR to set the stage, and substantiate my tongue-in-cheek referral to the craze about it.

Backstory

Taken from igtrcn.org

Taken from igtrcn.org

Editing with CRISPR, which is short-form for CRISPR-Cas9, uses sequence-specific guide RNA (gRNA) to target DNA for cutting by Cas9 nuclease, as depicted below. Guide RNA and Cas9 can be introduced into cells either encoded in a vector or as synthetic gRNA and synthetic Cas9 mRNA, which TriLink offers in either wild-type or base-modified forms of Cas9 mRNA. CRISPR for genome editing was publicly described in Science in 2012 by co-corresponding authors Jennifer A. Doudna, a biologist at the University of California, Berkeley, and the French microbiologist Emmanuelle Charpentier. But Feng Zhang, at the Broad Institute, was first to obtain a patent on the technique.

Not surprisingly, given the financial potential for DNA editing by CRISPR, which has been called the ‘biotech discovery of the century,’ there is ownership litigation. This dispute is getting rather ugly, if you will, according to an article in Science titled Accusations of errors and deception fly in CRISPR patent fight.

crispPotential financial gain aside, PubMed stats I found clearly substantiate the craze factor in numeric terms: >4,000 publications to date with a rapidly increasing trajectory, i.e. ~600 in 2014 and ~1,200 in 2015, which is an average of roughly 4 publications every day in that year!

By the way, in the chart above that I made for CRISPR publications in PubMed, there was only one report in 2002, which was the first publication to identify CRISPR. These Dutch investigators used computer analysis to find a novel family of repetitive DNA sequences that is present among both domains of the prokaryotes (Archaea and Bacteria), but absent from eukaryotes or viruses. They noted that “[t]his family is characterized by direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non-repetitive sequences. To appreciate their characteristic structure, we will refer to this family as the clustered regularly interspaced short palindromic repeats (CRISPR).” 

Taken from youtube.com

Taken from youtube.com

CRISPR was also selected as 2015 Science Breakthrough of the Year, and is featured in an interesting YouTube video that is definitely worth watching, in my opinion.

Enough said for CRISPR editing of DNA, let’s move on to RNA editing with CRISPR that offers a fundamentally different editing approach: whereas DNA editing makes permanent changes to the genome of a cell, CRISPR-based RNA-targeting approach may allow researchers to make temporary changes. Moreover, this can be adjusted up or down, and may one day provide greater specificity and functionality than existing methods for RNA interference (RNAi) using either siRNA or antisense oligos.

CRISPR Targeting RNA

Feng Zhang. Taken from mit.news.edu

Feng Zhang. Taken from mit.news.edu

At the risk of seeming to be too trendy, this section heading could have read “Feng Zhang 2.0” in that Zhang at the Broad Institute, along with co-corresponding author Eugene V. Koonin at NIH and uber-famous “Broadster” Eric Langer plus others on a large team, have characterized a new CRISPR system that targets RNA—but not DNA. In their recent Science publication they demonstrated that this new system involves a Class 2 type VI-A CRISPR-Cas effector—aptly abbreviated C2c2 (pronounced “see too, see too”)—that has RNA-guided RNase function.

The researchers originally identified C2c2 in the bacterium Leptotrichia shahii (L. shahii) in a systematic search for previously unidentified CRISPR systems within diverse bacterial genomes. They focused on C2c2 because its sequence contained two copies of a domain called higher eukaryotes and prokaryotes nucleotide-binding (HEPN) that has only been found in RNases. Mutating the putative catalytic site within either of C2c2’s HEPN domains demonstrated that none of the mutated enzyme versions could cut RNA in vitro, suggesting that both HEPN domains are necessary for C2c2 to work.

CRISPR-C2c2 from L. shahii reconstituted in E. coli to mediate interference of the RNA phage MS2 via crRNA facilitated by the two HEPN nuclease domains. Taken from Abudayyeh et al.

CRISPR-C2c2 from L. shahii reconstituted in E. coli to mediate interference of the RNA phage MS2 via crRNA facilitated by the two HEPN nuclease domains. Taken from Abudayyeh et al.

But C2c2 Cleaves Collateral RNA—a Case for “Lemons into Lemonade”?

Unlike Cas9, which cuts DNA only within the sequence dictated by the CRISPR gRNA, C2c2 was found to make cuts within the target sequence and adjacent, nonspecific sequences. While this collateral cleavage obviously presents a specificity problem, Zhang and his colleagues were able to create a deactivated C2c2 (dC2c2) variant by alanine substitution of any of the four predicted HEPN domain catalytic residues. To me this clever trick is like converting “lemons into lemonade” in that undesired non-specific cleavage is transformed into a programmable RNA-binding protein having potential utility.

For example, the investigators speculate that the ability of dC2c2 to bind to specified sequences could be used in the following ways:

  • Bring effector modules to specific transcripts in order to modulate their function or translation, which could be used for large-scale screening, construction of synthetic regulatory circuits, and other purposes.
  • Fluorescently tag specific RNAs in order to visualize their trafficking and/or localization.
  • Alter RNA localization through domains with affinity for specific subcellular compartments.
  • Capture specific transcripts through direct pull-down of dC2c2 in order to enrich for proximal molecular partners including RNAs and proteins.

Listen to Zhang’s Grad Students 

While the details of this seminal work published in Science is not easily summarized, its practical implications have been concisely translated, if you will, by first coauthor Omar O. Abudayyeh, and second coauthor Jonathan S. Gootenberg—both graduate student members of the Zhang lab—in three short videos that I encourage you to watch at this link.

Left: Omar Abudayyeh. Taken from zlab.mit.edu Right: Jonathan Gootenberg Taken from zlab.mit.edu

Left: Omar Abudayyeh. Taken from zlab.mit.edu Right: Jonathan Gootenberg Taken from zlab.mit.edu

Publication protocol generally lists coauthors in order of contribution, so in this C2c2 publication that has many coauthors, these fellows know what they’re talking about because they did lots of the lab work. Congrats to them, Feng Zhang (again), and all of the other contributors.

As always, your comments are welcomed and encouraged.

Chinese Scientists to Pioneer First Human CRISPR Clinical Trial

  • Chinese Team Begins First CRISPR-Based Anticancer Immunotherapy Clinical Study
  • US Consortium’s CRISPR Clinical Study OK’d by NIH Panel
  • Survey Indicates More Worry than Enthusiasm for Gene-Editing in Babies
Taken from jeantet.ch

Taken from jeantet.ch

Regular readers of my blog will recall a number of previous postings on gene editing using CRISPR-Cas9 (aka CRISPR), which has rapidly become the hottest trend in nucleic acid-based biotechnology and medical research. That opinion is partly based on the fact that this relatively new technology has already amassed thousands of publications, including 1,250 in 2015 alone! Additional evidence follows from the numerous start-up and established biopharma companies pursuing CRISPR-based therapeutics, which is “the biggest biotech discovery of the century” according to one report.

Now, even more exciting developments for CRISPR are on the horizon. Chinese researchers are poised for the first human clinical trial using CRISPR, and an analogous study in the US awaiting FDA approval. Both of these trials involve forms of cancer immunotherapy, which is a very hot field in itself, and is briefly introduced in the next section.

Cancer Immunotherapy

Cancer immunotherapy is the use of the immune system to treat cancer either actively, passively, or by a combination of these approaches, which exploit the fact that cancer cells often have macromolecules on their surface that can be detected by the immune system (aka tumor-associated antigens, TAAs). Active immunotherapy directs the immune system to attack tumor cells by targeting TAAs, whereas passive immunotherapies enhance existing anti-tumor responses and include the use of monoclonal antibodies, lymphocytes and cytokines.

Numerous antibody therapies have been approved by the FDA and other regulatory authorities worldwide. In contrast, active immunotherapies, which usually involve the removal of immune cells from the blood or from a tumor for reintroduction to the patient, have lagged in such approvals. In fact, the only US-approved cell-based therapy is Dendreon’s Provenge®, for the treatment of prostate cancer. A recent series of NY Times articles highlights some powerful examples of cancer immunotherapy, especially from the perspective of interviews with patients and their physicians.

Taken from howitworksdaily.com

Taken from howitworksdaily.com

For the purpose of this blog, I’ll add that adoptive T-cell therapy is a form of passive immunization by the transfusion of T-cells, which are found in blood and tissue and usually activate when they find “foreign” pathogens. These pathogens can be either infected cells, or antigen presenting cells present in tumor tissue, where they are known as tumor infiltrating lymphocytes. Although these cells can attack the tumor, the environment within the tumor is highly immunosuppressive, preventing immune-mediated tumor death.

As depicted below, T-cells specific to a tumor antigen can be removed from a tumor sample or filtered from blood. Subsequent activation and culturing is performed ex vivo, with the resultant cells being reinfused. Importantly, activation can take place through genetic engineering, such as gene editing by CRISPR.

Cancer specific T-cells can be obtained by fragmentation and isolation of tumor infiltrating lymphocytes, or by genetically engineering cells from peripheral blood. The cells are activated and grown prior to transfusion into the recipient (tumor bearer). Taken from Wikipedia.org

Cancer specific T-cells can be obtained by fragmentation and isolation of tumor infiltrating lymphocytes, or by genetically engineering cells from peripheral blood. The cells are activated and grown prior to transfusion into the recipient (tumor bearer). Taken from Wikipedia.org

CRISPR Goes Clinical in China

As I write this post, Chinese scientists at Sichuan University’s West China Hospital in Chengdu will reportedly become the first in the world to inject people with cells modified using the CRISPR gene-editing method. This landmark trial will involve patients with metastatic non-small cell lung cancer who have not responded to chemotherapy, radiation therapy and/or other treatments.

The team will extract T cells from the blood of the trial participants and then use CRISPR to knock out a gene encoding a protein called PD-1 that normally regulates the T cell’s immune response to prevent it from attacking healthy cells. As depicted below, this so-called checkpoint has been targeted by small molecule inhibitors (anti PD-1), but with somewhat limited success so far—notably including failure of a would-be billion-dollar drug (Opdivo®) recently reported by Bristol-Myers Squibb. Nevertheless, the presently envisaged PD-1 gene-edited cells will be amplified in the lab and re-introduced into the patient’s bloodstream to circulate and, hopefully, attack the cancer.

Taken from smartpatients.com

Taken from smartpatients.com

Potential Concerns of CRISPR Clinical Trials

While the Chinese trial may be groundbreaking, it is not without risk. There is concern that the edited T-cells could attack normal tissue as it’s well documented that CRISPR can result in gene edits at the wrong place in the genome. To help mediate this risk, the T-cells will be validated by biotechnology company MedGenCell—a collaborator on the trial—to ensure that the correct gene is knocked out before the cells are re-introduced into patients.  Since the primary purpose of this phase one trial is to determine if the approach is safe, participants will be closely monitored for side effects, and researchers will pay close attention to biological markers in the blood.

Some may say that this type of trial in humans is premature, but China has always tried to be a leader in CRISPR research. Carl June, a clinical researcher in immunotherapy at the University of Pennsylvania in Philadelphia explains, ‘China places a high priority on biomedical research.’ And Tetsuya Ishii, a bioethicist in Japan, is quoted in Nature magazine as saying that ‘When it comes to gene editing, China goes first.”

Initial CRISPR Clinical Trial in USA Awaiting Review Board and FDA Approvals

While the Chinese team seems positioned to be the first to conduct a CRISPR clinical trial, the US isn’t far behind. As reported earlier this summer, the Recombinant DNA Research Advisory Committee (RAC) at the NIH has approved an analogous—but genetically more complex—proposal to use CRISPR-edited T cells for cancer immunotherapy. The RAC reviews all proposals for human trials involving modified DNA that are conducted in the United States, and the investigators now have to convince review boards at their own institutions, and the FDA, to allow the trial. This will hopefully be done by the end of 2016.

The proposed trial is a collaborative effort involving the University of Pennsylvania, M.D. Anderson Cancer Center in Texas, and the University of California, San Francisco. This trial will be funded by a $250-million immunotherapy foundation formed in April 2016 by former Facebook president Sean Parker. According to a news item in Nature, The University of Pennsylvania will produce the edited cells, and will recruit and treat patients alongside the collaborating medical centers in Texas and California.

In this study, researchers will perform three CRISPR edits with T cells from patients with several types of cancers: 1. a gene for a protein engineered to detect and target cancer cells will be inserted, 2. a natural T-cell protein that could interfere with this process will be removed and 3. the gene for a protein that identifies the T cells as immune cells and prevents the cancer cells from disabling them will be removed. The researchers will then infuse the edited cells back into the patient.

Both of the studies being performed by the Chinese and US teams are very exciting to me. I will be paying close attention to the progress of these studies over the next few months and hope to report back to you with some very interesting and ground breaking results.

Survey Indicates Public Concern in the US About Gene Editing in Babies

A Pew Research Center pole focusing on concerns about gene editing was recently reported in Nature. The poll surveyed more than 4,700 people in the United States and the results indicate that more people are concerned than enthusiastic about gene editing.

The quadrants below (from 0-100%) show responses to the question, “How worried or enthusiastic do you feel about gene editing to reduce disease risk in babies?”

Taken from nature.com

Taken from nature.com

While these findings speak for themselves, I hasten to add that this same pole also asked “Have you heard or read about this topic?” The following replies (in quadrants from 0-100%) indicate that a substantial percentage of respondents who have not at all read about gene editing nevertheless expressed either worry or enthusiasm for gene editing. Ditto for those who read a little about gene editing.

babies

It would seem, then, that we should take this poll with a grain (or two) of salt as it apparently includes a substantial amount of uninformed opinion. This is not too surprising given the complex nature of gene editing and it’s relatively new position in research. We can see from the results of this poll that a significant amount of education may be needed to garner increased public support for gene editing. Hopefully, the results of the studies highlighted above will begin to pave this road.

Hope for the Best but Expect Complications

This section heading, which summarizes my parting comments about the advent of CRISPR-enabled clinical trials, is based upon my having participated in several decades of research on nucleic acid-based concepts for radically different approaches to traditional small-molecule therapeutics. First was the idea of using chemically modified antisense oligonucleotides to block gene expression, which encountered non-specificity issues, low potency, delivery, and a host of other issues that took two decades to sort through. Then there was the idea of using chemically modified short-interfering RNA (siRNA) for modulating gene expression via RNA interference (RNAi). This, too, encountered similar problems in reaching the clinic. Ditto for anti-microRNAs (antagomirs).

I’m hoping that CRISPR-based therapies meet with success far faster—and prove to be affordable to society. I won’t, however, be surprised if progress is slow—and quite expensive.

Are you excited about potential CRISPR-based therapies? Do you have concerns about their safety and efficacy? Do you believe the general public is ready to accept gene editing therapies? Please share your thoughts as your comments are always welcome.

DIY CRISPR Kit – Door to Democratization or Disaster?

  • Gene Editing with CRISPR is All the “Buzz”
  • Low-Cost CRISPR Kit Being Sold to DIY “Biohackers”
  • What is the Balance Between Democratization and Preventing Disaster?

The dictionary definition of democratization is the transition to a more democratic political regime. Since democracy emphasizes the role of individuals in society, democratization is generally perceived to be good. This political concept of democratization is being increasingly morphed, if you will, to describe the transition of science and technology from trained specialists in traditional labs to any individual, anywhere—including someone’s kitchen table.

Taken from oocities.org

Taken from oocities.org

Lest you get the impression I’m an elitist, and not in favor of fostering better understanding—and appreciation—of science by non-scientists everywhere, I definitely am not. I want the value of science to be widely appreciated. Even if I weren’t of that opinion, democratization of science and technology is already evident in this exemplary cartoon indicating how DNA is now familiar to virtually everyone. But I digress…

Taken from diy-bio.com

From diy-bio.com

It is evident that molecular biology has also undergone democratization based on emergence of so-called “do it yourself” (DIY) advocates of biology (DIY-BIO), which on the surface seems like a good thing. But, as I’ll expand upon below, DIY-BIO has morphed in a way which has elevated concerns that a well-intentioned DIY aficionado anywhere can now access genetically powerful CRISPR reagents that might inadvertently unleash a harmful home-made organism.

CRISPR Basics

First off, I should note that gene editing by CRISPR—thankfully short for “clustered regularly-interspaced short palindromic repeats”—actually involves another component named Cas9—short for CRISPR associated protein 9. Cas9 is an enzyme that recognizes single guide RNA (sgRNA) hybridized to one strand of specifically targeted DNA via the 5’end of sgRNA, as depicted in green in the mechanism below. The remaining sgRNA has a double-stranded “stem” (black, red) and loop (purple) internal structure, and a 3’ end with several stem-loop structures (red).

Taken from jeantet.ch

Taken from jeantet.ch

The scissors indicate Cas9 cutting both strands of DNA, which thus allows for insertion of so-called donor DNA and, consequently, enabling a variety of genetic manipulations in plants, bacteria, human or animal cells. Chemically synthesized sgRNA that target any gene of interest can be readily designed for purchase, along with Cas9 in the form of biosynthetic Cas9 mRNA encoding this necessary protein component.

CRISPR’s importance as an emerging, useful tool for gene editing is evident from the number of publications in PubMed that have approximately doubled each year since the seminal to give an estimated 2,500 publications indexed to CRISPR as a search term. Unfortunately (but perhaps not surprisingly given the billion-dollar implications), there is an ongoing dispute over inventorship involving the Broad Institute (see Feng Zhang patent), the University of California, and the University of Vienna.

Biohacker Promotes DIY CRISPR Kit

Josiah Zayner (Taken from http://www.ifyoudontknownowyaknow.com)

Josiah Zayner (Taken from http://www.ifyoudontknownowyaknow.com)

As mentioned in the introduction, self-proclaimed “biohackers” who are avid fans and practitioners of DIY molecular biology, have been busily “doing their thing” for some time now without much cautionary publicity. That’s changing, however, as a result of the advent of CRISPR together with relatively easy access to its sgRNA and Cas9 reagents. One case in point involves Josiah Zayner, who has a PhD from the Department of Biochemistry and Molecular Biophysics at the University of Chicago and now lives in the San Francisco Bay Area.

Zayner’s online biographical sketch states that he is “very active in Biohacking and DIY Science and run[s] an online Biohacking supply store The ODIN.” By visiting the website for The ODIN, which reportedly raised $65,000 by crowdfunding online via Indiegogo, you’ll find various items for conducting molecular biology experiments, along with an “about” page stating that “smaller groups of people, small labs or even DIY Scientists on their own can do amazing things if they have access to resources that are normally only available to large heavily funded labs and companies.”

While this seems all fine and good is some ways, the item offered by The ODIN that has led to controversy is the first-ever DIY kit for CRISPR. This, according to an article in The Mercury News, “raises the specter—deeply troubling to some experts—of a day when dangerous gene editing is conducted far from the eyes of government regulators, posing risk to the environment or human health”.

The article goes on to quote one expert who said The ODIN kit is sold for manipulating yeast and could never be used to alter human genes, while another expert cautioned that the kit can teach basic principles to do so with appropriate modifications. Another problem is inadvertent conversion of yeast into a harmful microorganism that might be accidentally spread.

Taken from mercurynews.com

Taken from mercurynews.com

While I share these concerns, it will be virtually impossible to prevent individuals or small groups intent on nefarious activities using CRISPR technology. On the other hand, I have to admit that I would be very concerned if I were living next door or otherwise nearby Josiah if he is indeed practicing what he’s preaching, so to speak, using CRISPR in his kitchen as pictured right.

CRISPRized Plants, Too

If you think that DIY is a passing fad with few devotees, think again. Aside from the main DIY-BIO website that you can peruse, a recent online article in Fusion talks about a couple of DIY enthusiasts doing things that make the hairs on my neck stand up, as the saying goes. For instance, David Ishee, a 30-year-old Mississippi resident who never attended college, does at-home experiments in his shed using online kits for growing plants, but will now use CRISPR to carry out gene editing.

Ishee reportedly will use software like DeskGen that advertises its “on-demand CRISPR libraries” for gene editing, and is quoted as saying “That gives me a lot of new options. Up until now, all the genetic edits I’ve made have been limited to plasmids and unguided genomic insertions. That limits the kinds of cells I can work with and the types of work I can do.”

So what will Ishee do? The answer is that nobody but he knows. If his genetically edited plants grow and seeds get carried by the wind, they could someday end up in your backyard. What then? Who knows? Could be creepy.

Possibly harmful, irreversible consequences of completely democratized CRISPR are completely unknown. Therein lies the essence of the problem that has many experts quite concerned, as reported in Fusion. I share that concern.

Parting Shot

In closing this brief story about DIY synthetic biology using CRISPR, I must say that I wish journalists writing for newspapers and other media would stick to news that is factual and not interpreted for commentary that is flat out wrong or intentionally provocative. My case in point is the following big font, bold letters headline:

“Finally, your chance to play God!”

This was used by time.com to recycle the aforementioned piece by The Mercury News. Shame on time.com for this misleading and totally wrong exclamation. But I digress…

I would greatly appreciate knowing your thoughts about DIY CRISPR by sharing them here as comments.

The Most Interesting Scientist in the World: George M. Church

  • Mind Boggling Breadth and Significance of Scientific Publications
  • Serial Entrepreneur and Science Advisor to Many Companies
  • Radical Advocate of Total Openness for Personal Genomics

While seeing for the umpteenth time a Dos Equis beer commercial featuring The Most Interesting Man in the World, I was suddenly inspired to write a blog about The Most Interesting Scientist in the World. After scrolling and polling my memory to decide who that would be, it was an easy decision to pick George M. Church, professor of genetics at Harvard. As I’ll briefly highlight herein, Prof. Church’s contributions continually span a mind boggling spectrum of science that cuts across academic theory, ground breaking “how to” methods, serial entrepreneurship, and—perhaps most importantly—radical openness for personal genomics.

George M. Church and The Most Interesting Man in the World: ‘I don’t always read science, but when I do it’s by George M. Church.’ (taken from Bing Images)

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