1 septillion reasons Dad’s CRISPR-Cas9 may already be Toast

May 16, 2017 |

In the rapid-fire tech and political world of 2017, a day feels like a month, a year is like a generation, and sometimes it feels like 90% of the population hasn’t heard of a technology wave before it is swamped by the next tsunami, and that may well be the case with the first wave of CRISPR-Cas technology.

It was voted “Breakthrough of the Year” in 2015 by AAAS and big companies are just now taking big licenses — but is CRISPR-Cas, as we knew it back a couple of centuries ago (i.e., in 2016), already toast? Is there another piece on the way to marry precision with throughput to move faster on yield.

What is CRISPR-Cas9 again?

If you know all about CRISPR, you can skip this paragraph in which we offer our CRISPR backstory.

CRISPR-Cas9 is a technique for making a cut at a desired point in a cell’s genome. You can pick the spot and do an edit. Amazing stuff. You can clip out junk genes, or add in useful ones. The promise is pretty obvious to anyone who has ever pruned a tree — you want Nature to direct all its energy to producing the target product you have in mind — whether it is peaches, fuel, or a therapeutic target.

Pruning directs that energy towards fruiting and away from branching. In that case, we’re editing the tree. But we can edit at the gene level, and that’s what breeding animals or plants is about. To get a desired trait, you breed and breed until Nature gives you what you want, and you double-cross to fix that trait so that it replicates on a consistent level.

That’s how we have boosted yields around the world. That’s why we have enough to eat, and fuel and fiber and everything else we get from biomass.

But editing through hybridizing is clunky, slow and imprecise. You may get the trait you want, but Nature may also cross a whole bunch of junk DNA is the process.

That’s where CRISPR-Cas comes in. You edit with complete precision. Snip, snip, you’re done. It’s a hyper-specific, gene level version of what any gardener does with a pair of pruning shears, yet takes the system of improving genomes, using the set of DNA that Nature gives us to work with, to another level.

The 3 Unmistakable Signs of CRISPR heat and CRISPR love

For CRISPR-Cas9, the medical, agricultural, and industrial applications abound, and we’ve seen the 3 unmistakable signs that people think there’s powerful value that can be unlocked.

1. Company formation amidst tsunamis of hype and gobs of venture capital.

2. Patent wars. Every important patent has a thousand parent, every useless patent is an orphan.

3.  If Friends of the Earth and their ilk are raising money by attacking it, you know it’s got value – that stream of bioethical chat about whether something that is not transgenic is still GMO and thereby to be controlled, feared and shamed, we’re seeing that for sure.

What’s enduring about the CRISPR revolution?

Undoubtedly, the breakthrough in establishing tools to edit the genetic code at the DNA level.

What’s the limitation?

Well, if you were designing something like the ideal, you’d be able to make a huge number of edits and make a huge number of changes at each edit point, and you’d be able to track back results to each individual edit. In other words, you’d like a technology such as CRISPR-Cas9 to have something like what you have in a word processing app when you do things like “find and replace”.  You’d like to go past one-at-a-time editing and do everything-at-once. Ideally.

1 septillion reasons that you need throughput — precision alone is not enough

As Matt Lipscomb, founder of Boulder-based DMC Limited and its own cool tech licensed out of Duke, explained not long ago to Duke’s Pratt School’s website editors:

“The number of potential combinations of biochemical reactions to engineer in a microbe is something on the order of a septillion. That’s a one with 24 zeroes after it,” said Matt Lipscomb, CEO and co-founder of DMC. “Even with the recent significant advances in lab automation, computing power and machine learning algorithms, it’s impossible to experimentally explore the entire design space.”

Even if you could run an experiment every second, it would take you 31 quadrillion years to go through the available options. Or roughly 1 million times the expected lifespan of the universe. So, you need speed, and you need trackability.

The world of microbe engineering, and the OPX Bio connection

The broad field of study is called (by some) microbe engineering, and in recent years we have seen a host of companies break out with different capabilities in that space. There are the big commercial biofoundries that are building up heft, like Zymergen and Ginkgo BioWorks — and companies in the orbit include Arzeda, Genomatica, Codexis, Twist Biosciences, and Amyris. For sure, Zymergen and Ginkgo will tell you that they can achieve very precise targets in performance whether a novel strain (Ginkgo) or in strain improvement (ZYmergen). They just get precision at very high speed.

Here’s an overview of the space from Ginkgo CEO Jason Kelly:

And there is work underway in establishing a big public BioFoundry, and we’ve covered that here.

In the CRISPR-Cas space, Caribou Biosciences is the spin-out that is in everyone’s spotlight. They’ve turned CRISPR-Cas into a licensable platform — and have bveen racking the licenses up at almost a one a week rate. And as they point out “through the use of multiple guide RNAs, Cas9 can enable multiplexed engineering of many sites in parallel.”

That’s the key, isn’t it?

Now, let’s turn to work we’ve been following for a number of years out of the like of the University of Colorado, the Colorado Center for Biorefining and Biofuels, and OPX Biotechnologies. OPXBio’s underlying tech was known as EDGE (Efficiency Directed Genome Engineering), and was eventually acquired by Cargill in 2016.

Ryan Gill was a co-founder of OPXBio and was the founding Managing Director at C2B2 and the Gill Lab has come up with another wonder, which has been licensed to a company known as Muse bio, which emerged in late 2015 — to some extent, out of the ashes of OPXBio, since long-time OPX’er Tanya Warnecke Lipscomb is CTO at Muse, and there are OPXers elsewhere around the halls.

Muse has a revolutionary capability which they describe in verbiage not aimed at the layperson as “high throughput massively-multiplexed CRISPR editing of proteins, pathways, and genomes.”

They add cryptically, “through our powerful bioinformatics and novel molecular approach, ForgeCraft generates low-cost libraries of thousands of designer protein, pathway, or genome variants each with specifically defined, trackable mutations. This allows the impact of specific changes to be determined through rapid selection and high throughput screening allowing research timelines and costs to be reduced.”

References to “multiplexed” and “massively-multiplexed” may evoke images of finding Guardians of the Galaxy on fifteen out of 36 screens at your local AMC this week, but it’s not entirely a bad way to start thinking about the space. In the end, AMC wants yield (that’s box office), through an optimal organization of the theater (that’s DNA).

The Netflix problem

So, here’s what Netflix discovered. Through streaming, they can give you all the moves you want at any time you want them. You have, conceptually, total flexibility (yes, we know that Outlander does not air on Netflix, but go with us for a minute). That’s more powerful than having to achieve choice by driving down to Blockbuster as in the old days, or getting lots of movies but at set times through HBO, or getting like one movie a week and at a set time, like network TV used to have with “Sunday Night at the Movies.”

Multiplex — which you could call “streaming” — that’s where the yield gets maximized — via lots of edit points and lots of edits — and you get the lowest cost film library. (Yes, we’ve strained the analogy enough). But here’s the world of microbe engineering, looked at from the point of view of precision and throughput.

Boulder vs Boston vs Berkeley

Which is to say, there’s much to admire in CRISPR-Cas, and CRISPR is the platform all the future technologies will be built upon, because it has taken precision to an entirely different universe. But the road to cash, cash, cash is via product, product, product, and you travel over a road called yield, yield, yield — the flexibility that comes with multiple editing points and gobs of edits is a powerful formula, and the new companies are going that way, fast.

Three Bs to remember in this space. Berkeley, Boston and Boulder.

They’re working hard in Berkeley and Boston on yield. The race is on. But don’t count out Boulder — they may have the horse to win. With Muse bio’s ForgeCraft generating “low-cost libraries of thousands of designer protein, pathway, or genome variants each with specifically defined, trackable mutations” — as soon as Muse gets some more development, the first-gen approaches to CRISPR-Cas may well be toast.

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