Synthetic biology: Impacting drug discovery

Gene editing

Mark Kotter, Founder and CEO of bit.bio, talks with Reece Armstrong about different approaches to synthetic biology and its applications in programming stem cells into mature, functional human cells for drug discovery and the creation of next generation.

In the last 10 years, synthetic biologists have developed new technologies that have led to some of the most innovative and important therapies on the market. Notable therapeutic modalities being advanced by synthetic biology include immunotherapy, CRISPR therapy, and tumour targeting therapies like Chimeric Antigen Receptor (CAR-T) cells. As such, synthetic biology is playing a vital role in the production of treatments for a range of conditions and hard- to-treat diseases.

Based in Cambridge, UK, bit.bio is a synthetic biology company that has developed a technology to program induced pluripotent stem cells (iPSCs) into any human cells of choice. These cells can be provided to companies and scientists involved in disease research and drug discovery. Also, bit. bio is using this technology to build its own in-house cell therapy pipeline. The company was founded in 2016 as a spin-out of the University of Cambridge and has raised approximately $200 million to help advance its novel cell identity coding platform.

Mark Kotter, Founder and CEO of bit.bio defines synthetic biology as “the engineering of biology,” but states that in order to do this you want to “enter a software paradigm.”

“So maybe a better phrase is programming biology,” he states.

Programming biology

For Kotter and bit.bio, the company views cells as if they are a computer with the nucleus and genes acting like the hard drive and computer programs that operate within.

In order to program biology, there are three things you need to be able to do, according to Kotter. “First, you have to read DNA. That’s, of course, the sequencing revolution. The next thing, you have to write code. That’s where DNA synthesis and CRISPR comes in. The third aspect, which people thought would be a given, is you have to be able to execute that genetic code –like pressing the enter button on a keyboard,” Kotter says.

Editing and executing code has never been particularly challenging in things like genetically engineered E. coli or yeast, two strains that have been used as foundational chassis for synthetic biology research and which have contributed to the development of small molecules and biopharmaceuticals.

When it comes to genetic editing for humans and other species however, “cells have defence mechanisms – a process called gene silencing – that actually resist the genetic manipulation or the activation of a new programmed state,” Kotter states, before going on to explain that “gene silencing has emerged as a mechanism that specifically constrains our ability to program human cells.”

Kotter further explains how the execution of code is recognised as a “big bottleneck when it comes to mammalian and especially human cells.” Some examples include industrial cell lines such as Chinese hamster ovary (CHO) cells and human embryonic kidney (HEK) 293 cells, having reduced long-term yields during manufacturing due to silencing1.

How do we overcome this?

bit.bio has discovered a way to utilise genomic safe harbour sites, which are areas of the genome that enable researchers to reprogram cells without the programs being silenced. This means that new genetic material can be integrated into these areas, and it will function in a fully predictable manner.

The company’s proprietary opti-ox (optimised inducible overexpression) technology is what bit.bio uses to execute these genetic programs in human stem cells. The synthetic biology platform is able to express transcription factor combinations that reprogram human iPSCs into highly defined and mature human cell types. The use of genomic safe harbour sites ensures it does so with remarkable consistency.

Using opti-ox, “we can edit and insert genetic information without disturbing the function of the cell,” Kotter says. At the recent International Society of Stem Cell Research (ISSCR) conference in Boston, Kotter presented the company’s latest consistency data from three different cell types reprogrammed with opti-ox, and these data confirm that bit.bio is truly making the manufacture of human cells an industrial process. Samples of cells were sequenced from independent opti-ox reprogrammed manufacturing lots for multiple cell types. Analysis of the samples show fewer than 1% differentially expressed genes in bulk-mRNA sequencing experiments between manufacturing lots.

This is important when you consider cell therapies, which rely on a consistent and stable supply of cells that match the needs of patients. Being able to manufacture human cells at scale and with consistency has great applications for therapies dependent on this supply chain. opti-ox relies on the precise activation of transcription factors to induce gene expression.

“What transcription factors do is they regulate gene expression. So this is the class of regulatory proteins that determine transcriptional state. It has been found that there is a class of transcription factors that act as master regulators that create cascades of transcription, sort of feedback loops, or gene regulatory networks that when activated, wholly define the identity of cells,” Kotter explains. The master regulator transcription factors define the transcriptional state of a cell, which dictates its function and identity. bit.bio’s opti-ox precision reprogramming platform is able to consistently activate these master regulators, executing the genetic code of every cell so they are reprogrammed to the same functional human cell every time.

The translation issue

The issue of translatability between animal and human models is well documented throughout drug discovery. “There’s a huge gap between human biology and the animal models that are currently used in drug development,” Kotter says. “I always take this example: there’s not a single mouse on this planet that has Alzheimer’s.”

Genetically modified mouse models have something which looks analogous to Alzheimer’s, and these models are then used to test potential candidate compounds in an attempt to develop therapies.

“In most cases, we’ve learned that the compound that has been able to treat the mouse disease that was created by scientists works very differently (or not at all) on the disease that we have, in our human condition,” Kotter says. “In order to close this ‘translation gap’, you need to use human cells that actually suffer from the condition of interest to increase your chances that drug development leads to something that works in humans.”

This issue of translation is something that extends into the very basis of research, in that experiments should be reproducible. “A basic premise of science is that if you can do an experiment, and someone else does this experiment it should be reproduced,” Kotter says.

However, this is unfortunately not the case and reports indicate at least two thirds of scientists cannot reproduce their peers’ work2.

“The real problem lies in the fact that there are very few biological standards,” Kotter says, referencing engineering standards such as millimetres and inches. “So the standard doesn’t have to be the ultimate truth, it just has to be the reference that people can use to benchmark their own results.”

But how does this relate to cells? Ensuring cell populations yield reproducible results is especially difficult due to biology’s inherent nature for change.

“Cell populations change when you culture them, cell lines behave differently in one lab versus another lab, largely because of the evolutionary pressures that are on cells,” Kotter explains.

Synthetic biology, Kotter states, can help overcome this issue by providing human cells that are identical every time, meaning they are standardised, and experiments using them are reproducible. In particular, stem cells, primary cells, and programmed, mature cell models based on iPSCs, the type bit.bio are offering in its portfolio, represent promising approaches for research.

Synthetic biology offers a democratisation of research, where reproducible experiments and translatable science sits at its core. Its applications in areas like cell therapies could very well help reduce costs for developers and bring effective treatments to millions of patients much sooner. On cell therapies, Kotter says: “The reason why cells can be so powerful as therapeutics is because they can do two things: they can replace lost cells, and they can also interact with the environment. So they’re intelligent medicines. This is the promise of cell therapies.”

“Now what we need to do is we need to get from the initial paradigm, which is patient specific, complex and expensive to a paradigm where it becomes a medicine which is available to everyone. And this is exactly what synthetic biology can address.”

DDW Volume 24 – Issue 3, Summer 2023

References:

  1. https://www.sciencedirect. com/science/article/pii/ S2405471222004641
  2. https://www.bbc.co.uk/news/ science-environment-39054778

Mark KotterBiography

Mark Kotter is a doctor, scientist, and serial entrepreneur. As a neurosurgeon, he treats patients with spinal cord injury. He is CEO & founder of bit.bio – a cell coding company empowering biomedical research and a new generation of cures through precision reprogrammed human cells.

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