Epigenetics and Beyond — The Dawn of CRISPR

Epigenetics Dispatch #2 — Don Dulchinos — neurosphere.org

Introduction

In an earlier article, I tried to bring developmental psychology theories up to date by proposing a biological mechanism driving movement across levels of existence (Clare Graves) or circuits (Tim Leary and Robert Anton Wilson); namely, the development of the science of epigenetics, especially as popularized by David Sloane Wilson in This View of Life. (I noticed a year after my article that D.S. Wilson himself described an ongoing partnership, that was already in progress before I wrote, with the Integral Community, whose founder Ken Wilber incorporates Graves’ developmental perspectives and models.) In my article I asked,

[H]ow does the evolution happen on the micro level — in our own lives and cultures? As a start, D.S. Wilson reminds us that variations in gene expression depend on life conditions — the entire gene repertoire is much greater than what we use in course of a lifetime. (Graves follower Beck loves to talk about life conditions — people don’t, indeed can’t evolve to higher levels until problems of existing and lower levels are faced and solved.)

So, epigenetics is operating upon us all the time, and genetic options are available to us. The trick is how to access more of the unexpressed genes inside us.

The Leary/Wilson circuit theory had seemed to me to get fuzzier in describing higher levels, especially lacking some mechanism for triggering higher states, but then I re-read a version of their work (Info-Psychology) and wrote

Circuits 7 and 8 seemed no more specific than they had been 10 years earlier, at least as I read it then. But wait! — “the Seventh [circuit] Brain learns to control, integrate, organize Neuro-genetic signals and manipulate Chromosomes.” Emphasis mine — well hello CRISPR gene editing, 20 years later!!

So transgenerational human cultural change counts as an evolutionary process, similar to genetic evolution, the immune system and our capacity to learn as individuals. The slow process of genetic evolution follows the fast evolution of cultural evolution. Traces of your grandparents’ cultural evolution are within you.

So having a framework, I wanted in this article (christened Epigenetics Dispatch #2 in a series) to present a summary (mostly for my own education) of what has been happening in CRISPR research, development and application. This would set the stage for investigating how gene editing, broadly speaking, might be or might become a tool for personal “evolution” (with or without the quotes) in one’s own lifetime. (That will be the subject of Epigenetics Dispatch #3.)

In particular, the key development that bears on my view of the 8 Circuit model is summarized in this statement:

CRISPR-Cas-based transcriptional activators allow genetic engineers to specifically induce expression of one or many target genes

To set the stage for that discussion, I’ve assembled the following notes; less an essay than a compilation.

First Generation Gene Therapy

Gene therapy has been around for 20 years, and yet is still in its early days as a common medical treatment. This appears partly due to our profit-driven medical environment (at least in the U.S.) A path to widespread commercialization, and thus availability of treatments, has not yet emerged.

A gene therapy treats a genetic or inherited disease by replacing, deactivating, modifying, or introducing genes (with the help of a vector) in targeted cells.

Several approved gene therapy medicines now exist. All involve taking a virus, replacing its harmful contents with a disease-treating gene, and injecting it into a person (or exposing the person’s cells to that virus in a dish and putting them back). Though effective, these treatments remain cumbersome to build and jaw-droppingly expensive: One recently approved gene therapy for people with an inherited bleeding disorder costs a record-breaking $3.5 million for a single-use vial, making it the most expensive drug in the world. (See Blue Matter, Commercializing Gene Therapies)

Progress has been made, but it has been slow (and expensive) going until recently. CRISPR is recently touted as providing an approach and toolkit for gene therapy. People (like me) know vaguely about CRISPR (and gene therapy generally) from general news coverage. What actually happens?

CRISPR Technology Overview

A basic overview from an editorial in the New York Times: “Gene editing is much newer technology but builds on the gains of gene therapy. Instead of using a virus, however, gene editing relies on a molecular machine called CRISPR, which can be instructed to repair a mutation in a gene in nearly any organism, right where that “typo” occurs…in the patients’ DNA. And so much substantive progress has been made in the field of genetic medicine that it’s clear scientists have now delivered on a remarkable dream: word-processor-like control over DNA.” [https://www.nytimes.com/2022/12/09/opinion/crispr-gene-editing-cures.html]

A more technical definition from Wikipedia:

CRISPR (an acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea.[2] These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral (i.e. anti-phage) defense system of prokaryotes and provide a form of acquired immunity.[2][3][4][5] CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.[6]

The actual manipulation of CRISPR sequences is facilitated by Cas9 (CRISPER-associated protein 9) technology.

Cas9 is an enzyme that uses CRISPR sequences as a guide to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms. [from Wikipedia}

Not directly relevant to this article, but the Nobel Prize in Chemistry in 2020 was awarded to two chemists for the development of CRISPR-Cas9, but they lost the patent case in 2022 to a different inventor at the Board Institute (Harvard and MIT). From the Broad Institute Web site:

In April, 2014, the USPTO granted US Patent №8,697,359 to Broad, MIT, and Dr. Feng Zhang. This patent (which draws priority from a provisional patent application filed on December 12, 2012) contained successful experiments.

This marked the world’s first engineering of CRISPR-Cas9 to be delivered and used to achieve mammalian genome editing. Zhang was the first to file a patent application that described and enabled such a method.

Since 2013, the Zhang Lab has openly shared CRISPR reagents and tools with more than 3,000 institutions in 75 countries through the nonprofit Addgene. For research by companies, Broad Institute licenses CRISPR IP non-exclusively and through the open “inclusive innovation” model to maximize opportunities for therapeutic development across human disease.

State of the Art — Business Development and Research Findings

Gene therapy has been available and used in food and farming industries for 20 years or so, accompanied by a patent and regulatory regime and not a little fear of GMO “Frankenfood”. (My personal view is GMO-based foods are not as insidious as the creation of patented, seedless crops that leave farmers at the mercy of the Archer Daniels Midland, Cargill and other dominant ag enterprises.) But only the last five years have seen an increase in use on humans, partly due to the emergence of CRISPR.

The first example of a person to be gene-edited with CRISPR occurred in 2019, for a disorder of red blood cell production. In recent years, CRISPR treatments have been applied to a range of conditions, including:

Congenital blindness

Sickle cell disease

Heart disease

Cancer

HIV

An initial use of gene editing to treat high cholesterol took place in mid-2022. It illustrates several fast moving dimensions of the technology

Base editing

The study also marks an early use of base editing, a novel adaptation of CRISPR that was first developed in 2016. Unlike traditional CRISPR, which cuts a gene, base editing substitutes a single letter of DNA for another.

The gene Verve is editing is called PCSK9. It has a big role in maintaining LDL levels and the company says its treatment will turn the gene off by introducing a one-letter misspelling.

Verve’s cholesterol-lowering treatment uses base editing, as do several other experimental therapies. A company called Beam Therapeutics, for example, is using the approach to create potential treatments for sickle-cell disease and other disorders.

Prime Editing

And then there’s prime editing, or “CRISPR 3.0.” This technique allows scientists to replace bits of DNA or insert new chunks of genetic code. It has only been around for a few years and is still being explored in lab animals. But its potential is huge.

That’s because prime editing vastly expands the options. “CRISPR 1.0” and base editing are somewhat limited — you can only use them in situations where cutting DNA or changing a single letter would be useful. Prime editing could allow scientists to insert entirely new genes into a person’s genome.

Synergy with mRNA Vaccine Development

One reason Verve’s base-editing technique is moving fast is that the technology is substantially similar to mRNA vaccines for covid-19. Just like the vaccines, the treatment consists of genetic instructions wrapped in a nanoparticle, which ferries everything into a cell.

While the vaccine instructs cells to make a component of the SARS-CoV-2 virus, the particles in Verve’s treatment carry RNA directions for a cell to assemble and aim a base-editing protein, which then modifies that cell’s copy of PCSK9, introducing the tiny mistake.

“The pandemic and the emergent need for vaccines [created] large-scale manufacturing capacity,” says Kiran Musunuru, a gene-editing expert at the University of Pennsylvania who cofounded Verve. That capacity “can be easily repurposed for genetic therapy,” he says, and “of course, abundant capacity means reduced prices.”

Research and Corporate Development

Following is a short selection of companies and institutions using CRISPR/Cas9, and some recent research examples and business partnerships.

CRISPR Therapeutics (founded 2014)

o CRISPR Therapeutics has established a portfolio of therapeutic programs across a broad range of disease areas including hemoglobinopathies, oncology, regenerative medicine and rare diseases.

o To accelerate and expand its efforts, CRISPR Therapeutics has established strategic partnerships with leading companies including Bayer, Vertex Pharmaceuticals and ViaCyte, Inc.

o Dr. Emmanuelle Charpentier, one of our scientific founders, co-invented CRISPR/Cas9 gene editing. [The Nobel Prize winner, not the patent holder.]

o Web site: www.crisprtx.com

CRISPR QC (founded 2022)

o Offers a CRISPR/Cas9 gene-editing tool and touts an “analytics platform [that] allows unparalleled insight into the factors that impact editing outcomes, such as cleavage and binding activity.”

o Web site: www.crisprqc.com

Intellia Therapeutics (founded 2015)

o Reported clinical data suggesting the CRISP R gene-editing therapy may offer cure for hereditary angioedema (HAE) ( a disease which causes recurrent episodes of swelling, sometimes life threatening)

Lund University Sweden

o Development and Validation of CRISPR Activator Systems for Overexpression of CB1 Receptors in Neurons (causing Alzheimer’s Disease or other neurological disorders

o Our results show that CRISPRa techniques could be successfully used in neurons to target overexpression of genes involved in synaptic transmission, and can potentially represent a next-generation gene therapy approach against neurological disorders.

- ArsenalBio (founded 2019)

o Recent $200 million financing round will help the company expand its programmable cell therapy research activities and grow its pipeline of therapeutic candidates for solid tumor malignancies across a range of cancer indications.

Current Industry Issues and Challenges

As seen from the Arsenal Bio funding round described above, capital is chasing CRISPR research and development as a new and promising field. The risk/reward ratio is daunting so far, but the sector is attracting significant capital. These are early days, not all clinical research has been positive, and the financials of the sector can be volatile.

Editas Medicine said Thursday that it will halt a study of its experimental CRISPR/Cas9 genome editing medicine EDIT-101 for the treatment of blindness due to Leber congenital amaurosis 10 and look for a partner for the programme.

CEO Gilmore O’Neill remarked that the findings from the BRILLIANCE study “provide a proof of concept and important learnings for our inherited retinal disease programmes.” Editas added that EDIT-101 was tolerated with no ocular serious adverse events or dose-limiting toxicities observed in the study, although shares in the company plunged as much as 20% on the news. https://firstwordpharma.com/story/5676763?aid=5676763

In a New York Times Op-Ed, Fyodor Urnov professor of molecular and cell biology at the University of California, Berkeley, and a gene editor at its Innovative Genomics Institute, lamented that CRISPR technology is not more widely available, but “the greatest obstacles are not technical but legal, financial and organizational.”

‌‌According to U.S. and European law, a detailed process is in place to ensure safety and efficacy of the experimental medicine. It starts with meticulous studies using human cells in a dish and in animals. This takes at least two years, and if everything checks out, scientists embark on the most expensive leg of the trip: making the CRISPR medicine, which has to be synthesized to comply with a regulatory standard known as good manufacturing practice. Designed to protect patients from faulty medicines, this U.S. federal requirement stretches out the making of clinic-grade CRISPR to a year and over $1 million, followed by over a year of animal testing. All of this happens before you can use it to treat a human being.https://www.nytimes.com/2022/12/09/opinion/crispr-gene-editing-cures.html

He argues that this system means investment in treatments are only aimed at conditions that constitute a large market, and calls for some special government intervention.

Investing public funding in CRISPR cures for rare diseases not only will help us treat people with uncommon mutations (a global community numbering hundreds of millions of people) but also can provide insights that can be infused into CRISPR clinical innovation for common diseases.

These are tough trade-offs, but the privatization of medical research for now means these are still early days for CRISPR.

Application to Personal Development — Dispatch #3

That said, it is interesting (if a little science-fictional) to speculate on the use of CRISPR technology. At this point, one can see the clear application of gene therapy and gene editing to “fixing errors” in the genetic code of an individual. This only proves the mutability of common genetic profiles found in the population.

But it still remains the case that we all carry genes encoded in our bodies that are not used, or “expressed”. The third dispatch in this series, coming soon, will address a series of questions around the possibility of using gene editing and related technologies to unlock higher level/circuit functioning, in a similar way to which Leary and Wilson felt the use of marijuana and LSD unlocked existing circuits 5 and 6 in their system.

- What are the mechanisms whereby epigenetic selection occurs?

- Do cultural, life conditions play a role?

- What unused genes are in there? Could they be identified in high-functioning individuals? Could they be “unlocked” using a form of gene editing?

- What did development pioneer Clare Graves have to say about brain structures he believed were activated as individuals progressed up the levels of human emergence?

- What did Leary say about “histones masking” genetic capabilities?

- Are there alternative interpretations for Circuit 7 than neurogenetic interventions?

- Is transgenerational human cultural change essentially an evolutionary, epigenetic process as well?