Tag Archives: gene editing

Precision targeting of the liver for gene editing

Apparently the magic is in the lipid nanoparticles. A March 1, 2021 news item on Nanowerk announced research into lipid nanoparticles as a means to deliver CRISPR (clustered regularly interspaced short palindromic repeats) to specific organs (Note: A link has been removed),

The genome editing technology CRISPR has emerged as a powerful new tool that can change the way we treat disease. The challenge when altering the genetics of our cells, however, is how to do it safely, effectively, and specifically targeted to the gene, tissue and organ that needs treatment.

Scientists at Tufts University and the Broad Institute of Harvard [University] and MIT [Massachusetts Institute of Technology] have developed unique nanoparticles comprised of lipids — fat molecules — that can package and deliver gene editing machinery specifically to the liver.

In a study published in the Proceedings of the National Academy of Sciences [PNAS] (“Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3”), they have shown that they can use the lipid nanoparticles (LNPs) to efficiently deliver the CRISPR machinery into the liver of mice, resulting in specific genome editing and the reduction of blood cholesterol levels by as much as 57% — a reduction that can last for at least several months with just one shot.

A March 2, 2021 Tufts University news release (also on EurekAlert but published March 1, 2021), which originated the news item, provides greater insight into and technical detail about the research,

The problem of high cholesterol plagues more than 29 million Americans, according to the Centers for Disease Control and Prevention. The condition is complex and can originate from multiple genes as well as nutritional and lifestyle choices, so it is not easy to treat. The Tufts and Broad researchers, however, have modified one gene that could provide a protective effect against elevated cholesterol if it can be shut down by gene editing.

The gene that the researchers focused on codes for the angiopoietin-like 3 enzyme (Angptl3). That enzyme tamps down the activity of other enzymes – lipases – that help break down cholesterol. If researchers can knock out the Angptl3 gene, they can let the lipases do their work and reduce levels of cholesterol in the blood. It turns out that some lucky people have a natural mutation in their Angptl3 gene, leading to consistently low levels of triglycerides and low-density lipoprotein (LDL) cholesterol, commonly called “bad” cholesterol, in their bloodstream without any known clinical downsides.

“If we can replicate that condition by knocking out the angptl3 gene in others, we have a good chance of having a safe and long term solution to high cholesterol,” said Qiaobing Xu, associate professor of biomedical engineering at Tufts’ School of Engineering and corresponding author of the study. “We just have to make sure we deliver the gene editing package specifically to the liver so as not to create unwanted side effects.”

Xu’s team was able to do precisely that in mouse models. After a single injection of lipid nanoparticles packed with mRNA coding for CRISPR-Cas9 and a single-guide RNA targeting Angptl3, they observed a profound reduction in LDL cholesterol by as much as 57% and triglyceride levels by about 29 %, both of which remained at those lowered levels for at least 100 days. The researchers speculate that the effect may last much longer than that, perhaps limited only by the slow turnover of cells in the liver, which can occur over a period of about a year. The reduction of cholesterol and triglycerides is dose dependent, so their levels could be adjusted by injecting fewer or more LNPs in the single shot, the researchers said.

By comparison, an existing, FDA [US Food and Drug Administration]-approved version of CRISPR mRNA-loaded LNPs could only reduce LDL cholesterol by at most 15.7% and triglycerides by 16.3% when it was tested in mice, according to the researchers.

The trick to making a better LNP was in customizing the components – the molecules that come together to form bubbles around the mRNA. The LNPs are made up of long chain lipids that have a charged or polar head that is attracted to water, a carbon chain tail that points toward the middle of the bubble containing the payload, and a chemical linker between them. Also present are polyethylene glycol, and yes, even some cholesterol – which has a normal role in lipid membranes to make them less leaky – to hold their contents better.

The researchers found that the nature and relative ratio of these components appeared to have profound effects on the delivery of mRNA into the liver, so they tested LNPs with many combinations of heads, tails, linkers and ratios among all components for their ability to target liver cells. Because the in vitro potency of an LNP formulation rarely reflects its in vivo performance, they directly evaluated the delivery specificity and efficacy in mice that have a reporter gene in their cells that lights up red when genome editing occurs. Ultimately, they found a CRISPR mRNA-loaded LNP that lit up just the liver in mice, showing that it could specifically and efficiently deliver gene-editing tools into the liver to do their work.

The LNPs were built upon earlier work at Tufts, where Xu and his team developed LNPs with as much as 90% efficiency in delivering mRNA into cells. A unique feature of those nanoparticles was the presence of disulfide bonds between the long lipid chains. Outside the cells, the LNPs form a stable spherical structure that locks in their contents. When they are inside a cell, the environment within breaks the disulfide bonds to disassemble the nanoparticles. The contents are then quickly and efficiently released into the cell. By preventing loss outside the cell, the LNPs can have a much higher yield in delivering their contents.

“CRISPR is one of the most powerful therapeutic tools for the treatment of diseases with a genetic etiology. We have recently seen the first human clinical trail for CRISPR therapy enabled by LNP delivery to be administered systemically to edit genes inside the human body. Our LNP platform developed here holds great potential for clinical translation,” said Min Qiu, post-doctoral researcher in Xu’s lab at Tufts.  “We envision that with this LNP platform in hand, we could now make CRISPR a practical and safe approach to treat a broad spectrum of liver diseases or disorders,” said Zachary Glass, graduate student in the Xu lab. Qiu and Glass are co-first authors of the study.

Here’s a link to and a citation for the paper,

Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3 by Min Qiu, Zachary Glass, Jinjin Chen, Mary Haas, Xin Jin, Xuewei Zhao, Xuehui Rui, Zhongfeng Ye, Yamin Li, Feng Zhang, and Qiaobing Xu. PNAS March 9, 2021 118 (10) e2020401118 DOI: https://doi.org/10.1073/pnas.2020401118

This paper appears to be behind a paywall.

Toronto’s ArtSci Salon and The Mutant Project March 15, 2021

The Mutant Project is both a book (The Mutant Project: Inside the Global Race to Genetically Modify Humans) and an event about gene editing with special reference to the CRISPR (clustered regularly interspaced short palindromic repeats) twins, Lulu and Nana. The event is being held by Toronto’s ArtSci Salon. Here’s more from their March 3, 2021 announcement (received via email),

The Mutant Project

A talk and discussion with Eben Kirksey

Discussants:

Dr. Elizabeth Koester, Postdoctoral fellow, Department of History, UofT [University of Toronto]

Vincent Auffrey, PhD student, IHPST [Institute for the History and Philosophy of Science and Technology], UofT

Fan Zhang, PhD student, IHPST, UofT

This event will be streamed on Zoom and on Youtube

Here is the link to register to Zoom on the 15th:

https://utoronto.zoom.us/meeting/registe/tZErcemoqzwrG9foNF5Ud86uJXdNeIzQSfDw

Event on FB: https://www.facebook.com/events/4033393163381012/

YouTube: https://www.youtube.com/watch?v=pEFfj3Ovsfk&feature=youtu.be

At a conference in Hong Kong in November 2018, Dr. He Jiankui announced that he had created the first genetically modified babies—twin girls named Lulu and Nana—sending shockwaves around the world. A year later, a Chinese court sentenced Dr. He to three years in prison for “illegal medical practice.”

As scientists elsewhere start to catch up with China’s vast genetic research program, gene editing is fueling an innovation economy that threatens to widen racial and economic inequality. Fundamental questions about science, health, and social justice are at stake: Who gets access to gene editing technologies? As countries loosen regulations around the globe, from the U.S. to Indonesia, can we shape research agendas to promote an ethical and fair society?

Join us to welcome Dr. Kirksey, who will discuss key topics from his book “The Mutant Project”.

The talk will be followed by a Q&A

EBEN KIRKSEY is an American anthropologist who finished his latest book as a Member of the Institute for Advanced Study in Princeton, New Jersey. He has been published in Wired, The Atlantic, The Guardian and The Sunday Times. He is sought out as an expert on science in society by the Associated Press, The Wall Street Journal, The New York Times, Democracy Now, Time and the BBC, among other media outlets. He speaks widely at the world’s leading academic institutions including Oxford, Yale, Columbia, UCLA, and the International Summit of Human Genome Editing, plus music festivals, art exhibits, and community events. Professor Kirksey holds a long-term position at Deakin University in Melbourne, Australia. For more information, please visit https://eben-kirksey.space/.

Elizabeth Koester currently holds a SSHRC [Social Science and Humanities Research Council of Canada] Postdoctoral Fellowship in the Department of History at the University of Toronto. After practising law for many years, she undertook graduate studies in the history of medicine at the Institute for the History and Philosophy of
Science and Technology at the University of Toronto and was awarded a PhD in 2018. A book based on her dissertation, In the Public Good: Eugenics and Law in Ontario, will be published by McGill-Queen’s University Press and is anticipated for Fall 2021.

Vincent Auffrey is pursuing his PhD at the Institute for the History of Philosophy of Science and Technology (IHPST) at the University of Toronto. His focus is set primarily on the social history of medicine and the history of eugenics in Canada. Secondary interests include the histories of scientific racism and of anatomy, and the interplay between knowledge and power.

Fan Zhang is a PhD student at the History of Philosophy of Science and Technology (IHPST) at the University of Toronto

Kirksey’s eponymous website,

CRISPR/Cas9 used successfully to edit SIV (simian immunodeficiency virus, which is similar to HIV) out of monkey genome

Before reading further please note, the research discussed in this posting is based on animal testing, which many people find highly disturbing.

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), or more familiarly CRISPR/Cas9, has been been used to edit simian immunodeficiency virus from infected monkeys’ cells according to a December 2, 2020 article by Matthew Rozsa for Salon.com (Note: Links have been removed),

With multiple coronavirus vaccines being produced as we speak, the COVID-19 pandemic appears to have an end in sight, though the HIV pandemic continues after more than 40 years. That might seem like a head-scratcher: why is HIV, a virus we’ve known about for decades, so much harder to cure than a virus discovered just last year? Part of the reason is that HIV, as a retrovirus, is a more complex virus to vaccinate against than SARS-CoV-2 — hence why a vaccine or other cure has eluded scientists for decades. 

Now, a surprising new study on a related retrovirus shows incredible promise for the potential to develop a cure for HIV, or human immunodeficiency virus. In an article published in the scientific journal Nature Communications, scientists revealed that they had used CRISPR – a genetic technology that can alter DNA and whose developers won the 2020 Nobel Prize in Chemistry [specifically, Jennifer Doudna and Emanuelle Charpentier received the Nobel for developing CRISPR-cas9 or CRISPR/Cas9 not CRISPR alone) — to successfully edit SIV (simian immunodeficiency virus), a virus similar to HIV, out of the genomes of non-human primates.  Specifically, the scientists were able to edit out the SIV genome from rhesus macaque monkeys’ infected cells.

For anyone who’s interested in how CRISPR was developed and the many contributions which have led to the current state-of-the-art for CRISPR gene editing, see the History subsection of Wikipedia’s CRISPR entry.

Getting back to Rozsa’s December 2, 2020 article,

“This study used the CRISPR CaS9 system, which has been described as molecular scissors,” Andrew G. MacLean, PhD, wrote to Salon. MacLean is an associate professor at the Tulane National Primate Research Center and the Department of Microbiology and Immunology at Tulane University School of Medicine and was a senior co-investigator of the study. “It uses a highly specific targeting system to cut out a specific portion of DNA that is necessary for HIV to be able to produce more virus.”

He added, “Our collaborators at in the Khalili Lab at Temple University have developed a method of ‘packaging’ this within a single so-called vector. A vector is a non-disease causing virus that is used as a carrier for the CRISPR CaS9 scissors to get it into the tissues of interest.”

The experiments with SIV are considered to be a gateway to understanding HIV, as HIV is believed to have evolved from SIV, and is genetically similar.

“The rhesus macaque model of HIV/AIDS is the most valuable model to test efficacy of new interventions or approaches for preventing or treating HIV infection, prior to human clinical trials,” Binhua Ling, PhD, associate professor at the Southwest National Primate Research Center, Texas Biomedical Research Institute, wrote to Salon. “This first proof-of-principal [emphasis mine] study on the rhesus macaque model indicates that this virus-vehicle-delivered-CRISPR system can reach many tissue sites of the body, and is able to effectively delete virus DNA in infected cells. This paves the way for applying the same technology to the human body, which could lead to a cure for HIV infection.”

Tricia H. Burdo, PhD, another senior co-investigator on the new study who works at the Lewis Katz School of Medicine at Temple University, explained to Salon by email that “HIV is in a class of viruses (retroviruses) that inserts itself into the DNA of the host, so you can really think of this now as a genetic disease” — in other words, the kind of thing that would be ripe for CRISPR’s scissors-like ability to remove errant or unwanted genetic material. Burdo notes that the CRISPR technology discussed in the article “cuts out this foreign viral gene.”

The study was conducted on eight Rhesus macaque monkeys. That is a very small number to start with and not all of the monkeys received the CRISPR/Cas9 treatment. From the ‘Animals used in the study and ethical statement‘ subsection of the study, “Animals were sacrificed for tissue collection 3 weeks after … .” Leaving aside how anyone may feel about ‘sacrificing …’, three weeks is not a long time for observation.

Should you be interested, there is a November 30, 2020 Tulane University news release announcing the research.

If you want to read the whole study, here’s a link and a citation,

CRISPR based editing of SIV proviral DNA in ART treated non-human primates by Pietro Mancuso, Chen Chen, Rafal Kaminski, Jennifer Gordon, Shuren Liao, Jake A. Robinson, Mandy D. Smith, Hong Liu, Ilker K. Sariyer, Rahsan Sariyer, Tiffany A. Peterson, Martina Donadoni, Jaclyn B. Williams, Summer Siddiqui, Bruce A. Bunnell, Binhua Ling, Andrew G. MacLean, Tricia H. Burdo & Kamel Khalili. Nature Communications volume 11, Article number: 6065 (2020) DOI: https://doi.org/10.1038/s41467-020-19821-7 Published: 27 November 2020

This paper is open access.

As Rozsa notes in his December 2, 2020 article, the Joint United Nations Programme on HIV/AIDS estimates that 32.7 million [24.8 million–42.2 million] people have died from AIDS-related illnesses since the start (1981?) of the epidemic to the end of 2019.

“transforming a plant is still an art” even with CRISPR

“Plus ça change, plus c’est la même chose (the more things change, the more things stay the same), is an old French expression that came to mind when I stumbled across two stories about genetic manipulation of food-producing plants.

The first story involves CRISPR (clustered regularly interspersed short palindromic repeats) gene editing and the second involves more ancient ways to manipulate plant genetics.

Getting ‘CRISPR’d’ plant cells to grow into plants

Plants often don’t grow from cells after researchers alter their genomes. Using a new technology, a team coaxed wheat (above) and other crops to more readily produce genome-edited healthy adult plants. Credit: Juan Debernardi

An October 13, 2020 news item on phys.org announces research about getting better results after a plant’s genome has been altered,

Researchers know how to make precise genetic changes within the genomes of crops, but the transformed cells often refuse to grow into plants. One team has devised a new solution.

Scientists who want to improve crops face a dilemma: it can be difficult to grow plants from cells after you’ve tweaked their genomes.

A new tool helps ease this process by coaxing the transformed cells, including those modified with the gene-editing system CRISPR-Cas9, to regenerate new plants. Howard Hughes Medical Institute Research Specialist Juan M. Debernardi and Investigator Jorge Dubcovsky, together with David Tricoli at the University of California, Davis [UC Davis] Plant Transformation Facility, Javier Palatnik from Argentina, and colleagues at the John Innes Center [UK], collaborated on the work. The team reports the technology, developed in wheat and tested in other crops, October 12, 2020, in the journal Nature Biotechnology.

An October 12, 2020 Howard Hughes Medical Institute (HHMI) news release, which originated the news item, provides more detail,

“The problem is that transforming a plant is still an art [emphasis mine],” Dubcovsky says. The success rate is often low – depending on the crop being modified, 100 attempts may yield only a handful of green shoots that can turn into full-grown plants. The rest fail to produce new plants and die. Now, however, “we have reduced this barrier,” says Dubcovsky, a plant geneticist at UC Davis. Using two genes that already control development in many plants, his team dramatically increased the formation of shoots in modified wheat, rice, citrus, and other crops.

Although UC Davis has a pending patent for commercial applications, Dubcovsky says the technique is available to any researcher who wants to use it for research, at no charge. A number of plant breeding companies have also expressed interested in licensing it. “Now people are trying it in multiple crops,” he says.

Humans have worked to improve plants since the dawn of agriculture, selecting wild grasses to produce cultivated maize and wheat, for example. Nowadays, though, CRISPR has given researchers the ability to make changes to the genome with surgical precision. They have used it to create wheat plants with larger grains, generate resistance to fungal infection, design novel tomato plant architectures, and engineer other traits in new plant varieties.

But the process isn’t easy. Scientists start out with plant cells or pieces of tissue, into which they introduce the CRISPR machinery and a small guide to the specific genes they’d like to edit. They must then entice the modified cells into forming a young plant. Most don’t sprout – a problem scientists are still working to understand.

They have tried to find work-arounds, including boosting the expression of certain genes that control early stages of plant development. While this approach has had some success, it can lead to twisted, stunted, sterile plants if not managed properly.Dubcovsky and his colleagues looked at two other growth-promoting genes, GRF and GIF, that work together in young tissues or organs of plants ranging from moss to fruit trees. The team put these genes side-by-side, like a couple holding hands, before adding them to plant cells. “If you go to a dance, you need to find your partner,” Dubcovsky says. “Here, you are tied with a rope to your partner.”

Dubcovsky’s team found that genetically altered wheat, rice, hybrid orange, and other crops produced many more shoots if those experiments included the linked GRF and GIF genes. In experiments with one variety of wheat, the appearance of shoots increased nearly eight-fold. The number of shoots in rice and the hybrid orange, meanwhile, more than doubled and quadrupled, respectively. What’s more, these shoots grew into healthy plants capable of reproducing on their own, with none of the defects that can result when scientists boost other development-controlling genes. That’s because one of the genes is naturally degraded in adult tissues, Dubcovsky says.

Caroline Roper, a plant pathologist at University of California, Riverside who was not involved in the work, plans to use the new technology to study citrus greening, a bacterial disease that kills trees and renders oranges hard and bitter.

To understand how citrus trees can protect themselves, she needs to see how removing certain genes alters their susceptibility to the bacterium — information that could lead to ways to fight the disease. With conventional techniques, it could take at least two years to generate the gene-edited plants she needs. She hopes Dubcovsky’s tool will shorten that timeline.  

“Time is of the essence. The growers, they wanted an answer yesterday, because they’re at the brink of having to abandon cultivating citrus,” she says.

For anyone who noticed the reference to citrus greening in the last paragraphs of this news release, I have more information aboutthe disease and efforts to it in an August 6, 2020 posting.

As for the latest in gene editing and regeneration, here’s a link to and a citation for the paper,

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants by Juan M. Debernardi, David M. Tricoli, Maria F. Ercoli, Sadiye Hayta, Pamela Ronald, Javier F. Palatnik & Jorge Dubcovsky. Nature Biotechnology volume 38, pages 1274–1279(2020) DOI: https://doi.org/10.1038/s41587-020-0703-0 First Published Online: 12 October 2020 Journal Issue Date: November 2020

This paper is behind a paywall.

Ancient farming techniques for engineering crops

I stumbled on this story by Gabriela Serrato Marks for Massive Science almost three years late (it’s a Dec. 5, 2017 article),

There are more than 50 strains of maize, called landraces, grown in Mexico. A landrace is similar to a dog breed: Corgis and Huskies are both dogs, but they were bred to have different traits. Maize domestication worked the same way.

Some landraces of maize can grow in really dry conditions; others grow best in wetter soils. Early maize farmers selectively bred maize landraces that were well-adapted to the conditions on their land, a practice that still continues today in rural areas of Mexico.

If you think this sounds like an early version of genetic engineering, you’d be correct. But nowadays, modern agriculture is moving away from locally adapted strains and traditional farming techniques and toward active gene manipulation. The goal of both traditional landrace development and modern genetic modification has been to create productive, valuable crops, so these two techniques are not necessarily at odds.

But as more farmers converge on similar strains of (potentially genetically modified) seeds instead of developing locally adapted landraces, there are two potential risks: one is losing the cultural legacy of traditional agricultural techniques that have been passed on in families for centuries or even millennia, and another is decreasing crop resilience even as climate variability is increasing.

Mexico is the main importer of US-grown corn, but that imported corn is primarily used to feed livestock. The corn that people eat or use to make tortillas is grown almost entirely in Mexico, which is where landraces come in.

It is a common practice to grow multiple landraces with different traits as an insurance policy against poor growth conditions. The wide range of landraces contains a huge amount of genetic diversity, making it less likely that one adverse event, such as a drought or pest infestation, will wipe out an entire crop. If farmers only grow one type of corn, the whole crop is vulnerable to the same event.

Landraces are also different from most commercially available hybrid strains of corn because they are open pollinating, which means that farmers can save seeds and replant them the next year, saving money and preserving the strain. If a landrace is not grown anymore, its contribution to maize’s genetic diversity is permanently lost.

This diversity was cultivated over generations from maize’s wild cousin, teosinte, by 60 groups of indigenous people in Mexico. Teosinte looks like a skinny, hairier version of maize. It still grows wild in some parts of Central America, but its close relatives have been found, domesticated, at archaeological sites in the region over 9,000 years old. These early maize cobs could easily fit in the palm of your hand – not big enough to be a staple crop that early farmers could depend upon for sustenance. Genetically, they were more similar to wild teosinte than to modern maize.

[] archaeologists also found that the cobs in Honduras, which is outside the natural range of teosinte, were larger than cobs of the same age from the original domestication region in southern Mexico. The scientists think that people in Honduras were able to develop more productive maize landraces because their crops were isolated from wild teosinte.

The size and shape of the ancient cobs from Honduras show that early farmers engineered the maize crop [emphasis mine] to make it more productive. They developed unique landraces that were well adapted to local conditions and successfully cultivated enough maize to support their communities. In many ways, they were early geneticists. [emphasis mine] …

We have a lot to learn from the indigenous farmers who were growing maize 4,000 years ago. Their history provides examples of both environmentally sound genetic modification and effective adaptation to climate variability. [emphases mine] …

Plus ça change …, eh?

New US regulations exempt many gene-edited crops from government oversight

A June 1, 2020 essay by Maywa Montenegro (Postdoctoral Fellow, University of California at Davis) for The Conversation posits that new regulations (which in fact result in deregulation) are likely to create problems,

In May [2020], federal regulators finalized a new biotechnology policy that will bring sweeping changes to the U.S. food system. Dubbed “SECURE,” the rule revises U.S. Department of Agriculture regulations over genetically engineered plants, automatically exempting many gene-edited crops from government oversight. Companies and labs will be allowed to “self-determine” whether or not a crop should undergo regulatory review or environmental risk assessment.

Initial responses to this new policy have followed familiar fault lines in the food community. Seed industry trade groups and biotech firms hailed the rule as “important to support continuing innovation.” Environmental and small farmer NGOs called the USDA’s decision “shameful” and less attentive to public well-being than to agribusiness’s bottom line.

But the gene-editing tool CRISPR was supposed to break the impasse in old GM wars by making biotechnology more widely affordable, accessible and thus democratic.

In my research, I study how biotechnology affects transitions to sustainable food systems. It’s clear that since 2012 the swelling R&D pipeline of gene-edited grains, fruits and vegetables, fish and livestock has forced U.S. agencies to respond to the so-called CRISPR revolution.

Yet this rule change has a number of people in the food and scientific communities concerned. To me, it reflects the lack of accountability and trust between the public and government agencies setting policies.

Is there a better way?

… I have developed a set of principles and practices for governing CRISPR based on dialogue with front-line communities who are most affected by the technologies others usher in. Communities don’t just have to adopt or refuse technology – they can co-create [emphasis mine] it.

One way to move forward in the U.S. is to take advantage of common ground between sustainable agriculture movements and CRISPR scientists. The struggle over USDA rules suggests that few outside of industry believe self-regulation is fair, wise or scientific.

h/t: June 1, 2020 news item on phys.org

If you have the time and the inclination, do read the essay in its entirety.

Anyone who has read my COVID-19 op-ed for the Canadian Science Policy may see some similarity between Montenegro’s “co-create” and this from my May 15, 2020 posting which included my reference materials or this version on the Canadian Science Policy Centre where you can find many other COVID-19 op-eds)

In addition to engaging experts as we navigate our way into the future, we can look to artists, writers, citizen scientists, elders, indigenous communities, rural and urban communities, politicians, philosophers, ethicists, religious leaders, and bureaucrats of all stripes for more insight into the potential for collateral and unintended consequences.

To be clear, I think times of crises are when a lot of people call for more co-creation and input. Here’s more about Montenegro’s work on her profile page (which includes her academic credentials, research interests and publications) on the University of California at Berkeley’s Department of Environmental Science, Policy, and Management webspace. She seems to have been making the call for years.

I am a US-Dutch-Peruvian citizen who grew up in Appalachia, studied molecular biology in the Northeast, worked as a journalist in New York City, and then migrated to the left coast to pursue a PhD. My indigenous ancestry, smallholder family history, and the colonizing/decolonizing experiences of both the Netherlands and Peru informs my personal and professional interests in seeds and agrobiodiversity. My background engenders a strong desire to explore synergies between western science and the indigenous/traditional knowledge systems that have historically been devalued and marginalized.

Trained in molecular biology, science writing, and now, a range of critical social and ecological theory, I incorporate these perspectives into research on seeds.

I am particularly interested in the relationship between formal seed systems – characterized by professional breeding, certification, intellectual property – and commercial sale and informal seed systems through which farmers traditionally save, exchange, and sell seeds. …

You can find more on her Twitter feed, which is where I discovered a call for papers for a “Special Feature: Gene Editing the Food System” in the journal, Elementa: Science of the Anthropocene. They have a rolling deadline, which started in February 2020. At this time, there is one paper in the series,

Democratizing CRISPR? Stories, practices, and politics of science and governance on the agricultural gene editing frontier by Maywa Montenegro de Wit. Elem Sci Anth, 8(1), p.9. DOI: http://doi.org/10.1525/elementa.405 Published February 25, 2020

The paper is open access. Interestingly, the guest editor is Elizabeth Fitting of Dalhousie University in Nova Scotia, Canada.

The CRISPR yogurt story and a hornless cattle update

Clustered regularly interspaced short palindromic repeats (CRISPR) does not and never has made much sense to me. I understand each word individually it’s just that I’ve never thought they made much sense strung together that way. It’s taken years but I’ve finally found out what the words (when strung together that way) mean and the origins for the phrase. Hint: it’s all about the phages.

Apparently, it all started with yogurt as Cynthia Graber and Nicola Twilley of Gastropod discuss on their podcast, “4 CRISPR experts on how gene editing is changing the future of food.” During the course of the podcast they explain the ‘phraseology’ issue, mention hornless cattle (I have an update to the information in the podcast later in this posting), and so much more.

CRISPR started with yogurt

You’ll find the podcast (almost 50 minutes long) here on an Oct. 11, 2019 posting on the Genetic Literacy Project. If you need a little more encouragement, here’s how the podcast is described,

To understand how CRISPR will transform our food, we begin our episode at Dupont’s yoghurt culture facility in Madison, Wisconsin. Senior scientist Dennis Romero tells us the story of CRISPR’s accidental discovery—and its undercover but ubiquitous presence in the dairy aisles today.

Jennifer Kuzma and Yiping Qi help us understand the technology’s potential, both good and bad, as well as how it might be regulated and labeled. And Joyce Van Eck, a plant geneticist at the Boyce Thompson Institute in Ithaca, New York, tells us the story of how she is using CRISPR, combined with her understanding of tomato genetics, to fast-track the domestication of one of the Americas’ most delicious orphan crops [groundcherries].

I featured Van Eck’s work with groundcherries last year in a November 28, 2018 posting and I don’t think she’s published any new work about the fruit since. As for Kuzma’s point that there should be more transparency where genetically modified food is concerned, Canadian consumers were surprised (shocked) in 2017 to find out that genetically modified Atlantic salmon had been introduced into the food market without any notification (my September 13, 2017 posting; scroll down to the Fish subheading; Note: The WordPress ‘updated version from Hell’ has affected some of the formatting on the page).

The earliest article on CRISPR and yogurt that I’ve found is a January 1, 2015 article by Kerry Grens for The Scientist,

Two years ago, a genome-editing tool referred to as CRISPR (clustered regularly interspaced short palindromic repeats) burst onto the scene and swept through laboratories faster than you can say “adaptive immunity.” Bacteria and archaea evolved CRISPR eons before clever researchers harnessed the system to make very precise changes to pretty much any sequence in just about any genome.

But life scientists weren’t the first to get hip to CRISPR’s potential. For nearly a decade, cheese and yogurt makers have been relying on CRISPR to produce starter cultures that are better able to fend off bacteriophage attacks. “It’s a very efficient way to get rid of viruses for bacteria,” says Martin Kullen, the global R&D technology leader of Health and Protection at DuPont Nutrition & Health. “CRISPR’s been an important part of our solution to avoid food waste.”

Phage infection of starter cultures is a widespread and significant problem in the dairy-product business, one that’s been around as long as people have been making cheese. Patrick Derkx, senior director of innovation at Denmark-based Chr. Hansen, one of the world’s largest culture suppliers, estimates that the quality of about two percent of cheese production worldwide suffers from phage attacks. Infection can also slow the acidification of milk starter cultures, thereby reducing creameries’ capacity by up to about 10 percent, Derkx estimates.
In the early 2000s, Philippe Horvath and Rodolphe Barrangou of Danisco (later acquired by DuPont) and their colleagues were first introduced to CRISPR while sequencing Streptococcus thermophilus, a workhorse of yogurt and cheese production. Initially, says Barrangou, they had no idea of the purpose of the CRISPR sequences. But as his group sequenced different strains of the bacteria, they began to realize that CRISPR might be related to phage infection and subsequent immune defense. “That was an eye-opening moment when we first thought of the link between CRISPR sequencing content and phage resistance,” says Barrangou, who joined the faculty of North Carolina State University in 2013.

One last bit before getting to the hornless cattle, scientist Yi Li has a November 15, 2018 posting on the GLP website about his work with gene editing and food crops,

I’m a plant geneticist and one of my top priorities is developing tools to engineer woody plants such as citrus trees that can resist the greening disease, Huanglongbing (HLB), which has devastated these trees around the world. First detected in Florida in 2005, the disease has decimated the state’s US$9 billion citrus crop, leading to a 75 percent decline in its orange production in 2017. Because citrus trees take five to 10 years before they produce fruits, our new technique – which has been nominated by many editors-in-chief as one of the groundbreaking approaches of 2017 that has the potential to change the world – may accelerate the development of non-GMO citrus trees that are HLB-resistant.

Genetically modified vs. gene edited

You may wonder why the plants we create with our new DNA editing technique are not considered GMO? It’s a good question.

Genetically modified refers to plants and animals that have been altered in a way that wouldn’t have arisen naturally through evolution. A very obvious example of this involves transferring a gene from one species to another to endow the organism with a new trait – like pest resistance or drought tolerance.

But in our work, we are not cutting and pasting genes from animals or bacteria into plants. We are using genome editing technologies to introduce new plant traits by directly rewriting the plants’ genetic code.

This is faster and more precise than conventional breeding, is less controversial than GMO techniques, and can shave years or even decades off the time it takes to develop new crop varieties for farmers.

There is also another incentive to opt for using gene editing to create designer crops. On March 28, 2018, U.S. Secretary of Agriculture Sonny Perdue announced that the USDA wouldn’t regulate new plant varieties developed with new technologies like genome editing that would yield plants indistinguishable from those developed through traditional breeding methods. By contrast, a plant that includes a gene or genes from another organism, such as bacteria, is considered a GMO. This is another reason why many researchers and companies prefer using CRISPR in agriculture whenever it is possible.

As the Gatropod’casters note, there’s more than one side to the gene editing story and not everyone is comfortable with the notion of cavalierly changing genetic codes when so much is still unknown.

Hornless cattle update

First mentioned here in a November 28, 2018 posting, hornless cattle have been in the news again. From an October 7, 2019 news item on ScienceDaily,

For the past two years, researchers at the University of California, Davis, have been studying six offspring of a dairy bull, genome-edited to prevent it from growing horns. This technology has been proposed as an alternative to dehorning, a common management practice performed to protect other cattle and human handlers from injuries.

UC Davis scientists have just published their findings in the journal Nature Biotechnology. They report that none of the bull’s offspring developed horns, as expected, and blood work and physical exams of the calves found they were all healthy. The researchers also sequenced the genomes of the calves and their parents and analyzed these genomic sequences, looking for any unexpected changes.

An October 7, 2019 UC Davis news release (also on EurekAlert), which originated the news item, provides more detail about the research (I have checked the UC Davis website here and the October 2019 update appears to be the latest available publicly as of February 5, 2020),

All data were shared with the U.S. Food and Drug Administration. Analysis by FDA scientists revealed a fragment of bacterial DNA, used to deliver the hornless trait to the bull, had integrated alongside one of the two hornless genetic variants, or alleles, that were generated by genome-editing in the bull. UC Davis researchers further validated this finding.

“Our study found that two calves inherited the naturally-occurring hornless allele and four calves additionally inherited a fragment of bacterial DNA, known as a plasmid,” said corresponding author Alison Van Eenennaam, with the UC Davis Department of Animal Science.

Plasmid integration can be addressed by screening and selection, in this case, selecting the two offspring of the genome-edited hornless bull that inherited only the naturally occurring allele.

“This type of screening is routinely done in plant breeding where genome editing frequently involves a step that includes a plasmid integration,” said Van Eenennaam.

Van Eenennaam said the plasmid does not harm the animals, but the integration technically made the genome-edited bull a GMO, because it contained foreign DNA from another species, in this case a bacterial plasmid.

“We’ve demonstrated that healthy hornless calves with only the intended edit can be produced, and we provided data to help inform the process for evaluating genome-edited animals,” said Van Eenennaam. “Our data indicates the need to screen for plasmid integration when they’re used in the editing process.”

Since the original work in 2013, initiated by the Minnesota-based company Recombinetics, new methods have been developed that no longer use donor template plasmid or other extraneous DNA sequence to bring about introgression of the hornless allele.

Scientists did not observe any other unintended genomic alterations in the calves, and all animals remained healthy during the study period. Neither the bull, nor the calves, entered the food supply as per FDA guidance for genome-edited livestock.

WHY THE NEED FOR HORNLESS COWS?

Many dairy breeds naturally grow horns. But on dairy farms, the horns are typically removed, or the calves “disbudded” at a young age. Animals that don’t have horns are less likely to harm animals or dairy workers and have fewer aggressive behaviors. The dehorning process is unpleasant and has implications for animal welfare. Van Eenennaam said genome-editing offers a pain-free genetic alternative to removing horns by introducing a naturally occurring genetic variant, or allele, that is present in some breeds of beef cattle such as Angus.

Here’s a link to and a citation for the paper,

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull by Amy E. Young, Tamer A. Mansour, Bret R. McNabb, Joseph R. Owen, Josephine F. Trott, C. Titus Brown & Alison L. Van Eenennaam. Nature Biotechnology (2019) DOI: https://doi.org/10.1038/s41587-019-0266-0 Published 07 October 2019

This paper is open access.

Gold nanoparticle loaded with CRISPR used to edit genes

CRISPR (clustered regularly interspaced short palindromic repeats) gene editing is usually paired with a virus (9, 12a, etc.) but this time scientists are using a gold nanoparticle. From a May 27, 2019 news item on Nanowerk (Note: Links have been removed),

Scientists at Fred Hutchinson Cancer Research Center took a step toward making gene therapy more practical by simplifying the way gene-editing instructions are delivered to cells. Using a gold nanoparticle instead of an inactivated virus, they safely delivered gene-editing tools in lab models of HIV and inherited blood disorders, as reported in Nature Materials (“Targeted homology-directed repair in blood stem and progenitor cells with CRISPR nanoformulations”).

A May 27, 2019 Fred Hutchinson Cancer Research Center news release (also on EurekAlert) by Jake Siegel, which originated the news item, expands on the theme, provides more detail,

It’s the first time that a gold nanoparticle loaded with CRISPR has been used to edit genes in a rare but powerful subset of blood stem cells, the source of all blood cells. The CRISPR-carrying gold nanoparticle led to successful gene editing in blood stem cells with no toxic effects.

“As gene therapies make their way through clinical trials and become available to patients, we need a more practical approach,” said senior author Dr. Jennifer Adair, an assistant member of the Clinical Research Division at Fred Hutch, adding that current methods of performing gene therapy are inaccessible to millions of people around the world. “I wanted to find something simpler, something that would passively deliver gene editing to blood stem cells.”

While CRISPR has made it faster and easier to precisely deliver genetic modifications to the genome, it still has challenges. Getting cells to accept CRISPR gene-editing tools involves a small electric shock that can damage and even kill the cells. And if precise gene edits are required, then additional molecules must be engineered to deliver them –adding cost and time.

Gold nanoparticles are a promising alternative because the surface of these tiny spheres (around 1 billionth the size of a grain of table salt) allows other molecules to easily stick to them and stay adhered.

“We engineered the gold nanoparticles to quickly cross the cell membrane, dodge cell organelles that seek to destroy them and go right to the cell nucleus to edit genes,” said Dr. Reza Shahbazi, a Fred Hutch postdoctoral researcher who has worked with gold nanoparticles for drug and gene delivery for seven years.

Shahbazi made the gold particles from laboratory-grade gold that is purified and comes as a liquid in a small lab bottle. He mixed the purified gold into a solution that causes the individual gold ions to form tiny particles, which the researchers then measured for size.

They found that a particular size – 19 nanometers wide – was the best for being big and sticky enough to add gene-editing materials to the surface of the particles, while still being small enough for cells to absorb them.

Packed onto the gold particles, the Fred Hutch team added these gene-editing components (diagram available [see below]):

A type of molecular guide called crRNA acts as a genetic GPS to show the CRISPR complex where in the genome to make the cut.

CRISPR nuclease protein, often called “genetic scissors,” makes the cut in the DNA. The CRISPR nuclease protein most often used is Cas9. But the Fred Hutch researchers also studied Cas12a (formerly called Cpf1) because Cas12a makes a staggered cut in DNA. The researchers hoped this would allow the cells to more efficiently repair the cut and while so doing embed the new genetic instructions into the cell. Another advantage of Cas12a over Cas9 is that it only requires one molecular guide, which is important because of space constraints on the nanoparticles. Cas9 requires two molecular guides.

Instructions for what genetic changes to make (“ssDNA”). The Fred Hutch team chose two inherited genetic changes that bestow protection from disease: CCR5, which protects against HIV, and gamma hemoglobin, which protects against blood disorders such as sickle cell disease and thalassemia.

A coating of a polyethylenimine swarms the surface of the particles to give them a more positive charge, which enables them to more readily be absorbed into cells. This is an improvement over another method of getting cells to take up gene editing tools, called electroporation, which involves lightly shocking the cells to get them to open and allow the genetic instructions to enter.

Then the researchers isolated blood stem cells with a protein marker on their surface called CD34. These CD34-positive cells contain the blood-making progenitor cells that give rise to the entire blood and immune system.

“These cells replenish blood in the body every day, making them a good candidate for one-time gene therapy because it will last a lifetime as the cells replace themselves,” Adair said.

Observing human blood stem cells in a lab dish, the researchers found that their fully loaded gold nanoparticles were taken up naturally by cells within six hours of being added and within 24 to 48 hours they could see gene editing happening. They observed that the Cas12a CRISPR protein partner was better at delivering very precise genetic edits to the cells than the more commonly used cas9 protein partner.

The gene-editing effect reached a peak eight weeks after the researchers injected the cells into mouse models; 22 weeks after injection the edited cells were still there. The Fred Hutch researchers also found edited cells in the bone marrow, spleen and thymus of the mouse models, a sign that the dividing blood cells in those organs could carry on the treatment without the mice having to be treated again.

“We believe we have a good candidate for two diseases — HIV and hemoglobinopathies — though we are also evaluating other disease targets where small genetic changes can have a big impact, as well as ways to make bigger genetic changes,” Adair said. “The next step is to increase how much gene editing happens in each cell, which is definitely doable. That will make it closer to being an effective therapy.”

In the study, the researchers report 10 to 20 percent of cells took on the gene edits, which is a promising start, but the researchers would like to aim for 50% or more of the cells being edited, which they believe will have a good chance of combatting these diseases.

###

Adair and Shahbazi are looking for commercial partners to develop the technology into therapies for people. They hope to begin clinical trials within a few years.

Here’s the diagram of a gold nanoparticle loaded with CRISPR,

Caption: Graphic of a fully loaded gold nanoparticle with CRISPR and other gene editing tools. Credit: Image courtesy of the Adair lab at Fred Hutch.

Here’s a link to and a citation for the paper,

Targeted homology-directed repair in blood stem and progenitor cells with CRISPR nanoformulations by Reza Shahbazi, Gabriella Sghia-Hughes, Jack L. Reid, Sara Kubek, Kevin G. Haworth, Olivier Humbert, Hans-Peter Kiem & Jennifer E. Adair. Nature Materials (2019) DOI https://doi.org/10.1038/s41563-019-0385-5Published 27 May 2019

This paper is behind a paywall.

October 2019 science and art/science events in Vancouver and other parts of Canada

This is a scattering of events, which I’m sure will be augmented as we properly start the month of October 2019.

October 2, 2019 in Waterloo, Canada (Perimeter Institute)

If you want to be close enough to press the sacred flesh (Sir Martin Rees), you’re out of luck. However, there are still options ranging from watching a live webcast from the comfort of your home to watching the lecture via closed circuit television with other devoted fans at a licensed bistro located on site at the Perimeter Institute (PI) to catching the lecture at a later date via YouTube.

That said, here’s why you might be interested,

Here’s more from a September 11, 2019 Perimeter Institute (PI) announcement received via email,

Surviving the Century
MOVING TOWARD A POST-HUMAN FUTURE
Martin Rees, UK Astronomer Royal
Wednesday, Oct. 2 at 7:00 PM ET

Advances in technology and space exploration could, if applied wisely, allow a bright future for the 10 billion people living on earth by the end of the century.

But there are dystopian risks we ignore at our peril: our collective “footprint” on our home planet, as well as the creation and use of technologies so powerful that even small groups could cause a global catastrophe.

Martin Rees, the UK Astronomer Royal, will explore this unprecedented moment in human history during his lecture on October 2, 2019. A former president of the Royal Society and master of Trinity College, Cambridge, Rees is a cosmologist whose work also explores the interfaces between science, ethics, and politics. Read More.

Mark your calendar! Tickets will be available on Monday, Sept. 16 at 9 AM ET

Didn’t get tickets for the lecture? We’ve got more ways to watch.
Join us at Perimeter on lecture night to watch live in the Black Hole Bistro.
Catch the live stream on Inside the Perimeter or watch it on Youtube the next day
Become a member of our donor thank you program! Learn more.

It took me a while to locate an address for PI venue since I expect that information to be part of the announcement. (insert cranky emoticon here) Here’s the address: Perimeter Institute, Mike Lazaridis Theatre of Ideas, 31 Caroline St. N., Waterloo, ON

Before moving onto the next event, I’m including a paragraph from the event description that was not included in the announcement (from the PI Outreach Surviving the Century webpage),

In his October 2 [2019] talk – which kicks off the 2019/20 season of the Perimeter Institute Public Lecture Series – Rees will discuss the outlook for humans (or their robotic envoys) venturing to other planets. Humans, Rees argues, will be ill-adapted to new habitats beyond Earth, and will use genetic and cyborg technology to transform into a “post-human” species.

I first covered Sir Martin Rees and his concerns about technology (robots and cyborgs run amok) in this November 26, 2012 posting about existential risk. He and his colleagues at Cambridge University, UK, proposed a Centre for the Study of Existential Risk, which opened in 2015.

Straddling Sept. and Oct. at the movies in Vancouver

The Vancouver International Film Festival (VIFF) opened today, September 26, 2019. During its run to October 11, 2019 there’ll be a number of documentaries that touch on science. Here are three of the documentaries most closely adhere to the topics I’m most likely to address on this blog. There is a fourth documentary included here as it touches on ecology in a more hopeful fashion than is the current trend.

Human Nature

From the VIFF 2019 film description and ticket page,

One of the most significant scientific breakthroughs in history, the discovery of CRISPR has made it possible to manipulate human DNA, paving the path to a future of great possibilities.

The implications of this could mean the eradication of disease or, more controversially, the possibility of genetically pre-programmed children.

Breaking away from scientific jargon, Human Nature pieces together a complex account of bio-research for the layperson as compelling as a work of science-fiction. But whether the gene-editing powers of CRISPR (described as “a word processor for DNA”) are used for good or evil, they’re reshaping the world as we know it. As we push past the boundaries of what it means to be human, Adam Bolt’s stunning work of science journalism reaches out to scientists, engineers, and people whose lives could benefit from CRISPR technology, and offers a wide-ranging look at the pros and cons of designing our futures.

Tickets
Friday, September 27, 2019 at 11:45 AM
Vancity Theatre

Saturday, September 28, 2019 at 11:15 AM
International Village 10

Thursday, October 10, 2019 at 6:45 PM
SFU Goldcorp

According to VIFF, the tickets for the Sept. 27, 2019 show are going fast.

Resistance Fighters

From the VIFF 2019 film description and ticket page,

Since mass-production in the 1940s, antibiotics have been nothing less than miraculous, saving countless lives and revolutionizing modern medicine. It’s virtually impossible to imagine hospitals or healthcare without them. But after years of abuse and mismanagement by the medical and agricultural communities, superbugs resistant to antibiotics are reaching apocalyptic proportions. The ongoing rise in multi-resistant bacteria – unvanquishable microbes, currently responsible for 700,000 deaths per year and projected to kill 10 million yearly by 2050 if nothing changes – and the people who fight them are the subjects of Michael Wech’s stunning “science-thriller.”

Peeling back the carefully constructed veneer of the medical corporate establishment’s greed and complacency to reveal the world on the cusp of a potential crisis, Resistance Fighters sounds a clarion call of urgency. It’s an all-out war, one which most of us never knew we were fighting, to avoid “Pharmageddon.” Doctors, researchers, patients, and diplomats testify about shortsighted medical and economic practices, while Wech offers refreshingly original perspectives on environment, ecology, and (animal) life in general. As alarming as it is informative, this is a wake-up call the world needs to hear.

Sunday, October 6, 2019 at 5:45 PM
International Village 8

Thursday, October 10, 2019 at 2:15 PM
SFU Goldcorp

According to VIFF, the tickets for the Oct. 6, 2019 show are going fast.

Trust Machine: The Story of Blockchain

Strictly speaking this is more of a technology story than science story but I have written about blockchain and cryptocurrencies before so I’m including this. From the VIFF 2019 film description and ticket page,

For anyone who has questions about cryptocurrencies like Bitcoin (and who doesn’t?), Alex Winter’s thorough documentary is an excellent introduction to the blockchain phenomenon. Trust Machine offers a wide range of expert testimony and a variety of perspectives that explicate the promises and the risks inherent in this new manifestation of high-tech wizardry. And it’s not just money that blockchains threaten to disrupt: innovators as diverse as UNICEF and Imogen Heap make spirited arguments that the industries of energy, music, humanitarianism, and more are headed for revolutionary change.

A propulsive and subversive overview of this little-understood phenomenon, Trust Machine crafts a powerful and accessible case that a technologically decentralized economy is more than just a fad. As the aforementioned experts – tech wizards, underground activists, and even some establishment figures – argue persuasively for an embrace of the possibilities offered by blockchains, others criticize its bubble-like markets and inefficiencies. Either way, Winter’s film suggests a whole new epoch may be just around the corner, whether the powers that be like it or not.

Tuesday, October 1, 2019 at 11:00 AM
Vancity Theatre

Thursday, October 3, 2019 at 9:00 PM
Vancity Theatre

Monday, October 7, 2019 at 1:15 PM
International Village 8

According to VIFF, tickets for all three shows are going fast

The Great Green Wall

For a little bit of hope, From the VIFF 2019 film description and ticket page,

“We must dare to invent the future.” In 2007, the African Union officially began a massively ambitious environmental project planned since the 1970s. Stretching through 11 countries and 8,000 km across the desertified Sahel region, on the southern edges of the Sahara, The Great Green Wall – once completed, a mosaic of restored, fertile land – would be the largest living structure on Earth.

Malian musician-activist Inna Modja embarks on an expedition through Senegal, Mali, Nigeria, Niger, and Ethiopia, gathering an ensemble of musicians and artists to celebrate the pan-African dream of realizing The Great Green Wall. Her journey is accompanied by a dazzling array of musical diversity, celebrating local cultures and traditions as they come together into a community to stand against the challenges of desertification, drought, migration, and violent conflict.

An unforgettable, beautiful exploration of a modern marvel of ecological restoration, and so much more than a passive source of information, The Great Green Wall is a powerful call to take action and help reshape the world.

Sunday, September 29, 2019 at 11:15 AM
International Village 10

Wednesday, October 2, 2019 at 6:00 PM
International Village 8
Standby – advance tickets are sold out but a limited number are likely to be released at the door

Wednesday, October 9, 2019 at 11:00 AM
International Village 9

As you can see, one show is already offering standby tickets only and the other two are selling quickly.

For venue locations, information about what ‘standby’ means and much more go here and click on the Festival tab. As for more information the individual films, you’ll links to trailers, running times, and more on the pages for which I’ve supplied links.

Brain Talks on October 16, 2019 in Vancouver

From time to time I get notices about a series titled Brain Talks from the Dept. of Psychiatry at the University of British Columbia. A September 11, 2019 announcement (received via email) focuses attention on the ‘guts of the matter’,

YOU ARE INVITED TO ATTEND:

BRAINTALKS: THE BRAIN AND THE GUT

WEDNESDAY, OCTOBER 16TH, 2019 FROM 6:00 PM – 8:00 PM

Join us on Wednesday October 16th [2019] for a series of talks exploring the
relationship between the brain, microbes, mental health, diet and the
gut. We are honored to host three phenomenal presenters for the evening:
Dr. Brett Finlay, Dr. Leslie Wicholas, and Thara Vayali, ND.

DR. BRETT FINLAY [2] is a Professor in the Michael Smith Laboratories at
the University of British Columbia. Dr. Finlay’s  research interests are
focused on host-microbe interactions at the molecular level,
specializing in Cellular Microbiology. He has published over 500 papers
and has been inducted into the Canadian  Medical Hall of Fame. He is the
co-author of the  books: Let Them Eat Dirt and The Whole Body
Microbiome.

DR. LESLIE WICHOLAS [3]  is a psychiatrist with an expertise in the
clinical understanding of the gut-brain axis. She has become
increasingly involved in the emerging field of Nutritional Psychiatry,
exploring connections between diet, nutrition, and mental health.
Currently, Dr. Wicholas is the director of the Food as Medicine program
at the Mood Disorder Association of BC.

THARA VAYALI, ND [4] holds a BSc in Nutritional Sciences and a MA in
Education and Communications. She has trained in naturopathic medicine
and advocates for awareness about women’s physiology and body literacy.
Ms. Vayali is a frequent speaker and columnist that prioritizes
engagement, understanding, and community as pivotal pillars for change.

Our event on Wednesday, October 16th [2019] will start with presentations from
each of the three speakers, and end with a panel discussion inspired by
audience questions. After the talks, at 7:30 pm, we host a social
gathering with a rich spread of catered healthy food and non-alcoholic
drinks. We look forward to seeing you there!

Paetzhold Theater

Vancouver General Hospital; Jim Pattison Pavilion, Vancouver, BC

Attend Event

That’s it for now.

Detecting off-target effects of CRISPR gene-editing

In amidst all the hyperbole about CRISPR (clustered regularly interspaced short palindromic repeats), the gene editing technology, you will sometimes find a mild cautionary note. It seems that CRISPR is not as precise as you might think.

Some months ago there was a story about research into detecting possible unanticipated (off target) effects from using CRISPR, from an April 19, 2019 news item on ScienceDaily,

Since the CRISPR genome editing technology was invented in 2012, it has shown great promise to treat a number of intractable diseases. However, scientists have struggled to identify potential off-target effects in therapeutically relevant cell types, which remains the main barrier to moving therapies to the clinic. Now, a group of scientists at the Gladstone Institutes and the Innovative Genomics Institute (IGI), with collaborators at AstraZeneca, have developed a reliable method to do just that.

An April 19, 2019 Gladstone Institutes press release by Julie Langelier, which originated the press release, provides details,

CRISPR edits a person’s genome by cutting the DNA at a specific location. The challenge is to ensure the tool doesn’t also make cuts elsewhere along the DNA—damage referred to as “off-target effects,” which could have unforeseen consequences.

In a study published in the journal Science, the two first authors, Beeke Wienert and Stacia Wyman, found a new way to approach the problem.

“When CRISPR makes a cut, the DNA is broken,” says Wienert, PhD, who began the work in Jacob E. Corn’s IGI laboratory and who is now a postdoctoral scholar in Bruce R. Conklin’s laboratory at Gladstone. “So, in order to survive, the cell recruits many different DNA repair factors to that particular site in the genome to fix the break and join the cut ends back together. We thought that if we could find the locations of these DNA repair factors, we could identify the sites that have been cut by CRISPR.”

To test their idea, the researchers studied a panel of different DNA repair factors. They found that one of them, called MRE11, is one of the first responders to the site of the cut. Using MRE11, the scientists developed a new technique, named DISCOVER-Seq, that can identify the exact sites in the genome where a cut has been made by CRISPR.

“The human genome is extremely large—if you printed the entire DNA sequence, you would end up with a novel as tall as a 16-story building,” explains Conklin, MD, senior investigator at Gladstone and deputy director at IGI. “When we want to cut DNA with CRISPR, it’s like we’re trying to remove one specific word on a particular page in that novel.”

“You can think of the DNA repair factors as different types of bookmarks added to the book,” Conklin adds. “While some may bookmark an entire chapter, MRE11 is a bookmark that drills down to the exact letter than has been changed.”

Different methods currently exist to detect CRISPR off-target effects. However, they come with limitations that range from producing false-positive results to killing the cells they’re examining. In addition, the most common method used to date is currently limited to cultured cells in the laboratory, excluding its use in patient-derived stem cells or animal tissue.

“Because our method relies on the cell’s natural repair process to identify cuts, it has proven to be much less invasive and much more reliable,” says Corn, PhD, who now runs a laboratory at ETH Zurich. “We were able to test our new DISCOVER-Seq method in induced pluripotent stem cells, patient cells, and mice, and our findings indicate that this method could potentially be used in any system, rather than just in the lab.”

The DISCOVER-Seq method, by being applied to new cell types and systems, has also revealed new insights into the mechanisms used by CRISPR to edit the genome, which will lead to a better understanding of the biology of how this tool works.

“The new method greatly simplifies the process of identifying off-target effects while also increasing the accuracy of the results,” says Conklin, who is also a professor of medical genetics and molecular pharmacology at UC San Francisco (UCSF). “This could allow us to better predict how genome editing would work in a clinical setting. As a result, it represents an essential step in improving pre-clinical studies and bringing CRISPR-based therapies closer to the patients in need.”

###

About the Study

The paper “Unbiased detection of CRISPR off-targets in vivo 1 using DISCOVER-Seq” was published by the journal Science on April 19, 2019. Gladstone’s Hannah L. Watry and Luke M. Judge (who is also at UCSF) contributed to this study. Other authors also include Christopher D. Richardson, Jonathan T. Vu, and Katelynn R. Kazane from IGI, Charles D. Yeh from ETH Zurich, as well as Pinar Akcakaya, Michelle J. Porritt, and Michaela Morlock from AstraZeneca.

The work was supported by Gladstone, the National Institutes of Health (grants EY028249 and HL13535801), the Li Ka Shing Foundation, the Heritage Medical Research Institute, the Fanconi Anemia Research Foundation, a Sir Keith Murdoch Fellowship from the American Australian Association, and an Early Career Fellowship from the National Health and Medical Research Council.

About the Gladstone Institute

To ensure our work does the greatest good, the Gladstone Institutes focuses on conditions with profound medical, economic, and social impact—unsolved diseases. Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. It has an academic affiliation with the University of California, San Francisco.

Before getting to the link and citation that I usually offer you might find this July 17, 2018 posting, The CRISPR ((clustered regularly interspaced short palindromic repeats)-CAS9 gene-editing technique may cause new genetic damage kerfuffle of interest. I wonder if this latest news affected the CRISPR market as the did the news in 2018.

In addition to the link in the press release, I am including a link and a citation for the study,

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq by Beeke Wienert, Stacia K. Wyman, Christopher D. Richardson, Charles D. Yeh, Pinar Akcakaya, Michelle J. Porritt, Michaela Morlock, Jonathan T. Vu, Katelynn R. Kazane, Hannah L. Watry, Luke M. Judge, Bruce R. Conklin, Marcello Maresca, Jacob E. Corn. Science 19 Apr 2019: Vol. 364, Issue 6437, pp. 286-289 DOI: 10.1126/science.aav9023

This paper is behind a paywall.

Money

Over the last 10 or more years, I have, on occasion made a point, of finding out about the funding for various non-profit agencies and projects. I find that sort of thing interesting and have hoped that my readers might feel the same way.

It seems that my readers and I might not be the only ones to care about the source of funding. Joi Ito who held appointments with Harvard University and the Massachusetts Institute of Technology (MIT) resigned from his various appointments on Sept. 7, 2019 after news of major donations from Jeffrey Epstein (a disgraced financier and sex offender) to MIT were revealed. From the Joi Ito’s entry on Wikipedia (Note: Links have been removed),

Joichi “Joi” Ito (伊藤 穰一 Itō Jōichi, born June 19, 1966) is a Japanese activist, entrepreneur and venture capitalist. He is the former director of the MIT Media Lab, and a former professor of the practice of media arts and sciences at MIT. He is a former visiting professor of practice at the Harvard Law School.[1][2]

Ito has received recognition for his role as an entrepreneur focused on Internet and technology companies and has founded, among other companies, PSINet Japan, Digital Garage and Infoseek Japan. Ito is a strategic advisor to Sony Corporation[3] and general partner of Neoteny Labs.[4] Ito writes a monthly column in the Ideas section of Wired.[5]

Ito resigned from his roles at MIT, Harvard, the John D. and Catherine T. MacArthur Foundation, the Knight Foundation, PureTech Health and The New York Times Company on September 7, 2019, following allegations of financial ties to sex offender and financier Jeffrey Epstein.[2][6][7]

Many, many institutions have accepted funds from sketchy characters and orgnaizations. It’s not new to academia, the sciences, or the arts. For a contemporary view of how some of this works, take a look at Anand Giridharadas’s 2018 book, Winners Take All. From the webepage for the book,

WINNERS TAKE ALL
The Elite Charade of Changing the World
 
An insider’s groundbreaking investigation of how the global elite’s efforts to “change the world” preserve the status quo and obscure their role in causing the problems they later seek to solve.

Former New York Times columnist Anand Giridharadas takes us into the inner sanctums of a new gilded age, where the rich and powerful fight for equality and justice any way they can–except ways that threaten the social order and their position atop it. We see how they rebrand themselves as saviors of the poor; how they lavishly reward “thought leaders” who redefine “change” in winner-friendly ways; and how they constantly seek to do more good, but never less harm. We hear the limousine confessions of a celebrated foundation boss; witness an American president hem and haw about his plutocratic benefactors; and attend a cruise-ship conference where entrepreneurs celebrate their own self-interested magnanimity.

I don’t recall any mention of Epstein in Giridharadas’s book but he did have this to say on Twitter about Epstein,

Anand Giridharadas‏Verified account @AnandWrites



Everything that made Epstein’s life possible remains in place after his arrest: the Caribbean tax havens, the hidden real-estate deals, the buying of politicians, the nonprofits that sell reputational glow, the editors who cover for people of their class.

7:34 PM – 8 Jul 2019

it can’t be easy to withstand the temptation to take the money and hope that the misdoings have been exaggerated or that they have stopped. I imagine Ito and others are under constant pressure to get funds.

AstraZeneca

One of the partners in this research about CRISPR, AstraZeneca, is a pharmaceutical company. In fact, it’s one of the largest in the world (from the AstraZeneca Wikipedia entry; Note: Links have been removed),

AstraZeneca plc[4] is a British-Swedish multinational pharmaceutical and biopharmaceutical company. In 2013, it moved its headquarters to Cambridge, UK, and concentrated its R&D in three sites: Cambridge; Gaithersburg, Maryland, USA (location of MedImmune) for work on biopharmaceuticals; and Mölndal (near Gothenburg) in Sweden, for research on traditional chemical drugs.[5] AstraZeneca has a portfolio of products for major disease areas including cancer, cardiovascular, gastrointestinal, infection, neuroscience, respiratory and inflammation.[6]

The company was founded in 1999 through the merger of the Swedish Astra AB and the British Zeneca Group[7][8] (itself formed by the demerger of the pharmaceutical operations of Imperial Chemical Industries in 1993). Since the merger it has been among the world’s largest pharmaceutical companies and has made numerous corporate acquisitions, including Cambridge Antibody Technology (in 2006), MedImmune (in 2007), Spirogen (in 2013) and Definiens (by MedImmune in 2014).

Controversies

Seroquel
In April 2010 AstraZeneca settled a qui tam lawsuit brought by Stefan P. Kruszewski for $520 million to settle allegations that the company defrauded Medicare, Medicaid, and other government-funded health care programs in connection with its marketing and promotional practices for the blockbuster atypical antipsychotic, Seroquel.[76]
In March 2011, AstraZeneca settled a lawsuit in the United States totalling $68.5 million to be divided up to 38 states.[77]
Nexium
The company’s most commercially successful medication is esomeprazole (Nexium). The primary uses are treatment of gastroesophageal reflux disease, treatment and maintenance of erosive esophagitis, treatment of duodenal ulcers caused by Helicobacter pylori, prevention of gastric ulcers in those on chronic NSAID therapy, and treatment of gastrointestinal ulcers associated with Crohn’s disease. When it is manufactured the result is a mixture of two mirror-imaged molecules, R and S. Two years before the omeprazole patent expired, AstraZeneca patented S-omeprazole in pure form, pointing out that since some people metabolise R-omeprazole slowly, pure S-omeprazole treatment would give higher dose efficiency and less variation between individuals.[78] In March 2001, the company began to market Nexium, as it would a brand new drug.[79]

In 2007, Marcia Angell, former editor-in-chief of the New England Journal of Medicine and a lecturer in social medicine at the Harvard Medical School, said in Stern, a German-language weekly newsmagazine, that AstraZeneca’s scientists had misrepresented their research on the drug’s efficiency, saying “Instead of using presumably comparable doses [of each drug], the company’s scientists used Nexium in higher dosages. They compared 20 and 40 mg Nexium with 20 mg Prilosec. With the cards having been marked in that way, Nexium looked like an improvement – which however was only small and shown in only two of the three studies.”[83]
Bildman fraud, and faithless servant clawback

Study
In 2004, University of Minnesota research participant Dan Markingson committed suicide while enrolled in an industry-sponsored pharmaceutical trial comparing three FDA-approved atypical antipsychotics: Seroquel (quetiapine), Zyprexa (olanzapine), and Risperdal (risperidone). University of Minnesota Professor of Bioethics Carl Elliott noted that Markingson was enrolled in the study against the wishes of his mother, Mary Weiss, and that he was forced to choose between enrolling in the study or being involuntarily committed to a state mental institution.[89] Further investigation revealed financial ties to AstraZeneca by Markingson’s psychiatrist, Stephen C. Olson, oversights and biases in AstraZeneca’s trial design, and the inadequacy of university Institutional Review Board (IRB) protections for research subjects.[90][unreliable source?] A 2005 FDA investigation cleared the university. Nonetheless, controversy around the case has continued. A Mother Jones article[89] resulted in a group of university faculty members sending a public letter to the university Board of Regents urging an external investigation into Markingson’s death.[91]

Is it ok to take money and/or other goods and services from them?

Innovative Genomics Institute (IGI)

Also mentioned as a partner in the research, is the Innovative Genomics Institute (IGI). Here’s more from the company’s Overview webpage (Note: Links have been removed),,

The IGI began in 2014 through the Li Ka Shing Center for Genetic Engineering, which was created thanks to a generous donation from the Li Ka Shing Foundation. [emphasis mine] The Innovative Genomics Initiative formed as a partnership between the University of California, Berkeley and the University of California, San Francisco. Combining the fundamental research expertise and the biomedical talent at UCB and UCSF, the Innovative Genomics Initiative focused on unraveling the mechanisms underlying CRISPR-based genome editing and applying this technology to improve human health. Early achievements include improving the efficiency of gene replacement and foundational work toward a treatment for sickle cell disease.

In late 2015, generous philanthropic donations enabled a bolder vision and broader mission for the IGI. With this expansion came a significant enhancement of the organization, and in January 2017, the IGI officially re-launched as the Innovative Genomics Institute.

As it turns out, there is a Li Ka-shing and he has a bit of a history with Vancouver (Canada). First, here’s more about him from the Li Ka-shing Wikipedia entry,(Note: Links have been removed),

Sir Li Ka-shing GBM KBE JP[4] (born 13 June 1928)[5][6] is a Hong Kong business magnate, investor, and philanthropist. As of June 2019, Li is the 30th richest person in the world, with an estimated net wealth of US$29.4 billion.[3] He is the senior advisor for CK Hutchison Holdings,[7] after he retired from the Chairman of the Board in May 2018;[8] through it, he is the world’s leading port investor, developer, and operator of the largest health and beauty retailer in Asia and Europe.[9]

Besides business through his flagship companies Cheung Kong Property Holdings and CK Hutchison Holdings Limited, Li Ka-shing has also personally invested extensively in real estate in Singapore and Canada. He was the single largest shareholder of Canadian Imperial Bank of Commerce (CIBC), the fifth largest bank in Canada, until the sale of his share in 2005 (with all proceedings donated, see below). He is also the majority shareholder of a major energy company, Husky Energy, based in Alberta, Canada.[48]

In January 2005, Li announced plans to sell his $1.2 billion CAD stake in the Canadian Imperial Bank of Commerce, with all proceeds going to private charitable foundations established by Li, including the Li Ka Shing Foundation in Hong Kong and the Li Ka Shing (Canada) Foundation based in Toronto, Ontario.[49]

His son Victor Li was kidnapped in 1996 on his way home after work by gangster “Big Spender” Cheung Tze-keung. Li Ka-shing paid a ransom of HK$1 billion, directly to Cheung who had come to his house.[53] A report was never filed with Hong Kong police. Instead the case was pursued by Mainland authorities, leading to Cheung’s execution in 1998, an outcome not possible under Hong Kong law. Rumours circulated of a deal between Li and the Mainland.[53] In interviews, when this rumor was brought up, Li brushed it off and dismissed it completely.

Li Ka-shing was well known here in Vancouver due to his purchase of a significant chunk of land in the city. This January 9, 2015 article by Glen Korstrum for Business in Vancouver notes some rather interesting news and contextualizes with Li’s Vancouver history,

Hong Kong billionaire Li Ka-shing is restructuring his empire and shifting his base to the Cayman Islands and away from the Chinese special administrative region.

His January 9 [2015] announcement came the same day that Forbes ranked him as Hong Kong’s richest man for the 17th consecutive year, with a total wealth of US$33.5 billion.

Li is best known in Vancouver for buying an 82.5-hectare parcel of land around False Creek for $328 million in 1988 along with partners, who included fellow Hong Kong tycoons, Lee Shau Kee and Cheng Yu Tung.

The group formed Concord Pacific, which redeveloped the site that had been home to Vancouver’s 1986 world’s fair, Expo ’86.

Li cashed out of Concord Pacific in the late 1990s and, in 2007, invested in Deltaport through his Hutchison Port Holdings.

Li’s biggest Canadian holding is his controlling stake in Husky Energy. …

Intriguing, yes? It also makes the prospect of deciding whose money you’re going to accept a bit more complicated than it might seem.

Gladstone Institutes

In what seems to be a decided contrast to the previous two partners, here’s more from the Gladstone Institutes, About Us, History webpage,

Born in London in 1910, J. David Gladstone was orphaned as a boy and came to North America at age 10. He began a career in real estate in Southern California at age 28, eventually making his fortune as the first developer to create the region’s enclosed shopping malls (such as the Northridge Fashion Center mall). His accidental death in 1971 left an estate valued at about $8 million to support medical students interested in research.

It soon became clear to the three trustees administering Mr. Gladstone’s trust that his legacy could support a far more substantial philanthropic enterprise. In 1979, they launched The J. David Gladstone Institutes under the leadership of Robert W. Mahley, MD, PhD, a leading cardiovascular scientist who at the time was working at the National Institutes of Health.

In 2010, after three decades of leading Gladstone, Dr. Mahley stepped down in order to return to more active research. That same year, R. Sanders “Sandy” Williams, MD, left Duke University, where he had been Dean of the School of Medicine—as well as Senior Vice Chancellor and Senior Advisor for International Strategy—to become Gladstone’s new president. The following year, the S.D. Bechtel, Jr. Foundation [emphasis mine] helped launch the Center for Comprehensive Alzheimer’s Disease Research with a generous $6M lead gift, while the Roddenberry Foundation [emphasis mine] gave $5 million to launch the Roddenberry Center for Stem Cell Biology and Medicine. Also in 2011, the independent and philanthropic Gladstone Foundation formed with the mission of expanding the financial resources available to drive’s Gladstone’s mission.

The S. D. Bechtel jr. mentioned is associated with Bechtel, an international engineering firm. I did not find any scandals or controversies in the Bechtel Wikipedia entry. That seemed improbable so I did a little digging and found a January 30, 2015 (?) article by Matthew Brunwasser for foreignpolicy.com (Note: A link has been removed),

Steamrolled; A special investigation into the diplomacy of doing business abroad.

One of Europe’s poorest countries wanted a road, so U.S. mega-contractor Bechtel sold it a $1.3 billion highway, with the backing of a powerful American ambassador. Funny thing is, the highway is barely being used—and the ambassador is now working for Bechtel.

Bechtel, the largest contractor by revenue in the United States and the third-largest internationally, according to an annual list compiled by the Engineering News-Record, has in recent years constructed expensive highways in Kosovo, Croatia, Romania, and Albania. A six-month investigation by the Investigative Reporting Program at the University of California at Berkeley Graduate School of Journalism has found that these highways were boondoggles for the countries in which they were constructed, and that members of governments and international institutions often saw problems coming before Bechtel (along with its Turkish joint venture partner, Enka) even began work on the roads.

My other source is a May 8, 1988 article by Walter Russell Mead for the Los Angeles Time,s

From San Francisco to Saudi Arabia, the Bechtel Group Inc. has left its mark around the world. Yet the privately owned Bechtel Group is one of the country’s most mysterious operations–or was, until the publication of Laton McCartney’s critical and controversial “Friends in High Places.”

Those who believe that “Dynasty” and “Falcon Crest” describe life at the top of America’s corporate pyramids will find a picture here that makes the most far-fetched TV plots look dull. One Bechtel executive was torn to pieces by an angry mob; another, kidnaped, survived two days in the trunk of a Mercedes that had been driven over the edge of a cliff but caught on an obstacle half way down. Wheeling and dealing from Beirut to the Bohemian Grove, Bechtel executives fought off Arab and Jewish nationalists, angry senators, bitter business rivals, and furious consumer groups to build the world’s largest construction and engineering firm.

Poor Bechtel sometimes seems damned if it does and damned if it doesn’t. No major corporation could undertake foreign operations on Bechtel’s scale without some cooperation from the U.S. government–and few companies could refuse a government request that, in return, they provide cover for intelligence agents. Given the enormous scope of Bechtel’s operations in global trouble spots–a $20-billion industrial development in Saudi Arabia, for example–it could only proceed with assurances that its relations with both Saudi and American governments were good. Where, exactly, is the line between right and wrong? [emphasis mine]

… The white elephants Bechtel scattered across the American landscape–particularly the nuclear power plants that threaten to bankrupt some of the country’s largest utility systems–are monuments to wasted talent and misdirected resources.

Finally, I get to the Roddenberry Foundation, which was founded by Gene Roddenberry’s (Star Trek) son. Here’s more from the About Us, Origin webpage,

Gene Roddenberry, creator of the Star Trek series, brought to his audiences meaningful and thought-provoking science fiction to “think, question, and challenge the status quo” with the intention of creating “a brighter future”. His work has touched countless lives and continues to entertain and inspire audiences worldwide. In 2010, Gene’s son Rod established the Roddenberry Foundation to build on his father’s legacy and philosophy of inclusion, diversity, and respect for life to drive social change and meaningfully improve the lives of people around the world.

While there are many criticisms of Mr. Roddenberry, there doesn’t seem to be anything that would be considered a serious scandal on the order of a Jeffrey Epstein or the whisper of scandal on the order of Sir Li Ka-shing or Bechtel.

Final comments

It’s a good thing when research is funded and being able to detect off-target effects from CRISPR is very good, assuming the research holds up to closer scrutiny.

As for vetting your donors, that’s tricky. Of course, Epstein was already a convicted sex offender when Ito accepted his funding for MIT but I cannot emphasize enough the amount of pressure these folks are under. Academia is always hungry for money. Hopefully this incident will introduce checks and balances in the donor process.

Greater mortality for the CRISPR twins Lulu and Nana?

Every time I think this CRISPR (clustered regularly interspaced short palindromic repeats) story is winding down, something new happens. The latest (I think) is in a June 3, 2019 news item on ScienceDaily,

A genetic mutation that a Chinese scientist attempted to create in twin babies born last year, ostensibly to help them fend off HIV infection, is also associated with a 21% increase in mortality in later life, according to an analysis by University of California, Berkeley, scientists.

The researchers scanned more than 400,000 genomes and associated health records contained in a British database, UK Biobank, and found that people who had two mutated copies of the gene had a significantly higher death rate between ages 41 and 78 than those with one or no copies.

Sarah Zhang’s June 3, 2019 article for The Atlantic provides an overview of the situation before exploring the current controversy,

In the 1990s, virologists in New York learned of a genetic mutation that would become one of the most famous ever discovered. They found it in a man who could not be infected with HIV. He turned out to be missing just 32 letters in a gene called CCR5, and remarkably, it was enough to make him resistant to the virus killing so many others. About 1 percent of people of European descent carry two copies of this mutation, now known as CCR5-Δ32.

In 2018, a Chinese scientist named He Jiankui made the mutation infamous when he attempted to use CRISPR to edit CCR5-Δ32 (pronounced “CCR5-delta-32”) into human embryos. He chose this mutation, he said, because the babies’ father was HIV-positive, and he wanted to make the resulting twin girls resistant to the virus. CCR5-Δ32 is also, after all, one of the most studied mutations.

He’s work immediately provoked outrage among scientists, who knew enough to know how much they did not know about the risks of altering CCR5. And now a new study suggests that CCR5-Δ32 is indeed harmful overall.

The girls’ CCR5 genes were altered, according to data He presented, but they do not exactly match the 32-letter deletion; it’s unclear whether either of them is actually resistant to HIV. Even if they were unable to get HIV, a body of research already suggested that CCR5-Δ32 made people more vulnerable to the flu and West Nile virus. A “good” mutation in the context of HIV can be “bad” in another context. No one knew, exactly, the net effect of a CCR5-Δ32 mutation.

For some reason, Zhang makes no mention of the possibly enhanced cognitive abilities that the twins may have as a consequence of the gene editing assuming that He Jiankui successfully edited the genes. (To my knowledge, the results and data have not been released for review by colleagues.)

Regardless, Zhang’s article provides a handy overview and update.

For anyone who’s interested in more detail about this latest research into mortality and CCR5, there’s a June 3, 2019 University of California at Berkeley news release (also on EurekAlert) by Robert Sanders, which also originated the ScienceDaily news item, details the latest research,

Previous studies have associated two mutated copies of the gene, CCR5, with a fourfold increase in the death rate after influenza infection, and the higher overall mortality rate may reflect this greater susceptibility to death from the flu. But the researchers say there could be any number of explanations, since the protein that CCR5 codes for, and which no longer works in those having the mutation in both copies of the gene, is involved in many body functions.

“Beyond the many ethical issues involved with the CRISPR babies, the fact is that, right now, with current knowledge, it is still very dangerous to try to introduce mutations without knowing the full effect of what those mutations do,” said Rasmus Nielsen, a UC Berkeley professor of integrative biology. “In this case, it is probably not a mutation that most people would want to have. You are actually, on average, worse off having it.”

“Because one gene could affect multiple traits, and because, depending on the environment, the effects of a mutation could be quite different, I think there can be many uncertainties and unknown effects in any germline editing,” said postdoctoral fellow Xinzhu “April” Wei.
Wei is first author and Nielsen is senior author of a paper describing the research that will appear online on Monday, June 3, in the journal Nature Medicine.

Mutation prevents HIV infection

The gene CCR5 codes for a protein that, among other things, sits on the surface of immune cells and helps some strains of HIV, including the most common ones, to enter and infect them. Jiankui He, the Chinese scientist who last November shocked the world by announcing he had experimented with CCR5 on at least two babies, said he wanted to introduce a mutation in the gene that would prevent this. Naturally-occurring mutations that disable the protein are rare in Asians, but a mutation found in about 11% of Northern Europeans protects them against HIV infection.

The genetic mutation, ∆32 (Delta 32), refers to a missing 32-base-pair segment in the CCR5 gene. This mutation interferes with the localization on the cell surface of the protein for which CCR5 codes, thwarting HIV binding and infection. He was unable to duplicate the natural mutation, but appears to have generated a similar deletion that would also inactivate the protein. One of the twin babies reportedly had one copy of CCR5 modified by CRISPR-Cas9 gene editing, while the other baby had both copies edited.

But inactivating a protein found in all humans and most animals is likely to have negative effects, Nielsen said, especially when done to both copies of the gene — a so-called homozygous mutation

“Here is a functional protein that we know has an effect in the organism, and it is well-conserved among many different species, so it is likely that a mutation that destroys the protein is, on average, not good for you,” he said. “Otherwise, evolutionary mechanisms would have destroyed that protein a long time ago.”

After He’s experiment became public, Nielsen and Wei, who study current genetic variation to understand the origin of human, animal and plant traits, decided to investigate the effect of the CCR5-∆32 mutation using data from UK Biobank. The database houses genomic information on a half million U.K. citizens that is linked to their medical records. The genomic information is much like that acquired by Ancestry.com and 23andMe: details on nearly a million individual variations in the genetic sequence, so-called single nucleotide polymorphisms (SNPs).

Two independent measures indicated a higher mortality rate for those with two mutated genes. Fewer people than expected with two mutations enrolled in the database, indicating that they had died at a higher rate than the general population. And fewer than expected survived from ages 40 to 78.

“Both the proportions before enrollment and the survivorship after enrollment tell the same story, which is that you have lower survivability or higher mortality if you have two copies of the mutation,” Nielsen said. “There is simply a deficiency of individuals with two copies.”

Because the ∆32 mutation is relatively common in Northern Europeans, it must have been favored by natural selection at some point, Nielsen said, though probably not to protect against HIV, since the virus has circulated among humans only since the 1980s.

Wei said that some evidence links the mutation to increased survival after stroke and protection against smallpox and flaviviruses, a group that includes the dengue, Zika and West Nile viruses.

Despite these possible benefits, the potential unintended effects of creating genetic mutations, in both adult somatic cells and in embryonic, germline cells, argue for caution, the researchers said.

“I think there are a lot of things that are unknown at the current stage about genes’ functions,” Wei said. “The CRISPR technology is far too dangerous to use right now for germline editing.”

Here’s a link to and a citation for the latest paper,

CCR5-∆32 is deleterious in the homozygous state in humans by Xinzhu Wei & Rasmus Nielsen. Nature Medicine (2019) DOI: https://doi.org/10.1038/s41591-019-0459-6 Published 03 June 2019

This paper is behind a paywall.

For those who have an insatiable appetite for detail, there’s my November 28, 2018 posting which covers what happened when the CRISPR twins, Lulu and Nana, was first announced, along with a few updates to January 23, 2019. The May 17, 2019 posting covers the news of possible cognitive advantages for the CCR5-Δ32 gene-edited twins and explores some of the social implications.