U$A

How genetic therapies transformed the lives of sickle cell patients

Washington (AFP) – Their stories are divided into before and after.

Issued on: 18/03/2024 

Physician-scientist John Tisdale of the National Institutes of Health, which ran a clinical trial for sickle cell disease treatment 

© Brendan Smialowski / AFP

First, those long years of pain which flooded every moment -- school, relationships, work.

And then -- after agonizing treatments -- what felt like the miracle of life after sickle cell disease (SCD).

Two Americans whose lives were turned around by newly approved treatments tell AFP they want others to benefit too.

But the eye-watering cost -- up to $3.1 million per course of treatment -- could limit access for other patients.

'Like coming to life'

Tesha Samuels was born in 1982 -- just before the invention of prenatal screening for SCD, an inherited red blood cell disorder.

SCD affects around 100,000 people in the United States and some 20 million worldwide.

Most people with the condition are Black. Scientists say this is because the sickle cell trait evolved to protect people exposed to malaria, so the risk of SCD is higher.

Doctors prepare a patient for blood work during her clinical trail in Washington, DC in February 2024

 © Brendan Smialowski / AFP

Those with the disease have abnormal hemoglobin -- the molecule that carries oxygen -- making their red cells hard and C-shaped like sickles.

Complications include anemia, bouts of extreme pain, organ damage and early death.

Tesha was diagnosed aged two and recalls a childhood in and out of hospital.

At seven, she suffered a life-threatening case of anemia and then aged 13 she had a stroke which led to monthly blood infusions.

Tesha said "the stigma of a Black child going to the hospital saying they're in pain" made her wait until things got unbearable.

As a young adult, Tesha saw the disease take the life of a dear friend named Mohammed, a fellow "sickle cell warrior" who would often end up in the same hospital as her.

She began studying at the prestigious Howard University hoping to become a doctor but her health forced her to drop out. She then tried community college but, once more, SCD meant couldn't finish.

"You downgrade your dreams based on your capacity in sickle cell," said Tesha.

As a newlywed in her twenties, she was dismayed at needing an intravenous medicine drip for eight hours every night to manage her condition.

Viral vector treatment has been trialed as a way to treat sickle cell disease 

© Valentin RAKOVSKY, Jean-Michel CORNU / AFP

But in 2018 her life turned a corner when she became one of the first ever people to receive an experimental gene therapy.

The procedure -- now marketed as Lyfgenia -- uses a modified virus to deliver a functional version of the hemoglobin-producing gene. .

First, doctors draw out stem cells from the bone marrow before modifying them in a lab. Then comes the hardest part -- chemotherapy to clear the way for the return of the treated cells.

In addition to losing all her hair, chemotherapy saw Tesha have a 16-hour nosebleed which left her in intensive care.

Her recovery was further complicated as her blood platelets, which are essential for blood clotting, took months to bounce back.

But when they did, her energy levels soared.

"It's almost like coming to life," Tesha said. "Here's this new life ahead of you. What do I want to do with it?"

Tesha went back to school to complete her degree.

A patient receives an echocardiogram in a followup visit during her clinical trail at the National Institutes of Health 

© Brendan Smialowski / AFP

She also started her own advocacy group, Journey to ExSCellence, to spread word of the treatment among the Black community.

"It looks like the cure, but we like to call this 'transformative,'" said physician-scientist John Tisdale of the National Institutes of Health, which ran the trial Tesha took part in.

Tisdale emphasized that each patient needed monitoring for 15 years to complete the study.

Childhood struggle

Jimi Olaghere's first memory of sickle cell goes back to when he was eight-years-old, playing soccer with other kids in his native Nigeria and needing to stop every five minutes for rest and water.

"I asked my mom, why am I different?" he remembers.

His parents sent him to live with his aunt in New Jersey where there was better health care but his childhood remained a struggle.

Jimi, 38, was unable to complete college and found his disease was too heavy a burden to place on most romantic partners, until he found his wife who was willing to embrace the challenge.

The disease also took a terrible toll.

His gallbladder was removed, he had a heart attack and lung clots. At his worst, he recalls spending 80 percent of his time in bed.

Moving to the warmer climate of Atlanta brought some relief, as it does for many with SCD.

Then, in 2019, he heard about a CRISPR gene therapy clinical trial. He applied to be tested for eligibility and received a "magical" voicemail telling him he was in.

Cell lines are prepared in a laboratory at the National Institutes of Health in Washington, DC 

© Brendan Smialowski / AFP

Thanks to the CRISPR-modified stem cell therapy he received, now marketed as Casgevy, Jimi is "basically living the dream now."

He has three children, thanks to IVF, and runs several small businesses.

Like Tesha, Jimi has raised his voice to advocate for others, particularly in Africa, where access to such treatment seems a far-off dream.

Tisdale, of the NIH, said the next step was reducing the physical burden of the treatment and making it cheaper.

It remains unclear how much private insurers will pay to offset the procedure's enormous costs.

But Medicaid, a US government-backed insurance program, has said it will pay for the therapies starting next year.

© 2024 AFP

 

It’s hearty, it’s meaty, it’s mold

Hacking the genome of fungi for smart foods of the future

Peer-Reviewed Publication

DOE/LAWRENCE BERKELEY NATIONAL LABORATORY

 

IMAGE: 

A GENE-EDITED FUNGAL CULTURE FROM VAYU HILL-MAINI'S RESEARCH, SEEN ON A DINNER PLATE. 

view more 

CREDIT: MARILYN SARGENT/BERKELEY LAB

With animal-free dairy products and convincing vegetarian meat substitutes already on the market, it’s easy to see how biotechnology can change the food industry. Advances in genetic engineering are allowing us to harness microorganisms to produce cruelty-free products that are healthy for consumers and healthier for the environment.

One of the most promising sources of innovative foods is fungi – a diverse kingdom of organisms that naturally produce a huge range of tasty and nutritious proteins, fats, antioxidants, and flavor molecules. Chef-turned-bioengineer Vayu Hill-Maini, an affiliate in the Biosciences Area at Lawrence Berkeley National Laboratory (Berkeley Lab), is exploring the many possibilities for new flavors and textures that can be made from modifying the genes already present in fungi.

“I think it's a fundamental aspect of synthetic biology that we’re benefiting from organisms that have evolved to be really good at certain things,” said Hill-Maini, who is a postdoctoral researcher at UC Berkeley in the lab of bioengineering expert Jay Keasling. “What we're trying to do is to look at what is the fungus making and try to kind of unlock and enhance it. And I think that's an important angle that we don’t need to introduce genes from wildly different species. We’re investigating how we can stitch things together and unlock what's already there.”

In their recent paper, publishing on March 14 in Nature Communications, Hill-Maini and colleagues at UC Berkeley, the Joint BioEnergy Institute, and the Novo Nordisk Foundation Center for Biosustainability studied a multicellular fungus called Aspergillus oryzae, also known as koji mold, that has been used in East Asia to ferment starches into sake, soy sauce, and miso for centuries. First, the team used CRISPR-Cas9 to develop a gene editing system that can make consistent and reproducible changes to the koji mold genome. Once they had established a toolkit of edits, they applied their system to make modifications that elevate the mold as a food source. First, Hill-Maini focused on boosting the mold’s production of heme – an iron-based molecule which is found in many lifeforms but is most abundant in animal tissue, giving meat its color and distinctive flavor. (A synthetically produced plant-derived heme is also what gives the Impossible Burger its meat-duping properties.) Next, the team punched up production of ergothioneine, an antioxidant only found in fungi that is associated with cardiovascular health benefits.  

After these changes, the once-white fungi grew red. With minimal preparation – removing excess water and grinding – the harvested fungi could be shaped into a patty, then fried into a tempting-looking burger.

Hill-Maini’s next objective is to make the fungi even more appealing by tuning the genes that control the mold’s texture. “We think that there's a lot of room to explore texture by varying the fiber-like morphology of the cells. So, we might be able to program the structure of the lot fibers to be longer which would give a more meat-like experience. And then we can think about boosting lipid composition for mouth feel and further nutrition,” said Hill-Maini, who was a Fellow of the Miller Institute for Basic Research in Science at UC Berkeley during the study. “I'm really excited about how can we further look at the fungus and, you know, tinker with its structure and metabolism for food.”

Though this work is just the beginning of the journey to tap into fungal genomes to create new foods, it showcases the huge potential of these organisms to serve as easy-to-grow protein sources that avoid the complex ingredients lists of current meat substitutes and the cost barriers and technical difficulties hindering the launch of cultured meat. Additionally, the team’s gene editing toolkit is huge leap forward for the field of synthetic biology as a whole. Currently, a great variety of biomanufactured goods are made by engineered bacteria and yeast, the single-celled cousins of mushrooms and mold. Yet despite humanity’s long history of domesticating fungi to eat directly or to make staples like miso, multicellular fungi have not yet been harnessed as engineered cellular factories to the same extent because their genomes are far more complex, and have adaptations that make gene editing a challenge. The CRISPR-Cas9 toolkit developed in this paper lays the foundation to easily edit koji mold and its many relatives.

“These organisms have been used for centuries to produce food, and they are incredibly efficient at converting carbon into a wide variety of complex molecules, including many that would be almost impossible to produce using a classic host like brewer’s yeast or E. coli,” said Jay Keasling, who is a senior scientist at Berkeley Lab and a professor at UC Berkeley. “By unlocking koji mold through the development of these tools, we are unlocking the potential of a huge new group of hosts that we can use to make foods, valuable chemicals, energy-dense biofuels, and medicines. It’s a thrilling new avenue for biomanufacturing.”

Given his culinary background, Hill-Maini is keen to ensure that the next generation of fungi-based products are not only palatable, but truly desirable to customers, including those with sophisticated tastes. In a separate study, he and Keasling collaborated with chefs at Alchemist, a two-Michelin-starred restaurant in Copenhagen, to play with the culinary potential of another multicellular fungus, Neurospora intermedia. This fungus is traditionally used in Indonesia to produce a staple food called oncom by fermenting the waste products left over from making other foods, such as tofu. Intrigued by its ability to convert leftovers into a protein-rich food, the scientists and chefs studied the fungus in the Alchemist test kitchen. They discovered N. intermedia produces and excretes many enzymes as it grows. When grown on starchy rice, the fungi produces an enzyme that liquifies the rice and makes it intensely sweet. “We developed a process with just three ingredients – rice, water, and fungus – to make a beautiful, striking orange-colored porridge,” said Hill-Maini. “That became a new dish on the tasting menu that utilizes fungal chemistry and color in a dessert. And I think that what it really shows is that there's opportunity to bridge the laboratory and the kitchen.”

Hill-Maini’s work on the gene editing research described in this article is supported by the Miller Institute at UC Berkeley. Keasling’s lab is supported by the Novo Nordisk Foundation. Both received additional support from the Department of Energy (DOE) Office of Science. The Joint BioEnergy Institute is a DOE Bioenergy Research Center managed by Berkeley Lab.

 

The small koji mold patty after frying.

CREDIT

Vayu Hill-Maini

First author Vayu Hill-Maini in the lab at the Joint BioEnergy Institute in Emeryville, California. 

CREDIT

Marilyn Sargent/Berkeley Lab

The petri dish on the left contains the natural koji mold, whereas the one on the right has been engineered to contain higher levels of a nutrient called ergothioneine and more heme – an iron-based molecule found in many organisms, but is especially abundant in animal tissues, which gives meat a distinctive flavor.

CREDIT

Marilyn Sargent/Berkeley Lab

Lawrence Berkeley National Laboratory (Berkeley Lab) is committed to delivering solutions for humankind through research in clean energy, a healthy planet, and discovery science. Founded in 1931 on the belief that the biggest problems are best addressed by teams, Berkeley Lab and its scientists have been recognized with 16 Nobel Prizes. Researchers from around the world rely on the Lab’s world-class scientific facilities for their own pioneering research. Berkeley Lab is a multiprogram national laboratory managed by the University of California for the U.S. Department of Energy’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science.

---

JOURNAL

Nature Communications

ARTICLE TITLE

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit

ARTICLE PUBLICATION DATE

14-Mar-2024

Infections from these bacteria are on the rise. New blood test cuts diagnosis time from months to hours

Tulane University researchers have designed a platform to perform blood-based diagnoses of nontuberculosis mycobacteria, simplifying and shortening a long-complicated procedure from 6 months to 2 hours.

TULANE UNIVERSITY

Inhaling nontuberculous mycobacteria is common for most people. The bacteria are found in water systems, soil and dust worldwide and, for many, cause no harm.

For those with underlying conditions, nontuberculous mycobacteria (NTM) can infect the lungs, causing symptoms similar to tuberculosis. Inflammation can cause a chronic and sometimes bloody cough as well as scarring, which can make respiratory infections like bronchitis and pneumonia more common. Due to the slow growth of the bacteria, proper diagnosis and treatment can take months.

In a new study, Tulane University researchers have developed a CRISPR-based platform for diagnosing NTM infections where blood testing can yield results in as little as two hours

The preliminary findings, published in the American Journal of Respiratory and Critical Care Medicine, showed that the blood test was able to accurately identify more than 93% of patients with an NTM infection. Rapid, accurate diagnosis has never been more important as cases of NTM infections have continued to increase annually, spreading from subtropical regions to more temperate zones in part due to global climate change.

“NTM infection is highly underestimated, and due to the slow diagnosis of it, patients with NTM infection are not effectively treated,” said Bo Ning, corresponding author and assistant professor of molecular biology at Tulane University School of Medicine. “Importantly, our blood test can analyze NTM DNA fragments in the bloodstream, thereby inferring a drug response, which is crucial for rapidly determining treatment plans, capabilities traditional diagnostic approaches cannot achieve.”

The blood test is specifically designed to detect mycobacteria avium complex (MAC), one of the most common types of NTM and the most common cause of NTM-induced pulmonary disease.

To identify an infection, the test detects fragments of NTM DNA in the bloodstream. Current diagnosis methods rely on analysis of long-term cultures of the slow-growing bacteria, which can lead to delays in diagnosis and treatment. And with more than 190 species of NTM, correctly diagnosing an infection can be difficult. 

“Currently, correct diagnosis and treatment can last more than six months,” Ning said. “Not only can our blood test provide same-day results, this test can be quickly performed in any clinics where blood can be drawn and does not require specialized training or equipment needed to analyze bacteria cultures.”

Ning said the United States may face rising NTM infections in the future and that accessible tests like this one are vital to staying ahead of it.

Going forward, he hopes to expand the types of NTM that CRISPR can detect and develop point-of-care tests for NTM detection.

“The goal is to reduce barriers to testing and diagnosis and prepare for a potential surge of NTM infections,” Ning said. 

The study was conducted in collaboration with Oregon Health & Science University.

---

JOURNAL

American Journal of Respiratory and Critical Care Medicine

DOI

10.1164/rccm.202303-0401OC 

ARTICLE TITLE

Serum Cell-free DNA-based Detection of Mycobacterium Avium Complex Infection

 

Revolutionary elephant iPSC milestone reached in Colossal’s Woolly Mammoth Project

Colossal scientists achieve global first; technology promises seminal advancements for engineering Woolly Mammoth phenotypes in in vitro cellular models, developmental biology, and attaining balance between senescence and cell growth

Business Announcement

COLOSSAL

 

IMAGE: 

ASIAN ELEPHANT IPSC COLONIES STAINED FOR PLURIPOTENCY FACTORS OCT4 (MAGENTA) AND SOX2(GREEN), NUCLEAR DNA HOECHST (BLUE) AND CYTOSKELETAL PROTEIN ACTIN (RED)

view more 

CREDIT: COLOSSAL BIOSCIENCES

Dallas, TX – March 06, 2024 - Colossal Biosciences (“Colossal”), the world’s first de-extinction company, announces today that their Woolly Mammoth team has achieved a global-first iPSC (induced pluripotent stem cells) breakthrough. This milestone advancement was one of the primary early goals of the mammoth project, and supports the feasibility of future multiplex ex utero mammoth gestation.

iPSC cells represent a single cell source that can propagate indefinitely and give rise to every other type of cell in a body. As such, the progress with elephant iPSCs extends far beyond this de-extinction project holding tremendous potential for studying cell development, cell therapy, drug screening, synthetic embryos, in vitro gametogenesis, and the use of iPSCs for nuclear transfer across all species. Invaluable for Colossal’s Woolly Mammoths, these cells can be multiplex-edited and differentiated to study cold adaptation traits like woolly hair growth and fat storage in cellular and organoid models.  

“In the past, a multitude of attempts to generate elephant iPSCs have not been fruitful. Elephants are a very special species, and we have only just begun to scratch the surface of their fundamental biology,” shared Eriona Hysolli, Head of Biological Sciences at Colossal Biosciences. “My early work in Dr. George Church’s laboratory had been partially successful with iPSC-like cells that led to the foundation of the cells we have currently developed. And now, using a multi-pronged approach to reprogramming we have the most successful efforts to date. The Colossal mammoth team persisted quite successfully as this progress is invaluable for the future of elephant assisted reproductive technologies, as well as advanced cellular modeling of mammoth phenotypes.”

The derivation of mouse iPSCs pioneered by Shinya Yamanaka in 2006 paved the way for using a  4-factor protocol to derive human, horse, pig, cattle, rabbit, monkey, ape, big cats, rhino and even avian species iPSCs among many more. While the medium where the cells grew required some tweaking depending on the species, it was surprising to observe how close to universal the reprogramming protocol was across species. Yet, elephant iPSCs still remained elusive.

“Elephants might get the "hardest to reprogram" prize, but learning how to do it anyway will help many other studies, especially on endangered species. This milestone gives us insights into developmental biology and the balance between senescence and cancer. It opens the door for obtaining gametes and other cell types without surgery on precious animals. It opens the door to establishing connections between genes and traits for both modern and extinct relatives – including resistance to environmental extremes and pathogens.  This collaboration has been a true pleasure and a colossal accelerant for our challenging project,” shared Colossal co-founder and renowned Harvard geneticist Dr. George Church.

Using chemical-based induction media first, followed by addition of transcription factors  Oct4, Sox2, Klf4, Myc +/- Nanog and Lin28, and p53 pathway suppression, the team has achieved the most successful reprogramming of elephant iPSCs yet. The approach differs from other more standard reprogramming protocols for other species due in part  to the complexities of the TP53 pathway in elephants as their genome contains up to 19 copies of TP53 retrogenes. TP53 is a core gene utilized by the cell to carefully regulate its growth so as not to become cancerous. Additionally, reprogramming, which in itself is quite long and inefficient for higher mammal species, takes longer for elephants. But, the successful iPSC cells now express multiple core pluripotency factors and are able to differentiate into the three germ layers that have the potential to give rise to each cell type in the body.

These newly reprogrammed iPSC cells have been validated through immunostaining, PCR of pluripotency and differentiation markers, transcriptomics analysis, embryoid bodies and teratoma formation. This work will be published in Bioarxiv with a peer-reviewed article in a scientific journal in progress. It is not the end of the elephant reprogramming journey, but this announcement marks the first successful steps. The mammoth stem cell team with team lead Evan Appleton are now focused on further maturing these cells, and pursuing additional iPSC generation strategies that have so far also been successful. This work will be shared in follow-up publications.

“We are most excited to use the cells we have developed to grow elephant gametes in a dish. While elephants have been a challenging species, this has been an incredibly unique opportunity with so much to learn and share now and in the near future,” shared team lead Evan Appleton.

“We knew when we set out on the Woolly Mammoth de-extinction project that it would be challenging but we’ve always had the best team on the planet focused on the task at hand,” stated co-founder and CEO of Colossal, Ben Lamm. “This is a momentous step, with numerous applications, that we are proud to share with the scientific community. Each step brings us closer to our long term goals of bringing back this iconic species.”

The team is also working to establish a mechanism that can explain why elephant cell reprogramming has been challenging. Doing so is critical to deriving iPSCs faster, achieving more advanced tri-lineage differentiation, particularly in vitro gametogenesis, which is crucial to test the full potential of the iPSCs. Once the iPSCs can be used to establish a model for synthetic elephant embryos, it will also be integral to understanding the long and complex elephant (and by association mammoth) development and gestation cycle.  This will be critical to Colossals’ re-wilding efforts which rely heavily on leveraging ex utero development for species preservation and restoration. All of these scientific developments hold extension possibilities across the field of developmental biology which have ramifications far beyond the current Colossal projects.

 Asian elephant iPSC colonies [VIDEO] | 

ABOUT COLOSSAL

Colossal was founded by emerging technology and software entrepreneur Ben Lamm and world-renowned geneticist and serial biotech entrepreneur George Church, Ph.D., and is the first to apply CRISPR technology for the purposes of species de-extinction. Colossal creates innovative technologies for species restoration, critically endangered species protection and the repopulation of critical ecosystems that support the continuation of life on Earth. Colossal is accepting humanity's duty to restore Earth to a healthier state, while also solving for the future economies and biological necessities of the human condition through cutting-edge science and technologies. To follow along, please visit: www.colossal.com

WEBSITE & SOCIALS

Websites: www.colossal.com
Twitter: https://twitter.com/itiscolossal
Instagram: ​​https://www.instagram.com/itiscolossal/
LinkedIn: https://www.linkedin.com/company/itiscolossal/
Facebook: https://www.facebook.com/itiscolossal
Hashtag: #itiscolossal

COLOSSAL PRESS CONTACTS:

R&CPMK /  Emily.mailaender@rcpmk.com

Prosek /  pro-colossal@prosek.com

---

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Cells

 

New disease testing component facilitates lower-cost diagnostics

Peer-Reviewed Publication

UNIVERSITY OF TEXAS AT AUSTIN

A new tool could reduce costs for diagnosing infectious diseases.

Biomedical researchers from The University of Texas at Austin have developed a new, less expensive way to detect nuclease digestion – one of the critical steps in many nucleic acid sensing applications, such as those used to identify COVID-19 and other infectious diseases.  

A new study published in the journal Nature Nanotechnology shows that this low-cost tool, called Subak, is effective at telling when nucleic acid cleavage occurs, which happens when an enzyme called nuclease breaks down nucleic acids, such as DNA or RNA, into smaller fragments. 

The traditional way of identifying nuclease activity, Fluorescence Resonance Energy Transfer (FRET) probe, costs 62 times more to produce than the Subak reporter.   

“To make diagnostics more accessible to the public, we have to reduce costs,” said Soonwoo Hong, a Ph.D. student in the lab of Tim Yeh, associate professor in the Cockrell School of Engineering’s Department of Biomedical Engineering, who led the work. “Any improvements in nucleic acid detection will strengthen our testing infrastructure and make it easier to widely detect diseases like COVID-19.”

The research team – which also included Jennifer Brodbelt, professor of chemistry at UT Austin's College of Natural Sciences, and MinJun Kim, professor of mechanical engineering in Southern Methodist University’s Lyle School of Engineering – replaced the traditional FRET probe with Subak reporter in a test called DETECTR (DNA endonuclease-targeted CRISPR trans reporter).

Subak reporters are based on a special class of fluorescent nanomaterials known as silver nanoclusters. They are made up of 13 silver atoms wrapped inside a short DNA strand. This organic/inorganic composite nanomaterial is too small to be visible to the naked eye and ranging from 1 to 3 nanometers (one billionth of a meter) in size.

Nanomaterials at this length scale, such as semiconductor quantum dots, can be highly luminescent and exhibit different colors. Fluorescent nanomaterials have found applications in TV displays and biosensing, such as the Subak reporters.

“We have very clear evidence from mass spectrometry that transformation from Ag13 to Ag10 underlines the green to red color conversion observed in the sample, after DNA template digestion,” Brodbelt said.

Subak reporters, which can be synthesized at room temperature in a single-pot reaction, cost just $1 per nanomole to make. In contrast, FRET probe – which employs complex steps to label a donor dye and a quencher – costs $62 per nanomole to produce.  

“These highly luminescent silver nanoclusters can be called quantum dots as they show strong size-tunable fluorescence emission due to quantum confinement effect,” Yeh said. “No one can precisely tune the cluster size (and the corresponding emission color) until our demonstration of Subak,” which highlights the innovation of this research. 

In addition to further testing the Subak reporter for nuclease digestion, the team also wants to investigate whether it can be a probe for other biological targets. 

The work is supported by a National Science Foundation grant to Yeh and Brodbelt.

---

JOURNAL

Nature Nanotechnology

DOI

10.1038/s41565-024-01612-6 

ARTICLE TITLE

A non-FRET DNA reporter that changes fluorescence colour upon nuclease digestion

COMPANY SEEKING APPROVAL TO SELL MEAT FROM GENE-HACKED PIGS

CRISPR-EDITED PIGS, COMING TO A PLATE NEAR YOU.

Pork Chopped

In the future, the roasted pork shoulder or the slices of seasoned country ham you eat may well come from gene-hacked pigs.

At least that's what the scientists at animal genetics outfit Genus hope will come to fruition, New Scientist reports, as they work on perfecting CRISPR-edited pigs designed to withstand the disease porcine reproductive and respiratory syndrome (PRRS), which has caused billions in losses for pig farmers.

"I think by and large the farmers are quite excited to have it, because this is a fairly devastating disease," Genus' Global Director of Regulatory and External Affairs Clint Nesbitt told the magazine.

Welfare Check

Genus is now awaiting for approval from the Food and Drug Administration, per New Scientist. If given the green light, the pigs would enter the history books as the first ever gene-edited domestic animal for mass meat consumption.

Once approved, Genus would be selling sperm from the gene-edited pigs that carry the modified genes. Subsequent breeding, it says, will yield porkers that will be totally immune to PRRS.

PRRS is a viral disease that harms the reproduction process and pigs' respiratory system. It first emerged in late 1980s and has impacted pigs all over the world except for Australia, New Zealand and Switzerland.

Farmers have tried to keep the disease in check with antibiotics, vaccines, isolating pigs, and cleaning and disinfecting pig breeding facilities. But industrial pig farms are often crowded and unhappy places that smell heavily of acrid feces, and hence they are breeding grounds for all sorts of diseases.

In the face of all that, genetics modification is a tempting solution. But animal welfare advocates say gene-edited farm animals will only cement the stranglehold that industrial farms have on the public and may even make the conditions worse for the animals.

"Keeping animals crowded together, and in stressful conditions, provides an ideal environment for pathogens to spread and evolve," anti-factory farm group Compassion in World Farming's research manager Catherine Jadav told New Scientist. "If PRRS-resistant pigs are used to perpetuate the current highly intensive model of pig farming, then other diseases will continue to develop – bringing disease after disease that ‘requires’ new gene-edited animals."

More on gene-edited pigs: Gene-hacked Pig Liver Successfully Filters Blood of Human Patient

Prices for new US drugs rose 35% in 2023, more than the previous year

FEBRUARY 24, 2024 

Pharmaceutical companies last year launched new US drugs at prices 35 per cent higher than in 2022, reflecting in part the industry's embrace of expensive therapies for rare diseases like muscular dystrophy, a Reuters analysis found.

The median annual list price for a new drug was US$300,000 (S$402,900) in 2023, according to the Reuters analysis of 47 medicines, up from US$222,000 a year earlier. In 2021, the median annual price was US$180,000, opens new tab for the 30 drugs first marketed through mid-July, according to a study published in JAMA.

PHOTO: Reuters graphics

More than half of the new products approved by the Food and Drug Administration in 2023 and 2022 were for orphan diseases, meaning they affect fewer than 200,000 Americans, and some are not expected to become big sellers. The orphan rate is slightly higher than the 49 per cent seen in the previous five years, opens new tab.


A high price is justified for a drug with a lot of value to patients, but "prices are just going up and up without any clear rationale as to why," said Dan Ollendorf, chief scientific officer at the Institute for Clinical and Economic Review (ICER), an influential group that evaluates the value and prices of medicines.

He said many rare disease and cancer drugs are not being priced relative to their benefit, but the lack of alternatives gives manufacturers negotiating leverage.

Reuters analysed 55 novel drugs approved by the FDA last year, up from 37 in 2022. The agency's biologic division approved 17 new products, including four gene therapies.

The analysis excludes vaccines and drugs used intermittently such as Pfizer's, opens new tab Covid-19 antiviral Paxlovid. It also excludes drugs that have not yet launched commercially.

Of the 47 medications included in the analysis, the highest price for drugs taken consistently was US$1.8 million a year for Regeneron's, opens new tab Veopoz for CHAPLE disease, an inherited condition diagnosed in fewer than 100 people worldwide in which parts of the immune system become overactive.


The lowest annual price was US$576 for diabetes drug Brenzavvy, sold by TheracosBio in partnership with Mark Cuban's Cost Plus Drugs online pharmacy.

ICER's Ollendorf said it is too early to tell whether TheracosBio will succeed with its strategy to "blow up" the typical drug contracting model by selling a medication in a widely-used class at a much lower price than the competition.

TheracosBio CEO Brian Connelly said Brenzavvy "sales are increasing at a great clip," but declined to provide details.

PHOTO: Reuters graphics

Market incentives

Gene therapies, which are one-time treatments, range in price from US$2.2 million for sickle cell disease treatment Casgevy from Vertex, opens new tab and CRISPR, opens new tab, to US$3.2 million for Sarepta's, opens new tab muscular dystrophy therapy Elevydis.

The US gives drug manufacturers market exclusivity, fee waivers, direct funding for research and development, and tax credits for such orphan treatments.

"We created a lot of incentives for innovation for rare diseases and the market responded," said Dana Goldman, director of the USC Schaeffer Center for Health Policy & Economics. "The hope is that eventually we will see some therapeutic competition in this space and bring prices down."

The 2022 Inflation Reduction Act limits how much drugmakers can raise prices for treatments offered under Medicare, the federal health plan for people age 65 and over. The legislation does not limit what can be charged for new medicines.

"It means you are encouraging companies to launch at high prices," Goldman said.

Drugmakers stress they do not determine what US patients end up paying. Many offer savings cards and other programs to reduce out-of-pocket costs, while health insurers can receive discounts and rebates from manufacturer list prices, especially if competing treatments are available.

Drugmakers also say new medicines offer cost-saving value, including the possibility of fewer emergency room visits and hospital stays.


Boston Consulting Group forecast that 24 per cent of 2023's new drugs will reach blockbuster status - annual sales of over US$1 billion - versus 35 per cent from 2022's crop.

As patents expire, lower-cost generics mitigate prescription drug price inflation, which in the 12 months through December was roughly in line with broader inflation at 3.3 per cent, according to US government data.

 

CRISPR-copies: New tool accelerates and optimizes genome editing

CABBI researchers publically share a new tool to revolutionize CRISPR gene editing

UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN INSTITUTE FOR SUSTAINABILITY, ENERGY, AND ENVIRONMENT

 

IMAGE: 

CRISPR-COPIES HAS APPLICATIONS IN SYNTHETIC BIOLOGY TOOLKIT CHARACTERIZATION, GENE THERAPY, AND METABOLIC ENGINEERING.

view more 

CREDIT: AASHUTOSH BOOB ET AL.

CRISPR/Cas systems have undergone tremendous advancement in the past decade. These precise genome editing tools have applications ranging from transgenic crop development to gene therapy and beyond. And with their recent development of CRISPR-COPIES, researchers at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) are further improving CRISPR’s versatility and ease of use.

“CRISPR-COPIES is a tool that can quickly identify appropriate chromosomal integration sites for genetic engineering in any organism,” said Huimin Zhao, CABBI Conversion Theme Leader and Steven L. Miller Chair of Chemical and Biomolecular Engineering (ChBE) at the University of Illinois. “It will accelerate our work in the metabolic engineering of non-model yeasts for cost-effective production of chemicals and biofuels.”

Gene editing has revolutionized scientists’ capabilities in understanding and manipulating genetic information. This form of genetic engineering allows researchers to introduce new traits into an organism, such as resistance to pests or the ability to produce a valuable biochemical.

With CRISPR/Cas systems, researchers can make precise, targeted genetic edits. However, locating optimal integration sites in the genome for these edits has been a critical and largely unsolved problem. Historically, when researchers needed to determine where to target their edits, they would typically manually screen for potential integration sites, then test the site by integrating a reporter gene to assess its cellular fitness and gene expression levels. It’s a time- and resource-intensive process.

To address this challenge, the CABBI team developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool can identify genome-wide neutral integration sites for most bacterial and fungal genomes within two to three minutes.

“Finding the integration site in the genome manually is like searching for a needle in a haystack,” said Aashutosh Boob, a ChBE Ph.D. student at the University of Illinois and primary author of the study. “However, with CRISPR-COPIES, we transform the haystack into a searchable space, empowering researchers to efficiently locate all the needles that align with their specific criteria.”

In their paper published in Nucleic Acids Research, the researchers demonstrated the versatility and scalability of CRISPR-COPIES by characterizing integration sites in three diverse species: Cupriavidus necator, Saccharomyces cerevisiae, and HEK 293T cells. They used integration sites found by CRISPR-COPIES to engineer cells with increased production of 5-aminolevulinic acid, a valuable biochemical that has applications in agriculture and the food industry.

In addition, the team has created a user-friendly web interface for CRISPR-COPIES. This incredibly accessible application can be used by researchers even without significant bioinformatics expertise.

A primary objective of CABBI is the engineering of non-model yeasts to produce chemicals and fuels from plant biomass. Economically producing biofuels and bioproducts from low-cost feedstocks at a large scale is a challenge, however, due to the lack of genetic tools and the cumbersome nature of traditional genome-editing methods. By enabling researchers to swiftly pinpoint genomic loci for targeted gene integration, CRISPR-COPIES provides a streamlined pipeline that facilitates the identification of stable integration sites across the genome. It also eliminates the manual labor involved in designing components for CRISPR/Cas-mediated DNA integration.

For crop engineering, the tool can be used to increase biomass yields, pest resistance, and/or environmental resilience. For converting biomass to valuable chemicals — for instance, by using the yeast S. cerevisiae — CRISPR-COPIES can be used to engineer cells with significantly greater yields.

This versatile software is designed to simplify and accelerate the strain construction process, saving researchers both time and resources. Researchers around the world in both academia and industry can benefit from its utility in strain engineering for biochemical production and transgenic crop development.

Co-authors on this study include ChBE Ph.D. student Zhixin Zhu, ChBE visiting student Pattarawan Intasian, and Bioengineering Ph.D. student Guanhua Xun; Carl R. Woese Institute for Genomic Biology (IGB) Software Developers Manan Jain and Vassily Petrov; IGB Biofoundry Manager Stephan Lane; and CABBI postdoc Shih-I Tan.

— Article by CABBI Communications Specialist April Wendling

---

JOURNAL

Nucleic Acids Research

DOI

10.1093/nar/gkae062 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

CRISPR-COPIES: An in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

ARTICLE PUBLICATION DATE

13-Feb-2024

Not too late to repair: gene therapy improves advanced heart failure in animal model

Peer-Reviewed Publication

BAYLOR COLLEGE OF MEDICINE

Heart failure remains the leading cause of mortality in the U.S. During a heart attack blood stops flowing into the heart. Without oxygen, part of the heart muscle dies. The heart muscle does not regenerate, instead it replaces dead tissue with a scar made of cells called fibroblasts that do not help the heart pump. If there is too much scarring, the heart progressively enlarges, or dilates, weakens and eventually stops working.

“The current thought is that advanced or chronic heart failure, a stage in which the cardiac muscle has become too weak, is a point of no return. The present understanding is that it is not possible to stimulate a heart in this condition to generate new heart cells to repair itself and that only palliative treatment is available to patients,” said corresponding author Dr. Tamer M. A. Mohamed, associate professor of surgery and medicine and director of cardiac regeneration at Baylor College of Medicine. “In this study published in the journal Cardiovascular Research, we show that advanced heart failure can be treated to improve cardiac function in an animal model.”

In a previous study, Mohamed and his collaborators had successfully used gene therapy to improve acute cardiac dysfunction in animals. Their method effectively and specifically delivered genes that promote proliferation to heart cells, generating new heart muscle. This approach not only strengthened the heart improving its ability to keep the blood flowing, but also prevented typical subsequent congestion in the liver, kidneys and lungs in rats and pigs.

“In this study, we did something that had not been done before,” Mohamed said. “We intervened with the same gene therapy but not during acute heart failure or early in the disease as in our previous experiments, but late in the disease during the chronic phase four weeks after cardiac injury had severely damaged the heart.”

Four months after treating the animals, the researchers checked cardiac function and heart structure. “We were surprised to see evidence of significant heart cell proliferation, a marked reduction in scar size and a significant improvement in cardiac function,” said first author Dr. Riham R E Abouleisa, assistant professor of surgery- cardiothoracic surgery at Baylor. “Although heart dilation and lung congestion associated with chronic heart failure were not improved, the treatment partially improved liver and kidney functionality.”

The findings show for the first time that contrary to expectations, it is possible to induce heart cell proliferation during advanced states of heart failure and improve heart function, with some beneficial effects on the liver and kidneys’ functions.

“Our work has important implications for the large group of patients with advanced heart failure for whom there are currently no treatments to improve their condition,” Mohamed said. “This approach offers the possibility of developing future new therapies for this deadly disease.”

Other authors on this study include: Xian-Liang Tang, Qinghui O, Abou-Bakr M. Salama, Amie Woolard, Dana Hammouri, Hania Abdelhafez, Sarah Cayton, Sameeha K. Abdulwali, Momo Arai, Israel D. Sithu, Daniel J. Conklin and Roberto Bolli. The authors are affiliated with one or more of the following institutions: Baylor College of Medicine, University of Louisville, Zagazig University, Alfaisal University and University of Manchester.

This work was supported by the National Institutes of Health grants (F32HL149140, R01HL147921, P30GM127607, R15HL168688, R01HL166280 and HL78825) and by the American Heart Association grant 16SDG29950012.

###

---

JOURNAL

Cardiovascular Research

DOI

10.1093/cvr/cvae002 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Gene therapy encoding cell cycle factors to treat chronic ischemic heart failure in rats