UC Berkeley wins chance to reclaim lucrative gene editing patent
The U.S. Patent Trial and Appeal Board ruled in 2022 that the patent for so-called CRISPR technology belonged to the Broad Institute, affiliated with Harvard and the Massachusetts Institute of Technology, which had published a study in 2012 describing how the technology could be used to alter genes in plants and animals.
The board rejected a competing claim from the University of California, whose scientists had reported on the use of CRISPR technology to alter DNA six months before the Broad study. The patent board said the UC Berkeley report was the first of its kind but did not apply directly to genes in plants and animals.
But the U.S. Court of Appeals for the Federal Circuit ruled Monday that UC had presented evidence that its findings could be developed and applied to genes in all living creatures.
The patent board cited the UC scientists' 'experimental difficulties and … statements of doubt' about the application of their newly discovered technology, but failed to consider evidence that 'routine methods or skill' could enable the scientists to clear those hurdles and show that they were the original source of the information, Judge Jimmie Reyna wrote in the 3-0 ruling.
The court ordered the patent board to reconsider UC's contention that its study was the original breakthrough.
'This could end up being a big windfall for the University of California,' said Jacob Sherkow, a professor of law and medicine at the University of Illinois who has followed the issue for more than a decade.
He said the Broad Institute was paid $400 million in one of its first contracts with companies seeking to license the CRISPR technology. That contract and others already signed are not at risk, Sherkow said, but if Broad loses the patent, 'no one will sign a future license with them.'
Jeff Lamken, an attorney for UC in the case, said the ruling would enable the patent board to 're-evaluate the evidence under the correct legal standard and confirm what the rest of the world has recognized: that the (UC scientists) were the first to develop this groundbreaking technology for the world to share.'
The Broad Institute said in a statement that it was 'confident' the patent board 'will reach the same conclusion and will again confirm Broad's patents, because the underlying facts have not changed.'
The UC team was led by biochemist Jennifer Doudna and also included French scientist Emmanuelle Charpentier. In 2020, those two won the Nobel Prize in chemistry for their research on CRISPR, the first time two or more women had won that prize without a male partner.
In its 2022 ruling, the patent board cited Doudna's statement that the UC study had one shortcoming: 'We weren't sure if (the technology) would work in eukaryotes,' the cells found in plants and animals. The board noted that the scientists had experienced several failures in experiments with fish and human cells, and concluded that – unlike the Broad Institute study six months later – UC's report was 'not yet a definite and permanent reflection of the complete invention as it (would) be used in practice.'
But the appeals court said the patent board should have allowed UC to show that its scientists had made the crucial findings in their 2012 report and could take the final steps by using ordinary scientific methods and skills.
Try Our AI Features
Explore what Daily8 AI can do for you:
Comments
No comments yet...
Related Articles
Yahoo
20 hours ago
- Yahoo
Scientists Found a Hidden Trigger That Could Make Your Eyes Regenerate
Here's what you'll learn when you read this story: Many groups in the animal kingdom have the remarkable ability to regenerate their eyes, but mammals are not one of them—at least, not yet. A new study analyzed the genetic mechanisms behind the ocular regenerative ability of the golden apple snail to see if a similar technique could be used in human eyes. Although separated by hundreds of millions of years of evolution, human eyes and apple snail eyes retain remarkable similarities, both physically and genetically. Talk to most freshwater biologists, and you likely won't find much love for the golden apple snail. An invasive species outside of South America, this freshwater snail (Pomacea canaliculata) is both extremely resilient and what is known as a prolific organism, meaning it makes a lot of babies. This is a one-two punch of bad news for conservationists. But in a strange twist of fate, these particular attributes of the golden apple snail—along with its impressive ability to regenerate its eyes when damaged—made it the perfect test subject for Alice Accorsi, an assistant professor of molecular and cellular biology at the University of California (UC) Davis. So much so, in fact, that Accorsi was surprised no other study had yet detailed exactly how these snails wield such impressive powers of regeneration. 'When I started reading about this, I was asking myself, why isn't anybody already using snails to study regeneration?' Accorsi, the lead author of the new study, said in a press statement. 'I think it's because we just hadn't found the perfect snail to study, until now. A lot of other snails are difficult or very slow to breed in the lab, and many species also go through metamorphosis, which presents an extra challenge.' In the experiment, Accorsi and her team developed methods to tweak the apple snail's genome, hoping to better understand why it can regrow its eyes—an enviable ability that vertebrates (including humans) can't seem to achieve. Although separated by more than 600 million years of evolution, humans and apple snails both have camera-type eyes that make use of a system of corneas, lens, and retinas. Accorsi also said that many of the genes that participate in human eye development can be found in these snails as well. An apple snail's ocular regeneration process takes a month from start to finish. In the first 24 hours, the amputated wound heals and unspecialized cells congregate in the area before building new ocular hardware. By day 15, all parts of the eye's structure (including the optic nerve) are present, but the snail requires a few more weeks to fully mature. During this incredible process, scientists analyzed gene expression in the snail's genome, and found that immediately upon amputation, 9,000 genes expressed themselves at different rates than they did in a normal apple snail. The team then used CRISPR/Cas9 techniques to edit a snail embryo's genome—specifically, a gene known as Pax6, which is also known to control the development of the brain and eye in humans. 'The idea is that we mutate specific genes and then see what effect it has on the animal, which can help us understand the function of different parts of the genome,' Accorsi said in a press statement. When the snail embryo had two non-functional copies of the gene—one from each parent—eyes didn't develop at all once the snail reached maturation. Future studies will investigate if the manipulation of the gene in adult snails similarly impacts regeneration. 'If we find a set of genes that are important for eye regeneration, and these genes are also present in vertebrates, in theory we could activate them to enable eye regeneration in humans,' Accorsi said in a press statement. The idea of regenerating human eyes isn't new. A study published earlier this year in the journal Nature Communications showed evidence of the 'first successful induction of long-term neural regeneration in mammalian retinas,' according to the researchers, by inhibiting the PROX1 protein that can block retinal cell types in animals, including ones that could help restore vision to those suffering from retinitis pigmentosa. Similarly, this research was inspired by the amazing eye-regenerating abilities of the zebrafish. We humans may be the one with the big brains of the animal kingdom, but the varied biology of Earth's incredible creatures still has so much to teach us. Get the Issue Get the Issue Get the Issue Get the Issue Get the Issue Get the Issue Get the Issue Get the Issue You Might Also Like Can Apple Cider Vinegar Lead to Weight Loss? Bobbi Brown Shares Her Top Face-Transforming Makeup Tips for Women Over 50 Solve the daily Crossword
Scientific American
a day ago
- Scientific American
How RNA Unseated DNA as the Most Important Molecule in Your Body
In 1957, just four years after Francis Crick and other scientists solved the riddle of DNA's structure—the now famous double helix—Crick laid out what he called the 'central dogma' of molecular biology, which his colleague James Watson later said implied that biological information flows inexorably from DNA to RNA to proteins. Although Watson was oversimplifying, the message was that the purpose of the double helix in our chromosomes is to hold, in encoded form, blueprints for the proteins that build and maintain our bodies. DNA's chemical cousin, RNA, was the messenger that carries DNA instructions from the double helix in the cell's nucleus to the protein-making machinery, called the ribosome, scattered around the cell. Molecular biology's mission, it seemed, was to decipher those genetic instructions. But in recent years researchers have discovered a dizzying array of 'noncoding' RNA (ncRNA) molecules that do something other than ferry DNA instructions for proteins. They perform a surprisingly wide range of biochemical functions. It now seems that our genome may be at least as much a repository of plans for vital, noncoding RNA as it is for proteins. This shift in thinking has been 'revolutionary,' says Thomas Cech, who shared the 1989 Nobel Prize in Chemistry with Sidney Altman for discovering RNA molecules, called ribozymes, that can catalyze biochemical reactions. 'DNA is old stuff, 20th-century stuff,' Cech says. 'It's a one-trick pony. All it does is store biological information, which it does exquisitely well. But it's inert—it can't do anything without its children, RNA and proteins.' RNA is created when an enzyme called RNA polymerase reads a DNA sequence and builds a corresponding RNA molecule—a process known as transcription. The discovery, over the past three decades, of thousands of previously unknown noncoding RNAs 'has been mind-blowing,' says Maite Huarte, a molecular biologist at the University of Navarra in Pamplona, Spain. Noncoding RNA plays many roles, often involving the regulation of other genes—for example, determining whether protein-coding genes get transcribed to messenger RNA (mRNA) and how (or if) that molecule is edited and then translated into a protein. In this case, RNA seems to control how cells use their DNA. These functions turn the popular central dogma, which was a one-way street from DNA to mRNA to proteins, into an open system with information flowing in all directions among DNA, proteins, cells and organism. On supporting science journalism If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. Equally fascinating, Huarte says, is that ncRNAs don't belong to just one family of molecules. 'RNA is highly versatile, and nature exploits this versatility,' she says. Scientists have known since the 1950s that ribosomes contain ribosomal RNA and use transfer RNA to collect amino acids that are stitched together in proteins. But for a long time those seemed like anomalies. Then, in the 1980s, Cech and Altman discovered a new type of ncRNA: ribozymes that cleave and edit themselves and other RNAs. And in the 1990s researchers began to find human ncRNAs that had regulatory functions. A gene called XIST, involved in the 'silencing' of one of the two X chromosomes in the cells of chromosomal females, encoded not a protein but a long noncoding RNA that appears to wrap around the chromosome and prevent its transcription. 'Textbooks 25 years ago confidently stated that RNA consisted of [three types]. Now there are hundreds, likely many thousands, of other types.' —Thomas Cech University of Colorado Boulder Meanwhile molecular biologists Victor Ambros and Gary Ruvkun found short noncoding RNA molecules that interact with mRNA to silence a corresponding gene. This extra layer of gene regulation—controlling whether an mRNA is used to make a protein—seems to be an essential feature in the growth of complex organisms. Scientists have linked genetic mutations that hinder gene regulation by ncRNAs to a wide range of diseases, including cancers. 'We're getting closer to some really exciting biomedical applications,' Huarte says. 'From new diagnostic tools to innovative, targeted therapies, the potential of ncRNAs is huge.' Cech says it was a 'big surprise' RNA could perform such diverse roles. That surprise was apparent in 2012 when scientists working on an international project called ENCODE reported that as much as 80 percent of our DNA has biochemical function in some cells at some point, and much of that DNA is transcribed into RNA, challenging the long-held belief that most of our genome is 'junk' accumulated over the course of evolution. This is not a consensus view. Some researchers argue that, on the contrary, most of the RNA transcribed from DNA but not translated into protein is 'noise,' made because the transcription machinery is rather indiscriminate. Such noise will indeed be the end result for some transcription. It now appears that known noncoding genes outnumber genes encoding proteins by a factor of about three, according to some estimates. It's often hard, however, to figure out just what the RNA is doing. Some of these molecules might get transcribed only in particular types of cells or at a particular stage in embryonic development, so it would be easy to miss their moment of action. 'They are incredibly cell-type specific,' says molecular biologist Susan Carpenter of the University of California, Santa Cruz. But because of that, she says, 'the more we look, the more we find.' Ambiguities notwithstanding, the rise of RNA has transformed molecular biology. 'Textbooks 25 years ago confidently stated that RNA consisted of messenger RNA, transfer RNA and ribosomal RNA,' Cech says. 'Now there are hundreds, likely many thousands, of other types.' The 21st century, he says, 'is the age of noncoding RNA.' We have much more to learn. We don't know how much functional ncRNA there is, let alone what the many varieties do. And 'when we answer one question, it raises 10 new ones,' Carpenter says. As scientists discover more about the many types and roles of RNA, medical researchers may discover potential therapeutic applications, yet the more profound implications are about how life works. For complex organisms to be viable, it's simply not enough to have a 'genetic blueprint' that gets read. They need to be able to change, on the fly, how their genes get used. RNA seems to offer incredibly responsive and versatile ways of doing that.
Forbes
2 days ago
- Forbes
Growing Almost Anything From Almost Anything
One of the most interesting applications of AI is the ability to use it to analyze and design materials in the 'real world.' And that's an understatement. It's one thing to create digital playgrounds or do deep research on some intangible concept. It's quite another thing to improve the design of molecular compounds, i.e. drugs or other chemical compositions. It's probably no coincidence that one of the most heralded innovations with AI is the Alphafold project which won a Nobel prize for science. The idea of inventing proteins through automated research led to enormous changes in how we approach both pharmaceutical research and clinical science in general. Notwithstanding all of the amazing progress we have done to date, we're not done yet. There's much more to come, and those involved in this kind of science are paying attention to what's happening as we game all of this out. Growing Things 2.0 In a recent TED Talk, David Kong shows us how some of this cutting-edge design works. He mentions a project where it's possible to 'nucleate' and edit DNA. When I looked this up, the idea of 'nucleating' just means forming something into a nucleus or cluster. He then refers to how scientists 'design and build genetic circuits,' which, he suggests, are large pieces of DNA. I was about to look this up, too, but then realized that Kong describes it himself: 'We put (DNA) inside cells, on cells who behave like circuits from electronics or computer science, (and) we learn all about cell-free systems, which can help us understand the origins of life on Earth, or they can be used in applied ways, and freeze dried, and used as sensors to detect pathogens and pollutants in fabrics and textiles.' He also mentions the ability to build completely synthetic genomes from bacteria or yeast, which speaks to a kind of modern alchemy that explores previously uncharted waters. And in a way, that's what all of this is about – alchemy. Kong goes over what's happening in a MIT Harvard global synthetic biology class. Students, he said, program a robot to dispense brightly colored E. coli bacteria in the shape of a design that they created. Psychedelic Results 'After growing on black agar plates for 24 hours, a living artwork flowed under UV light,' he said. The student base, he pointed out, is diverse. 'We have students that are computer scientists, mechanical engineers, urban planners, management students, artists, designers, almost any type of creative or technical background … in the course,' he said. 'And the course has really grown tremendously in recent years, more than doubling our number of accepted students to almost 1300 from MIT Harvard and all around the world. And some of our students are even high school students or even retirees that join us each and every year.' Working Wonders As more of this alchemy, Kong cited projects built to break down temperature-sensitive materials, or deploy nanosensors to surveil environments. One student, he related, used a bioreactor to study indigenous microorganisms. Research Anywhere And then there's the versatility and portability of these project goals. In older times, scientists needed a dedicated lab, because of equipment and mechanical tools. Now, it's different. '(This research) could be (done) anywhere in the world,' he said. 'It could be across the street, in their dorm rooms, Ghana, London in the U.K., wherever our students happen to be.' In fact, Kong adds another quasi-superlative to one that was already in his lexicon: instead of just 'how to grow almost anything from almost anything else,' the phrase becomes 'how to grow almost anything from almost anything else, almost anywhere.' Let's take that a step further, though, because in subsequent narration of other lab work, Kong describes how another student figured out that processes could also be untethered from hands-on access to source material. 'He started to realize that you could take … lab modules like biological production, where organisms are being engineered to produce molecules like lycopene and beta carotene, and they could be programmed totally remotely,' he said. There's a lot more in the video. But this is a good start to understanding the 'modern magic' that goes into learning systems on the cutting edge of today's AI world, and what one of our speakers called the 'secret sauce' enterprise parties can apply to push the envelope with innovation.
