The work, which is published online today in Nature in the paper “In situ targeted base editing of bacteria in the mouse gut,” was a team effort by the scientists at Eligo, led jointly by Jesus Fernandez-Rodriguez, PhD, (Eligo’s VP of Technology), David Bikard, PhD, (Eligo co-founder and head of the Synthetic Biology Group at Institute Pasteur), and Xavier Duportet, PhD, (Eligo’s CEO and chairman).

Before this report, notes Bikard, “it was still an outstanding question whether it would even be possible to genetically modify a whole target bacterial population in an animal. There could have been fundamental barriers that would’ve made this impossible. But here we show that we can do it!”

Eligo’s advance, which combined research in both vector engineering and payload modification, is exciting on two fronts: it could open the door to new microbiome genome-editing therapeutic modalities. And it launches a microbiome-editing toolbox that has been previously unavailable.

This work is “ushering in a new era of microbiome engineering,” notes Rodolphe Barrangou, PhD, professor at North Carolina State University and editor-in-chief of The CRISPR Journal. “This proof-of-concept study is just not for E. coli or the mouse gut microbiome; it can be used much more widely, for all kinds of things, and can be deployed at scale.”

Brady Cress, PhD, principal investigator of microbiome editing technologies at the Innovative Genomics Institute at the University of California, Berkeley, agrees. Cress told GEN that this is “a massive step forward that opens the door to rewriting our microbiomes for optimal health.”

Tweaking, not altering

Duportet co-founded Eligo with Bikard a decade ago; the two friends were still in training when they had the idea for the company—Duportet was a graduate student at MIT, Bikard a postdoctoral fellow in Luciano Marraffini PhD’s lab at the Rockefeller University. (Marraffini and Tim Lu, MD, PhD, are Eligo’s other scientific co-founders.) Today, Duportet and Bikard are a dynamic duo—with Duportet at the helm of the company and Bikard a scientific advisor, who remain close friends while collaborating scientifically.

Current microbiome approaches are typically based on altering the compositions of the bacteria. The idea is to introduce bacterial species to change the balance (like probiotics) or to remove others. Eligo’s focus here was different. The idea is not to kill the bacteria but rather, as Duportet explains, to “inactivate its pathogenic potential and leave the bacteria in place.”

“If you are trying to target bacteria that has a niche,” notes Bikard, “completely removing it from the niche might be very challenging. Unless there is something else there to take its place, it will just grow back. So, it is a better strategy to disarm it, rather than kill it.”

Two-fold

Eligo’s new data are not the first to demonstrate editing of the microbiome in vivo, however. In May 2023, research from the Danish company SNIPR Biome was published in Nature Biotechnology in a paper entitled, “Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice.” In it, the researchers identified eight phages (after screening a library of 162 phages) that delivered a CRISPR-based gene-editing payload that resulted in a reduction of E. coli in the mouse gut. In the SNIPR Biome study, the E. coli were killed by CRISPR.

It has been known for a decade—since Bikard and Marrafini’s Nature Biotechnology paper in 2014—that cutting the bacterial chromosome with CRISPR-Cas kills bacteria efficiently. But the first generation of gene-editing tools were not very efficient tools, notes Bikard. They could be used in a lab setting to make modifications but most of the bacteria would be killed in the process. Therefore, if the goal is to make modifications in vivo, and maintain the bacterial population, the first generation of CRISPR tools for bacteria “would not cut it.”

The game changed when base editing—a more precise form of genome editing developed in the Broad Institute lab of David Liu, PhD—entered the toolbox. Eligo worked to bring together their knowledge in genome editing and delivery to allow for efficient editing of bacteria without changing the composition of the microbial population.

When targeting E. coli strains colonizing the mouse gut, Eligo’s technology modified the target gene in more than 90% of the bacteria, reaching up to 99.7% in some cases. These modifications remained stable for at least 42 days.

Barrangou notes that the penetrance of the edits showed remarkable efficiency. “They are setting the bar,” he told GEN. “Being able to do it is one thing. But being able to do it with that kind of longevity and efficiency is practically important and sets the stage for new opportunities in the field.”

For Bikard, working out the gene editing was not as big a hurdle as the delivery. Eligo modified the site fibers on a phage chassis (from phage lambda) to target specific bacterial strains. The phage vector can be modified to target different bacterial strains or species with additional engineering.

Cress thinks of it as “a reprogrammable platform” for targeting different bacteria. That said, while this research provides an impressive blueprint using the most well-studied phage-bacteria pair, Cress notes that expanding it to other microbes will necessitate developing efficient genetic tools for non-model bacteria and a deeper understanding of the genetics and biology of less well-studied phages.

Another advance, Duportet notes, is that his team was able to demonstrate the same efficiency of editing using a non-replicative plasmid in the target bacteria. This is an additional benefit because they don’t maintain a transgene in the microbiome of the animals.

Long road ahead

The long-term goal at Eligo is to develop therapeutics—not necessarily for infectious diseases. The interest extends to those that would change the genetic content of the microbiome that alter a factor of host–focused diseases.

One example where this could be applicable is the delivery of a base editor to commensal intestinal E. coli that express the toxin colibactin, to inactive its mutagenic potential, therefore preventing the progression of human colorectal tumors.

But there is a long road ahead and challenges remain. One, notes Cress, is that this approach uses short-lived delivery of gene editing machinery to make gene disruptions, but other types of edits like gene insertions take longer to write (e.g. CRISPR-associated transposases) and thus will likely require different delivery approaches. Another point Cress considers is that “the type of edits made in this study could potentially revert through natural mutation, making gene removal a more durable solution than gene disruption.”

This study also raises new questions. Teasing apart the genetic network of the microbiome is in its infancy. Do researchers have enough knowledge to use this new tool?

“It’s important to have the genome editing tools,” notes Barrangou. But in the end, “what really matters is knowing what to target. Knowing what to target and what edit you want is part of the secret sauce.”

But Bikard reckons that this work will help answer some of those questions. This will be an extraordinary tool for researchers, he says, because it offers the possibility to probe gene function directly in the animal. He is excited to use it in his academic lab on the other side of Paris from Eligo’s base.

Duportet hopes that scientists will use the method and is happy to issue “a call for collaboration.” “We cannot work on everything, and we cannot find all the targets to edit,” he notes. “But we have the knowledge to design the vectors and the payloads to make it happen.”

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MORF-057 is a selective oral small molecule inhibitor of α4β7 integrin developed using the company’s Morphic Integrin Technology (MInT) platform. MORF-057 is now under study in two Phase II trials in ulcerative colitis (UC), and a third in Crohn’s disease.

In releasing first quarter results in April, Morphic said it was enrolling patients in the Phase IIb EMERALD-2 trial (NCT05611671) assessing MORF-057 in ulcerative colitis, and anticipated dosing its first patient during the second quarter in the Phase II GARNET trial (NCT06226883) evaluating MORF-057 in patients with moderate-to-severe Crohn’s disease.

Morphic is expected to disclose additional details on the studies when it releases second quarter results later this summer. The company had not announced a release date at deadline.

Should MORF-057 generate positive data and win approvals, it could potentially challenge Takeda Pharmaceutical’s already-marketed intravenous, subcutaneous, and injector pen versions of its injectable drug Entyvio^® (vedolizumab), an integrin receptor agonist indicated for moderately and severely active UC and Crohn’s. For the fiscal year ending March 31, Entyvio generated blockbuster sales of ¥800.9 billion ($4.986 billion), up 14% from ¥702.7 billion ($4.375 billion) a year earlier.

Another α4β7 integrin receptor antagonist, Biogen’s Tysabri (natalizumab), carries indications in Crohn’s disease as well as muscular sclerosis. Tysabri generated $464.7 million last year, down nearly 5% from $488.4 million in 2022.

“Morphic has always believed that the immense potential of MORF-057 to benefit patients suffering from IBD could be optimized by the ideal strategic partner. Lilly brings unparalleled resources and commitment to the inflammation and immunology field,” Morphic CEO Praveen Tipirneni, MD, said in a statement.

Added Daniel Skovronsky, MD, PhD, Lilly’s chief scientific officer: “Oral therapies could open up new possibilities for earlier intervention in diseases like ulcerative colitis, and also provide the potential for combination therapy to help patients with more severe disease.”

“We are eager to welcome Morphic colleagues to Lilly as this strategic transaction reinforces our commitment to developing new therapies in the field of gastroenterology, where Lilly has made significant investments to deliver first-in-class molecules for the benefit of patients,” added Skovronsky, who is also president, Lilly Research Laboratories and president, Lilly Immunology.

Investors and at least one analyst shared Lilly’s enthusiasm for the deal. Morphic shares traded on Nasdaq zoomed 75% today, to $55.74, while Lilly shares barely budged, inching up 0.4% to $918.00.

“A good outcome”

Michael Yee, an equity analyst with Jefferies, wrote today in a research note that he viewed the deal favorably since Morphic won’t have Phase IIb data to read out on MORF-057 till the first half of next year, and would need “significant” additional capital to run costlier Phase III studies and commercialize the drug worldwide.

“We see this as a good outcome for holders as it provides nearly full value of the Phase IIB data ahead of having to go through the up/down risk of data in H1:25,” Yee wrote. “MORF has prev[iously] spoken about a global partnership or strategic options. We think this is a good outcome and would have been where the stock probably would have traded up to if data were positive in H1/25 (approx[imately] up 50–100%).

In such a scenario, Yee explained, Morphic’s shares would be consistent with Jefferies’ 12-month price target of $60 and “Buy” rating on the stock: “Overall we think it’s a good deal for MORF shareholders.”

Yee added that because Morphic’s pipeline showed little overlap with that of Lilly, he did not foresee a challenge to the deal from the U.S. Federal Trade Commission (FTC), which has opposed some recent biotech merger and acquisition (M&A) deals on antitrust grounds.

Morphic’s pipeline also includes four preclinical programs:

• MORF-088, a family of small molecule αVβ8 integrin inhibitors being developed for myelofibrosis and a combination immuno-oncology approach to treat solid tumor indications.
• A family of small molecule α5β1 inhibitors with potential indications in severe pulmonary hypertensive disease, including pulmonary arterial hypertension, based on research showing that fibronectin integrin inhibition suppresses pulmonary arterial smooth muscle cell proliferation.
• A family of small molecule candidates targeting non-integrins including TL1-A and IL-23, which according to Morphic have potential as treatments for IBD through monotherapy and possibly in combination with other IBD treatment mechanisms including α₄β_7.
• A family of next generation α4β7 inhibitors for gastrointestinal indications using the MInT platform. The next-gen candidates have enhanced selectivity, potency, and pharmacokinetic profiles compared with first-generation inhibitors like MORF-057.

Lilly immunology pipeline

Lilly’s immunology pipeline is headed by mirikizumab (LY3074828), an interleukin 23 (IL-23) inhibitor under regulatory review as a treatment for Crohn’s disease. Mirikizumab is now marketed under the name Omvoh (mirikizumab-mrkz) as a treatment for moderately to severely active ulcerative colitis in adults, after winning FDA approval last October.

Lilly has not furnished sales figures for Omvoh, instead lumping the drug with four other products in a “New Products” category that nearly quadrupled its combined sales during Q1, from $600 million to $2.39 billion—a jump driven by its tirzepatide-based diabetes and weight loss drugs Mounjaro^® and Zepbound^®.

Also in Lilly’s immunology pipeline are seven Phase II candidates in five key indications (atopic dermatitis, hidradenitis suppurativa, multiple sclerosis, psoriasis, and rheumatoid arthritis), as well as three Phase I candidates for undisclosed autoimmune diseases.

Lilly plans to acquire via tender offer all outstanding shares of Morphic at $57 a share, a 79% premium over Morphic’s closing stock price Friday of $31.84 a share—and an 87% premium to the 30-day volume-weighted average trading price of Morphic’s common stock ending Friday.

The boards of Lilly and Morphic have approved the transaction, which is expected to close in the third quarter subject to customary closing conditions, including the tender of a majority of outstanding shares of Morphic’s common stock.

Lilly said it would reflect the Morphic acquisition in upcoming financial results and financial guidance after it determines whether to account for the deal as a business combination or an asset acquisition, including any related acquired in-process research and development charges, according to Generally Accepted Accounting Principles (GAAP) upon closing.

“My deepest thanks go to the entire Morphic Team for their expertise, creativity and tenacity. We are also grateful to the investigators and patients who have contributed to the success of MORF-057 thus far, and we eagerly anticipate the path forward for MORF-057 and other integrin medicines under Lilly’s stewardship,” Tipirneni added.

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The research, published today in Science in a report entitled “A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction,” was led by Pamela Ting, PhD, associate director of hematology at Novartis Biomedical Research. Ting leads a team of 40 co-authors, including Jay Bradner, MD, PhD, the former president of Novartis Institutes for BioMedical Research, who left the company in 2022 and joined Amgen late last year. Developing small-molecule drugs for SCD has been a long-standing interest of Bradner’s, dating back almost 15 years to research he performed on histone deacetylase inhibitors in collaboration with Stuart Schreiber, PhD, and colleagues at the Broad Institute.  

Over the past decade or more, predating her own arrival at the company in 2015, Ting estimates that Novartis has screened some two million compounds in the search for a promising compound to take to the clinic. Along the way, the company briefly pursued its own CRISPR gene editing strategy, following a similar path to the approach that Vertex Pharmaceuticals took in developing Casgevy by boosting HbF production. (Although Novartis and collaborators published promising initial clinical data last year, the company decided to shelve the gene editing program.) 

Despite the remarkable clinical success of the CRISPR ex vivo approach—the first American patient in the Vertex trial, Victoria Gray, celebrated the fifth anniversary of her stem cell transfusion earlier this week—it is clear that this demanding (and expensive) ex vivo strategy will not help the millions of patients in Africa and beyond—a point that Ting and colleagues hit home in their report in Science.  

“Regrettably,” Ting and her co-authors write, “substantial challenges exist for [hematopoietic stem and progenitor cell] therapies to reach most SCD patients, who live in medically underserved communities and low and middle-income countries. Safe, efficacious, and globally accessible HbF-inducing medicines therefore remain an important unmet need.” 

Fyodor Urnov, PhD, director of technology and translation at the Innovative Genomics Institute, told GEN that the 2023 approval of Casgevy provided definitive clinical evidence that the strategy of upregulating HbF is “a safe and effective approach to resolve major symptoms of sickle cell disease.” The new work builds on the theme of modulating a transcription factor to upregulate HbF, but this time using a small molecule. “Even people who live and breathe CRISPR will agree that, on balance, such a small molecule could have a wider global reach than gene editing,” Urnov said. 

“There is a pressing need for oral agents that can more effectively induce fetal hemoglobin,” agreed hematologist Vijay Sankaran, MD, PhD, professor of pediatrics at Harvard Medical School. (Sankaran played a key role in cementing the HbF upregulation strategy to treat SCD 15 years ago.) He called the new Novartis report impressive and “exciting work and identifies a promising new target for fetal hemoglobin induction.” 

Screen time 

The Novartis study falls into a category known as “molecular glue pharmacology.” The researchers recognized that very small modifications to the chemical structure of a class of drug compounds that mediate targeted protein degradation (TPD) could profoundly affect the choice of protein for degradation. (A good example was work published by Novartis colleagues last year on the discovery of selective glue degraders for cancer immunotherapy).

“This was a big conceptual leap,” Ting explained. “You could do just a little bit of work around a fundamental structure and then broadly look for changes to the substrate selectivity.”

She added: “We decided, if this [chemical] library is capable of drugging a new class of transcription factors, then we should think about how we can apply it to an age-old problem that, at the root, is really a question of how do we regulate genes? And can we target transcription factors to regulate gene expression?” 

Ting’s team embarked on a screen of a library of almost 3,000 compounds that target cereblon, a component of the E3 ubiquitin ligase complex that is involved in targeted protein degradation. Using a cellular assay that detected the upregulation of HbF) in erythroblasts, Novartis researchers identified scores of candidate molecules before whittling down the list and focusing on “compound C” for further study.   

After mass spectrometry experiments showed that this chemical targeted the WIZ transcription factor, Ting’s group renamed the drug candidate dWIZ-1. The WIZ target was emphatically confirmed by CRISPR gene knock-out experiments. All told, these results suggested that WIZ was a previously unrecognized repressor of HbF expression. dWIZ-1 could recruit WIZ to the cereblon-ubiquitin ligase complex to trigger targeted protein degradation. The Novartis researchers continued experiments with a modified molecule termed dWIZ-2. 

The Science report is packed with multiple types of experiments—molecular assays, mouse and non-human primate models, protein modeling using AlphaFold, and X-ray crystallography. Part of the rationale, Ting says, “was to convince ourselves that by every measurement that we could think of, we could see a reproducible effect.”  

Some of the most important data in the report are results administering dWIZ-2 in a trio of cynomolgus monkeys. This in vivo study monitored the animals for 28 days and showed robust up-regulation of the γ-globin gene and HbF production in virtually all peripheral reticulocytes. “We saw almost pan-cellular HbF expression, which is very promising,” Ting said, and no signs of cytotoxicity. Curiously, one of the three animals was termed a non-responder. Ting calls it “the coolest monkey, because I feel like it must be telling us something and I don’t know what it is!” 

The Novartis team found evidence for WIZ binding directly at the β-globin locus, which was unexpected. “Seeing WIZ for the first time is quite surprising for such a deeply studied locus,” Ting said. “For whatever reason, the globin locus seems to be highly sensitive to the loss of WIZ.” What is striking, she adds, is that “there is relatively strong overlap with binding sites for BCL11A,” the transcription factor that Vertex successfully targets in its Casgevy cell therapy.

“That’s where we leave it in the paper, as a bit of a teaser, something that we hope that we can further study in the future and that others will be inspired to study.”  

Dealbreaker 

As Ting readily acknowledges, there are still many unanswered questions, including the specificity of the inhibition. WIZ naturally binds at many spots in the genome, including a dozen or more in the β-globin gene cluster. “For whatever reason, when we modulate WIZ, the effects are fairly moderate and fairly mild,” Ting said. And the results in the non-human primates bode well. “We hope with these new chemical probes that this is something that we can continue to study and understand in the long run,” Ting says.  

“I think the [Novartis] approach is promising, but with the current data it’s difficult to know what degree of HbF induction a human would experience,” said Vivien Sheehan, MD, PhD, associate professor and director of Sickle Cell Translational Research at Emory University School of Medicine in Atlanta. Sheehan, who first heard these results presented at the American Society of Hematology conference late last year, would like to see additional quantification data including HbF measurements using high-performance liquid chromatography. She also observes that “the lack of myelosuppression is promising for a potential combined therapy with hydroxyurea.”  

Sankaran cautions that the non-specific effects of targeting WIZ lead to expression changes of hundreds of genes in erythroblasts. “More studies are needed before and during human clinical studies,” he said. A rigorous assessment of the safety of systemic WIZ degradation will be needed. “That could be a dealbreaker,” Sheehan says. 

Understandably, Ting would not be drawn on a timeline for progress into the clinic, but her closing comments underlined her team’s belief in the program. “What we’re really focused on now is making sure that we’ve found a molecule that can really go all the way to patients,” she said. “We are highly committed to sickle cell patients around the world. We see the unmet need,” she said. “We’re progressing as quickly as possible, and we really have our eye on a medicine that will reach patients where they are.” 

Nevertheless, while a small-molecule drug should prove both more affordable and accessible in the countries where most SCD live, IGI’s Urnov cautions that access to drug therapies outside the U.S. is by no means guaranteed. For example, a decade ago, Gilead slashed the price of its drug Solvadi by almost 99 percent in order to provide meaningful access to hepatitis patients in Egypt. The Novartis study, Urnov says, offers “an important opportunity to think ahead to how to solve this challenge when and if a medicine based on this work is approved in the U.S.” 

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10x says its Xenium Prime 5K Pan-Tissue and Pathways panel features enhanced chemistry enabling the increase in the number of cells capable of being imaged compared with previous gene expression panels ranging from the company’s 247-gene mouse brain panel to the 379-gene mouse tissue atlassing panel.

“It has a lot of the content that people have asked for from our custom panels,” Ben Hindson, PhD, 10x’s co-founder and CSO, told GEN Edge. “It’s a nice panel in terms of pretty comprehensive coverage of the transcriptome, and it should also enable customers to just take their samples and get lots of really informative data after the run is complete.”

With 5,000 genes, the new panel is designed for comprehensive profiling of cell types and states and cell signaling pathways across multiple tissue and disease types, according to 10x. The panel can be customized with up to 100 additional genes, including isoforms, exogenous sequences such as guide RNAs (gRNAs) and barcodes, chimeric antigen receptor T-cell (CAR-T) transcripts, and viruses.

The breadth of the panel has attracted interest from potential customers within biopharma, as well as academic researchers specializing in single-cell research.

Covers 80% of requests

“I would say it covers about 80% of the requests that we’ve gotten from all those customers that we’ve worked with on either the tissue-specific or the disease-specific panel. It pretty well encompasses a lot of the most common requests, but it also offers customers customization for those who maybe feel that there’s something that’s not quite included that should be.”

What makes the other 20% of requests a no-go for adding to the panel? A combination of feedback from early-access customers and the utility value of the genes: “I would say that some genes aren’t that interesting, and they take up a lot of real estate and don’t give you as much information. So, we try to take those off the list per se, because they’re not very informative.”

The list price for Xenium Prime 5K is $7,500 for each slide. Each run is two slides, making the total cost per run $15,000 in the United States. Xenium Prime 5K also delivers improvements from previous panels that include enhanced per-gene sensitivity, improved specificity and spatial fidelity, integrated multimodal cell segmentation, a workflow compatible with both fresh frozen and FFPE samples—plus the ability to let researchers analyze up to 472 mm² of human or mouse tissue in six days or less—speed, and throughput that the company calls industry-leading.

While Xenium Prime 5K may feature fewer genes than NanoString’s panel, Hindson said 10x has focused heavily on the panel’s performance: “For the most part, we’re pleased with how those landed in terms of sensitivity, specificity, and throughput, together with in-line data analysis and data processing that’s happening while the instrument’s running, so when it’s done,  you get your data and you go off and start analyzing.”

And while numerous research areas can benefit from the panel, Hindson said, the biggest potential opportunity for gleaning knowledge through Xenium Prime 5K is in oncology as researchers delve into the tumor microenvironment, looking at the single-cell resolution, how cells are programmed, how close they are to one another, and how they may interact with each other.

“I think there’s potential for new biomarkers based on the spatiality data as well. I think that’s why at conferences like AACR [the American Association for Cancer Research], there’s just a tremendous amount of excitement for looking at this high content, in situ data for studying the tumor microenvironment and then looking for potential new therapies, looking for why therapies may have worked in one patient and not in the other.”

10x formally announced the launch of the panel in late May, four months after co-founder and CEO Serge Saxonov, PhD, first announced Xenium Prime 5K among a series of product improvements planned for this year in January at J.P. Morgan’s 42^nd Annual Healthcare Conference.

NanoString launches 6K panel

The following month at the annual Advances in Genome Biology and Technology (AGBT) 2024 conference in Orlando, FL, NanoString announced the launch and full commercial release of its CosMx Human 6K Discovery Panel, the first single-cell spatial panel enabling research scientists to measure over 6,000 RNA targets, representing nearly every human biological pathway.

“From the technical perspective, we pushed the envelope harder than anybody else by far,” Joe Beechem, PhD, NanoString’s CSO and senior vice president of research and development, told GEN in an exclusive interview from AGBT.

Human 6K enables analysis of 6,175 genes with 20 control targets, and the ability to customize up to 200 additional targets of interest.

“The applications that we built this panel for were very broad. We went after all of translational biology, with a strong focus on cancer, immunology, and neuroscience. Those are hallmarks for us here at NanoString, the biggest areas of translational research,” Erin Piazza, PhD, associate director of bioinformatics with NanoString, told GEN Edge recently. “But we also looked at many other applications things crossing all of physiology endocrinology and metabolism, cardiovascular disease, developmental biology. We cast a very broad net with this panel, with the hope that most researchers, especially in the translational space, would be able to take advantage of it.”

Beyond numbers

The more genes a panel can accommodate, the better for researchers, though Piazza added that NanoString’s approach goes beyond numbers:

“Researchers love plex. When offered panels of varying size, larger is almost always preferred because it reduces the concern that the researcher has missed important findings. It reveals deeper biological insights and conserves precious tissue samples,” Piazza said.

“While we are delivering to the market the highest plex panels available, our approach is more than sheer numbers,” she said. “Our value proposition to researchers is providing biologically curated high-plex data that meaningfully advances their understanding of a broad variety of translational and discovery research areas.”

NanoString says its approach to content development starts with knowing what genes to include, and which to exclude through a proprietary pruning process, and also includes curating single-cell data based on feedback from key opinion leaders. The company will often share a draft of the genes it wants to feature in a panel under a nondisclosure agreement before locking in a final list, Piazza said.

“If you select the wrong dataset, you make the wrong choices. So we’re very cautious about ensuring that the single cell datasets that we did make decisions based on were as broad as the application areas we wanted to cover,” Piazza explained. “You want to look at normal tissues, disease tissues. What those genes are doing in those contexts informs the decisions you make while you prune. So, there’s a heavy lift of a panel. But we’re really, really pleased with how it turned out.”

NanoString will not disclose the list price for CosMx Human 6K or other products, citing numerous variables. Human 6K is designed for use with NanoString’s CosMx Spatial Molecular Imager (SMI), which offers single-cell RNA and protein imaging with what the company says is the most precise cell segmentation and highest plex available. CosMx SMI also delivers cell typing and spatial context, and accurately measures the transcriptional programs within cells that result in disease or health, according to NanoString.

Piazza said her company’s 6,000-plex panel will someday give way to an even larger panel. During AGBT, NanoString demonstrated what it said was true single-cell whole transcriptome analysis capabilities, releasing the first such public data set.

NanoString expects to make a whole transcriptome panel product commercially available in 2025.

“We’re calling the 6K panel high plex today, but hopefully tomorrow it will be the mid-high plex, as we’ve started already talking about our CosMx whole transcriptome panel,” Piazza said.

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Kisunla is the first amyloid plaque-targeting therapy with evidence to support stopping therapy when amyloid plaques are removed, which according to Lilly can reduce both the number of infusions needed as well as the treatment cost.

The FDA based its approval of Kisunla on positive data from the Phase III TRAILBLAZER-ALZ 2 trial (NCT04437511), in which people least advanced in the disease showed the strongest results 18 months after receiving the drug. Treatment with Kisunla significantly slowed clinical decline in two groups: Patients with low to medium levels of tau protein, and patients mirroring the overall population, which also included participants with high tau levels.

According to Lilly, patients treated with Kisunla who were less advanced in their disease showed a significant slowing of decline of 35% compared with placebo on the integrated Alzheimer’s Disease Rating Scale (iADRS), which measures memory, thinking, and daily functioning. In the overall population, a statistically significant 22% showed response to treatment based on the iADRS.

Among the two groups analyzed, participants treated with Kisunla had up to a 39% lower risk of progressing to the next clinical stage of disease compared with placebo patients. And among patients in the group mirroring the overall population, Kisunla reduced amyloid plaques on average by 61% at six months, 80% at 12 months, and 84% at 18 months compared to the start of the study.

“Very meaningful results”

“Kisunla demonstrated very meaningful results for people with early symptomatic Alzheimer’s disease, who urgently need effective treatment options. We know these medicines have the greatest potential benefit when people are treated earlier in their disease, and we are working hard in partnership with others to improve detection and diagnosis,” Anne White, executive vice president and president of Lilly Neuroscience, said in a statement.

The positive data led to a recommendation in favor of the drug last month by the FDA’s Peripheral and Central Nervous System Drugs Advisory Committee. Through two 11–0 votes, the advisory panel unanimously concluded that it was effective in treating patients with mild cognitive impairment, based on available data—and that the benefits of the drug outweighed its risks.

Lilly had been pursuing FDA approval for Kisunla since July 2022. The pharma giant initially expected a decision in the first quarter of this year, only to be told in May the agency would decide after hearing from the advisory committee.

Akash Tewari, an equity analyst with Jefferies, has projected peak annual sales for Kisunla of $2.9 billion—below the $4.6 billion projected by a consensus of analysts, asserting that Leqembi has shown an incrementally better risk-benefit profile in early AD patients. Tewari expects a commercial launch for Kisunla in the fourth quarter of this year.

Lilly has set a list price of $695.65 per vial for Kisunla, or about $32,000 for a year of treatment. That’s about 21% above the $26,500 annual list price in patients of typical weight for Leqembi^® (lecanumab-irmb), an Alzheimer’s treatment marketed by Eisai and Biogen which gained full approval four days short of a year ago (Leqembi received accelerated approval in January 2023). The costs for patients needing six and 18 months of treatment have been set at, respectively, $12,522 and $48,696.

“Duration of Kisunla regimen will differ across pts [patients],” Tewari wrote in a research note, “so we’ll need to see how real-world data w/ Kisunla looks.” He noted that the average time to negative amyloid beta level was ~47 weeks in the TRAILBLAZER-ALZ2 trial.

Alzheimer’s has been a notoriously difficult indication for drug developers. Only a handful of drug successes have ever reached the market, most of which have merely slowed progression of symptoms by six to twelve months.

A 2014 Cleveland Clinic study found a 99.6% failure rate of clinical trials for AD drug candidates between 2002 and 2012. That study found high attrition rates for AD treatments, with 72% of agents failing in Phase I, 92% failing in Phase II, and 98% failing in Phase III.

Reshaping AD drug landscape

Kisunla is also the second new drug in as many years that is expected to reshape the AD drug landscape following decades of failures by big pharmas and small biotechs alike. The other is Leqembi, a recombinant humanized immunoglobulin gamma 1 (IgG1) monoclonal antibody designed to treat Alzheimer’s by targeting aggregated soluble and insoluble forms of amyloid beta (Aβ).

The FDA is reviewing Eisai’s Supplemental Biologics License Application (sBLA) for a monthly intravenous maintenance dosing form of Leqembi, with the agency setting a Prescription Drug User Fee Act (PDUFA) target action date of January 25, 2025.

Leqembi is one of two amyloid-targeting Alzheimer’s drugs from Eisai and Biogen to win FDA approval in recent years. The other is Aduhelm^® (aducanumab-avwa), which won a controversial but historic FDA accelerated approval in 2021 as the first therapy indicated for reducing clinical decline in AD patients and the first therapy to tie improved clinical outcomes to removing amyloid beta. Aduhelm became the first treatment approved with an Alzheimer’s indication since 2003.

However, in January Biogen ended commercialization of Aduhelm following disappointing sales and the failure of the drug to gain reimbursement from the Centers and Medicaid and Medicare Services. The latter triggered Biogen’s initial rounds of cost-cutting in 2022, as well as the departure of the company’s previous CEO Michel Vounatsos, since succeeded by current CEO Christopher Viehbacher. Biogen said it would instead shift resources to commercialization of Leqembi and development of other pipeline candidates designed to treat Alzheimer’s.

The disruption caused by Aduhelm, Leqembi and now Kisunla has fueled development of new Alzheimer’s therapies by other biopharma giants, and several smaller biotechs—including Alzheon, which last month completed a $100 million Series E financing, and Cognition Therapeutics, which has shown clinical success for its lead candidate CT1812.

Howard Fillit, MD, co-founder and chief science officer for the Alzheimer’s Drug Discovery Foundation (ADDF), hailed the FDA approval of Kisunla.

“It’s promising to see that some patients essentially enter remission, where they achieve full amyloid clearance with no resurgence in substantial plaque buildup for several years to follow,” Fillit stated. “This approval is emblematic of the new era of Alzheimer’s research where we now have the first class of disease-modifying drugs that will eventually be used in combination with novel therapies—based on the biology of aging—that target all the underlying complexities of this disease.”

“This milestone will not only catalyze the next generation of therapies, but also reframe how we deliver treatments,” Fillit added.

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The company is on track for an early 2025 launch of a first-in-human Phase I trial of lead candidate ABS-101, CEO Sean McClain told GEN Edge, with an interim data readout expected in the second half of next year.

Absci is in IND-enabling studies for ABS-101, which is designed to treat inflammatory bowel disease (IBD) by targeting tumor necrosis factor-like cytokine 1A (TL1A). The company began those studies earlier this year after selecting a primary and a backup development candidate from three versions of ABS-101.

The primary candidate was selected based on its profile seen in mouse PK studies, the potency it showed in in vitro assays, and its binding affinity, as well as its manufacturability and developability.

“The candidate that had the best attributes across the board is the one we advanced as the actual candidate,” McClain said. “The backup had the same potency, similar affinity, and similar half-life. There were just some attributes on the developability side that weren’t as good as the actual candidate itself. But it still was a strong candidate.”

In releasing first-quarter results last month, Absci also presented preclinical data showing that all three versions of ABS-101 could bind both the TL1A monomer and trimer—activity that the company said could potentially lead to differentiated clinical efficacy.

“This is really exciting because it allows us to potentially—and we’ll find it out in the clinic—be able to go after patient populations that competitor molecules are unable to,” McClain said.

All three versions of ABS-101 demonstrated high affinity, high potency, favorable developability, and extended half-life. In addition, using its de novo AI model, Absci has designed ABS-101 toward a specific epitope with the aim of achieving superior potency and lower immunogenicity.

At the 42^nd Annual J.P. Morgan Healthcare Conference in January, Absci presented preclinical data on ABS-101 from multiple biophysical and cellular assays showing it to demonstrate equal or superior potency to two other TL1A-targeting drug candidates—RVT-3101, Roche’s TL1A-directed antibody candidate being developed for IBD, including ulcerative colitis (UC) and Crohn’s disease (CD); and Tulisokibart (MK-7240), which Merck & Co. is developing to treat immune-mediated diseases, including UC, CD, and other autoimmune conditions.

Later this year, Absci plans to share additional preclinical data, including results from nonhuman primate studies of ABS-101, likely via press release and data package.

Two additional candidates

Also in Absci’s pipeline are two additional preclinical candidates. One is ABS-201, a lead optimization phase drug to be developed for an undisclosed dermatological indication that according to the company has significant unmet need.

“I will say that we view this as an underappreciated target similar to TL1A,” McClain said.

TL1A was underappreciated, he said, until 2022 when Tulisokibart, then known as PRA023, generated positive clinical data as the lead candidate of Prometheus Biosciences—which Merck acquired last year for $10.8 billion.

“We think this derm target [ABS-] 201 is a very similar type of profile,” McClain asserted.

Absci expects to have a primary candidate for ABS-201 by the end of the year, at which point the company plans to release preclinical data. The company says ABS-201 has potential to be a best-in-class antibody showing high efficacy following once monthly or less frequent, low-volume, subcutaneous injection.

The other preclinical candidate in Absci’s pipeline is ABS-301, a lead optimization phase, fully human antibody that is designed to bind to a novel target discovered through Absci’s Reverse Immunology platform.

“We took a patient sample that had an extraordinary immune response, took the antibodies from the tertiary lymphoid structure, and then did a protein panel screen to find out what antigens or targets it was binding to. And that ended up allowing us to discover ABS-301, a novel I/O target,” McClain said.

He said the mode of action for ABS-301 will be validated in in vivo studies that are expected to be completed in the second half of this year: “This will be like essentially preclinical proof-of-concept similar to a Phase II POC [proof-of-concept].

Absci considers ABS-301 a potentially first-in-class immuno-oncology candidate. ABS-301’s target, which has not been disclosed, is an immune evasion strategy to limit immune infiltration and turn tumors immunologically “cold.” Absci reasons that ABS-301 treatment in cancer may release immune suppression and permit immune cells to infiltrate the tumor, allowing for a robust anti-tumor response.

Oncology and immunology and inflammation

Oncology and immunology and inflammation (I&I) have emerged as Absci’s key therapeutic areas of interest. In addition to -101, -201, and -301, Absci said, it expects to advance at least one additional internal asset program to a lead-identification stage this year.

The company’s pipeline could also grow if it succeeds in growing current collaborations with biopharma partners and establishing new ones. Absci has said it expects to sign drug creation partnerships with at least four additional partners this year, of which at least one could be a multi-program partnership.

Absci continues to make further progress on its existing drug creation partnerships and anticipates signing additional drug creation partnerships with at least four partners in 2024, including one or more multi-program partnerships.

“We are on track to achieve that goal,” McClain said. “We look to partner anywhere from a drug candidate phase, where we have preclinical proof of concept, all the way to a Phase II. There are a lot of factors that end up going into that, like what are the costs of the clinical trials? What is our own internal domain expertise? I think something like ABS-301, where we don’t have as strong of I/O expertise, that may get partnered sooner rather than later, but there’s a lot of factors that go into when we go about partnering.”

Absci finished the first quarter with $58.831 million in cash, cash equivalents, and another $102.712 million in short-term investments—enough of a “runway,” the company says, to fund its operations into the first half of 2027.

For the full fiscal year, Absci said, it expects to use approximately $80 million in cash, cash equivalents, and short-term investments—including expected costs associated with completing the IND-enabling studies for ABS-101 with an undisclosed contract research organization.

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Ginkgo Bioworks Holdings (DNA) shares tumbled 26% in the three trading days since the company disclosed plans to chop an estimated 400+ jobs. That’s not so bad considering that the shares have cratered 82.5% in just the past six months, from $1.77 on December 27, 2023.

Ginkgo started the week trading at 42 cents a share, then slid 12% to 37 cents on June 24, the day the company publicly quantified the extent of the job cutbacks it warned it would carry out back in May.

In a regulatory filing, Ginkgo revealed plans to eliminate “at least 35% of its workforce”—which would translate to at least 426 jobs, based on the 1,218 employees it reported as of December 31, 2023, according to its Form 10-K annual report for last year.

The layoffs were completed June 24, Ginkgo co-founder and CEO Jason Kelly posted on X the following day, adding that his company “had to let go of many truly excellent Bioworkers.”

“This was the hardest change we’ve made at @Ginkgo and it’s on myself and leadership for the decisions that led up to it,” Kelly acknowledged.

The job cuts includes 158 positions based in Cambridge, MA (Ginkgo is headquartered in neighboring Boston), and a total 47 positions based in Emeryville, CA, according to Worker Adjustment and Retraining Act (WARN) notices filed in Massachusetts and California, respectively.

Ginkgo stated that it expects to spend at least $12 million in severance and related separation costs related to the job cuts, with additional details to come in its second quarter earnings results, its next quarterly earnings call with analysts, and in an amended regulatory filing.

The workforce reduction came more than a month after Ginkgo on May 9 disclosed a multi-year cost-cutting plan that it warned would include “an expected reduction in labor expenses of at least 25%” and a planned consolidation of certain of its facilities.

That appears to explain why the falloff in Ginkgo stock was less than seen for many companies in the throes of job and cost cutting. Ginkgo shares skidded the rest of the week to 32 cents Tuesday, then 29 cents Wednesday before bouncing back, rising nearly 9% to 31 cents Thursday and up another 12% to 35 cents Friday as of 11:05 a.m. ET.

ARK sells off shares

Another significant reason behind the stock decline was a significant selloff of shares by a longtime investor and public supporter of Ginkgo.

Two electronic transfer funds (ETFs) of ARK Investment Management (ARK Invest)—the high-profile firm led by chief investment officer and portfolio manager Catherine D. (Cathie) Wood—sold off a combined 71,785,189 shares of Ginkgo stock totaling $26,225,932 early this past week.

ARK Innovation ETF (ARKK) and ARK Genomic Revolution ETF (ARKG) sold a combined 41,587,888 shares valued at $17,649,899 on Monday (based on the day’s closing price of 42 cents a share)—followed two days later by the ETFs selling off a combined 30,197,301 shares valued at $8,576,033 (based on Wednesday’s closing share price of 28 cents).

As of Friday, ARKK held 23,187,357 Ginkgo shares with a market value of $7,169,530.78. The fund’s ownership stake in Ginkgo carries a percentage or “weight” of 0.12%, the 34^th highest percentage among the 36 companies in which the fund holds shares, ARKK disclosed on its web page.

ARKG held 24,796,421 shares in Ginkgo, with a market value of $7,667,053.37 as of Friday—a weight of 0.6%, the 38^th highest percentage among the 42 companies in which the fund holds shares, ARKG disclosed.

ARKK invests in companies that offer “disruptive innovation,” which it defines as the “introduction of a technologically enabled new product or service that potentially changes the way the world works” in fields that include DNA technologies and the “genomic revolution”; automation, robotics, and energy storage; artificial intelligence and the “next generation” Internet; and fintech.

ARKG concentrates on healthcare and other sectors “expected to substantially benefit from extending and enhancing the quality of human and other life.”

Convergence prediction

“The more we unearth the possibilities—the storage possibilities of DNA, the financial industry will understand the convergence of biology and all kinds of technology,” Wood predicted at a panel discussion held during Ginkgo Ferment 2021, a company-sponsored conference. “I don’t think the financial world is ready for what’s about to happen.”

Ginkgo shares have largely freefallen since then, careening 96% from the $11.15 share price the synthetic biology powerhouse commanded when it went public in September 2021. The stock climbed to its all-time high two month later, reaching $15.86 on November 8, 2021.

“Gingko was one of the most hypnotic companies ever to have graced the Boston Biotech ecosystem,” commented Vincent Ling, PhD, in a LinkedIn post that explained he was speaking for himself and not for Takeda Pharmaceutical, where he is senior director, Center for External Innovation.

He noted that when Ginkgo went public on the New York Stock Exchange in 2021, it acquired the former “DNA” ticker of Genentech, a member of the Roche Group.

“Gingko was founded on the audacious premise of synthetic biology on mass scale, lab automation, and revolutionizing life itself … —as a service CRO. As a service business model where molecule IP would be exploited by partners and not by Gingko, it was difficult for many veterans in the industry to imagine discovery upsides akin to those seen in biotechs or pharma,” Ling observed.

Stung by Scorpion

A far more pointed criticism of Ginkgo’s business model was detailed three years ago in a stinging report by short seller Scorpion Capital. Scorpion denounced Ginkgo as employing “a hocus-pocus business model” and carrying out “a colossal scam.”

“Behind the synthetic biology and ‘Foundry’ hype, Ginkgo is a glorified contract research organization that does commodity yeast strain engineering,” Scorpion Capital contended in October 2021. “Ginkgo is nothing more than a commodity strain engineering CRO, and a crappy one at that according to its own related-party ‘customers.’”

Kelly responded to the Scorpion Capital report with a statement to various news outlets that said in part: “Our focus at Ginkgo is increasing the scale of our platform so we can deliver more cell programs to customers.  We were doing that yesterday, we’re doing it today, and we’ll be doing it tomorrow.”

Kelly defended the use by startups of Ginkgo’s platform to launch platforms after securing capital and other resources from the company: “We don’t think that is a problem—starting a biotech company should be as easy as launching a website!  We’re happy we make it easy for companies to start on Ginkgo’s platform and hopefully more entrepreneurs hear about our platform.”

“Hire them!”

This week in his post on X, Kelly extolled the virtues of the staffers that Ginkgo laid off.

“People come to Ginkgo because they want to develop new technologies at the very edge of what is possible in biological engineering, DNA design tools, automation, and more these are truly amazing folks with unique skills,” Kelly wrote. “[T]hey are lifelong alumni of Ginkgo and we are very sad to be losing them and you should be very happy to hire them!”

“Ginkgo has been focused over the last couple of weeks on doing right by our departing employees. Now we will be looking forward,” Kelly declared.

“Looking forward” should include even more cost cutting, Kelly was advised Wednesday in a reply on X by @VoodooScientific, a Los Angeles company that has developed the Viriato precision enzyme system for distillers of spirits seeking to enhance the smoothness of their beverages.

“Wishing Ginkgo the best! PLEASE, to give the best chances, slash expenses FAR deeper than whatever you are planning. That’s in your control, revenue isn’t and will be less than you’d think for quite a while. Spend more later, the grand vision can wait,” Voodoo Scientific added on Wednesday.

Last year, Voodoo Scientific joined Ginkgo to launch a partnership designed to help distillers produce ultra-premium spirit products by applying Ginko enzyme services such as ultra-high throughput screening, machine learning-guided protein design, and optimized proprietary bacterial and fungal host strains.

Kelly—who also chairs the U.S. National Security Commission on Emerging Biotechnology—asserted that Ginkgo “remains very well capitalized,” having ended the first quarter with nearly $850M in cash and essentially no debt, staffed with incredible talent and containing an unparalleled aggregation of technology in bioengineering from automation to AI.”

Ginkgo ended Q1 with $840.440 million in cash and cash equivalents, down 11% from the $944.073 million it reported in the year-ago quarter. The company finished the first quarter with a net loss of $165.911 million, improved from a net loss of $204.969 million on revenue that plummeted 53% year-over-year, to $37.944 million from $80.702 million.

Ginkgo has blamed its revenue falloff on an expected ramping down of the portion of its biosecurity business focused on COVID-19 testing in “K-12” elementary and high schools. But the company also saw its cell engineering revenues fall by 18%, to $27.889 million during Q1 this year from $34.096 million in the first three months of 2023.

“I’m deeply thankful for the incredible effort that has gone into building the assets we have today, especially from departing employees, and we will make the most of them as we continue to make biology easier to engineer,” Kelly added.

Leaders & laggards

• Alnylam Pharmaceuticals (ALNY) shares jumped 34.5% on June 24, after the company reported positive topline results from the Phase III HELIOS-B trial (NCT04153149) assessing vutrisiran as a treatment for ATTR amyloidosis with cardiomyopathy (ATTR-CM). Vutrisiran achieved a 28% reduction in the composite of all-cause mortality and recurrent cardiovascular events in the overall population, and a 33% reduction in the monotherapy populations. The study also showed statistically significant improvements across all secondary endpoints in both the overall and monotherapy populations, Alnylam said. Alnylam plans to proceed with global regulatory submissions starting later this year, including filing a supplemental New Drug Application with the FDA using a Priority Review Voucher.
• eFFECTOR Therapeutics (EFTR) shares plunged 76% from $1.17 to 28 cents on June 24, after the company announced that it had terminated its staff and will seek potential strategic alternatives for its development programs as it winds down operations. eFFECTOR also said it will voluntarily request a delisting of its securities and expects them to be delisted in the near term. The company also named Craig R. Jalbert as CEO, president, treasurer, and secretary, as well as the board’s sole member. Last month, eFFECTOR claimed its cash, cash equivalents, and short-term investments totaling $25.4 million (up 38% from $18.4 million on December 31, 2023) were sufficient to fund operations into the first quarter of 2025.

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Physician-scientist Matthew Porteus, MD, PhD, has been a mainstay in the genome editing field for more than two decades. He trained at Stanford University Medical School before completing his residency and hematology/oncology fellowship at Boston Children’s Hospital/Dana Farber Cancer Institute. During his postdoctoral research at Caltech with Nobel laureate David Baltimore, Porteus began his journey in gene targeting, in particular homologous recombination, as a means to repair disease genes. He has been on the Stanford faculty since 2010, treating patients with sickle cell disease and other hematological disorders at the Lucille Packard Children’s Hospital. 

Porteus is a scientific co-founder of CRISPR Therapeutics, the company that launched the exa-cel CRISPR trial that culminated in the approval of Casgevy in December 2023. With the latest companies he has co-founded—first Graphite Bio, now Kamau Therapeutics— Porteus remains steadfast in translating the promise of homologous recombination to the benefit of patients with sickle cell disease. 

In this wide-ranging interview with GEN editorial director Kevin Davies, PhD, Porteus candidly discusses some of the scientific milestones along his 25-year genome editing journey, including an update on the clinical translation of homologous recombination to treat patients with sickle cell disease. 

(This interview has been edited for length and clarity. A longer version has been published in the June 2024 issue of The CRISPR Journal.) 

Kevin Davies: Matt, what’s your impression of the current state of gene therapy and gene editing? 

Matthew Porteus: The approvals in December 2023 of Casgevy [Vertex Pharmaceuticals/CRISPR Therapeutics] and Lyfgenia [Bluebird Bio] are super exciting to see. Within a decade, a discovery made in a test tube translated to an approved therapy for a disease that has a large unmet medical need. I’m proud to have made my contributions to that process.  

That said, this is a first step but we’re nowhere close to where we need to go on multiple axes. From an efficacy standpoint, I’d argue that it’s not as good as a bone marrow transplant. If I could do an allogeneic bone marrow transplant as easily as doing an autologous transplant, the results are still better. Then there’s the issue of cost and accessibility. Certainly, an autologous transplant (using the patient’s own cells) is going to be more accessible because it’s a much less complicated procedure. 

The manufacturing, of course, is more complicated. If you had a patient and they had a perfect allogeneic transplant match, that’s the direction you would probably go. If you have a matched sibling donor—a perfect HLA match donor without sickle cell disease or even with sickle cell trait—the trials exclude you from getting a gene therapy or gene-edited product because the results there are so spectacular. It’s when you don’t have that donor that you look for alternative sources. That is 85% or more of patients who don’t have that gold-standard matched sibling donor.  

Davies: You have a long history in the genome editing space, going back to the early 2000s. Can you summarize some of those early landmark studies?  

Porteus: I started thinking about this during my MD/PhD training. During my PhD work, I would argue the work that led to the first Nobel Prize in genome editing was performed. Mario Capecchi and Oliver Smithies showed that you could get targeted integration at measurable frequencies in mouse embryonic stem cells. Maybe we should start calling that the first Nobel in gene editing—they called it ‘gene targeting’ but the reality is that’s what a lot of us are doing.  

The second thing was taking care of patients with sickle cell disease during medical school and recognizing the gulf between the contributions this disease had made to our understanding. of almost everything—blood development, genomic regulation, genomic structure, molecular pathophysiology—and that we did nothing that was driven by that understanding. We had this tremendous genetic and pathophysiological understanding— but it wasn’t being translated.  

At the beginning of my career, I thought I could go into lentiviral gene therapy. But I wanted to develop homologous recombination—the Smithies-Capecchi approach to this disease—because the basis is a single nucleotide change in a single gene. We know the cell that you need to fix because allogeneic transplant shows us—as Guido Lucarelli called it ‘allogeneic gene therapy.’ John Tisdale (NIH) called it ‘whole genome therapy.’ We knew fundamentally what needed to be done. 

Luckily, I found a postdoctoral mentor—David Baltimore—who was willing to say go at it. He admits he treats his trainees with ‘benign neglect’ in his words! But that was what I needed. Maria Jasin and others had shown that if you make a DNA break, the homologous recombination pathway is stimulated.¹ I was part of a group showing how to take an engineered nuclease at the time—zinc-finger nuclease (ZFN)—and create a genome-specific break.² Other than Sangamo, no one can really make good ZFNs. There was a real barrier because it was so difficult to engineer them. Many of us spent a decade doing the best we could with them.  

Casgevy is not based on gene correction or homologous recombination. And the recognition that DNA breaks can lead to site-specific indels (insertions/deletions), we need to really give Dana Carroll credit. He published a paper using ZFNs showing that you could make mutations in specific genes.³ And since that was a relatively simpler process, it really has exploded. I thought TALENs were going to be really transformative but just as they were getting off the ground, we have the 2012–2013 discoveries of CRISPR.  

Davies: You were a co-author on the famous Nature paper in 2005 that introduced us to the term ‘genome editing.’ How did your collaboration with Sangamo come about? 

Porteus: I was talking to Srinivasan Chandrasegaran, who biochemically had said ‘I can link a ZFN to the Fok I-chimeric nuclease domain.’ He had collaborated with Carroll. We needed to engineer these systems into mammalian cells and had shown how to use nucleases in a mammalian cell to get high frequencies of gene targeting. I could fix the GFP gene. And I was finishing up my postdoctoral work with David who said, ‘you need to talk to Sangamo…’ I remember visiting Casey Case, the CSO of Sangamo at the time…That prompted a collaboration as I was transitioning to my independent faculty position and their enterprise on engineering ZF proteins and then coupling them to the nuclease domain, which led to the Nature paper.⁴ It was the first demonstration that you could engineer a nuclease to target an endogenous sequence in a genome. In all the prior experiments, you inserted your target site first, and then retargeted it.  

Davies: Not long after the CRISPR gene editing papers in 2012–13, you became a scientific co-founder of CRISPR Therapeutics. How did you get involved with them?  

Porteus: I make the distinction that gene editing is a process and CRISPR is a tool to start the process. But any protein that makes a DNA break initiates the gene editing process. CRISPR just happened to be this amazingly powerful, easy-to-use specific tool. There was a clear excitement—it caught the attention of investors who wanted to start biotech companies. Investors were looking to people who knew about gene editing and some came knocking on my door. I started talking to some of the VCs and through those conversations became a scientific founder of CRISPR Therapeutics, got to know [co-founders] Sean Foy, Rodger Novak, and Emmanuelle Charpentier. They clearly had a sense that they had a hold of something. One of the things I think I can take credit for is pointing them in the direction that sickle cell disease and β-thalassemia were the perfect first indication.  

Sickle cell disease needed and deserved this attention. It was the right [patient] size, it had a large unmet medical need, the biology was well understood, and there were a lot of approaches that one could take. My lab has continued to work on directly correcting the mutation that causes the disease by homologous recombination because that’s where I got started.  

But the biology of understanding that fetal hemoglobin (HbF) could counteract the effects of sickle hemoglobin and that there were pathways that controlled the levels of HbF, and that there were people in the world who had genetic changes causing hereditary persistence of fetal hemoglobin, pointed people to the idea that perhaps a faster approach was homologous recombination—to harness the indel-based approach that Dana Carroll had [published]. I helped CRISPR Therapeutics work through potential targets with CRISPR-Cas9. 

They ended up building on the biology that came from Daniel Bauer and Stuart Orkin on BCL11A.⁵ The first approaches in fact were by Sangamo to target BC11A itself. We quickly learned that if you inactivate the protein, you disrupt stem cell function. When Dan identified this key enhancer—we helped them a bit with some TALENs [to show] that you could inactivate BC11A being turned on in the red cell lineage without inactivating all of its key functions in hematopoietic stem cells and B cells. 

They built on that target, but if you look at some of the subsequent programs that are targeting HbF, they’re targeting other pathways in BCL11A, the binding sites. They’re making changes that match what has been found in people. We often go back to the Orah Platt [Boston Children’s Hospital] paper showing that 8–9 is the level of HbF that starts to differentiate between less severe disease.⁶ And of course, hydroxyurea is a small molecule showing that if you upregulated HbF, you decrease the severity of the disease…  

The second part that I contributed to was that CRISPR-Cas, as originally discovered, simply didn’t work in hematopoietic stem cells (HSCs). Delivering the system as a plasmid, as DNA expression molecules, simply didn’t work. We at Stanford, in collaboration with Agilent, showed that you could deliver it as a Cas9 protein complexed to a synthetic guide molecule, with the guide molecule having modifications at the end. This probably serves a couple of purposes, one of which is to protect it from degradation, the other maybe is to shelter it from being recognized as a foreign molecule. I suspect that was a highly effective way of getting genome editing to occur in a range of primary cell types and keeping those cells healthy. You could deliver plasmids to CD34 cells and they would just die like a dog because cytoplasmic DNA is sensed as a viral infection and you get this robust type 1 interferon response. This was a way to deliver that nuclease in a highly efficient fashion to get that break where you wanted and maintain the quality of the cells. It’s that approach using the CRISPR-RNP complex that’s being used to manufacture Casgevy. 

CRISPR Therapeutics-Vertex found a good guide RNA, you have your target, you treat a patient, you see Victoria Gray doing fantastically well.⁷ The pace of their trial enrollment was appropriately slow, then you see this huge acceleration and the number of patients they enrolled. It is super exciting to see the results in Victoria basically generalize [to others] and the approval in December 2023. 

Davies: Let’s talk about your former company, Graphite Bio. What was the origin of the name? 

Porteus: We went through several names as most companies do, but we picked the name because the very first structure that Rosalind Franklin published was of graphite! So it was a call out to her contributions to our understanding of the structure of DNA that leads to sickle cell disease as a genetic disease. 

Davies: Do you still believe that direct correction of the pathogenic mutation will work better than upregulating HbF? 

Porteus: I certainly think it will be, it’s an approach that still is going to be the gold standard. Casgevy is still not a treatment of the root cause. This still has not been done for any disease—to take the pathologic variant and change it to the non-pathologic variant. That has not been done yet. [The HbF approach] is great but it’s a workaround, making mutations to compensate for the pathologic variant.…  

Even as we were supporting and advising CRISPR Therapeutics on their program, in my academic lab, we were building the technology to get high frequencies of gene correction in the endogenous beta-globin gene. We developed it with CIRM support from Stanford, generous philanthropic support from some Bay Area supporters, and got to the place where we could submit an IND and then raise capital to run the clinical trial. We made the decision to start Graphite Bio to run that clinical trial, and then maybe to more broadly develop the HDR [homology directed repair] platform. The company got started when times were good in the biotech investing world. Raising capital is always challenging but they were able to raise capital.  

Davies: The story of Graphite didn’t end the way you had planned it. There was an adverse event after you dosed your first patient? 

Porteus: The patient received her own cells in August 2022. When you get chemotherapy following a bone marrow transplant, there’s always a period where you wait for the cells to engraft and start making new red blood cells and platelets. Her period lasted longer than we expected but she was discharged from the hospital, she was doing fine, she felt great. But the treating team decided to stimulate her bone marrow by putting her on a growth factor for stem cells—a thrombopoietin agonist—which is being used in other bone marrow failure settings. But it wasn’t written into the protocol. And because we started an off-protocol medicine for a finding that was related to the drug product—slow engraftment— that triggered the SAE [serious adverse event] reporting. She was home! There were some [erroneous] reports, one even reported that she had died. She called her treating physician and said, ‘I’m not dead!’ Nonetheless, it was clear that the process that had come out of Stanford needed improvement….

Davies: So Graphite was at a crossroads. One could imagine a scenario where the company regrouped and decided to carry on—but you didn’t do that?  

Porteus: The company had appropriately decided to pause it on its own. After that [the patient’s] bone marrow started to recover. It was reported at ASH 2023 [American Society of Hematology] that she’s now transfusion independent, she’s off all her growth factors and clinically she’s doing great. There are some laboratory findings that we’ll continue to study and report in the future. 

It was clear it was going to take another 12–18 months to take the improvements had been identified both academically and within Graphite to treat the next patient. It was clear that the manufacturing process was too hard on the cells, but it was going to take another 12–18 months to get the manufacturing down and reboot the clinical trial. Graphite, the board and the investors thought that it was not in the best interest for that company to continue the program. 

So it came back to me because that makes sense. I got a lot of advice, thought long and hard. They were willing to do whatever I wanted to do. Some people said, ‘You should take it back to your Stanford lab and reboot it there.’ But I don’t think that works because we were ready to go. So instead, I started another company called Kamau Therapeutics…. 

Basically, the entire genome editing program has been transferred from Graphite into Kamau. We’re in the process of closing our seed funding. The trial was never closed, so we’re just reopening it under different names, the same general sites, with this markedly improved manufacturing process, some tweaks to the clinical protocol around cell dose and utilization of growth factors. We hope to treat the next patient with Nula-cel in 2025. 

Davies: We now have two approved therapies, priced at $2.2 and $3.1 million. Do you think those are fair prices?  

Porteus: One part of me agrees with what Julia Kanter (University of Alabama) has publicly said, which is that these patients and these therapies deserve that price: the benefit to patients absolutely justifies the lifelong savings and the indirect costs. [These prices] are not out of line for the prices for similar therapies. Lenmeldy, which just got approved for metachromatic leukodystrophy, got listed at $4.25 million! Why should sickle cell drugs be priced any less than any of the other peer drugs? 

That said, the price is clearly going to be a barrier to patients getting access. Where is the price coming from? Well, it’s coming from companies that are driven by shareholder value that need to make a return, and they develop the drugs and that’s the system we work in. It’s also driven by the fact that these autologous ex vivo manufactured therapies are expensive to make. Once you have a small molecule drug, you can make kilograms. If it’s an antibody and they do a 25,000-liter bioreactor run, one lot gives you doses for thousands, if not 10,000 patients. Every [gene editing] dose has to be manufactured specifically. So right now, there’s just a cost of goods that’s high.  

Some people said that’s why we need to figure out how to give an in vivo gene editing drug, but I’d argue right now the in vivo gene therapies are just as expensive and just as inaccessible as ex vivo therapies. So yes, it could get you there, but AAV gene therapies are also $3 million. There’s not a big difference. In terms of treating patients in Africa and India where most patients are, ex vivo therapy is pretty much [considered] a non-starter. But I don’t believe that.  

I think the other challenge with in vivo is the HSC is a pretty special cell. So in vivo editing and the Intellia programs are super exciting and the Verve Therapeutics programs are exciting in some senses. But delivery is challenging, even in the liver. The liver is designed to take up things. Macrophages are designed to take up things. HSCs are not designed to take up anything! They’re designed to be sheltered and protected. I think we’ve got a lot of biologic work to be done to find the right way to deliver an editor to that cell. 

In contrast, I think ex vivo autologous engineering is now, to me, an engineering problem. How do you stick process engineers on this and make the cost of goods cheaper, make the process cheaper and scalable? Instead of having five people make one product, can you have one person make ten products? I think engineering is something we are really good at and there are solutions out there and solutions being developed. The story of monoclonal antibodies is the analogy I turn to: once considered impossible to be a scalable drug and now a platform that is considered standard. I hope to be part of the story where autologous genetically engineered cell therapies go through a similar developmental process. 

I think we need competition. I’m going to put my effort in making ex vivo therapy as cheap as possible. Let’s set a bar that in vivo has to get to.  

Matthew Porteus, MD, PhD, is a physician-scientist at Stanford University School of Medicine, Palo Alto, CA. Kevin Davies, PhD, is Editorial Director of GEN.

A longer version of this interview has been published in the June 2024 issue of The CRISPR Journal. 

References

1. Urnov F. Genome Editing B.C. (Before CRISPR): Lasting lessons from the “Old Testament. Crispr J 2018;1(1):34–46.
2. Porteus MH, Baltimore D. Chimeric nucleases stimulate gene targeting in human cells. Science 2003;300(5620):763.
3. Carroll D. Genome engineering with zinc-finger nucleases. Genetics 2011;188(4):773–782.
4. Urnov FD, Miller JC, Lee Y-L, et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 2005;435(7042):646–651.
5. Orkin SH, Bauer DE. Emerging genetic therapy for sickle cell disease. Annu Rev Med 2019;70:257–271.
6. Platt OS, Brambilla DJ, Rosse WF, et al. Mortality in sickle cell disease—Life expectancy and risk factors for early death. New Engl J Med 1994;330:1639–1644.
7. Gray V, Thomas U, Davies K. Warrior spirit: An interview with Victoria Gray, sickle cell pioneer. Crispr J 2024;7(1):5–11.

The post A Story of Perseverance: An Interview with Matthew Porteus appeared first on GEN - Genetic Engineering and Biotechnology News.

Can GeoVax Labs’ dual-antigen COVID-19 vaccine succeed where leading messenger RNA (mRNA)-based jabs developed during the pandemic have faded, clinically and commercially?

The company will begin to find out as it launches a 10,000-participant Phase IIb trial comparing the efficacy, safety, and immunogenicity of its next-generation, dual-antigen COVID-19 vaccine GEO-CM04S1 to one of the current FDA-approved COVID vaccines—a study being funded by the Biomedical Advanced Research and Development Authority (BARDA).

BARDA has awarded GeoVax approximately $24.3 million through its Rapid Response Partnership Vehicle (RRPV) to fund the manufacturing of clinical materials for the randomized, double-blinded Phase IIb trial, as well as regulatory and other support activities for the study. GeoVax could receive up to $45 million through RRPV based on meeting technical and scientific milestones.

Through its Clinical Studies Network, BARDA will also award approximately $343 million from its Project NextGen program to fully fund an as-yet-undisclosed contract research organization (CRO) that will carry out the Phase IIb trial. The Network offers services for Phase I through IV clinical trials of medical countermeasure candidates such as vaccines and treatments.

Investors responded to the BARDA award announcement June 18 by sending GeoVax shares rocketing 71% from $1.11 to $1.90. Those shares have fluctuated early this week, surging another 30% to $3.03 on Monday before dipping 27% to $2.20 on Tuesday.

GeoVax Chairman, President, and CEO David A. Dodd told GEN his company and the CRO have worked for over a year in preparation for the start of the Phase IIb trial.

GEO-CM04S1 is based on GeoVax’s MVA viral vector platform, which supports the presentation of multiple vaccine antigens to the immune system in a single dose.

Two-prong attack

While current COVID-19 vaccines such as Pfizer/BioNTech’s Comirnaty and Moderna’s Spikevax are mRNA vaccines targeting the Spike protein, GeoVax’s GEO-CM04S1 mounts a two-prong attack on SARS-CoV-2 by encoding for both the spike (S) and nucleocapsid (N) antigens of the virus. The vaccine is designed to induce both durable neutralizing antibody and T-cell-based immunity against current and future variants of SARS-CoV-2 by attacking parts of the virus that are less likely to mutate over time.

By pursuing a more broadly functional engagement of the immune system, GEO-CM04S1 is designed to protect against severe disease caused by continually emerging variants of COVID-19—and thus should not require frequent and repeated modification or updating, according to GeoVax.

GEO-CM04S1 is already under study in three Phase II trials. One trial is assessing GEO-CM04S1 as a primary vaccine in immunocompromised blood cancer patients who have received cell transplants or CAR-T therapy (NCT04977024). The study’s open-label portion has generated data showing GEO-CM04S1 to be highly immunogenic in these patients, inducing both antibody responses, including neutralizing antibodies, and T-cell responses.

“We expect that this year there will be another update. We also expect that as we go into early 2025, we anticipate expanding that trial to additional sites in North America as well as in the U.K.,” Dodd said.

The other two trials are evaluating GEO-CM04S1 as a:

• Booster vaccine for healthy adults who have previously received the Pfizer or Moderna mRNA vaccines (NCT04639466). The trial was fully enrolled in September 2023 and final results are expected in the fourth quarter, reflecting a 12-month tracking of study patients.
• Booster vaccine in immunocompromised patients with chronic lymphocytic leukemia (CLL), a high-risk population for which current mRNA vaccines and monoclonal antibody (MAb) therapies have been shown to offer inadequate protective immunity (NCT05672355). GeoVax expects to read out data in the fourth quarter.

‘The reason why that becomes important to us is, if the data looks good, we may very well initiate our own company sponsored CLL trial,” Dodd said. “The various discussions we’ve been having with regulatory authorities indicate that there may be an expedited pathway for registration by focusing on such a high-risk group that is recognized as not being satisfied or addressed adequately by what is out there right now.”

GeoVax says its COVID-19 vaccine is potentially more durable than current FDA-approved COVID-19 jabs, which have been shown to lose effectiveness within two to six months.

“We’re showing protective immunity from the original Wuhan through the Omicron XBB1.5 variant, so it offers breadth of protection across the variants as well as durability,” Dodd said.

Longer durability

GeoVax says its studies to date have shown the effectiveness of GEO-CM04S1 to last twice as long as the two to six month range of current COVID-19 vaccines: “Our durability currently is coming in from our clinical trials at 8 to 12 months,” Dodd added.

And where Pfizer/BioNTech and Moderna developed COVID-19 vaccines aimed at protecting the general population from the virus, GeoVax says its COVID-19 jab is intended for immunocompromised adults who are more likely to potentially experience severe COVID-19 symptoms, hospitalization, and increased risk of death, yet are less likely to respond adequately to current COVID-19 vaccines.

The number of immunocompromised adults is estimated at between 50 million and 70 million people in the U.S. and up to 300 million worldwide.

“We’re not planning on going toe to toe with the current vaccines,” Dodd said. “From day one of moving forward with our vaccine, we have focused on going after the populations for whom the pandemic has never ended, the immunocompromised populations who have medical conditions that have depleted their body’s ability to respond to COVID or SARS-CoV-2.”

“These patients remain at risk of severe disease, hospitalization, and risk of death. They’re under active medical care they’re being managed by hematological oncologists, or they might be managed by the nephrologist, or by the endocrinologist if they have diabetes. They have medical conditions in which they are under active medical care. That’s different than the general population,” Dodd explained.

By focusing on immunocompromised patients, GeoVax reasons it can maximize potential revenue for its vaccine as revenues for the approved COVID-19 jabs has plunged with the pandemic evolving into an endemic.

$7.4B U.S. revenue potential

In its corporate overview presentation to investors this past spring, GeoVax estimated the market revenue potential for GEO-CM04S1 in the  U.S. alone at $7.4 billion—just below the combined $8 billion in combined 2024 global sales that Pfizer has projected for both its COVID-19 vaccine Comirnaty^® (co-marketed with BioNTech) and its COVID-19 drug Paxlovid^®.

Dodd says GeoVax is updating its revenue projection because the spring forecast was based on an older estimate of just 20 to 25 million immunocompromised Americans—while the National Health Interview Survey of the U.S. Centers for Disease Control and Prevention cites between 50 million to 70 million Americans with compromised immune systems.

“From a business standpoint, we believe that we have the opportunity with our vaccine to be the lead vaccine to be used among people with compromised immune systems, because they’re not benefiting from what is currently out there,” Dodd said.

GeoVax has not furnished a peak annual sales estimate for GEO-CM04S1

Last year, Comirnaty generated $11.220 billion in direct sales and alliance revenues, down 70% from $37.806 billion in 2022, while Paxlovid generated only $1.279 billion in 2023, down 93% from $18.933 billion a year earlier.

Moderna’s COVID-19 vaccine Spikevax racked up $6.7 billion in 2023 sales, a 64% plunge from $18.4 billion in 2022. For this year, Moderna has only disclosed a $4 billion combined sales projection for its respiratory vaccine franchise, which includes Spikevax as well as its respiratory syncytial virus (RSV) vaccine mRESVIA (mRNA-1345), approved by the FDA on May 31.

The BARDA award marks a milestone for GeoVax. Based in the Atlanta suburb of Smyrna, GA, GeoVax was founded in 2001 with the initial focus of developing an HIV vaccine, based on research by Harriet Latham Robinson, the company’s founder and chief scientific officer emeritus.

Pivot from HIV

Dodd joined GeoVax’s board in 2010, and the following year was first elected chairman. As chairman, Dodd oversaw the company’s pivot away from HIV in 2014 after it failed to attract funding from investors or the NIH to advance its vaccine past Phase IIa.

The company began pursuing vaccine development based on its MVA platform, with early signs of success. GeoVax’s Ebola Zaire vaccine, for example, showed 100% protection in non-human primates given a single dose without any adjuvants, while the company also developed vaccines for Ebola Sudan and Marburg virus.

“We’re not planning on carrying those forward on our own funding, but we’re in discussions right now” with potential partners to move toward Phase I studies, Dodd said. Should those talks yield one or more agreements, he said, the resulting studies “will be done through funding by non-dilutive means.”

Dodd took on the additional roles of president and CEO in 2018, intent on enabling GeoVax to develop its pipeline by growing and broadening the company’s financing.

As COVID-19 began to wreak havoc on the world, GeoVax began a program to develop a vaccine for the virus. That sent the company’s stock, then trading Over the Counter, zooming from 13 to 50 cents a share. But by June 2020, with the world upended by the pandemic, GeoVax was down to five employees and $100,000 in available cash.

Three months later, GeoVax closed on a $12.8 million public offering and up-listed its publicly traded shares and warrants from the Over the Counter market to Nasdaq.

In 2021, GeoVax acquired its two main pipeline programs, shelling out undisclosed sums for an exclusive license from City of Hope to develop GEO-CM04S1 two months after the company bought exclusive rights to the cancer drug Gedeptin^® from PNP Therapeutics.

Gedeptin is now in a Phase I/II trial (NCT03754933) in patients with advanced head and neck cancer. Initial study results from the first trial of the Phase II portion are expected to be announced within the next two to three weeks, Dodd said, to be followed by plans for an expanded Phase II study of Gedeptin, then a combination study evaluating Gedeptin with an immune checkpoint inhibitor.

The FDA has granted Gedeptin orphan drug status for the intra-tumoral treatment of anatomically accessible oral and pharyngeal cancers, including cancers of the lip, tongue, gum, floor of mouth, salivary gland and other oral cavities.

Also in GeoVax’s pipeline is GEO-MVA, a vaccine for smallpox and Mpox being developed for adult men at high risk of Mpox. GeoVax aims to become the first U.S. based supplier of a vaccine for Mpox and smallpox (Copenhagen-based Bavarian Nordic began commercial launch of the currently sole FDA-approved Mpox vaccine, Jynneos^® [MVA-BN] in April), plus satisfy interest from the federal government in replenishing and re-stocking the Strategic National Stockpile with a domestic-sourced smallpox vaccine.

Progress report

GeoVax plans later this year to disclose its progress toward an expedited regulatory registration pathway. “Frankly, we believe that our first product to be registered and commercialized could very easily be GEO-MVA as a standalone vaccine,” Dodd said. “I’m not saying it will be commercialized. But we’ll have updates on that, because development is being driven by a heavy regulatory strategy, as you might imagine.”

GeoVax’s pipeline also includes a half dozen preclinical programs—including a treatment for solid tumor cancers, and vaccines for pan-coronavirus, Ebola Zaire, Ebola Sudan, Marburg virus, and Zika.

“Those products will advance to the degree that there is non-dilutive, let’s say external collaboration, business development, or co-development funding. We’re not allocating a lot of time to those if any,” Dodd said.

Despite data showing 100% protection in a single dose for its Zika virus candidate, Dodd said, “it has not been a priority, because there are others out there that are going after it.”

“That’s one program that is held in discussions if there are potential partners, and whatever form of a transaction they may end up thinking about,” Dodd added. “Our focus is, number one, the [BARDA-funded] Project NextGen program for GEO-CM04S1, then number two, both the GEO-CM04S1 Phase II programs and the Gedeptin program.”

Project NextGen is a $5 billion program designed to speed up development of next-generation COVID-19 vaccines, drugs, and enabling technologies that lower costs, speed production, increase efficacy, and improve access to those vaccines and drugs. Project NextGen is led by BARDA and the NIH’s National Institute of Allergy and Infectious Diseases (NIAID).

To date, BARDA says, it has spent more than $2 billion in Project NextGen funding to support development of next generation vaccines, treatments, and enabling technologies. BARDA is part of the U.S. Department of Health and Human Services (HHS)’s Administration for Strategic Preparedness and Response (ASPR).

GeoVax finished the first quarter with a $5.58 million net loss, up from a $4.038 million net loss in Q1 2023, and no grant revenue either quarter. The company reported a $26 million net loss in 2023, nearly double its $14 million net loss the previous year.

GeoVax has grown its workforce to about 25 people, Dodd said, up from the 17 the company reported in its Form 10-K annual report for 2023. That workforce is expected to grow over time through a combination of full-time and contracted employees: “We’re actually going through all that planning right now of what our timing will be and our options for staffing up.”

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Unquestionably, we will emerge from this revolutionary period with modified views of components of cells and how they operate, but only, however, to await the emergence of the next revolutionary phase that again will bring startling changes in concepts. —Barbara McClintock, Nobel laureate (1983)

 “Everything in the last 14 years of genome editing has been based on CRISPR. We have been whipping this horse for a decade and a half, but we need more programmable functions with complexity beyond the molecular scissors that cut RNA and DNA.” So says Patrick Hsu, PhD, co-founder of the Arc Institute, in whose lab the next revolutionary phase of genome engineering may have just been unearthed, even as the CRISPR revolution has barely begun.  

In January of this year, researchers in Hsu’s laboratory (he is also assistant professor of bioengineering and Deb Faculty Fellow at the University of California, Berkeley) posted a preprint on bioRxiv in which they claim to have discovered a new class of natural single-effector RNA-guided systems.¹ That story, now peer reviewed, is published online today in Nature.  

These systems retain the key property of programmability from RNAi and CRISPR, while enabling large-scale genome design beyond RNA and DNA cleavage. These modular, bi-specific bridge RNAs can be reprogrammed to enable sequence-specific fundamental DNA rearrangements, potentially accelerating the advancement of genome design (Fig 1).² 

“This is a much more complex molecular machine,” Hsu continues. “We’re excited about the potential of this for eventually achieving chromosome-scale genome engineering, where you can do long-range insertions, deletions, and genome translocations.” 

Complex genome assembly 

Hsu is a self-described technologist—he creates the genome engineering and biological design tools of tomorrow. As a graduate student at Harvard University, he worked with his mentor Feng Zhang, PhD, building some of the foundational components of CRISPR as a genome engineering tool.³ But Hsu came to realize that manipulating RNA might be a more flexible technique than making permanent, and sometimes unintended, changes to the genetic code. In 2018, Hsu and his team, which included Arc Institute co-founder Silvana Konermann, PhD, developed CasRx as a programmable RNA-binding module for efficient targeting of cellular RNA, enabling a general platform for transcriptome engineering and future therapeutic development with RNA targeting CRISPR.⁴  

Hsu believes that one of the greatest challenges today is the manipulation of eukaryotic genomes, particularly the integration and manipulation of large, multi-kilobase (kb) DNA sequences, which limits the rapidly growing fields of synthetic biology, cell engineering, and gene therapy. According to Hsu, who is quite the science historian, the prevailing modern genome editing method has been stuck on a road paved with milestones that began with the initial work of Mario Capecchi, PhD, in 1980 on the insertion of DNA into mammalian cells,⁵ Martin Evans PhD’s work in 1986 on chimeric mice,⁶ and then work from both Oliver Smithies, PhD, and Capecchi to successfully create specific modifications in the genomes of mice.^7,8   

“That was generally an attempt to do an insertion reaction, which is only one way to do genome editing,” Hsu told me. “Funnily enough, what happens today with base editing or prime editing—while exciting—is arguably even smaller in scope. You’re making single-nucleotide polymorphism changes or tens of bases, rather than the multigene-sized cassettes that we originally [envisioned]… Generally, all of this has been small-scale single-locus changes.” 

Hsu argues that CRISPR-Cas molecular scissors require a complex multistep process to make an edit that, in chemistry terms at least, has very low purity. “You mostly get indels, and only a small amount of time you get the edit, which then leads to chromosomal translocations and large lesions,” said Hsu.  

“You’re trying to create this chemical reaction that’s just not very predictable. Certainly, there are highly optimized cases like ex vivo T-cell engineering, where billions of dollars have been invested into this problem to get it to work right. [Scientists] will hang their hat on that and say that CRISPR is high efficiency and specificity. But generalizing this success to other cell types or in vivo has been really hard—it’s a fundamental mechanistic limitation.” 

Hsu is not alone in this view. In 2019, Harvard Medical School geneticist George Church, PhD, memorably referred to CRISPR as a “blunt axe” that performs “genome vandalism.” Instead of looking to take a major leap forward, Hsu said the genome engineering field is in a battle over bragging rights that centers around the size, toxicity, specificity, and efficiency of their nucleases.  

Some recently developed gene editing assemblies, such as PASTE and PASSIGE (both developed by former colleagues of Hsu’s at the Broad Institute), are showing considerable promise in their own right, although they require several distinct components to be delivered to a given cell.⁹   

By contrast, Hsu is trying to reframe the conversation completely. Hsu, who was already working on a solution to evolve the genome engineering field, did what many talented scientists have done in the past—he turned to nature for inspiration. For example, during conception, there’s a large amount of recombination and genomic rearrangements from crossover events at chromosomal scale between genes from the mother and father that results in the unique individuals that we are.  

Another example is Deinococcus radiodurans, a bacterium that is extremely resistant to radiation and other environmental stresses. When the organism is being battered by radioactivity, their genomes can shatter, but they always find a way to reassemble a complete genome. And then there are mobile genetic elements (MGEs), which brings us to the great Barbara McClintock, PhD. 

About 80 years after Gregor Mendel worked with peas in an abbey garden in (what is now) the Czech Republic to describe the transmission of genetic traits (before anyone knew genes existed), McClintock began experiments on maize kernels at the Cold Spring Harbor Laboratory that would lead to her profound discoveries on transposable elements.^10,11 McClintock observed that genetic elements can change position on a chromosome, causing nearby genes to become active or inactive, and that this correlated with the redistribution of genetic traits in maize as well as other organisms.¹² 

In her 1983 Nobel Prize lecture, McClintock spoke about genetic shocks created by MGEs that create selective pressures and, thus, new gene functions—even the origin of new species.¹³ “[McClintock] was one of the original people who discovered these elements, one of the first people that realized that they’re actually really powerful driving forces for genetic diversification in new functions,” said Hsu. “We’ve just been fascinated by these transposons and genomic elements and what else could be out there.” 

That framework got Hsu to begin examining large serine recombinases (LSRs). “The reason we did our LSR research in the first place, was not really to find recombinases per se—it was to solve this core technological problem of modern gene editing.” 

The bridge RNA recombinase mechanism 

A few years ago, two members of the Hsu lab, graduate student Nicholas Perry and computational biologist Matt Durrant, PhD, were working on LSRs (Fig 2). One of the perks of working in the non-profit Arc Institute is that it affords scientists no-strings-attached, multi-year funding.¹⁴ Perry and Durrant decided to sift through a huge genomic and metagenomic database that Durrant had been compiling for MGEs (Box 1).  

Upon investigating a family of cut-and-paste MGEs called IS110s, which all had a gene encoding a RuvC-like domain—one of the key nuclease domains in the Cas9 nuclease—the Arc team wondered if it might encode a whole RNA-guided transposase system.^15,16 This made sense to Durrant, as IS110 elements scarlessly excise themselves from the genome and generate a circular form as part of their transposition mechanism (Fig. 3). 

“Patrick threw around the idea that maybe there’s some kind of RNA-guided transposase out there,” Durrant recalled. “At that point, I had just been staring at sequences for so long that I felt like I had built up an intuition for what would be worth pursuing.” 

Hsu’s and Durrant’s hypothesis sent Perry on a quest to discover whether there could be some sort of RNA that existed, a pre-requisite for any sort of RNA-guided transposase system. Their first clue came from secondary structure analysis of a particular IS110 sequence, called IS621, which was predicted to contain an RNA with a 5′ stem loop and two large internal loops. Perry set out to demonstrate that an RNA was expressed from this sequence. 

Meanwhile, Durrant circled back to an idea that Hsu had pushed him to implement called covariation analysis to predict base-pairing interactions between the non-coding RNA (ncRNA) and the target or donor DNA.¹⁷ This comparative analysis method asks whether pairs of nucleotides change in tandem at specific positions of aligned DNA and RNA, which would indicate evolutionary pressure to conserved base-pairing interactions between ncRNA positions and target or donor positions. Projecting this covariation pattern onto the canonical IS621 sequence and ncRNA secondary structure, Durrant saw that the first internal loop may base-pair with the target DNA.  

“It was a really messy initial analysis… but we got lucky enough that it worked,” said Durrant. “We saw this signal of bits of the non-coding ends that co-vary with the target. It was the most exciting moment of my whole career, when it became clear that these are probably programmable.” 

Durrant immediately messaged Perry, who was at a CRISPR conference in Boston, saying they had to talk immediately. Perry hurriedly left the meeting and covertly called Durrant, wary of any potential eavesdroppers who might pick up on their findings about RNA-guided transposases. Although the team gave some thought to publishing the computational results alone, Durrant said there was “some sliding scale of confidence and doubt… We tried to deeply understand how everything worked.” 

For the next few months, Perry was buried in experiments to try to assemble pieces of the puzzle that had been predicted by Durrant’s computational analysis. On a Sunday morning, which happened to be his birthday, Perry was looking through data when he got confirmation for an experiment showing that a promoter on the circular form of IS621 expressed an encoded ncRNA that formed a functional complex with a transposase. 

“I spent probably six months before getting any conclusive positive data about the expression of a non-coding RNA, observing them transpose and showing that they worked in an orthogonal system, trying to engineer the system,” said Perry. “If we couldn’t even get these to function in the cell type that they’re native in, then how could we ever learn anything more about them? You can wish that they’re programmable, but if there’s no observable function, does it really matter?” 

Perry was able to confirm a mechanism for a programmable target loop, and a short time later, they repeated the whole process for identifying and confirming that the second loop was a programmable donor loop. This suggested to Perry and Durrant that the RNA acts as a “bridge” between target and donor DNA to enable recombination by the IS621 recombinase (Box 2). 

Then came the eureka moment, where the entire picture of their computational and experimental data came together. Perry and Durrant had discovered a single-effector recombinase system that uses a bridge RNA with two distinct binding loops that can be independently reprogrammed to bind and recombine diverse DNA sequences (Fig. 4). “We realized it was programmable on both [the donor and target] ends, which was completely unprecedented,” said Perry. 

The team went on to demonstrate that the modularity of each loop of the bridge RNA can facilitate the recombinase system to execute sequence-specific insertions, inversions, and excisions. This meant that the bridge RNA-guided single effector system provided “a unified, programmable, and modular mechanism for the fundamental DNA rearrangements required for genome design,” says Hsu. “We discovered a conceptually distinct mechanism of RNA-guided self recognition for a mobile genetic element and capitalized upon this mechanistic feature to enable a new method of genetic engineering.” 

A GUI for genome engineering 

Since the early days of bacterial artificial chromosomes (BACs) and yeast artificial chromosomes (YACs), assembling large sections of DNA has been technically incredibly challenging. As the field has moved towards making synthetic minimal genomes, the field has been limited to relatively short DNA synthesis and assembly techniques. With the concept of genome design in mind, Hsu explains the significance of these bridge RNAs in computer terms—they’re basically like a program that allows the user to install and uninstall packages. 

“The Xerox Alto was the first computer ever sold with a mouse and a graphical user interface (GUI),” said Hsu. “It was invented just off the street from where Arc [Institute] is today at Xerox PARC. It gave humans for the first time a simple and intuitive way to interact with information. Guide RNAs act like that mouse cursor to interact with nucleic acids in a large genome. What we’ve been doing so far is basically punching individual nucleotides and changing them, like punch-card programming. We want something that can operate at a much higher level of abstraction to design genomes. That’s where all of this is going.” 

Nature has invented it, and there are probably many more programmable systems. And Hsu will keep on looking to see what other biotechnology doors he can unlock. 

References 

1. Durrant MG, Perry NT, Pai JJ, et al. Bridge RNAs Direct Modular and Programmable Recombination of Target and Donor DNA. 2024;2024.01.24.577089; doi: 10.1101/2024.01.24.577089.
2. Herrera RJ, Garcia-Bertrand R, Salzano FM. Genomes, Evolution, and Culture: Past, Present, and Future of Humankind. Wiley; 2016.
3. Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotech 2013;31:827-32. doi: 10.1038/nbt.2647
4. Konermann S, Lotfy P, Brideau NJ, et al. Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell 2018;173(3):665-676.e14; doi: 10.1016/j.cell.2018.02.033.
5. Capecchi MR. High efficiency transformation by direct microinjection of DNA into cultured mammalian cells. Cell 1980;22(2, Part 2):479–488; doi: 10.1016/0092-8674(80)90358-X.
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