Volatile macroeconomic events are magnified in life science and healthcare applications, which are capital intensive, long-term investments with associated regulatory, safety, and commercial risks.
New technology is naturally exciting at first, but the reality of commercialization soon hits. Demonstrating efficacy and safety takes time. Many gene-editing companies set very high expectations from the get-go, and, unfortunately, position themselves for potential failure if funds are needed midstream during a difficult financial environment.
To put this challenge in perspective, it is helpful to remember that antibody applications developed slowly, starting with reagents for research then moving to diagnostics before jumping into therapeutics. Today, based on the accumulated knowledge base, therapeutic monoclonal antibodies have grown even more complex and specific. The concepts were there decades ago but the market needed time to mature.
A cycle of high expectations, reality crashes, and resurgence is not atypical for novel therapeutic approaches, including the gene-editing field, which is widely acknowledged to hold tremendous promise. A recent example from late last April is the U.S. FDA approval of Prime Medicine’s IND application, which gives the company the go-ahead to test its first next-generation product candidate, PM359, in a Phase I/II clinical trial in pediatric and adult patients with chronic granulomatosis disease (CGD).
Also in 2024, a Nature Biomedical Engineering article detailed a novel gene-editing approach, PASSIGE (prime-editing-assisted site-specific integrase gene editing), which couples the programmability of prime editing with the ability of recombinases to precisely integrate large DNA cargoes exceeding 10 kilobases.1 It is said that “patience is a virtue,” and these and other successes support the belief that full promise of gene editing is coming to fruition, despite temporary setbacks.
“Base editing is very precise and versatile, but any editing technology alone is not sufficient for success,” emphasized Giuseppe (Pino) Ciaramella, PhD, president at Beam Therapeutics. “You need an end-to-end infrastructure for technology optimization, manufacture, and therapy delivery. Delivery is an enabler where it works well in the liver, but current methods do not go everywhere in the body.”
The company realized from its inception that delivery and manufacturing capabilities were strategic assets and invested in a manufacturing facility in North Carolina and lipid nanoparticle (LNP) technology. In 2022, it also cofounded and has since collaborated with Orbital Therapeutics to expand LNP development for delivery to other tissues.
“Our competitive advantage is our entire optimized drug discovery and delivery engine. We were fortunate that, in the beginning, we were operating in a constructive market environment,” Ciaramella pointed out. “In the current environment, a company would struggle to put all of those pieces together.”
The BEAM-302 base editor corrects the mutation in alpha-1 antitrypsin deficiency (AATD) carried by 95% of those afflicted. The A in the E324 mutation is changed to a G, resulting in a corrected SERPINA1 gene. [Beam Therapeutics]
Beam Therapeutics’ pipeline focuses on two franchises–hematology and liver genetic diseases. In hematology, the lead indication is sickle cell disease. The long-term, life-cycle plan starts with an ex vivo approach, BEAM-101, in which patients undergo a conditioning regimen, such as treatment with busulfan, the standard of care in hematopoietic stem cell (HSC) transplantation. However, busulfan’s associated toxicity limits treatment to the most severely affected population.
The next-generation BEAM-103/BEAM-104 enables a non-toxic conditioning strategy for ex vivo transplants–called ESCAPE–that uses base editing to make multiple edits simultaneously. An additional guide makes a single base change to a receptor that allows a proprietary antibody to target and kill only unedited cells, providing a survival advantage to edited cells. A survival advantage for edited cells may also prove valuable in enabling more efficient in vivo editing of stem cells in the bone marrow, potentially eliminating the need for transplant altogether.
The lead indication in liver genetic disease is alpha-1 antitrypsin deficiency (AATD). AATD affects 100,000 individuals in the U.S., where 95% carry the same mutation that causes the protein to misfold and accumulate to toxic levels in the liver. The mutation also prevents the protein from going to the lungs to provide protection from proteases. “With BEAM-302 we target the liver and restore the function of the gene so the protein can be secreted. Initial clinical trial results are encouraging,” said Ciaramella.
The Axiomer
ADAR-mediated RNA editing technology uses a novel mechanism distinct from gapmers, splicing oligonucleotides, siRNA, or other RNA modalities. The technology is based on oligonucleotides referred to as “editing oligonucleotides”, or EONs, designed to recruit endogenous ADAR enzymes to make single, highly specific, and targeted adenosine-to-inosine (A-to-I) changes in RNA.
Single base changes in RNA, in lieu of editing DNA, is an alternative approach to genome-editing therapeutics. “Thousands of G-to-A mutations in the human population cause disease,” said Gerard Platenburg, PhD, CSO, ProQR. The technology is also designed to change amino acids, which could modulate protein expression and activity or alter proteins to provide a new function.
The Axiomer platform has evolved over the last decade. The first generation included a hairpin structure designed to recruit endogenous ADAR for precise adenosine editing. To increase activity and stability, the second generation uses a much shorter oligonucleotide with no hairpin structure.
“Our versatile approach is capable of targeting a variety of RNA species, organs, and a wide range of diseases and offers a long-lasting therapeutic effect without the need for frequent dosing, while also avoiding the risks of permanent genetic changes or irreversible DNA damage,” Platenburg explained.
A trial will begin this year with AX-0810 that targets NTCP, the main transporter of bile acids into the liver. AX-0810 uses GalNAc for efficient delivery to the liver and aims to introduce a protective variant on a wild-type RNA to positively impact cholestatic diseases.
While the initial pipeline program is focused on a liver-originating disease, ProQR also has a partnership with Lilly that currently includes up to 10 targets, with an option for an additional five. In addition, work is progressing with CNS-targeted Axiomer-editing oligonucleotides. Research demonstrated that RNA editing can be successfully achieved in key regions of the nervous system, across species, with durable effects.
The CNS pipeline includes programs targeting Rett Syndrome, a devastating and progressive neurodevelopmental disorder caused by variants in the transcription factor in the MECP2 gene. “We believe Axiomer offers an elegant approach to restoring physiological MECP2 levels while avoiding the risk associated with MECP2 overexpression and are partnered with the Rett Syndrome Research Trust to advance our approach,” said Platenburg.
A common thread in genome-editing therapies has been a relatively simple, localized single alteration of genetic sequence. However, many diseases result from loss-of-function genetic variants that are often spread throughout the affected gene.
According to Gregory Davis, PhD, head of Research and Technology at Sangamo Therapeutics, more general strategies that aim to repair genes in a “one-shot-fits-all” approach would typically involve the targeted insertion of a wild-type version of the full gene cDNA, a “super-exon,” directly into an early exon or intron of the endogenous target gene.
Recombinases have long been used to insert genetic payloads into cells without relying on endogenous DNA repair machinery or creation of a double-strand break (DSB). Switching to non-reversible “programmable” integrases represents a major simplification and derisking of targeted gene insertion.
“To address targeted integration of large DNA constructs into desired genomic loci, we sought to use our core expertise in protein-DNA interactions to engineer the protein-DNA interface of large serine integrases (LSIs),” explained Davis. “We discovered a zinc finger-like helix within Bxb1 that we can reprogram.”
The versatile protein-guided next-generation Modular Integrase (MINT) platform is designed to enable large-scale genome editing. The platform works by first reprogramming the LSI Bxb1 to recognize a relevant target site, then it co-delivers the modified Bxb1 with a donor carrying the genetic payload and irreversibly swaps DNA strands between the genomic target site and a slightly different target site in a synthetic donor construct. [Sangamo]
The next-generation Modular Integrase (MINT) platform is a versatile protein-guided method designed to enable large-scale genome editing. The MINT platform works by first reprogramming the LSI Bxb1 to recognize a target site at the relevant genomic locus. Then, it co-delivers the modified Bxb1 with a donor carrying the genetic payload. The mechanism irreversibly swaps DNA strands between the genomic target site and a slightly different target site in a synthetic donor construct.
The enzyme is completely responsible for the integration (theoretically tens of kilobases), keeps very tight control of the reaction, and does not leave free DNA ends that can cause undesired events. LSI-only DNA recognition reduces the number of components that need to be delivered, simplifies the editing to a single step, and minimizes any potential risks associated with the installation of the wild-type Bxb1 target site currently required for existing LSI approaches.
“We are currently exploring opportunities for the MINT platform with our neurology programs,” Davis said. “We are collaborating externally on other therapeutic applications and there is strong interest for agricultural use and other applications.”
“Base editing provides a precise, predictable single base change outcome with a homogenous genotype at the end, within and across the cells,” said Amanda Haupt, business unit manager of base editing at Revvity. “Cells are generally healthier since they do not undergo a stressful DNA repair response. Less chance also exists for DNA and chromosomal aberrations and abnormal pathway behavior.”
Active areas of base-editing research include the types of base changes (currently A-to-G or C-to-T), genome targets and bystander editing, which becomes less relevant when making knock-out models. Shorter engineered deaminase wingspans can increase target specificity. Different designs or enzymes can already overcome many existing challenges, according to Haupt.
The Pin-point
base-editing platform is based on an aptamer-recruited arrangement. Other base editors tether together the DNA targeting element and the deaminase. The Pin-point platform is a three-part system that assembles at the DNA target site through interaction with the guide RNA scaffold. Advantages include high flexibility and customization to swap out nucleases and deaminases to increase specificity or to target different genomic regions.
Importantly, the platform can be leveraged to do different jobs at one time. “Because we use an aptamer, which is basically like a handle to recruit deaminases, we can use different handles for different deaminases to very specifically do different jobs at different places,” said Haupt. “We can also use guide RNAs that do not have a handle at all to open up the DNA for knock-in. With the appropriate guide RNAs we can do edits and knock-ins at the same time.”
The development of an allogeneic CAR T cell in a single step in which four proteins were knocked out and a CAR knocked-in with a single base-editing system demonstrated the possibilities.2
Base editing is an excellent tool for creating research models, including differentiated stem cells. Revvity provides licensable assets and support services for preclinical through clinical applications, including custom library and model development to inform drug discovery.
Inscripta’s mission to leverage the advances of CRISPR technology and implement whole-genome engineering has progressed to a focus on the development of molecules and ingredients beyond drug-based medicine. Previously, companies failed to deliver on this potential, creating skepticism about biotechnology in the larger commercial market.
“The best way to combat skepticism is with products. We leverage biology and data science for industrial applications to develop ingredients that replace a chemical or plant-extracted supply,” said Sri Kosaraju, CEO at Inscripta. “Our technology is unique because of its ability to explore the whole genome, at scale. Our products using scalable engineered strains fall under the umbrella of bioengineering and the bioeconomy.”
The first product, a well-aging cosmetic ingredient that is currently in biomanufacturing, demonstrates the feasibility of Inscripta’s approach. Several other bioengineered products are in the pipeline to offer more stable, consistent supply chains.
Incripta’s platform enables rapid exploration of changes to both understood and uncharacterized parts of the genome. The technology edits at scale – hundreds or thousands of edits at a time. Successful hits are combined, making it even more powerful.
The technology platform has three main components. Specific technologies include MADzyme
nucleases that can be licensed or used for academic research. The main component, called CRISPR-enabled trackable genome engineering, CREATE
, enables editing at scale and traceability due to a unique genetic barcode delivered with each edit.
To date, industrial applications of genome-editing technology have failed to show their potential. Inscripta’s approach uses evolved MADzyme nucleases to enable precise whole-genome
engineering with minimal disruption resulting in healthy, productive, and stable strains. [Inscripta]
GenoScaler
pulls together the process and creates the surrounding high-throughput workflow. “We use AI and ML to leverage the massive amount of data we generate. Success in the bioeconomy means costs must decrease through both efficient strain engineering and manufacturing for our commercial partners,” said Kosaraju. “We plan to be part of the next generation of companies that demonstrate the promise and the opportunity in the bioeconomy.”
Although the optimization and opening of fermentation capacity is a current issue, government grants are available to increase U.S. domestic manufacturing capacity, on-shoring supply chains to add capacity and domestic jobs.
References
The post Gene Editing Marches On Despite Missed Beats appeared first on GEN - Genetic Engineering and Biotechnology News.
New technology is naturally exciting at first, but the reality of commercialization soon hits. Demonstrating efficacy and safety takes time. Many gene-editing companies set very high expectations from the get-go, and, unfortunately, position themselves for potential failure if funds are needed midstream during a difficult financial environment.
To put this challenge in perspective, it is helpful to remember that antibody applications developed slowly, starting with reagents for research then moving to diagnostics before jumping into therapeutics. Today, based on the accumulated knowledge base, therapeutic monoclonal antibodies have grown even more complex and specific. The concepts were there decades ago but the market needed time to mature.
A cycle of high expectations, reality crashes, and resurgence is not atypical for novel therapeutic approaches, including the gene-editing field, which is widely acknowledged to hold tremendous promise. A recent example from late last April is the U.S. FDA approval of Prime Medicine’s IND application, which gives the company the go-ahead to test its first next-generation product candidate, PM359, in a Phase I/II clinical trial in pediatric and adult patients with chronic granulomatosis disease (CGD).
Also in 2024, a Nature Biomedical Engineering article detailed a novel gene-editing approach, PASSIGE (prime-editing-assisted site-specific integrase gene editing), which couples the programmability of prime editing with the ability of recombinases to precisely integrate large DNA cargoes exceeding 10 kilobases.1 It is said that “patience is a virtue,” and these and other successes support the belief that full promise of gene editing is coming to fruition, despite temporary setbacks.
Planning for success
“Base editing is very precise and versatile, but any editing technology alone is not sufficient for success,” emphasized Giuseppe (Pino) Ciaramella, PhD, president at Beam Therapeutics. “You need an end-to-end infrastructure for technology optimization, manufacture, and therapy delivery. Delivery is an enabler where it works well in the liver, but current methods do not go everywhere in the body.”
The company realized from its inception that delivery and manufacturing capabilities were strategic assets and invested in a manufacturing facility in North Carolina and lipid nanoparticle (LNP) technology. In 2022, it also cofounded and has since collaborated with Orbital Therapeutics to expand LNP development for delivery to other tissues.
“Our competitive advantage is our entire optimized drug discovery and delivery engine. We were fortunate that, in the beginning, we were operating in a constructive market environment,” Ciaramella pointed out. “In the current environment, a company would struggle to put all of those pieces together.”
The BEAM-302 base editor corrects the mutation in alpha-1 antitrypsin deficiency (AATD) carried by 95% of those afflicted. The A in the E324 mutation is changed to a G, resulting in a corrected SERPINA1 gene. [Beam Therapeutics]
Beam Therapeutics’ pipeline focuses on two franchises–hematology and liver genetic diseases. In hematology, the lead indication is sickle cell disease. The long-term, life-cycle plan starts with an ex vivo approach, BEAM-101, in which patients undergo a conditioning regimen, such as treatment with busulfan, the standard of care in hematopoietic stem cell (HSC) transplantation. However, busulfan’s associated toxicity limits treatment to the most severely affected population.
The next-generation BEAM-103/BEAM-104 enables a non-toxic conditioning strategy for ex vivo transplants–called ESCAPE–that uses base editing to make multiple edits simultaneously. An additional guide makes a single base change to a receptor that allows a proprietary antibody to target and kill only unedited cells, providing a survival advantage to edited cells. A survival advantage for edited cells may also prove valuable in enabling more efficient in vivo editing of stem cells in the bone marrow, potentially eliminating the need for transplant altogether.
The lead indication in liver genetic disease is alpha-1 antitrypsin deficiency (AATD). AATD affects 100,000 individuals in the U.S., where 95% carry the same mutation that causes the protein to misfold and accumulate to toxic levels in the liver. The mutation also prevents the protein from going to the lungs to provide protection from proteases. “With BEAM-302 we target the liver and restore the function of the gene so the protein can be secreted. Initial clinical trial results are encouraging,” said Ciaramella.
RNA single base changes
The Axiomer
Single base changes in RNA, in lieu of editing DNA, is an alternative approach to genome-editing therapeutics. “Thousands of G-to-A mutations in the human population cause disease,” said Gerard Platenburg, PhD, CSO, ProQR. The technology is also designed to change amino acids, which could modulate protein expression and activity or alter proteins to provide a new function.
The Axiomer platform has evolved over the last decade. The first generation included a hairpin structure designed to recruit endogenous ADAR for precise adenosine editing. To increase activity and stability, the second generation uses a much shorter oligonucleotide with no hairpin structure.
“Our versatile approach is capable of targeting a variety of RNA species, organs, and a wide range of diseases and offers a long-lasting therapeutic effect without the need for frequent dosing, while also avoiding the risks of permanent genetic changes or irreversible DNA damage,” Platenburg explained.
A trial will begin this year with AX-0810 that targets NTCP, the main transporter of bile acids into the liver. AX-0810 uses GalNAc for efficient delivery to the liver and aims to introduce a protective variant on a wild-type RNA to positively impact cholestatic diseases.
While the initial pipeline program is focused on a liver-originating disease, ProQR also has a partnership with Lilly that currently includes up to 10 targets, with an option for an additional five. In addition, work is progressing with CNS-targeted Axiomer-editing oligonucleotides. Research demonstrated that RNA editing can be successfully achieved in key regions of the nervous system, across species, with durable effects.
The CNS pipeline includes programs targeting Rett Syndrome, a devastating and progressive neurodevelopmental disorder caused by variants in the transcription factor in the MECP2 gene. “We believe Axiomer offers an elegant approach to restoring physiological MECP2 levels while avoiding the risk associated with MECP2 overexpression and are partnered with the Rett Syndrome Research Trust to advance our approach,” said Platenburg.
Bigger payloads
A common thread in genome-editing therapies has been a relatively simple, localized single alteration of genetic sequence. However, many diseases result from loss-of-function genetic variants that are often spread throughout the affected gene.
According to Gregory Davis, PhD, head of Research and Technology at Sangamo Therapeutics, more general strategies that aim to repair genes in a “one-shot-fits-all” approach would typically involve the targeted insertion of a wild-type version of the full gene cDNA, a “super-exon,” directly into an early exon or intron of the endogenous target gene.
Recombinases have long been used to insert genetic payloads into cells without relying on endogenous DNA repair machinery or creation of a double-strand break (DSB). Switching to non-reversible “programmable” integrases represents a major simplification and derisking of targeted gene insertion.
“To address targeted integration of large DNA constructs into desired genomic loci, we sought to use our core expertise in protein-DNA interactions to engineer the protein-DNA interface of large serine integrases (LSIs),” explained Davis. “We discovered a zinc finger-like helix within Bxb1 that we can reprogram.”
The versatile protein-guided next-generation Modular Integrase (MINT) platform is designed to enable large-scale genome editing. The platform works by first reprogramming the LSI Bxb1 to recognize a relevant target site, then it co-delivers the modified Bxb1 with a donor carrying the genetic payload and irreversibly swaps DNA strands between the genomic target site and a slightly different target site in a synthetic donor construct. [Sangamo]
The next-generation Modular Integrase (MINT) platform is a versatile protein-guided method designed to enable large-scale genome editing. The MINT platform works by first reprogramming the LSI Bxb1 to recognize a target site at the relevant genomic locus. Then, it co-delivers the modified Bxb1 with a donor carrying the genetic payload. The mechanism irreversibly swaps DNA strands between the genomic target site and a slightly different target site in a synthetic donor construct.
The enzyme is completely responsible for the integration (theoretically tens of kilobases), keeps very tight control of the reaction, and does not leave free DNA ends that can cause undesired events. LSI-only DNA recognition reduces the number of components that need to be delivered, simplifies the editing to a single step, and minimizes any potential risks associated with the installation of the wild-type Bxb1 target site currently required for existing LSI approaches.
“We are currently exploring opportunities for the MINT platform with our neurology programs,” Davis said. “We are collaborating externally on other therapeutic applications and there is strong interest for agricultural use and other applications.”
One system, multiple jobs
“Base editing provides a precise, predictable single base change outcome with a homogenous genotype at the end, within and across the cells,” said Amanda Haupt, business unit manager of base editing at Revvity. “Cells are generally healthier since they do not undergo a stressful DNA repair response. Less chance also exists for DNA and chromosomal aberrations and abnormal pathway behavior.”
Active areas of base-editing research include the types of base changes (currently A-to-G or C-to-T), genome targets and bystander editing, which becomes less relevant when making knock-out models. Shorter engineered deaminase wingspans can increase target specificity. Different designs or enzymes can already overcome many existing challenges, according to Haupt.
The Pin-point
Importantly, the platform can be leveraged to do different jobs at one time. “Because we use an aptamer, which is basically like a handle to recruit deaminases, we can use different handles for different deaminases to very specifically do different jobs at different places,” said Haupt. “We can also use guide RNAs that do not have a handle at all to open up the DNA for knock-in. With the appropriate guide RNAs we can do edits and knock-ins at the same time.”
The development of an allogeneic CAR T cell in a single step in which four proteins were knocked out and a CAR knocked-in with a single base-editing system demonstrated the possibilities.2
Base editing is an excellent tool for creating research models, including differentiated stem cells. Revvity provides licensable assets and support services for preclinical through clinical applications, including custom library and model development to inform drug discovery.
Building the Bioeconomy
Inscripta’s mission to leverage the advances of CRISPR technology and implement whole-genome engineering has progressed to a focus on the development of molecules and ingredients beyond drug-based medicine. Previously, companies failed to deliver on this potential, creating skepticism about biotechnology in the larger commercial market.
“The best way to combat skepticism is with products. We leverage biology and data science for industrial applications to develop ingredients that replace a chemical or plant-extracted supply,” said Sri Kosaraju, CEO at Inscripta. “Our technology is unique because of its ability to explore the whole genome, at scale. Our products using scalable engineered strains fall under the umbrella of bioengineering and the bioeconomy.”
The first product, a well-aging cosmetic ingredient that is currently in biomanufacturing, demonstrates the feasibility of Inscripta’s approach. Several other bioengineered products are in the pipeline to offer more stable, consistent supply chains.
Incripta’s platform enables rapid exploration of changes to both understood and uncharacterized parts of the genome. The technology edits at scale – hundreds or thousands of edits at a time. Successful hits are combined, making it even more powerful.
The technology platform has three main components. Specific technologies include MADzyme
To date, industrial applications of genome-editing technology have failed to show their potential. Inscripta’s approach uses evolved MADzyme nucleases to enable precise whole-genome
engineering with minimal disruption resulting in healthy, productive, and stable strains. [Inscripta]
GenoScaler
Although the optimization and opening of fermentation capacity is a current issue, government grants are available to increase U.S. domestic manufacturing capacity, on-shoring supply chains to add capacity and domestic jobs.
References
- Pandey, S. et al. Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing. Nat Biomed. Eng 9, 22–39 (2025). doi:10.1038/s41551-024-01227-1
- Porreca I. et al. An aptamer-mediated base editing platform for simultaneous knockin and multiple gene knockout for allogeneic CAR-T cells generation. Mol Ther. 2024 Aug 7;32(8):2692-2710. doi: 10.1016/j.ymthe.2024.06.033
The post Gene Editing Marches On Despite Missed Beats appeared first on GEN - Genetic Engineering and Biotechnology News.