Over the next year, a series of clinical milestones and regulatory decisions—what companies and investors like to call “inflection points”—will set for years to come the direction of what has been until now the fledgling biotech segment focused on genome editing.

Yet this week, investors received a reminder that in genome editing, inflection points don’t always lead to big stock gains: Beam Therapeutics (BEAM) shares skidded 12% in early trading, reaching a new 52-week low as it slid from $20.80 to $18.36, after the company announced a restructuring and reprioritization of its pipeline of base editing therapies that will include elimination of about 100 jobs—some 20% of its workforce.

Beam said it will prioritize development of its ex vivo and in vivo sickle cell disease programs—including BEAM-101, which applies the company’s Engineered Stem Cell Antibody Paired Evasion (ESCAPE) non-genotoxic conditioning strategy, and in vivo delivery to hematopoietic stem cells (HSCs).

Beam also said it will:

• Prioritize development of its in vivo base editor BEAM-302 for the treatment of alpha-1 antitrypsin deficiency (AATD).

• Conduct an initial clinical trial in the U.S. assessing BEAM-301 as a treatment for glycogen storage disease 1a (GSD1a).
• Seek partnerships for BEAM-201 and other potential ex vivo CAR-T programs, including ongoing research to create next-generation allogeneic cell therapies with multiplex base editing. For BEAM-201, Beam plans to generate a focused clinical dataset in T-cell acute lymphoblastic leukemia (T-ALL).
• Focus near-term spending on research and platform applications that apply Beam’s in vivo editing capabilities in the liver, targeting both rare genetic and common disorders, as well as select opportunities in hematology and immunology/oncology.
• Pause its hepatitis B virus program and seek for it a partner “given the requirement of specialized development and commercial capabilities.”

“From the beginning, Beam’s strategy has been to develop base editing technology broadly across a diverse portfolio of programs and delivery modalities, and our science and pipeline continue to progress across the board,” Beam CEO John Evans stated. “In this challenging market environment, however, we need to make the difficult decision to focus our resources on those clinical programs and research areas we believe have the highest potential for near-term value creation, while continuing to build a strong company for the future.”

Intellia Therapeutics (NTLA) shares fell about 3% on Wednesday from $29.05 to $27.96, and dipped another 3% on Thursday, to $27.10, despite the company sharing more positive news.

Intellia’s NTLA-2001 became the first first-ever investigational in vivo CRISPR-based gene editing therapy cleared to enter late-stage clinical development when the FDA cleared the company’s Investigational New Drug (IND) application for NTLA-2001 for the treatment of transthyretin (ATTR) amyloidosis with cardiomyopathy. The decision paves the way for a global Phase III study of NTLA-2001 that is expected to start by year-end 2023.

In a statement, Intellia president and CEO John Leonard, MD, said the company will share details about that pivotal trial on its third-quarter earnings call with analysts, set for November 9.

“Details on trial design at 3Q call Nov 9 should clarify next steps and further move the stock. We expect (+)ve [positive] readthrough to other editing cos [companies] too,” Jefferies equity analyst Maury Raycroft, PhD, wrote Wednesday in a research note. “The bar for FDA has been unclear, and NTLA now sets precedent for others to follow.”

He said Intellia had noted to him that while global trial start-up activities will start, “actual dosing may begin early ’24 depending on how fast things move.”

Raycroft added that he and other Intellia watchers will be seeking more specifics about the size and duration of the Phase III trial compared to the pivotal trials for other non genome-edited therapy developers of ATTR amyloidosis-caused cardiomyopathy treatments.

Pfizer (PFE) crossed the proverbial finish line first when it won FDA approval in 2019 for its wild-type or hereditary ATTR amyloidosis treatments, Vyndaqel^® (tafamidis meglumine) and Vyndamax^® (tafamidis). Each uses a different form of active ingredient tafamidis (micronized meglumine salt and free acid form, respectively), and each is taken a different dosage.

The Pfizer drugs are expected to be joined soon by treatments being developed by other companies—a group that includes Anlylam Pharmaceuticals (ALNY), BridgeBio Pharma (BBIO), and the tandem of Ionis Pharmaceuticals and AstraZeneca (IONS/AZN). Those treatments “pose substantial headwinds” to Intellia’s NTLA-2001, observed David Nierengarten, PhD, managing director and head of equity research focusing on biotech for Wedbush Securities, according to Investor’s Business Daily.

However, whatever headwinds Alnylam posed to Intellia have been significantly stilled.

As Raycroft commented, Alnylam saw a setback to development of patisiran for cardiomyopathy of ATTR amyloidosis on October 9 when the FDA refused to approve Alnylam’s supplemental NDA for the RNA interference (RNAi)-based therapy already marketed as Onpattro^® for polyneuropathy of hereditary ATTR amyloidosis in adults. Instead, the agency sent Alnylam a Complete Response Letter stating that data from the company’s Phase III APOLLO-B trial (NCT03997383) had not established the clinical meaningfulness of patisiran’s treatment effects in ATTR amyloidosis. Alnylam responded by saying it was no longer pursuing the additional indication in the U.S.

Earlier this year, BridgeBio and Ionis/AstraZeneca announced positive Phase III results for their ATTR amyloidosis candidates—acoramidis and eplontersen, respectively.

Intellia is among a half-dozen genome editing therapy developers with key clinical and regulatory inflection points to watch in coming months. Following is a roundup of those companies, their anticipated events, and recent actions by analysts covering the company:

Beam Therapeutics (BEAM)

Inflection Points: BEAM restructured operations and reprioritized its pipeline on Thursday (see above), listing first its ex vivo and in vivo sickle cell disease programs, which include BEAM-101—for which the company anticipates reporting initial data in 2024 on multiple patients from its Phase I/II BEACON trial (NCT05456880) assessing BEAM-101 in severe SCD.

In August, BEAM said it anticipated having enough currently consented patients to fill a three-patient sentinel cohort and launch an expansion cohort. Beam will continue adding additional patients to the BEACON trial through the end of year and beyond, until it reaches a total target of 45 treated patients. The trial has an estimated primary completion date of February 1, 2025.

Significance: BEAM-101 is an ex vivo therapy that produces base edits designed to potentially alleviate the effects of SCD by mimicking genetic variants seen in individuals who have hereditary persistence of fetal hemoglobin.

Other catalysts: BEAM is also prioritizing development of BEAM-302 in AATD, saying in August it expected to submit a regulatory filing in the first quarter of 2024 to begin a clinical trial. A similar filing is expected in the first half of 2024 for BEAM-301 in GSD1a, with BEAM saying Thursday that an initial clinical trial is still planned.

BEAM-301 is a liver-targeting lipid nanoparticle (LNP) formulation of base editing reagents designed to correct the R83C mutation—the most common mutation responsible for causing GSD1a. BEAM-302 is a liver-targeting LNP formulation of base editing reagents designed to correct the PiZ allele, the most common gene variant associated with severe AATD.

However, BEAM is seeking a partner for BEAM-201, for which it dosed the first patient with BEAM-201 in a Phase I/II trial (NCT05885464) assessing the CD7+ relapsed/refractory T-ALL/T-LL (T-cell lymphoblastic leukemia) in August. The trial has an estimated primary completion date of December 2031. BEAM-201 is, according to Beam, the first quadruplex-edited, allogeneic CAR-T cell therapy candidate in clinical-stage development, and the first treatment with a base editing candidate in the U.S.

Analyst action: Cantor Fitzgerald’s Rick Bienkowski on Tuesday lowered his firm’s 12-month price target on Beam shares 43%, from $56 to $32, but maintained its “Overweight” rating.

Caribou Biosciences (CRBU)

Inflection Point: CRBU expects to begin patient enrollment in the Phase I AMpLify trial by mid-2024. AMpLify is designed to assess the safety and tolerability of a single administration of CB-012 for relapsed or refractory acute myeloid leukemia (r/r AML) at dose level 1 (25×10⁶ CAR-T cells). The FDA has cleared Caribou’s IND for the trial, the company said Wednesday.

Caribou said it is beginning Part A of AMpLify, a 3+3 dose escalation design that will evaluate the safety and tolerability of CB-012 at ascending dose levels to determine the maximum tolerated dose and/or the recommended doses for expansion. Part B, the dose expansion portion, has as its primary objective determining antitumor response, assessed by overall response rate (ORR), after a single dose of CB-012. AMpLify will include patients who have not responded to or relapsed after standard treatment and will exclude patients who have been treated with more than three prior lines of therapy and patients with proliferative disease.

Significance: According to CRBU, CB-012 is the first allogeneic CAR-T cell therapy with both checkpoint disruption through a PD-1 knockout, and immune cloaking through a B2M knockout and B2M–HLA-E fusion transgene insertion.

Analyst action: Nothing since July 26, when HC Wainwright’s Robert Burns lowered his firm’s price target 8%, from $25 to $23, but maintained its “Buy” rating.

CRISPR Therapeutics (CRSP) and Vertex Pharmaceuticals (VRTX)

Inflection points: The FDA’s Cellular, Tissue, and Gene Therapies Advisory Committee will meet October 31 to recommend how the agency should act on exagamglogene autotemcel (exa-cel), the companies’ autologous, ex vivo CRISPR/Cas9 gene-edited for severe sickle cell disease (SCD) and transfusion-dependent beta thalassemia.

The FDA, which typically heeds the advice of its “adcomms,” has set for December 8 its Prescription Drug User Fee Act (PDUFA) target action date on the companies’ biologics license application (BLA) for exa-cel in SCD. In beta thalassemia, the agency has set a PDUFA date of March 30, 2024.

Significance: If approved, exa-cel would be the first CRISPR-Cas9 gene-edited therapy to win FDA approval.

Other catalysts: Cardiovascular candidate CTX310, which applies in vivo editing of the ANGPTL3 gene, is expected to enter the clinic by year’s end; Atherosclerotic cardiovascular disease candidate CTX320 is expected to begin clinical trials in the first half of 2024.

Analyst action: Cantor Fitzgerald’s Eric Schmidt on Tuesday downgraded CRSP shares from “Overweight” to “Neutral.” Mizuho’s Salim Syed, however, initiated coverage of CRSP on September 27 with a “Buy” rating.

Editas Medicine (EDIT)

Inflection Point: Editas’ EDIT-301, an ex vivo autologous CRISPR gene edited gene-edited CD34+ hematopoietic stem and progenitor cell therapy candidate, received the FDA’s Regenerative Medicine Advanced Therapy (RMAT) designation on Monday. EDIT-301 is on track to dose 20 total sickle cell disease (SCD) patients in the Phase I/II RUBY trial (NCT04853576), and deliver a clinical update on the study, by the end of this year, the company said in August.

In June, Editas presented positive initial clinical safety and efficacy data from the RUBY trial in an oral presentation at the European Hematology Association (EHA) Hybrid Congress in Frankfurt, Germany, and in a company-sponsored webinar.

Significance: In EDIT-301, patient-derived CD34⁺ hematopoietic stem and progenitor cells are edited at the gamma globin gene (HBG1 and HBG2) promoters, where naturally occurring fetal hemoglobin (HbF) inducing mutations reside, by a highly specific and efficient proprietary engineered AsCas12a nuclease. Red blood cells derived from EDIT-301 CD34⁺ cells have shown a sustained increase in fetal hemoglobin production, which according to Editas could provide a one-time, durable treatment benefit for people living with severe SCD and TDT.

The RUBY trial marked the first time that a novel type of CRISPR gene-editing technology—CRISPR/CA12—was used in a human clinical study to alter the defective gene, according to the scientists.

Other catalysts: SCD is one of two indications for which Editas is developing EDIT-301; the other is transfusion-dependent beta thalassemia (TDT), for which Editas also has a clinical update planned by year’s end, from the Phase I/II EDITHAL trial (NCT05444894). Editas presented positive initial clinical safety and efficacy data from the first EDITHAL patient in June, in a company-sponsored webinar.

Analyst action: J.P. Morgan’s Brian Cheng on Wednesday upgraded his firm’s rating on EDIT stock from “Underweight” to “Neutral,” and announced a price target of $8 a share. However, Cantor Fitsgerald’s Eric Schmidt downgraded EDIT on Tuesday from “Overweight” to “Neutral.” Last month, Stifel’s Dae Gon Ha upgraded the stock from “Hold” to “Buy” and nearly doubled his firm’s price target, from $9 to $17.

Intellia Therapeutics (NTLA)

Inflection Point: Intellia said Wednesday its NTLA-2001, being co-developed with Regeneron Pharmaceuticals (REGN), won FDA clearance of its IND application for a trial assessing the in vivo CRISPR-based therapy as a treatment of transthyretin (ATTR) amyloidosis with cardiomyopathy. The decision paves the way for a global Phase III study of NTLA-2001 that is expected to start by the end of this year. In a statement, Intellia President and CEO John Leonard, MD, said the company will share details about that pivotal trial on its third-quarter earnings call with analysts, set for November 9.

Significance: NTLA-2001 is the first first-ever investigational in vivo CRISPR-based gene editing therapy cleared to enter late-stage clinical development when the FDA cleared. If approved by the agency, it could potentially be the first single-dose treatment for ATTR amyloidosis, according to Intellia.

Other catalysts: NTLA-2002, an in vivo CRISPR-based treatment candidate for hereditary angioedema, earlier this month was granted the European Medicines Agency (EMA)’s Priority Medicine (PRIME) designation. NTLA-2002 is set to start a global pivotal Phase III trial as early as Q3 2024 “subject to regulatory feedback,” Intellia said in August, following release of positive Phase I data including extended data announced in June. According to Intellia, NTLA-2002 is the first single-dose investigational treatment being explored in clinical trials for the potential to continuously reduce kallikrein activity and prevent attacks in people with HAE.

Analyst action: Nothing since September 13, when Cantor Fitzgerald’s Rick Bienkowski maintained his firm’s “Overweight” rating and $65 a share price target on the stock.

Prime Medicine (PRME)

Inflection Point: PRME expects to submit an IND in 2024 for its first clinical candidate to the FDA, the company’s co-founder, prime editing and base editing pioneer David R. Liu told an investor conference earlier this month.

While the company has not identified that candidate, its pipeline shows only one of its 18 programs has reached the phase of IND-enabling studies—a blood-targeting candidate for chronic granulomatous disease (CGD), designed to be administered ex vivo. Additional IND filings are anticipated in 2025, Prime Medicine said in a company presentation to investors last month.

Significance: If Prime wins FDA clearance for its IND, it could be the first drug developer to bring a base edited therapy into the clinic. By contrast, base editing technology, first disclosed in 2016 by Liu’s lab—is under investigation in six ongoing clinical trial.

Other catalysts: Three other programs in Prime’s pipeline are in lead optimization phases—a Wilson’s disease candidate targeting liver tissue and using lipid nanoparticle (LNP) delivery; a retinitis pigmentosa/rhodopsin candidate targeting eye tissue and using adeno-associated virus (AAV) vector delivery; and a neuromuscular tissue targeting candidate for Friedreich’s ataxia also delivered via AAV. The rest of Prime Medicine’s programs are in preclinical discovery phases.

Analyst action: BMO Capital’s Kostas Biliouris initiated coverage of PRME on October 9 with an “Outperform” rating and a price target of $19 a share. A month earlier on September 6, JonesTrading’s Justin Walsh initiated coverage with a “Buy” rating and a price target of $20 a share.

Leaders & Laggards

• Aldeyra (ALDX) shares plunged 66% on Monday, from $5.43 to $1.83, after it disclosed that according to minutes of a late-cycle review meeting with the FDA, the company “needs to conduct an additional clinical trial to satisfy efficacy requirements for reproxalap as a treatment for signs and symptoms of dry eye disease. Aldeyra quoted from the minutes: “[i]t does not appear that you have data to support the clinical relevance of the ocular signs to support your dry eye indication.” As a result, Aldeyra acknowledged, “the FDA may not be in the position to approve the NDA [New Drug Application] for reproxalap on or about the Prescription Drug User Fee Act (PDUFA) target action date of November 23, 2023 or afterwards, and it may issue a Complete Response Letter.”
• Assembly Biosciences (ASMB) shares rocketed 71%, from 73 cents to $1.25, after the company announced a 12-year partnership with Gilead Sciences (GILD) to advance R&D of novel antiviral therapies, focusing initially on herpes, hepatitis B, and hepatitis D viruses. Gilead agreed to pay Assembly Bio an initial $100 million consisting of $84.8 millionupfront and a $15.2 million equity investment. Gilead also agreed to pay at least $45 million per program after clinical proof-of-concept is achieved to opt into exclusive rights for each of Assembly Bio’s current and future programs,. If Gilead opts-in to any program, it will pay Assembly Bio up to $330 million per program tied to achieving regulatory and commercial milestones, plus royalties. Assembly Bio is also be eligible to receive three separate $75 million collaboration extension payments toward funding future R&D. Gilead shares rose 2% from $79.20 to $80.48.
• Evelo Biosciences (EVLO) shares plummeted 59% on Tuesday, from $2.91 to $1.20, after the company acknowledged that it had begun exploring strategic alternatives after its moderate psoriasis candidate EDP2939 failed the Phase II EDP2939-101 trial. EDP2939 missed the study’s primary endpoint of achieving a statistically significant difference in the proportion of patients who achieved an outcome of a 50% improvement from baseline in Psoriasis Area and Severity Index (PASI) score (PASI-50) between EDP2939 and placebo after 16 weeks of daily treatment. Evelo added that EDP2939 went from being inferior to placebo at week 16 (19.6% vs 25%) to being superior at the week 20 follow-up visit (33.9% vs. 26.9%).
• Nkarta (NKTX) shares more than doubled, zooming 112% on Tuesday from $1.48 to $3.14, after the company said the FDA had cleared its IND application to evaluate NKX019, its allogeneic, CD19-directed CAR NK cell therapy for lupus nephritis (LN). The company plans to launch a multi-center, open label, dose escalation clinical trial designed to assess the safety and clinical activity of NKX019 in patients with refractory LN. The study is designed to enroll up to 12 patients, with the first patient expected to be enrolled in the first half of 2024. Nkarta also disclosed plans to eliminate 18 jobs—about 10% of its workforce—among cost containment measures designed to extend its projected cash runway by one year into 2026.

Alex Philippidis is Senior Business Editor of GEN.

The post StockWatch: For Genome Editing, Inflection Points Crowd the Calendar appeared first on GEN - Genetic Engineering and Biotechnology News.

Carlsbad, CA—Durhane Wong-Rieger, PhD, president and CEO of the Canadian Organization for Rare Diseases and chair of a global alliance for patient organizations called Rare Diseases International, recalled a recent conference where he found himself speaking between panels with a patient advocate from Zimbabwe.

The woman, whom Wong-Rieger regards as one of the smartest and most involved patient advocates he knows, told him she would not go to any more sessions on cell and gene therapy because she didn’t want to hear about therapies that she or her patients would never get.

Wong-Rieger immediately realized the truth in her statement: many people who are in dire health conditions have no access to what may be a life-saving treatment.

“We really don’t have any rules for [cell and gene therapies] as we’re all saying this is the most amazing breakthrough in terms of therapies—truly lifesaving therapies,” said Wong-Rieger. “But the problem is we can’t give them to everybody. Unfortunately for us in this whole space, how do we get to doing what is the right thing?”

While Wong-Rieger doesn’t have the answer, he thinks that evolving ethics are at the heart of what will allow the field of cell and gene therapy get there.

A North Star

Ethics often gets a bad rap for being prohibitive, but for J. Benjamin Hurlbut, PhD, associate professor, School of Life Sciences, Arizona State University, that’s just plain wrong. Hurlbut believes that ethics is primarily about innovation and limits themselves can be sources of creativity and innovation.

“This is a domain where lives are at stake, and it makes this industry a different kind of industry than other industries because the stakes associated with the work, how the work is done, what the work means, and the name of the public goods the work has undertaken have a greater significance than in the automobile and smartphone industries,” said Hurlbut.

Tim Hunt, JD, CEO of the Alliance for Regenerative Medicine (ARM), has been mulling over the ethics of cell and gene therapy for months because, ultimately, this is the business of permanently altering people’s DNA or irreversibly transplanting cells.

“For too many of our patients—millions of people around the world—the status quo represents death or serious disability,” said Hunt. “No one runs out and takes gene therapy, a gene editing regimen, or cell therapy because they feel great and healthy. Patients are in difficult shape.”

Rob Perez, operating partner at the global growth equity firm General Atlantic, feels similarly about ethics, which he defines as a set of moral principles that helps one navigate challenging problems and situations.

“If we can have more conversations and come to more alignment on what an ethical code or ethical standards could be for the industry, it can help to be a north star on how we want to operate and how we want to make those very difficult decisions,” said Perez. “That’s always been a really important part of how I can deal with the most challenging questions, the most challenging decisions, and the most challenging complexities in operating a business.”

Value and accessibility

While the goal of many cell and gene therapies is to cure diseases and completely return a patient to full health, an incremental change in the patient’s health, which also can greatly affect a whole family, is understated. Somebody having to walk or sit for the rest of their time can be incredible in terms of that benefit.

Tay Salimullah, vice president, Global Head of Value and Access, Novartis Gene Therapies, was part of the team that led the first FDA-approved cell therapy, Kymriah, and is currently on a team working on a treatment for spinal muscular atrophy. He says defining patient success happens before one even begins to define value and economics.

“You have to actually understand the journey—the days, weeks, months, years—it takes families to try and get care,” said Salimullah. “It’s like a diagnostic odyssey where they can’t even actually then find out who’s going to treat them in what center. And that’s before even getting to the transaction of buying a gene therapy!”

For Salimullah, it’s all about democratizing access to gene therapies. Salimullah thinks carefully about how polarizing cell and gene therapy can be, especially regarding pricing.

“How can you have a $2-million gene therapy and leave babies to die?” asked Salimullah.

He believes in a self-imposed responsibility that looks for ways to find new opportunities where patients worldwide get access not only in the United States but in Europe and other environments. Salimullah thinks that the theme of democratizing access is dependent on finding the right people who can reinvent a playbook. But who is going to set that up? Will anyone take responsibility and apply it globally?

Janet Lambert, former CEO of ARM and now a consultant at The Densmore Group, believes the global democratization of cell and gene therapies will rely on public-private partnerships. That is a steep hill to climb.

“We’ve had such trouble successfully commercializing advanced therapies, and it is my view that getting it right and getting the economic base that’s necessary from the U.S. and Europe for these therapies is going to be absolutely essential to succeeding in global reach,” she said. “And we have a lot of work left to do there.”

The failed system of responsibility                             

Hurlbut thinks that it’s important to address whether the way of doing innovation in health for the public good is suited to the kind of innovation that is happening in cell and gene therapy. If it isn’t going to serve people as well as it can, then it’s no good.

“All the different stakeholders engage with the sector to ask pretty hard questions about whether the way business as usual is playing out is the best way for that business to play out,” said Hurlbut. “And if things change, some businesses may get broken. But that’s the way things should go if the question is about the broader purpose of this domain, which is to heal people, to treat people.”

According to Hurlbut, an obvious issue to address is pricing, because the sticker shock is so profound that it’s easy for people to protest such steep prices and blast the entire industry of cell and gene therapy as useless.

As he is not a health economist, Hurlbut doesn’t claim to have the answer. However, he said if the regimen is unsustainable for the long run such that society cannot benefit from the good things that its investments have produced, then it’s a failure. Hurlbut said that thinking about these kinds of questions—such as whether cell and gene therapy is economically sustainable—has ethical stakes.

“Is the right way to ask questions about that life in terms of healthcare costs saved, future economic productivity, or to count the various beings and pile them up and say, look, there’s value here?” said Hurlbut. “Maybe that’s the way that one has to convince some set of actors, but maybe that’s the wrong way to ask questions about children’s lives.”

Hurlbut goes one step further, suggesting that, depending on a particular society or government, the decision on whether to get treated or not could be taken completely out of the hands of the patient at the earliest of life stages, even before birth, for all sorts of reasons like cost-savings—the more people who are “cured,” the less of an economic burden on that society. Hurlbut brings up a situation for which he has unique insight—that of He Jankui and the IVF embryos that he gene-edited—noting that one of the central arguments for this infamous experiment that was undertaken in China a few years ago is that it’s a lot easier and a lot cheaper to do it in one cell than to do it in many.

Hurlbut thinks that thinking through this ethical problem highlights that with the system that gets put in place—the drug makers, the regulators, the insurance companies, the health systems—no singular actor is responsible, but instead, it’s the collective actions of the community put in place—and that’s where things can go wrong because it results in failures of responsibility, compassion, and recognition of what is at stake.

After all, there is a dark side to gene therapy, and not every company working on cell or gene therapy is thinking about how their technology may contribute to applications that they would never endorse and, even, abhor, such as genetic cleansing.

Changing the path of humanity 

Even in a world where accessibility and economics for cell and gene therapies get worked out ethically, there’s another set of questions lying in wait that are top of mind for Lambert. For example, if a person chooses to get treated with gene therapy and it reaches the germline, genetic changes will be made in the patient and possibly in their children and generations to come.

Similarly, who is responsible for whether a child with a disease will get gene therapy? Does it fall into the hands of the parents?

“One of the most profound conversations I had in my time at ARM was with a mom who had signed her child up for a safety study,” said Lambert. “And even though this was a very well-educated mom, she felt profound guilt about having done that and that her child was, therefore, ineligible to get a therapeutic dose, which in that particular case turned out to be different than the safety trial dose.”

When it comes to gene editing, Lambert thinks that a major challenge in deciding what is a disease, what’s worth preventing, and what needs to be prevented.

At the end of the day, cell and gene therapy is not about eliminating or customizing people—it’s about treating patients.

The post Meeting on the Mesa: Without Ethics, Cell and Gene Therapy Will Fail appeared first on GEN - Genetic Engineering and Biotechnology News.

Carlsbad, CA—The timing of the Cell & Gene Meeting on the Mesa appears to have been prearranged with the help of a crystal ball. Members of the cell and gene therapy field are anxiously awaiting the FDA’s review of three submissions before the end of 2023: two treatments for sickle cell disease—exa-cel (Vertex and CRISPR Therapeutics) and lovo-cel (Bluebird)—as well as Bristol Myers Squibb and 2Seventy Bio’s Abecma for earlier multiple myeloma.

The sector is at an inflection point. There’s a lot of excellent science and exciting clinical results. Still, it remains to be seen whether that will translate into commercial success—a major focus of this week’s Alliance for Regenerative Medicine (ARM) conference. 

Regulatory approval

All eyes, therefore, are on Nicole Verdun, MD, the new permanent director of the FDA’s Office of Therapeutic Products (OTC), which is within the Center for Biologics Evaluation and Research (CBER). Verdun’s plate has a healthy serving of cell and gene therapy clinical trials for rare and serious diseases, which typically do not fit the testing paradigm of a randomized clinical trial. According to Verdun, who will be working hand in hand with CBER director Peter Marks, MD, PhD, the key to the approval of cell and gene therapies for conditions with just a handful of patients is a mix of communication and regulatory flexibility.

“We have INDs open for diseases where there are 11 patients in the United States,” said Verdun. “There needs to be increased communication earlier on in the development process, and there has to be consideration for the disease, the benefit-risk for how rare it is, and we have to do what we can to partner to get more of these therapies to patients that need them.”

To get right at this, Verdun highlighted the “Support for clinical Trials Advancing Rare disease Therapeutics” (START) Pilot Program. Three chosen START participants must be sponsors of cell and gene therapies for rare diseases and serious conditions currently in clinical trials under an active Investigational New Drug Application (IND). These participants will be able to receive regular advice and ad hoc communication with FDA staff to talk about product-specific development issues, such as clinical study design, choice of the control group, and fine-tuning the choice of the patient population. START will begin accepting applications between January 2 and March 1, 2024. 

Manufacturing and commercialization

 As more cell and gene therapies begin to move into the clinic, there is growing attention on manufacturing, which may be the major bottleneck for creating commercialized products.

Automation and artificial intelligence (AI) will be major disruptors to the manufacturing and commercializing cell and gene therapy. The efforts made by Cellares with its Cell Shuttle to integrate batch processing and automation into the assembly process serve as evidence of this. But automation and AI will not be enough.

According to Ann Lee, PhD, chief technical officer at Prime Medicine, there are three key factors to developing commercial-grade manufacturing. The first is picking the right people, because getting a cell and gene therapy program into the clinic requires a breadth of expertise that will likely not be found in a single individual. The second is data infrastructure, because to generate data that will be submitted for an IND or BLA submission, processes need to be in place where it is retrievable, tracked, and analyzed. Third, Lee said that regardless of going the internal or external route, the process needs to be transparent because no cell or gene therapy will be approved if the manufacturing process is a black box.

Some key factors go into choosing to partner with an external CDMO for manufacturing or bringing it in-house, often touted as the best way to control one’s destiny. While many have approached the manufacturing of cell and gene therapies with the view to putting all their manufacturing capabilities into the hands of partner CDMOs, some have decided to take this on to various degrees to gain increased control of their medicine’s destiny.

For cell therapies, some of this may come down to whether a company’s approach uses allogeneic or autologous cells. Sumit Verma, senior vice president of Global Strategic Manufacturing at Iovance Biotherapeutics, said that, while there is a lot of allogeneic work being done and CAR T having that success rate, autologous cell therapy has its place as a potentially unrivaled personalized medicine but is incredibly challenging from a logistics side. “For the patient’s benefit, being able to manufacture [an autologous cell therapy] batch is a key concept that I think you’re going to see a lot more maturity next year,” said Verma.

With two autologous cell therapy, using patient-specific tumor-infiltrating lymphocytes and peripheral blood lymphocytes (PBL), Iovance has taken an approach to investing in both their own manufacturing capabilities, as evidenced by their recent investment in establishing the Iovance Cell Therapy Center (iCTC)—a 136,000-square-foot facility in Philadelphia.

While Intellia Therapeutics will also be opening a new manufacturing facility in Waltham, Massachusetts, in 2024, chief business officer Derek Hicks said that in this market environment, he wouldn’t be surprised if there are more deals featuring a shared partnership between manufacturing and smaller biotechs.

“When you think about manufacturing, it’s not just that shared risk,” said Hicks. “It is how can you work with someone that actually helps you accelerate because we’re trying to get these products to patients. The research is moving very quickly, so how do you ensure that manufacturing doesn’t stop you from bringing things forward? These are the things that we all need to think about.”

Healthcare systems

Bob Smith, senior vice president of the Global Gene Therapy Business at Pfizer, said a lot of his concern for getting cell and gene therapies commercialized is related to the healthcare systems in the U.S. and abroad.

“A lot of healthcare systems have a negative innovation bias in the way that they evaluate and value the innovations that our sector is developing,” said Smith. “No individual company is going to be able to overcome this, and I think we need to think about how we communicate not just with the healthcare systems and how they evaluate not just the regulatory aspects, but now really the value of what we’re bringing to patients.”

For example, Smith points to some European markets where sometimes there isn’t a price approval for a year and a half after the regulatory approval.

“Think about the burden that is on small midsize companies that don’t have a balance sheet like [Pfizer does],” said Smith. “We can absorb that financial hit, but it’s going to put a tremendous financial strain on capital-intensive companies, and we need to really think through how we can change that paradigm to be much more efficient, principally for the benefit of patients but also, quite frankly, for the sustainability of the sector.”

Phil Cyr, senior vice president at Precision Value & Health, said that historically, a lot of payers and health technology organizations have been very focused on cost-effectiveness, but that they’ll also be looking at the budget impact and affordability, especially as cell and gene therapy begin to move into more prevalent diseases, which he believes will happen. Cyr thinks that the way to overcome this is by developing an evidence base to discourage people from thinking about sticker price and more towards long-term value.

“How do you go to a payer with a three to four-year window and make them understand that [gene therapy] will benefit them?” said Cyr. “I can think of one payer that actually built a model to figure out how long they needed to keep that member in their plan to recoup the money.”

For these reasons, organizations like Express Scripts and Cigna’s Embarc will play a key role in the future of gene therapies by helping protect customers from the high cost of gene therapy drugs and ensure access for those who need them.

 Expectations for 2024

Much is riding on the cell and gene therapy submissions that are due to be reviewed by the FDA before the end of this year. If they are successful, its possible that there will be a change in sentiment within the investor community—not to mention patients.

Next year, the Cell and Gene Therapy Meeting on the Mesa will move to Phoenix, Arizona, as the conference has maxed out its current capacity at the Park Hyatt Aviara Resort in northern San Diego. If the FDA approves these initial submissions, the new venue will likely be filled in 2024. But what if they’re not approved? All it takes is one bad batch that will reflect poorly on the entire industry.

As regulatory submissions and clinical data trickle in, there has to be a high standard. But standardization will not be achievable by a single business entity or the FDA alone. This new and evolving field will require organizations like ARM to unite different voices. That’s exactly what’s happening right now at the Cell and Gene Meeting on the Mesa.

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Carlsbad, CA—Across the board, biotech investing in 2023 has seen a retraction from the high levels seen the past three years: venture investment has dropped and companies large and small have lost value. However, that doesn’t mean that biotech investors have lost interest or abandoned ship. In fact, with the FDA reviewing submissions for three cell and gene therapies in Q4, investors are looking beyond the discovery and development phase and into the manufacturing and commercialization of these potentially revolutionary medicines—a theme that has taken hold at the 2023 Cell and Gene Meeting on the Mesa.

To get there, cell and gene therapy companies will have to do more than fly by on the seat of their pants, hoping to just live another day. Instead, there’s a sentiment amongst investors that now is the time to show a vision for the long run if biotech hopes to have financial support to carry them through until the headwinds die down and into the tailwinds for smooth sailing. 

Is this the new normal?

According to Dynamk Capital’s market analysis, the size and count of deals—mergers and acquisitions (M&A) and initial public offerings (IPOs)—have dropped from the 2020 to 2022 levels through the pandemic. But with three quarters complete in 2023, their analysis shows that the industry numbers are on par with 2018 and 2019 levels, perhaps even higher. Beyond some outliers such as Danaher’s acquisitions of Aldevron and Cytiva as well as the Thermo-PPD deal, Daniella Kranjac, founding partner and managing director at Dynamk Capital, said the trend for deals is pretty healthy.

While recent transactions aren’t pulling in deals of 20x revenue as seen during the pandemic, they’re also not at the 3–6x revenue multiples seen in 2018–2019. The industry is at the “new normal,” she said, which is in the 10–15x range.

Valerie Dixon, managing director at Morgan Stanley, says it is less a “new normal”, and more of a reversion to the historical mean. It is foolish to hope for the same “irrational exuberance” of the market to return to pandemic levels and that things won’t change back to how they were in 2020 and 2021, she said.

“They’re not going to be saved by a white knight and get 15x as much revenue for their company. That’s not happening!”

Kicking the can down the road

While some investors, board members, and founders have been trying to stay afloat in the turbulent economic climate, Dixon said the perception that they can just kick the can down the road and stretch their cash for another two to four quarters is irrational, even in the context of recent geopolitical events—Russia and Ukraine and now Israel and Palestine.

“You can’t manage your balance sheet anticipating World War III,” said Dixon. “You need to be managing your own business for a two to three-year timeframe, not for next quarter or making that month’s quota.” Instead, Dixon believes that managing a biotech business today requires creating long-term, enduring, profitable growth. That’s what funders think is most credible.

“When you can tell a story about how you’re investing for long-term growth, then [the investors] will be there for your expansion capital or your growth capital when you need it,” said Dixon. “If they take that long-term mindset with you, that means that you can have confidence that they’re going to have capital that’s going to grow with you along the way. It’s not growth at any cost; it’s making sure you’re doing responsible growth and you’re hitting… milestones that will get you to that next inflection point.”

While Sean Mackay, Operating Partner at Casdin Capital, is excited about the numerous companies with great products in great markets, he won’t invest in a company if they can’t support their own operating expenses. For Mackay, it comes down to the return on investment from capital.

Consistency is key, Mackay insisted. He wants to know that a prospect’s revenue isn’t random and that a particular move is devoted to a big market that the company is creating or disrupting, which is harder to do. A company’s capital-raising process has to increase the number of shots on goal and, thus, increase the probability of raising the money. To succeed, Mackay says companies need to be creative and expand their funnel instead of just hopping to the next shiny thing.

To IPO or not IPO

Although there have been signs of life for investing in healthcare and biotech—nine deals so far in 2023 (eight in biotech)—today, only three are trading around issue price. Some 2021 biotech IPOs, Dixon notes, are trading as low as 85% below the original issue price.

“Just because you’re going public doesn’t mean everything’s great,” said Dixon, who has led Morgan Stanley’s efforts in life sciences tools and diagnostics. “You still have to pay attention to aftermarket performance… and not just be the first one out of the gate. Be consistent in execution and a good steward of the capital that you raise. Maybe they [went] public too early, took their eye off the ball, or any number of factors—all those things play into the success of an IPO.”

Kranjac’s guidance to founders trying to get term sheets done in this market environment and the near future is to make sure they are thinking about who they bring to the table— board members and investors who understand the market and can be helpful in terms of forging additional relationships, whether for investments, operations, or talent.

There is no magic wand to secure a deal sheet for financing, but Kranjac shared the advice she can give the founder of an early-stage company: although they may have the luxury of being pre-revenue and not having reportables on a monthly or quarterly basis, they should be raising as much money as possible.

“In this environment, the guidance that we’re giving our portfolio companies, and even companies that we’re looking at going forward, is don’t wait,” said Kranjac. “There were a number of folks that early in the year said, ‘We’re going to wait until the fall when the market’s better or until [JP Morgan] 2024, when things are going to be great. Don’t wait!”

As to how to value a company, Mackay said that during the 2019 and 2022 period, research analysts might have understood the liquidation value for a sale. But when there’s no M&A activity, that number is more difficult to calculate. The huge push by big pharma to invest in new therapeutic modalities like cell and gene therapies is evidence, according to Mackay, that the industry’s “tailwinds” appear to be very strong.

Dead cells don’t cure cancer

A major early theme of the 2023 Meeting on the Mesa has been manufacturing and commercialization. Along these lines, while the panelists are all excited about the development of cell gene therapies and the enabling tools that go along with them, they’re keeping a close eye on companies involved in manufacturing and commercialization.

Kranjac agreed that bioproduction is exciting because there are going to be many such medicines. And those are exactly the types of companies, like RoosterBio, Curi Bio, and CellFE, that Dynamk has been adding to its portfolio.

“You can’t take your eyes off the ball on the manufacturing process and the tools that help with potency, stability, purity, and quality control—dead cells don’t cure cancer,” said Dixon. “When there are huge acquisitions with outsourced manufacturing and you start seeing the Thermo Fishers and Danahers making multi-billion-dollar acquisitions in the space to have capacity for cell gene therapies, that’s a wake-up call.”

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Now, for the first time, genome editing has generated chickens partially resistant to infection by influenza virus A. The findings, which indicate that multiple genetic modifications would be required to curtail viral escape, present a potential strategy to help mitigate the spread of avian influenza into farmed poultry from wild bird sources.

This work was published in Nature Communications in the paper, “Creating resistance to avian influenza infection through genome editing of the ANP32 gene family.”

Avian influenza is widely dispersed across Asia, Europe, Africa, and the Americas representing a threat to wild bird species, economic costs to farmers, and risk to human health. Poultry vaccination against avian influenza has not yet been reliable due to the rapid antigenic drift of field viruses and is controversial owing to political and economic implications. In chickens, avian influenza relies on the host protein ANP32A for its life cycle, which represents a potential target for creating virus-resistant birds.

Researchers edited the ANP32A gene in chicken germ cells to restrict influenza A activity. More specifically, the authors used CRISPR/Cas9 to generate homozygous gene-edited chickens containing two ANP32A amino acid substitutions that prevent viral polymerase interaction. They found that fully-grown chickens were resistant to a physiological dose of influenza A exposure from other infected birds and displayed increased resilience. After a challenge with influenza A virus, nine of the ten edited chickens remained uninfected.

However, when the researchers infected with a higher dose (1,000 times higher,) breakthrough infections occurred. The influenza virus, they found, had mutated to be able to use the edited chicken ANP32A. Unexpectedly, the authors wrote, “this virus also replicated in chicken embryos edited to remove the entire ANP32A gene and instead co-opted alternative ANP32 protein family members, chicken ANP32B and ANP32E.”

The birds showed no adverse health or egg-laying productivity effects when monitored for over two years. The authors suggest that additional editing and deletion of the other associated genes (ANP32B and ANP32E) in chicken cells would prevent virus replication.

The findings suggest gene editing as a possible route to create chickens resistant to infection by avian influenza. However, the authors caution that further study is needed to ensure animal health is not impacted and that multiple edits to the ANP32 family of genes might be required to eliminate the possibility of viral evolution.

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NEW YORK—David R. Liu, PhD, the genome editing pioneer whose Broad Institute lab developed both base editing and prime editing technologies over the past decade, told an audience of investors that prime editing is on track to join base editing in human clinical trials in less than a year.

“Likely the first clinical trial will be in 2024,” Liu said, speaking via video at the Chardan 7^th Annual Genetic Medicines Conference, held this week in New York City. “Prime editors, we anticipate, will be in the clinic next year.”

Liu is a co-founder of Prime Medicine, the publicly traded company formed to commercialize prime editing by developing treatments based on applying the technology’s “search and replace” approach to genome editing.

In releasing second-quarter results in August, Prime Medicine conveyed the possibility of a first trial for its gene editing technology next year by publicly including among its anticipated upcoming milestones: “Complete first IND filing as early as 2024.” Additional IND filings are anticipated in 2025, Prime Medicine said in a company presentation to investors last month.

By contrast, base editing technology, first disclosed in 2016 by Liu’s lab—is under investigation in six ongoing clinical trials.

Prime Medicine has not yet released which of its 18 pipeline programs will be selected as its first clinical-phase candidate.

IND-enabling candidate

According to Prime Medicine’s presentation last month, only one of its programs has reached the phase of IND-enabling studies—a blood-targeting candidate for chronic granulomatous disease (CGD), designed to be administered ex vivo.

Three other programs are in lead optimization phases—a Wilson’s disease candidate targeting liver tissue and using lipid nanoparticle (LNP) delivery; a retinitis pigmentosa/rhodopsin candidate targeting eye tissue and using adeno-associated virus (AAV) vector delivery; and a neuromuscular tissue targeting candidate for Friedreich’s ataxia also delivered via AAV.

The rest of Prime Medicine’s pipeline programs are in preclinical discovery phases.

During the conference, Liu noted that AAV has fallen out of favor with some gene therapy developers, concerned about harm to patients from needed redosing, as that will often induce high-titer neutralizing antibodies that make it difficult for a second AAV dose to be effective. That’s less likely to be a problem in genome editing, Liu asserted, as long as the editing therapy is effective enough to be a one-time treatment.

“If you look at some of the new generation AAVs that have liver detargeting, that go to previously challenging organs like the brain or muscle or lung, even in primates in some cases, I actually think those AAVs are going to be powerful tools for the delivery of these gene editing agents, especially because we anticipate that we will only need to deliver them once to effect a permanent benefit for the patient,” Liu said.

Both prime and base editing are designed to engineer precise base substitutions while avoiding double-stranded DNA breaks (as occurs in CRISPR-Cas9 gene editing). As a postdoctoral fellow in Liu’s lab, Alexis Komor, PhD, spearheaded the development of the first base editing technology, which could install specific base substitutions (C to T or G to A) without cleaving DNA. Eighteen months later, her colleague Nicole Gaudelli, PhD, developed a complementary adenine (A to G) base editor. Both base editing approaches were detailed in separate papers published in Nature.

In 2019, Liu, former postdoc Andrew Anzalone MD, PhD, and colleagues detailed prime editing in Nature. In prime editing, the desired edit is supplied in an extension to the guide RNA, which is then converted to DNA using the enzyme reverse transcriptase. The technology can introduce targeted insertions, deletions, and all 12 possible base-to-base conversions.

Generating positive results

In May, Liu and colleagues published in Nature Biotechnology a paper entitled “Efficient prime editing in mouse brain, liver and heart with dual AAVs”, in which they sought to address bottlenecks limiting AAV-mediated prime editing in vivo by developing AAV-PE vectors with increased PE expression, stability of prime editing guide RNA, and modulation of DNA repair.

The study detailed how two dual-AAV systems were developed—v1em and v3em PE-AAV. They generated positive results by enabling therapeutically relevant levels of prime editing in mouse brain (up to 42% efficiency in cortex), liver (up to 46%) and heart (up to 11%).

The group declared that the results represented “the first prime editing in postnatal brain and heart and substantially higher AAV-mediated in vivo prime editing efficiencies than have been previously reported in the liver.”

The dual-AAV systems were also used to install the rare Apolipoprotein E Christchurch (APOE3 R136S) variant in vivo for Alzheimer’s disease in astrocytes, and the dominant variant of proprotein convertase subtilisin/kexin type 9 (PCSK9) Q152H (mouse Pcsk9 Q155H), associated with a reduction in low-density lipoprotein (LDL) cholesterol levels and protection from coronary artery disease in hepatocytes.

“Our results advance the potential of prime editing for basic research and therapeutic applications and establish optimized PE-AAV systems as an effective in vivo PE delivery method,” Liu and colleagues concluded in the study.

Correcting CGD mutation

Also in May, Prime Medicine researchers presented updated preclinical data showing the potential of prime edited cells to correct the causative mutation of chronic granulomatous disease (CGD) at the American Society of Gene and Cell Therapy (ASGCT) 26^th Annual Meeting, held in Los Angeles.

In an abstract, “Prime Editing of Human CD34+ Long-Term Hematopoietic Stem Cells Precisely Corrects the Causative Mutation of p47phox Chronic Granulomatous Disease and Restores NADPH Oxidase Activity in Myeloid Progeny,” the researchers reported greater than 90% prime editing in CD34⁺ cells from four donors—a finding they said showed their technology to be highly reproducible.

“These data show that prime editing precisely corrects the ΔGT mutation at NCF1 in p47phox CGD patient CD34+ cells and restores NADPH oxidase activity and myeloid cell function in progeny of these PE-corrected cells, thus representing a potential curative approach for p47phox CGD patients,” the Prime Medicine researchers concluded.

Earlier data showed the ability of prime editing to correct a CGD causative mutation in CD34⁺ cells ex vivo, with the prime edited CD34⁺ cells engrafting long-term in vivo and editing levels greater than 92%.

During the ASGCT conference—which featured a presidential symposium keynote address by Liu—Prime Medicine highlighted its Prime Editing Assisted Site-Specific Integrase Gene Editing (PASSIGE) platform, showcasing its potential application to generate multiplex-edited chimeric antigen receptor (CAR)-T cells for the treatment of some cancers and immune diseases, without the use of viruses.

Liu co-founded Prime Medicine with Anzalone, currently the company’s head of the prime editing platform. Anzalone detailed his creation of prime editing and career in genome editing earlier this year in an exclusive interview on GEN Edge’s video interview series “Close to the Edge”, and published in our sister journal GEN Biotechnology.

Genome editing methods

Base and prime editing, Liu told conferees, were two of three different ways that have emerged for editing the genomes of human cells currently that meet the criteria of reasonably efficient and reasonably specific, used by hundreds of laboratories, and well-validated. The third, he said, was using CRISPR nucleases, which can result in gene disruption and creation of indels.

There are three base-editing candidates now in clinical trials:

• BEAM-101: Beam Therapeutics—co-founded by Liu with Feng Zhang, PhD, and Keith Joung, MD—is assessing BEAM-101, delivered via autologous bone marrow transplant, to treat severe sickle cell disease in adults in the Phase I/II BEACON trial (NCT05456880). Beam said in August it had enough consented patients to fill its sentinel cohort and begin an expansion cohort. Beam expects to report initial patient data from BEACON in 2024.
• BEAM-201: Beam last month dosed the first patient in a Phase I/II trial (NCT05885464) evaluating BEAM-201, a multiplex base-edited CAR-T cell therapy for the treatment of relapsed/refractory T-cell acute lymphoblastic leukemia and lymphoma (T-ALL/T-LL).
• VERVE-101: Verve Therapeutics is studying VERV-101—the first in vivo base editing therapy to reach the clinic—to treat heterozygous familial hypercholesterolemia (HeFH) in the Phase Ib heart-1 trial (NCT05398029), enrolling patients in New Zealand and the U.K. Verve expects to complete patient enrollment outside the U.S. after the FDA placed a hold on its IND application pending additional data.

The progression of base and prime editing from research papers to preclinical to clinical trials have both been swift, Liu observed. “These are breathtakingly fast transitions from academia to actual clinical applications,” Liu said, paying tribute to numerous laboratories advancing these technologies. “There are, for example, more than 1,000 research papers published on base editors and prime editors,” he said.

“Our lab has not published most of those,” Liu quipped, drawing laughs. “And it’s something that has really helped establish the robustness of the technology, de-risk it, improve it, and given us and the patient communities some confidence that it can be deployed in ways that are useful for helping patients.”

Alex Philippidis is Senior Business Editor of GEN.

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Through their newly reported studies, the team created a library of possible AsCas12f mutations and selected which to combine and engineer into activity-enhanced, enAsCas12f enzyme variants with 10 times more editing ability than the original unmutated enzyme. The engineered AsCas12f has been tested in mice and could potentially be used to develop more effective treatments for patients, the researchers suggested.

Study lead Osamu Nureki, PhD, at the University of Tokyo department of biological sciences, and colleagues across universities in Japan, reported on their development in Cell, in a paper titled “An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.” In their paper, the team concluded, “Taken together, enAsCas12f variants could offer a minimal genome-editing platform for in vivo gene therapy.”

The gene-editing tool CRISPR has given researchers the ability to replace and alter segments of DNA, and scientists are applying the technology in fields as diverse as malaria prevention and crop production. In more recent years human trials have started, that aim to use CRISPR-based technology to address genetic disorders.

Two widely used genome-editing tools in human cells are SCas9 and AsCas12a, but there are limitations, the authors noted. “… their relatively large size poses a limitation for delivery by cargo-size-limited adeno-associated virus vectors.” The common way to deliver genetic material into a host cell is to use a modified virus as a carrier. Adeno-associated viruses (AAVs) are not harmful to patients, can enter many different types of cells to introduce CRISPR enzymes like Cas9, and have a lower likelihood of provoking an undesired immune response compared to some other methods. However, like any parcel delivery service, there is a size limit. Its large size means that Cas9 can lack efficiency when used for gene therapy. “Cas9 is at the very limit of this size restriction, so there has been a demand for a smaller Cas protein that can be efficiently packaged into AAV and serve as a genome-editing tool,” said Nureki.

The multi-institutional team worked to develop a smaller Cas enzyme that would prove just as active, but more efficient than Cas9. They used as their starting point AsCas12f, from the bacteria Axidibacillus sulfuroxidans. The advantage of this enzyme is that it is one of the most compact Cas enzymes found to date (422 amino acids) and less than one-third the size of Cas9. In previous tests it had shown “low but detectable” genome-editing activity in human cells, the team noted. “Therefore, AsCas12f shows great promise as a miniature genome-editing tool that can be packaged into a single AAV vector.”

Nureki and colleagues combined structural analysis and deep mutational scanning (DMS) methods to identify potential modifications to the enzyme that would improve its effectiveness in human cells. “The DMS approach combines exhaustive protein mutagenesis and functional screening with deep sequencing, enabling the assessment of the effects of thousands of mutations in a single experiment,” the authors explained. “The synergistic effects of these mutations, coupled with guide RNA [gRNA] engineering, remarkably enhanced the genome-editing efficiency of AsCas12f in human cells to levels comparable with those of both SpCas9 and engineered Cas12a effectors.”

“Using a screening method called deep mutational scanning, we assembled a library of potential new candidates by substituting each amino acid residue of AsCas12f with all 20 types of amino acids on which all life is based,” Nureki continued. “From this, we identified over 200 mutations that enhanced genome-editing activity. Based on insights gained from the structural analysis of AsCas12f, we selected and combined these enhanced-activity amino acid mutations to create a modified AsCas12f. This engineered AsCas12f has more than 10 times the genome-editing activity compared to the usual AsCas12f type and is comparable to Cas9, while maintaining a much smaller size.”

The researchers commented in their paper, “The synergistic effects of these mutations, coupled with guide RNA engineering, remarkably enhanced the genome-editing efficiency of AsCas12f in human cells to levels comparable with those of both SpCas9 and engineered Cas12a effectors.”

The investigators carried out animal trials with the engineered AsCas12f system, partnering it with other genes and administering it to live mice. The encouraging results indicated that engineered AsCas12f has the potential to be used for human gene therapies, such as treating hemophilia.

The team discovered numerous potentially effective combinations for engineering an improved AsCas12f gene-editing system, and acknowledged the possibility that the selected mutations may not have been the most optimal of all the available mixes. As a next step, computational modeling or machine learning could be used to sift through the combinations and predict which might offer even better improvements.

And as the authors noted, by applying the same approach to other Cas enzymes, it may be possible to generate efficient genome-editing enzymes capable of targeting a wide range of genes. “The compact size of AsCas12f offers an attractive feature for AAV-deliverable gRNA and partner genes, such as base editors and epigenome modifiers. Therefore, our newly engineered AsCas12f systems could be a promising genome-editing platform … Moreover, with suitable adaptations to the evaluation system, this approach can be applied to enzymes beyond the scope of genome editing.”

Nureki concluded, “Elevating AsCas12f to exhibit genome-editing activity comparable to that of Cas9 is a significant achievement and serves as a substantial step in the development of new, more compact genome-editing tools. For us, the crucial aspect of gene therapy is its potential to genuinely help patients. Using the engineered AsCas12f we developed, our next challenge is to actually administer gene therapy to aid people suffering from genetic disorders.”

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Panelists:

Fyodor Urnov, PhD
Scientific Director
Innovative Genomics Institute

Tom Foti
VP & General Manager
Protein Business Unit
Aldevron

Tim Morris
Manager Upstream Development
Aldevron

Originally Aired: October 12, 2023
Time: 10:00 am PT, 1:00 pm ET, 19:00 CET

In this live webinar, one of the pioneers of human genome editing—Dr. Fyodor Urnov—will lay out the urgent challenge facing the clinical genome editing community in terms of expanding the public health impact of CRISPR-Cas. A formidable financial, logistical, and regulatory hurdle in all genetic therapies is attaining scalable clinic-grade manufacture of the experimental therapeutic. The current costs, timelines, and requirements in that space make the vast majority of genetic disease intractable in a practical sense.  

Dr. Urnov will discuss the unique nature of CRISPR-Cas as a platform technology that brings the promise of leveraging nonclinical and manufacturing information from one disease indication to another, potentially without repeating redundant, costly, and time-consuming nonclinical studies. The non-viral delivery of CRISPR-Cas, including as a Cas9 ribonucleoprotein (RNP), is a strong case study in this regard, where key aspects of the manufacturing framework could be leveraged between disease indications. Dr. Urnov will assess the latest progress in clinical genome editing and discuss how further progress could be enabled by creative academia-industry partnerships to develop and reduce to real-world-practice manufacturing innovation in the “CRISPR-Cas as a therapeutic platform” space. 

Following this live presentation, Dr. Urnov took audience questions moderated by Aldevron leaders Tom Foti and Tim Morris.

Produced with support from:

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Due to his preexisting peripheral vascular disease and complications with internal bleeding, UMMC and several other leading transplant hospitals determined that Faucette was not a good candidate for a conventional transplant with a human heart. Faucette’s heart failure had progressed to the point where death was imminent without the transplant.

On Friday, September 15, the U.S. Food and Drug Administration granted emergency approval for the surgery via its single-patient investigational new drug (IND) “compassionate use” pathway in the hope of saving the patient’s life. This procedure for approval is used when a patient has no other choice and only an experimental medical product—in this case, a genetically altered pig’s heart—to treat a serious or potentially fatal illness.

Beating immune rejection

According to organdonor.gov, there are currently about 110,000 people in the United States on the transplant waiting list, and more than 6,000 people die each year while still waiting. Xenotransplantation, in which organs are harvested from animals and then transplanted into humans, presents its own set of challenges but has the potential to save many lives. In addition to the potential for a xenotransplant to spread a disease from animal to human, there is also the risk that the recipient’s immune system will reject the foreign organ, which can be fatal to the patient. 

To prevent the rapid rejection of pig organs by humans due to antibody-mediated rejection, three genes were knocked out in the donor pig. To make the pig’s immune system accept the human heart, scientists inserted six human genes. The donor pig underwent 10 distinct gene edits, including the deletion of a gene that was thought to be responsible for the abnormal growth of heart tissue.

Immunosuppression after a transplant traditionally involves blocking signaling pathways by targeting the CD40 receptor. Studies have shown that blocking CD40L (CD154) stops the co-stimulatory signaling pathways for CD40 and CD11. This may make immunosuppressants more effective and safer by lowering the risk of side effects like lymphopenia, diabetes, high blood pressure, and others.

Faucette is being treated with standard anti-rejection medications and a novel antibody therapy called tegoprubart, developed by Eledon Pharmaceuticals (Nasdaq: ELDN). Tegoprubart is an anti-CD40 Ligand (CD40L) inhibitor still being studied. It stops rejection by blocking a key way immune cells rejecting something talk to each other. In animal models of xenograft rejection, tegoprubart has been shown to extend the time that xenograft organs continue to function significantly.

The lessons learned after the first operation

In January 2022, the pioneering transplant team, widely regarded as the best in cardiac xenotransplantation, performed the first-ever successful xenotransplantation on David Bennett. The UMMC research team spent five years honing the surgical technique on non-human primates before they performed the first surgery on Bennett in 2022. Over more than three decades of xenotransplant research, Muhammad M. Mohiuddin, MD, has published studies showing that a heart from a genetically modified pig can continue to beat when transplanted into the abdomen, even for three years.

Nearly two years have passed since Mr. Bennett received the first genetically modified cardiac xenotransplant, and in that time, faculty scientists at UMSOM have been studying his experience. The results of their initial study were published in the New England Journal of Medicine, and those of their subsequent, more in-depth investigation were published in The Lancet. They showed that the pig heart continued to work normally for weeks after being transplanted into the patient, with no evidence of acute rejection. It is likely that a combination of factors, including Mr. Bennett’s poor health that required him to spend six weeks on a heart-lung bypass machine before his transplant, led to his death from heart failure.

Muhammad M. Mohiuddin, MD, who serves as the program’s scientific director, and Bartley P. Griffith, MD, who surgically transplanted the pig heart into the first and second patients at UMMC, led the procedure. The xenotransplantation laboratory at UMSOM received the genetically modified pig from United Therapeutics Corporation via its Blacksburg, VA-based xenotransplantation subsidiary, Revivicor.

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When Gerardo Ramos, PhD, retired from his position as the Head of R&D at Syngenta and began an advisory role at Flagship Pioneering, he became very interested in one question inspired by the use of microbiomes in human health: what if the microbiome of insects could be modulated to affect their population dynamics, reducing their impact on crop yields and making agriculture more sustainable for the future?

“Our company tried to translate human therapeutic science into agriculture,” said Ramos, who is now Director and Chief Scientific Officer at Invaio Sciences. “There’s a lot of microbiome knowledge in [Flagship Pioneering] companies in the human segment, and we transported this into the insect world.”

Ramos and his colleagues explored several options, landing on what they thought was the lowest-hanging fruit: exploiting the microbiome to regulate insect populations. And just as in human health, they ran into the problem of delivery—how do you deliver biologically active compounds with target specificity?

“Most of the problems driving the negative impact of agriculture on the environment have to do with how things are delivered,” said Ramos. “If you spray an insecticide, 95% goes everywhere, and maybe 4-5% goes where it should go. For the insect microbiome, we looked for a mode of getting the biological active compounds into the gut of the insect without spraying.”

That’s what led to Invaio’s work on their microinjection technology, known as Trecise, to deliver biologically active substances to a tree’s vascular system, which would reach the insect’s gut upon feeding.

Saving Florida’s Oranges

Last month, on August 29, Invaio announced news of the first regulatory approval for commercial use of Trecise technology. Invaio’s technology will be used to deliver a biologically active compound for the suppression of citrus greening disease in Florida oranges. Citrus greening disease, also known as Huanglongbing, has wreaked havoc on the Florida citrus industry and resulted in significant yield and profit losses since 2006.

“We are deploying our mechanical precision delivery system to improve efficacy and reduce the volumes of pesticides used,” said Ramos. “To enter a market as a small company, we have chosen a problem that is unsolved, and one of the biggest agricultural problems at the moment is citrus greening. It destroyed the [citrus] industry in Florida and if we don’t control it, it will do the same in Brazil and [wherever citrus is produced].”

The culprit that spreads the disease is the Asian citrus psyllid, which introduces a slow-growing bacteria that grows in the tree’s vascular system and eventually kills the tree. Trecise injects ArborBiotic, which is Invaio’s version of a registered bactericide called oxytetracycline hydrochloride.

Ramos said that spraying oxytetracycline hydrochloride is not very efficient because it won’t get into the tree’s vascular system, where the disease spreads. But with Trecise, they can achieve excellent control of the bacteria and see an improvement in the trees’ health and the quality of the juice using less than 10% of the substance.

“That’s our first product on the market just after four years of company, which I think is a very good milestone,” said Ramos. “We have had a fantastic response from the farmers. Everybody wants the system, and we’ll be very happy to deliver it. But this is just the beginning.”

Biological Delivery Systems                        

The next logical step for the company’s R&D efforts was to move beyond mechanical precision delivery technology, which Ramos said is mostly suitable for big plants and trees. To do so, Ramos and his team exploited biological delivery systems from the Flagship ecosystem to create two different types of systems.

Exosomes served as inspiration for the first.

“A few years ago, it was discovered that plants also have exosomes, and when plants get attacked by external disease agents—fungal, bacterial, or insect—they produce defense peptides and proteins, which are encapsulated in exosomes,” said Ramos. “We isolated exosomes from plants and were trying to encapsulate biologically active compounds in these exosomes but we realized that this was not scalable.”

So, Ramos and his team moved to using natural oils, like soy- and sunflower-based oils, which are available on huge scales. Ramos said that with these nature-derived lipid nanoparticles, (NLPs), they can encapsulate small molecules as well as peptides and RNA, which opened up an entirely new molecular space to mine.

“There are not many peptides or proteins used in agriculture at the moment because you cannot deliver them—they’re not stable or amenable to the use of the spray,” said Ramos.

Building off the NLPs, Invaio developed another type of encapsulation, which they call microbially derived particles (MDPs). These are a bit larger than a nanoparticle. Scientists at Invaio use bacterial cells from GRAS microbes and turned them into programmable particles. Next, they modified these microbes to make them non-replicative and programmed them to produce biologically active compounds that MDPs encapsulate within the microbe for delivery.

“What we have is a system that is at both your production and delivery, and you can modify the surface of these MDPs to target them to particular plant tissues, stabilize them against the UV impact in the field, or make them more adherent to the surface where applied,” said Ramos.

This non-replicating microbe-derived delivery system works in the plant and pest microenvironments to improve crop system health. MDPs can be adapted to work with RNA, proteins, peptides, and any other programmable biological actives.

Ramos said that both the NLPs and MDPs can be targeted but use very different methods. MDPs work through molecular targeting, whereas NLPs can be targeted depending on the matrix composition to reach different plant tissues, such as the leaves or roots.

At the end of the day, what drives Ramos and the team at Invaio is the notion that the way agriculture is performed—the maintenance, harvesting, and processing of the crops—is not sustainable; it has a major impact on the environment, climate, and people’s health. Ramos believes that they will one day be able to manage agricultural systems in a way that’s better for society and the environment.

To make agriculture more sustainable in the future, Ramos says his team had to start small, which is why they chose to target a destructive disease that has no known solution. The existing strategy is to just kill the vector insect, which requires large amounts of insecticides and results in a detrimental impact on biodiversity and the environment. Ramos wants to position this solution so that the farmer can protect their existing trees as well as replant and reestablish groves in a way that the benefits grove economics, society and the environment — including improved carbon capture. This is just the very first step towards that vision.

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