Tag Archives: immune-system

The Needle Issue #7

10 Jun
Juan-Carlos-Lopez
Juan Carlos Lopez
Andy-Marshall
Andy Marshall

Ex vivo HSC lentiviral gene therapies have been on the market for nearly a decade, with six products approved and at least 55 now in clinical testing for rare inherited diseases, HIV infection or cancer. And yet, their commercial success remains in question. Bluebird Bio—which was valued at $10 billion only a few years ago and successfully shepherded to market Zynteglo against transfusion-dependent β-thalassemia, Skysona for early cerebral adrenoleukodystrophy, and Lyfgenia for sickle-cell disease (SCD)—was sold earlier this year to private-equity firms Carlyle and SK Capital for a measly $29 million. Last November, the company had treated only 57 patients (35 for Zynteglo; 17 for Lyfgenia and 5 for Skysona), with just 28 of 70 medical centers across the US ready to treat patients due to delays in accreditation and training of personnel. In Europe, Orchard Therapeutics halted marketing and production of a treatment for severe combined immunodeficiency caused by adenosine deaminase mutations (Strimvelis) after six years, forcing Fondazione Telethon to take over production. Even market uptake of Vertex’s much-heralded CRISPR/Cas9 BCL11a SCD therapy Casgevy has been sluggish.

These subpar commercial launches relate to the complexity of ex vivo lentiviral gene therapy: patient identification and qualification is lengthy; HSC mobilization and sourcing efficiencies vary due to patient heterogeneity; and manufacture and distribution processes remain lengthy and convoluted (sometimes requiring repetition if a poor quality product batch is generated). From first evaluation, patients are required to make several hospital visits over a period (of up to a year) and must undergo punishing conditioning regimes with lymphodepletive bisulfan before infusion, which itself carries infertility and cancer risks. All of these challenges have added impetus to the search for alternative and more efficient approaches for carrying out HSC gene therapy.

A group led by Alessio Cantore and Luigi Naldini, from the San Raffaele Telethon Institute for Gene Therapy in Milan, Italy, report in Nature that it may be possible to obviate these challenges by delivering recombinant lentiviral vectors in vivo soon after birth, when HSCs continue to circulate in the bloodstream in large numbers and are beginning their transition from the liver (where they are located in the fetus) to bone marrow (where they remain through adulthood).

Cantore, Naldini and their colleagues started by measuring the number of circulating HSCs in neonatal, 1-, 2- and 8-week-old mice, looking at the peripheral blood, spleen, liver and bone marrow. They found that HSCs were present in the circulation right after birth and that their number immediately declined. These cells could be transduced with lentiviruses, successfully engrafted, and persisted in the mice for several months.

To show that these HSCs could be harnessed to treat genetic disorders, the team tried to correct three mouse models of disease — adenosine deaminase deficiency, autosomal recessive osteopetrosis and Fanconi anemia. Although the therapeutic effect of the cells varied depending on the disease, the results provided compelling evidence for the potential for in vivo gene transfer to HSCs.

The authors reported that human neonates also have circulating HSCs in high numbers. And although the therapeutic window in the mouse only existed during the neonatal period, it was possible to lengthen it by mobilizing the HSCs from their niche in two-week-old animals using protocols in clinical use (granulocyte-colony stimulating factor/CXCR4 antagonist Plerixafor) These observations raise the possibility of therapeutically targeting HSCs in newborns, potentially opening the gates to treatment of a variety of inherited conditions.

Compared with the headaches of ex vivo manipulation, the authors’ concept of simply injecting a lentiviral gene therapy into a newborn to bring about a genetic cure is certainly alluring. But reducing this to clinical practice will require optimization of many different factors. How to account for the heterogeneity and fragility of patient HSCs in a particular disease? How to measure the cellular activation/metabolic state of HSCs in newborns and assess the affect on amenability to lentiviral transduction in the hostile milieu of blood? What effect would shear stress in circulation have on lentiviral transduction efficiencies in situ? What would be the selective engraftment advantage provided to HSCs after engraftment of a particular gene? And what would be the potential safety implications of off-target transduction events in cells other than HSCs, given instances of dysplastic syndromes have been reported with ex vivo lentivectors?

Current ex vivo lentiviral gene therapy like Lyfgenia and Zynteglo infuse between 3–5×106 gene-modified CD34+ HSCs/kg in a patient. The challenge for in vivo lentiviral gene therapy will be to achieve transduction efficiencies that transduce as many cells and obtain similar engraftment rates in the rapidly turning over HSC population. Beyond these issues, there are additional practical challenges: can genetic testing of an infant happen fast enough to take advantage of the short therapeutic window for which an in vivo lentiviral HSC therapy could work?

Clearly, the new work raises many intriguing questions for the lentiviral gene therapy space. And for newborns with genetic diseases, such as severe immunodeficiencies or Fanconi anemia, in vivo HSC gene therapy may open up new treatment options.

The Needle Issue #5

28 May
Juan-Carlos-Lopez
Juan Carlos Lopez
Andy-Marshall
Andy Marshall

Last week’s ASGCT 2025 provided a stark contrast between excitement around DNA- and RNA-editing platforms and commercial interest in traditional gene replacement and cell therapy. Over the past few months, Pfizer decided to stop the commercialization of its hemophilia B gene therapy Beqvez, lentiviral gene therapy flagship Bluebird Bio agreed to acquisition by private-equity firms Carlyle and SK Capital Partners, and earlier this month, Vertex announced its was discontinuing its gene-therapy programs.The remarkable clinical progress achieved with base editing modalities over the past year was highlighted in an ASGCT keynote by Kiran Musunuru of the University of Pennsylvania on the ultra-rare condition carbamoyl-phosphate synthetase 1 (CPS1) deficiency. The fact that the UPenn group were able to design, preclinically validate and bring the treatment to a child in just 7 months is staggering:

Source: New England Journal of Medicine

Writing in the New England Journal of Medicine, the team led by Musunuru and Rebecca Ahrens-Nicklas describe the development of a personalized base-editing therapy with guide RNAs designed to remove the UGA stop codon in a neonate diagnosed with a Q335X variant of CPS1. Using an adenine base-editor, the team designed a bespoke, corrective therapy delivered in vivo using lipid nanoparticles (LNPs) comprising an ionizable amino lipid (ALC-0307), cholesterol, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and a PEG lipid (ALC-0159).

After preclinical validation in cell lines, mice and non-human primates, the authors administered two intravenous doses of the base editor, dubbed ‘k-abe’ — 0.1 mg/kg at seven months of age and 0.3 mg/kg one month later. Following treatment, the patient tolerated increased dietary protein and showed a reduced need for ammonia-scavenging medication, with no serious adverse events. Long-term clinical outcomes and safety remain under evaluation.

One of the most striking features of the study is the speed of therapy development—from diagnosis to treatment in a mere seven months, during which the team had to create cell and mouse models of the disease, screen various base editors with guide RNAs covering the site of the mutation to identify the most efficient approach, carry out toxicological assays in non-human primates, and obtain FDA regulatory approval to treat the child. The workflow reported represents a blueprint for rapid development of customized gene-editing therapies for patients with ultra-rare variants and provides one of the first glimpses of a coming era in advanced therapeutics.

The FDA has taken a very progressive attitude regarding N-of-1 therapies that involve platform technologies such as base editing. An accompanying Editorial in the NEJM, authored by Peter Marks, former Director of the FDA’s Center for Biologics Evaluation and Research, elaborates on the need for a regulatory approach that takes advantage of the data from the elements that remain consistent from one therapeutic product to the next, while allowing the customization required for individual patients — in the case of base editors, a short sequence of guide RNA.

Of course, despite the openness of regulatory authorities, several hurdles remain before bespoke DNA and RNA editing therapies becomes a reality. Among them, manufacturing, scalability and distribution are particularly problematic, and represent the biggest challenges for big pharma to address before widespread adoption of such approaches. Also, existing lipid nanoparticles preferentially travel to the liver. Targeting other organs remains a huge challenge for the field so ultrarare liver disease will remain the option in reach for base editing in the near term. But despite these concerns, we think that the report by Musunuru and his colleagues is a milestone in the development of genetic medicines and underscores the potential of gene-editing approaches to deliver bespoke cures for ultra-rare diseases.

The Needle Issue #4

20 May
Juan-Carlos-Lopez
Juan Carlos Lopez
Andy-Marshall
Andy Marshall

Lipid nanoparticles (LNPs), like those used in the FDA-approved siRNA drug Onpattro, remain the delivery vehicle of choice for mRNAs, gene-editing and base-editing therapies. One drawback of intravenously administered LNPs is adsorption of apolipoprotein E triggers rapid liver uptake via low-density lipoprotein (LDL) and other receptors on hepatocytes. This results in a relatively short half-life and limit application of LNPs in other organs. Peter Cullis, from the University of British Columbia, and his team report in Nature Communications a new LNP design that promises to enhance their lifetime in the blood.

In previous work, the team had established that LNPs consisting of an oil droplet of ionizable lipid like MC3, surrounded by a monolayer of bilayer-forming lipids like egg sphingomyelin and cholesterol, further surrounded by a proper lipid bilayer lasted longer in the circulation. In their new study, they systematically modified the ratio of bilayer lipid to ionizable lipid (RB/I) and found that LNPs with RB/I=4 showed liposomal morphology, high mRNA encapsulation efficiency, and excellent transfection properties in vitro and in vivo. Moreover, these LNPs with high proportions of bilayer forming lipids lasted longer in the circulation and showed higher transfection efficacy in lymph nodes and pancreas than Onpattro-like LNPs.

Cullis and his colleagues propose that the prolonged blood circulation lifetime is attributed to reduced plasma protein adsorption. The transfection competency of liposomal LNP systems is attributed to export of the solid core containing mRNA from the LNP as the endosomal pH is lowered. Their transfection potency, in turn, appears to depend on the cytoplasmic release of complexes that include mRNA and ionizable lipid, complexes that are generated as the endosome matures and its pH decreases. This work represents a promising strategy to increase the therapeutic index of drugs delivered by LNPs.

The new LNPs are being developed by Nanovation Therapeutics, a preclinical startup co-founded by Cullis in 2021. In September, Nanovation clinched a $600 million deal with Novo Nordisk to license worldwide rights to its long-circulating LNPs for extra hepatic delivery of two base-editing therapies for rare genetic diseases, and up to five additional targets in cardiometabolic and rare diseases. Cullis is a serial entrepreneur who has founded several companies around lipid-based delivery systems for nucleic acid-based drugs, including Inex Therapeutics/Protiva Biotherapeutics/Tekmira/Arbutus Pharma and subsequently Acuitas Therapeutics, which developed the MC3 LNP for Onpattro in collaboration with Alnylam Pharmaceuticals. The group also collaborated with Drew Weissman of the University of Pennsylvania on LNPs for mRNA vaccines, which lead to their use in mRNA COVID-19 vaccines.

To be a broad platform for the liver and beyond, LNPs must compete with several other delivery modalities, such as viral vectors and conjugates. In liver delivery, triantennary GalNAc-conjugated siRNAs, which target asialoglycoprotein receptors on hepatocytes, are now the delivery vehicle of choice for liver-targeted siRNAs. Apart from circulation lifetime, another issue that LNPs must contend with is organ accessibility due to fenestrations in blood vessels. In the case of the liver, pancreas, and bone marrow, pores are greater than 60 nm, allowing LNPs access to tissue. For mRNA vaccines, blood filtering lymph nodes also represent an excellent LNP target. However, tissues, such as brain (with its accompanying blood brain barrier), muscle and kidney have much tighter fenestrations (<15 nm), presenting an uphill delivery challenge for intravenous LNPs.

The Needle Issue #3

13 May
Juan-Carlos-Lopez
Juan Carlos Lopez
Andy-Marshall
Andy Marshall

A growing stable of biopharma companies are developing biparatopic antibodies, which hit the same target via two non-overlapping epitopes. Compared with monospecific mAbs, such antibodies display enhanced binding through increased avidity, slower target dissociation, improved internalization, and greater specificity against drug target families where members share significant structural similarity. Now in the Journal of Clinical Investigation, a group at the Broad led by William Sellers describes biparatopic mAbs that inhibit fibroblast growth factor receptor 2 fusions, which are found in a variety of cancers, including intrahepatic cholangiocarcinomas (ICCs).

Sellers and his team showed that their mAbs inhibit signaling through FGFR2 fusions and inhibit ICC proliferation. They generated a panel of 15 biparatopic antibodies from 6 parental human antibodies and systematically tested them for their anti-proliferative activity on cells expressing FGFR2 fusions. Two showed greater potency than the parental antibodies, both in vitro and in vivo. Moreover, these biparatopic antibodies potentiated the action of FGFR2 inhibitors on cancer cells, and their inhibitory effect persisted, even against FGFR2 fusions with mutations that drive drug resistance. Mechanistically, the biparatopic antibodies promoted internalization and lysosomal degradation of FGFR2 fusions.

Sellers is also a scientific founder of Cambridge, Mass-based RedRidge Bio, which was funded in March via an undisclosed Series A venture round. Another recent startup, Attovia, took its first VHH biparatopic nanobody program against IL-31 into the clinic earlier this year and is collaborating with SciNeuro Pharmaceuticals on a neurology target.

The FGFR2 fusion work follows in the footsteps of studies by Regeneron demonstrating that biparatopic antibodies are effective inhibitors of oncogenic fusions of other receptor tyrosine kinases (RTKs). In that work, Regeneron researchers targeted fusions of another FGFR family member, FGFR3. In theory, the approach should be generalizable to any cancer arising from RTK fusions.

Biparatopic antibodies can work either in cis (binding the same target twice) or trans (binding two different molecules of the same target; e.g., to facilitate receptor clustering). Although they have been in clinical testing since 2011, it took until 2022 for the first biparatopic product to reach the market. Nanjing, China-based Legend Biotech (now J&J) got FDA approval for a T-cell therapy against refractory multiple myeloma featuring a chimeric antigen receptor (CAR) based on two single-domain antibodies targeting two different epitopes on B-cell maturation antigen (BCMA). Last November, FDA also gave the green light to Jazz Pharmaceuticals and Zymeworks’s zanidatamab, a biparatopic mAb that binds HER2 in trans and is indicated for patients with HER2-positive biliary tract cancer.

Similar to the antibody drug conjugate (ADC) space, a commercial stampede is currently underway in China to develop biparatopic mAbs against HER2, with at least 4 companies (Xuanzhu Biopharm, Alphamab Oncology, Chia Tai Tianqing Pharmaceutical and Beijing Mabworks) with products in clinical development. Given that big pharma has yet to make major announcements around biparatopic mAbs—notwithstanding AstraZeneca’s/Medimmune’s discontinued effort to develop MEDI4276, an anti HER2 ADC based on a biparatopic scaffold— the recent co-development partnership deal between Pierre Fabre Laboratorie and RedRidge Bio likely augurs more deal activity around this antibody modality in the near future.