Gene Therapy Briefs

The U.S. Food and Drug Administration (FDA) Endocrinologic and Metabolic Drugs Advisory Committee recommended approval of two drug candidates for homozygous familial hypercholesterolemia (HoFH), following review meetings on October 17 and 18. In so doing, the advisory panel accepted the lowering of low-density lipoprotein (LDL) as a suitable surrogate end point for drugs to combat the rare genetic form of high cholesterol, an orphan disease affecting several hundred U.S. patients—but also expressed the need for better surrogates for cardiovascular morbidity and mortality.

Although the FDA has been able to confirm cholesterol reduction for most mass-market drugs designed to reduce lipids, the agency has had the benefit of results of confirmatory trials that are not typically feasible to conduct for orphan drugs. Panel members discussed alternative measurements that could also show efficacy, such as coronary calcium.

By a 13-to-2 vote, the panel supported eventual FDA approval of lomitapide, concluding that developer Aegerion Pharmaceuticals (www.aegerion.com) provided sufficient efficacy and safety data to support marketing of the drug for HoFH when used as an adjunct to a low-fat diet and other lipid-lowering therapies.

The FDA has assigned a Prescription Drug User Fee Act (PDUFA) action date of December 29 for completion of its review of the New Drug Application (NDA) for lomitapide.

By a 9-to-6 vote, the panel recommended FDA approval of KYNAMRO (mipomersen sodium), concluding that Sanofi's Genzyme unit (www.genzyme.com) and Isis Pharmaceuticals (www.isispharm.com) provided sufficient safety and efficacy data to support marketing the drug to patients with HoFH who are at severe cardiovascular risk.

“There is still a great need for the HoFH patients, who have exhausted conventional medications and still have LDL cholesterol levels two to four times above normal,” David Meeker, Genzyme's president and CEO, said in a statement.

The FDA's PDUFA date for completing its NDA review of KYNAMRO is January 29, 2013. An application for marketing approval of the drug is pending in the European Union.

Sanofi's Genzyme unit (www.genzyme.com) will develop and commercialize in Japan and the Asia-Pacific market RNA interference (RNAi) therapeutics (Alnylam Pharmaceuticals, www.alnylam.com) that target transthyretin (TTR) for transthyretin-mediated amyloidosis (ATTR). Through its ALN-TTR program, Alnylam maintains rights to develop and commercialize medicine in the rest of the world, including the United States and Europe.

Under an exclusive alliance announced October 22, Genzyme will make an up-front cash payment of $22.5 million to Alnylam, and agreed to pay undisclosed development milestone payments and tiered royalties expected to yield an effective rate in the mid-teens to mid-twenties on Genzyme's sales of ALN-TTR products in their territory.

Alnylam's ALN-TTR program includes ALN-TTR02, now in a phase 2 clinical trial; and ALN-TTRsc, a subcutaneously administered RNAi therapeutic in late-stage preclinical development.

“As the lead program in our ‘Alnylam 5×15’ product strategy, we also view this program as a key part of building Alnylam for the future,” said John Maraganore, Ph.D., Alnylam's CEO, in a statement.

In July, Alnylam presented positive clinical results from its ALN-TTR02 phase 1 trial demonstrating up to 94% knockdown of serum TTR protein levels. Suppression of TTR, the disease-causing protein in ATTR, was found to be rapid, dose dependent, durable, and specific after just a single dose. The drug was found to be safe and well tolerated. Alnylam is now enrolling patients in a phase 2 multidose study of ALN-TTR02 in people with ATTR, and plans to launch a phase 3 pivotal study of ALN-TTR02 by the end of 2013.

BioTime (www.biotimeinc.com) signed a nonbinding letter of intent to acquire the stem cell therapy assets of Geron (www.geron.com), which last year said it would leave the field and focus instead on its cancer drug candidate imetelstat.

According to a Geron statement November 15, Geron will give its intellectual property and other assets related to its human embryonic stem cell (hESC) programs to BioTime Acquisition Corporation (BAC), a recently formed, wholly owned subsidiary of BioTime. In return, BioTime will give BAC $5 million in cash, $30 million in BioTime common shares, warrants to purchase 8 million shares of BioTime at a prespecified price, rights to use certain hESC lines, and minority stakes in two of BioTime's subsidiaries.

Geron stockholders would receive shares representing 21.4% of BAC's common stock, plus warrants to purchase 8 million shares of BioTime common stock at a prespecified price. BioTime would own the remaining 71.6% of the subsidiary, with an undisclosed private investor owning about 7% of the outstanding BAC common stock.

BioTime would also receive warrants that would enable it to increase its ownership in BAC by about 2%, which would dilute the Geron stockholders' ownership in BAC to 19.2%. BAC would also be committed to pay to Geron royalties on the sale of products that are commercialized in reliance on Geron patents acquired by BAC.

In a separate statement, BioTime announced it had entered into a separate nonbinding letter of intent with the undisclosed investor for $10 million in financing for the acquisition of Geron assets. That includes $5 million cash to BAC for the 7% stake in the subsidiary, plus warrants to buy about another 350,000 additional shares of BAC common stock at $5 per share, with a 3-year term.

Also, the unnamed investor will invest $5 million in BioTime by purchasing 1.35 million BioTime common shares at about $3.70 per share, and warrants to purchase 650,000 more BioTime common shares at $5 per share and a 3-year term.

The nonbinding agreement and financing letter were announced almost a month after BioTime addressed Geron shareholders in an open letter, proposing to form a new publicly traded company that would own all of Geron's stem cell assets and some of BioTime's. According to the proposal, Geron could own up to 45% of the company, which would also hold $40 million in shares of BioTime as well as shares of some BioTime subsidiaries focused on stem cells. Geron shareholders would also receive about $13 million in BioTime stock purchase warrants.

The letter was signed by BioTime CEO Michael D. West, Ph.D., and Thomas Okarma, Ph.D., CEO of BioTime Acquisition Corporation, a recently formed, wholly owned subsidiary of BioTime. Significantly, both are former Geron executives: Dr. Okarma was Geron's CEO from 1999 until 2011, when he stepped down amid speculation that he and his board differed on how the company should move forward. Dr. West was Geron's founder and first CEO from 1990 to 1992.

The offer attracted interest from a Geron investor: Jonathan C. Woolf, managing director of British & American Investment Trust PLC, told shareholders in a letter that Geron should work with BioTime to combine assets.

ENCODE, the Encyclopedia of DNA Elements, has assigned some sort of function to four-fifths of the genome, including more than 70,000 “promoter” regions where proteins bind to control gene expression, and nearly 400,000 “enhancer” regions that regulate expression of distant genes.

The work represents some of the key findings of a 5-year international study of the regulation and organization of the human genome by ENCODE, formed to catalogue the “functional” DNA sequences that lurk between the genes, learn when and in which cells these sequences are active, and trace their effects on how the genome is packaged, regulated, and read.

Although the human genome consists of about 3 billion DNA base pairs, only a small percentage of DNA actually encodes proteins. For years, scientists have sought to learn the roles and functions of the remaining genetic information, sometimes referred to as “junk DNA.”

According to ENCODE, however, more than 80% of the human genome is associated with biological function. Proteins switch genes on and off regularly, and can do so at distances far from the genes they regulate. The consortium also determined sites on chromosomes that interact, the locations where chemical modifications to DNA can influence gene expression, and how the functional forms of RNA can regulate the expression of genetic information.

A subset of ENCODE, called the GENCODE Consortium, was established to accurately map and annotate the complex system of genes and regulatory regions—much of it transcribed into RNA—across the human genome, both manually and through computational methods.

The ENCODE consortium encompassed more than 440 scientists in 32 laboratories in the United States, the United Kingdom, Spain, Singapore, and Japan, performing more than 1600 sets of experiments on 147 types of tissue. The results were published in one main integrative paper and five other papers in the journal Nature, 18 papers in Genome Research, and six papers in Genome Biology.

In one Genome Research paper, Derrien and colleagues (2012) analyzed GENCODE data on more than 9500 long noncoding RNA (lncRNAs), of which only about 100 have been characterized with cellular function until now. According to that paper, approximately one-third of lncRNAs have arisen in the primate lineage, suggesting that there may be important lncRNA functions yet to be discovered.

Researchers at Spain's Center for Genomic Regulation (CRG; www.crg.es) designed specific zinc finger proteins (ZFPs) that recognize and specifically bind to more than 35 repetitions of the nucleotides CAG—the DNA sequence whose overrepetition in the gene encoding the mutant protein “Huntingtin” is the cause of Huntington's disease.

By binding, the ZFPs are acting to reduce expression of the gene containing these repeats, which would prevent the development of Huntington's disease, as well as reduce the production of the Huntingtin protein.

“When applying this treatment to a transgenic mouse model carrying the human mutant Huntingtin gene, we observed a delayed onset of the symptoms,” Mireia Garriga-Canut, first author of the study and researcher at the CRG's Gene Network Engineering group, said in a statement.

The research was published in the journal Proceedings of the National Academy of Sciences (Garriga-Canut et al., 2012).

“The next step is to optimize the design for an effective and durable treatment for patients. This would pave the way to find a therapy for Huntington's disease,” said one of Garriga-Canut's colleagues on the study, Carmen Agustín Pavón, Ph.D., now a postdoctoral student in the laboratory of Angela Roberts, at the University of Cambridge.

The study was funded by the European Commission's FP7 program as well as Spain's Ministry of Science and Innovation.

Lonza (www.lonza.com) will manufacture Celladon's enzyme replacement therapy MYDICAR (AAV1/SERCA2a) to a cGMP grade for future clinical trials, under a process transfer and GMP manufacturing agreement. MYDICAR is the subject of a 200-patient phase 2b clinical trial initiated in August in NYHA class III/IV heart failure patients.

MYDICAR, the lead product of Celladon (www.celladon.net), targets the key enzyme deficiency in advanced heart failure by restoring levels of the SERCA2a gene, which regulates calcium cycling and contractility in heart muscle cells. With MYDICAR, the SERCA2a gene is delivered using recombinant adeno-associated virus (AAV) as the vector, while MYDICAR is delivered in a single dose directly to the heart during routine outpatient cardiac catheterization procedures, similar to angiograms.

“We will be producing materials for Celladon beginning at the 1000-liter scale and likely expanding to 2000 liters, which our recently completed and validated GMP suite was specifically designed to support,” David Enloe, Lonza's head of virus-based therapeutics, said in a statement.

The companies agreed to negotiate a supply agreement if Celladon intends to start commercial scale manufacture of MYDICAR.

MYDICAR's molecular target is an enzyme found in the sarcoplasmic reticulum (SR) critical to the contraction of the cardiac muscle cell. The SR is a cellular organelle that regulates the contraction and relaxation of cardiac muscle cells by coordinating the contraction and relaxation of calcium ions (Ca²⁺). The heart muscle's ability to contract is determined by a continual reloading of the SR with Ca²⁺ to “stage” for the next cycle of contraction. SERCA2a is the key factor that enables the reloading of the SR with Ca²⁺.