Allele Publication Explains cGMP Generation of Induced Pluripotent Stem Cells

The discovery that adult somatic cells can be reprogrammed to pluripotent stem cells has given the biomedical community a powerful platform for personalized medicine. However, the translation of cell therapies from bench to bedside holds a significant challenge. Realizing the clinical potential for stem cells requires their production under current Good Manufacturing Practice (cGMP) regulations enforced by the FDA. A new protocol ( published by scientists at Allele and detailed in this quarter’s issue of Current Protocols in Stem Cell Biology, reveals key conditions required for converting adult fibroblasts to induced pluripotent stem cells (iPSCs) under cGMP regulations.1

The patent-pending protocol is an update to a previous protocol that describes how to reprogram fibroblasts to iPSCs using mRNA. “The system of using mRNA to reprogram fibroblasts presents itself as a very favorable candidate for generating iPSCs for cell therapy” according to the senior author of the paper and CEO of Allele, Dr. Jiwu Wang, “our company is committed to developing stem cell based therapies using this protocol and through the establishment of our own stem cell GMP facilities here in California”. mRNA transfection is “footprint free”, meaning no insertions or alterations have been made to the genome. Transfection of mRNA is also “cleanup free,” because mRNA transcripts are supplied to the cells in the culture medium only for the time required to induce pluripotency. Furthermore, genomic analyses of iPSCs reprogrammed using mRNA indicate that this method of conversion is unlikely to introduce problematic mutations.2

The new version of the protocol describes reprogramming technology that utilizes all cGMP-certified reagents and vessels, meaning that every material is manufactured under guidelines that allow for ancillary use in manufacturing processes related to cell therapy. All materials described in the protocol – from cell medium and components to the coating for tissue culture plates – were meticulously evaluated at every step of generating and storing iPSCs. For truly cGMP produced cell lines, all processes should take place in certified cleanrooms with qualified equipment and thoroughly trained operators.

Establishing a cGMP process for any product intended for human use is a daunting undertaking. Unlike drugs and small-molecule pharmaceuticals, stem cells are living entities whose production cannot be chemically synthesized. Therefore, special considerations must be made – particularly for making individual cell lines – to help assure the highest safety and quality of downstream stem cell products. Adhering to cGMP regulations infuses high quality into the design and manufacturing process at every step. Through rigorous testing, researchers at Allele have identified critical parameters for generating iPSCs from fibroblasts that are cGMP-compliant, and are optimistic that the methods described in this recent publication will serve as a launch pad for the development of future cell products and therapies.


  1. Ni Y, Zhao Y, Warren L, Higginbotham J, Wang J. cGMP Generation of Human Induced Pluripotent Stem Cells with Messenger RNA. Current Protocols in Stem Cell Biology,2016; 39:4A.6.1-4A.6.25.
  2. Bhutani K, Nazor KL, Williams R, et al. Whole-genome mutational burden analysis of three pluripotency induction methods. Nature communications. 2016;7:10536.


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Thursday, November 10th, 2016 cGMP, iPSCs and other stem cells No Comments

The NIH Awards Allele with Grant for the Development of a New Antibody Therapy for Treating Alzheimer’s Disease


The National Institute on Aging of the NIH has awarded a grant to Allele Biotechnology and Pharmaceuticals (“Allele”) to develop a new antibody therapy for treating Alzheimer’s disease. Alzheimer’s disease is the most common cause of dementia, but there are currently no treatments to stop or reverse its progression.

Alongside academic collaborators, scientists at Allele have revealed a strong correlation between a previously uncharacterized target gene and Alzheimer’s disease. They discovered that expression of the gene reduces beta-amyloid production and tau phosphorylation, two components of plaque formation in Alzheimer’s disease. Furthermore, high levels of this protein in the brain can counteract loss of synapses and cognitive impairments in mice.

Allele will generate a panel of antibodies that recognize this protein with the goal of employing one of these antibodies as a therapeutic drug candidate. The antibodies’ unique size and shape allow them to pass the blood-brain barrier to reach crucial regions of the brain, and each antibody can be easily modified and engineered to heighten its therapeutic potential. Researchers at Allele hope that an antibody treatment will improve the function of its target protein in the brains of Alzheimer’s patients and ultimately reduce pathogenesis of the disease.

Recombinant antibodies represent one of the most important classes of biological therapeutics: 80% of the best selling drugs on the market are antibodies; immune checkpoint therapies and CAR-T cell therapies rely on antibodies. Continuously seeking unique antibodies against high value targets is a key focus of Allele, along with its induced pluripotent stem cell (iPSC) programs and iPSC-based drug screening projects. With the support of the new NIH grant, Allele will not only move closer to finding antibody drug candidates in fighting one of the most devastating diseases, but also generate long-needed research tools for other scientists to further study Alzheimer’s disease. For example, fusion of these antibodies to fluorescent proteins such as mNeonGreen can be used to image Alzheimer’s disease-related factors in cultured neurons, astrocytes, oligodendrocytes, or “minibrain”-like organoids derived from human iPSCs.

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Allele Receives NIH Award to Fund the Development of Large-Scale Stem Cell Production


The NIH’s National Heart, Lung, and Blood Institute has awarded Allele Biotechnology and Pharmaceuticals (“Allele”) a Phase 1 SBIR grant to develop a novel manufacturing system to produce stem cell-derived human tissue and cells for clinical therapy. By increasing the scale of production and reducing the cost of manufacturing, Allele is confident that this system will overcome a considerable roadblock for clinical applications of stem cells, which is to produce a sufficient amount of therapeutic material at a manageable cost.

At the core of translating this potentially game-changing technology into medically-beneficial applications is the use of induced pluripotent stem cells (iPSCs), which hold unprecedented promise of providing any type of immune-matched cells of unlimited quantity. Allele has already developed a patented method of reprogramming somatic cells into iPSCs, secured industrial licensees using this technology, and initiated cGMP procedures for clinical applications.

Further moving iPSCs into commercially viable clinical cell therapies still requires overcoming one major barrier: the prohibitive cost of manufacturing iPSC-derived cells, mostly due to the need of expensive clinical-grade growth factors and cytokines. For example, the estimated cost of the growth factors and cytokines needed to produce a typical transfusion of platelets is $87,252.

Ultimately, Allele’s goal is to create clinical-grade iPSCs and control their differentiation into specific cell types at a scale large enough to satisfy the clinical demand. “We have been diligently working on removing the use of protein factors through our own proprietary protocols to generate many clinically-relevant cell types, including beta cells, mesenchymal stem cells, neural progenitor cells, oligodendrocytes, liver, and heart cells,” said Dr. Jiwu Wang, Allele’s CEO and the Principle Investigator of the new NIH grant. “By developing a recombinant protein-independent, real-time adjusted culture system under this project, we are confident that—as many groundbreaking technologies such as genome sequencing have done—the manufacturing process will mature and the costs will come down to eventually benefit everybody.”

Allele’s plan gained trust from the NIH scientific review panel, which gave it a near-perfect score. With this funding, Allele’s researchers will move even faster towards the goal of bringing iPSC products to clinical applications. Successful efforts will also likely provide a vehicle for genome-editing technologies such as CRISPR to be delivered into patients.

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Stem Cell Therapies: What’s Approved, What Isn’t, and Why Not?

With acceptance of stem cell therapies growing, so have controversies surrounding regulations.

Desperate to heal sports injuries, top professional athletes have been known to pay tens of thousands of dollars for experimental stem cell treatments that many used to find controversial. But now, stem cell therapies have become more mainstream and are no longer limited to professional athletes. Stem cell clinics offer both medical and non-medical treatments with claims of improving aesthetics and quality of life.

One recent study found over 400 websites – with the largest portion in the United States – advertising stem cell-based therapies (1); another found over 570 U.S. clinics offering stem cell interventions (2), giving more evidence that the market for stem cell therapies in the U.S. is growing at an accelerated rate. Yet these therapies are too often based on unfounded claims and lack proper clinical trials or authorized regulation. Despite what some clinics claim, very few stem cell treatments are currently available that are actually approved by the Food and Drug Administration (FDA). Hematopoietic stem cells harvested from bone marrow are routinely used in transplant procedures to treat patients with cancer or other blood or immune system disorders. Banking of umbilical cord blood is FDA-regulated and its use is approved for certain indications. Otherwise, consumers should be wary of claims by stem cell clinics implying FDA-approval.

So why aren’t more FDA-approved stem cell therapies available?

The FDA has strict regulations on using stem cell products in humans. In most cases, stem cell-based products are categorized the same way as pharmaceutical drugs. Therefore, each new therapy must go through a rigorous process including pre-clinical animal trials, phased clinical studies, and pre-market review by the FDA prior to offering the treatment in the clinic.

And with stringent regulatory requirements comes prohibitive costs. Research animals, Phase I-III clinical trials, and the regulatory demands for good manufacturing practice (GMP) labs result in an extraordinarily costly process that may hinder the progress of new therapies. The cost of developing a new drug has even been estimated to reach billions of dollars.

Nevertheless, a complete lack of regulation of stem cell therapies – as is seen in many of the stem cell clinics springing up worldwide – is clearly problematic. Alarmingly, many clinics advertise claims related to medical diseases for which there is no scientific consensus that supports their safety or efficacy. Premature commercialization of unproven therapies not only puts patients at risk, but also jeopardizes the credibility of still-developing stem cell products.

One of the most exciting outlooks for stem cell therapy is the prospect of using one’s own stem cells for personalized medicine. Should the development of an autologous stem cell product really be regulated the same way as a pharmaceutical drug, which is aimed at treating huge populations of people? If not, how should stem cell products be regulated?

In an effort to make the transition of novel stem cell products to the clinic more seamless, some countries have made significant changes in regulations. For instance, in 2014, Japan broke out a separate regulatory system for stem cell products that softened legislation dramatically to require only limited safety and efficacy data. Some argue that countries with softer regulations and less stringent safety and efficacy milestones, such as Japan, have poised themselves to become the likely pioneers in the field of regenerative medicine.

Regulatory frameworks for the clinical application of stem cell products are still evolving in most countries, including the U.S. In March, the Reliable and Effective Growth for Regenerative health Options that improve Wellness (REGROW) Act was introduced to congress. This change in legislation would remove some of the regulatory hurdles that hinder the progress of biologic therapies.

Regardless, the FDA needs to establish a more reasonable regulatory system that can evaluate the safety and efficacy of stem cell products in a more efficient manner.

1.  Berger, I., et al., Global Distribution of Businesses Marketing Stem Cell-Based Interventions. Cell Stem Cell, 2016. 19(2): p. 158-62.
2.  Turner, L. and P. Knoepfler, Selling Stem Cells in the USA: Assessing the Direct-to-Consumer Industry. Cell Stem Cell, 2016. 19(2): p. 154-7.


CRISPR: Growing in Popularity, But Problems Remain

The CRISPR gene-editing technology is taking the scientific world by storm, but researchers are still uncovering the platform’s potential and pitfalls.

The “Democratization” of Gene Editing
The idea of modifying human genomes using homology directed repair (HDR) has been around for decades. HDR is a widely-used repair mechanism to fix double-strand breaks in the cell’s DNA. By supplying an exogenous, homologous piece of DNA to the cell and increasing the probability of HDR occurring, changes in the DNA sequence can be introduced to the targeted area.

Some of the first gene editing platforms taking advantage of HDR used engineered endonucleases such as zinc finger nucleases (ZFNs) and transcription activator like effector nucleases (TALENs). Both ZFNs and TALENs required a custom protein to target a specific DNA sequence, making them pricey and very difficult to engineer. The more recently developed CRISPR/Cas9 platform works differently: instead of using a protein, the Cas enzyme uses a small guide RNA to locate the targeted DNA, which is then cut. CRISPR is more low tech and “user-friendly” than other platforms, as users are no longer required to do the onerous chore of protein engineering. Now, the ability to modify genomes can be done without extensive training or expensive equipment. CRISPR can be used for knocking out genes, creating reporter or selection genes, or modifying disease-specific mutations—by practically anyone with basic knowledge of molecular biology.

The CRISPR Revolution
Because of its relative simplicity and accessibility, it is no wonder that life scientists from all over the world are eager to incorporate CRISPR into their research. One of the most remarkable things about CRISPR technology is how quickly its popularity has allowed the platform to evolve. The discovery revealing that CRISPR can be used for RNA-programmable genome editing was first published in 2012 (1). Since then, about 2,000 manuscripts have been published including this technology and millions of dollars have been invested into CRISPR-related research and start-up companies. Scientists have developed a myriad of applications for CRISPR, which can be used in practically any organism under the sun. The popularity and progress of gene editing promises revolutionary advancements in virtually every scientific field: from eradicating disease-carrying mosquitoes to creating hypoallergenic eggs and even curing genetic diseases in humans.

There is no doubt that CRISPR has enormous potential – the widespread interest and rapid progress are evidence of that. The main reason CRISPR has been so widely adapted is because development and customization is way less labor-intensive and time-consuming than previous methods. But material preparation is a miniscule part of the CRISPR platform. Contrary to popular belief, just because CRISPR is easier to use than other methods of gene editing, it is not “easy.”

Hitting the Bull’s-Eye
To understand the limitations of this gene editing technology, it’s important to understand more about how CRISPR works. The CRISPR/Cas9 system functions by inducing double-strand breaks at a specific target and allowing the host DNA repair system to fix the site of interest. Cells have two major repair pathways to fix these types of breaks, Non-Homologous End Joining (NHEJ) and homology directed repair (HDR). NHEJ is faster and more active than HDR and does not require a repair template, so NHEJ is the principle means by which CRISPR/Cas9-induced breaks are repaired. If the editing goal is to induce insertions or deletions through NHEJ to cut out a part of a gene, then using the CRISPR platform is less complicated. But directing CRISPR to correct a gene with exogenous DNA does not work very well, as the rate of HDR occurring at the site of interest is often very low, sometimes less than 1%. For precise genome-editing through CRISPR, it is essential to have HDR while minimizing damaging NHEJ events.

Increasing the rate of HDR is not trivial. Recent research has shown that the conditions for the two repair pathways vary based on the cell type, location of the gene, and the nuclease used (2). Besides, optimizing CRISPR to better control HDR versus NHEJ events is only half the battle. One of the greatest challenges in using CRISPR is to be able to quickly and accurately detect different genome-editing events. Many scientists measure changes by sequencing. A more sophisticated method is to use droplet digital PCR (ddPCR) (3), but many labs have limited accessibility to ddPCR systems. After screening multiple clones and detecting the desired genetic edit comes what is usually the most laborious and time-consuming step: pure clonal isolation. Because each individual cell is affected by CRISPR independently, isogenic cell lines must be established.

Improving CRISPR
CRISPR has become the gold standard for many scientists now that the potential to perform gene editing has become so universal. Top journals expect isogenic lines for characterizing genes and mutations, and many researchers feel pressured to include such experiments to stay competitive in grant proposals. Moreover, a federal biosafety committee has recently approved the first study in patients using this genome-editing technology. To keep up with the pace of this rapidly moving field, significant improvements in CRISPR technology need to be made.

First, a better grasp of the basic principles behind CRISPR is likely to lead to improvements in targeting and efficiency. For example, understanding how the cell type, locus, and genomic landscape affect the targeting and cutting of Cas9 could lead to higher efficiencies of HDR. Similarly, engineering Cas9 and the guide RNA to maximize on-target activity could also accelerate the technology’s success. Screening the ability of the guide RNA to target the intended sequence can be performed in vitro by assessing the Cas9-mediated cuts on a PCR-amplified fragment of DNA; this method often gives a good indication of what to expect in cells. Another hindrance to CRISPR technology is that currently, all methods to detect genome changes require destruction of the cells of interest. Development of an assay to detect chromosomal changes in live cells – reminiscent of live-cell RNA detection – would immensely improve the processes of clonal screening and isolation.

Besides the technical challenges that come with maximizing on-target edits is that Cas9 frequently has off-target effects, producing insertions or deletions at unintended sites. Online algorithms can predict where some of these cuts are likely to occur, but currently, there is no efficient method to identify all possible off-target sites (4). To complicate things further, no two human genomes are identical. Due to genetic variation, predicting off-target effects based on reference genomes remains a challenge. Because so much of the hype around CRISPR surrounds the potential to treat human diseases, it is imperative to make sure that CRISPR does not introduce detrimental changes elsewhere in the genome before therapeutic use in humans. Standard screening methods and biological assays need to be established to robustly assess potential damage done to other sites in the genome and to measure its impact on cell function and mutagenesis.

Despite its shortcomings, the hub of activity surrounding CRISPR has been astounding. And with the force of thousands of scientists working on this technology, the possibilities for the future of CRISPR are boundless.




  1. Jinek, M., et al., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012. 337(6096): p. 816-21.
  2.  Miyaoka, Y., et al., Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci Rep, 2016. 6: p. 23549.
  3.  Hindson, B.J., et al., High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem, 2011. 83(22): p. 8604-10.
  4.  Stella, S. and G. Montoya, The genome editing revolution: A CRISPR-Cas TALE off-target story. Bioessays, 2016. 38 Suppl 1: p. S4-s13.