Thursday, December 31, 2015

Gizmodo.com mentions Sangamo in 2016 "Breakthrough" Article

http://gizmodo.com/these-are-the-science-stories-we-ll-be-watching-in-2016-1749459257

Human trials are also set to begin with gene-editing tools. California-based Sangamo Biosciences is planning to test enzymes to correct a gene defect that causes hemophilia. The study, which was just approved by the FDA, will be the first in vivo protein replacement platform for the treatment of Hemophilia B. The company, in cooperation with Biogen, will also begin trials to determine if a similar technique can be used to boost hemoglobin in people with the blood disorder, beta thalassaemia.

Tuesday, December 29, 2015

Sangamo Presentation Makes USC's Top News List for 2015

One in a series showcasing a year of university highlights

Fasting and football, research on baldness and HIV, and some impressive construction projects – these and more were Trojan topics in the news in 2015. Here are some of the USC News stories you made among our most popular for the year.

...

Are we really on the road to a cure for HIV/AIDS?

T cell under attack by HIV
This human T cell (blue) is under attack by HIV (yellow), the virus that causes AIDS. The virus specifically targets T cells, which play a critical role in the body’s immune response against invaders like bacteria and viruses. (Photo/courtesy of National Institute of Allergy and Infectious Diseases, National Institutes of Health)


Something wonderful sometimes happens when scientists and the public get together to talk about research. All the jargon, all the technical language falls away, and it becomes instead a conversation between the two groups with most at stake: the people in need of a treatment or cure and the people trying to develop it. One such get-together happened in July, when the California Institute for Regenerative Medicine (CIRM) joined with the AIDS Project Los Angeles to hold a Town Hall event in West Hollywood called “HIV Matters — Countdown to a Cure: California Leads the Way.” Nearly 120 people showed up to listen to stem cell scientists from USC, City of Hope, Calimmune and Sangamo Biosciences — all of whom are using CIRM funding to develop new treatments and hopefully even cures for HIV/AIDS.

Monday, December 28, 2015

Great NATURE article on Sangamo's HIV program

Disease: Closing the door on HIV

Although yet to complete clinical trials, genome editing has already shown promise against a globally important disease.

Sceptical is an understatement for Jim Riley's first thoughts when, ten years ago, he learned that scientists at Sangamo BioSciences wanted to use genome-editing technologies to treat patients with HIV. “I thought they were insane,” recalls Riley, a microbiologist at the University of Pennsylvania in Philadelphia. “I thought there was no way you could do this at a high-enough efficiency to have a really meaningful effect.”
What the Sangamo researchers were planning was remarkable indeed. Their goal was not merely to control the symptoms of HIV/AIDS, but to directly modify the genes of adults who were HIV positive to eliminate their susceptibility to the virus. One of HIV's primary means of entering immune cells, including helper T cells and macrophages, entails latching onto a cell-surface protein called C-C chemokine receptor type 5 (CCR5). A small percentage of people — roughly 10% of those of European descent — carry a deletion that removes 32 nucleotides from the gene that encodes CCR5. The resulting receptor is truncated and impossible for the virus to grasp. This means that homozygous individuals — those who inherited the mutation from both their mother and their father — are essentially resistant to the most commonly transmitted strain of HIV.
To replicate this desirable trait, scientists at Sangamo, a biopharmaceutical company based in Richmond, California, have been working closely with academic researchers across the United States, including — once he overcame his initial surprise — Riley and his team at the University of Pennsylvania. The project uses one of the more established tools of genome engineering, zinc-finger nuclease (ZFN) technology. Sangamo's product, SB-728, contains a set of engineered protein parts called zinc fingers that bind to specific sites within the CCR5 gene. These zinc fingers are linked to a nuclease enzyme that can cut the DNA. In 2008, Riley's team showed that SB-728 is capable of efficiently and specifically snipping out a chunk of the CCR5 gene in cultured human T cells (E. E. Perez et al. Nature Biotechnol. 26, 808816; 2008).
These findings offered tantalizing proof of concept that such editing might provide real protection for patients.

Berlin and beyond

There is a medical precedent for thinking that this approach will work against HIV. Back in the 1990s, US student Timothy Ray Brown became infected with the virus while studying in Berlin, Germany. About a decade later, he developed acute myeloid leukaemia. Things got even worse when his first two courses of chemotherapy, given to treat the leukaemia, caused his kidneys to fail. So doctors discontinued his antiretroviral drugs, which meant that his viral load started to climb. Yet, remarkably, it was this combination of leukaemia and HIV that proved to be Brown's salvation.
In 2007, he received a stem-cell transplant at Charité, a large teaching hospital in Berlin. The blood stem cells that Brown received were carefully chosen for him. Normally, doctors verify only that the tissues of the donor and the recipient match — for blood stem cells they check a marker called human leukocyte antigen — but in Brown's case, the medical team also screened potential donors homozygous for the CCR5 mutation. After radiation therapy, the blood stem cells that Brown received, and from which his T cells developed, were therefore immune to HIV. After a few rounds of treatment, Brown was soon in remission. His T-cell levels rose, and he has remained disease free without the need for antiretroviral drugs.
Brown's recovery was inspirational for researchers contemplating CCR5 as a target for genome editing. “There aren't many genes that I'm aware of where knocking them out doesn't do any harm, but instead has a therapeutic benefit,” says Paula Cannon, a specialist in gene therapy and infectious disease at the University of Southern California in Los Angeles, who began her research of ZFNs as a tool for modifying CCR5 in 2007.

Into the clinic

“The take-home for me was that the engineered cells got into patients and lasted longer than were expected.”
The early success of SB-728 in replicating the CCR5 mutation, coupled with the story of the Berlin patient, as Brown became known, made researchers optimistic for clinical trials of the therapy. Between 2011 and 2013, researchers at the University of Pennsylvania, including immunotherapist Carl June and HIV specialist Pablo Tebas, used SB-728 to modify the genomes of helper T cells (the main target of HIV) obtained from 12 volunteers who were HIV positive. The researchers then cultivated the cells and transplanted them back into the donors. All the patients experienced a boost in their T-cell count, and each patient established a small, but stable subpopulation of immune cells with edited CCR5 genes. When treatment with antiretroviral drugs was interrupted to test whether the gene edits worked on their own, some patients saw transient reductions in their viral load (P. Tebas et al. N. Engl. J. Med. 370, 901910; 2014). “The take-home for me was that the engineered cells got into patients and lasted longer than were expected,” says Cannon, who was not directly involved in the study.
The next challenge was how to make this immune protection more potent and durable. One approach is to generate a larger population of ZFN-modified T cells. So, in a separate study, three patients were given a mild dose of chemotherapy to reduce their immune-cell populations before transplantation. As an added boost to the therapy, in addition to editing helper T cells, the researchers also used SB-728 to modify killer T cells, which can also be destroyed by HIV infection.
Gerard Julien/AFP/Getty Images
Timothy Ray Brown is disease-free after receiving HIV-immune blood cells.
“By creating a little more space and relying on the homeostatic factors that maintain T-cell levels, the cells have a better chance of survival and of giving rise to long-lasting cell populations,” explains Riley. Two of the three patients experienced a profound drop in viral load, and they have not had to take antiretroviral treatment for more than a year.
How many cells must have their CCR5 genes edited to keep HIV at bay is not clear, however. About 5% of circulating T cells were successfully edited in the most recent trials, but Cannon points out that there are also populations of T cells hiding in tissues, which makes the total pool a lot bigger than estimates from circulating cells would suggest. A fully modified T-cell population would be a tall order, but it may be possible to achieve protection even with a relatively small proportion of edited cells, according to Hans-Peter Kiem, a gene-therapy researcher at the Fred Hutchinson Cancer Research Center in Seattle, Washington. Kiem's group uses primate models to study the clinical potential of genome-edited immune cells. “If we only protect about 20% of the cells, we get a very robust boost in the immune response against HIV,” says Kiem, referring to a 2013 study in which he tested the extent to which genetically modified stem cells protect pig-tailed macaques from simian HIV.

Looking ahead

Kiem thinks that the critical factor for building immunity against HIV is engraftment — the extent to which transplanted cells incorporate themselves into the tissues of the recipient's body. He and Cannon are separately exploring whether SB-728 might perform better if it is applied to haematopoietic stem cells — the common precursor of all of the various blood and immune cell subtypes — rather than to a few varieties of fully developed immune cells. “Then we can hit the T cells as well as monocytes, macrophages and other cell types that can be infected by, or serve as reservoirs for, HIV,” explains Kiem.
However, stem cells are more difficult to cultivate and edit than T cells, and must be carefully maintained to ensure that they retain their developmental flexibility. Using stem cells also means more serious side effects for patients, who will have to undergo an aggressive course of chemotherapeutic 'conditioning' before treatment. “It kills some of the stem cells in the bone marrow to make room for the engineered cells — and it's not a trivial thing to undergo,” cautions Cannon. This strategy is also slower to have an effect: it takes between six months and a year before the stem cells fully replenish the mature T-cell population. Cannon is involved with a newly launched clinical trial at the City of Hope Hospital in Duarte, California, which aims to explore how well these cells engraft into the bone marrow of 12 patients with HIV, and how many HIV-proof immune cells they each produce.
The therapeutic landscape for HIV has changed significantly in the ten years since Sangamo began pursuing this project. For a start, many patients can now keep their viral loads in check indefinitely by taking standard antiretrovirals. Nonetheless, a significant minority do not respond to these drugs.
Dale Ando, Sangamo's chief medical officer, is intrigued by the potential for a 'one-hit' treatment as opposed to having to take lifelong medication. “With antiretroviral therapy, there is a significant toll on the brain and heart, and increased risk of cancer, as well as chronic inflammation from long-term HIV infection,” he says. By comparison, and leaving aside the effects of the associated chemotherapies, SB-728 has not been linked to any serious side effects. So far, all the data on SB-728 have assuaged the most immediate concerns about ZFNs — that off-target edits elsewhere in the genome may have damaging or carcinogenic consequences.
Perhaps more importantly, these HIV studies have helped to clear a regulatory path for future genome-editing therapeutic programmes. “We've had multiple discussions on T cells, stem cells and in vivo genome editing, so the US Food and Drug Administration (FDA) is quite comfortable,” says Ando. As mainstream attention shifts to another genome-editing technology, CRISPR–Cas9, many believe that the FDA will find itself on familiar turf when drug applications that use the newer tool are filed.
From Cannon's perspective, much of the credit for this rapid progress belongs to the HIV patient community, whose political activism and hunger for a cure has helped to push genome editing into the clinic. “They've gotten us to this stage with this new therapy very quickly,” she says, “and hopefully it will have benefits for all sorts of other diseases in the future.”

Author information

Affiliations

  1. Michael Eisenstein is a freelance writer based in Philadelphia, Pennsylvania.

  2. http://www.nature.com/nature/journal/v528/n7580_supp/full/528S8a.html

Thursday, December 24, 2015

Sangamo Biosciences (SGMO) Short Interest Update- Slight Decline

Sangamo Biosciences (SGMO) Short Interest Update


DATE                                   SHORT INTEREST
12/15/15                              11,153,021 (7.79 days to cover)
11/30/15                              11,483,202
11/13/15                              11,088,163                      
10/30/15                              11,668,561 
10/15/15                              12,821,197    
9/30/15                                12,619,596
9/15/15                                10,882,795
8/31/15                                10,150,146
8/14/15                                  9,488,474
7/31/15                                  9,207,150
7/15/15                                  9,205,202
6/30/15                                  9,387,951
6/15/15                                  9,393,825
5/29/15                                  8,938,987
5/15/15                                  8,668,559
4/30/15                                  8,198,983
4/15/15                                  8,050,307
3/31/15                                  8,285,803
3/13/15                                  8,441,291
2/27/15                                  8,939,000
2/13/15                                  9,268,065
1/30/15                                  9,082,814
1/15/15                                  9,387,913

The State of the State - Sangamo Biosciences

Recap from Sangamo literature displaying 2015 progress

http://files.shareholder.com/downloads/SGMO/0x0x866935/9D598B9D-5EB9-4176-8DE4-170AA1622038/SGMO_One-Pager_Dec2015_vFINAL.pdf



Wednesday, December 23, 2015

Biotech Showcase 2016 - January 11-13 in San Francisco

From the Partnering360.com website:
Sangamo Biosciences is actively seeking partners for its clinical and preclinical programs, including:
1. SB-728-T in HIV
SB728-T is an ex-vivo autologous ... (must login to read further, please leave further info as a comment if you have it)

Tuesday, December 22, 2015

Nature.com mentions Sangamo in "Science to Look out for in 2016"

http://www.nature.com/news/the-science-to-look-out-for-in-2016-1.19073

Cut-and-paste genes

Human trials will get under way for treatments that use DNA-editing technologies. Sangamo Biosciences in Richmond, California, will test the use of enzymes called zinc-finger nucleases to correct a gene defect that causes haemo-philia. Working with Biogen of Cambridge, Massachusetts, it will also start a trial to look at whether the technique can boost a functional form of haemo-globin in people with the blood disorder β-thalassaemia. Scientists and ethicists hope to agree on broad safety and ethical guidelines for gene editing in humans in late 2016. And this year could see the birth of the first gene-edited monkeys that show symptoms of the human disorders they are designed to model.

Monday, December 21, 2015

This Should be a Very Interesting Session at Cell & Gene Therapy World, January 27, 2016

Holmes v Gregory Mano a Mano

Focus Session 1

Genome editing: How do the major platforms compare in both in vivo and ex vivo settings?


11:45 - 11:50
11:50 - 12:10
12:10 - 12:30
12:30 - 12:50
TALEN®-based targeted genome modifications for improved CAR T-cell adoptive immunotherapy
12:50 - 13:10

Friday, December 18, 2015

Science magazine names CRISPR ‘Breakthrough of the Year’

n its year-end issue, the journal Science chose the CRISPR genome-editing technology invented at UC Berkeley 2015’s Breakthrough of the Year.
Science magazine cover about CRISPR
The genome editing system called CRISPR earned Science’s 2015 Breakthrough of the Year laurels. Illustration by Davide Bonazzi/@SalzmanArt, courtesy of Science.

A runner-up in 2012 and 2013, the technology now revolutionizing genetic research and gene therapy “broke away from the pack, revealing its true power in a series of spectacular achievements,” wrote Science correspondent John Travis in the Dec. 18 issue. These included “the creation of a long-sought ‘gene drive’ that could eliminate pests or the diseases they carry, and the first deliberate editing of the DNA of human
 The implications of editing human embryos drove UC Berkeley inventor Jennifer Doudna to convene a discussion of CRISPR ethics in Napa in January, which led to an international summit in Washington early this month and a consensus statement to hold off on using gene-editing technologies to alter human eggs, sperm or embryos – so-called germline gene-editing – until more is known about the long-term implications of making hereditary changes to the human genome.
CRISPR, or CRISPR-Cas9, has invaded every other area of genetics, however, leading to genetically modified pigs, beagles and wheat. “Longer-lasting tomatoes, allergen-free peanuts and biofuel-friendly poplars are all on the drawing board,” Travis wrote. And biomedical applications are blossoming as scientists apply CRISPR to diseases such as diabetes, AIDS and cancer.
“In short, it’s only slightly hyperbolic to say that if scientists can dream of a genetic manipulation, CRISPR can now make it happen,” Travis concluded. “It’s the simple truth. For better or worse, we all now live in CRISPR’s world.”
UC Berkeley scientists also contributed to two runners-up for Breakthrough of the Year. Barbara Romanowicz and her team in the Department of Earth and Planetary Science published a report in September that helped show that “plumes of hot rock rising from the bottom of the mantle do exist,” according to Science. And John Dueber and his team in the Department of Bioengineering played a key role in engineering yeast to produce opiods.
Visit Science magazine’s website to read more about the Breakthrough of the Year and the runners-up.

http://news.berkeley.edu/2015/12/18/science-magazine-names-crispr-breakthrough-of-the-year/

Piper Jaffray's Schimmer makes 2016 Sangamo HIV Prediction

  • Joshua Schimmer of Piper Jaffray commented in a note that he is "eager to hit the reset button" within the biopharma sector.
  • Schimmer presented a list of potential outcomes and events in 2016 which represent contrarian views or ones that investors "aren't even contemplating."
  • The analyst noted some of his calls may be provocative and low-probability events.
It's been a "very long and tiring" year within the biotech sector, at least according to Joshua Schimmer of Piper Jaffray.

8. Sangamo Biosciences, Inc. SGMO 2.76%'s HIV program will prove to be a "black swan."
Schimmer suggested that investors may be "overlooking the upside potential" in Sangamo's HIV program as an out-licensing candidate. The analyst added that "tangible" progress on a partnership marks a "real potential source of upside" in the coming year.


Read more: http://www.benzinga.com/analyst-ratings/analyst-color/15/12/6060652/piper-jaffray-makes-15-provocative-predictions-for-bioph#ixzz3ugvTAVdH

Phacilitate Cell and Gene Therapy World January 2016

Ed Lanphier and Geoff Nichol speaking.
http://www.bioleaders-forum.com/

Thursday, December 17, 2015

Interesting Theory

HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene

Abstract

Highly active antiretroviral therapy (ART) has successfully turned Human immunodeficiency virus type 1 (HIV-1) from a deadly pathogen into a manageable chronic infection. ART is a lifelong therapy which is both expensive and toxic, and HIV can become resistant to it. An alternative to lifelong ART is gene therapy that targets the CCR5 co-receptor and creates a population of genetically modified host cells that are less susceptible to viral infection. With generic mathematical models we show that gene therapy that only targets the CCR5 co-receptor fails to suppress HIV-1 (which is in agreement with current data). We predict that the same gene therapy can be markedly improved if it is combined with a suicide gene that is only expressed upon HIV-1 infection.

http://www.nature.com/articles/srep18088

FBI arrests Turing Pharmaceuticals CEO Martin Shkreli: Witness

Reuters
Martin Shkreli, a lightning rod for growing outrage over soaring prescription drug prices, was arrested by the FBI on Thursday after a federal investigation involving his former hedge fund and a pharmaceutical company he previously headed.
The securities fraud probe of Shkreli, who is now chief executive officer of Turing Pharmaceuticals and KaloBios Pharmaceuticals, stems from his time as manager of hedge fund MSMB Capital Management and CEO of biopharmaceutical company Retrophin, a person familiar with the matter said.
Shares of KaloBios fell about 50 percent in premarket trading.
Retrophin said it has 'fully cooperated' in government investigations of Shkreli, and declined further comment.
Turing sparked controversy earlier this year after news reports that it had raised the price of Daraprim, a 62-year-old treatment for a dangerous parasitic infection, to $750 a tablet from $13.50 after acquiring it.
Shkreli, 32, was expected to be charged on Thursday for illegally using Retrophin assets to pay off debts after MSMB lost millions of dollars, the source said.
The probe, by federal prosecutors in Brooklyn, dates back to at least January when Retrophin said it received a subpoena from prosecutors seeking information about its relationship with Shkreli.
That subpoena also sought information about individuals or entities that had invested in funds previously managed by Shkreli, Retrophin said in a regulatory filing.
A noon ET press conference on the arrest is scheduled at the U.S. Attorney's Office in Brooklyn, N.Y.

Wednesday, December 16, 2015

Spark Prices Secondary at $47

Spark Therapeutics Announces Pricing of Public Offering
PHILADELPHIA, Dec. 15, 2015 (GLOBE NEWSWIRE) -- Spark Therapeutics, Inc. (“Spark”) (NASDAQ:ONCE) announced today the pricing of an underwritten public offering of 3,000,000 shares of its common stock at a public offering price of $47.00 per share, before underwriting discounts. The offering consists of 2,000,000 shares being sold by Spark and 1,000,000 shares being sold by The Children’s Hospital of Philadelphia Foundation (“CHOP”), resulting in aggregate net proceeds of approximately $88.4 million to Spark and approximately $44.2 million to CHOP, after deducting underwriting discounts and before offering expenses. In addition, Spark and CHOP have granted the underwriters of the offering an option for a period of 30 days to purchase up to an additional 450,000 shares at the public offering price, less the underwriting discount. Spark will not receive any proceeds from the sale of shares by CHOP.
The offering is expected to close on or about December 21, 2015, subject to satisfaction of customary closing conditions. A registration statement relating to these securities was declared effective by the Securities and Exchange Commission on December 15, 2015.
J.P. Morgan Securities LLC, Cowen and Company, LLC and Evercore Group L.L.C. will act as bookrunning managers for the offering. SunTrust Robinson Humphrey, Inc. will act as lead manager and Roth Capital Partners, LLC will act as co-manager. This offering is being made only by means of a prospectus, copies of which may be obtained from: J.P. Morgan Securities LLC, c/o Broadridge Financial Solutions, 1155 Long Island Avenue, Edgewood, NY 11717, or by telephone at (866) 803-9204; Cowen and Company, LLC c/o Broadridge Financial Services, 1155 Long Island Avenue, Edgewood, NY, 11717, Attn: Prospectus Department, by calling (631) 274-2806 or by faxing (631) 254-7140; or Evercore Group L.L.C., 55 East 52nd Street, New York, NY 10055, Attn: Prospectus Department or by telephone at (212) 849-3486.
This press release shall not constitute an offer to sell or the solicitation of an offer to buy, nor shall there be any sale of, these securities in any state or jurisdiction in which such offer, solicitation or sale would be unlawful prior to registration or qualification of these securities under the securities laws of any such state or jurisdiction.

Tuesday, December 15, 2015

SGMO: The Rodney Dangerfield of Gene Therapy

Blogger creates list of top RNAi and gene therapy companies.... forgets our friends in Richmond.
http://rnai.technology/rnai-type/top-rani-gene-therapy-companies/

Top RNAi and gene therapy companies

Saturday, December 12, 2015

Protocol Change to Stem Cell HIV Study

ClinicalTrials.gov Identifier:
NCT02500849

OLD:
At 9-12 months after SB-728mR-HSPC infusion, subjects who are aviremic with CD4 cell counts 500 cells/L and have 1% CCR5-modified CD4 cells within the peripheral blood detected by pentamer PCR will undergo an ATI. 

NEW:
At 9-12 months after SB-728mR-HSPC infusion, subjects who are aviremic with CD4 cell counts 600 cells/L and have 1% CCR5-modified CD4 cells within the peripheral blood detected by pentamer PCR will undergo an ATI. 

ADDITION:
- The SB-728mR-HSPC product passed all release testing

Ages Eligible for Study increased from 65 to 75

https://clinicaltrials.gov/ct2/show/NCT02500849?term=NCT02500849&rank=1

AWESOME Interview with Dr. Fyodor Urnov (published by Insights.bio)

The power and promise of zinc finger nuclease mediated genome editing

Fyodor Urnov, PhD, is Project Leader and Senior Scientist at Sangamo
BioSciences, Inc. where he co-developed human genome editing with engineered
zinc finger nucleases (ZFNs). Dr Urnov previously led the company’s
research and development efforts in deploying genome editing for crop trait
engineering (in partnership with Dow Agrosciences) and in generation of engineered
cell lines for manufacturing, improved generation of transgenic animals
and as research reagents (in partnership with Sigma-Aldrich). In his current
role as Project Leader for the Hemoglobinopathies, Dr Urnov heads Sangamo’s
collaboration with Biogen to develop genome editing as a one time, lasting
treatment for beta-thalassemia and sickle cell disease. Dr Urnov is also an associate
adjunct professor in the department of Molecular and Cell Biology at
the University of California, Berkeley. Dr Urnov received his PhD from Brown
University and holds a BSc in Biology from Moscow State University. He is an
author on more than 60 scientific publications and an inventor on more than

90 issued and pending US patents related to ZFN technology.

QQ You have been working in the field of gene editing for
a number of years – can you briefly explain how you
got into this area and your particular expertise?

I received my PhD from Brown University where I studied how
proteins bind to DNA and turn genes on and off; following this I
conducted my postdoctoral research at the NIH doing more of the
same. Then 15 years ago I was brought into Sangamo with the goal of
trying to build next-generation approaches to dealing with the challenge
of genetic disease. As I’m a basic scientist and not a physician, at that time
my background was not in any particular genetic disease; however, I found
it thrilling that a general solution to the problem of how to change the sequence
of DNA with high efficiency and precision inside the nucleus of
living human cells in fact emerged out of the basic investigations of protein–
DNA interactions, mechanisms of DNA repair, processes that most people
think are rather fundamental and haven’t an immediate applied relevance.
This is probably the second time
in the history of biomedicine where
something this basic has had such a
translational impact; the first instance
was the discovery of recombinant
DNA which emerged from studies of
bacterial defence and resulted in the
development of recombinant insulin
and monoclonal antibodies. Genome
editing arose from the studies of protein–DNA interactions, mechanisms
of double strand break repair, understanding how to deliver nucleic acids
to cells, and yet here we are with the conceptual equivalent of Microsoft
Word for the human genome.


QQ And why is it that we are now starting to see so much
excitement and interest in gene editing?


In many ways we’ve always wanted to do this haven’t we? The
notion of improving the human predicament by changing DNA
is an old one and probably on some level predates the discovery
of DNA in the late nineteenth century. We first showed that human
genes can be rewritten with high precision and efficiency nearly a decade
ago and at the time it wasn’t clear to us whether we would be able
to make it sufficiently broad and useful, in other words could we make
various types of edits, not just correct genes as we did initially for the
genetic mutation that gives rise to bubble boy disease – or severe combined
immune deficiency (SCID)? Would we be able to knock genes
out? What about more than one gene at a time? Would we be able to
integrate genes into specific locations to allow their sustained function?
Or edit the genes of model organisms important in biomedicine such
as the rat or pig? Over the 6 years that followed our initial discovery of
human genome editing, we and our collaborators in academia as well
as other academic groups who have been using zinc finger nucleases
(ZFNs) demonstrated conclusively that the answer to those questions
is an affirmative yes.
Yet whilst it was evident that genome editing will change the way people
approach experimentation both in basic research and translational settings,
the main question that remained was: how do you make that initial double
strand break in the DNA?
Then two discoveries were made essentially back to back that expanded
the access of the average researcher to the tools required to make that initiating
break. The first was our discovery of a second nuclease class called
TAL effector nucleases (TALENs) that are assembled using more Lego-like
principles than ZFNs, which are more sophisticated set of molecular scissors.
Then of course most recently Emmanuelle Charpentier and Jennifer
Doudna made their landmark discovery that Cas9 is an RNA-guided
nuclease. The field immediately realized that the previous 7 or 8 years
of toolbox building that we’d generated with ZFNs and then with
TALENS, could be taken and deployed wholesale to the cause of
genome editing with CRISPR/Cas9. All the tools existed but the
path to initiating the break was the question and that’s what Cas9
has made so easy for everyone.
An additional factor that has also impacted the advancement of
gene editing is that gene sequencing has become cheap and very efficient.
We have the means of editing genes but of course we need to
know what to edit and to what form. That part of the puzzle is what
facile sequencing has really enabled.
You can sequence different organisms to understand the basis of
trait differences or sequence the DNA of a patient who is presenting
with a particular condition. Before the emergence of gene editing,
you would just stare at that sequence and feel helpless; but now with
not one but three different gene editing platforms available it is easy
to understand why people empowered with the ability to not just
read DNA but change it, are doing so.

 Q:At Sangamo you work with Zinc Fingers – what
benefits are unique to using this specific type of
nuclease?
As you can imagine this is a topic I could talk about at considerable
length. The challenge in using a nuclease for the treatment
or prevention of disease is twofold: potency and specificity.
Zinc fingers are the best studied and most sophisticated nuclease
platform for which both the potency and specificity metrics meet
the demands of deployment at clinical scale. As an example, in collaboration
with Biogen we are advancing genome editing of human
hematopoietic stem and progenitor cells (HSPCs) as a potential
treatment for the b-hemoglobinopathies – sickle cell disease and
b-thalassemia. We discovered that the human genome contains a
specific region which if disabled by genome editing creates a disease-
protective phenotype in the erythrocyte progeny of the edited
HSPCs. Remarkably, as we’ve shown in this work recently published
in Nature Methods, it is a highly specific process – you have to cut
to within one base pair of a specific position in the human genome
to create that desired protective effect. Now this highlights a unique
benefit of the ZFN platform in that it allows the placement of that
double-strand break to that level of precision.
The other challenge is of molecular specificity and we’ve focused
on ensuring that the nucleases we build attain clinical-grade specificity
with respect to genome-wide action. ZFNs are of course
Mother Nature’s own invention for engaging specific loci in the human
genome – they co-evolved with the human genome to allow
the potent and specific regulation of specific gene loci. In many ways
we are borrowing her invention and developing ways to engineer
the zinc fingers to attain maximum potency and specificity of action
It is this ability to cut very precisely where we need to cut and to
do so while maintaining clinical-grade specificity of action within
the nucleus that drives our reliance specifically on the ZFNs rather
than the other nuclease platforms.

Q Sangamo is one of the leaders in moving gene
editing from the preclinical into the clinical
setting – with a couple of INDs accepted by the
FDA for HIV and b-hemoglobinopathies – can
you tell us about some of the key challenges in
making this translation step?


12 years ago, following the first demonstration that
we could engineer ZFNs to create a double-strand break,
we very quickly realized that there are numerous downstream
considerations that you must address before this
can become clinically actionable. The first consideration is
that of deploying this approach in the cell type or setting that is
clinically relevant. With specific focus on our programs in HIV
and b-hemoglobinopathies, the challenge was how to genome
edit at clinical-scale potency and specificity in a whole patient
dose of cells – millions and potentially billions of human T cells
or HSPCs. The challenge of cell husbandry and safe and effective
delivery of the nuclease was a critical issue for us to resolve, but
I’m delighted to report that after a great deal of work we have
charted a path to ex vivo genome editing of T cells and human
HSPCs.
The second consideration is building a panel of assays to evaluate
the preclinical safety of genome editing prior to the cells
being transplanted into patients in our trial. Here we have benefited
greatly from an essentially collaborative effort with the
regulatory authorities – FDA and NIH – in building a comprehensive
panel of assays. These enable us to assess the safety of our
genome editing approach in a way that is appropriately balanced
relative to the risk–benefit profile in the context of a particular
disease indication.
In summary, deploying your nuclease to make the DNA break
in the right cell type and then assessing the specificity and safety
of that editing in a manner that is commensurate with what you
are trying to achieve clinically has been a formidable challenge
that I’m delighted to report we have overcome. We are advancing
to the clinic an approach for in vivo genome editing and have
just received unanimous approval for our clinical study protocol
for hemophilia B and MPS I (Hurler Syndrome) from the NIH
Recombinant DNA Advisory Committee (RAC). Once reviewed
by the FDA, this trial will be the first in vivo genome editing for
any nuclease platform.

Q As a trailblazer in clinical gene editing, Sangamo
has paved an unchartered path through the
regulatory landscape – what are the key learnings
from this experience with regulatory bodies?
\
Dialogue is essential. The specific branch of the FDA that we
work with is CBER – the Center for Biologics Evaluation and Research
– they fully understand that cell and gene therapies are experimental,
that we’re not developing a small molecule for a particular
disease indication with an existing history of preclinical and clinical
development. The FDA has an established path for the progressive
discussion of both assaying the safety as well as the clinical issues for
proposed clinical deployment.
Over the past decade we have
benefited tremendously from
being able to engage the FDA
in reviewing our proposals,
receiving very constructive
feedback and addressing that
feedback. I‘m very proud to
report that not only are we in
clinical trials with autologous
edited T cells but that we have
an open IND for the editing of HSPCs in HIV. We are also on track
for filing an IND for in vivo genome editing before the end of 2015
as well as an IND for b-thalassemia in the first half of next year. The
reason I mention these timelines is that when I talk about a dialogue
with the agency this isn’t hypothetical – we are in discussions and
regulatory dialogue with them all the time and they have been a
great partner to work with. And the other agency is of course the
NIH RAC which is staffed by people who have been working in the
field of cell and gene therapy their entire lives and so they have been
really constructive with their feedback as well.

Q When moving to the clinical setting, what are the
potential safety risks and how do you mitigate these?

The first thing to understand is that this is very much disease
indication specific and I can give you some insight into
how we approach safety in our ex vivo therapy for beta-hemoglobinopathies.
We have built a comprehensive panel of assays
that assess the safety of genome editing to both the genome and
the “stemness” phenotype of human HSPCs. What’s interesting is
that having watched this field over the last decade, the technology
just does not stand still. The world around us continues to develop
new approaches to evaluate biological systems that really didn’t exist
even 10 years ago. When I was a graduate student in the early 1990s
at Brown I used to perform a procedure called Sanger sequencing
and it took me a month to determine the DNA sequence of 1000
base pairs; yet today we have next generation sequencing where for
a fraction of the cost and within 48 hours you can determine the
DNA sequence of thousands of loci or sequence the entire genome
in a population of cells.
Assays evolve and our ways of looking at the safety of gene editing
has also evolved as the technology becomes more sophisticated. An
important thing to understand is that when we assess the safety of
what we are doing, we don’t really stand still with respect to what our
clinical-grade reagents are. The research-stage reagents that we utilize
to obtain initial read outs of efficacy with ZFNs both in vitro and potentially
in animal models, we can assess their safety rather rapidly and
then, if necessary, essentially optimize the reagents further to attain
maximum on-target and genome-wide specificity read outs.


Q Sangamo’s lead product for HIV targets the
CCR5-encoding gene – can you briefly explain
the scientific rationale behind the selection of this
target and your approach to disrupt this gene?

The age of genomics has brought us this remarkable discovery
that natural selection has non-uniformly distributed
disease-relevant alleles in humans. We are all familiar with lactase-
persistent alleles that are more prevalent in parts of the world
where people drink milk. And in the mid-90s here in the San Francisco
Bay area, the remarkable observation was made that some people
who have been exposed to HIV appear to remain overt disease
symptom free. It was very rapidly determined by DNA sequencing
that these individuals are ‘natural mutants’ – namely they are homozygous
for the loss-of-function allele of a gene called CCR5 which
encodes the co-receptor for HIV entry into the cell.
Timothy Ray Brown at this point is probably one of the best
known names in biomedicine – but he’s not a scientist, he is in fact
the famous Berlin patient who has been effectively cured of his HIV
infection by allogeneic bone marrow transplant of HSPCs that are
homozygous for this disease-protective allele of CCR5. Whilst this
is fantastic for Timothy, this approach is just not scalable worldwide
to HIV patients. We reasoned therefore, that based on this
very strong epidemiological and public health data indicating that
people homozygous for the knock out allele of CCR5 are protected
from infection by R5 tropic HIV. Furthermore, looking at Timothy
Ray Browns’ experience we posited that you could attempt to
recreate this HIV-protective genotype in the cells of HIV-positive
individuals in the hopes of essentially creating a compartment of the
immune system that is protected from HIV infection.

Q In collaboration with the University of
Pennsylvania, you have treated over 70 HIV
patients with this ZFN-mediated gene editing
approach – can you share with us some of your
clinical experiences and outcomes to date?

We are excited to report that the treatment is well tolerated
to date and that we have evidence of an antiviral effect including
subjects that have demonstrated control of viral load for
an extended period while remaining off anti-retroviral therapy
(ART). For example in our most recent cohort, we have shown that
two out of our three subjects have sustained functional control of viral
load in the absence of ART. We also have a cohort of immunologic
non-responders that we were
happy to see have demonstrated
a decrease in the size of their
HIV reservoir at 36 months.
We were greatly encouraged by
how well this has gone and now
have a Phase 1 study, for which
we have an open IND, for the
same approach but this time in
HSPCs and this study is being
conducted at the City of Hope in Southern California. And you may
we have an open IND, for the
same approach but this time in
HSPCs and this study is being
conducted at the City of Hope in Southern California. And you may
ask: “why go from T-cells to stem cells?” The logic here is that we are
attempting to protect additional compartments of the hematopoietic
tree from HIV infection, for example macrophages and dendritic cells.

Q How durable does this response appear to be?
Will there be a need or option to re-dose patients?

Re-dosing is an option and we are evaluating the delivery
of ZFNs to the T cells in the form of in vitro transcribed messenger
RNA (mRNA) which absolutely gives us the option
to re-dose. With respect to the durability of response, we’ve seen
modified cells persisting in our subjects out over 4 years post-transplant
– the longest time point studied to date. Granted, 4 years is
not a lifetime, but we are greatly encouraged by the durability we’ve
observed so far.

Q HIV is renowned for its ability to evade immune
detection through its presence in latent
reservoirs in the body – can gene editing impact
these reservoirs and cure patients vs functionally
cure?

Looking at the cohorts 1 through 3 in one of our earlier
studies, for whom we have up to 36 months of follow-up
data, one could argue that the answer to this question is yes.
We’ve observed a mean 0.9 log decrease in HIV reservoir in nine
out of nine subjects and in some individuals this decrease is actually
substantially greater. We are excited to observe an increase in genome
editing in the CD4+ central stem cell memory compartment
and whilst I’m not an immunologist, my qualified immunologist
colleagues assure me that this compartment of the immune system
lasts the lifetime of a human. Therefore, being able to modify those
cells and potentially protect them from HIV infection gives us great
hope that we are in fact creating a lifetime effect.

Q Whilst HIV is a global healthcare issue, large
patient populations are found within developing
nations – do you think therefore that it’s possible
that gene editing technologies will one day
replace existing ART which is currently a cheaper
and comparatively easy to deliver to patients?
This as you can imagine is a topic that we think about a lot at
Sangamo and the issue of cost is nuanced. ART really changed
the prognosis of patients with HIV but it is a lifetime treatment and
patients must take multiple pills daily. When I was in high school

I was a huge fan of Queen and it was such a tragedy when Freddie
Mercury succumbed to the disease; and it’s fantastic – as a basketball
fan – to see Magic Johnson is alive and well. But we must contend
with the fact that the life-time cost of ART is not unsubstantial. The
big hope of course with genome editing is that one creates a functional
cure with a one-time treatment or a potentially short regimen
of re-dosing.
The other issue to consider regarding ART is that it’s evident
that there are certain patients who are immunologic non-responders,
whose immune system never completely recovered
from the initial assault from the virus. Helping these people is
a real challenge and that’s why we enrolled them in some of our
cohorts. Ultimately ours is an experimental therapy still in clinical
development, but as I mentioned, to date the treatment has
been well tolerated and we have some people with viral control
in the absence of ART.
In addition to cost, a lifetime regimen of ART is clearly associated
with side effects that in many patients, create serious non-compliance
issues, namely they have to make a choice of whether to take
the medication or not. Our hope is that this will be a non-issue with
a genome editing approach because a human being once edited will
not need to comply with a therapy anymore as the therapy will have
been complete.

Q Sangamo is also applying ZFN gene editing to the
hemoglobinopathies – can you tell us about the
selected target and how it was identified?

As I sometimes point out to my colleagues – I love being
second. My colleague Michael Holmes, PhD, at Sangamo was the
scientific leader responsible for taking our first genome editing approach
to the clinic. As mentioned, the approach to editing CCR5
in HIV patients was based upon epidemiologic and public health
data that showed that there is a naturally occurring disease-protective
genetic variation – namely the knockout mutation of CCR5.
In reference to my point of going second, I am the scientific leader
in our collaboration with Biogen where we are looking to deploy
the same fundamental principle – which is to rely on naturally occurring
disease-protective genetic variation – to the hemoglobinopathies,
the most prevalent genetic diseases globally. In Thailand alone
there are 300,000 people with b-thalassemia; 100,000 people with
sickle cell disease in the USA and that many neonates born annually
with sickle cell disease in Nigeria alone. Therefore they truly represent
a substantial public health burden.
One of the remarkable things about these diseases is the large
variability in clinical presentation of the disease: some individuals
are relatively disease free whilst others are severely ill despite having
the same underlying genetic mutation. This led people to study this
disparity and 4 years ago studies started to emerge that this is in
fact due to the protective effects of mutations at other loci in the
genome. These individuals are not single but double mutants; they
have the disease-causing mutation and then they have a disease-protective
mutation in addition. Researchers started to look at where
that disease-protective variation lies and were greatly surprised to

find it in the gene bcl11a. Now the name of this gene is actually a

find it in the gene bcl11a. Now the name of this gene is actually a
misnomer – it should really be called multi-functionally important
human gene that happens to be the key regulator of human fetal
globin! In utero or immediately post birth we produce a different
b-hemoglobin to that which we make as adults. This hemoglobin
is call fetal hemoglobin, which is quickly shut off and its synthesis
in our erythrocytes is replaced by adult hemoglobin. In individuals
with sickle cell disease or b-thalassemia, they are in this unfortunate
position whereby Mother Nature doesn’t realize that their adult
hemoglobin is the mutant form and thus when they switch from a
perfectly functioning fetal hemoglobin to mutant adult hemoglobin
they develop the disease. That is unless they have this second mutation
in bcl11a in which case the switch in hemoglobin production is
incomplete and they synthesize sufficient levels of fetal hemoglobin
throughout life which protects them from the fact that their adult
hemoglobin is mutant.
Greatly encouraged by the fact that there are people with much
milder or essentially no disease symptoms if they have this protective
mutation, our strategy is to recreate this disease-protective genetic
variation in HSPCs of people with b-thalassemia and subsequently
with sickle cell disease. I hope that that we will create a one-time
approach that will be broadly applicable against both of these hemoglobinopathies
where we take HSPCs from a person with either disease,
genetically engineer them in a way that selectively eliminates
expression of the bcl11a from the erythropoietic tree, transplant the
cells back into the subject and cross all fingers other than zinc in
the hope that we get a sustained elevation of fetal hemoglobin. If
we achieve that elevation then we know that will confer protection
against the disease.

Q You are also working on in vivo applications
for diseases such as hemophilia and lysosomal
storage disorders – what are the main differences
and challenges in applying gene editing in vivo
versus ex vivo?

Deployment in vitro is carried out in a more controlled environment:
you harvest the T or stem cells from a subject and
they are either in a bag or a cuvette in front of the operator at
all times. Therefore you build non-clinical safety assays and efficacy
assays that are focused on the fact that you are working with cells
that are in front of you. With in vivo genome editing you develop
your genome editing tool, deliver it to the subject but then Mother
Nature takes her course so the challenge there, that we believe we
have successfully met, is to build a comprehensive panel of preclinical
safety and efficacy assays that adequately assess the potency and
specificity of that approach.
One of the things that I find remarkable and most translationally
exciting about the in vivo genome editing approach – and I must
credit my colleagues Edward Rebar, PhD, and Michael Holmes,
PhD, who are leading the development of our in vivo editing – is
that we are potentially able to treat a range of monogenic disorders
by the targeted editing of just one locus. In essence, we believe we
are building an in vivo protein replacement platform and the strategy
here was to identify a human gene that is expressed to a very
high level in the human liver but is
also non-essential so that its loss of
expression causes no ill effects. And
one such gene is albumin. The data
we have generated thus far support
the hypothesis that for monogenic
diseases such as lysosomal storage
disorders or hemophilia B, we will
be able to replace the human albumin
gene in the liver of an affected
individual with the open reading frame of the gene which is disabled
by mutation. Following genome editing with ZFNs, the hepatocyte,
which is our natural ‘engine’ for the secretion of protein into the
bloodstream, no longer secretes albumin but now faithfully secretes
the protein we have just integrated into it. I find this truly thrilling
– this notion that we have for lack of a more elegant term, a ‘plug
and play’ locus on the human genome that we are hopeful we can
develop as a broad approach for the treatment of monogenic diseases
that are addressable in this way.

Q Sangamo is collaborating with Biogen and Shire
on the development of couple of clinical products
– what are the key considerations when looking
to collaborate with industry partners?

In many ways the proverbial saying: “it takes a village to
raise a child” is highly relevant here. We’ve discussed the tremendous
efforts in academia upon which we have relied in building
this gene editing platform. As we move toward the clinic, for the
specific indications that we are targeting which affect a large number
of people worldwide, being able to collaborate with a company like
Biogen or Shire is wonderful because they bring the extraordinary
might that big biotech and big pharma possess. Obviously it’s good
to be able to work with someone who is also focused on the same
therapeutic areas that we are targeting, but more than that - they
need to be excited about the fact that this is not a small molecule or
a biologic. We are building genome editing as a therapeutic modality
and we are hopeful to look for synergy – which is certainly the
case with Biogen and Shire. We are the genome editing people, we
live and breathe zinc finger nucleases, so it’s incredibly important to
be able to partner with organizations that have their own expertise
that is relevant to the disease indication we are pursuing.

Q How do you envisage the field evolving over the
next 5 years – what progress do you hope to see?

I am very much a glass half full kind of person – I am thrilled
about the progress that has been made so far. Over the next 5
years we will have data, not only from the more advanced stages of
clinical development of our genome editing in T cells in HIV but
also of this approach in our trial of CCR5 editing in HSPCs. Following
on from this will be the application of genome editing of HSPCs
for b-thalassemia or sickle cell diseases. Data from deploying editing
in HSPCs for these three indications will really teach the field more
broadly about what genome editing ex vivo can do to address the
challenge of infectious and monogenic diseases of the blood. Should
the data look good, which I’m incredibly optimistic that they will,
then this will fundamentally change the way we think about dealing
with those diseases clinically.
Following closely on from this is our approach of genome editing
in vivo and our initial approach to rewriting the gene expression
programme of the hepatocyte to become an in vivo protein synthesis
machine. Once again, if we are able to demonstrate that the liver
genome was rewritable safely and effectively allows an improvement
in the predicament of patients with hemophilia or lysosomal storage
diseases, again I think the field as a whole will start to look very
differently at how we approach the clinical management of these
conditions.
Last but not least, if you had told me when I was a graduate student
that 20 years from now you will be able to engineer molecular
scissors that will be able to within base pair precision disable a locus
in the human genome in a clinical-scale dose of HSPCs that would
then retain every metric of viability and functionality to allow an
autologous transplant for the treatment of HIV or beta thalassemia,
I don’t know how I would have reacted, but that would have sounded
incredibly futuristic and yet here we are. The lesson from this
and from other developments of technologies, such as deep sequencing,
is that we should not underestimate the progress of technology.
Engineering of nucleases, of cell husbandry, cell processing and of
course delivery modalities is advancing at a pace that is just breath
taking. Therefore good and accurate prognoses for the next 5 years
are hard to provide because who knows what is currently being invented.
My take on this is really formulated by Alan Kay who was
one of the pioneers of computer science: “the best way to predict the
future is to invent it”. I am very much a believer in that paradigm
– we are currently inventing what the next 5 years are going to look
like. Exciting they will be, that’s for sure.

http://insights.bio/cell-and-gene-therapy-insights/2015/12/11/dr-fyodor-urnov-the-power-and-promise-of-zinc-finger-nuclease-mediated-genome-editing/