Interesting Data presented at International Aids Conference 2016

https://www.buzzfeed.com/azeenghorayshi/repeating-the-berlin-patient?utm_term=.aodGGEgvq#.fiObbNGnj

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Some of the patients received transplants with the mutation, and others did not. By comparing these two groups, the researchers wanted to see whether Brown’s cure was the result of the CCR5 mutation, or of simply getting infused with foreign cells. (Bone marrow transplants often come with “graft-versus-host disease,” which kills off the body’s native cells and, some speculate, could be involved in wiping out HIV.)
The trial’s initial results are encouraging, Wensing said, though it’s still unclear whether the results are due to the CCR5-altered cells, the bone marrow transplant itself, or the standard antiretroviral medications.
Of the three individuals who have made it three years since their transplants, two received normal bone marrow cells and one received the HIV-resistant type. One of the individuals who received the normal type cells luckily avoided graft-versus-host disease. The other two — one of whom had HIV-resistant cells, and one of whom didn’t — did experience graft-versus-host. Both of these individuals now have undetectable levels of their own immune cells in their blood, but also have undetectable levels of HIV. The other patient has low levels of their own immune cells and HIV still detectable in their blood.
It will take some work to determine how the various factors are at play, but Wensing says the worst is over since the three patients are healthy and cancer-free. The next step will be deciding whether the patients will go off their antiretroviral medications, to see whether the bone marrow transplants were solely responsible for eradicating their HIV.
The researchers did not present any results from the other three patients in the trial, who got their transplants less than three years ago.

Do CRISPR enthusiasts have their head in the sand about the safety of gene editing?

https://www.statnews.com/2016/07/18/crispr-off-target-effects/

At scientific meetings on genome-editing, you’d expect researchers to show pretty slides of the ribbony 3-D structure of the CRISPR-Cas9 molecules neatly snipping out disease-causing genes in order to, everyone hopes, cure illnesses from cancer to muscular dystrophy. Less expected: slides of someone kneeling on a beach with his head in the sand.

Yet that is what Dr. J. Keith Joung of Massachusetts General Hospital showed at the American Society of Hematology’s workshop on genome-editing last week in Washington. While the 150 experts from industry, academia, the National Institutes of Health, and the Food and Drug Administration were upbeat about the possibility of using genome-editing to treat and even cure sickle cell disease, leukemia, HIV/AIDS, and other blood disorders, there was a skunk at the picnic: an emerging concern that some enthusiastic CRISPR-ers are ignoring growing evidence that CRISPR might inadvertently alter regions of the genome other than the intended ones.

“In the early days of this field, algorithms were generated to predict off-target effects and [made] available on the web,” Joung said. Further research has shown, however, that such algorithms, including one from MIT and one called E-CRISP, “miss a fair number” of off-target effects. “These tools are used in a lot of papers, but they really aren’t very good at predicting where there will be off-target effects,” he said. “We think we can get off-target effects to less than 1 percent, but we need to do better,” especially if genome-editing is to be safely used to treat patients.

That, of course, is the hope of companies including Editas Medicine, which Joung cofounded, CRISPR Therapeutics, Caribou Biosciences, and Sangamo BioSciences, which all presented at the ASH workshop.

Read More

They’re going to CRISPR people. What could possibly go wrong?

Off-target effects occur because of how CRISPR works. It has two parts. RNA makes a beeline for the site in a genome specified by the RNA’s string of nucleotides, and an enzyme cuts the genome there. Trouble is, more than one site in a genome can have the same string of nucleotides. Scientists might address CRISPR to the genome version of 123 Main Street, aiming for 123 Main on chromosome 9, only to find CRISPR has instead gone to 123 Main on chromosome 14.
In one example Joung showed, CRISPR is supposed to edit a gene called VEGFA (which stimulates production of blood vessels, including those used by cancerous tumors) on chromosome 6. But, studies show, this CRISPR can also hit genes on virtually every one of the other 22 human chromosomes. The same is true for CRISPRs aimed at other genes. Although each CRISPR has zero to a dozen or so “known” off-target sites (where “known” means predicted by those web-based algorithms), Joung said, there can be as many as 150 “novel” off-target sites, meaning scientists had no idea those errors were possible.
One reason for concern about off-target effects is that genome-editing might disable a tumor-suppressor gene or activate a cancer-causing one. It might also allow pieces of two different chromosomes to get together, a phenomenon called translocation, which is the cause of chronic myeloid leukemia, among other problems.
Many researchers, including those planning clinical trials, are using web-based algorithms to predict which regions of the genome might get accidentally CRISPR’d. They include the scientists whose proposal to use CRISPR in patients was the first to be approved by an NIH committee. When scientists assure regulators that they looked for off-target effects in CRISPR’d cells growing in lab dishes, what they usually mean is that they looked for CRISPR’ing of genes that the algorithms flagged.
As a result, off-target effects might be occurring but, because scientists are doing the equivalent of the drunk searching for their lost keys only under the lamppost, they’re not being found.

Read More

Federal panel approves first use of CRISPR in humans

One little-appreciated feature of CRISPR’s DNA-cutting enzyme is that it doesn’t stop at one. Even if the enzyme cuts its intended target, the risk of off-target cutting remains. The enzyme “still has energy to bind with off-target sites,” Joung said, so “it can still cleave those sites.”
Scientists from some of the leading genome-editing companies said they are confident they will be able to minimize off-target CRISPR’ing, by picking “high-quality” guide RNAs, among other methods. While “bad” RNAs hit as many as 152 wrong targets, studies show, good ones hit only one, and the algorithms “capture most of” the potential off-target effects, said Dr. Bill Lundberg, chief scientific officer of CRISPR Therapeutics. Still, he conceded, “At the end of the day we’re taking a cell where we can’t predict a priori where the edit has happened.”
Scientists have recently recognized another reason to worry about off-target effects: No two people’s genomes are identical. Off-target-identifying methods, which are based on a composite or “reference” human genome, might indicate that there are no stretches of DNA that CRISPR can mistakenly snip. But because of random mutations and genetic variations, some patients might have additional “123 Main Street”s, attracting CRISPR and its DNA-cutting enzyme where they’re not supposed to go.
“There are a significant percent of sites, more than I would have thought,” where that might happen, said Joung, “and it varies by ethnic group.”
Said Andrew May, chief scientific officer of Caribou: “There is going to have to be some consideration of that” as genome-editors try to bring CRISPR to patients.

Sharon Begley can be reached at sharon.begley@statnews.com
Follow Sharon on Twitter @sxbegle

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Fred Hutch HIV cure program extended, expanded

The National Institutes of Health today awarded a second five-year round of funding to defeatHIV, a public-private research group based at Fred Hutchinson Cancer Research Center that has spent the last five years investigating the use of genetically modified, HIV-resistant blood stem cells as a potential cure for the virus that causes AIDS.
“We’re excited and honored to be able to continue defeatHIV’s work and keep Fred Hutch at the center of HIV cure research, particularly in the area of cell and gene therapy,” said defeatHIV co-director Dr. Keith Jerome, a Fred Hutch virologist.
The new $23.5 million award will allow the group to tackle three new approaches that build on its earlier work. They include:

• Exploring CAR T-cell therapy, a type of immunotherapy that already is being hailed as a potent anti-cancer weapon, against HIV, in partnership with Seattle-based biopharmaceutical company Juno Therapeutics
• Using gene therapy to induce production of a synthetic “super antibody” to target HIV
• Adding a therapeutic vaccine to boost the proliferation and function of genetically modified HIV-resistant cells

All three new tactics have in common a focus on using the immune system to eradicate or at least control HIV.
“We’ve learned that the immune response — the patient’s immune system — plays a critical role in controlling HIV, just like in cancer,” said defeatHIV co-director Dr. Hans-Peter Kiem, a Fred Hutch stem cell transplant and gene therapy researcher. “It’s set the stage for the next generation of studies to further mobilize and harness the immune system to fight HIV.”
An ambitious agenda
DefeatHIV was one of six groups nationwide to receive a total of $150 million over the next five years from the NIH’s Martin Delaney Collaboratory: Towards an HIV-1 Cure program. That is double the number of research collaborations funded in the program’s first iteration in 2011.
The three original groups ­— based at Fred Hutch, the University of California San Francisco and the University of North Carolina at Chapel Hill — received funding again for new projects. Three new groups were added, based at George Washington University in Washington, D.C., the Wistar Institute in Philadelphia and Beth Israel Deaconess Medical Center in Boston.
Named in honor of a late HIV/AIDS activist who served on the advisory committee for the National Institute of Allergy and Infectious Diseases, or NIAID, the Martin Delaney program strongly encourages collaboration within and among research groups and between scientists and private industry. The goal is to translate research into the clinic as rapidly as possible.
“The two greatest challenges remaining in HIV/AIDS research are finding a cure and developing a safe and effective preventive vaccine,” said NIAID Director Dr. Anthony S. Fauci in a statement announcing the awards. “A simple, safe and scalable cure for HIV would accelerate progress toward ending the HIV/AIDS pandemic.”
Moving therapies to clinical trials is an ambitious aim considering that until about eight years ago, curing HIV was considered all but impossible.
The biggest success story for HIV came in 1996, when combination antiretroviral treatment turned the virus from a certain death sentence to a chronic manageable disease, at least for those who have access to the drugs and can tolerate them. But hopes that this treatment would eventually cure infection were dashed when scientists learned that the virus, which integrates itself into a person’s own DNA, can hide out in cells, dormant and out of reach of the drugs. Some likened HIV to the proverbial cockroach that can survive a nuclear blast: Stop treatment, and the virus comes back.
But in at least one case — that of Timothy Ray Brown — the virus did not roar back after the blast. In 2008, the world learned about the Seattle-born Brown, who while living in Berlin had undergone two grueling bone marrow transplants to treat acute myeloid leukemia. In what proved to be a successful attempt to also cure Brown’s HIV infection, his Berlin doctor found a stem cell donor who carried two copies of a rare gene mutation that confers natural resistance to the virus. Brown stopped taking antiretroviral drugs after the first transplant in 2007 and shows no sign of HIV.
In its first five years, defeatHIV used Brown’s cure as a blueprint for developing a less toxic therapy than the one he endured by seeking to genetically engineer resistance in an infected person’s own immune cells. In preclinical experiments, Kiem’s lab has successfully modified blood stem cells using a gene editing technique that employs molecules called zinc-finger nucleases and returned the resistant stem cells to repopulate the immune system.  Research into this approach will continue under a separate five-year grant to Kiem’s lab from the National Heart, Lung and Blood Institute, a division of the NIH. The biopharmaceutical company Sangamo Biosciences, which developed zinc-finger nucleases, will continue as a defeatHIV partner.
New approaches, new partners
The first new approach — engineering HIV-resistant and anti-HIV T cells — will be led by Fred Hutch virologist Dr. Larry Corey and immunology and infectious disease experts Drs. David Rawlings and Thor Wagner of the University of Washington and Seattle Children’s, along with Juno Therapeutics.
Researchers at Fred Hutch and elsewhere have been working on still-experimental therapies that genetically reprogram patients’ own T cells — a type of white blood cell that searches out and destroys pathogens — with synthetic receptors called chimeric antigen receptors, or CARs, to kill cancer cells bearing a particular marker. There are now dozens of clinical trials underway of CAR T cells for cancer, with promising early results.
DefeatHIV proposes to transfer this approach from cancer to HIV by producing CAR T cells that target markers expressed by cells that harbor HIV.
Corey, whose early work in treating herpes laid the groundwork for antiretroviral treatment for HIV and who now leads the world’s largest network for testing preventive HIV vaccines, will discuss the CAR T-cell approach as the keynote speaker at the upcoming 2016 Conference on Cell and Gene Therapy for HIV Cure on Aug. 4-5 at Fred Hutch.
The second new approach — genetically engineering the production of a synthetic broadly neutralizing antibody — will be led by Dr. Michael Farzan, professor of immunology and microbial science at the Scripps Research Institute in Jupiter, Florida. Farzan made headlines last year for developing a lab-made molecule that is more powerful than any antibody humans produce against HIV. In preclinical models, Farzan’s lab used a virus to insert a gene into muscle cells to direct production of this “super antibody” and showed that it protected against HIV infection. Farzan described his research at the 2015 Conference on Cell and Gene Therapy for HIV Cure, hosted by defeatHIV at Fred Hutch, which cemented the scientists’ decision to work together, according to Jerome.
The defeatHIV proposal calls for pairing each of these two new strategies with a latency-reversing agent developed by the biotechnology company Gilead  Biosciences to “wake up” the reservoir of dormant HIV so infected cells can be targeted by CAR T cells or Farzan’s broadly neutralizing antibodies. Reducing the viral reservoir is seen as key to an HIV cure.
Preclinical and limited human trials in Kiem’s and others’ labs have already shown that genetically modifying stem and T cells not only makes them resistant to HIV infection but improves immune function overall. So for the third new tactic, defeatHIV will seek to boost that immune response by adding a therapeutic vaccine. (A vaccine given before infection is called a preventive vaccine; it helps healthy people set up defenses against infection. Therapeutic vaccines are designed to treat people after they are infected by strengthening the body’s natural immune response. So far, neither type of vaccine has been successfully developed for HIV.)
“Even a small percentage of gene-edited cells help orchestrate an immune response against the virus,” said Jerome. “So we thought we could build on that going forward by adding a therapeutic vaccine.”
Leading the vaccine effort will be University of Washington microbiologists Dr. Jim Mullins, who already has a vaccine in clinical trials, and Dr. Deb Fuller.
In addition to its new partners, Jerome and Kiem stressed the continued partnership with the volunteer community members who make up its Community Advisory Board, or CAB.
“Our CAB is the model for community involvement around cure. It’s the greatest partner we could hope for,” said Jerome. “Representatives from the CAB are at pretty much all of our planning meetings to listen, to advise as we talk about clinical trials, for information flow in both directions. They wrote an incredibly strong section of the proposal for the grant.”
Hope and caution
The plan is that at least one and maybe more of these three strategies will be ready for clinical trials in the next four to five years, Jerome and Kiem said. And unlike clinical trials that tried to replicate Timothy Ray Brown’s transplant cure, the new strategies will not require testing in people with both HIV and cancer.
“Before, we talked about that we would have to test in patients with malignancies because we needed high-dose irradiation and chemotherapy for the transplant procedure,” harsh treatments that would only be appropriate if needed to also treat cancer, said Kiem.
In fact, efforts elsewhere to replicate Brown’s cure in patients who needed stem cell transplants as a last-resort cancer treatment have so far failed to show the same results. In part, these are often very ill patients to begin with; in most cases, they died from the cancer or the transplant before it could be determined whether their HIV was gone. Brown remains the only known person in the world to be cured of HIV.
As excited as the Hutch researchers are about the new, less toxic approaches and as optimistic as they are about getting to clinical trials, they remain cautious when it comes to using the word “cure,” whether for cancer or HIV.
“We’ve become a bit more careful in terms of the words ‘HIV cure,’” said Kiem, who works with both cancer and HIV patients. “It is difficult to determine whether every single cancer cell has been eliminated in the body after a bone marrow transplant. Yet we know we can cure the cancer because in many patients it does not return even after five or 10 years, and we know the immune system plays a critical role.”
HIV and the HIV reservoir pose a similar challenge. So far, there are no good tests or markers to tell for sure whether HIV might be still hiding in a few cells.
“It will take time to determine whether HIV has the potential to return, and we think just like in cancer, therapies establishing a solid immune system and response that can recognize HIV will be an important and critical part in our HIV cure effort,” Kiem said. “If HIV can be made undetectable, it is first like a remission and then after several years we will know whether it is a cure, just like in cancer. Many investigators have also come to the conclusion that this is a very reasonable first step and expectation.”

UPENN Receives HIV Grant

PHILADELPHIA—(July 13, 2016)—The Wistar Institute is pleased to announce that the National Institutes of Health (NIH) has awarded a nearly $23 million Martin Delaney Collaboratories for HIV Cure Research grant to the BEAT-HIV: Delaney Collaboratory to Cure HIV-1 Infection by Combination Immunotherapy (BEAT-HIV Delaney), a consortium of top HIV researchers led by co-principal investigators Luis J. Montaner, D.V.M., D.Phil., director of the HIV-1 Immunopathogenesis Laboratory at The Wistar Institute Vaccine Center, and James L. Riley, Ph.D., research associate professor at the Perelman School of Medicine at the University of Pennsylvania.
The Philadelphia-based BEAT-HIV Delaney project is one of six grants awarded by the Delaney initiative, joining a highly-selective group of U.S.-led teams charged with advancing the global efforts to develop a cure for HIV. The five-year award promotes a preeminent partnership of more than 30 leading HIV investigators from The Wistar Institute, the University of Pennsylvania, Philadelphia FIGHT, Rockefeller University, VA San Diego Healthcare System, Johns Hopkins University, the University of Nebraska-Lincoln, and the University of Utah working with government, non-profit, and industry partners to test combinations of several novel immunotherapies under new preclinical research and clinical trials.
With 37 million people now living with HIV worldwide and 17 million receiving antiretroviral therapy, the Martin Delaney Collaboratories for HIV Cure Research initiative reflects the interest in HIV cure research that has grown into a global priority over the last five years and follows President Obama’s call for increased HIV cure research.
“The lifelong stigma, economic burden on society, strain on healthcare resources, and sheer toll on human life across the globe makes finding a cure a top priority,” said Montaner. “Together we’re building on our teams’ extensive established efforts to move forward and make those next transformative steps that will bring us closer to an HIV cure.”
Three Research Pillars
Incorporating three distinct areas of study, the goals of the BEAT-HIV Delaney project are to investigate where HIV hides after therapy and test novel clinical strategies aimed at an HIV cure that eliminates the hidden virus. The first area of study or “pillar” will identify where and how HIV hides so researchers can better assess if proposed clinical strategies can eradicate the virus. This pillar links three research teams who will measure HIV in the body, determine how HIV persists after therapy, access new areas in the body that have not been studied before where HIV may hide, and distinguish HIV by “fingerprinting” or “barcoding” to determine the fate of each infected cell. The BEAT-HIV Delaney research team plans to develop clear criteria to evaluate reductions in the virus beyond what is measured in the clinic.
The second pillar focuses on stimulating the immune system with which we are all born (innate immunity) through a combination immunotherapy approach using highly-potent antibodies against HIV together with pegylated interferon alpha 2b. The researchers plan to conduct the first human clinical trial combining these two therapeutic strategies (which have been tested separately and have shown activity in reducing HIV in humans) with the expectation that a boosted innate immune system empowered with unique antibodies to target HIV-infected cells will achieve greater reductions in HIV than observed previously. In addition, the researchers will look to develop novel DNA-based delivery systems that may make administering anti-HIV treatments more simple and effective than by transfusions.
The third pillar will bring together two promising gene therapy strategies, independently tested in humans, with the goal of engineering, growing and administering killer cells that are uniquely empowered to find and kill HIV-infected cells. The proposed gene therapy strategy is based on the success of small human trials of killer T-cells (Chimeric Antigen Receptor [CAR] T-cell therapy). Earlier studies showed that killer T-cells can be generated and administered safely. The research team will repeat these studies and for the first time safeguard the new killer cells from being attacked by HIV when “activated” by removing the CCR5 protein. HIV needs this protein to infect and kill the killer cells, so removing it can “protect” killer cells so they can continue to proliferate and kill HIV-infected cells. The ability of cells to remain unaffected by HIV in the absence of CCR5 has already been shown clinically, but this strategy has not yet been joined with gene therapy in making killer cells.
“The results of this trial are expected to show for the first time what the long-term effects of these killer cells can be in finding and eradicating HIV,” said Riley.
The BEAT-HIV Delaney project benefits from decades-long partnerships in the Philadelphia HIV community. Philadelphia FIGHT, a comprehensive AIDS care and service organization, and Penn Center for AIDS Research (CFAR) will ensure community input and outreach as research develops. The three main research pillars will be supported by separate smaller teams that include longstanding industry partners Merck & Co., Inc., Sangamo BioSciences, Inc. and Inovio Pharmaceuticals, Inc.

Juno Therapeutics Reports Clinical Hold on the JCAR015 Phase II ROCKET Trial

Jul. 7, 2016-- Juno Therapeutics, Inc. (NASDAQ:JUNO), a biopharmaceutical company focused on re-engaging the body’s immune system to revolutionize the treatment of cancer, today announced that it has received notice from the U.S. Food and Drug Administration (FDA) that a clinical hold has been placed on the Phase II clinical trial of JCAR015 in adult patients with relapsed or refractory B cell acute lymphoblastic leukemia (r/r ALL), known as the “ROCKET” trial. The clinical hold was initiated after two patient deaths last week, which followed the recent addition of fludarabine to the pre-conditioning regimen.
Juno has proposed to the FDA to continue the ROCKET trial using JCAR015 with cyclophosphamide pre-conditioning alone. In response, the FDA has requested that Juno submit, as a Complete Response to the Clinical Hold: a revised patient informed consent form, a revised investigator brochure, a revised trial protocol, and a copy of the presentation made to the agency yesterday. Juno will submit the requested information to the FDA this week.