Public-Private Consortium Aims to Cut Preclinical Cancer Drug Discovery from Six Years to Just One

Scientists from two U.S. national laboratories, industry and academia today launched an unprecedented effort to transform the way cancer drugs are discovered by creating an open and sharable platform that integrates high-performance computing, shared biological data from public and industry sources and emerging biotechnologies to dramatically accelerate the discovery of effective cancer therapies.

The goal of the consortium – Accelerating Therapeutics for Opportunities in Medicine (ATOM) – is to create a new paradigm of drug discovery that would reduce the time from an identified drug target to clinical candidate from the current approximately six years to just 12 months. ATOM aims to transform cancer drug discovery from a time-consuming, sequential and high-risk process into an approach that is rapid, integrated and with better patient outcomes — using supercomputers to pretest many molecules simultaneously for safety and efficacy.

The consortium comprises the Department of Energy’s Lawrence Livermore National Laboratory (LLNL), GSK, the National Cancer Institute’s Frederick National Laboratory for Cancer Research (FNLCR), and the University of California, San Francisco (UCSF). ATOM welcomes additional public and private partners who share the vision.

“The goals of ATOM are tightly aligned with those of the 21st Century Cures Act, which aims in part to enable a greater number of therapies to reach more patients more quickly,” said FNLCR Laboratory Director David Heimbrook. “Although initially focused on precision oncology – treatments targeted specifically to the characteristics of the individual patient’s cancer – the consortium’s discoveries could accelerate drug discovery against many diseases.”

ATOM will develop, test and validate a multidisciplinary approach to drug discovery in which modern science, technology and engineering, supercomputing simulations, data science and artificial intelligence are highly integrated into a single drug-discovery platform that can untimately be shared with the drug development community at large.

“As we have learned more about what modern supercomputers can do, we’ve gained confidence that this approach can make a big difference in creating medicines,” said John Baldoni, senior vice president, R&D at GSK. “We must do all that we can to reduce the time it takes to get medicines to patients. GSK is working to set a precedent with pharmaceutical companies by sharing data on failed compounds.”

GSK will initially contribute chemical and in vitro biological data for more than 2 million compounds from its historic and current screening collection, as well as preclinical and clinical information on 500 molecules that have failed in development but could help accelerate development of new compounds by providing knowledge about the underlying biology of candidate compounds and that of the human body. Combined with data on successful drugs, GSK’s offering represents a broad base of information for ATOM researchers. In addition, GSK will provide expertise in drug discovery and development, computational chemistry and biology.

The ATOM team will combine data provided by GSK with publicly available data, and that of future consortium members, to generate new dynamic models that can better predict how molecules will behave in the body compared to the current iterative and time-consuming practices. In this effort, LLNL will contribute its best-in-class supercomputers, including its next-generation system Sierra, as well as its expertise and innovative approaches to modeling and simulation, cognitive computing, machine learning and algorithm development. More broadly, by tackling the ambitious challenge of cancer therapies, ATOM will drive technologies vital to the core missions of the Department of Energy and National Nuclear Security Administration (NNSA).

“ATOM is a novel public-private partnership that draws on the lab’s unique capabilities to create a paradigm change in drug development,” said LLNL Director Bill Goldstein. “It will help to strengthen U.S. leadership in high-performance computing and, by speeding the discovery of therapeutics, contribute to biosecurity.”

For its part, FNLCR will contribute from its wealth of scientific expertise in precision oncology, computational chemistry and cancer biology, as well as support for open sharing of data sets and predictive modeling and simulation tools. UCSF will provide expertise from a long history of innovation in drug discovery and medicine to improve the lives of patients.

“We at UCSF are eager to lend our expertise to this effort,” said UCSF Chancellor Sam Hawgood, MBBS. “UCSF scientists and clinicians have long been leaders in drug discovery, therapeutics, and cancer biology with the UCSF Helen Diller Family Comprehensive Care Center among the top-ranked cancer institutes in the country. Our role with ATOM is therefore in lock step with UCSF’s mission of advancing health worldwide.”

ATOM welcomes additional public and private partners who share the vision of the consortium, which will have physical headquarters in the Mission Bay neighborhood of San Francisco, adjacent to UCSF’s newest campus.

Good-Guy Bacteria May Help Cancer Immunotherapies Do Their Job

Individuals with certain types of bacteria in their gut may be more likely to respond well to cancer immunotherapy, researchers at the Harold C. Simmons Comprehensive Cancer Center found in a study of patients with metastatic melanoma.

The incidence of melanoma has been increasing over the past 40 years. Immunotherapies have dramatically improved the outlook for patients with metastatic melanoma in the past half-dozen years, but still only about half of these patients go into remission.

UT Southwestern cancer researchers analyzed the gut bacteria of 39 melanoma patients who were treated with immunotherapies and found a strong association between a good response and the presence of particular bacteria.

“Our research suggests there were certain good-guy bacteria that are needed to optimize the effectiveness of checkpoint inhibitors. These bacteria somehow prime your immune system so that it’s better able to attack cancer cells and kill them,” said senior author Dr. Andrew Koh, Associate Professor of Pediatrics and Microbiology with the Simmons Cancer Center.

Rick Spurr, former CEO of Zix, a company that provides email encryption services for banks and health care facilities, volunteered for the study that helped identify the link. The grandfather of six was diagnosed with metastatic melanoma, which was discovered on his lungs while he was fighting off a bout of pneumonia.

Mr. Spurr was treated with an every-other-week infusion of nivolumab, an immunotherapy drug that acts by lifting a brake on the immune system, allowing the body’s natural defenses to go into overdrive.

“I felt virtually no side effects from the treatment,” he said. “I started the treatment in the summer and I was skiing in November.”

Researchers found he had the beneficial gut bacteria and suspect this microbiome contributed to the outcome. As a group, patients who responded well to the immunotherapy had three specific bacteria:

  • Bacteroides thetaiotaomicron
  • Faecalibacterium prausnitzii
  • Holdemania filiformis

All three are common normal flora in the human intestinal tract.

After identifying the link, researchers looked for a potential reason for the association between the helper bacteria and immunotherapy effectiveness. “Is it something the bacteria are making? We examined metabolites in these subjects and found the strongest correlation between anacardic acid, present in cashews and mangoes, and the beneficial bacteria,” Dr. Koh said.

Researchers plan to follow up on the current research, which appears in the journal Neoplasia, with larger clinical studies.

“While these preliminary observations do not establish a firm causal connection between gut microbes and immunotherapy efficacy, they may lead eventually to a probiotic cocktail that could be given along with immunotherapy to enhance the chance of response,” said Dr. Koh, Director of Pediatric Hematopoietic Stem Cell Transplantation at UT Southwestern.

The research was supported by the Roberta I. and Norman L. Pollock Fund, the Melanoma Research Fund, the T. Boone Pickens Cancer Research Fund, the Cancer Prevention and Research Institute of Texas, and the National Institutes of Health.

The Harold C. Simmons Comprehensive Cancer Center is the only NCI-designated Comprehensive Cancer Center in North Texas and one of just 49 NCI-designated Comprehensive Cancer Centers in the nation. Simmons Cancer Center includes 13 major cancer care programs. In addition, the Center’s education and training programs support and develop the next generation of cancer researchers and clinicians. Simmons Cancer Center is among only 30 U.S. cancer research centers to be designated by the NCI as a National Clinical Trials Network Lead Academic Participating Site.

About UT Southwestern Medical Center

UT Southwestern, one of the premier academic medical centers in the nation, integrates pioneering biomedical research with exceptional clinical care and education. The institution’s faculty has received six Nobel Prizes, and includes 22 members of the National Academy of Sciences, 18 members of the National Academy of Medicine, and 14 Howard Hughes Medical Institute Investigators. The faculty of more than 2,700 is responsible for groundbreaking medical advances and is committed to translating science-driven research quickly to new clinical treatments. UT Southwestern physicians provide care in about 80 specialties to more than 100,000 hospitalized patients, 600,000 emergency room cases, and oversee approximately 2.2 million outpatient visits a year.

New Ovarian Cancer Immunotherapy Study Poses Question: Can Microbiome Influence Treatment Response?

Roswell Park Study with pembrolizumab in untried combination is first ovarian cancer clinical trial to incorporate gut flora analysis

A new clinical study underway at Roswell Park Cancer Institute is the first to test the combination of the immunotherapy pembrolizumab with two other drugs as treatment for recurrent epithelial ovarian cancer, and is also the first ovarian cancer clinical trial to incorporate analysis of patients’ microbiomes — the bacteria present in the human gut and other organs.

This new study, led by Principal Investigator Emese Zsiros, MD, PhD, FACOG, Assistant Professor of Oncology in Roswell Park’s Department of Gynecologic Oncology and Center for Immunotherapy, is a phase II clinical trial that will enroll approximately 40 patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer, and will evaluate the impact of the combination of the PD1-targeting antibody pembrolizumab (Keytruda) with intravenous bevacizumab (Avastin) and oral cyclophosphamide (Cytoxan) on antitumor immune responses and on progression-free survival.

Pembrolizumab has been approved by the U.S. Food and Drug Administration for treatment of advanced melanoma, some metastatic non-small cell lung cancers and recurrent squamous cell head/neck carcinoma, but has only been tested in a small number of ovarian cancer patients, as a single drug and showing modest response. The investigators say a strong scientific rationale supports their hypothesis that the combination of pembrolizumab with two other drugs that have already been approved to treat ovarian cancer — bevacizumab and low-dose oral cyclophosphamide — may have much broader benefit for patients.

“Our biggest hope is that by trying these three drugs in combination, we can significantly extend the lives of patients with recurrent ovarian cancer. We also hope to minimize the side effects associated with chemotherapy drugs, and to markedly improve the quality of our patients’ lives,” says Dr. Zsiros. “We will be looking at potential biomarkers that will tell us who can most benefit from this therapy combination and to better understand how cancer cells and immune cells communicate with one another so that we can design better medications to kill cancer efficiently.“

As part of this study, the clinical team will analyze blood, tumor, stool, vaginal and skin microbiome samples, looking to identify possible associations between these markers with clinical outcomes and tumor response. The study, which is supported by a grant from Merck & Co. Inc., maker of pembrolizumab, will be one of the first to analyze these bacteria to determine possible associations with response to immunotherapeutic agents in patients with cancer.

“We’re looking at how to improve our immune defenses to cancer, but we’re looking at it from a variety of angles,” says Dr. Zsiros. “There’s a whole new area of research suggesting that what’s going on in our gut, our gut flora, has a huge influence on your overall health and happiness, and this study will extend that work into some new directions.”

According to the National Cancer Institute, epithelial ovarian cancer is one of the most common gynecologic malignancies, and is the fifth most frequent cause of cancer death in women.

 

New Model For Understanding Myeloma

All cancers originate from an earlier, or precursor, state — such as a benign or asymptomatic condition. To develop new approaches to cancer prevention, scientists have attempted to grow tumor cells from precursor states in animal models. Myeloma — a type of cancer that forms in white blood cells — is an example of a cancer that is preceded by a condition called monoclonal gammopathy.

In a new study, Yale professors Madhav Dhodapkar, Richard Flavell, and their co-authors describe new mouse models, wherein mice carry human versions of six genes that are essential for growth of tumor cells. The found that when the humanized mice were injected with tumor and non-tumor cells, both cell types were able to grow. The finding provides a potential new approach to understanding how myeloma develops and how to prevent it.

Yale Study Identifies New Way To Suppress Lung Tumors

Lung cancer cell growth depends on certain proteins that require the addition of sugar molecule chains to become active. Scientists have long thought that the addition of these sugar chains is like an on or off switch, and that blocking their addition would be harmful. Now a Yale-led research team has identified a new blocking mechanism that acts more like a dimmer switch and potently inhibits lung tumor cell growth.

Senior author Joseph Contessa and his co-authors screened hundreds of thousands of chemical compounds to uncover a new inhibitor that reduces the addition of sugar chains without harming non-tumor cells. Based on this finding, the research team plans to test the compound in preclinical studies as a potential new strategy for treating lung cancer — the leading cause of cancer death nationwide.

JCAR014 Clinical Data Published In Science Translational Medicine: Patients With Advanced Lymphoma In Remission After T-Cell Therapy

In a paper published today in Science Translational Medicine, researchers from Fred Hutchinson Cancer Research Center shared data from an early-phase study of patients with advanced non-Hodgkin lymphoma (NHL) who received JCAR014, a Chimeric Antigen Receptor (CAR) T cell treatment, and chemotherapy. CAR T cells are made from a patient’s own immune cells that are then genetically engineered to better identify and kill cancer cells.

The paper reported the results of the first 32 patients in a dose-finding trial of JCAR014 following a round of chemotherapy, called lymphodepletion, designed to create a more favorable environment for the CAR T cells to grow in the patient’s body. Key findings of the study demonstrated the importance of the choice of lymphodepletion regimen and the effects of different doses of CAR T cells. 50 percent of the 18 patients who were evaluable for efficacy after receiving CAR T cells and chemotherapy agents fludarabine and cyclophosphamide (Cy/Flu) had a complete response, which compares favorably to the 8 percent complete response rate in patients who received JCAR014 plus cyclophosphamide-based chemotherapy without fludarabine. As previously reported, dose-limiting toxicities were observed in some patients in this dose-finding study who received the highest CAR T-cell dose. The study continues with the intermediate CAR T-cell dose.

In patients that received Cy/Flu lymphodepletion and the intermediate dose of JCAR014, the data showed a promising early efficacy and side effect profile. Specifically:

• Overall Response rate: 82 percent (9/11)
• Complete Response rate: 64 percent (7/11)
• Severe Cytokine Release Syndrome: 9 percent (1/11)
• Severe neurotoxicity: 18 percent (2/11)

JCAR014’s hallmark is its use of a one-to-one ratio of helper (CD4+) and killer (CD8+) CAR T cells, which join forces to kill tumor cells that produce CD19, a molecule found on the surface of many blood cancer cells, including lymphoma and leukemia. By controlling the mixture of T cells that patients receive, the researchers can see relationships between cell doses and patient outcomes that were previously elusive. The data also suggest that with a defined one-to-one composition of cells, efficacy of treatment is increased, while toxic side effects are minimized.

“With the defined composition treatment, we are able to get more reproducible data about the effects of the cells – both the beneficial impact against the cancer and any side effects to the patient,” said Fred Hutch clinical researcher Dr. Stan Riddell, one of the senior authors of the paper, along with Dr. David Maloney. “We are then able to adjust the dose to improve what we call the therapeutic index – impact against the tumor, with lower toxicity to the patient.”

“This study shows that at the right dose of CAR T cells and lymphodepletion, we can achieve very good response rates for NHL patients who have no other treatment options,” said Dr. Cameron Turtle, an immunotherapy researcher at Fred Hutch and one of the study leaders.

For Juno Therapeutics (NASDAQ: JUNO), these insights from the JCAR014 study are key to its development of JCAR017, a similar product candidate for the treatment of CD19 positive blood cancers. Like JCAR014, JCAR017 uses a one-to-one ratio of helper and killer CAR T cells, and the company believes it has the potential to be a “best-in-class” treatment for non-Hodgkin lymphoma, chronic lymphocytic leukemia, and adult and pediatric acute lymphoblastic leukemia. JCAR017 is currently in a phase I, multi-center study.

“We are encouraged by the efficacy and duration of response that we are seeing with defined composition CAR T treatment in patients with lymphoma and other B-cell malignancies,” said Mark J. Gilbert, Juno’s Chief Medical Officer. “We hope that the insights from JCAR014 will make it possible to bring more life-saving treatments to more patients with blood cancers.”

In addition to Fred Hutch researchers, the study team also included scientists from Juno and the University of Washington. Juno provided one of the trial’s sources of funding, along with the National Institutes of Health, Washington state’s Life Science Discovery Fund and the Bezos Family Foundation.