Disabling critical ‘node’ revs up attack when cancer immunotherapies fall short

Today’s checkpoint inhibitor drugs target receptors such as PD1 and CTLA-4, which act as a type of “off switch” on a T cell to prevent it from attacking other cells. Inhibiting these pathways with one or a more of the drugs releases these “brakes” so the immune system can fight the disease. However, over half … Continue reading “Disabling critical ‘node’ revs up attack when cancer immunotherapies fall short”

Today’s checkpoint inhibitor drugs target receptors such as PD1 and CTLA-4, which act as a type of “off switch” on a T cell to prevent it from attacking other cells. Inhibiting these pathways with one or a more of the drugs releases these “brakes” so the immune system can fight the disease. However, over half of patients on the drugs relapse or their cancer progresses.

“The proposed approach has some elegance to it — rather than try to figure out all inhibitory pathways that the tumor has enabled, find a critical pathway that regulates many of the inhibitory signals and cripple that instead,” said senior author Andy J. Minn, MD, PhD, an assistant professor of Radiation Oncology in the Perelman School of Medicine at the University of Pennsylvania. “Interferon signaling is like a critical node in a network. Disable it and a large part of that network collapses.”

Using breast cancer and melanoma mouse models, Minn, first-author Joseph L. Benci, a graduate student in Penn’s Cell and Molecular Biology Graduate Group, and their colleagues from the departments of Radiation Oncology, Abramson Family Cancer Research Institute and Penn’s Parker Institute for Cancer Immunotherapy showed that prolonged interferon signaling in tumor cells increased resistance to checkpoint inhibitors through multiple inhibitory pathways, and that blocking this response resulted in improved survival and powerful tumor responses.

Authors on the paper also include Robert Vonderheide, MD, DPhil, the Hanna Wise Professor in Cancer Research, Amit Maity, MD, PhD, a professor of Radiation Oncology, and E. John Wherry, PhD, a professor of Microbiology and director of the Institute for Immunology at Penn.

Studies have shown that combining checkpoint inhibitors, ipilimumab and pembrolizumab, for instance, as well as adding radiation therapy, as described in a Penn paper from the same researchers in Nature in 2015, elicits promising tumor responses in patients. But many still do not respond because of additional unidentified “brakes.”

Researchers modeled this unknown resistance in breast cancer and melanoma mouse models with various lab techniques, including the genetic tool CRISPR, and found that treating the mice with checkpoint inhibitors (against PD1 and/or CTLA4) with or without radiation, along with the JAK inhibitor ruxolitinib, effectively restored complete responses and long-term survival in mice with tumors that are normally highly resistant to therapy. Inhibiting this pathway could also bypass the need for multiple checkpoint inhibitors: one checkpoint inhibitor (anti-CTLA4) and the JAK inhibitor in the breast cancer mouse model resulted in a 100 percent complete response and survival.

JAK inhibitors, U.S. Food and Drug Administration-approved drugs to treat myelofibrosis and psoriasis, target the well-studied interferon pathway, typically considered to be immunostimulatory. However, the authors found that over time interferon signaling changes how cells respond epigenetically to molecular signals in the tumor, switching from stimulatory to suppressive, similar to what happens in a chronic viral infection. Thus, blocking it switched off the tumor’s resistance in mice.

“To our surprise, blocking interferon driven resistance not only antagonizes multiple inhibitory pathways that hinders combination therapies in mice,” Minn said, “but it may also provide a general strategy to the challenge of designing complex combination checkpoint blockade therapies that seek to address the well-known problem of resistance.”

Downgrading the number of checkpoint inhibitors for therapy has its advantages, given the severe and sometimes life-threatening toxicities that come along with combination therapies, including autoimmune complications such as colitis and fatal myocarditis.

“There is a real translational implication here,” Minn said. “Because the interferon signaling pathway is targetable pharmacologically, we could perhaps mimic what we did in mice using JAK inhibitors that already exist for other purposes.”

The team is looking to begin a new clinical study in lung cancer patients based on their findings in the upcoming months. The researchers also identified two potential biomarkers, MX1 and IFIT1, that may help identify tumors in patients under the influence of this interferon suppression.

Rare childhood disease linked to major cancer gene

According to Niall Howlett, URI associate professor of cell and molecular biology and Rhode Island’s leading expert on Fanconi anemia, the disease is characterized by birth defects, bone marrow failure and increased cancer risk. He said the genes that play a role in the development of the disease are also important in the development of hereditary breast and ovarian cancer.

Howlett’s new study now establishes a molecular link between Fanconi anemia and a gene strongly associated with uterine, prostate and brain cancer. This research was published this month in the journal Scientific Reports, with URI graduate student Elizabeth Vuono as lead author.

About 1 in 150,000 children in the United States is born with Fanconi anemia.

“People often ask why we study such a rare disease,” said Howlett, who has been studying Fanconi anemia for nearly 20 years. “First and foremost, there is no cure or effective treatments for it. So a greater understanding of the molecular basis of Fanconi anemia is critical to address this need.”

In addition, Howlett said there are countless examples of how the study of Fanconi anemia has greatly benefited the general population. The first umbilical cord blood transplant, for example, was performed with a Fanconi anemia patient. Bone marrow transplants have become much safer and more effective because of studies with Fanconi anemia patients. And new breast and ovarian cancer genes have been discovered as a result of studies on the molecular biology of Fanconi anemia.

Howlett’s current research is another example of the broader impact of Fanconi anemia studies.

The URI researcher speculated about the existence of a biochemical link between Fanconi anemia and PTEN. Mutations in PTEN occur frequently in uterine, prostate and brain cancer.

“The PTEN gene codes for a phosphatase — an enzyme that removes phosphate groups from proteins,” explained Howlett. “Many Fanconi anemia proteins have phosphate groups attached to them when they become activated. However, how these phosphate groups are removed is poorly understood.”

Howlett said that cells from Fanconi anemia patients are characteristically sensitive to a class of drugs widely used in cancer chemotherapy called DNA crosslinking agents.

“So we performed an experiment to determine if Fanconi anemia and PTEN were biochemically linked,” he said. “By testing if cells with mutations in the PTEN gene were also sensitive to DNA crosslinking agents, we discovered that Fanconi anemia patient cells and PTEN-deficient cells were practically indistinguishable in terms of sensitivity to these drugs. This strongly suggested that the Fanconi anemia proteins and PTEN might work together to repair the DNA damage caused by DNA crosslinking agents.”

By using epistasis analysis, a genetic method that determines if genes work together, Howlett and his research group found that the Fanconi anemia proteins and PTEN do indeed function together in this repair pathway.

“Before this work, Fanconi anemia and PTEN weren’t even on the same radar,” said Howlett. “This is really important to understanding how this disease arises and what its molecular underpinnings are. The more we can find out about its molecular basis, the more likely we are to come up with strategies to treat the disease.”

Howlett’s research is equally important to cancer patients who do not have Fanconi anemia. He said that since his study found that cells missing PTEN are highly sensitive to DNA crosslinking agents, it should be possible to predict whether a particular cancer patient will respond to this class of chemotherapy drug by conducting a simple DNA test.

“We can now predict that if a patient has cancer associated with mutations in PTEN, then it is likely that the cancer will be sensitive to DNA crosslinking agents,” he said. “This could lead to improved outcomes for patients with certain types of PTEN mutations.”

Researchers uncover more genetic links to brain cancer cell growth

In a report on one of the two findings, published online Sept. 20 in Acta Neuropathologica, the investigators identified alterations in a protein known as ATRX in human brain tumors that arise as part of a genetically inherited condition known as neurofibromatosis type 1 (NF1). The disorder, marked initially by benign tumors on nerves, often leads to brain cancer, and although most NF1-related malignancies are nonaggressive, a fraction are “high-grade” and difficult to treat, experts say.

Study leader Fausto J. Rodriguez, M.D., associate professor of pathology at the Johns Hopkins University School of Medicine and member of the Johns Hopkins Kimmel Cancer Center, says the new study sought to sort out what makes the more aggressive NF1-related tumors genetically different from low grade tumors and normal, healthy cells.

Research from other scientists at Johns Hopkins, he says, had suggested that some tumors, particularly those that affect the nervous system, have mutations in the ATRX gene, which produces proteins that appear to maintain the length of telomeres, repetitive segments of DNA on the ends of chromosomes that typically shorten each time a cell divides. Telomere shortening limits the number of divisions that cells can undergo. By keeping telomeres long, ATRX mutations give cells the ability to endlessly divide, a hallmark of cancer.

To see what role ATRX mutations might play in NF1-related brain cancers, Rodriguez and his colleagues examined samples of both high- and low-grade gliomas — tumors that arise from parent cells of nerve-supporting cells called glia — which were removed by surgery from 27 patients with NF1.

They tested the samples for longer telomeres that weren’t the product of a protein called telomerase, which helps maintain telomere length in healthy cells and more commonly in other cancers. This nontelomerase-associated telomere lengthening is known as alternative lengthening of telomeres or ALT. They also tested for loss of the protein product of ATRX caused by mutations in this gene.

About a third of the 27 samples had ALT and loss of the ATRX protein. The presence of both factors occurred in seven of 12 patients with high-grade tumors but only two of 14 with low-grade cancers.

If further studies confirm the role of the mutation, Rodriguez says, researchers might be able to develop anticancer agents to target cells with ATRX mutations or ALT to limit telomere length. In the meantime, he adds, gaining a better understanding of aggressive NF1-related tumors allows researchers to develop more realistic models of these cancers in the lab.

In a second study, described online Oct. 14 in Modern Pathology, the Johns Hopkins investigators sought a genetic source that could accurately identify subsets of low-grade pediatric gliomas, the most frequent tumors of the central nervous system in children. Unlike many other types of cancerous tumors, low-grade pediatric gliomas appear to have few genetic mutations, leaving the biology of these cancers a mystery, says Rodriguez.

In an effort to unravel that mystery, Rodriguez and his colleagues focused on the ways those cancer cells regulate the expression of genes or whether they make their constituent proteins. One way to control expression, he explains, is through microRNA, small pieces of noncoding genetic material that control whether a gene’s protein is generated from the DNA blueprints inside cell nuclei.

The researchers analyzed the amounts of 800 different microRNAs in nine different types of low-grade gliomas or related cancers. Of all of these, one in particular caught the researchers’ eyes: a microRNA called miR-487b, which was consistently underexpressed in tumor tissue compared to healthy cells.

To pin down the role of this microRNA, the researchers artificially increased its levels in lines of laboratory-grown human cancer cells that appeared to make too little of it, in turn bringing down the levels of the protein it affects. Unlike unaltered cancer cells, these new cells formed 30 percent fewer colonies and had decreased levels of other proteins, such as Nestin, by a third. Nestin is known to be important in both early development and in cancers.

Eventually, Rodriguez says, physicians might be able to look at the levels of this and other microRNAs in blood or cerebrospinal fluid to test for the presence of cancer. Researchers might also be able to target microRNAs directly, altering their levels to make cancer cells less likely to form tumors.

“By gaining a better understanding of the fine genetic differences between cancers and healthy tissues, we can develop better therapeutic or prognostic strategies,” he says. Funding for the studies was provided by the Childhood Brain Tumor Foundation, the Pilocytic/Pilomyxoid Astrocytoma Fund, and Lauren’s First and Goal.