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Epigenetic Drugs Reset Genes in Breast, Colon Cancers But Didn’t Shrink Tumors

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--Two clinical trials suggest promise for using these medications in combination with other cancer therapies

Two clinical trials using combinations of drugs meant to change cancer epigentics —or the way tumors express genes — failed at shrinking colon and breast tumors. However, these trials open the door for others currently in the works to combine epigenetic therapies with chemotherapy, immunotherapy and other treatments that could be more successful, Johns Hopkins researchers report in two new studies.

Cells operate using instructions not only from the four nucleotides that make up DNA, but also from so-called epigenetic, or “above the genome,” modifications — molecules that attach to DNA or to proteins that closely interact with this genetic molecule to switch genes off or on. For example, methyl groups that attach to genes can turn them off, preventing them from producing proteins. Histone deacelytalses, which remove molecules that attach to the protein “spools” that DNA coils around and allows DNA to coil more tightly, can also dampen gene expression.

Scientists have long known that cancer cells tend to express DNA abnormally because of epigenetic changes, particularly those that affect genes that would normally suppress tumors or allow them to be attacked by the immune system, explains Nita Ahuja, M.D., professor of urology, surgery and oncology at the Johns Hopkins University School of Medicine. However, she adds, lab work in cells and animal models of cancer has suggested that drugs that remove these abnormal epigenetic marks could be effective cancer treatments.

“It’s very hard to change someone’s DNA. It’s the hardware of the cell. But epigenetics is the software. It has some plasticity to it,” says Ahuja. “It’s been the dream for many of us in this field that we could harness that plasticity to treat cancer.”

While one epigenetic therapy, 5-azacitidine, has already been approved to treat a group of cancers involving the bone marrow and blood known as myelodysplastic syndrome, single epigenetic therapies haven’t shown promise for solid tumors such as those in colon cancer. Thus, Ahuja, fellow study leader Nilofer Azad, M.D., associate professor of oncology at the Johns Hopkins University School of Medicine, and colleagues launched a multi-institutional study to test two different epigenetic therapies on colon cancer in combination: 5-azacitidine, which removes DNA methylation, and entinostat, which inhibits histone acetylation.

The trial, detailed in the Feb. 5, 2017, Oncotarget, enrolled 47 colon cancer patients from April 2010 to December 2011, all of whom had failed multiple lines of traditional cancer treatments and had few options left. Thirty-seven of these patients underwent tumor biopsies before they started treatment, which involved subcutaneous shots of 5-azacitidine and taking entinostat orally. After two months of therapy, 18 of these patients underwent a second tumor biopsy.

Few patients had concerning side effects, suggesting that these drugs were safe to administer. Analyses of the collected tissue showed that the drugs reduced DNA methylation in 13 of these patients. However, none of the 47 experienced any shrinkage of their tumors, the primary goal of the study, says Azad. “Overall, this is a negative trial. We didn’t meet our primary endpoint,” she says.

However, she says, the fact that these drugs did appear to positively affect DNA methylation in the majority of patients suggests that epigenetic therapies could be effective in combination with other cancer therapies. For example, some cancers develop a resistance to chemotherapy or other treatments over time, an effect likely due to epigenetic changes. By removing epigenetic marks, these tumors might become susceptible to treatments they resisted before.

A second team of researchers, led by Vered Stearns, M.D., professor of oncology at the Johns Hopkins University School of Medicine, and Roisin M. Connolly, M.D., assistant professor of oncology at the school of medicine, tested this strategy in breast cancer patients in a trial detailed online on Dec. 15, 2016, in Clinical Cancer Research. The team launched a multicenter study that gave the same epigenetic drug combination to 40 breast cancer patients. Twenty-seven of these had a subtype called hormone-resistant breast cancer, and thus didn’t respond to commonly used hormone-blocking medications that can prevent cancer growth. Another 13 patients had triple-negative breast cancer, a subtype that’s known to be particularly aggressive and has few treatment options. Like the colon cancer patients in the other trial, each of these 40 breast cancer patients had failed multiple lines of treatment.

Similar to the patients in the colon cancer trial, 95 percent of those in the breast cancer trial had pre-treatment biopsies, then 60 percent of these underwent a subsequent biopsy after two months of treatment. Tissue analyses showed that the majority of these patients also had reduced DNA methylation. However, unlike the colon cancer trial, a single patient in the hormone-resistant group experienced significant tumor shrinkage.

As cancers in other hormone-resistant patients began to progress, the researchers offered them the option to restart hormone-blocking therapy, an idea that they thought might have positive results if the epigenetic therapies had removed methylation responsible for hormone resistance. Sure enough, a second patient experience significant tumor shrinkage after starting this protocol.

The fact that even two patients experienced positive outcomes on this trial is a promising start, says Stearns. “We need to go back to the lab and get a better understanding of these tumors and their biology to figure out which subset of patients is most likely to benefit from these treatments,” she says. “Even though we didn’t meet the endpoints that were prespecified for this study, we’ve generated several really interesting hypotheses that could lead to more effective treatments for some patients in the future.”

One of those hypotheses, says Connolly, is that epigenetic therapies appear to take significantly longer to work than traditional cancer chemotherapies. “There’s a suggestion that maybe with longer treatment, particularly with adding hormone-blocking therapy or other agents, a larger population of patients might benefit.”

She and the other researchers are also planning to test combining these medications with immunotherapies, cancer treatments that have shown limited success for some tumor types and no success for others. By “hitting the reset button” for tumor cells with epigenetic therapies, Connolly says, researchers may be able to significantly increase the response rate for immunotherapy treatments.

Both trials were funded by Stand Up to Cancer, a program of the Entertainment Industry Foundation, administered by the American Association for Cancer Research (AACR). The colon cancer trial received additional funding from the AACR Jeanette Littlefield Grant, the Conquer Cancer Foundation and the Mayo Clinic-Phase II Consortium grant N01-CM-2011-00099. The breast cancer trial received additional funding from the Cancer Therapy Evaluation Program, National Cancer Institute (grants MCR-0019-P2C, U01 CA070095 and UM1CA186691); Specialized Programs of Research Excellence in Breast Cancer (P50 CA88843), the Microarray Core (NIH grants P30 CA006973) and Analytical Pharmacology Core of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins (NIH grants P30 CA006973 and UL1 TR 001079), the Shared Instrument Grant (1S10RR026824-01), the Clinical Protocol and Data Management facilities (P30 CA006973 and P30CA 047904) and the Bioinformatics Core (P30 CA006973), the Pennsylvania Department of Health, QVC and Fashion Footwear Association of New York (FFANY), the Cindy Rosencrans Fund for Triple Negative Breast Cancer Research, and Lee Jeans and the Entertainment Industry Foundation.

Other Johns Hopkins researchers who participated in the colon cancer trial include Anup Sharma, Thomas Brown, Prakriti Medvari, Hariharan Easwaran, Ihab Kamel, Ross Donehower and Stephen Baylin. Other Johns Hopkins researchers who participated in the breast cancer trial include Huili Li, Zhe Zhang, Michelle A. Rudek, Stacie C. Jeter, Shannon A. Slater, Penny Powers, Antonio C. Wolff, John H. Fetting, Nita Ahuja, Leslie Cope, Stephen B. Baylin and Cynthia A. Zahnow.