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Insight & Intelligence™ : May 5, 2014

Cancer Vaccines in the Omics Era

New technologies and approaches are leading to new breakthroughs.
  • Richard A. Stein, M.D., Ph.D.

Until a few decades ago, cancer was mostly viewed as a genetic condition in which a single mutated cell clone survived and gave rise to a homogeneous tumor in which all cells shared the same genotype. However, a classical experiment published in 1977 revealed that individual clones derived from murine melanoma cells, when transplanted into syngenic mice, varied greatly in terms of their ability to produce metastatic tumors.

Following this initial evidence of broad heterogeneity in terms of the metastatic capability of individual cancer cells, many recent studies based on modern DNA sequencing technology revealed that multiple different clones can survive and are represented in the malignant tumor. Thus, the tumor cell population is not homogeneous but distinctly heterogeneous.

“There are as many as 80 functional mutagenic clones in colon cancer, and that number may is even higher in lung and breast cancer,” says Michael G. Hanna Jr., Ph.D., chairman and CEO at Vaccinogen. Over time, studies on different cancer samples allowed the mutational landscapes of the malignant tumors to be characterized and compared. Approximately 80 distinct mutations have been characterized for colon cancer, with as few as three of these being shared by tumors from two different patients. However, a major shortcoming of many cancer vaccines developed in the past was that only one or several common antigens were used to immunize against the whole tumor.

“In colon cancer, generating a vaccine targeting those one or few most common mutations is similar to a situation in which we needed to immunize against diverse influenza strains but we would miss one or more of them,” Dr. Hanna added. “We have actually experienced this limited vaccination program over the last few years.” This explains why most cancer vaccines that over the past decade reached Phase II or III clinical trials failed to show clinical benefits.

Besides the inter-tumor heterogeneity, significant intra-tumor heterogeneity has been described for malignant tumors. As a result, the different clones are not equally distributed within the tumor.

“Since tumors are so heterogeneous, we decided that the only rational approach is to use a patient’s own whole tumor as the source of cells for the vaccine,” Dr. Hanna said. This unequal distribution of the different clones within the tumor explains why a biopsy may not provide an accurate representation of all the mutations that are present. He adds, “Using the whole autologous tumor allowed us to embrace the genomic heterogeneity of the tumor cells, and to ensure a more robust immune response, because those cells represent the entire antigenic diversity of the primary tumor.” 

Preventing Recurring Cancers

In several dose and regimen optimization studies conducted since 1985, when they started implementing this approach, Dr. Hanna and colleagues eventually reported a significant improvement in the overall survival and recurrence-free survival of the participants in colon cancer clinical trials. “Not only did we see a robust immune response, but we also a recent independent review of the patient samples showed that the immunologic memory and thus clinical benefit can persist for as long as 15 years,” Dr. Hanna commented.

There is an additional reason explaining why many cancer vaccine studies have failed in the past: according to Dr. Hanna, “Many studies used vaccines to treat established disease, and if we consider the same principle as in infectious diseases, this would be similar to immunizing a patient that already developed polio with the polio vaccine.”

We now know that there are immune suppressor molecules in established tumors and a great deal of effort is going into identifying these and developing drugs to block or interfere with them. While we have no guarantee that this will result in improve treatment in this underserved population of advanced disease patients, in the approach that Dr. Hanna and colleagues pioneered, the primary tumor is used, after surgery, not to treat established disease, but to prevent recurrences. “And the result that we are seeing is a significantly higher recurrence-free survival,” he added.

Immunogenicity Issues

“The ability to have the genomes of literally thousands of different cancer patients has really accelerated the development of molecular targeted therapies, including targeted immunotherapy,” says Mary L. Disis, M.D., professor of Medicine at the University of Washington. One of the major difficulties in using the immune system to target cancer cells is that for many solid tumors, the preexisting immune response against endogenous antigens expressed by cancer cells is quantitatively very limited. This opens the need to identify immunogenic proteins that are present in all patients.

“One of the advantages that genomics offers us is the possibility to have a dataset that we can mine to look for proteins that could be potential candidate antigens for a vaccine,” she said. In addition to targeting the immune system to recognize and attack the cancer cells, an essential aspect of the therapeutic approaches involves the need to specifically eradicate the cells that actively drive the malignant transformation. “We are able to use -omics medicine to identify vaccine candidates,” she adds, “but a significant challenge emerges when it gets down to determine the immunogenicity of those candidates, or the characteristics of the immune response that they generate, or whether those candidates are even capable of being immunogenic.”

“In the omics era, we are finding new and attractive cancer vaccine targets, but in some patients we may not know what the most effective tumor rejection antigen is,” says James L. Gulley, M.D., Ph.D., chief, genitourinary malignancies branch at the National Cancer Institute, NIH. Many previous studies revealed that, in certain cancers, mutations are encountered more frequently. This suggested that an underlying immune response may exist against these mutated antigens, and immune checkpoint inhibitors may be able to unlock this immune response leading to clinical responses. In other instances, certain proteins, such as brachyury, are overexpressed in malignant tumors as compared to nontransformed tissue, providing another opportunity to target the immune response as a therapeutic approach in malignancies.

“It may not even matter so much what we initiate the immune response against, because once the immune cell learns how to take a tumor cell apart, the proteins are processed and presented by the antigen-presenting cells back to the immune system, and maybe other targets that are more relevant in the patient may be presented and mount a much broader immune response than the one to the initial antigen,” Dr. Gulley commented.

During this process, called antigen spreading or antigen cascade, the immune response initiated against an antigen ends up in being subsequently directed against multiple different tumor targets, which may be very specific for that patient’s tumor and may become more clinically relevant over time. As a result of this iterative process, the immune system is able develop a better response against that tumor. “Over time, we and others have seen this in patients and there is evidence that this broader immune response is associated with improved patient outcomes,” Dr. Gulley reported.


A recurring challenge in the field of cancer vaccines concerns the development of biomarkers, which may have a predictive value or may be used to monitor evolution after therapeutic interventions. “In the past, we focused mostly on blood and serum biomarkers, and those are important,” Dr. Gulley said, “but in the future we have to explore what is going on at the level of the tumor, and we need to look not only at the protein, cytokine, and chemokine expression, but also at the types of cells that are present in the tumor microenvironment,”

“Incorporating genomics and proteomics into cancer vaccines will be the driving force in understanding which genes are turned on or off at various moments,” said Leaf Huang, professor of molecular pharmaceutics at the University of North Carolina at Chapel Hill. Research in Dr. Huang’s group focuses on developing therapeutic cancer nanovaccines.

“In cancer, different molecules are expressed at different stages of the disease and, additionally, there are marked heterogeneities among the cancer cells in the same person,” Dr. Huang said. As a result, the immune system will be exposed to different antigens at different stages during the disease.

In their experimental strategy to develop a vaccine against melanoma, Dr. Huang and colleagues took advantage of the fact that tyrosinase-related protein 2 (TRP-2), which is part of the melanin synthesis pathway, is expressed by most melanoma patients. By delivering a peptide derived from this protein, together with an adjuvant, to dendritic cells, Dr. Huang and colleagues were able to elicit a powerful, systemic immune response. “This is only one particular example, but many other cancers express different types of antigens, and it is crucial to perform a proteomic and genomic analysis of cancer cells,” he said.

The omics sciences marked a series of conceptual changes that reshaped the field of cancer biology. In addition to providing new and more in-depth perspectives on cellular and molecular processes involved in malignant transformation, these advances are opening new diagnostic and therapeutic opportunities including the design of biomarkers and cancer vaccines. These new directions in cancer research are a testimony of the interdisciplinarity that characterizes the transition from the bench to bedside and fuels progress in biology and medicine.