To Root Out Cancer Immunotherapies Dig Deeper

Investigators Can Work More Systematically against Cancer’s Escape Mechanisms

Immunotherapy has done more than just scratch beneath the surface of cancer. In recent years, immunotherapy has started to undermine melanoma, non-small cell lung cancer, kidney cancer, bladder cancer, head and neck cancers, and Hodgkin’s lymphoma.

Immunotherapy, a growing body of research suggests, may topple cancers resistant to other treatments. Also, immunotherapy has shown that in some circumstances, it may cause fewer side effects than those associated with standard chemotherapy.

Despite these promising developments, immunotherapy sometimes fails. Patients may not respond to immunotherapy, or they may respond initially before ultimately experiencing relapse or recurrence. Patients may also suffer autoimmune-like consequences if their immune systems are overactivated.

Immunotherapy’s uneven record against cancer is hard to explain. Although immunotherapy has brought many cancer vulnerabilities to light, many interactions between tumors and the immune system remain hidden. It is among these hidden interactions, researchers feel, that new therapeutic opportunities will be found.

Existing cancer immunotherapies include monoclonal antibodies, immune checkpoint inhibitors, and cancer vaccines. These therapies all help the immune system to fight cancer, either by boosting the immune system’s ability to destroy cancer cells or counteracting signals that protect the tumor from attack. Quite a few cancer immunotherapies have been approved by the FDA, including pembrolizumab, a checkpoint inhibitor celebrated, among other reasons, for its role in shrinking former President Jimmy Carter’s brain tumors.

Up-and-coming cancer immunotherapies are being designed to thwart newly characterized immune-evasion mechanisms. For example, several novel cancer immunotherapy approaches were discussed at the recent Protein and Antibody Engineering Summit (PEGS) Europe. At this event, speakers described how second-generation immunotherapies that will surpass first-generation immunotherapies. Also, speakers described how they are developing new tools to advance immunotherapy design and discovery.

Treating the Incurable

The effectiveness of current immunotherapy treatments varies between patients and between cancers. For example, some patients with multiple myeloma, a bone marrow cancer remain incurable. Patients relapse or their cancers become resistant even to the latest treatments.

To develop a new approach against multiple myeloma, scientists at Aduro Biotech Europe recently collaborated with Kenneth C. Anderson, M.D, director of the Lebow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center at Dana-Farber Cancer Institute. The research team conducted a preclinical study to determine how APRIL (a proliferation-inducing ligand) promotes the growth and survival of multiple myeloma cells.

“What we uncovered with Ken Anderson is that APRIL is a crucial protective factor. In the bone marrow, it is responsible for the proliferation and survival of the remnants of cancer cells, as well as for maintaining the immune suppression environment,” stated John Dulos, Ph.D., director of Aduro Biotech Europe.

Aduro plans to begin a Phase I trial of BION-1301, a humanized antibody. BION-1301 is designed to prevent APRIL from binding to two receptors, B-cell maturation antigen (BCMA) and transmembrane activator and calcium modulator (TACI), which are expressed on the surface of multiple myeloma cells (Figure 1).

Figure 1. Mechanism of action of BION-1301, a humanized antibody that is a key investigational candidate in Aduro Biotech Europe’s pipeline.

According to Dr. Dulos, other clinical approaches focus only on BCMA. He explained that Aduro is taking the unique approach of focusing on APRIL to specifically targetremnant tumor cells in the bone marrow and break down the [tumor’s] protective environment. “We hope,” he said, “that this approach will be a benefit to patients and prevent the relapses we’ve seen up to now.”

Dr. Dulos also presented new pharmacokinetic and pharmacodynamics data collected from nonhuman primates. “We are pretty excited about these findings,” he remarked. “They replicate some aspects we’ve seen in mouse models and really show that our compound is pharmacologically active. We are very comfortable advancing it into the clinic.”

A Second Generation

New treatments hope to overcome difficulties in combatting the powerful immunosuppressive effects of tumors. Immunosuppressive effects can limit the ability of checkpoint inhibitor therapies to “activate” lymphocytes. Such effects can prevent checkpoint inhibitors from boosting the effectiveness of T cells against cancer.

iTeos Therapeutics is developing an immunotherapy treatment designed to simultaneously activate T cells to attack a tumor while destroying the regulatory T (Treg) cells that protect cancer cells from T-cell attack. “By using one antagonist antibody that targets several pathways, we increase the activation of T cells and at the same time deplete immunosuppressive Treg cells,” said Gregory Driessens, Ph.D., project leader at iTeos.

The treatment is a monoclonal antibody designed to target TIGIT (T cell immunoreceptor with Ig and ITIM domains), an immunosuppressive receptor expressed on the surface of T and natural killer (NK) cells (Figure 2). By binding to the TIGIT receptor, the antibody prevents the induction of the immunosuppressive signal mediated by binding of the natural ligand poliovirus receptor (PVR), which allows PVR to bind to another protein, CD226. CD226 is also expressed on the surface of T cells and increases their functionality. In a normal situation, CD226 is typically outcompeted by TIGIT for the same ligand.

Figure 2. Anti-TIGIT antibody mechanism of action. [iTeos Therapeutics]

Dr. Driessens asserted that the functional and binding properties associated with the dual mechanism of action of iTeos’ anti-TIGIT antibody will allow the company to develop a best-in-class anti-TIGIT antibody. iTeos is currently completing preclinical studies and expects to have the antibody in clinical trials by early 2019.

Reducing the Risk

Other speakers at PEGS Europe focused on technologies that can generate alternatives to antibodies for immunotherapy applications. One such technology is called Affimer®. Currently under development by Avacta Life Sciences, Affimer is an engineered protein scaffold derived from stefin A, a human protease inhibitor. The core scaffold has two loops of nine amino acids. Each of the 18 amino acids found in these loops can be changed, leading to the generation of a huge library of molecules that, once screened, can potentially bind to an immunotherapy target, such as a cell-surface receptor such as PD-L1.

Amrik Basran, Ph.D., chief scientific officer at Avacta, talked about one of the company’s immune checkpoint inhibitor programs. Specifically, he cited a program called AVA-004, which targets PD-L1 and is at preclinical stage. Like other checkpoint inhibitors, AVA-004 works by “releasing the brakes” on the immune system to destroy cancer cells.

“We decided to go into the area with immune checkpoint inhibitors because there’s a lot of interest in these types of targets and a need to develop new medicines,” said Dr. Basran. “Also, I saw that, with the Affimer technology, we might be able to do things differently.”

According to Dr. Basran, Avacta uses phage-display techniques to screen its library, capturing and enriching everything that binds to the target protein before another round of selection. By the end of two or three rounds, this screening approach identifies a range of target-binding Affimer molecules. These Affimers can be combined speedily with other Affimers to create a multitargeting molecule (Figure 3). “The technology has several advantages, including the speed at which one can generate binders to a target with relatively high affinity,” he asserts.

Figure 3. Affimer® molecules can be chained together to bind multiple targets. [Avacta Life Sciences]

Another advantage of Affimers for immunotherapy, according to Avacta, is their smallness. They are described as being 10 times smaller than antibodies. “The smaller the protein you can make, the more tissue penetration you should have, which is important when you’re thinking of treating solid tumors, where you need to get the protein inside the tumor to get the effect,” Dr. Basran explained.

PEGS Europe also highlighted the development of novel tools for basic immunotherapy research and the development of new treatments. For example, one presentation focused on human cell microarray screening.

“We have a unique technology. No one else is doing anything similar,” asserted Jim Freeth, Ph.D., managing director of Retrogenix. The technology, Dr. Freeth explained, is used to express (membrane) proteins on the surface of human cells. According to Dr. Freeth, human cell microarray screening is already used for immunotherapy development by pharmaceutical companies and academic clients.

“When we started the company in 2009, we weren’t going to be focused on membrane proteins,” recalled Dr. Freeth. “We developed where the demand came.”

The tool uses an array of expression vectors encoding about 4,500 full-length human plasma membrane proteins spotted onto slides. Human cells grown over the top overexpress these proteins on their surface. The client’s molecule can then be applied to the slide and the location of the bindings analyzed (Figure 3).

Identifying Interactions

The advantage of human cell microarray screening, Dr. Freeth maintained, is that it makes use of correctly folded, full-length membrane proteins. Also, these proteins are expressed in human cells, so they’re “very physiologically relevant.”

The Retrogenix tool, Dr. Freeth continued, boasts high success rates and generates few false positives. “We’ve had seven publications in mostly high-impact journals,” he pointed out. This form of recognition, Dr. Freeth suggested, “really validates the technology.”

The tool is being used in immunotherapy for identifying immune checkpoint interactions (Figure 4), where “the client may have a checkpoint protein of interest, but doesn’t know what the counter receptor or binding partner is.” Other applications include identifying off-target effects that could cause toxicity in chimeric antigen receptor T-cell (CAR-T) therapies. In these therapies, T cells are taken from patients and engineered to express a protein, the CAR. The modified T cells, which are now able to activate an immune response, are put back into the patient.

Figure 4. Identification of a specific off-target receptor for an immune checkpoint monoclonal antibody. [Retrogenix]

The possibility that human cell microarray screening could be used to advance immunotherapy while curbing toxicity, noted Dr. Freeth, is “something that’s generated a lot of interest in the last 18 months.”

A Detailed View

“It’s very important for academia and companies to have software that doesn’t require specialist computer skills,” said Michael Blank, Ph.D., chief scientific officer of AptaIT. The company launched its AptaAnalyzer™ software in May 2017 with the aim of providing an intuitive tool biomedical researchers could use to analyze next-generation sequencing (NGS) data from B-cell receptors (BCRs) or from screening experiments. AptaAnalyzer, it happens, is well suited to immunotherapy development.

“What we’re doing is analyzing big data—hundreds of millions of sequences,” explained Dr. Blank. The software offers a range of analytical tools for, among other things, examining which sequences are enriched during multiple rounds of phage-display experiments. The software can cluster sequences into families and, within a family of proteins, see which amino acids might be essential for binding and which can be replaced.

According to Dr. Blank, these functions can help companies get a detailed insight into how they might optimize an immunotherapy treatment or biopanning experiment. “Our revolution is that we can look inside the procedure and identify what’s really relevant,” he asserted.

AptaIT plans to expand the AptaAnalyzer software with a module for analyzing data from T-cell receptors. At present, AptaIT is developing different ways of clustering sequences intelligently into families. The company is also collecting sequences to help develop machine-learning algorithms. “We will make intelligent software that helps you identify relevant sequences in terms of functionality, affinity, and solubility,” he said.


Vivienne Raper Ph.D. , is a Freelance Journalist.