Unlocking the dark genome: New cancer antigens for next-generation immunotherapies

Human Health

8minAudiovisual content

We explore the dark genome to find tumor-specific signals that could power novel targeted immunotherapies for cancer.

On the screens in Boehringer Ingelheim’s Cancer Antigen Discovery lab in Vienna, a tumor doesn’t appear as a lump. It appears as a pattern: Thousands of individual cells, some harmless, some dangerous.

“Everything we do starts with a basic question,” says Ralf Leonhardt, scientific director, who leads the discovery of cancer antigens derived from the “dark genome” at Boehringer Ingelheim. “How can we give the immune system better information about which cells to attack and which to spare?”

Cancer immunotherapy and the search for better cancer antigens

Modern cancer immunotherapy depends on more than powerful immune cells. It depends on what they are told to look for. “Immunotherapy has huge potential to seek out and destroy cancers,” Alina Neunkirchner, principal scientist in oncology research, explains. “But first we have to identify the target proteins, we also call them antigens, that specifically mark only on the cancer cells.”

Cancer antigens act like small flags on the surface of cells.

These antigens act like molecular flags on the surface of cells. If they appear on tumor cells but not on healthy tissue, they can guide T-cell engagers, therapeutic cancer vaccines and other immune-based therapies precisely to their targets.

By creating a physical link between T-cells and tumor cells, T-cell engagers can activate T-cells against tumor cells, potentially resulting in their destruction.

In practice, most known tumor antigens have been far from perfect. “When we’re trying to discover tumor antigens, they usually fall into one of two categories,” Ralf says. “Either they’re very abundant and shared across patients, but not really specific for the tumor cell … or they’re very highly specific but restricted to very few patients.”

The first group is too unspecific; the second too rare. “What we’re trying to find,” he summarizes, “are antigens that are shared across patients, abundant and at the same time highly tumor specific.”

That is where the dark genome comes in.

Dark genome research and cryptic antigens for cancer immunotherapy

For many years, the search for cancer immunotherapy targets focused on familiar parts of the genome—the regions known to code for classical proteins. Large stretches of DNA were bundled into broad categories such as “non-coding” or dark genome and largely ignored. “If you imagine the genome as a map,” Ralf says, “the dark genome used to be the big grey area with a question mark on it.”

Everything we do starts with a basic question: How can we give the immune system better information about which cells to attack and which to spare?

Ralf Leonhardt, scientific director

New sequencing and proteomics technologies have changed that picture. Scientists can now see that some of these previously overlooked regions do give rise to small protein fragments that are presented on the surface of cells. Some of those fragments show up mainly on tumor cells and hardly at all on healthy tissue. This makes them compelling candidates for a new class of tumor-specific antigens. In scientific discussions they are often referred to as dark-genome-derived antigens, or more simply “cryptic antigens”.

For our researchers, the dark genome has turned from a blank corner of the map into a potential source of exactly the kind of targets we’ve been missing.

From tumor samples to antigens at our Vienna site

At our site in Vienna, we’re using two complementary research approaches to discover new antigens: One starts with the tumor cells, and the other with the T cells.

“When we start with tumor cells, we run extensive scans to find which parts of the dark genome are particularly active in cancers,” Ralf explains. “Next, we unravel which of these active elements are presented as antigens to patrolling T cells. The ones that are presented and recognized by the immune system may become powerful targets for future immunotherapies.”

Alina’s team works from the opposite side, focusing on the T cells that have already entered the tumor: “We extract T cells from tumor samples,” she explains. These tumor-infiltrating lymphocytes are immune cells that have already moved into the tumor micro-environment. “We sequence their T cell receptors and try to identify the antigens they recognize.”

We extract T-cells from tumor samples. We sequence their T-cell receptors and try to identify the antigens they recognize.

Alina Neunkirchner, principal scientist in oncology research at Boehringer Ingelheim

Those receptors point towards antigens the immune system is trying to see. Bioinformatic analyses then scan across the whole genome—including dark regions—to predict which DNA sequences could produce matching antigen fragments.

Antigens recognized by T-cell receptors from tumor-infiltrating lymphocytes are likely to be strong tumor antigens, “antigens that have the potential to lead to tumor rejection,” as she puts it.

Prediction is only the first filter. “My lab validates the predicted cancer antigens by demonstrating that they are immunogenic and therefore good targets for our cancer vaccine platform,” Lotte Spel, principal scientist in our oncology research, says. “We do this by mimicking in the lab those conditions that are needed in the human body at the very first moment an immune response is initiated.”

My lab validates the predicted cancer antigens by demonstrating that they are immunogenic and therefore good targets for our cancer vaccine platform.

Lotte Spel, principal scientist in oncology research

Only candidates that trigger a strong, specific immune response in these assays move forward. The most promising include antigens that are:

• highly specific to tumor cells,
• abundant (high expression levels) on tumor cells,
• and shared across patients.

These are the cryptic antigens that could help shape next-generation immunotherapies for people with cancer.

From dark genome targets to future cancer immunotherapy

Validating a new antigen is the start of a new path. Some of the antigens discovered by our colleagues from the Cancer Antigen Discovery team are already feeding into concepts for therapeutic cancer vaccines and T-cell engagers.

“The mission of our Cancer Antigen Discovery group in Vienna,” Ralf says, “is to develop novel immunotherapies that have the potential to transform the lives of patients with cancer.”

Dark genome research is still young. Many questions remain about which cryptic antigens will prove most relevant, how stable they are as tumors evolve and how best to integrate them into real-world treatment strategies.

But what was once a quiet, unexplored part of our DNA is rapidly becoming a new source of possibilities. For the immune system—and for patients who may one day benefit from these next generation immunotherapies—those possibilities begin with better information about which cells truly need to be stopped by our body’s guardians.

Shaping connections

We connect overlooked genomic regions with tumor data and T-cell insight to surface hidden antigens. By linking research, computation and translational ideas, we build a path from concept to potential immunotherapies. These connections aim to give the immune system clearer targets—and people more precise treatment options.