Lung Tumor Location Determines How the Immune System Responds

Researchers from VIB and the Vrije Universiteit Brussel have developed a new method to study how the immune system behaves in lung tumors. They created one of the most detailed immune maps to date of lung adenocarcinoma, the most common form of lung cancer. Their results were published in Nature Communications. 

“Whether a therapy works or not depends heavily on how immune cells behave in real tumors,” says Prof. Damya Laoui (VIB-VUB Center for Inflammation Research). “If our models do not accurately reflect the biology of patients, we can draw incorrect conclusions. With this work, we are bringing preclinical research a step closer to the clinic.”

Lung cancer accounts for nearly 20% of all cancer-related deaths, making it the leading cause of cancer mortality worldwide. New therapies are usually first tested in preclinical models in which tumor cells are implanted under the skin of mice. These models are practical, but they do not mirror the unique immune environment of the lung, which makes translation to human patients difficult.

Prof. Laoui's team therefore developed a model for lung adenocarcinoma in which the tumor grows directly into the lung. An important advantage is that the researchers can analyze tumors individually, separate from the surrounding healthy lung tissue. This is also how patient samples are analyzed in the hospital.

When the team compared their model with datasets of human lung tumors, it turned out to correspond strongly with what is seen in patients. For instance, they found poorly functioning natural killer cells in tumors and an increase in suppressive and exhausted T cell types, among other things.

“Our goal was to build a model that truly reflects what we see in patients,” says Pauline Bardet (VIB-VUB), PhD student and co-first author of the study. “By placing the tumor in its natural environment - the lung - we see immune dynamics that are completely absent in subcutaneous models.”

A new technique to determine the location of immune cells: SEPARATE-Seq

An important innovation in the study is SEPARATE-Seq (Streptavidin Enabled PARtitioning And Tag Evaluation for RNA-Sequencing). In organs such as the lung, immune cells are located in different compartments: in blood vessels, in the tissue itself, or in the airways. Depending on their location, they have a different impact, which is why researchers want to gain insight into this. With classical technologies, it is difficult to distinguish between immune cells that actually penetrate a tumor and cells that only pass through the blood. SEPARATE-Seq solves this problem by 'labeling' immune cells in the bloodstream.

“The location of a cell matters enormously,” explains Prof. Damya Laoui. “An immune cell in a blood vessel receives very different signals than a cell located in the tumor tissue. With SEPARATE-Seq, we can finally map that difference at the level of individual cells.”

The method can also be used in other diseases where different populations of immune cells need to be distinguished from one another.

By combining SEPARATE-Seq with other technologies such as spatial transcriptomics, the researchers were able to see not only which immune cells are present, but also exactly where they are located within the tumor.

“We have developed a lung cancer model that closely resembles how tumors grow in patients,” says Prof. Damya Laoui (VIB-VUB Center for Inflammation Research). “In combination with a new method to track cells, we can see the difference between immune cells that are actually located within the tumor tissue and cells that simply pass through the bloodstream. That distinction is crucial. It shows us much more clearly how immune cells change as soon as they invade a tumor.”

The analyses revealed striking patterns that also occur in human tumors, which underscores the importance of the model for clinical research.

“With this combination of spatial and molecular information, we can see how immune cells specialize in specific 'niches' within the tumor,” says Lize Allonsius, PhD student and co-first author of the study. “It shows how strongly the tumor environment can alter the functioning of the immune system.”

Reference: Bardet PMR, Allonsius L, Hadadi E, et al. Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq. Nat Commun. 2026. doi: 10.1038/s41467-026-72247-5