LMU Munich, Charité University Hospital Berlin, and the BIFOLD institute at the Technical University of Berlin have created a single-cell atlas for lung cancer and linked it to clinical data.

Recent advances in cancer biology have shown that a tumor is not a uniform mass. It consists of many different cancer cells and is embedded in an environment of immune cells, connective tissue, and blood vessels. This variety is a significant factor in determining whether a tumor spreads and how well a therapy works. While single-cell approaches are considered pioneering instruments in cancer research, their translation into clinical practice has been limited to date, primarily due to a lack of large patient datasets with comprehensive clinical histories.

Researchers from LMU Munich, Charité University Hospital Berlin, and the Berlin Institute for the Foundations of Learning and Data (BIFOLD) at the Technical University of Berlin have now created a comprehensive single-cell atlas for lung cancer. This atlas was then linked to the clinical outcomes of patients using AI. With their model, the researchers were able not only to identify tumor cell types that particularly contribute to the development of metastases, but also to predict interactions between tumor cells and the cells of the surrounding microenvironment that are closely connected to disease outcome. The study has now been published in the journal Nature Cancer.

Capturing tumor cells and their environment in detail

One of the world’s leading causes of cancer-related deaths, lung cancer is markedly heterogeneous. Even within a tumor, cancer cells differ considerably in their aggressiveness. The conventional classification according to tumor size and lymph node involvement does not adequately capture this variety. And although single-cell technologies can make this variety visible, there has been a lack of large datasets that connect single-cell profiles with clinical follow-up data.

“For the LuCaS+ atlas, our team analyzed tumor tissue from 454 lung cancer patients,” explains Professor Frederick Klauschen from LMU. “To do this, we used a method that had rarely been used before on this scale: With the help of single-cell RNA sequencing, we were able to read out the activity of over 2,000 genes per cell nucleus from archived tissue samples and thus draw on clinical histories with long follow-ups.”

In total, the researchers captured the gene activity in more than 2.5 million individual cells. Using machine learning methods, they were able to find patterns within the data. This allowed them to define numerous groups of tumor cells, as well as groups of immune system, connective tissue, and blood vessel cells, that correlate with clinical outcomes.

Recognizing aggressive tumor cells before metastases occur

Using this clinical data, the researchers determined the metastatic potential for each tumor cell group. This approach allows the identification of patients who have a high risk of developing metastases despite their tumors being in early stages where adjuvant therapy is not typically administered after surgery. These findings were validated in an independent patient cohort. “When working with millions of cells, classical evaluation methods come up against their limits,” says Professor Klaus-Robert Müller, BIFOLD director and professor at TU Berlin. “Our machine learning methods, by contrast, recognize even the tiniest differences between individual cell types. This makes it possible to link these patterns directly to the clinical outcomes of the respective patients.”

Interplay of tumor and environment opens new therapeutic avenues

In a second step, the team incorporated the microenvironment – that is, the immune, connective tissue, and blood vessel cells that surround and interact with the tumor. From the joint analysis of the metastatic potential of tumor cells and their specific microenvironment, the researchers developed a model that predicts clinical outcomes significantly better than traditional parameters. The model recognized patients with a higher risk of relapse than conventional evaluations would indicate – and also patients whose prognosis is more favorable than previously reckoned. At the same time, it showed which interactions between tumor and microenvironment influence the course of the disease.

“LuCaS+ is freely available to scientists. The goal is to derive new therapeutic approaches and treatment strategies, which will then have to be tested in cell culture and animal models,” says Dr. med. Simon Schallenberg of Charité.