These new insights could help develop better, personalized treatments for T-ALL. Research group leader and Oncode Investigator dr. Ruben van Boxtel explains: 'This could lead to therapies that are better suited to the genetic characteristics of each patient's leukemia. This increases the chances of success and reduces side effects. For children with cancer, this means a greater chance of recovery and a better quality of life during and after treatment.'
In T-ALL, there are malignant T-cells in the blood and bone marrow. T-cells are important cells of the immune system. When they become malignant, they grow rapidly and outcompete healthy blood cells. As a result, children with T-ALL often have a shortage of healthy blood cells. In the Netherlands, approximately 30 children are diagnosed with T-ALL each year.
Vera Poort is the first author of this study, which was published in Cancer Research, and a PhD candidate in Van Boxtel's research group. Together with colleagues, she used advanced techniques to examine the DNA of individual leukemia cells. This allowed them to observe how these cells behaved and changed at the onset of leukemia.
Advanced techniques in leukemia research
‘In our research, we use various techniques. With flow cytometry, we can look at different types of cells. The leukemia cells pass one by one through a laser beam. This allows us to see which proteins are present on the surface and how the cells behave,' explains Poort. ‘Then, we analyzed the DNA of individual leukemia cells. The technique we used for this is called "single-cell whole genome sequencing". We partly developed this technique ourselves, and it has been previously published. It enables us to analyze the complete DNA of a single cell.’
A family tree of leukemia Cells
By combining single-cell sequencing and whole genome sequencing, Poort and her colleagues were able to create a family tree of the leukemia cells. This showed exactly when the leukemia cells branched off. ‘With this technique, we could accurately measure the genetic changes in the cells and observe how the leukemia cells behaved and changed during disease development,’ says Poort. ‘Through this family tree, we can go back in time and determine what happens exactly when the disease originates. This is unique and crucial to understand how cancer develops. In a way, we are like time travelers.’
In the family tree, they observed that the ends of the different branches contained the same type of cells. This means that the characteristics of the leukemia cells remain stable. Poort explains this finding: ‘What is special about our study is that we examined the differences in tumor cells over time in a new way. Researchers always thought that many differences meant that tumor cells constantly changed. Treatments often don't work if the tumor cells keep changing. However, we now show that in T-ALL, most changes occur at the onset of the disease. After that, the characteristics of the cells remain quite stable. We also saw that recurrence of the disease often begins with those early changes.’
T-ALL is not the same for every child
The researchers also discovered that this form of leukemia is not the same for every child. In 26 out of 31 patients, they found different appearances of the cells. Most children had two to four different appearances in their leukemia. Even children with the same DNA abnormalities had different types of leukemia cells. Younger children often had more cell variation, while older children had less. Poort: ‘This means that physicians may be able to tailor treatment to the different cell types in each child. This way, we can provide better and more targeted treatments.’
The disease originates from more developed T-cells
An important discovery was that the leukemia cells often originate from healthy T-cells that are already somewhat developed, rather than from primitive cells. ‘All acute lymphoblastic leukemias are immature cells, but there are different levels of immaturity,’ says Poort. ‘We show that T-ALL can originate from a more developed cell, which then can take on the characteristics of a less developed cell.’
Epigenetic changes in leukemia cells
Another relevant finding is that leukemia cells undergo not only genetic but also epigenetic changes. Epigenetic changes are adaptations in the cell that do not reside in the DNA itself but affect how the DNA is used. ‘The epigenetic changes that cause cancer-promoting genes are often so significant that you see few differences between the cells themselves. But on the outside of the cell, there are small differences,’ explains Poort.
‘Thanks to our family tree, we were able to determine that the cells branched off at different times and retained certain characteristics. Our method of analysis showed that the epigenetic differences indeed correspond with the mechanisms in the cell, which was previously not clearly visible.’
‘Our findings demonstrate that leukemia cells develop and change in different ways,’ says Van Boxtel. ‘This insight is important for developing new therapies that can target these cells at an early stage. By studying genetic and epigenetic changes, we hope to find new ways to stop the growth of malignant cells.’