Chronic Myeloid Leukemia, or CML, is a cancer that begins in the blood-forming cells of the bone marrow, causing it to produce an excessive number of white blood cells. Over the past few decades, advancements in understanding the genetics of CML have led to targeted treatments. These therapies have transformed the prognosis for many individuals, shifting the disease from a rapidly progressing illness to a manageable chronic condition. Their effectiveness is rooted in targeting the specific genetic flaw that drives the cancer, making this genetic basis central to controlling CML.
The Foundational Genetic Anomaly in CML
The defining characteristic of Chronic Myeloid Leukemia is a specific genetic abnormality known as the Philadelphia chromosome. This isn’t an inherited chromosome but rather one that forms during a person’s lifetime in a bone marrow cell. It is the result of a translocation, an event where pieces of two different chromosomes break off and switch places. In CML, a section of chromosome 9 and a section of chromosome 22 exchange material, creating an altered, shorter chromosome 22.
The direct molecular outcome of this chromosomal swap is the creation of a new, abnormal fusion gene called BCR-ABL1. This gene is formed by joining the ABL1 gene from chromosome 9 with the BCR gene on chromosome 22. While the normal ABL1 gene produces a protein that helps regulate cell growth and division, the fused BCR-ABL1 gene is different. It produces a protein that is constantly active, functioning as a hyperactive tyrosine kinase.
This unregulated BCR-ABL1 protein sends continuous signals to the bone marrow’s stem cells, instructing them to proliferate uncontrollably. The result is the massive overproduction of white blood cells, particularly neutrophils, that is characteristic of CML. The protein also makes it difficult for these leukemic cells to undergo apoptosis, or programmed cell death, allowing them to accumulate.
How Treatment-Resistant Mutations Emerge
The primary treatment for CML involves a class of drugs called Tyrosine Kinase Inhibitors (TKIs). These medications are designed to specifically block the action of the BCR-ABL1 protein, fitting into its active site to prevent it from sending growth signals. This targeted approach is highly effective for most patients, leading to deep and lasting remissions. The success of these drugs, however, can be challenged by the development of new genetic changes within the cancer cells.
Over time, additional point mutations can arise in the BCR-ABL1 gene itself. These secondary changes occur as the leukemia cells divide and alter the gene’s sequence, which in turn changes the structure of the BCR-ABL1 protein. This change in shape can alter the site where the TKI drug is meant to bind, much like a key no longer fitting a changed lock.
This process leads to what is known as acquired resistance, where a TKI that was once effective loses its ability to control the leukemia. More than 50 different mutations have been identified that can cause resistance to the first-generation TKI, imatinib. The most well-known of these is the T315I mutation, often called the “gatekeeper” mutation. This specific change blocks the binding of most first and second-generation TKIs, historically making it very difficult to treat. The emergence of such mutations is a primary reason why CML treatment is re-evaluated.
Methods for Detecting CML Mutations
Clinicians monitor patients with CML closely to ensure their treatment remains effective. Testing for BCR-ABL1 mutations is performed when there are signs of treatment failure or a suboptimal response. These signs can include a rise in white blood cell counts or molecular tests showing that the amount of the BCR-ABL1 gene in the blood is increasing.
The main laboratory methods used to detect these mutations are Polymerase Chain Reaction (PCR) and DNA sequencing. PCR-based techniques can be designed to look for specific, known mutations with high sensitivity. For a broader analysis, direct DNA sequencing of the BCR-ABL1 kinase domain is used. Sanger sequencing has been the standard method, though it has a sensitivity limit of about 15-20%, meaning it may miss mutations present at low levels.
More advanced techniques like Next-Generation Sequencing (NGS) offer greater sensitivity and can detect mutations that are present in a very small fraction of cancer cells. NGS can also identify multiple mutations at once, including compound mutations where two or more changes exist on the same BCR-ABL1 gene. Another highly sensitive method, droplet digital PCR (ddPCR), can be used to track specific mutations like T315I with high precision.
Adjusting Treatment Based on Mutation Type
The results of mutation testing directly influence how a patient’s CML treatment is managed. Identifying a specific mutation in the BCR-ABL1 gene provides a clear reason for treatment resistance and helps guide the selection of a subsequent therapy. The choice of the next TKI depends on the particular mutation found, as different mutations confer varying degrees of resistance to different drugs.
For instance, if a patient on a first-generation TKI like imatinib develops resistance due to many types of mutations, switching to a second-generation TKI such as dasatinib, nilotinib, or bosutinib is often effective. These drugs were designed to overcome many of the mutations that cause imatinib resistance. However, their effectiveness varies depending on the specific mutation. For example, some mutations may respond well to dasatinib but not nilotinib, and vice versa, making the mutation profile a guide for drug selection.
The T315I mutation presents a unique challenge because it confers resistance to all first and second-generation TKIs. For patients who develop this specific mutation, a different class of drugs is required. Ponatinib, a third-generation TKI, was specifically developed to be effective against T315I-mutated CML. More recently, a drug called asciminib, which binds to a different site on the BCR-ABL1 protein, has also been approved for patients with the T315I mutation, offering another valuable option.