CML and BCR::ABL1 Monitoring

The fusion

Chronic myeloid leukemia (CML) is driven by the Philadelphia chromosome, a balanced translocation t(9;22)(q34;q11) that fuses BCR on chromosome 22 to ABL1 on chromosome 9. The fusion gene, BCR::ABL1, makes a constitutively active tyrosine kinase that drives myeloid proliferation.

Where BCR breaks determines the transcript and protein ¹:

Knowing the transcript at diagnosis matters because the monitoring assay must detect it. Standard quantitative assays target e13a2 and e14a2; atypical transcripts need specialized assays ².

Diagnosis and treatment

CML is diagnosed by finding the Philadelphia chromosome (karyotype), the fusion (FISH), or the transcript (RT-PCR). It’s treated with tyrosine kinase inhibitors (TKIs): imatinib, dasatinib, nilotinib, and bosutinib first-line ². Most patients now have a near-normal life expectancy, and molecular monitoring is how their treatment is managed.

Quantitative monitoring

Response is monitored by quantitative RT-PCR of BCR::ABL1 transcripts in peripheral blood, every 3 months until response is established ². The result is a ratio: BCR::ABL1 transcripts divided by a control gene (usually ABL1, sometimes GUSB or BCR) in the same sample. The control corrects for RNA quantity and quality, and a minimum number of control transcripts is required for a result to count as deeply negative.

The International Scale

Ratios from different labs once couldn’t be compared. The International Scale (IS) fixes this: each lab derives a conversion factor against reference material, so a result of 0.1% IS means the same thing everywhere. The IS sets 100% as the standardized baseline from the original trials, so log reductions read directly:

²

Milestones

ELN 2020 milestones ²:

Missing milestones, losing MMR, or rising transcripts prompt a check of adherence, kinase domain mutation analysis, and a change of TKI ².

Patients with sustained deep response (MR4 or better for at least two years, among other criteria) may try treatment-free remission: stopping the TKI with frequent PCR monitoring, monthly at first, and restarting if MMR is lost ².

Kinase domain mutations

Resistance often comes from point mutations in the ABL1 kinase domain that stop a TKI from binding. They’re found by sequencing the BCR::ABL1 kinase domain (Sanger, or NGS for lower-level variants) in patients with failure or warning responses ².

The famous one is T315I, the “gatekeeper” mutation, resistant to imatinib, dasatinib, nilotinib, and bosutinib. ELN 2020 named ponatinib as the only TKI then active against it ²; in October 2021 FDA also approved asciminib, which binds a different site on the kinase, for CML with T315I ³.

Worked example

A patient’s BCR::ABL1 results (% IS): diagnosis 85%, 3 months 6%, 6 months 0.8%, 12 months 0.25%.

• 3 months: 6% ≤10%, optimal.
• 6 months: 0.8% ≤1%, optimal.
• 12 months: 0.25% is above 0.1% but below 1%: warning. Check adherence and drug interactions, test for kinase domain mutations, and monitor closely; a change of therapy may be considered.

What to take from this

CML is driven by BCR::ABL1 from t(9;22); p210 (e13a2/e14a2) is typical of CML and p190 (e1a2) of most Ph+ ALL. Response is monitored by quantitative RT-PCR as a ratio to a control gene, reported on the International Scale. The milestones are ≤10% at 3 months, ≤1% at 6, and ≤0.1% (MMR) at 12; MR4 is 0.01% and MR4.5 0.0032%. Failing milestones calls for kinase domain sequencing, and T315I responds only to ponatinib or asciminib.