Interferon-α Revisited: Individualized Treatment Management Eased the Selective Pressure of Tyrosine Kinase Inhibitors on BCR-ABL1 Mutations Resulting in a Molecular Response in High-Risk CML Patients.

Bone marrow transplantation or ponatinib treatment are currently recommended strategies for management of patients with chronic myeloid leukemia (CML) harboring the T315I mutation and compound or polyclonal mutations. However, in some individual cases, these treatment scenarios cannot be applied. We used an alternative treatment strategy with interferon-α (IFN-α) given solo, sequentially or together with TKI in a group of 6 cases of high risk CML patients, assuming that the TKI-independent mechanism of action may lead to mutant clone repression. IFN-α based individualized therapy decreases of T315I or compound mutations to undetectable levels as assessed by next-generation deep sequencing, which was associated with a molecular response in 4/6 patients. Based on the observed results from immune profiling, we assumed that the principal mechanism leading to the success of the treatment was the immune activation induced with dasatinib pre-treatment followed by restoration of immunological surveillance after application of IFN-α therapy. Moreover, we showed that sensitive measurement of mutated BCR-ABL1 transcript levels augments the safety of this individualized treatment strategy

Additional file 2: Table S2. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

The sequences of designed primers for amplification of selected promoters of SLC and ABC genes including annotations of transporters. (XLSX 11 kb

Additional file 5: Figure S1. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

A colormap of genotypes distribution among optimally and non-optimally responding patients to first-line imatinib treatment at 12 months. Each square illustrates each genotyped SNP for each patient. Red squares = minor allele homozygotes; pink squares = heterozygotes; white squares = major allele homozygotes; gray square = not analyzed. Figure S2. Genotype frequencies of the rs460089 and rs460271 in patients with optimal and non-optimal response to imatinib at 12 months. 1 – Initial cohort of 83 patients; 2 – An independent group of added patients. Note – the graphs illustrate frequencies of genotypes of rs460089, which exactly reflect genotypes frequencies of rs460271. Figure S3. Genotype frequencies of a. rs13180043 (SLC22A5) and b. rs1050152 (SLC22A4, exon 9) in patients with optimal and non-optimal response to imatinib at 12 months. Note – the graph a. illustrates frequencies of genotypes of rs13180043, which exactly reflect genotypes frequencies of rs4646298, rs13180169, rs1310186, and rs13180295. Figure S4. Relative mRNA levels of SLC22A4 and SLC22A5 in tested cell lines. a. Graph shows expression in all eight cell lines. b. Graph shows expression of cell lines carrying rs460089-GG_rs2631365-TC or rs460089-GC_rs2631365-TC genotypes. (DOCX 687 kb

Additional file 4: Table S4. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

Identified SNPs in amplified region including whole promoters of 19 selected genes in the cohort of 83 CML patients. (XLSX 20 kb

Summary of sequential lines of treatment, therapy responses and mutation status.

<p>Summary of sequential lines of treatment, therapy responses and mutation status.</p

Patient’s characteristics.

<p>Patient’s characteristics.</p

Dynamics of total and mutated BCR-ABL1 transcript levels.

<p>(A) Patient no 1: The patient achieved MMR on solo IFN-α and maintained MMR for 88 months; the T315I mutation was persistently undetectable for 62 months due to the overall low levels of total BCR-ABL1 transcripts. (B) Patient no 2: Compound mutations M351T/F317L (100%) developed after sequential therapy with imatinib and dasatinib. The patient has now been on IFN-α/nilotinib therapy with undetectable mutations for 29 months. MR⁵ was achieved on the 15^th month of the combined treatment. (C) Patient no 3: Poor compliance to imatinib treatment within the 24^th– 30^th month; the T315I mutation burden decreased on solo IFN-α therapy down to undetectable levels after the combination of IFN-α and nilotinib. The patient achieved MR⁵ in the 22^nd month from IFN-α treatment initiation. (D) Patient no 4: The T315I mutation decreased on solo IFN-α therapy and was not detected for the subsequent 46 months on solo nilotinib therapy. The relatively slow reduction of the BCR-ABL1 transcript level and MMR achievement might have been caused by a problematic compliance to nilotinib. (E) Patient no 5: The T315I mutation decreased on solo IFN-α therapy, but the F317L and E255V mutations appeared and expanded. Death of this patient was related to lung tuberculosis. (F) Patient no 6: IFN-α therapy did not contribute to the T315I reduction and response improvement. Therefore, the patient has been switched to ponatinib with CCgR achievement after 7 months from ponatinib treatment initiation. IMA-imatinib, NILO-nilotinib, DASA-dasatinib, IFN-α –interferon alpha, HU-hydroxyurea, PONA-ponatinib. Note: A mutation burden of 0% represented undetectable levels of mutated BCR-ABL1 transcripts when the sequencing depth was 1,000 to 8,000 sequence reads per each nucleotide position.</p