Clonal Hematopoiesis Detected at the Time of Tyrosine Kinase Inhibitor Cessation Is Associated with Delayed Molecular Recurrence after Treatment-Free Remission in Patients with CML

Background Treatment-free remission (TFR) is a goal of therapy. However, ~50% of patients who attempt TFR will relapse, which mostly occurs by 6 months. The acquisition of somatic mutations in hematopoietic cells is common with age (clonal hematopoiesis, CH). Through next-generation sequencing studies we identified CH in patients in deep molecular remission. CH variants provide a selective growth advantage to cells, driving their clonal expansion. The clones also give rise to mutated immune effector cells with a proinflammatory profile that exacerbate diseases with a chronic inflammatory component, such as atherosclerosis. CH variants could potentially influence TFR, either by outcompeting an emerging residual CML clone or by altering immune function, which is known to play an important role in TFR.

Aim To determine whether CH variants present at the time of therapy cessation could influence TFR.

Methods

An RNA-based hybridization capture sequencing method targeting 17 of the most frequently mutated CH genes was developed and applied to samples of 138 patients who attempted TFR. CH variants met strict criteria for pathogenicity based on their potential to confer growth and survival advantages. The CH status was confirmed by repeat testing of samples of 28 patients. The method reproducibly detected variants with a variant allele frequency (VAF) of ≥0.4%.

Results The median follow-up for the 138 patients was 66 months from the TFR attempt. Molecular recurrence was defined as loss of major molecular response (MMR, BCR::ABL1 ≤0.1%). The probability of TFR was 64.5% at 6 months, 59.4% at 12 months and 51.0% at 84 months.

CH variants were detected in 61/138 patients (44%): 107 variants in 12 genes. Multiple variants, range 2 - 7, were detected in 26 patients (19%). The median VAF was 0.9%, range 0.4 - 44%. Variants most frequently occurred in TET2 (44% of variants), DNMT3A (25%), PPM1D (7.4%) and ASXL1 (6.5%). The average age at cessation was 59.6 years, range 33 - 85. The average age of patients with CH was higher than those without CH: 64.7 versus 55.5 years, P < .0001. Only 3/13 patients (15%) aged ≤40 had CH compared with 6/7 patients (86%) ≥80.

CH was significantly associated with TFR to 36 months after cessation. The optimal criteria for TFR prediction were at least one CH variant of VAF >2% or >2 variants (CH >2%/>2). Thirty-one of 138 patients (22%) had CH of VAF >2% (n = 24) or >2 variants (n = 7). The probability of TFR for these 31 patients was significantly higher than for the remaining patients when assessed at 6, 12, 24 and 36 months after cessation, Figure. The probability of TFR at 6 months was 90.3% for patients with CH >2%/>2 versus 57.0% for the remaining patients, P = .001. The probability of TFR at 36 months was 65.9% versus 51.2%, P = .049.

A landmark analysis was performed at 12 months for the 74 patients who maintained TFR at 12 months. MMR was subsequently lost in 8/74 patients and the probability of TFR at 84 months was 86.9%. CH >2%/>2 occurred for 23/74 patients (31%). The probability of late molecular recurrence was higher among the patients with CH >2%/>2: 27.3% versus 5.5% for the remaining patients, P = .009.

Overall, molecular recurrence occurred for 12/31 patients (39%) with CH >2%/>2 and 53/107 of remaining patients (50%). Time to molecular recurrence after cessation was longer for patients with CH >2%/>2 than the remaining patients: median 12.5 months versus 3.5 months, P < .0001. The longer time to molecular recurrence was linked to a different pattern of loss of MMR. The median time between first loss of MR4 (BCR::ABL1 ≤0.01%) and loss of MMR was 145 days for patients with CH >2%/>2 and 28 days for remaining patients, P = .0007. BCR::ABL1 values more frequently fluctuated before loss of MMR in patients with CH >2%/>2: 8/12 patients (67%, fluctuation over 120-1335 days) versus 6/53 (11%, fluctuation over 85-715 days) in the remaining patients, P =.016.

Conclusion CH may improve the probability and duration of TFR, delaying the time to molecular recurrence, which has implications for patient selection and monitoring. Patients with CH who are eligible for therapy cessation have an excellent prospect of remaining drug-free for 1-2 years but their long term prospects of sustained TFR may be less certain compared to other patients, given the slower dynamics of relapse. Delayed relapse could be due to competition for clonal dominance between residual leukemic cells and larger CH clones, or modulation of the immune microenvironment.

Branford:Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Qiagen: Honoraria; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Shanmuganathan:Amgen: Other: Meeting sponsorship; Novartis: Honoraria. Yeung:Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria; Pfizer: Honoraria; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Honoraria, Research Funding. Ross:Celgene: Research Funding; Keros: Consultancy; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria. Yong:Celgene: Honoraria; BMS: Honoraria, Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hughes:Enliven: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Novartis: Consultancy, Research Funding.