Immune-Related Signatures Predict Prognosis in Chronic Myeloid Leukemia (CML) Patients Receiving the 3rd-Generation Tyrosine-Kinase Inhibitors (3G-TKIs)

Background Growing evidence revealed that immune-related signatures are related to tumorigenesis and prognosis. However, it is rarely explored in CML.

Objectives To explore the novel immune-related signatures for predicting the prognosis and to clarify the immune-related molecular subgroups in CML patients receiving 3G-TKI therapy.

Methods RNA sequencing was performed on blood samples from CML-CP/AP patients who were resistant to prior imatinib and/or 2G-TKI therapy and subsequently received 3G-TKI therapy. Based on the gene expression profiles (GEPs), xCell algorithm in the “IOBR” R package was applied to assess the proportions of immune cell infiltration and calculate the Immune/Stroma Scores. Different immune-related subgroups were classified using unsupervised consensus clustering. Cox regression models were used to identify the co-variates associated with outcomes.

Results 151 patients with available blood samples receiving olverembatinib (n = 120, 80%) or ponatinib (n = 31, 20%) therapy were enrolled in the study. 64 (42%) patients received ≥ 3 prior TKI therapy. Median age at the start of 3G-TKI therapy was 37 years (IQR, 27-47 years). Median follow-up was 46 months (IQR, 33-65 months). 72 (48%) patients achieved CCyR by 12 months; 63 (42%), MMR by 24 months. 32 (21%) patients transformed to AP or BP by 60 months. At baseline, patients not achieving CCyR, MMR or transformed to the advanced phases had the significantly lower proportions of B cells (p < 0.001), class-switched memory B cells (p < 0.001), memory B cells (p < 0.001), basophils (p < 0.002), MSC (p = 0.012), NK (p = 0.003) and NKT (p = 0.01) cells, Tregs (p = 0.01), as well as the immune Score (p = 0.002), but the significant higher proportions of CMP cells (p = 0.007), GMP cells (p < 0.001), HSC (p < 0.001), MEP (p < 0.001), macrophages (p = 0.005), mast cells (p = 0.002), megakaryocytes (p = 0.007), as well as the stromaScore (p = 0.008) than those achieving CCyR, MMR or did not transformed. Subsequently, serial blood samples from 118 patients receiving 3G-TKI therapy at least one year were analyzed. It was further found that the immune cell subsets with significant differences at baseline. Additionally, the proportions of CMP (p = 0.001-0.002), GMP (p < 0.001), HSC (p = 0.008-0.01), mast cells (p = 0.01-0.02), MEP (p = 0.002-0.003) and megakaryocytes (p = 0.04-0.05) were significantly increased after treatment in patients without achieving CCyR, MMR or transformation. Moreover, patients with transformation had the significantly lower proportions of CD4⁺ naive/memory T cells (p = 0.001-0.008), CD4⁺ Tcm/Tem (p = 0.001-0.002) and CD8⁺ Tcm/Tem cells (p = 0.002-0.006).

Based on the GEPs of 151 patients before 3G-TKI therapy, 2 distinct immune-related subgroups (C1 [n = 53] and C2 [n = 98]) were identified using unsupervised consensus clustering, and the C2 subgroup exhibited activated immune pathways and a higher percentage of immune cells compared to the C1 subgroup. The proportion of CD4⁺ native/memory T cells (p = 0.002-0.006), CD4⁺ Tem/Tcm (p < 0.001), CD8⁺ native/memory T cells (p < 0.001), CD8⁺ Tem/Tcm (p < 0.001), NK cells (p < 0.001) and naive/memory B cells (p = 0.007-0.03) in the C2 subgroup were significantly-higher than those in the C1; whereas the proportion of HSC (p < 0.001), MEP (p < 0.001), erythrocytes (p < 0.001), macrophages (p = 0.001), GMP (p < 0.001) and CMP (p < 0.001) in the C1 subgroup were significantly-higher than those in the C2. Patients in the C1 subgroup receiving 3G-TKI therapy had the worse PFS (p < 0.001) and CML-related survival (p = 0.017) than those in the C2 subgroup. Moreover, the immuneScore and stromaScore calculated by xCell algorithm were significantly-associated with PFS and CML-related survival. Multi-variable Cox analyses further indicated that the immune-related subgroups C1, the lower immuneScore and the higher stromaScore were significantly-associated with the worse PFS and CML-related survival. Sensitive analyses were performed in patients receiving olverembatinib therapy, and the same results were obtained.

Conclusions We revealed the characteristics and dynamic changes of immune cell subsets under the heterogeneous treatment response patterns of 3G-TKI, and identified a subgroup (C1) with the unique immune-related signature associated with worse outcomes in CML patients receiving 3G-TKI therapy, which is a promising biomarker to distinguish the prognosis, the molecular and immune characteristics.