Detection of residual disease in chronic myeloid leukemia utilizing genomic next generation sequencing reveals persistence of differentiated Ph⁺ B cells but not bone marrow stem/progenitors

Abstract

Persistence of leukemic stem cells (LSCs) results in the recurrence of chronic myeloid leukemia (CML) after the administration of tyrosine kinase inhibitors (TKIs). Thus, the detection of minimal residual disease (MRD) with LSC potential can improve prognosis. Here, we analyzed 115 CML patients and found that CD25 was preferentially expressed on the phenotypic stem and progenitor cells (SPCs), and TKI therapy decreased the number of CD25-positive cells in the SPC fraction. To detect MRD harboring BCR-ABL1 fusion DNA, we developed a highly-sensitive method using patient-specific primers and next-generation sequencing. By using this method, we identified that in patients who achieved molecular remission, almost all residual CD25-positive SPCs were BCR-ABL1-negative. Moreover, in some patients BCR-ABL1 was detectable in peripheral B cells but not in SPCs. We conclude that CD25 marks LSCs at diagnosis but does not mark MRD following TKI treatment and that analysis of peripheral B cells can allow sensitive detection of MRD.

Keywords:

• Chronic myeloid leukemia
• minimal residual disease
• tyrosine kinase inhibitor
• CD25

Acknowledgments

The authors thank all patients who participated in this study. We thank Y. Niizuma, A. Tajima, K. Yanai, S. Yamanaka, M. Haraguchi, M. Furuhashi, and A. Azizi for technical support and laboratory management; and E. Lamar, D. Martinez-Krams and J. Morriss for preparation of the manuscript. D.K. was supported in part by a KAKENHI grant from MEXT/JSPS (19K17877), JB Research Grants and the Takeda Science Foundation. H. Kasahara was supported in part by a KAKENHI grant from MEXT/JSPS (JP19J00502). H. Kobayashi was supported in part by a KAKENHI grant from MEXT/JSPS (19K17847) and a grant from the National Center for Global Health and Medicine (29-1015). Y.K. was supported in part by a KAKENHI Grant from MEXT/JSPS (26221005). K.T. was supported in part by KAKENHI Grants from MEXT/JSPS (18H02845, 18K19570), grants from the National Center for Global Health and Medicine (26-001, 29-2007), AMED grants (JP18ck0106444, JP18ae0201014) and grants from the Ono Medical Research Foundation, the Kanzawa Medical Research Foundation and the Takeda Science Foundation.

Author contributions

D.K., H. Kasahara, K.S., S.F., H. Kobayashi, S.T., R.Y., K.Y., Y.Y., N.K., T.A., H. Katagiri, N.S., T.H., T.Y., T. Sasaki and K.T. performed the study and analyzed data; M.S., T.K., J.K., T. Shimizu, M. Matsushita, H.N., Y.K., M. Murata, T.M., T. Sasaki, S.O. and K.T. provided scientific advice and materials; D.K., H. Kasahara and K.T. wrote the manuscript; and K.T. and S.O. conceived the project and supervised the research.

Disclosure statement

No potential conflict of interest was reported by the author(s).