Methods and compositions for identifying leukemic stem cells

A method of guiding treatment of a subject having or diagnosed with acute lymphocytic leukemia (ALL) or lymphoid blast crisis chronic myeloid leukemia (LBC CML) at increased risk of relapse after chemotherapy alone, comprising:

• (a) obtaining a biological cell sample from the subject;
• (b) isolating mononuclear cells from the sample of (a);
• (c) allowing the cells of (b) to take up a fluorescence substrate for the enzyme aldehyde dehydrogenase (ALDH) and labeling the cells with an anti-CD34 monoclonal antibody and an anti-CD38 monoclonal antibody, in combination with an anti-CD19 monoclonal antibody;
• (d) isolating CD34+CD38− mononuclear cells from the cells of (c) using flow cytometry;
• (e) measuring the ALDH activity of the cells of (d);
• (f) comparing the levels of ALDH activity in the cells of (e) with the levels of ALDH activity in the cells of a reference sample;
• and
• (g) identifying cells of (f) that have a high level of ALDH activity (CD34+CD3831 ALDHhigh) in the sample from the subject when compared to the level of ALDH activity of the CD34+CD38− cells in the reference sample;
• and
• h) assaying the CD34+CD38−ALDHhigh cells identified in (g) for the presence or absence of CD19 on the surface of the CD34+CD38−ALDHhigh cells, wherein the presence of CD19 cells on the surface of the CD34+CD38−ALDHhigh cells identifies the subject as being more likely to relapse after chemotherapy alone relative to a subject lacking said cells;
• and
• (i) administering a treatment to the subject, selected from immunotherapy, an anti-body based therapy, hematopoietic stem cell transplantation, and/or chimeric antigen receptor T cell therapy with or without chemotherapy to decrease the subject's risk of relapse.