Methods and compositions for identifying leukemic stem cells

1. 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 + CD38 31 ALDH high ) 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 − ALDH high cells identified in (g) for the presence or absence of CD19 on the surface of the CD34 + CD38 − ALDH high cells, wherein the presence of CD19 cells on the surface of the CD34 + CD38 − ALDH high 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.

2. The method of claim 1 , further comprising assaying the cells of (d) for the presence or absence of CD3, CD5, CD20, CD22, CD25, CD33, CD40, CD42, CD44, CD45, CD47, CD90, CD96, CD123, CD133, CD138, CD235a, IL1RAP, PD1, and/or PDL1 on the cells.