WO2009146495A1

WO2009146495A1 - Method for predicting engraftment potential

Info

Publication number: WO2009146495A1
Application number: PCT/AU2009/000701
Authority: WO
Inventors: David Jonathon Gottlieb; Kenneth Francis Bradstock; Mary Mirella Sartor; Vicki Antonenas
Original assignee: Sydney West Area Health Services; The University Of Sydney
Priority date: 2008-06-03
Filing date: 2009-06-03
Publication date: 2009-12-10

Abstract

The invention relates to methods for the identification of proliferating stem cells in products for transplantation, and uses thereof. More specifically, the invention relates to methods for predicting the engraftment potential of stem cells following transplantation by determining their proliferative capacity.

Description

METHOD FOR PREDICTING ENGRAFTMENT POTENTIAL

Technical Field

Background Bone marrow transplantation (BMT) and peripheral blood stem cell transplantation

(PBSCT) are procedures used primarily for the restoration of stem cells destroyed by high doses of chemotherapy and/or radiation therapy.

The field of bone marrow transplantation (BMT) originally developed without the benefit of bioassays for enumeration of stem cells present within bone marrow grafts. In contrast, the technique of peripheral blood stem cell transplantation (PBSCT) arose from observations of greatly increased numbers of hematopoietic progenitor cells (HPC) in the blood in patients recovering from myelosuppressive chemotherapy. Subsequently, it was found that myeloid colony stimulating factors could be used to achieve similar effects. The clinical application of PBSCT was initially strongly dependent on stem cell assays carried out on leucapheresis products obtained from patients, in order to demonstrate that sufficient numbers of stem cells were present to allow adequate engraftment in the transplant recipient.

Colony assays, such as the granulocyte-macrophage colony-forming assay (CFU- GM), while serving as a useful bioassay for the presence of stem cells, were associated with a number of significant limitations and problems. These included a lack of standardization of assay variables (source, type and combinations of cytokines, choice of serum batches), subjective interpretation of results, and a 10-14 day culture period before a result could be obtained. Furthermore, although a correlation was found between the CFU-GM content of apheresis products and engraftment, this was not absolute, and there were a significant minority of cases with discordance between graft stem cell content and speed of engraftment.

With the recognition that stem cells could be detected in the blood by flow cytometry using the CD34 marker, it was realised that the number of circulating CD34⁺ cells in the blood was a reliable surrogate for stem cells. Subsequently, the utility of CD34 cell assays has been demonstrated in clinical studies, which have shown correlations between the CD34⁺ cell content of autologous stem cell collections and speed of neutrophil and platelet recovery after high dose chemotherapy and autografting. Correlative data suggest a minimum number of 2 million CD34⁺ cells/kg is required for autografts, below which a higher risk of delayed neutrophil and platelet recovery is seen. However, engraftment can be delayed with higher numbers of CD34⁺ cells in some patients, while others have been found to engraft at an acceptable rate with less than 2 million CD34⁺ cells/kg. Hence, the enumeration of CD34⁺ cells in autologous stem cell collections can be an unreliable predictor of engraftment success in some patients.

There is a need for alternative and improved assays capable of evaluating stem cells in apheresis products, bone marrow harvests, and cord blood collections for the prediction of engraftment success following transplantation. There is also a need for functional stem cell assays for allogeneic unrelated donor transplants wherein cell numbers are frequently a limiting factor and delayed engraftment arising from the transportation of stem cell products represents a substantial clinical problem.

Summary

In a first aspect, the invention provides a method for predicting the engraftment potential of a cell population containing one or more stem cells, said method comprising the steps of culturing one or more of the stem cells from the population with at least one growth factor and determining the proliferative capacity of the one or more stem cells in response to said at least one growth factor, wherein said proliferative capacity predicts the engraftment potential of the cell population following transplantation.

In one embodiment of the first aspect, the steps of culturing one or more of the stem cells and determining the proliferative capacity are performed simultaneously. In one embodiment of the first aspect, the method further comprises a step of identifying one or more stem cells in said cell population prior to or concurrent with determining the proliferative capacity.

In one embodiment of the first aspect, the method comprises the additional step of determining the number of stem cells present in said population of cells. hi one embodiment of the first aspect, the proliferative capacity of one or more stem cells is determined using a fluorescent dye assay.

In one embodiment of the first aspect, the fluorescent dye assay utilises a fluorescent dye selected from the group consisting of carboxyl-fluorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKH, Dapi, Hoechst, thiazole orange, and propidium iodide.

In one embodiment of the first aspect, the fluorescent dye assay comprises the step of detecting the fluorescent signal emitted by the dye using a flow cytometer. In one embodiment of the first aspect, the one or more stem cells in a cell population are identified by the presence or absence of one or more cellular markers.

In one embodiment of the first aspect, the one or more cellular markers is selected from the group consisting of CD7, CDlO, CD13, CD14, CD15, CD19, CD33, CD34, CD38, CD45, CD61, CD64, CD68, CD71, CD90 (Thy-1), CDI lO, CD117, CD123, CD 124, CD 133 , HLA-DR, Glycophorin A and combinations thereof.

In one embodiment of the first aspect, the presence or absence of said cellular markers is determined using one or more antibodies.

In one embodiment of the first aspect, the one or more antibodies are conjugated to a fluorochrome. In one embodiment of the first aspect, the one or more antibodies are identified by flow cytometry. hi one embodiment of the first aspect, the stem cell is a hematopoietic stem cell.

In one embodiment of the first aspect, the stem cell is a hematopoietic progenitor cell. In one embodiment of the first aspect, the cell population is a clinical sample.

In one embodiment of the first aspect, the clinical sample is derived from bone marrow, peripheral blood, or cord blood.

In one embodiment of the first aspect, the transplantation is autologous, syngeneic, or allogeneic. In one embodiment of the first aspect, the at least one growth factor is selected from the group consisting of stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), FLT-3/FLK- 2 ligand, stromal cell-derived factor- 1 (SDF-I), tumor necrosis factor-alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13, and combinations thereof.

In one embodiment of the first aspect, the cell population is a stem cell-enriched population or a purified stem cell population. In a second aspect, the invention provides a kit for determining the engraftment potential of a cell population containing one or more stem cells, the kit comprising: (i) one or more growth factors (ii) one or more agents for determining the proliferative capacity of stem cells, and optionally (iii) one or more agents for detecting the presence or absence of one or more cellular markers expressed by stem cells or subpopulations of stem cells.

In one embodiment of the second aspect, the one or more growth factors are selected from the group consisting of stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M- CSF), FLT-3/FLK-2 ligand, stromal cell-derived factor- 1 (SDF-I), tumor necrosis factor- alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13, and combinations thereof. In one embodiment of the second aspect, the one or more agents for determining the proliferative capacity of stem cells is a fluorescent dye selected from the group consisting of carboxyl-fluorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKH, Dapi, Hoechst, thiazole orange, and propidium iodide. In one embodiment, the one or more agents for determining the proliferative capacity of stem cells is an antibody.

In one embodiment of the second aspect, the one or more cellular markers is selected from the group consisting of CD7, CDlO, CD13, CD14, CD15, CD19, CD33, CD34, CD38, CD45, CD61, CD64, CD68, CD71, CD90 (Thy-1), CDIlO, CDl 17, CD 123 , CD 124, CD 133 , HLA-DR, Glycophorin A, and combinations thereof.

Abbreviations

BMT bone marrow transplantation

BrDU bromodeoxyuridine CFSE carboxyl-fiuorescein-succinimidyl ester

CFU-GM colony-forming unit-granulocyte/rnacrophage

CXCR4 CXC chemokine receptor 4

G-CSF granulocyte colony-stimulating factor

GM-CSF granulocyte-macrophage colony-stimulating factor HLA human leukocyte antigen

HLA-DR human leukocyte antigen DR

HPC hematopoietic progenitor cells

HSC hematopoietic stem cells Ig Immunoglobulin

PBSCH peripheral blood stem cell harvest

PBSCT peripheral blood stem cell transplantation

Definitions

As used in this application, the singular form "a", "an" and "the" include plural references unless the context clearly dictates otherwise. For example, the term "a stem cell" also includes a plurality of stem cells.

As used herein, the term "comprising" means "including". Variations of the word "comprising", such as "comprise" and "comprises," have correspondingly varied meanings. Thus, for example, a polynucleotide "comprising" a sequence encoding a protein may consist exclusively of that sequence or may include one or more additional sequences.

As used herein, the term "stem cells" encompasses hematopoietic stem cells (HSC) and hematopoietic progenitor cells (HPC). "Hematopoietic stem cells" are self-renewing, multipotent cells which are not committed to any particular cell lineage and are capable of differentiating into any type of hematopoietic cell. "Hematopoietic progenitor cells" are lineage-committed cells derived from HSC that have not undergone terminal differentiation. HPC may be capable of differentiating into single or multiple cell lineages. HPC may be myeloid progenitor cells and lymphoid progenitor cells. Accordingly, HPC include, but are not limited to megakaryocyte/platelet progenitor cells, erythrocyte/erythroblast progenitor cells, granulocyte progenitor cells, monocyte and macrophage progenitor cells, lymphocyte progenitor cells, dendritic cell progenitor cells and mast cell progenitor cells.

As used herein, "apheresis" refers to the process by which blood from a patient is separated into one or more component parts, wherein at least one of the component parts is a stem cell that is collected. The unused components of the blood may be returned into the circulation to the patient. Included within the scope of "apheresis" are "peripheral blood stem cell transplantation" (PBSCT) and "leucapheresis". Stem cells collected by apheresis may be used in autologous, syngeneic, or allogeneic transplants. As used herein, the term "growth factor" includes within its scope any biological substance that functions to regulate the proliferation, growth, differentiation, or maturation of stem cells.

As used herein, the terms "antibody" and "antibodies" include IgG (including IgGl, IgG2, IgG3, and IgG4), IgA (including IgAl and IgA2), IgD, IgE, or IgM, and IgY, whole antibodies, including single-chain whole antibodies, and antigen-binding fragments thereof. Antigen-binding antibody fragments include, but are not limited to, Fab, Fab' and F(ab')2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (sdFv) and fragments comprising either a VL or VH domain. The antibodies may be from any animal origin. Antigen-binding antibody fragments, including single-chain antibodies, may comprise the variable region(s) alone or in combination with the entire or partial of the following: hinge region, CHl, CH2, and CH3 domains. Also included are any combinations of variable region(s) and hinge region, CHl, CH2, and CH3 domains. Antibodies may be monoclonal, polyclonal, chimeric, multispecific, humanized, and human monoclonal and polyclonal antibodies which specifically bind the biological molecule.

As used herein, the terms "marker" and "cellular marker" refer to any component on the surface of a cell or within the interior of a cell that may be used for the detection and/or identification and/or isolation of that cell. Accordingly, markers and cellular markers may be used to detect one or more cells within a mixed population of cells, and/or may provide a means by which specific cells within a mixed population can be enriched, purified, or separated. Non-limiting examples of markers and cellular markers include cellular proteins and nucleic acids which may be detected using methods known in the art such as by the use of antibodies capable of specifically binding to the protein or nucleic acid.

As used herein, the term "fluorescent dye assay" refers to any assay in which a fluorescent dye is used for the detection of proliferating cells. The fluorescent dye maybe a membrane-permeable dye that passes through the cell membrane and is retained in the cell interior. Membrane-permeable fluorescent dyes include but are not limited to DNA- binding fluorescent dyes, cytoplasmic dyes and covalent-coupling fluorescent dyes. The fluorescent dye may be capable of inserting into and/or being retained in the cell membrane. In general the fluorescent dye retained in the interior of a cell or retained in the cell membrane are distributed equally between daughter cells upon cell division, and hence the relative intensity of the fluorescent signal emitted by the dye is decreased by approximately half in each successive generation of dividing cells. Examples of fluorescent dye assays for detecting cell proliferation include, but are not limited to assays that utilise carboxyl-fluorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein , PKH, Dapi, Hoechst, thiazole orange, or propidium iodide. As used herein, the term "engraftment potential" refers to the capacity of transplanted stem cells to reproduce and/or produce differentiated hematopoietic cells upon migrating into and colonising the bone marrow and/or lymphoid tissue of a subject. The term also encompasses the capacity of transplanted stem cells to undergo events surrounding or leading up to engraftment, including tissue homing and tissue colonisation. The degree of stem cell engraftment following transplantation may be evaluated or quantified using standard techniques in the art including, for example, by detecting an increase or decrease in the number of hematopoietic and/or mature blood cells in the circulation, by chimerism analysis of peripheral blood or bone marrow cells to detect the proportions of donor and recipient haematopoiesis, by cytogenetic analysis or fluorescence in situ hybridisation of peripheral blood or bone marrow cells to detect the proportions of donor and recipient haematopoiesis.

As used herein, the term "proliferative capacity" refers to the ability of stem cells to undergo cell division. The proliferative capacity of stem cells may be measured by any method known in the art including, but not limited to, the enumeration of stem cells before and after stimulation with a suitable growth factor, fluorescent dye assays, incorporation of BrdU in the DNA of proliferating cells, incorporation of radio-labelled analogues such as ³H-thymidine into the DNA of proliferating cells and/or the detection of cellular markers of proliferation.

As used herein, the term "kit" refers to any delivery system for delivering materials. In the context of proliferation assays for determining the engraftment potential of a cell population containing one or more stem cells, such delivery systems may include systems that allow for the storage, transport, or delivery of reaction reagents (for example labels, reference samples, supporting material, etc. in the appropriate containers) and/or supporting materials (for example, buffers, written instructions for performing the assay etc.) from one location to another. For example, kits may include one or more enclosures, such as boxes, containing the relevant reaction reagents and/or supporting materials.

As used herein, the term "fragmented kit" refers to a delivery system comprising two or more separate containers that each contains a subportion of the total kit components. The containers may be delivered to the intended recipient together or separately. For example, a first container may contain one or more growth factors for use in an assay, while a second container contains an agent for determining the proliferative capacity of stem cells. Indeed, any delivery system comprising two or more separate containers that each contains a subportion of the total kit components are included in the term "fragmented kit." In contrast, a "combined kit" refers to a delivery system containing all of the components of a reaction assay in a single container (e.g., in a single box housing each of the desired components). The term "kit" includes both fragmented and combined kits.

Any discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is solely for the purpose of providing a context for the present invention. It is not to be taken as an admission that any or all of these matters form part of the prior art base or were common general knowledge in the field relevant to the present invention before the priority date of this application. For the purposes of description all documents referred to herein are incorporated by reference.

Brief Description of the Figures

The invention will now be described by way of example with reference to the accompanying figures.

Figures IA- 1C are dot plots obtained from a flow cytometry analysis of proliferating CD34 stem cells derived from cord blood cells cultured with a combination of GM-CSF, G-CSF, IL-3, SCF, TPO, Flt-3, and IL-6 for 72 hours. CD34⁺ cells were identified by first gating cells based on forward and side scatter characteristics (Figure IA) followed by gating on CD34/7AAD/CD14/CD45 stained cells (Figure IB). Proliferating CD34⁺ cells were identified by CFSE fluorescence (Figure 1C). Figure 2 is a histogram plot showing the proliferative response of purified CD34⁺ cells derived from PBSCH collected from a normal donor undergoing apheresis after mobilization with 4 days of treatment with G-CSF, and then cultured with GM-CSF, G- CSF, IL-3, SCF, TPO, Flt-3, and IL-6. The proliferative response was detected by carboxyl-fluorescein-succinimidyl ester (CFSE) fluorescence after 24, 48, 72 and 96 hours of culture.

Figure 3 is a histogram plot showing the proliferative response of CD34⁺ CD45⁺ CD 14^" cells derived from unrelated banked cord blood stimulated with SCF, GM-CSF and IL-6, detected by carboxyl-fluorescein-succinimidyl ester (CFSE) fluorescence after 24, 48 and 72 hours of culture. Figure 4 is a graph showing the proliferative response of CD34⁺ CD45⁺ CD 14^" cells in apheresis products (n=8) and cord blood (n=12) and the proliferative response of

CD34⁺ cells purified from apheresis products from normal donors (n=4), as detected by carboxyl-fluorescein-succinimidyl ester (CFSE) fluorescence after 24, 48, and 72 hours of culture.

Figure 5 is a table showing engraftment data obtained after transplantation of stem cell products used for proliferation assays. The column labelled ANO500 depicts the time (in days) taken after transplantation to achieve an absolute neutrophil count of over 0.5 x 10⁹/L in the blood. Abbreviations: relat = related, unrelat = unrelated, hid = haplo- identical, NA = not available, TNC = total nucleated cells, ANC = absolute neutrophil count, PLT = platelet count, D = day post-transplant, Tx = transplant.

Detailed Description

The invention relates to the finding that the proliferative potential of stem cells and individual subsets thereof may be used to predict their engraftment potential upon transplantation. Accordingly, the invention provides a means by which the functional capacity of stem cells and their individual subsets derived from sources such as apheresis products, bone marrow harvests, and cord blood collections may be assessed for engraftment potential in procedures involving the transplantation of such cells. The transplant may be autologous, syngeneic, or allogeneic. The methods described herein provide a faster and more efficient means of determining the engraftment potential of stem cells in comparison to previously described methods such as the granulocyte- macrophage colony-forming assay (CFU-GM), which requires a 10-14 day culture period. The methods of the invention comprise the application of at least one growth factor to a sample containing stem cells. The cells are exposed to the growth factor or growth factors for a period of time sufficient to allow cell division. Stem cells in the sample are identified and their proliferative response determined, for example, by comparison to the proliferation of stem cells in a control sample to which the at least one growth factor was not applied. The proliferative response of stem cells in the sample provides indication of their engraftment potential upon transplantation. In general, stem cells with normal or increased proliferative responses are predicted to engraft successfully. Stem cells with a low proliferative response are, in general, predicted to have a reduced engraftment potential. Stem cells that do not show a proliferative response are generally predicted to have little or no potential for engraftment. The proliferative capacity of stem cells in a sample may also be used in combination with stem cell enumeration to predict the engraftment potential of stem cells following transplantation.

Stem CeUs Stem cells for use in accordance with the invention may be derived from any source. For example, the stem cells may be present in, or enriched/purified from, apheresis products, bone marrow harvests, or cord blood collections. The proliferative capacity of stem cells may also be determined upon thawing samples derived from apheresis products, bone marrow harvests, or cord blood collections that were previously frozen.

The principles and practice of apheresis are well known in the art and are described, for example, in "Apheresis: Principles and Practice of Apheresis", McLeod, Price, and Drew (Eds), (1997), American Association of Blood Banks (AABB). In the context of the present invention, apheresis refers to a process by which one or more stem cells is separated from the blood of patient or a donor patient while the remainder of the blood may be returned into the circulation of that patient. The patient or donor may receive stem cell mobilisation treatment prior to apheresis for a period of time sufficient to increase the number of circulating stem cells. For example, the patient or donor may be administered granulocyte colony-stimulating factor (G-CSF) and/or CXCR4 antagonists. Stem cells for use in accordance with the invention may be obtained from umbilical cord blood. Methods for obtaining umbilical cord blood are known in the art and described, for example, in US Patent No. 6102871, US Patent No. 6461645 and US Patent No. 6179919, the contents of which are incorporated herein by reference. In general, methods for obtaining umbilical cord blood involve the collection of cord blood from the ^' cut end of the umbilical cord into a sterile collection container containing an anticoagulant.

The invention contemplates the use of stem cells obtained from the bone marrow. Bone marrow cells may be obtained from iliac crest, femora, tibiae, spine, rib or other medullary spaces. Methods and devices for the aspiration of bone marrow from a donor are well known in the art, and described in, for example, in US Patent No. 4486188 and US Patent No. 4481946, the contents of which are incorporated herein by reference. Bone marrow removed from the donor may be replicated or preserved for future replication.

The invention also contemplates the use of stem cells purified or enriched from apheresis products, bone marrow harvests, or cord blood collections, for example, by physical or immunological separation techniques. Methods for isolating enriched populations stem cells are known in the art, and are described for example, in US Patent No. 506162, US Patent No. 5681559, PCT/US 1994/09760, PCT/US 1994/08574 and PCTYUS 1994/10501, the contents of which are incorporated herein by reference. Stem cell fractions may be enriched or purified from samples using known techniques including density centrifugation, counter-flow centrifugal elutriation, or affinity chromatography. Immunomagnetic cell separation systems may be used to purify stem cells or stem cell subpopulations from mixed cell populations. Examples of commercially available kits suitable for immunomagnetic cell separation include the mini MACS kit (Miltenyi Biotech, Inc., CA, USA) and the Easy Sep kit (Stem Cell Technologies, Vancouver, Canada). Stem cell populations may be enriched or purified by cell sorting or the use of packed columns.

Stem cells for use in accordance with the invention may be maintained or expanded in culture. For example, stem cells may be placed in a medium containing an effective amount of insulin-like growth factor (IGF) and at least one of thrombopoietin (TPO), stem cell factor (SCF), or fibroblast growth factor (FGF) under conditions suitable for expansion. Culture conditions for the maintenance or expansion of stem cells are known in the art and described, for example, in Ueda et al. J. CHn. Invest. (2000) 105:1013-1021, the disclosure of which is incorporated herein by reference.

The invention further contemplates the use of stem cells that have been preserved and stored, for example, by cryopreservation. Methods for the cryopreservation of stem cells are described, for example, in Stiff PJ, "Cryopreservation of hematopoietic stem cells" in: Bone Marrow Transplantation (1994), Forman SF, Blume KG, Thomas ED (Eds), Blackwell Scientific Publications (see pages 299-308). Methods by which stem cells derived from cord blood may be preserved are described in, for example, US Patent No. 6461645, the contents of which is incorporated herein by reference. Non-limiting examples of systems for freezing bone marrow are disclosed in US Patent No. 4117881 and US Patent No. 4107937, the contents of which are also incorporated herein by reference. hi the context of the present invention, stem cells encompass both hematopoietic stem cells (HSC) and hematopoietic progenitor cells (HPC). HSC are pluripotent stem cells with self-renewal capacity and are capable of sustained differentiation into cell types of any hematopoietic lineage. For example, HSC may differentiate into cells of the myeloid lineage including, but not limited to, neutrophils, basophils, eosinophils, megakaryocytes, platelets, erythrocytes, dendritic cells, monocytes and macrophages. Alternatively, HSC may differentiate into cells of the lymphoid lineage including, for example, T lymphocytes, B lymphocytes and natural killer cells.

HSC may be identified by the presence or absence of one or more specific markers on the surface of the cell or within the interior of the cell. Alternatively or additionally, HSC may be identified by measuring the expression of genes which encode such markers.

In a preferred embodiment of the invention, HSC are identified by detecting the presence of CD34 on the cell surface. Accordingly, HSC may be identified as CD34⁺ cells. HSC do not generally express markers associated with lineage commitment such as, for example, CD38. Accordingly, in one embodiment of the invention, HSC may be identified as CD34⁺CD38^" cells. Additionally or alternatively, HSC may be identified by the expression of CDl 17 (c-kit) and/or CD133. Additionally or alternatively, HSC of the invention may be identified by the absence of other lineage-associated markers, such as CD7, CDlO, CD13, CD19, CD33, CD45, CD71, CDI lO, and Glycophorin A.

Hematopoietic progenitor cells (HPC) in the context of the present invention are cells derived from a hematopoietic stem cell that have not undergone terminal differentiation. HPC of the invention may be oligopotent thus being capable of differentiating into multiple types of blood cells, or unipotent and thereby being capable of differentiating into a single type of blood cell. In a preferred embodiment of the invention, HPC are identified by detecting the presence of CD34 and CD38 on the cell surface. Accordingly, the HPC of the invention may be identified as CD34⁺CD38⁺ cells. Additionally or alternatively, HPC may be identified by the expression of lineage- . associated markers, including but not limited to CD7, CDlO, CD13, CD19, CD33, CD45, CD68, CD71, CD90 (Thy-1), CDl 10, CD123, CD124, HLA-DR and Glycophorin A.

HPC for use in the invention may be myeloid progenitor cells. Myeloid progenitor cell may be identified as CD34⁺CD38⁺CD33⁺ cells. Myeloid progenitor cells may be early myeloid progenitor cells or late-myeloid progenitor cells. Early myeloid progenitor cells may be identified as CD34⁺CD38⁺CD33⁺CD15⁺ cells. Late myeloid progenitor cells may be identified as CD34⁺CD38⁺CD33⁺CD15^" cells. HPC may be granulomonocytic progenitor cells. Granulomonocytic progenitor cells may be identified as CD34⁺CD38⁺CD64⁺ cells, or CD34⁺CD38⁺CD64⁺CD71^low cells. HPC may be megakaryocytic progenitor cells identified as CD34⁺CD38⁺CD61⁺ cells or CD34⁺CD38⁺CD61⁺CD110⁺ cells. HPC may be T lymphocyte progenitor cells or B lymphocyte progenitor cells. T lymphocyte progenitor cells may be identified as CD34⁺CD38⁺CD7⁺ cells. B lymphocyte progenitor cells may be identified as CD34⁺CD38⁺CD19⁺ cells. HPC may be erythroid progenitor cells or late erythroid progenitor cells. Erythroid progenitor cells may be identified as CD34⁺CD45⁺CD71⁺ cells. Late-erythroid HPCs may be identified as CD34⁺CD71⁺CD64^" cells. The skilled addressee will recognise that the cellular markers and combinations of cellular markers listed above are not limiting, and accordingly HSC/HPC may be identified by detecting the presence or absence of other additional cellular markers or other additional combinations of cellular markers known in the art.

Stem cells of the invention may be identified by flow cytometry. Flow cytometry techniques allow the identification of different cell types in a non-homogeneous sample (immunophenotyping) and are known in the art. The general principles of flow cytometry, and assays for the preparation of cells for use in flow cytometry are described in "Current Protocols in Cytometry", Robinson, Darzynkiewic, Hyun, Orfao, Rabinovitch, (Eds.), (2007); "Current Protocols in Immunology", Coligan J.E., Kruisbeek A.M., Margulies D.H., Shevach E.M., Strober W. (Eds.), (2007) (see for example, Unit 5); U.S. Patent No. 4727020; U.S. Patent No. 4704891 and U.S. Patent No. 4599307, the contents of which are incorporated herein by reference. In general, stem cells of the invention may be incubated with antibodies under suitable conditions such that the antibody specifically binds to one or more target markers on the surface of the cell. Additionally or alternatively, the cell membrane may be permeabilised allowing antibodies to enter the interior of the stem cell whereupon one or more internal target markers may be bound by the antibodies.

Stem cells with bound antibodies may be combined with suitable reagents or buffer solutions for application to a flow cytometer. In general, labelled stem cells are passed substantially one at a time through one or more sensing regions in the cytometer wherein each cell is exposed to one or more light sources. Upon passing through the light source within the flow cell, light scattered and absorbed (or fluoresced) by each cell may be detected by one or more photodetectors. Side scattered light is generally used to provide information on cell structure while forward scattered light is generally used to provide information on cell size. In addition the fluorescence emitted by fluorochrome molecules conjugated to antibodies upon exposure to the one or more light sources may be used to detect the presence of different types of stem cells possessing certain marker profiles. The detected scattered and/or emitted light may be stored in computer memory for analysis. Additionally or alternatively, specific defined parameters of scattered and emitted light from each cell passing through the sensing region may be used as a basis for the cytometer to separate stem cells from other cells in a clinical sample, and/or separate mixed populations of stem cells into individual populations of stem cells. The proliferative potential of stem cells and individual subsets of stem cells may be used to predict engraftment potential in procedures involving the transplantation of such cells. The transplant may be an autologous transplant, a syngeneic transplant, or an allogeneic transplant. Donors for allogeneic transplants may be related or unrelated to the recipient. Donors for allogeneic donor transplants will, in general, share a similar human leukocyte antigen (HLA) type to the recipient. The recipient of an allogeneic transplant may be administered one or more immunosuppressive medications to alleviate graft- versus-host disease.

The autologous, syngeneic or allogeneic transplant may be used to increase the number of hematopoietic and/or mature blood cells in the circulation in a subject in need thereof. For example, the transplant may be used following chemotherapy or radiotherapy used for the treatment of hematological malignancies such as leukaemia, lymphoma and multiple myeloma, or solid-tumour cancers including breast and ovarian cancers. Additionally or alternatively, the transplant may be used for the treatment of inherited immunodeficiency disorders. Examples of inherited immunodeficiency disorders include Krabbe disease, severe combined immunodeficiency disorder (SCID), thalassemia, aplastic anaemia and sickle cell anaemia. The skilled addressee will recognise that the methods of the invention are applicable to transplants used for other applications in addition to those referred to above, which are provided for the purpose of exemplification only.

Growth Factors

Blood cells develop from hematopoietic stem cells (HSC), which can undergo self- renewal or differentiate into a multilineage committed hematopoietic progenitor cells (HPC), being either common lymphoid progenitors or common myeloid progenitors. Cells of the lymphoid lineage develop from common lymphoid progenitor cells, and predominantly undergo maturation in lymphoid tissue. Cells of the myeloid lineage develop from common myeloid progenitor cells, and predominantly undergo maturation in the bone marrow. In accordance with the methods of the present invention, stem cells are exposed to at least one growth factor capable of inducing a proliferative response. Suitable growth factors include any substance capable of inducing proliferation of stem cells. The at least one growth factor may induce proliferation in a specific subset of stem cells or multiple stem cell subsets in a given stem cell population. In addition to inducing proliferation, the at least one growth factor may affect other functional aspects of stem cells (or subsets thereof) including, for example, differentiation, maturation and survival.

Examples of growth factors that may be used to induce proliferation of stem cells and subsets thereof include, but are not limited to, stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM- CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), FLT-3/FLK-2 ligand, stromal cell-derived factor- 1 (SDF-I)₅ tumor necrosis factor-alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13 and combinations thereof. The skilled addressee will recognise that these are non-limiting examples and other growth factors or combinations of different growth factors known in the art may be utilised when carrying out the methods of the invention.

Growth factors for use in the methods of the invention may be produced naturally or manufactured by alternative means. For example, recombinant forms of several growth factors have been produced, including granulocyte-macrophage colony simulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), IL-3, macrophage colony simulating factor (M-CSF) or colony stimulating factor 1 (CSF-I), and stem cell factor (SCF), each of which may be used in the methods of the invention. Non-limiting examples of growth factors for use in the invention are provided below.

Stem cell factor (SCF) may be used to induce the proliferation of stem cells. SCF has broad activities involving hematopoietic, pigment and primordial germ cell lineages, and promotes proliferation and survival of human megakaryocyte, erythroid and granulocyte/macrophage progenitors. SCF is involved in the differentiation of hematopoietic stem cells (HSC) into common myeloid progenitor cells (CMP) and has a role in the generation of granulocytes.

Additionally or alternatively, thrombopoietin (TPO) may be used to induce the proliferation of stem cells. TPO promotes survival and proliferation in megakaryocytes and is a primary regulatory factor for megakaryocytopoiesis and thrombopoiesis, regulating platelet production and the development of megakaryocytes and their progenitors.

Additionally or alternatively, erythropoietin (EPO) may be used to induce the proliferation of stem cells. EPO a primary regulatory factor for erythopoiesis and promotes the proliferation and differentiation of erythroid precursor cells. Additionally or alternatively, granulocyte-macrophage colony stimulating factor (GM-CSF) may be used to induce the proliferation of stem cells. GM-CSF is an essential survival and proliferation factor for granulocyte, macrophage and eosinophil lineage cells from the progenitor stage to maturity, and is involved in the growth and differentiation of these cells.

Additionally or alternatively, granulocyte colony simulating factor (G-CSF) may be used to induce the proliferation of stem cells. G-CSF is an activation factor for hematopoietic restricted granulocyte lineage cells, and is involved in their proliferation, differentiation and survival. Receptors for GM-CSF exist on most types of myeloid progenitor cells, mature monocytes, neutrophils, eosinophils, basophils, and dendritic cells.

Additionally or alternatively, macrophage colony stimulating factor (M-CSF) may be used to induce the proliferation of stem cells. M-CSF is involved in the generation of monocyte/macrophage cells from their cellular precursors. M-CSF also targets macrophages and stimulates multiple responses, including proliferation, cytokine and inflammatory modulator release, cytotoxicity and pinocytosis.

Additionally or alternatively, the proliferation of stem cells may be induced by various cytokines. Non-limiting examples of suitable cytokines include the FLT-3/FLK-2 ligand, IL-3, IL-6 and IL-I l, which may be used singularly or in combination with each other and/or in combination with one or more growth factors. The FLT-3/FLK.-2 ligand acts on primitive hematopoietic (multi-lineage) progenitor cells that express the flt3 receptor, and promotes the survival, proliferation, and differentiation of hematopoietic progenitors in synergy with other growth factors such as SCF. Interleukin 3 (IL-3) is a multifunctional cytokine, which among other things supports the early development and proliferation of multi-potential hematopoietic progenitor cells, including those of the macrophage, neutrophil, mast cell and megakaryocyte lineages. Interleukin 6 (IL-6) is also a multifunctional cytokine which acts on a wide range of cell types. In combination with other cytokines, it is known to act upon fibroblasts, myeloid progenitor cells, T-cells, B-cells, and hepatocytes. Interleukin- 11 (IL-Il) is a pleiotropic cytokine that enhances the proliferation of factor-dependent growth of early multipotent progenitors as well as later progenitors committed to either the erythroid or megakaryocyte lineage. Within the hematopoietic system, the effects of IL-11 largely manifest only through combination with other cytokines. IL-11 has generally acted as a synergistic factor serving to augment the responses to primary growth factors, particularly IL-3 and steel factor (SF), the ligand for the c-kit receptor. Stem cells used in accordance with the methods of the invention may be cultured using standard methods known in the art. Techniques and conditions for culturing stem cells are described in, for example, Current Protocols in Stem Cell Biology. Bhatia, Elefanty Fisher Patient Schlaeger and Synder (Eds), (2007), the contents of which are incorporated herein by reference. Stem cells may be cultured in semi-solid media such as soft agar or methylcellulose containing a source of hematopoietic growth factors, with the assay end-point being the number of colonies of mature cells being produced from individual stem cells, as described in Metcalf, D, "The hematopoietic stem and progenitor cells demonstrable using in vitro cloning techniques" In: "The hematopoietic colony stimulating factors", Metcalf D (Ed), (1984), New York, Elsevier (see pages 27-54), the contents of which are incorporated herein by reference.

Detection of Proliferating Stem Cells

Methods for the detection of proliferating stem cells suitable for use in accordance with the invention are known in the art and include, for example, fluorescent dye assays, incorporation of BrdU in the DNA of proliferating cells, incorporation of radio-labelled analogues such as ³H-thymidine into the DNA of proliferating cells, and the detection of cellular markers of proliferation. In general, the proliferative capacity of an aliquot of stem cells from a sample may be used to predict the engraftment potential of the sample from which the aliquot was derived.

The proliferative capacity of stem cells may be assessed using a fluorescent dye assay. Fluorescent dye assays are well known in the art, and are described, for example in Parish CR. Immunol Cell Biol, (1999), 77(6):499-508; Lyons AB and Parish CR, Journal of Immunological Methods., (1994), 171 :131-137; Horan et al, Methods in Cell Biology, (1990), 33:460-490; Lyons AB, J Immunol Methods, (2000), 21:243(l-2):147-54; Quah et al, Nat Protoc. (2007), 2(9):2049-56; "Current Protocols in Cytometry", Robinson, Darzynkiewicz, Hoffman, Nolan, Orfao, Rabinovitch, and Watkins (Eds), (2007) (see for example pp 9.11.1-9.11.9); Traycoff et al, Blood, (1995) 85:2059-2068; Young et al, Blood, (1996), 87;545-556; Gothot et al, Experimental Hematology (1998), 26:562-570; Glimm and Eaves, Blood, (1999), 94:2161-2168, and Oostendorp et al, Blood, (2000), 95:855-862, the contents of which are incorporated herein by reference.

Non-limiting examples of fluorescent dye assays for detecting and/or quantifying proliferating stem cells include assays that utilise carboxyl-fluorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKH, Dapi, Hoechst, thiazole orange, or propidium iodide. The skilled addressee will recognise that other fluorescent dyes may be utilised in the methods of the invention which are not limited to use of the specific dyes mentioned above.

In a preferred embodiment of the invention, the proliferative response of stem cells is detected using carboxyl-fluorescein-succinimidyl ester (CFSE). Enriched or purified stem cells or a clinical sample containing stem cells are exposed to CFSE which passes through the cell membrane by passive diffusion. The CFSE within the cell remains colourless and non-fluorescent until cellular esterases cleave the acetate groups yielding fluorescent carboxyfluorescein succinimidyl ester. The succinimidyl ester group is able to react with amine-containing residues of cellular proteins forming fluorescent conjugates. Upon cell division, CFSE labelling is distributed approximately equally among daughter cells, which possess approximately half the fluorescence of undivided cells. Accordingly, upon exposure to one or more growth factors, each successive generation in a population of proliferating stem cells labelled with CFSE may be identified by a halving of cellular fluorescence intensity (excitation/emission maxima approximately 495/525 nm) that is readily detectable, for example, by using a flow cytometer or a fluorescence microplate reader.

In one embodiment of the invention, stem cells labelled with a succinimidyl ester dye, such as CFSE are exposed to one or more growth factors and detected by flow cytometry. The stem cells may be sourced from a clinical sample containing stem cells or a sample of enriched or purified stem cells. Flow cytometry may be used to simultaneously detect the fluorescing succinimidyl ester dye incorporated in the cell in combination with one or more fluorochrome-conjugated antibodies bound to one or more cellular markers capable of identifying a stem cell or a subpopulation thereof. The marker or combination of markers may thus be used to distinguish proliferating stem cells from other cells present in the sample and/or to identify specific subpopulations of proliferating stem cells within the general stem cell population. In one embodiment, one or more cell viability markers are detected in combination with the fluorescing succinimidyl ester dye incorporated in the cell and one or more fluorochrome-conjugated antibodies bound to one or more cellular markers capable of identifying a stem cell or a subpopulation thereof. In one embodiment, the viability marker is 7AAD.

Accordingly, the proliferative response of stem cells identified in the sample is used to predict their engraftment potential following transplantation. The proliferative capacity of stem cells identified in the sample may be used in combination with stem cell enumeration to predict the engraftment potential of stem cells following transplantation. In accordance with the methods of the invention, proliferating stem cells may be detected vising bromodeoxyuridine (5-bromo-2-deoxyuridine, BrdU), a synthetic thymidine analogue that incorporates into cellular DNA generally during the S-phase of cell division. Assays that utilise BrdU for the detection of cell proliferation are known in the art and described, for example, in "Current Protocols in Cytometry", Robinson, Darzynkiewicz, Hoffman, Nolan, Orfao, Rabinovitch, and Watkins (Eds), (2007) (see for example unit 7.7), the contents of which are incorporated herein by reference. BrdU may be applied to enriched or purified stem cells or a clinical sample containing stem cells which are exposed to one or more growth factors. Antibodies specific for BrdU may then be used to detect BrdU incorporated into the DNA of stem cells thus providing a means of detecting proliferating stem cells. Binding of the antibody may require denaturation of the DNA which may be achieved, for example, by exposing the cells to acid or heat. Antibodies specific for BrdU may be conjugated to fluorochromes allowing detection, for example, by flow cytometry, immunohistochemistry or other means known in the art. Alternatively, antibodies specific for BrdU may be bound to a substrate allowing colorimetric or chemiluminescent detection. For example, antibodies specific for BrdU may be bound to peroxidase facilitating detection by application of a peroxidase substrate.

In one embodiment of the invention, stem cells proliferating in response to one or more growth factors are labelled with one or more fluorochrome-conjugated antibodies specific for BrdU and identified by flow cytometry. In another embodiment, additional fluorochrome-conjugated antibodies capable of identifying a stem cell or determining stem cell viability are used in combination with one or more BrdU-specific fluorochrome- conjugated antibodies. Accordingly, proliferating stem cells may be distinguished from other cells present in the sample, and specific subpopulations of proliferating stem cells within the stem cell population may also be identified.

Proliferating stem cells may be identified by the detection of one or more cellular markers indicative of cell division including, but not limited to, Ki-67, michrochromosome maintenance protein 2 (Mcm2/BM28), microchromosome maintenance protein 6 (Mcm6), and cdcό. Cellular markers associated with cell division may be detected using one or more antibodies capable of specifically binding to the cellular marker. The cellular marker may be present on the surface of the cell or in the interior of the cell. The antibodies may be conjugated to a fluorochrome allowing detection, for example, by flow cytometry, immunohistochemisty or by other means known in the art. Alternatively, the antibody may be bound to a substrate allowing colorimetric or chemiluminescent detection. In one embodiment, stem cells proliferating in response to one or more growth factors are labelled with one or more fluorochrome-conjugated antibodies specific for one or more cellular markers associated with cell division and identified by flow cytometry. In a further embodiment, additional fluorochrome-conjugated antibodies for the identification of stem cells or subsets thereof are used in combination with fluorochrome- conjugated antibodies specific for markers associated with cell division, and the labelled cells detected by flow cytometry. Accordingly, proliferating stem cells may be distinguished from other cells present in the sample, and the information used to predict the engraftment potential of the stem cells following transplantation. In another embodiment of the invention, the proliferative capacity of stem cells so identified in the sample is used in combination with stem cell enumeration to predict the engraftment potential of stem cells following transplantation.

Proliferating stem cells may be detected by incorporation of a radioactive label into the DNA of the cell during division. For example, radioactive H-thymidine may be used to label cellular DNA of enriched or purified stem cells exposed to one or more growth factors. Cell proliferation assays utilising ³H-thymidine are described, for example, in "Current Protocols in Immunology," John E. Coligan, Ada M. Kruisbeek, David H. Margulies, Ethan M. Shevach, Warren Strober (Eds), (2007) (see in particular Appendix 3D), the contents of which are incorporated herein by reference. Enriched or purified stem cells (or subpopulations thereof) may be incubated under suitable culture conditions with one or more growth factors and ³H-thymidine for a period sufficient to allow cell division, during which time the ³H-thymidine is incorporated into the DNA of dividing stem cells. Proliferating stem cells undergoing cell division incorporate radioactive thymidine into their DNA, and the degree of radioactivity will therefore increase in proliferating stem cells. Following incubation the cells may be harvested and lysed. The cell fragments and DNA can be passed through a filter membrane allowing the collection of DNA on the filter membrane. The filter membrane can then be dried and the amount of radioactivity measured in a scintillation counter. Proliferating stem cells may then be detected by the increased emission of radioactivity from the isolated DNA. The proliferative capacity of an aliquot of stem cells from a sample as determined by ³H- thymidine assay may be used to predict the engraftment potential of the sample from which the aliquot was derived.

The skilled addressee will recognise that the methods for assaying and detecting stem cell proliferation described above are non-limiting examples and other suitable methods known in the field may be utilised. In general, stem cells with normal or increased proliferative responses are predicted to have the potential to engraft successfully. Stem cells with a low proliferative response are, in general, predicted to have a reduced engraftment potential. Stem cells that do not show a proliferative response are generally predicted to have little or no potential for successful engraftment. A person skilled in the art may readily determine whether the proliferative response of a particular sample of stem cells is low, normal or increased by comparison with the levels of proliferation observed in a group of stem cell samples derived from different subjects measured under the same assay conditions.

The proliferative capacity of stem cells in a sample may be used in combination with stem cell enumeration to predict the engraftment potential of stem cells following transplantation. In general, a minimum number of 2 million CD34⁺ stem cells displaying normal or increased proliferative capacity/kg can be predictive of successful engraftment.

Kits The invention provides kits for determining the engraftment potential of a cell population containing one or more stem cells, the kit comprising one or more growth factors, one or more agents for determining the proliferative capacity of stem cells and optionally one or more agents for detecting the presence or absence of one or more cellular markers expressed by stem cells or subpopulations of stem cells. Any suitable growth factor or combination of growth factors may be included in kits of the invention. Non-limiting examples of growth factors include stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), FLT-3/FLK-2 ligand, stromal cell-derived factor- 1 (SDF-I), tumor necrosis factor-alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13, and combinations thereof.

Kits of the invention may include any agent or agents suitable for determining the proliferative capacity of stem cells, including but not limited to, fluorescent dyes (e.g. carboxyl-fluorescein-succinimidyl ester (CFSE)₅ carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKH, Dapi, Hoechst, thiazole orange, or propidium iodide), BrdU, radio-labelled analogues (e.g. ³H-thymidine), and agents capable of detecting cellular markers of proliferation (e.g. Ki-67, microchromosome maintenance protein 2 (Mcm2/BM28), michiOchromosome maintenance protein 6 (Mcm6), and cdcό) such as antibodies.

The kits may also include any agent capable of detecting the presence or absence of one or more cellular markers expressed by stem cells or subpopulations of stem cells facilitating their identification. Examples of such markers include, but are not limited to, CD7, CDlO, CD13, CD14, CD15, CD19, CD33, CD34, CD38, CD45, CD61, CD64, CD68, CD71, CD90 (Thy-1), CDI lO, CDl 17, CD123, CD124, CD133, HLA-DR and Glycophorin A.

The kits may comprise any number of additional components, non-limiting examples of which include reagents for cell culture, reference samples, buffers, labels, and written instructions for performing the assay.

Engraftment

The degree of stem cell engraftment following transplantation may be evaluated using standard techniques in the art. In general, hematologic recovery in a stem cell transplant recipient may be indicative of successful engraftment. In particular, . hematologic recovery involving a significant proportion of cells derived from donor stem cells is indicative of successful engraftment. Methods for enumerating various types of blood cells in the circulation are known to the skilled addressee and typically involve cell counting using automated electronic cell counters that provide differential white blood cell counts as well as red blood cell and platelet counts.

For example, neutrophil counts are a primary measure of hematologic recovery and may be indicative of the degree of stem cell engraftment in a recipient. In particular, an increase in neutrophils derived from donor stem cells is an indicator of successful engraftment. In general, neutrophils constitute about 45%-75% of circulating white blood cells (normal ranges are known in the art) but counts may be significantly lower in patients requiring a stem cell transplant. Hence, in the clinical setting of stem cell transplantation, a recovery in the number of circulating neutrophils may be considered indicative of successful stem cell engraftment. This may be confirmed by demonstrating that a significant number of newly generated neutrophils are derived from donor stem cells using standard methods in the art including, for example, analysis of sorted myeloid cells using cytogenetic testing, or measurements of individual DNA variations between donor and recipient determined pre-transplant to demonstrate the origin of the cell population. The degree of stem cell engraftment may also be assessed by assessing T lymphocyte counts in a recipient. For example, T lymphocyte counts in a recipient taken before and after transplantation may be compared to determine the degree of stem cell engraftment. A clinically relevant recovery of T lymphocyte counts in a transplant recipient is generally considered to be indicative of successful stem cell engraftment. This may be confirmed by demonstrating that a significant number of newly generated T lymphocytes are derived from donor stem cells using standard methods in the art including, for example, analysis of sorted T lymphocytes using cytogenetic testing, or measurements of individual DNA variations between donor and recipient determined pre- transplant to demonstrate the origin of the cell population.

Standard platelet and T lymphocyte counts and ranges for healthy individuals are known in the field. Additional indicators of T cell recovery may be utilised, such as an increased response to PHA-induced proliferation.

Treatment Regimens

The methods of the invention are predictive of the degree of stem cell engraftment, and therefore find application in treatment strategies for transplant- associated disorders (e.g. cancer, leukaemia, lymphoma, myeloma, myelodysplasia, genetic disease, immune deficiencies, aplastic anaemia and autoimmune disorders).

For example, the capacity to predict the level of stem cell engraftment prior to transplantation may be used to improve therapeutic responses and clinical outcomes including, but not limited to the alleviation of disease symptoms, stabilisation or remission of disease or delayed disease progression, and/or prolonged survival after transplantation. An assessment of stem cell engraftment potential prior to transplantation is also critical when the availability of the appropriate donor material is limited.

Alternatively, the methods of the invention may be used to assist in the prevention of diseases, conditions or symptoms thereof that may otherwise develop when stem cell engraftment is low or fails in a recipient.

In general, predicting the engraftment potential of stem cells in accordance with the methods of the invention may be beneficial in the treatment and/or prevention of diseases and conditions including leukopenia, neutropenia, thrombocytopenia, lymphopenia, abnormal migration of hematopoietic cells and hematopoietic stem cell cytopenia. These diseases or conditions may arise following stem cell transplantation and/or chemotherapy. Alternatively, they may arise independently of such treatments.

The invention will now be described with reference to specific examples, which should not be construed as in any way limiting the scope of the invention. Examples

Example 1 : Derivation of Stem Cells

Cells were derived from patient samples enriched for HSC/HPC. Adult patients being prepared for high dose chemotherapy and autologous stem cell transplantation received stem cell mobilization treatment with high-dose cyclophosphamide and granulocyte colony-stimulating factor (G-CSF: Filgrastim, Amgen, Australia) given at a dose of 5 micrograms per kg patient weight every 12 hours for 10 days, and then underwent leukapheresis. Leukapheresis was performed approximately 10 days later when the white cell count in an EDTA blood sample reached 1.0 xlO⁹/L as measured on an Advia 120 automated cell counter (Bayer Diagnostics), and when the number of CD34⁺ cells in the blood exceeded 20 per microlitre as measured on a FacsCalibur flow cytometer (Becton Dickinson), according to methods described in Padley et al. Journal of Clinical Apheresis. 1991, 6: 77-80. The apheresis product was then prepared for cryopreservation by addition of 10% DMSO, and then frozen at -I⁰C per minute in a rate- controlled biological freezer as described in Lasky et al. Transfusion, 1986: 26: 331-4. , Cells in apheresis products were stored in the vapour phase of a liquid nitrogen tank at - 186⁰C indefinitely. Cells from pilot vials were thawed rapidly in a 37⁰C water bath. An aliquot of the thawed leukapheresis product was used for the CD34 proliferation assay. hi some cases, HSC apheresis samples taken from normal donors undergoing stem cell mobilization with G-CSF underwent CD34⁺ cell selection using an immunomagnetic clinical scale cell separation system (Clinimacs Device, Miltenyi Biotec, Germany) according to methods described in Perseghin et al. Stem Cells and Development. 2005, 14(6): 740-743, the contents of which are incorporated by reference. Purification of CD34⁺ cells by this method resulted in a highly purified CD34⁺ cell population (mean purity 80.3%, n=4) as measured by flow cytometry.

Umbilical cord blood derived from the placental vein immediately after delivery was used as an alternative source of stem cells for use in the proliferation assay. These samples were obtained in the practice of clinical transplantation from unrelated donor Cord Blood Banks. A small aliquot of cryopreserved cord blood was thawed as described in Sartor et al. Bone Marrow Transplantation. 2005, 36:199-204. Thawed cells were not purified prior to use in the proliferation assay. Example 2: Stem Cell Culture

Culture of HPC was carried out under the following standard conditions. Cells from pilot vials frozen at the time of storage of autologous leukapheresis products, or from frozen cord blood units, were thawed rapidly by placing pilot vials in a 37° C water bath, and washing twice in XV20 medium (Gambrex) by diluting with 10 mis of medium, centrifuging at 1600 rpm, and resuspending in 5 mis medium, in order to remove dimethysulphoxide. Purified CD34⁺ cells were prepared as described in example 1 above.

Cells were incubated with carboxyfluroescein diacetate succinimidyl ester (CFSE) prepared to a final concentration of 5 μM. A 5mM stock solution of CFSE (Bioscientific) was prepared by weighing lOmg of CFSE and dissolving in 3.6mls DMSO (Wack- Chemie), with lOμl aliquots of CFSE then stored at -20⁰C until used. A working solution was prepared by thawing lOμl aliquot of stock CFSE and diluting with 90μl of PBS (Oxoid). For CFSE staining, 1 μl of CFSE solution was added to 200μl of cell suspension (containing 2 x 10⁶ cells) for 10 minutes at 37⁰C then washed once in cold medium. Cells were resuspended at a concentration of 2 x 10 /ml in XV20 medium containing 10% fetal calf serum (BioWhittikar) and the following cytokines; GM-CSF (500U/μl), G-CSF (200U/μl), IL-3 (10 μg/ml), SCF (10 μg/ml), TPO (lOμg/ml), Flt-3 (10 μg/ml), IL-6 (20 μg/ml) (all cytokines were purchased from Chemicon). Control cells were prepared in the same manner, but without cytokines. Several additional samples of cord blood cells (thawed but not purified) were prepared and cultured as above in a less complex culture medium mixture of SCF and IL-3. Cells were placed in sterile tubes (Becton Dickinson 352054) in 1 ml of the above medium in a humidified incubator at 37 ⁰C in 5% CO₂ in air for up to 96 hours.

Example 3: Detection of proliferating stem cell populations

AU samples were prepared for flow cytometry using lOOμL of suspension containing 2-5 x 10⁵ cells per ml from the above cultures. Cells were then labelled with anti-CD34 antibody conjugated with Phycoerythrin (5μl) (CD34-PE; HPCA2 clone, Becton Dickinson), 7-AAD (lOμl) (viability probe, Catalogue Number 555816, Becton Dickinson), CD 14 conjugated with PerCP (5μl) (Clone MOP9, Becton Dickinson) and CD45 conjugated with APC (5μl) (Clone 2Dl, Becton Dickinson). Cell suspensions containing antibodies were then incubated for 15 minutes at 2O⁰C. Cells were then washed once in phosphate buffered saline, and analysed on a FACS Calibur flow cytometer (Becton Dickinson) using Cellquest software. A minimum of 100,000 events were collected, and viable CD34⁺ cells were identified by gating on forward and side scatter and CD34 expression. Dead cells and monocytes were excluded by their positive staining for CD 14 and 7AAD. CD45 was used to discriminate mature leukocytes from erythrocytes and HSC/HPC. Viable CD34 cells were then examined for CFSE staining (Figure 1).

Purified CD34⁺ cells were analysed for proliferation based on CFSE labelling at various time points following incubation in a 6 growth factor combination for 4 days. Discrete populations of proliferating CD34⁺ were observed at cells at 48, 72 and 96 hours of culture (Figure 2). Unpurified cord blood cells exposed to a simplified cocktail of growth factors (SCF,

GM-CSF, and IL-6) showed equivalent levels of CD34⁺ cell proliferation (Figure 3) compared with the 6 factor combination (GM-CSF, G-CSF, IL-3, SCF, TPO, Flt-3, IL-6) shown in Figure 2.

Figure 4 shows the results of proliferation assays conducted on purified CD34⁺ purified cells derived from apheresis products (n=4), apheresis products (n=8) and cord blood (n=12). Four independent samples of purified CD34⁺ cells showed a mean of 76% (range 75-80%) dividing cells at 48 hours and 97% (range 94-98%) at 72 hours (Figure 4). Similar levels of proliferation in CD34⁺ cells were detected using apheresis products (PBSCH) from 8 different patients (Figure 4), with a mean of 59% (range 50-70) dividing cells at 48 hours and 96% (range 92-98%) at 72 hours. Comparable levels of cell division were detected in 12 cord blood samples (Figure 4).

Example 4: Correlation between stem cell proliferative capacity and engraftment Engraftment was measured, according to conventionally accepted definitions, as the day that the absolute neutrophil count in the patient's peripheral blood reached 0.5 x 10⁹ per litre, as measured on an Advia 120 Hematology analyser (Bayer Diagnostics). A venous blood sample collected into EDTA anticoagulant was generally used for these counts. AU patients were receiving BMT for treatment of a form of hematological malignancy, such as leukaemia or lymphoma.

Purified CD34⁺ cells from 3 of the 4 normal donors were transplanted into 3 MHC- haploidentical related recipients. As shown in Figure 5, all 3 patients showed evidence of neutrophil recovery between 7-10 days post-transplant. 10 of 12 cord blood units analysed were transplanted into 8 unrelated recipients (2 patients received double cord blood unit transplants) and neutrophil engraftment occurred 17-38 days post-transplant. Finally, 7 of 8 autologous or allogeneic PBSCH were transplanted, with neutrophil engraftment occurring between day 9 and 19.

These clinical data demonstrate that all stem cell products, which showed clear evidence of proliferative capacity in the in vitro assay described above, had subsequent in vivo engraftment in BMT recipients.

Claims

1. A method for predicting the engraftment potential of a cell population containing one or more stem cells, said method comprising the steps of: culturing one or more of the stem cells from the population with at least one growth 5 factor; and determining the proliferative capacity of the one or more stem cells in response to said at least one growth factor, wherein said proliferative capacity predicts the engraftment potential of the cell population following transplantation. o

2. The method according to claim 1, wherein the steps of culturing one or more of the stem cells and determining the proliferative capacity are performed simultaneously.

3. The method according to claim 1 or claim 2, further comprising a step of identifying one or more stem cells in said cell population prior to or concurrent with the step of determining the proliferative capacity. s

4. The method according to any one of claims 1 to 3, comprising the additional step of determining the number of stem cells present in said population of cells.

5. The method according to any one of claims 1 to 4, wherein said proliferative capacity of one or more stem cells is determined using a fluorescent dye assay.

6. The method according to claim 5, wherein said fluorescent dye assay utilises a0 fluorescent dye selected from the group consisting of carboxyl-fiuorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKLH, Dapi, Hoechst, thiazole orange, and propidium iodide.

7. The method according to claim 5 or claim 6, wherein said fluorescent dyes assay comprises the step of detecting a fluorescent signal emitted by the dye using a flow cytometer.

8. The method according to any one of claims 3 to 7, wherein said one or more stem cells in said cell population are identified by the presence or absence of one or more cellular markers. 0

9. The method according claim 8, wherein said one or more cellular markers is selected from the group consisting of CD7, CDlO, CD13, CD14, CD15, CD19, CD33, CD34, CD38, CD45, CD61, CD64, CD68, CD71, CD90 (Thy-1), CDI lO, CDl 17, CDl 23, CDl 24, CDl 33, HLA-DR, Glycophorin A, and combinations thereof.

10. The method according to claim 8 or claim 9, wherein the presence or absence₅ of said cellular markers is determined using one or more antibodies.

11. The method according to claim 10, wherein said one or more antibodies are conjugated to a fluorochrome.

12. The method according to claim 11, wherein said one or more antibodies conjugated to a fluorochrome are identified by flow cytometry.

13. The method according to any one of claims 1 to 12, wherein said stem cell is a hematopoietic stem cell.

14. The method according to any one of claims 1 to 12, wherein said stem cell is a hematopoietic progenitor cell.

15. The method according to any one of claims 1 to 14, wherein said cell population is a clinical sample.

16. The method according to claim 15, wherein said clinical sample is derived from bone marrow, peripheral blood, or cord blood.

17. The method according to any one of claims 1 to 16, wherein said transplantation is autologous, syngeneic, or allogeneic.

18. The method according to any one of claims 1 to 17, wherein said transplantation is used for the treatment of a hematological malignancy.

19. The method according to any one of claims 1 to 18, wherein the at least one growth factor is selected from the group consisting of stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), FLT-3/FLK-2 ligand, stromal cell-derived factor- 1 (SDF-I), tumor necrosis factor-alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13, and combinations thereof.

20. The method according to any one of claims 1 to 19, wherein said cell population is a stem cell-enriched population or a purified stem cell population.

21. A kit for determining the engraftment potential of a cell population containing one or more stem cells, the kit comprising:

(i) one or more growth factors,

(ii) one or more agents for determining the proliferative capacity of stem cells; and optionally

(iii) one or more agents for detecting the presence or absence of one or more cellular markers expressed by stem cells or subpopulations of stem cells.

22. The kit according to claim 21, wherein the one or more growth factors are selected from the group consisting of stem cell factor (SCF), thrombopoietin (TPO), erythropoietin (EPO), granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony simulating factor (G-CSF), macrophage colony stimulating factor (M- s CSF), FLT-3/FLK-2 ligand, stromal cell-derived factor- 1 (SDF-I), tumor necrosis factor- alpha (TNF-α), transforming growth factor beta (TGFβ), interleukin 1, interleukin 2, interleukin 3, interleukin 4, interleukin 5, interleukin 6, interleukin 7, interleukin 8, interleukin 11, interleukin 12, interleukin 13, and combinations thereof.

23. The kit according to claim 21 or claim 22, wherein the one or more agents foro determining the proliferative capacity of stem cells is a fluorescent dye selected from the group consisting of carboxyl-fluorescein-succinimidyl ester (CFSE), carboxyfluorescein succinimidyl ester diacetate (CFDA SE), carboxylic acid diacetate succinimidyl ester (DFFDA, SE), calcein, PKH, Dapi, Hoechst, thiazole orange, and propidium iodide.

24. The kit according to any one of claims 21 to 23, wherein said one or more5 cellular markers is selected from the group consisting of CD7, CDlO, CDl 3, CD 14,

CD15, CD19, CD33, CD34, CD38, CD45, CD61, CD64, CD68, CD71, CD90 (Thy-1), CDIlO, CDl 17, CD123, CD124, CD133, HLA-DR, Glycophorin A, and combinations thereof.