# Patent

## Title
Method for expansion of stem cells and the use of such cells

## Abstract

The present invention demonstrates that SALL4A and SALL4B are strong positive regulators of hematopoetic stem cell expansion. HSCs receiving expression of SALL4A or SALL4B are able to achieve a high-level of expansion. Cultures of SALL4-transduced cells results in extensive HSC expansion with over 1000-fold higher levels than controls within 2 to 3 weeks and expanded HSCs show no or very little maturation. Moreover, the expansion occurs quite rapidly with significant HSC growth in just a few days. In addition, SALL4-induced HSC expansion exhibits no impairment of hematopoietic cell differentiation. SALL4 appears to function in the maintenance of an undifferentiated proliferation state and block cell differentiation for HSCs.

## Background
This application is a §371 national state of PCT International Application No. PCT/US52011/048819, filed Aug. 23, 2011, claiming the benefit of U.S. Provisional Application No. 61/376,122, filed Aug. 23, 2010, the contents of each of which are hereby incorporated by reference in their entirety.


This invention was made with government support under grant number HL087984 awarded by the National Institute of Health. The government has certain rights in the invention.


Throughout this application, various publications are referred to by arabic numerals in parentheses. Full citations for these publications are presented in a References section immediately before the claims. Disclosures of the publications cited in the References section in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as of the date of the methods and apparatuses described herein.
FIELD OF THE INVENTION
The present invention relates to ex vivo expansion of a stem cell population using a polypeptide having the expansion enhancement activity of a Sal-like (SALL) polypeptide and the use of such cells.
BACKGROUND OF THE INVENTION
Stem cells have the potential to develop into many different cell types in the body during early life and growth. Stem cells can be divided into two broad categories: embryonic and adult. In a developing embryo, stem cells can differentiate into all of the specialized embryonic tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing specialized cells, but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues. Adult stem cells can differentiate into multiple pathways. Mesenchymal stem cells are adult stem cells which give rise to a variety of cell types: bone cells (osteocytes), cartilage cells (chondrocytes), fat cells (adipocytes), and other kinds of connective tissue cells such as those in tendons. Neural stem cells are adult stem cells in the brain which give rise to its three major cell types: nerve cells (neurons) and two categories of non-neuronal cells—astrocytes and oligodendrocytes. Epithelial stem cells are adult stem cells in the lining of the digestive tract occur in deep crypts and give rise to several cell types: absorptive cells, goblet cells, paneth cells, and enteroendocrine cells. Skin stem cells are adult stem cells which occur in the basal layer of the epidermis and at the base of hair follicles. The epidermal stem cells are adult stem cells which give rise to keratinocytes, which migrate to the surface of the skin and form a protective layer. The follicular stem cells can give rise to both the hair follicle and to the epidermis.
Hematopoietic stem cells (HSCs) are rare adult stem cells that have been identified in fetal bone marrow, fetal liver, umbilical cord blood, adult bone marrow, and peripheral blood, which are capable of differentiating into three cell lineages including myeloerythroid (red blood cells, granulocytes, monocytes), megakaryocyte (platelets) and lymphoid (T-cells, B-cells, and natural killer) cells. These HSCs are used in clinical transplantation protocols to treat a variety of diseases including malignant and non-malignant disorders. Expansion of HSCs has important clinical applications since the relative inability to expand hematopoietic stem cells ex vivo imposes major limitations on the current use of HSC transplantation. There is shortage of HSCs used for patient treatments related to bone marrow transplantation or genetic disorders. For allogenic bone marrow transplantation, only one third of all patients who would potentially benefit from an HSC transplant will find a suitable human leukocyte antigen (HLA)-matched related donor.
This is especially true in cases where the number of available stem cells is limiting. This includes cord blood-derived stem cells for transplantation into adults and infusion of multiple cord blood units. While these procedures are possibly effective in increasing the overall incidence of engraftment they have not overcome the problem of the slow pace of hematopoietic recovery. Delayed myeloid engraftment after umbilical cord blood transplantation (UCBT) is often associated with increased early transplant related morbidity and mortality. This remains the primary obstacle for the successful use of cord blood as an alternative source of stem cells for allogeneic transplantation and novel strategies are required to overcome this problem.
Bone marrow stem cells have been used to treat a variety of diseases: leukaemia, inflammation, immunology, inborn anomalies of the blood and immune system, aplastic anaemia, and haemoglobinopathies. However, it is difficult and time-consuming to find a matching donor. Only one in three patients will find a suitable donor and many patients die due to being unable to find a proper donor. In addition, finding a proper match is especially problematic for African-Americans, Hispanics, Native Americans and people of mixed ethnicity. Therefore, it is demanding to develop a process for growing hematopoetic stem cells, which may eliminate the need for human donors. Creating a cell bank containing different haplotype of marrow stem cells might enable cells from one donor to generate enough supply for more than 1,000 recipients.
Stem cells may also hold the key to the fight against HIV. Possible methods of manipulating blood cells to make them resistant to HIV infection, includes genetically altering receptors on stem cells that differentiate to T cells. The modified stem cells can then be expanded and introduced to patients with HIV.
At present the standard sources of HSCs are bone marrow and peripheral blood. To obtain marrow cells, donors must undergo multiple aspirations to collect several thousand milliliters of bone marrow, a procedure that is carried out under general anaesthesia. To collect HSCs from the peripheral blood, the donor must be treated with granulocyte colony-stimulating factor to increase the number of circulating HSCs. Both of these procedures entail some risk and significant cost.
An important newer source of HSCs is umbilical cord blood (UCB). Umbilical Cord blood has major advantages over other sources of HSCs, such as from bone marrow and mobilized peripheral blood. Not only is UCB readily available from many of the nearly 50 UCB banks across the U.S., it also shows increased tolerance for mismatches with the host major histocompatability complex (MHC).
In addition to relatively widespread availability, these HSCs have several useful properties, including their decreased ability to induce immunological reactivity. In many cases, use of UCB incurs significantly less graft-versus-host disease compared to other sources of HSCs.
Yet, while there are clear advantages associated with the use of UCB, there are key issues that constitute a critical barrier to expanded use of this source of hematopoietic stem cells. An obstacle to the successful use of umbilical cord blood as a source of stem cells for allogenic transplantation is delayed myeloid engraftment. This results in increased early transplant related morbidity and mortality following umbilical cord blood transfusion. Despite intensive and expensive supportive care, there is still >50% treatment-related mortality during the first 100 days post-transplant due to delayed immune system and platelet recovery which leaves patients vulnerable to opportunistic infections. Infusions of multiple cord blood units have been used as a possible approach to increase overall engraftment, but to date have not solved the problem of slow hematopoetic recovery.
Another barrier to expanded use of UBC is limited HSC numbers per cord at harvest. As cell dose has been shown to be a major determinant of engraftment and survival after UCB transplantation, low stem cell numbers represents the most significant barrier to successful UCB stem cell transplantation.
The ability to expand ex vivo, prior to transplantation, the stem cell components of a single cord blood unit will greatly increase the viability of this treatment modality. Infusing patients with larger numbers of stem cells as opposed the limited cells available in an unexpanded cord blood unit, should greatly increase the likelihood of successful engraftment.
The expansion of non-hematopoietic adult stem cells, including stem cells isolated from organs such as brain, heart, liver, pancreas, kidney, lung, etc., has important clinical applications, particularly as an external source of cells for replenishing missing or damaged cells of tissues or organs.
Moreover, stem cell gene therapy for hematologic genetic disorders is constrained by the inefficiency of gene transfer into early hematopoietic progenitors and stem cells. The barrier that needs to be overcome is to expand the population of genetically modified cells so that sufficient modified cells can be obtained before applied to humans. For instance, children with severe sickle cell disease can be cured with bone marrow transplants. In the case of sick cell disease, one does not need to completely destroy the recipient bone marrow but merely to replace it with enough healthy or genetically corrected stem cells so as to produce sufficient quantities of healthy red blood cells.
Expansion of hematopoietic stem cells (HSCs) has remained an important goal to develop advanced cell therapies for bone marrow transplantation and many blood disorders. During the last two decades, since the first hematopoietic growth factors were identified, there have been numerous attempts to expand HSCs in vitro using purified growth factors that are known to regulate HSCs. However, these attempts have met with limited success. For example, the hematopoietic growth factors fetal liver tyrosine kinase (Flt3) ligand, stem cell factor, and interleukins 6 and 11 promoted self-renewal of murine hematopoietic stem cells. However, only a limited expansion of hematopoietic stem cells compared with fresh input cells was observed (1-3).
Although a number of pluripotent embryonic stem (ES) cell genes are identified, none have emerged as a robust factor for HSC expansion. They exhibit either a limited or no role in expansion of HSCs as reported in the literature. The best studies of pluripotent genes reported to date are OCT4 and Nanog and both are unable to induce expansion of HSCs. This conclusion is also supported by our studies that there is no significant effect on HSC expansion in the tissue culture with forced expression of these genes using a viral vector.
Activation of Notch-1 in cell intrinsic pathways has been studied as a possible means to increase expansion of HSCs, and the studies have shown that the activation of these pathways is able to maintain HSCs with lympho-myeloid repopulation potential. Overexpression of HOXB4 is the most effective method for stem cell expansion reported to date. Recently, Antonchuk et al. showed that retroviral overexpression of HOXB4 for 10 to 14 days in vitro could increase the number of repopulating HSCs by 40-fold compared with fresh bone marrow stem cells (4).
However, even 40-fold increase in repopulating HSCs is not sufficient for a variety of purposes.
SUMMARY OF THE INVENTION
The present invention discloses a method for expanding a stem cell population using Sal-like (SALL) polypeptide.
The Sal-like (SALL) family (also called Hsal), comprised of SALL1 transcript variant 1 (SEQ ID No:1 [NCBI Reference Sequence: NM002968.2]), SALL1 transcript variant 2 (SEQ ID No:2 [NCBI Reference Sequence: NM001127892.1]), SALL2 (SEQ ID No:3 [NCBI Reference Sequence: NM_005407.1]), SALL3 (SEQ ID No:4 [NCBI Reference Sequence: NM_171999.2]), SALL4a (SEQ ID No:5 [GenBank: AY172738.1]), and SALL 4b (SEQ ID No:6 [GenBank: AY170621.1]), was originally cloned based on a DNA sequence homology to the Drosophila gene sal. In a related aspect, nucleic acid sequences comprising the sequences set forth as SEQ ID Nos: 1, 2, 3, 4, 5, and 6 encode amino acids in the sequences set forth as SEQ ID Nos: 7, 8, 9, 10, 11, and 12, respectively.
In humans, members of the SALL family, including SALL4, play an important role in normal development. Parallel to its important role in development, the SALL gene family has been found to be expressed in human and murine ES cells and during early development. SALL4 is expressed in the 2-cell stage of the embryo, similar to OCT4, while expression of SOX2 and NANOG begins in the blastocystic stage of embryonic development (1-3). Our group and others have shown that the embryonic stem cell (ESC) factor, SALL4, plays a vital role in maintaining ES cell pluripotency and in governing decisions affecting the fate of ES cells through transcriptional modulation of Oct4 and Nanog (4, 6, 8-10). We and others have also shown that SALL4 can activate OCT4 and interact with Nanog (9-11), and the SALL4/OCT4/Nanog transcriptional core network is essential for the maintenance of “stemness” of ES cells. By 10.5 days postcoitum, SALL4 is detectable mainly in the stem/progenitor populations in various organ systems including the brain and bone marrow of the embryo and later in the adult. This may suggest that SALL4 is not only involved in ESCs but also in adult stem cells (12-14).
This invention provides a method for expanding a stem cell population ex vivo, the method comprising providing to the stem cell population a polypeptide having the expansion enhancement activity of a Sal-like (SALL) polypeptide in an amount effective to expand the stem cell population ex vivo.
This invention further provides a composition for enhancing the expansion of a stem cell population in a subject, the composition comprising SALL polypeptide in an effective amount for the expansion of the stem cell population, and a culture media.
This invention further provides a method for identifying an agent for the expansion of a stem cell population, the method comprising (a) obtaining a candidate agent; (b) exposing a stem cell from the population to the candidate agent and (c) determining whether a SALL polypeptide is up-regulated in the stem cell, wherein if SALL polypeptide is up-regulated, then the agent is determined to be an agent for the expansion of the stem cell population.
This invention further provides a method for treatment or prophylaxis of diseases, disorders, or abnormalities in a subject requiring a stem cell or an expanded stem cell derived therefrom, the method comprising a) obtaining a stem cell population, b) providing to the stem cell population a SALL polypeptide in an amount effective to expand the stem cell population, and c) transplanting the expanded stem cell population to the subject in an amount effective for the treatment or prophylaxis of the diseases, disorders, or abnormalities of the subject.
This invention further provides a stem cell bank, comprising genetically distinct stem cell populations, wherein the stem cell populations have been expanded according to methods of the claims.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Schematic diagram of the SALL4A and SALL4β isoforms demonstrating the variable number of zinc finger domains possessed by each. The HSCs were transduced with either the SALL4A or SALL4B gene using a lentiviral transfection system.
FIG. 2. Bright field and fluorescent images of human bone marrow CD34+ cells. Bright field (left) and fluorescent (right) images illustrating the infection efficiency of lentiviral constructs containing GFP+SALL4A, GFP+SALL4B, and GFP only. Images were taken 48 hours post infection with lentiviruses.
FIG. 3. (A) HSCs transduced with SALL4A and SALL4B are able to survive and expand rapidly 7 days after lentiviral infection. (B) CD34+ cells isolated from peripheral blood stem cells of 3 different patients. CD34+ cells were isolated from the stem cell pool using magnetic anti-CD34+ human microbeads. The CD34+ enriched cells were transduced with SALL4A and imaged under bright field and fluorescent microscopy. All three samples from the various patients were successfully transduced with SALL4A and expanded rapidly in culture. In addition, SALL4-induced HSCs are able to expand when growth factor concentrations are decreased.
FIG. 4. Bright field and fluorescent images of human bone marrow CD34+ cells transduced with GFP (i and ii) or representative SALL4 isoform, B (v and vi) 9 days post infection. Initially, 50,000 CD34+/CD38− cells were plated. High magnification of SALL4B-transduced HSC clusters (vii, and viii). The GFP cell clusters signified positive overexpression of SALL4B. With SALL4B overexpression, HSC cell clusters are able to survive and are rapidly expanding at 9 days post infection.
FIG. 5. Cell expansion of SALL4-induced HSCs versus control cells. At two days following lentiviral infection, similar amounts of HSC clones are visible in both the GFP-transduced and SALL4-transduced cell cultures. At 11 days post infection, the SALL4-transduced HSCs are proliferating and expanding. Notice the formation of proliferating cell clusters in the HSCs overexpressing SALL-4 compared to the low number of cells in the GFP-induced control HSCs.
FIG. 6. 16 days post lentiviral infection, SALL4-induced HSCs continue to expand while control cells undergo cell death or differentiation. 16 days after infection, control GFP-transduced cells have depleted from the cell culture due to differentiation and death. In contrast, in HSCs overexpressing SALL4A or SALL4B, cells continue to expand and survive. Multiple healthy expanding clusters are visible throughout the cell culture.
FIG. 7. (A) Growth curves of CD34+ cells transduced with SALL4A, SALL4B, or GFP and cultured in media containing 75% less cytokines. After transduction, 50,000 cells of each group were cultured in stringent conditions in which normal cytokine concentrations were decreased by 75%. HSCs transduced with SALL4A or SALL4B continued to survive and expand over 7 days while control cells growth halted at day 5. (B) Fold expansion of CD34+/CD38− cells 14-days post infection of Lenti-SALL4A or −SALL4B versus control. Cells transduced with SALL4A demonstrated a 368 fold increase of CD34+/CD38− cells over control while those transduced with SALL4B showed a 384 fold increase. (C) Phenotypic analysis of SALL4-induced hematopoietic stem cells 31 days post lentiviral infection. Human-specific antibodies CD34-PE and CD38-APC were utilized to compare SALL4-transduced HSCs versus 3-day control cells. 31 days after lentiviral infection, the aged SALL4-induced cells continued to demonstrate similar phenotypic ratios compared to control cells for CD34+/C38−. FLOW analysis was carried out on three separate samples. Therefore, many of these aged cells still attained progenitor characteristics and had the ability to differentiate into various cells lines. (D) 31-day old SALL4-induced HSCs attain blast-like morphology. Aged 31-day old SALL4-induced HSCs were Wright-Giemsa stained. Many cells showed blast-like morphology including large nuclei and scant cytoplasm. These cells represented a population of undifferentiated cells still visible 31 days after SALL4-lentiviral infection and expansion.
FIG. 8. Representative phenotypic analysis of SALL4-induced hematopoietic stem cells 14 days post lentiviral infection (n=4). Human-specific antibodies CD34-PE and CD38-APC were utilized to compare SALL4-transduced HSCs versus 3-day control cells.
FIG. 9. A single SALL4-induced GFP-positive cluster can be dissociated and expanded to form new HSC clusters. A single 7-day old cluster overexpressing SALL4 was picked from an initial cell culture, gently dissociated, and replated into a single well of a 48-well plate. 4 days later, the HSCs were able to expand and form new proliferating healthy cell clusters leading to a net increase in the number of clones.
FIG. 10. 18-day old SALL4-induced HSCs attain blast-like morphology. Aged 18-day old SALL4-induced HSCs were placed in a cytospin and giemsa stained. Many cells showed blast-like morphology including large nuclei and scant cytoplasm. These cells represented a population of undifferentiated cells still visible 18 days after SALL4-lentiviral infection and expansion.
FIG. 11. CFU progenitors are GFP-positive. HSC cells selected for CFU assays were GFP-positive which verified that the cells were successfully transduced and overexpressing SALL4.
FIG. 12. Various CFU colonies are able to differentiate from SALL4-induced HSCs. Aged SALL4-induced HSCs were plated in Methocult and observed for CFU colonies. Numerous lineages were observed in CFU assays utilizing the SALL4-induced HSCs including BFU-E, CFU-GM, and CFU-GEMM colonies. These data demonstrated that the aged HSCs transduced with SALL4 were capable of differentiating into different blood cell lineages.
FIG. 13. SALL4-induced HSCs are able to expand when growth factor concentrations are decreased by 50%. When SALL4-transduced HSCs were cultured in growth media containing 50% less cytokines, they were still able to survive and expand 6 days post lentiviral infection. Furthermore, when growth factor concentrations were decreased to 25% of original values, the SALL4-transduced HSCs continued to proliferate. In contrast, control cells had undergone cell death by day 6.
FIG. 14. SALL4-induced HSCs successfully proliferate when growth factors are decreased by 25%. SALL4-induced HSCs are able to expand when growth factor concentrations are decreased by 50%. When Sall4-transduced HSCs were cultured in growth media containing 50% less cytokines, they were still able to survive and expand 6 days post lentiviral infection. Furthermore, when growth factor concentrations were decreased to 25% of original values, the SALL4-transduced HSCs continued to proliferate. In contrast, control cells had undergone cell death by day 6.
FIG. 15. Model of SALL4-mediated ex vivo HSC expansion. The primary culture was divided and transduced with a SALL4 or GFP control. The viable HSCs without SALL4 overexpression decreased in number due to differentiation or death leading to a net HSC decline. In contrast, HSCs in which SALL4 was overexpressed, many clones were able to survive and expand in the culture. A net HSC expansion was exhibited with numerous expanding clusters throughout the culture.
FIG. 16. Phenotypic analysis of SALL4-induced hematopoietic stem cells 14 and 23 days post lentiviral infection. Human-specific antibodies CD34-PE and CD38-APC were utilized to compare SALL4-transduced HSCs versus control cells. 14 (top) and 23 (bottom) days after lentiviral infection, the aged SALL4-induced cells continued to demonstrate similar phenotypic ratios compared to control cells for CD34+/C38−. Therefore, many of these aged cells still attained progenitor characteristics and had the ability to differentiate into various cells lines.
FIG. 17. SALL4 binds to important HSC signaling genes.
FIG. 18. CD34+ cells isolated from peripheral blood stem cells of 3 different patients. CD34+ cells were isolated from the stem cell pool using magnetic anti-CD34+ human microbeads. The CD34+ enriched cells were transduced with SALL4A and imaged under brightfield and fluorescent microscopy. All three samples from the various patients were successfully transduced with SALL4A and expanded rapidly in culture.
FIG. 19. Growth curves of SALL4 induced 32D cells cultured only with G-CSF. 32D cells were transduced with SALL4A, SALL4B, or GFP lentivirus then cultured for three days in growth media containing IL-3. On the 4th day, 15000 cells were aliquoted from each group and placed in new growth media with G-CSF and without IL-3. Cell growth was monitored daily and the viable number of cells in each group was recorded. In cells that were transduced with SALL4A, an 8-fold increase in the number of cells was observed from day 1 to 7. Cells that were transduced with SALL4B exhibited a 7-fold expansion of cells. In contrast, cells that were only transduced with GFP and WT (no lentiviral infection) demonstrated a decrease in the number of cells over the same period with almost all the cells undergoing cell death by day 5.
FIG. 20. Wright-Giemsa staining of 32D cells. Morphology of 32D cells with IL3 alone (A), transduced with SALL4A with G-CSF (B) and with G-CSF alone (C). Cells given IL3 or transduced with SALL4A continue to demonstrate blast-like morphology (A or B), while the cells not transduced with SALL4A and given G-CSF exhibit neutrophil morphology (C).
FIG. 21. The HA-SALL4A and His-SALL4B or HA-SALL4B and His-SALL4A transfected lysate of 293 cells were mixed with equal amounts and blotted with Anti-HA and Anti-His showing the present of these proteins in the lysates. Each lysate mixture was used to pull-down with Anti-HA antibody and resulting precipitated protein mixtures were subjected to Western blotting using antibodies against His tag.
FIG. 22. (A) Various CFU colonies are able to differentiate from SALL4-induced HSCs. Aged SALL4-induced HSCs were plated in Methocult and observed for CFU colonies. Numerous lineages were observed in CFU assays utilizing the SALL4-induced HSCs including CFU-GEMM, BFU-E, and CFU-GM colonies. These data demonstrated that the aged HSCs transduced with SALL4 were capable of differentiating into different blood cell lineages. (B) Number of CFU colonies formed from SALL-4 induced hematopoietic stem cells. The number of CFU colonies was counted 13-18 days after SALL-4 induced or GFP-induced cells were cultured in CFU Methocult media. The representative data from day 18 are shown. (C) Types of CFU colonies formed at day 18.
FIG. 23. (A) After one month of cell culture, CD34+ cells transduced with SALL4A or SALL4B had 1780 and 1463 fold increases respectively relative to control cells. Values are means±s.d. (B) Furthermore, SALL4 transduced cells showed 9.32 fold increases for SALL4A and 8.88 fold increases for SALL4B versus controls for the total number of LTC-ICs after one month. Values are means±s.d. (C) Overall, SALL4A transduced cells had a total fold CD34+/CD38− stem cell expansion 16776 over control while SALL4B transduced cells showed 13320 fold increases. Values are means±s.d. (D) Representative flow cytometry analysis 4 weeks post-injection for CD45+ human leukocytes from peripheral blood of NOD/SCID recipients transplanted with SALL4A- or SALL4B-transduced HSCs. (E) Representative flow cytometry profile 4 weeks post-injection of a mouse exhibiting multilineage repopulation of human cells by engrafted cells. While the negative control animal showed no engraftment of human cells, the experimental animal showed both CD15+ myeloid and CD19+ lymphoid human cell engraftment. (F) and Flow analysis of secondary and tertiary bone marrow transplant NOD/SCID mice. The animals were positive for CD45+ cells in both secondary (2.74%) and tertiary (3.29%) transplants. When the CD45+ population in the tertiary transplant was analyzed further for specific lineages, CD33 myeloid and CD19/CD3 lymphoid cells were positively measured (G). (H) Amount of human chimerism in the peripheral blood of NOD-SCID mice transplanted with 20,000 (SALL4A (▪), SALL4B (▴), or GFP (♦)) or 40,000 (SALL4A (□), SALL4B (Δ), or GFP (⋄)) initial human CD34+ cells. (I) Limiting-dilution analysis of CD34+ bone marrow cells injected into NOD-SCID mice (n=72) after lentiviral transfection with SALL4A (□), SALL4B (▴), or GFP (∘).
FIG. 24. SALL4-induced expansion of 32D cells proliferate after the removal of IL-3 and addition of G-CSF. Three days after the removal of IL-3 and addition of G-CSF to the growth media of the cells, the SALL4A- and SALL4B-induced cells continue to expand while the GFP induced cells exhibit a decrease in cell number. At 7 days, the SALL4A- (i) and SALL4B-induced (ii) cells continue to proliferate while the control cells (iii) have undergone cell death.
FIG. 25. (A) Schematic representation of human His-TAT-SALL4B construct. This construct was generated by cloning the human SALL4B cDNA into a pTAT-pET28b vector (gift from S. F. Dowdy, University of California, San Diego). (B) Affinity purification of His-TAT-SALL4B as detected by Coomassie blue-stained SDS-PAGE. CL, clear lysates with 0.1 mM IPTG induction for 3 h; FT, flow through; W, wash; E, eluates. The band indicated by the arrow was further identified by LC-MS/MS as shown in part (D). (C) Western blot of purified His-TAT-SALL4B by using anti-6×His tag mouse monoclonal antibodies. W, wash; E, eluates. (D) Identification of purified His-TAT-SALL4B protein by LC-MS/MS. A representation of sequence coverage with purified SALL4B in part (B). The peptides of His-TAT-SALL4B identified by LC-MS/MS are in black color. The percentage of sequence coverage in the specified band was 34% (58 peptides).
FIG. 26. Human bone marrow CD34+ cells expand at a higher rate when treated with TAT-SALL4B protein. (A) Brightfield images of CD34+ cells after 3 days of protein treatment. (B) Fold increase and total cell number (C) of TAT-SALL4B treated bone marrow cells versus control cells treated solely with BSA. (D) Number of CFU colonies formed from hematopoietic stem cells treated with TAT-SALL4B protein compared to unmanipulated CD34+ cells.
FIG. 27. Number of CFU colonies formed from SALL-4 induced hematopoeitic stem cells. The number and type of CFU colonies were counted 13-18 days after SALL-4 induced or GFP-induced cells were cultured in CFU methocult media.
FIG. 28. Multilineage repopulation of engrafted human cells in NOD/SCID mice. Representative flow cytometry profile of mouse bone marrow exhibiting multilineage repopulation of human cells by engrafted cells. The experimental animals showed CD3+/CD19+ lymphoid, CD15+ myeloid, and Glycophorin-4A+ erythroid human cell engraftment 15 weeks post-injection.
FIG. 29. Western blot of the purification of His-TAT SALL4β isolated from Sf9 cells infected with the baculovirus. Antibodies used were anti-SALL4, (Abnova, Taipei City, Taiwan) 1:2000; and anti-mouse HRP [goat], Abnova, 1:2000.
FIG. 30. Sf9 cells infected with baculovirus; 4th day.
FIG. 31. TAT-SALL4B increase the proliferation of mouse whole bone marrow cells.
FIG. 32. Bone marrow recovery in SALL4 treated animals with expansion of marrow cells (experimental design).
FIG. 33. Expansion of bone marrow cells after injection of TAT-SALL4B
FIG. 34. Comparisons of bone marrow cell expansion after peritoneal injections of PBS, G-SCF and SALL4B in mice. Histological sections of bone marrow cavity showing expansion of marrow cells.
FIG. 35. CFC numbers of bone marrow cells from PBS, SALL4B or G-CSF treated mice. C57B/6 mice were lethally irradiated (7Gy) and received treatment from 24 hours after irradiation for 7 days. At day 8, mice bone marrow cells were isolated and cultured in MethoCult for CFC assays. Per 20,000 whole bone marrow cells, the day 7 CFCs of PBS, SALL4B and G-CSF group were 6±1.41, 11.3±2.51 and 18±2.82 respectively (P values of PBS vs SALL4B, PBS vs G-CSF, SALL4B vs G-CSF are <0.05).
FIG. 36. Fold increase of HSCs (Scal1+/c-kit+) vs control (PBS) from animals treated with SALL4B, G-CSF, or PBS.
FIG. 37. Fold increase of long-term engraftment of human UCB in the peripheral blood of NOD-SCID mice. Approximately 20,000 cord blood derived-CD34+ cells were transplanted into sub-lethally irradiated NOD/SCID mice and treated with 2 μg/day SALL4B protein for 7 days and then 2 μg/day every other day for an additional week. CD45 cells (UCB cells) 16 weeks post-transplant compared to PBS treated controls will be measured by flow cytometry.
FIG. 38. SALL4B enhances long-term engraftment of human cord blood cells in NOD/SCID mouse. 20,000 human cord blood CD34+ cells were transplanted into NOD/SCID mice 24 hours after sub-lethal irradiation (2.5Gy). Mice were treated with 2 μg TAT-SALL4B protein or PBS for 2 weeks (once a day for the first week and once every other day for the second week). Mice bone marrow cells were collected 4 months post transplantation and analyzed by flow cytometry for CD45 positive cells (engrafted core blood cells).
FIG. 39. SALL4B increases CFC numbers of peripheral blood (PB). Wild type C57B/6 mice received PBS or 6 μg TAT-SALL4B protein injection (intraperitoneal injection) for 5 days and PB were collected 2 hours after last injection. The nucleated cells from peripheral blood of injected mice were used for CFC (colony forming progenitor cell) assays. CFC numbers on Day 7 were counted under microscope.



DETAILED DESCRIPTION OF THE INVENTION
Exemplary Embodiments of the Invention
This invention provides a method for expanding a stem cell population, the method comprising providing to the stem cell population a polypeptide having the expansion enhancement activity of a Sal-like (SALL) polypeptide in an amount effective to expand the stem cell population.
In one embodiment, the stem cell is an adult stem cell.
In some embodiments, the stem cell is in or derived from the brain, liver, heart, kidney, skin, pancreas, bladder, gall bladder, large intestine, small intestine, stomach, skeletal muscle, or lung.
In another embodiment, the stem cell is a hematopoietic stem cell.
In yet another embodiment, the hematopoietic stem cell is in or derived from umbilical cord blood, peripheral blood, bone marrow, or spleen. In yet another embodiment, the hematopoietic stem cell is a human stem cell.
In some embodiments, methods for expanding a stem cell population also comprise administration of a SALL polypeptide in combination with a stimulating factor. In some embodiments, the stimulating factor is G-SCF, GM-CSF, M-CSF, a stem cell factor, or FMS-like tyrosine kinase-3 (FLT-3).
In some embodiments, the stem cell population is expanded ex vivo.
In some embodiments, the stem cell population is expanded in vivo. In another embodiment, stem cell population is cultured in media comprising 50 ng/ml FMS-like tyrosine kinase-3 (FLT-3), 50 ng/ml Thrombopoietin (TPO), and/or 50 ng/ml Stem cell factor (SCF).
In another embodiment, the stem cell population is cultured in media comprising 25 ng/ml FMS-like tyrosine kinase-3 (FLT-3), 25 ng/ml Thrombopoietin (TPO), and/or 25 ng/ml Stem cell factor (SCF).
In one embodiment, the SALL polypeptide is attached to a transport moiety capable of crossing a cell membrane, thereby transporting the SALL polypeptide into the cell.
In another embodiment, the transport moiety is a HIV-1 transactivator of transcription (TAT) peptide, a Chariot protein, an arginine-rich peptide, an Antennapedia-derived penetratin peptide, a herpes simplex virus type 1 VP22 protein, or a +36 GFP.
In another embodiment, SALL for use in the present invention may be in the form of a nucleic acid or a polypeptide.
In one embodiment, the SALL polypeptide comprises amino acids in the sequence set forth in SEQ ID No: 7, 8, 9, 10, 11 or 12.
In one embodiment, SALL polypeptide is encloded by nucleotide sequence comprising SEQ ID No: 1, 2, 3, 4, 5 or 6.
In another embodiment, the stem cell population is provided with SALL polypeptide comprising amino acids in the sequence set forth in SEQ ID No: 7, 8, 9, 10, 11 and/or 12.
In one embodiment, a cell in the population is transduced with a viral vector comprising nucleotides encoding the SALL polypeptide, thereby providing the SALL polypeptide to the stem cell population.
In another embodiment, the viral vector is derived from, but are not limited to, adenoviruses, baculoviruses, parvoviruses, herpesviruses, poxviruses, adeno-associated viruses, Semliki Forest viruses, vaccinia viruses, and retroviruses.
In one embodiment, the exogenous SALL gene is transiently expressed in the stem cell.
In another embodiment, nucleotides encoding the SALL polypeptide comprise sequence as set forth in SEQ ID No: 1, 2, 3, 4, 5 or 6.
In another embodiment, the nucleotides encoding the SALL polypeptide are expressed under the control of an inducible promoter.
In another embodiment, SALL polypeptide for use in the present invention may be exogenous or endogenous. Preferably, SALL polypeptide is exogenous. In the present invention, an exogenous SALL polypeptide is provided to a cell, thereby promoting the expansion of the cell. In this case, an endogenous SALL polypeptide may be supplemented with an exogenous SALL polypeptide to enhance the effect thereof.
In one embodiment, the stem cell population is expanded 10-fold, 20-fold, 50-fold, 100-fold, or 1000-fold.
This invention further provides a composition for enhancing the expansion of a stem cell population in a subject, the composition comprising SALL polypeptide in an effective amount for the expansion of the stem cell population, and a culture media. In one embodiment, the composition further comprises stem cells.
This invention further provides a method for identifying an agent for the expansion of a stem cell population, the method comprising (a) obtaining a candidate agent; (b) exposing a stem cell from the population to the candidate agent and (c) determining whether a SALL polypeptide is up-regulated in the stem cell, wherein if SALL polypeptide is up-regulated, then the agent is determined to be an agent for the expansion of the stem cell population. In one embodiment, the candidate agent may be provided in a library. In another embodiment, the invention provides an agent for the expansion of a stem cell obtained by the above-described screening method.
This invention further provides a method for treatment or prophylaxis of diseases, disorders, or abnormalities in a subject requiring a stem cell or an expanded stem cell derived therefrom, the method comprising a) obtaining a stem cell population, b) providing to the stem cell population a SALL polypeptide in an amount effective to expand the stem cell population, and c) transplanting the expanded stem cell population to the subject in an amount effective for the treatment or prophylaxis of the diseases, disorders, or abnormalities of the subject.
In one embodiment, the present invention may target hematopoietic and circulatory (blood cells, etc.) diseases, disorders or abnormalities, including, but are not limited to, anemia (e.g., aplastic anemia (particularly, severe aplastic anemia), renal anemia, cancerous anemia, secondary anemia, refractory anemia, etc.), cancer or tumors (e.g., leukemia); and after chemotherapy therefor, hematopoietic failure, thrombocytopenia, acute myelocytic leukemia (particularly, a first remission (highrisk group), a second remission and thereafter), acute lymphocytic leukemia (particularly, a first remission, a second remission and thereafter), chronic myelocytic leukemia (particularly, chronic period, transmigration period), malignant lymphoma (particularly, a first remission (high-risk group), a second remission and thereafter), multiple myeloma (particularly, an early period after the onset), and the like. The present invention also targets heart failure, stenocardia, cardiac infarction, arrhythmia, valvular heart diseases, myocardial/pericardial diseases, congenital heart diseases (e.g., atrial septal defect, ventricular septal defect, arterial duct patency, tetralogy of Fallot), arterial diseases (e.g., arterial sclerosis, aneurysm, etc.), venous diseases (e.g., phlebeurysm, etc.), and lymph vessel diseases (e.g., lymphatic edema), sickle cell disease, and treatment of radiation induced injuries, autoimmune diseases, cerebral palsy, critical limb ischemia, degenerative joint disease, diabetes type 2, heart failure, multiple sclerosis, osteoarthritis, rheumatoid arthritis, and spinal injury.
The invention further provides a stem cell bank, comprising genetically distinct stem cell populations, wherein the stem cell populations have been expanded according to the methods of the subject invention.
This invention provides a method for expanding a stem cell population in a subject, comprising increasing the amount of SALL polypeptide in the subject.
This invention further provides a method for increasing the size of a progenitor cell population in a subject the method comprising the method comprising increasing the amount of SALL polypeptide in the subject.
In some embodiments, increasing the amount of SALL polypeptide in the subject comprises introducing into the subject the SALL polypeptide.
In some embodiments, increasing the amount of SALL polypeptide in the subject comprises introducing into the subject a nucleic acid molecule having nucleotides in a sequence encoding the SALL polypeptide.
In some embodiments, the nucleotides encoding the SALL polypeptide comprise nucleotides in the sequence as set forth as SEQ ID No: 1, 2, 3, 4, 5 or 6.
In some embodiments, the SALL polypeptide comprises a transport moiety capable of crossing a cell membrane, thereby transporting the SALL polypeptide into the cell.
In some embodiments, the protenitor cell is a hematopoeitic projenitor cell population.
Aspects of the invention also provide methods of enhancing the long-term engraftment of hematopoietic stem cells in a subject. In some embodiments, the hematopoietic stem cells are derived from a donor.
Non-limiting examples of diseases, disorders, or abnormalities in a subject requiring a stem cell or an expanded stem cell derived therefrom include but are not limited to severe aplastic anemia, leukopenia, neutropenia, acute radiation syndrome, multiple myeloma, non-Hodgkin's lymphoma, and Hodgkin's lymphoma. Methods of the present invention may be used in combination with various cancer treatment which are known to produce side effects such as a decrease in the number of white blood cells such as chemotherapy, radiation therapy, and bone marrow transplantation.
Each embodiment disclosed herein is contemplated as being applicable to each of the other disclosed embodiments. Thus, all combinations of the various elements described herein are within the scope of the invention.
It is understood that where a parameter range is provided, all integers within that range, and tenths thereof, are also provided by the invention. For example, “0.2-5 mg/kg/day” includes 0.2 mg/kg/day, 0.3 mg/kg/day, 0.4 mg/kg/day, 0.5 mg/kg/day, 0.6 mg/kg/day etc. up to 5.0 mg/kg/day.
Definitions
Stem cell as used herein refers to a cell having the ability to both self-renew indefinitely and differentiate to produce at least one functional, terminal cell type.
Progenitor cell as used herein refers to a cell having a limited ability to self-renew and which differentiates to produce at least one functional, terminal cell type.
Hematopoietic cells as used herein refer to cells normally found in the blood as well as cells that give rise to cells normally found in the blood, such as cells found in the bone marrow. In this context “normally” includes the situation where a person is treated to alter the number or quality oc cells in the blood of bone marrow.
Hematopoietic stem cells as used herein refers to multipotent stem cells that give rise to all blood cell types.
“Expanding” as used herein refers to increasing the number of stem cells by proliferation of the stem cells, as opposed to converting cells which are not stem cells into stem cells.
Sal-like (SALL) gene or polypeptide is used herein to comprise SALL1, SALL2, SALL3, and SALL4, which were originally cloned based on a DNA sequence homology to the Drosophila gene sal. SALL4 comprises SALL4a and SALL4b.
Viral vector is used herein to mean a vector that comprises all or parts of a viral genome which is capable of being introduced into cells and expressed. Such viral vectors may include native, mutant or recombinant viruses. Such viruses may have an RNA or DNA genome. Examples of suitable viral vectors include, but are not limited to, adenoviruses, baculoviruses, parvoviruses, herpesviruses, poxviruses, adeno-associated viruses, Semliki Forest viruses, vaccinia viruses, and retroviruses and hybrid vectors.
A “transport moiety” is used herein to mean a polypeptide that is capable of crossing a cell membrane and can transport a polypeptide of the present invention into a stem cell. Examples of transport moities include but are not limited to, HIV-1 transactivator of transcription (Tat) peptide, a ChariotTM protein, an arginine-rich peptide, an Antennapedia-derived penetratin peptide, a herpes simplex virus type 1 VP22 protein, and a +36 GFP. In embodiments in which a SALL polypeptide is attached to a transport moiety, “attached” can be covalently attached.
The term “amount effective” means the amount of the subject polypeptide or stem cell that will elicit the biological or medical response of a cell, tissue, system, animal or human that is being sought by the researcher, veterinarian, medical doctor or other clinician.
A “construct” is used to mean recombinant nucleic acid which may be a recombinant DNA or RNA molecule, that has been generated for the purpose of the expression of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleic acids. In general, “construct” is used herein to refer to an isolated, recombinant DNA or RNA molecule.
The term “capable of engraftment” is used in here to refer to the ability of a hematopoietic cell to implant into the bone marrow for an extended period of time, e.g. at least one year. Implantation may be detected directly, (e.g. by biopsy) or by the production of progeny cells in the blood.
Transduction is used to refer to the introduction of genetic material into a cell by using a viral vector. As used herein a transduced cell results from a transduction process and contains genetic material it did not contain before the transduction process, whether stably integrated or not.
The phrase “culture media” is used to mean any of the standard culture media for culturing stem cells.
“Nucleic acid sequence” as used herein refers to an oligonucleotide, or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin which may be single- or double-stranded, and represent the sense or antisense strand. Similarly, “amino acid sequence” as used herein refers to an oligopeptide, peptide, polypeptide, or protein sequence, and fragments or portions thereof, and to naturally occurring or synthetic molecules.
Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
Stem Cells
Stem cells of the present invention (e.g., adult stem cells, and hematopoietic stem cells) include all those known in the art that have been identified in mammalian organs or tissues. Stem cells may include, but are not limited to pluripotent stem cells, mesenchymal stem cells, hematopoietic stem cells, myeloid stem cells, and lymphoid stem cells. The best characterized is the hematopoietic stem cell. The hematopoietic stem cell, isolated from bone marrow, blood, cord blood, fetal liver and yolk sac, is the progenitor cell that generates blood cells or following transplantation reinitiates multiple hematopoietic lineages and can reinitiate hematopoiesis for the life of a recipient. (See Fei, R., et al., U.S. Pat. No. 5,635,387; McGlave, et al., U.S. Pat. No. 5,460,964; Simmons, P., et al, U.S. Pat. No. 5,677,136; Tsukamoto, et al., U.S. Pat. No. 5,750,397; Schwartz, et al., U.S. Pat. No. 5,759,793; DiGuisto, et al., U.S. Pat. No. 5,681,599; Tsukamoto, et al, U.S. Pat. No. 5,716,827; Hill, B., et al. 1996.) When transplanted into lethally irradiated animals or humans, hematopoietic stem cells can repopulate the erythroid, neutrophil-macrophage, megakaryocyte and lymphoid hematopoietic cell pool.
It is well known in the art that hematopoietic cells include multipotent stem cells (e.g., a lymphoid stem cell), and/or progenitor cells committed to specific hematopoietic lineages. The progenitor cells committed to specific hematopoietic lineages may be of T cell lineage, B cell lineage, dendritic cell lineage, Langerhans cell lineage and/or lymphoid tissue-specific macrophage cell lineage. Hematopoietic stem cell and progenitor cell lineages are discussed in Sieburg et al. 2006, Schroeder et al. 2010, Dykstra et al. 2007, and U.S. Pat. No. 7,994,114, the contents of which are incorporated herein by reference.
Hematopoietic stem cells can be obtained from blood products. A “blood product” as used in the present invention defines a product obtained from the body or an organ of the body containing cells of hematopoietic origin. Such sources include unfractionated bone marrow, umbilical cord, peripheral blood, liver, thymus, lymph and spleen. It will be apparent to those of ordinary skill in the art that all of the aforementioned crude or unfractionated blood products can be enriched for cells having “hematopoietic stem cell” characteristics in a number of ways. For example, the blood product can be depleted from the more differentiated progeny. The more mature, differentiated cells can be selected against, via cell surface molecules they express. Additionally, the blood product can be fractionated selecting for CD34+ cells. CD34+ cells are thought in the art to include a subpopulation of cells capable of self-renewal and pluripotentiality. Such selection can be accomplished using, for example, commercially available magnetic anti-CD34 beads (Dynal, Lake Success, N.Y.). Unfractionated blood products can be obtained directly from a donor or retrieved from cryopreservative storage.
Hematopoietic stem cells may be harvested or collected prior to expansion of the stem cell population ex vivo. “Harvesting” hematopoietic progenitor cells is defined as the dislodging or separation of cells from the matrix. This can be accomplished using a number of methods, such as enzymatic, non-enzymatic, centrifugal, electrical, or size-based methods, or preferably, by flushing the cells using media (e.g. media in which the cells are incubated). The cells can be further collected, separated, and further expanded using the subject invention and generating larger populations.
Methods for isolation of hematopoietic stem cells are well-known in the art, and typically involve subsequent purification techniques based on cell surface markers and functional characteristics. The hematopoietic stem and progenitor cells can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac, and give rise to multiple hematopoietic lineages and can reinitiate hematopoiesis for the life of a recipient. (See Fei, R., et al., U.S. Pat. No. 5,635,387; McGlave, et al., U.S. Pat. No. 5,460,964; Simmons, et al., U.S. Pat. No. 5,677,136; Tsukamoto, et al., U.S. Pat. No. 5,750,397; Schwartz, et al., U.S. Pat. No. 5,759,793; DiGuisto, et al., U.S. Pat. No. 5,681,599; Tsukamoto, et al., U.S. Pat. No. 5,716,827; Hill, B., et al. 1996.) For example, for isolating hematopoietic stem and progenitor cells from peripheral blood, blood in PBS is loaded into a tube of Ficoll (Ficoll-Paque, Amersham) and centrifuged at 1500 rpm for 25-30 minutes. After centrifuigation the white center ring is collected as containing hematopoietic stem cells.
Stem cells may be isolated from other tissues such as the brain, liver, heart, kidney, skin, and lung.
Stem Cell Transplantation
Stem cell transplantation can be used as part of the treatment for blood disorders such as leukemia, certain types of lymphoma (including Hodgkin lymphoma), aplastic anemia, thalassemia, sickle cell anemia, and some congenital metabolic or immunodeficiency disorders (such as chronic granulomatous disease). Certain types of stem cells may also be used as transplants for those whose bone marrow was destroyed by the high doses of chemotherapy or radiation therapy used to treat some cancers.
Stem cells may be the subject's own cells (autologous transplantation) or those of a donor (allogeneic transplantation). When the subject's own stem cells are used, they may be collected before chemotherapy or radiation therapy, “in vivo collection”, because these treatments may damage stem cells. They may be injected back into the body after the treatment, such as increasing or expanding “in vivo expansion” the quality of the cells being expanded.
Current methods for stem cell storage involve collection of stem cells from embryonic cord blood and the collection of stem cells from blood donations. The utility of these techniques are limited because of the small proportion of total number of stem cells in the peripheral blood and because only a limited amount of blood may be collected from a blood transfusion. An advantage of using stem cells from an adult is that the subject's own cells can be expanded in culture using the methods described in the present invention and then reintroduced into the subject. Thus, there is also an unmet need in collecting human stem cell population for long term cryogenic storage, for example in a stem cell bank, and for the eventual thawing of the cryopreserved cell population for the treatment of a disease by autologous transfer. Preservation of stem cells for cyrostorage is well known in the art. For example, see Culture of human stem cells (Wiley-Liss, 2007), and Cryopreservation and freeze-drying protocols (Humana Press, 2007). These documents are hereby incorporated by reference.
The expanded stem cell population of the present invention may be used to treat hematopoietic and circulatory (blood cells, etc.) diseases, disorders or abnormalities. Examples of the diseases, disorders or abnormalities include, but are not limited to, anemia (e.g., aplastic anemia (particularly, severe aplastic anemia), renal anemia, cancerous anemia, secondary anemia, refractory anemia, etc.), cancer or tumors (e.g., leukemia); and after chemotherapy therefor, hematopoietic failure, thrombocytopenia, acute myelocytic leukemia (particularly, a first remission (highrisk group), a second remission and thereafter), acute lymphocytic leukemia (particularly, a first remission, a second remission and thereafter), chronic myelocytic leukemia (particularly, chronic period, transmigration period), malignant lymphoma (particularly, a first remission (high-risk group), a second remission and thereafter), multiple myeloma (particularly, an early period after the onset), and the like. The present invention also targets heart failure, stenocardia, cardiac infarction, arrhythmia, valvular heart diseases, myocardial/pericardial diseases, congenital heart diseases (e.g., atrial septal defect, ventricular septal defect, arterial duct patency, tetralogy of Fallot), arterial diseases (e.g., arterial sclerosis, aneurysm, etc.), venous diseases (e.g., phlebeurysm, etc.), and lymph vessel diseases (e.g., lymphatic edema), sickle cell disease, and treatment of radiation induced injuries, autoimmune diseases, cerebral palsy, critical limb ischemia, degenerative joint disease, diabetes type 2, heart failure, multiple sclerosis, osteoarthritis, rheumatoid arthritis, and spinal injury.
Methods for stem cell transplantation for treatment of diseases, disorders or abnormalities in humans are well know in the art. For example, see Manual of Stem Cell and Bone Marrow Transplantation (Cambridge University Press, 2009), Stem cell transplantation: biology, processing, and therapy (Wiley-VCH, 2006), and Practical Hematopoietic Stem Cell Transplantation (Wiley-Blackwell, 2007). These documents are hereby incorporated by reference.
Stem Cell Engraftment
Bone marrow regeneration after transplant is a function of proper engraftment of transplanted cells. In preferred embodiments, engraftment of transplanted cells is long term engraftment of the cells. In some embodiments, the invention encompasses improved engraftment of hematopoietic stem cells (HSCs) derived from human umbilical cord blood. Embodiments of the present invention are useful for the treatment of various diseases such as marrow failure disorders, various genetic diseases, and hematopoietic malignancies.
In cases in which hematopoietic stem cells (HSCs) from a donor are transplanted into the host, embodiments of the invention are useful to increase the donor cells' chimerism with host cells. As used herein, chimerism is the coexistence of two genetically distinct types of cells in a single organism. Once chimerism has been established, the HSCs may proliferate within the host.
As disclosed herein intraperitoneally injected TAT-SALL4 protein dramatically stimulates chimerism and stem cell long-term engraftment. The SALL polypeptides described herein may be used to significantly increase survival, expansion and engraftment or chimerism of transplanted cells in the marrow or a niche in accordance with embodiments of the invention.
Aspects of the present invention relate to gene therapy, particularly as applied to hematopoietic stem cells and hematopoietic progenitor cells, to transduced cells and methods of obtaining them, and to methods of using them to provide prolonged engraftment of modified hematopoietic cells in subjects.
Polypeptides
The present invention emcompasses a polypeptide having the expansion enhancement activity of a Sal-like polypeptide. The term “a polypeptide having the expansion enhancement activity of a Sal-like polypeptide” refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the invention as measured in a particular biological assay.
It will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of SALL may exist within a population (e.g., the human population). Such genetic polymorphism in the SALL gene may exist among individuals within a population due to natural allelic variation. As used herein, the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding a SALL polypeptide, preferably a mammalian SALL polypeptide. Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of the SALL gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in SALL that are the result of natural allelic variation and that do not alter the functional activity of SALL are intended to be within the scope of the invention. The present invention encompasses nucleotide variations and resulting amino acid polymorphisms in SALL polypeptide which are substantially homologous to the SALL nucleotides disclosed herein.
To determine the percent homology of two amino acid sequences, or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one protein or nucleic acid for optimal alignment with the other protein or nucleic acid). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in one sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the other sequence, then the molecules are homologous at that position. As used herein, amino acid or nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”. The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent homology equals the number of identical positions/total number of positions times 100).
The present invention discloses experimental results of overexpressing SALL4a and SALL4b polypeptides in HSCs and demonstrates that overexpression of both of these polypeptides enhances the expansion of HSCs ex vivo. SALL4a and SALL4b are isomers of the SALL gene, and are 1053 and 616 amino acids long, respectively. However, even though SALL4b lacks over 400 amino acids present in SALL4a, it is nonetheles capable of enhancing the expansion of HSCs as disclosed herein to the level of SALL4a. Therefore, not all amino acids of SALL4a are required for the expansion enhancement activity of a Sal-like polypeptide. According to ALIGN Query (GENESTREAM SEARCH network server IGH Montpellier, France), the overall sequence identity among SALL4a and SALL4b is 57.5%. However, the sequence alignment of SALL4a and SALL4b polypeptides using the ExPASy (Expert Protein Analysis System) proteomics server reveals two domains in SALL4a that may be important for biological activity of these polypeptides in HSCs. Putative domain 1 of SALL4a and SALL4b includes the first 385 N-terminal amino acids of SALL4a and SALL4b, and reveals 98.7% sequence identity among the two polypeptides. Putative domain 2 includes C-terminal 822-1053 amino acids of SALL4a and C-terminal 385-616 amino acids of SALL4b, and reveals 97% sequence identity among the two polypeptides. Based on this information, it is possible to readily prepare additional peptides that have enhancement activity of SALL4a or SALL4b.
The invention also encompasses polypeptides having a lower degree of identity to a polypeptide having the expansion enhancement activity of a Sal-like polypeptide but having sufficient similarity so as to perform one or more of the same functions performed by the SALL polypeptides. Similarity is determined by conserved amino acid substitution. Such substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics. Conservative substitutions are likely to be phenotypically silent. Typically seen as conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu, and Ile; interchange of the hydroxyl residues Ser and Thr, exchange of the acidic residues Asp and Glu, substitution between the amide residues Asn and Gln, exchange of the basic residues Lys and Arg and replacements among the aromatic residues Phe, Tyr. Guidance concerning which amino acid changes are likely to be phenotypically silent are found in Bowie et al. (1990) Science 247:1306-1310.
According to ALIGN Query, the overall sequence identity of each one of SALL1 transcript variant 1, SALL1 transcript variant 2, SALL2, and SALL3, with SALL4a is 38.1%, 37.1%, 28.1%, and 38.4%, respectively.
As used herein, a polypeptide (or a region of the polypeptide) is substantially homologous to a polypeptide having the expansion enhancement activity of a Sal-like polypeptide when the amino acid sequences are at least about 25-30%, 30-35%, 35%-40% 40-45%, 45-50%, 50-55%, 55-60%, typically at least about 70-75%, more typically at least about 80-85%, and most typically at least about 90-95% or more homologous. A substantially homologous amino acid sequence, according to the present invention, will be encoded by a nucleic acid sequence hybridizing to the nucleic acid sequence, or portion thereof, of the sequence shown in SEQ ID NO: 1, 2, 3, 4, 5, and/or 6 under stringent conditions.
The invention further encompasses nucleic acid molecules that differ from the disclosed nucleotide sequences encoding the SALL polypeptide due to degeneracy of the genetic code. These nucleic acids therefore encode the same Sal-like polypeptide as those encoded by the nucleotide sequence shown in SEQ ID NO: 1, 2, 3, 4, 5, and/6.
A nucleic acid fragment encoding “a polypeptide having the expansion enhancement activity of a Sal-like polypeptide” can be prepared by isolating a portion of SEQ ID NO: 1, 2, 3, 4, 5, and/or 6, that encodes a polypeptide having a Sal-like polypeptide biological activity, expressing the encoded portion of Sal-like polypeptide (e.g., by recombinant expression ex vivo), and assessing the activity of the encoded portion of Sal-like polypeptide.
Increasing the Amount of a SALL Polypeptide in a Subject
The amount of a SALL polypeptide may be increased in a subject by a variety of means, including agents that increase the expression of the SALL polypeptide, administration of the SALL polypeptide, and introducing into the subject nucleotides encoding the SALL peptide.
Agents that may be used increase the expression of a SALL peptide include but are not limited to peptides, peptide-mimetics, oligonucleotides, small molecule compounds, and RNA interference inducing molecules.
Administration of a SALL polypeptide to a subject may be nasal, pulmonary, parenteral, i.v., i.p., intra-articular, transdermal, intradermal, s.c., topical, intramuscular, rectal, intrathecal, intraocular, and buccal all using dosage forms well known to those of ordinary skill in the pharmaceutical arts. Preferred routes of administration for SALL polypeptides include i.v. and i.p.
A SALL polypeptide can be administered in admixture with suitable pharmaceutical diluents or carriers (collectively referred to herein as a pharmaceutically acceptable carrier) suitably selected with respect to the intended form of administration and as consistent with conventional pharmaceutical practices. The unit may be in a form suitable for topical, intravenous or direct injection or parenteral administration.
General techniques and compositions for making dosage forms useful in the present invention are described in the following references: 7 Modern Pharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1979); Pharmaceutical Dosage Forms: Tablets (Lieberman et al., 1981); Ansel, Introduction to Pharmaceutical Dosage Forms 2nd Edition (1976); Remington's Pharmaceutical Sciences, 17th ed. (Mack Publishing Company, Easton, Pa., 1985); Advances in Pharmaceutical Sciences (David Ganderton, Trevor Jones, Eds., 1992); Advances in Pharmaceutical Sciences Vol 7. (David Ganderton, Trevor Jones, James McGinity, Eds., 1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugs and the Pharmaceutical Sciences, Series 36 (James McGinity, Ed., 1989); Pharmaceutical Particulate Carriers: Therapeutic Applications: Drugs and the Pharmaceutical Sciences, Vol 61 (Alain Rolland, Ed., 1993); Drug Delivery to the Gastrointestinal Tract (Ellis Horwood Books in the Biological Sciences. Series in Pharmaceutical Technology; J. G. Hardy, S. S. Davis, Clive G. Wilson, Eds.); Modern Pharmaceutics Drugs and the Pharmaceutical Sciences, Vol. 40 (Gilbert S. Banker, Christopher T. Rhodes, Eds.). These references in their entireties are hereby incorporated by reference into this application.
The present invention also provides for increasing the amount of a SALL polypeptide in a subject by introducing into the subject nucleotides encoding the SALL polypeptide. In some embodiments, the nucleotides encoding the SALL polypeptide comprise nucleotides in the sequence as set forth as SEQ ID No: 1, 2, 3, 4, 5 or 6. The nucleotides encoding the SALL polypeptide may be operably linked to an expression regulatory sequence such as a promoter, and may be introduced into the subject through the use of a suitable vector as described hereinbelow.
Vectors
Different types of vectors can be used for transduction or transformation of stem cells. These include plasmid or viral vectors. Retroviral vectors have been used widely so far in gene therapy, particularly those based on Moloney murine leukemia virus (MoMLV). Vectors based on murine retroviruses can be used for high efficiency transduction of cells, however, they require that the cells be active in cell division. Transduction of HP cells with murine retroviral based vectors therefore requires activation of the cells.
Lentiviral vectors, a subclass of the retroviral vectors, can also be used for high-efficiency transduction (Haas et al 2000, Miyoshi et al 1999, Case et al 1999) and are able to transduce non-dividing cells, not needing the induction of HP cells into cell cycle. This would avoid the loss of pluripotency that cell-cycle induction might cause in some of the cells. Other groups of retroviruses such as spumaviruses, for example the foamy viruses (Vassilopoulos et al 2001) are also capable of efficiently transducing non-dividing cells.
Other types of viral vectors that can be used in the invention include adenoviral vectors (Fan et al 2000, Knaan-Shanzer et al 2001, Marini et al 2000), adeno-associated viral (AAV) vectors (Fisher-Adams et al 1996), SV40 based vectors (Strayer et al 2000), or forms of hybrid vectors (for example Feng et al, 1997). Adenoviral vectors can be readily produced at high titers and can transduce non-dividing cells.
AAV vectors are non-pathogenic, transduce both proliferating and non-proliferating cells including CD34+ cells, and integrate stably into the cellular genome (Grimm and Kleinschmidt 1999). Moreover, they do not induce a host immune response and can be produced in helper-free systems. AAV vectors can effectively transduce CD34+ cells in long-term cultures (Chaterjee et al 1999).
Integrating vectors, such as retrovirus or lentivirus, are often used for gene therapy, however, random integration of these vectors, together with the oncogenic nature of some of the inducing genes, pose a risk of cancer formation. For this reason, non-integrating methods, such as adenovirus, baculovirus, or transient transfection of plasmids capable of episomal expression, are preferred. Vectors which result in non-integration of the introduced gene into the cell genome are preferred. Viral vectors which allow transient expression of the introduced gene are also preferred. Vector which have a short life-cycle in the host cell are also preferred.
Naturally-occurring constitutive promoters control the expression of essential cell functions. As a result, a gene under the control of a constitutive promoter is expressed under all conditions of cell growth. Exemplary constitutive promoters include the promoters for the following genes which encode certain constitutive or “housekeeping” functions: hypoxanthine phosphoribosyl transferase (UPRT), dihydrofolate reductase (DHFR) (Scharf mann et al., 1991, Proc. Natl. Acad. Sci. USA, 88:4626-4630), adenosine deaminase, phospho glycerol kinase (PGK), pyruvate kinase, phospho glycerol mutase, the actin promoter (Lai et al., 1989, Proc. Natl. Acad. Sci. USA, 86:10006-10010), and other constitutive promoters known to those of skill in the art. In addition, many viral promoters function constitutively in stem cells. These include: the early and late promoters of SV40; the long terminal repeats (LTRS) of Moloney Leukemia Virus and other retroviruses; and the thymidine kinase promoter of Herpes Simplex Virus, among many others. Accordingly, any of the above-referenced constitutive promoters can be used to control transcription of a heterologous gene insert.
Genes that are under the control of inducible promoters are expressed only or to a greater degree, in the presence of an inducing agent, (e.g., transcription under control of the metallothionein promoter is greatly increased in presence of certain metal ions). Inducible promoters include responsive elements (REs) which stimulate transcription when their inducing factors are bound. For example, there are REs for serum factors, steroid hormones, retinoic acid and cyclic AMP. Promoters containing a particular RE can be chosen in order to obtain an inducible response and in some cases, the RE itself may be attached to a different promoter, thereby conferring inducibility to the recombinant gene. Thus, by selecting the appropriate promoter (constitutive versus inducible; strong versus weak), it is possible to control both the existence and level of expression of an agent in the genetically modified cell. Selection and optimization of these factors for expression of a gene insert is deemed to be within the scope of one of ordinary skill in the art without undue experimentation, taking into account the above-disclosed factors.
Method of producing and using viral vectors for gene therapy are well known in the art. For example, see Gene transfer: delivery and expression of DNA and RNA: a laboratory manual (CSHL Press, 2007), Viral vectors for gene therapy: methods and protocols (Humana Press, 2003), Gene Therapy Protocols: Volume 2: Design and Characterization of Gene Transfer Vectors (Humana Press, 2008), and Gene and cell therapy: therapeutic mechanisms and strategies (CRC Press, 2008). These documents are hereby incorporated by reference.
Protein Transduction
Protein transduction may be used as an alternative to viral vectors for the delivery of proteins into stem cells. Protein tranduction is the internalisation of proteins into the cell, from the external environment. This process relies on the inherent property of a small number of proteins and peptides of being able to penetrate the cell membrane. The transducing property of these molecules can be conferred upon proteins which are expressed as fusions with them. Examples of peptides that can be used for protein transduction of the polypeptides on the subject invention include the following:
Antennapedia Peptide: The antennapedia motif is derived from a family of Drosophila homeoproteins, a class of trans-activating factors involved in the developmental process. These proteins recognise and bind DNA through a 60 amino acid carboxy-terminal region arranged in three-helical sequences, called the homeodomain. The homeodomain of antennapedia (AntpHD) is capable of translocating across neuronal membranes and is conveyed to the nucleus.
Herpes Simplex Virus VP22 Protein: The herpes simplex virus type 1 (HSV-1) VP22 protein is a structural polypeptide forming the major component of the virus tegument situated between the envelope and capsid regions of the mature virion. It is a small basic protein, approximately 38 kDa in size, encoded by the UL49 gene.
HIV TAT Protein Transduction Domain: The HIV-1 trans-activator gene product, TAT, has been shown to be a regulator of transcription in latent HIV and is essential for HIV replication. It is an 86 amino acid protein made from two exons of 72 and 14 amino acids, respectively.
Chariot Protein: Chariot is a 2843 dalton peptide and forms a non-covalent complex with the protein of interest (Active Motif, inc.).
Other examples of peptides that can be used for protein transduction include arginine-rich peptides (15), and +36 GFP (16).
Method of preparing peptides for protein transduction are well known in the art. For example, see Cell-penetrating peptides: Handbook of (CRC Press, 2006), Cell-penetrating peptides: processes and applications (CRC Press, 2002), Protein transduction: delivery of recombinant Tat-PTD fusion proteins into target cells (University of Tromsø, Institute of Medical Biology, 2000), and Protein analysis and purification: benchtop techniques (Springer, 2005). These documents are hereby incorporated by reference.
This invention will be better understood by reference to the Experimental Details which follow, but those skilled in the art will readily appreciate that the specific experiments detailed are only illustrative of the invention as described more fully in the claims which follow thereafter.
Methods
Isolation and SALL4-lentiviral Infection of Human cd34+ Cells
Normal human bone marrow CDd34+ cells were purchased (AllCells, Emeryville, Calif., USA) and single cell suspensions were generated in StemSpan SFEM (Stemcell Technologies, Vancouver, BC, Canada) for 24 hours. Next, 105 cells/well were plated in a 12-well plate. The cells were cultured in StemSpan SFEM containing 10% FBS and 1% pen/strep (Gibco, Carlsbad, Calif., USA). Additionally, the media was supplemented with 100 ng/ml FLT-3, 100 ng/ml TPO and 100 ng/ml SCF (ProSpec, Rehovet, Israel). SALL4 lentivirus particles at an MOI between 10-20 were added to the bone marrow cells at 37° C. For controls, GFP-only lentivirus particles were added to the bone marrow cells at similar MOIs. The cells were infected for 2.5 hours and recovered in culture medium for 24 hours. The next day the cells were once again infected for 2.5 hours, rinsed, and plated for experimental expansion.
Expansion of SALL4-transduced Human CD34+ Cells
The SALL4-transduced CD34+ cells were expanded in 12-well plates under normal culture conditions (StemSpan SFEM containing 10% FBS and 1% pen/strep supplemented with 100 ng/ml FLT-3, 100 ng/ml TPO and 100 ng/ml SCF). In addition, cells were cultured in more stringent conditions in which recombinant cytokine concentrations were decreased to see if the SALL4-transduced cells were still capable of surviving and expanding. In one experiment, cells were cultured in media containing 50% less cytokines (50 ng/ml FLT-3, 50 ng/ml TPO and 50 ng/ml SCF). In an additional trial, cells were cultured in media containing 75% less growth factors (25 ng/ml FLT-3, 25 ng/ml TPO and 25 ng/ml SCF). Cells were monitored for two months and observed with brightfield and fluorescent microscopy.
Expansion of SALL4-transduced Isolated CD34+ Cells from Patient Samples Peripheral blood stem cells were obtained from the Blood Marrow Stem Cell Laboratory at Stony Brook, N.Y., USA. CD34+ cells were isolated from the stem cell pool using the CD34 human Microbead kit and MiniMACS separation columns (Miltenyi Biotec Inc., Auburn, Calif., USA). After the CD34+ cells were isolated, the cells were transfected with lentivirus and cultured in the same manner as mentioned earlier.

CFU Assay of Bone Marrow Cells

Tubes of MethoCult® (StemCell Technologies, Vancouver, BC, Canada) medium were thawed overnight in a 4° refrigerator. The next morning tubes were vortexed to ensure all components were thoroughly mixed. SALL4-transduced or GFP-transduced CD34+ cells were then prepared at 10× the final concentration required. Cell suspensions of 1×106 cells per mL were prepared and duplicated the concentrations with different concentrations (2-4 folds). 0.3 mL of cells were added to 3 mL of MethoCult® medium (STEMCELL Technologies Inc, Vancouver, BC, Canada) for duplicate cultures. Tubes were once again vortexed to ensure all cells and components were thoroughly mixed and allowed to stand for 5 minutes for bubbles to dissipate. A 16 gauge blunt-end needle attached to a 3 cc syringe was used to dispense the cells and MethoCult® medium into culture dishes. 1.1 mL of cells were dispensed per 35 mm dish. The methylcellulose medium and cells were distributed evenly by gently tilting and rotating each dish. The two dishes were placed into a 100 mm petri dish and a third, uncovered 35 mm dish containing 3 mL of sterile water was also added. All 3 dishes were then covered within the 100 mm petri dish. The cells were incubated for 14-16 days at 37° C. with 5% CO2 and 95% humidity. The BFU-E, CFU-GM and CFU-GEMM colonies were observed with brightfield and fluorescent microscopy. In addition, CFUs were counted under the microscope 10-18 days after the cells were plated in MethoCult® medium. A colony with more than 100 cells was counted as a positive colony.
Flow Cytometry and Phenotyping of Cells
FLOW was conducted with Phycoerythrin (PE)-conjugated antibody to CD34, allophycocyanin (APC)-conjugated antibody to CD38, and PerCP-Cy5.5-conjugated antibody to CD45 were used for cell sorting (BD Biosciences, Franklin Lakes, N.J., USA). The presence of human cells in NOD-SCID mouse bone marrow was determined using CD45-PE antibody. Myeloid cells were tracked by CD15-APC or CD33-APC antibody and lymphoid cells were tracked by CD19-PE or CD3-PE antibody.
Cell Counting and Growth Curve Experiments
SALL4A-transduced, SALL4B-transduced, and control cells were counted every 24 hours for seven days using a hemocytometer. Before counting, cells were gently aspirated with a 200 ml pipet tip in order to dissociate cell clusters into individual cells.
Long-Term Culture Assays
LTC-IC assays using human CD34+ cells were conducted under bulk or limiting dilution conditions in MethoCult® media. In order to calculate the total LTC-IC number, the frequency of LTC-ICs was determined from secondary cultures. This calculated number was then multiplied by the total number of cells present after 4-week primary long-term cultures.
NOD/SCID Mice Repopulating Cells (SRCs) Assays
4×103, 8×103, 2×104, or 4×104 2-day old GFP-only or 14-day old cultured SALL4A or SALL4B expressing human CD34+ bone marrow cells along with 2×105 CD34− accessory cells were injected into irradiated (2,5 Gy) NOD-LtSz-scid/scid (NOD-SCID) mice on day 0. Seven weeks after transplantation, peripheral blood samples were analyzed by flow cytometry for the presence of CD45+ cells. Mice were scored as positive for human engraftment when at least 0.5% CD45+ human cells were detected among mouse peripheral blood cells. Stem cell initiating cell frequency was determined by the reciprocal of the concentration of test cells that gave 37% negative mice. Animal experiments were performed according to the investigator's protocols approved by the Stony Brook University Institutional Animal Care and Use Committee (IACUC).
Serially Transplanted Studies
Mice BM cells were harvested from the tibiae and femurs of highly engrafted primary recipient mice 16 weeks post-transplantation. After removal of red blood cells by lysis buffer, half of the BM cells from each recipient mouse was transplanted into one secondary sub-lethally irradiated (2.5 Gy) NOD/SCID mouse. Five weeks after transplantation, the percentage of human CD45+ cells in peripheral blood of the secondary recipient mouse was analyzed by flow cytometry as described. Tertiary transplants were conducted in the same manner and flow cytometry was conducted on bone marrow cells to analyze CD45+, CD33+, CD19+, and CD3+ cells 10-weeks post transplantation.
Expression and Purification of His-TAT-SALL4A/B
For expression of TAT-SALL4 in E. coli, the human SALL4B gene was doubly digested with the restriction endonucleases SalI and NotI, and ligated into a pTAT-pET28b vector, a 6×His-taq protein expression vector bearing the T7 promoter, kanamycin resistance and pTAT Peptide/Protein Transducing Domain (PTD). The plasmids with the correct gene sequences were then transformed into E. coli strain BL21 (DE3). The 6×His-fused human SALL4B was expressed with 0.1 mM IPTG induction for 3 h and then purified by using a Ni-NTA affinity column (Qiagen, Valencia, Calif., USA). The purity of the purified His-TAT-SALL4B was further determined based on SDS-PAGE and LC-MS/MS.
SDS-PAGE and Western Blot
Proteins were loaded on 12.5% one-dimensional SDS-PAGE for protein separation, followed by staining with Coomassie brilliant blue R-250 and destained in 10% methanol/7% acetic acid. For Western blot analysis, the SDS-PAGE was transferred to poly-(vinylidene difluoride) (PVDF) membranes (Millipore, Billerica, Mass., USA). After transfer, the membranes were saturated with 5% w/v nonfat dry milk in TBS/0.1% Tween 20 at 4° C. overnight, followed by incubation with the primary antibodies overnight at 4° C. Primary antibodies against human SALL4 and 6×His-tag were purchased from Abcam (Cambridge, UK). After three washes with TBS/0.1% Tween 20, the membranes were incubated with a solution of peroxidase-conjugated secondary antibodies (Abcam, Cambridge, UK). After 1-h incubation at room temperature, the membranes were washed three times with TBS/0.1% Tween 20 and the membrane blots were developed by using ECL substrates (Millipore).
In-Gel Digestion and LC-MS/MS
Gel bands were cut and digested in-gel with trypsin. Peptides were resuspended in 50 μl 0.1% formic acid/2% acetonitrile. 10 μl of the peptide was injected into Orbitrap at the Stony Brook University Proteomics Center for 1D LC/MS/MS analysis.
Growth and Maintenance of Insect Cells
Sf9 insect cells were grown in Sf900-II SFM (Gibco) media supplemented with 10% FBS (Gibco) and 1% antibiotic/antimycotic (Cellgro). Media was filtered through ExpressPLUS 0.22 uM filtration unit (Millipore) before use. Cells were maintained at counts between 0.5 and 5.0×106 cells per mL, at 27° C. in either spinner flasks (Wheaton) or tissue culture shaker flasks (Fisher, Pittsburgh, Pa., USA).
Infection of Sf9 Cells with Baculovirus Containing His-TAT SALL4B Construct
Cells reaching a count of 2.5×106 cells per mL were infected with baculovirus containing the His-TAT SALL4B cDNA, which had been freshly amplified in Sf9 cells. Final volume was 100 mL in a Wheaton 250 mL spinner flask. Infected cells continued to incubate at 27° C. for 4 days before harvesting.
Lysis of Sf9 Cells, and his-TAT hSALL4B Purification
Cells were centrifuged at 500×g for 10 minutes. The supernatant was saved as virus stock. The cell pellet was resuspended in 20 mL lysis buffer containing 50 mM NaH2PO4 (pH 8.0), 0.3 M NaCl, protease inhibitor cocktail, PMSF, and 1% NP40 (IGEPAL). Following a 30 minute incubation on ice, the lysate was cleared by centrifugation at 10,000 g for 15 minutes at 4°.
Cleared lysate was added to Ni-NTA beads (Qiagen) washed 4 times with lysis buffer. 200 uL of beads were added for every 4 mL of lysate. To limit nonspecific binding, 10 mM imidazole was added. The solution was incubated on a rotator at 4o for up to 2 hours, then loaded onto a gravity flow column, and the flowthrough was collected. The beads were washed first with 10 mL lysis buffer with 20 mM imidazole, then with 10 mL lysis buffer with 80 mM imidazole. Elution was performed with lysis buffer and 250 mM imidazole, collected in 1.5 mL fractions, up to 10 mL. All lysates and fractions were analyzed by 8% PAGE-SDS and immunoblotting using a 1:2000 dilution of anti-SALL4 (Abnova). His-TAT SALL4B typically eluted in fractions 2 and 3. These were pooled and dialyzed overnight against PBS—in Slide-A-Lyzer cassettes (Pierce, Rockford, Ill., USA), and protein concentration was determined (BioRad, Hercules, Calif., USA).
Statistical Analysis
Results are reported as means±s.d. Values with p<0.05 were considered to be statistically significant.
EXPERIMENTAL DETAILS
Example 1
Ex Vivo Expansion of SALL4-overexpressing Human HSC
To gain insight into the magnitude of SALL4-induced HSC expansion, the effects of SALL4 overexpression in human bone marrow CD34 positive cells following lentiviral transduction was investigated. The SALL4A and SALL4B cDNAs were incorporated into a vector carrying the GFP reporter gene that facilitated isolation and tracking of transduced cells. SALL4A and B are two splicing isoforms generated through internal splicing (FIG. 1).
Normal human CD34+ cells were cultured for 2 days with growth media containing h-FLT-3, h-SCF, and h-TPO. After 48 hours, the cells were divided into six groups of 3×104 cells and placed into separate wells of a 12-well plate. The cells were then transduced with either a SALL4A, SALL4B, or GFP (control) human lentivirus for 2.5 hours. After two hours, the cells were allowed to recover in growth media. 24 hrs later, the cells were once again transduced with the aforementioned lentiviruses for 2.5 hours. The next day, the cells were observed for GFP positive cells. It was noted that approximately 40% of the cells were fluorescent (FIG. 2).
The cells were observed daily for the next 14 days following the second lentiviral infection. They were observed qualitatively with bright field and fluorescent microscopy. During the first 48 hours, the cells transduced with either SALL4A or SALL4B expanded 10-fold and regularly formed GFP-positive cell clusters. In contrast, those cells transduced solely with GFP expanded approximately 2-fold but did not form many clusters. Instead, single cell or few small GFP-positive clusters were seen. After 7 days, the expansion cells appeared to be observed solely in the SALL4-transduced cells (FIG. 3A). After 8 to 11 days in complete growth media, those cells transduced with SALL4A or SALL4B expanded 200-400 fold (FIGS. 4 and 5). On the other hand, cells transduced only with GFP expanded 5-fold at most (FIGS. 4 and 5). Furthermore, the SALL4 transduced cells continued to survive and expand 16-days post lentiviral infection. These cells were able to expand 800-1000 fold without significant maturation over the first 2 to 3 weeks of culture while the majority of control cells had undergone death or differentiation (FIG. 6). Therefore, the expansion of cells was observed solely in the SALL4-transduced cells. The expansion experiments were repeated three times. In all trials, the SALL4A or SALL4B transduced human CD34+ cells were able to grow in the liquid culture medium, retain their undifferentiated appearance, and continue to grow for more than 2 months. Similar experiments were carried out utilizing CD34+ cells isolated from peripheral blood stem cells from patient samples. Our initial findings demonstrate that successful survival and expansion of these cells is also possible.
Similar experiments were carried out utilizing CD34+ cells isolated from mobilized peripheral blood stem cells which were collected from patients and cryopreserved. Three samples from different patients showed promising results in CD34+ cell expansion (FIG. 3B). Cells transduced with SALL4A or SALL4B expanded approximately 130-fold while control cells expanded 12-fold at most (FIG. 7A). Furthermore, when these SALL4-transduced cells were grown for 14 days, the CD34+/CD38-population increased 369 fold for SALL4A and 384 fold for SALL4B (FIG. 7B) and maintained stem cell immunophenotypes (n=4)(FIG. 8). At 31 days of cell culture, the SALL4-transduced expanding cells still retained progenitor or stem cell immunophenotypes (n=2) (FIG. 7C) and primitive cell morphology (FIG. 7D). At the end of expansion, approximately 90% of the cells were expressing GFP. In contrast, control cells ceased to proliferate or were no longer viable after two weeks post-infection. SALL4 induced cells continued to expand with CD34+/CD38− or CD34+/CD38+ ratios similar to that of the original cells the culture began with (FIG. 7).
The expansion experiments were repeated at least 12 times using a variety of sources for the CD34+ cells (Table 1). In all trials, the SALL4A or SALL4B transduced human CD34 cells were able to expand in the liquid culture medium for more than 2 months and demonstrated similar percentages of cell populations (15% CD34+/CD38−, 17% CD34+/CD38+) to 31-day old cells, as demonstrated by flow cytometry.







TABLE 1







Sources of CD34+ Cells








Source of CD34+ cells
Source





AllCells
27 yrs; female; Filipino/



Caucasian


AllCells
27 yrs; female; Filipino/



Caucasian


AllCells
32 yrs; male; Caucasian


AllCells
32 yrs; trials; Caucasian


AllCells
32 yrs; male; Caucasian


SBUMC Bone Marrow Transplant Lab
Confidential


SBUMC Bone Marrow Transplant Lab
Confidential


SBUMC Bone Marrow Transplant Lab
Confidential


AllCells
22 yrs; male; Caucasian


AllCells
22 yrs; male; Caucasian


AllCells
22 yrs; male; Caucasian


AllCells
22 yrs; male; Caucasian









Example 2
Single SALL4-induced CD34+ Cell Clusters Readily Expand in Culture
From days 5-14 large GFP-positive cell clusters could readily be observed throughout the cell cultures transduced with SALL4A or SALL4B. In order to see if these clusters could serve as a seed for further expansion, single cell clusters were picked from the parental plate and placed into individual wells of a 48-well plate. The cluster was gently dissociated by aspiration through a 100 μl pipet tip. The next day (day 6-15) new small GFP positive cell clusters began to form again (FIG. 9). These clusters were allowed to expand for 5 days with complete growth media and began to grow at a similar rate as seen in the initial parental plates (FIG. 9). Therefore, it is possible to select SALL4-transduced cell clusters and expand them 200-400 fold over 7 days.
To further illustrate the survival and expansion capabilities of the aged SALL4-transduced HSC colonies, 18-day old cells were placed in a cytospin and Giemsa stained to observe their morphology. Interestingly, more than 90% of the cells exhibited blast-like morphology with large nuclei and scant cytoplasm (FIG. 10). These cells resembled undifferentiated cells. In addition, aged SALL4-transduced HSCs were cultured in Methocult and scored for CFUs. The SALL4-transduced GFP positive HSCs were able to differentiate into variable CFU colonies including BFU-E, CFU-GM, and CFU-GEMM (FIGS. 11 and 12). Therefore, the HSC SALL4 induced cells still had the ability to form a variety of blood lineages similar to wild type CD34 cells.
Example 3
Ex Vivo SALL4 Induced Expansion of Human Hematopoietic Stem Cells Under Stringent Conditions
In order to demonstrate that SALL4 induced HSCs were capable of expanding at a faster rate and higher volume compared to controls, cell culture experiments were conducted in which recombinant cytokine concentrations were decreased significantly. If the SALL4 transduced HSCs were able to successfully grow at these more stringent conditions, we could solidify our findings that SALL4 is pertinent for the maintenance of an undifferentiated proliferation state and blocking cell differentiation of HSCs.
Cell culture experiments were conducted in which recombinant growth factor concentrations were decreased by 50 or 25% for both SALL4 induced HSCs and control cells. Cell growth was monitored during the first week. Interestingly, cells transduced with SALL4A or SALL4B were still able to survive and expand beyond 6 days of culture (FIGS. 13 and 14). In contrast, control cells had undergone cell death by day 6 and no viable colonies could be observed. In addition, under these conditions, SALL4 transduced human CD34+ cells were able to maintain their undifferentiated appearance and continue to grow for more than 2 months in the liquid medium.
This provides the first evidence that under stringent growth conditions, in which the concentrations of necessary recombinant cytokines is reduced, SALL4 induced HSCs still have the survival and expansion capacity of those that are cultured at 100% concentrations. This proves SALL4 plays a key role for maintaining HSCs in an undifferentiated proliferation state.
This is the first data to illustrate that transduction of bone marrow CD34+ cells with SALL4 offer a means to successfully expand HSC cells. HSCs without SALL4 overexpression decreased in number due to differentiation or death leading to a net HSC decline. In contrast, HSCs in which SALL4 was overexpressed, many clones are able to survive and expand in the culture. A net HSC expansion was exhibited with numerous expanding clusters throughout the culture (FIG. 15). This data increases our knowledge on how HSC self-renew and expand. Furthermore, this knowledge could be transferred for protocols to expand clinically useful numbers of HSC for bone marrow transplantation and targeted gene therapy for hematologic disorders.
In other experiments, SALL4-transduced cells were grown in culture with various combinations of the growth factors SCF, TPO, and FLT-3L. After 14 days of culture, it was noted that the growth and survival of SALL4-transduced cells were independent of FLT-3L, partially dependent on TPO, and dependent on SCF (Table 2).







TABLE 2







Dependence of SALL4-Transduced


Cells on Certain Growth Factors











Cytokine
SALL4A
SALL4B







FLT-3
Independent
Independent



TPO
Partially Dependent
Partially Dependent



SCF
Dependent
Dependent










Example 4
Morphology and Phenotyping of Aged SALL4-Induced HSCs
In order to demonstrate that the SALL4-induced HSCs had progenitor characteristics after being aged for several weeks, cytpospins and giemsa staining of the cells was conducted at different time points. Interestingly, both 16 and 31 days after lentiviral infection the cells morphology highly resembled progenitor cells with large nuclei and scant cytoplasm (FIG. 10). In addition, FLOW analysis was conducted and showed the ratios of CD34+/CD38− cells were similar in controls versus aged SALL4-induced cells at two distinct time points (FIG. 16). This was a key finding because the cells still demonstrated an undifferentiated progenitor state at a high percentage even after being cultured for several weeks.
Previous studies have illustrated that SALL4 plays an important role in both cell survival and apoptosis. In addition, SALL4 has the ability to bind to the promoter regions of numerous genes that play a key role in HSC expansion and renewal including BMI1, WNT1, and TGFB1 (FIG. 17).
Example 5
Overexpression of SALL4 Inhibits Granulocytic Differentiation in the 32D Cell Line
To further determine how SALL4 effects stem cell growth, studies were extended to the myeloid progenitor cell line, 32D where it is normally expressed. 32D cells proliferate as undifferentiated blasts when maintained in IL-3, but differentiate into mature neutrophilic granulocytes when stimulated with G-CSF.
32D cells were cultured for 3 days with growth media containing IL-3. On the third day, the cells were divided into six groups of 5×104 cells and placed into separate wells of a 12-well plate. The cells were then transduced with either a SALL4A, SALL4B, or GFP (control) human lentivirus for 2 hours. After two hours, the cells were allowed to recover in growth media. 24 hrs later, the cells were once again transduced with the aforementioned lentiviruses. The next day, the cells were observed for GFP positive cells. It was noted that approximately 30% of the cells were fluorescent. The cells were allowed to expand for 48 hours in full growth media supplemented with IL-3. After the 48 hours, the cells were collected, washed, and re-plated to new wells containing growth media without IL-3, but supplemented with G-CSF.
The cells were observed daily for the next seven days qualitatively with bright field and fluorescent microscopy and also counted with a hemacytometer. Throughout days 1-7, the cells transduced with SALL4A or SALL4B continued to expand at a steady rate even though IL-3 was removed from the growth media. The 32D-SALL4A or 32D-SALL4B proliferated at a 3-fold or 6-fold higher rate than the control counterpart after 3 days of culture in G-CSF (FIG. 18). The control, 32D cells died after 5-6 days in G-CSF but 32D-SALL4A and 32DSALL4B cells grew indefinitely in culture when IL-3 was removed, and replaced with G-CSF. Furthermore, these cells behaved identically to unmodified 32D cells (FIGS. 18 and 19). Expression of SALL4A or SALL4B permitted continued growth of cells in an undifferentiated state. While the control 32D cells exhibited appropriate granulocyte maturation, 32D-SALLA or 32D-SALL4B cells did not show significant granulocytic maturation with their morphology very similar to the 32D-SALL4 parent population. 32D cells proliferate as undifferentiated blasts when maintained in IL-3 (FIG. 20 iv), but differentiate into mature neutrophilic granulocytes when stimulated with G-CSF (FIG. 20 vi). SALL4 transduced 32D cells grew indefinitely without IL-3, and retained undifferentiated blast morphology when given G-CSF (FIG. 20 v). This study indicates that hematopoietic stem cell differentiation can be blocked by constitutive expression of SALL4.
Example 6
Interactions of SALL4A and SALL4B In vitro
To determine if the SALL4A or SALL4B protein forms homodimers or heterodimers in vitro, SALL4A or SALL4B were tagged with either HA or His (six histitine residues) and anti-HA pull-down assays was performed. As shown in FIGS. 21A and B, HA-SALL4A and His-SALL4B or HA-SALL4B and His-SALL4A proteins were expressed. Anti-HA pull down assays were performed. As seen in FIG. 21C, either His-SALL4A or His-SALL4B was pulled down by either HA-SALL4A or HA-SALL4B.
Example 7
Functional Analysis of SALL4 Induced CD34+ Cells In vitro
To further study the proliferation potential of the SALL4-transduced HSCs without an excess of special cytokines, colony-forming unit (CFU) assays were conducted. The CFU progenitors used for the study were initially GFP-positive signifying the expression of SALL4 protein (FIG. 11) and were cultured for at least one month in media containing the cytokines SCF, TPO, and FLT-3L. The CFU assays, conducted in methocult media without these cytokines, revealed that these cells could form various colonies including CFU-GM, CFU-GEMM, and BFU-E (FIG. 22A). In addition, the one month-old transduced cells had the capability to form similar numbers of CFU colonies compared to 2-day old GFP-transduced control cells when counted 18 days after the CFU assay was initialized (FIGS. 22B and 22C). Without wishing to be bound by any scientific theory, this study may indicate that SALL4 works in conjunction with other cytokines in order to block HSC differentiation and that other cytokines may by needed to inhibit differentiation.
To further test whether the transfer of SALL4 can lead to the long term expansion of human hematopoietic progenitors, SALL4A- and SALL4B-transduced cells were cultured for one month. After 31 days of culture there was a 1780-fold increase for SALL4A and 1463-fold increase for SALL4B in total CD34+ cells numbers compared to controls (FIG. 23A) (control cells ceased to expand after 10 to 12 days). Furthermore, SALL4 transduced cells showed 9.32 fold increases for SALL4A and 8.88 fold increases for SALL4B versus controls for the total number of LTC-ICs after one month (FIG. 23B). Overall, SALL4A transduced cells had a total fold CD34+/CD38− stem cell expansion of 16700 over control while SALL4B transduced cells showed 13300 fold increases although there was not a statistically significant difference between the two SALL4 isoforms (FIG. 23C).
Example 8
Expansion was Associated with Enhanced Stem Cell Repopulation Capacity In vivo
Xenotransplantation assays were transformed to test if SALL4 mediated cells are able to override the regulatory machinery in the marrow-niche to control their differentiation, repopulation capacity, and stem cell output. Phenotypic analysis revealed that both SALL4A- (n=9) and SALL4B-transduced (n=10) cells were capable of positive cell engraftment into NOD/SCID mice (FIG. 23D) 4 weeks post-injection. In addition, experimental animals (n=8) demonstrated myeloid (CD15+) and lymphoid (CD19+) lineages 4 weeks post-injection (FIG. 23E) indicative of a myeloid/lymphoid differentiation process. Bone marrow from animals (n=4) 15 weeks post-injection were analyzed using flow cytometry and still exhibited three lineage differentiation, including CD3+/CD19+ lymphoid, CD15+ myeloid, and Glycophorin-4A+ erythroid lineages (FIG. 24).
To further determine if SALL4-induced cells bear a long-term engraftable property, secondary and tertiary transplantations were conducted with bone marrow harvested from primary animals injected with human CD34+ cells. Flow analysis demonstrated that 8 weeks post-injection, animal marrows still had CD45+ cells (2.74%) but did not attain significant CD34+ cells (<0.24%) showing no leukemic effect.
In addition, the CD45+ population were positive for CD3+ (2.97%)/CD19+ (0.89%) lymphoid, CD15+ (14.1%) myeloid, and Glycophorin-4A+(5.6%) lineages. This showed that successful bone marrow transplantation from one animal to another was possible and that cells could differentiate properly in the bone marrow niche. In addition, tertiary transplantations were conducted with bone marrow harvested from secondary transplant animals. 10 weeks post transplant, the animals still exhibited CD45+ (3.29%) cells within their bone marrow (FIGS. 23F and 23G). Further analysis of the CD45+ population demonstrated the cells were positive for myeloid and lymphoid lineages similar to that of the second transplant (FIGS. 23F and 23G).
After 4 weeks of culture, the ability of SALL4A or SALL4B to increase the repopulating capacity of human cells into NOD/SCID was demonstrated by a strong enhancement in the level of chimerism in mice transplanted with SALL4A or SALL4B-transduced cells. The proportion of CD45+ cells with SALL4A was 3.84% (0.34-12.89%; n=12) and with SALL4B was 2.98% (0.41-9.41%; n=12) compared to 0.52% (0.03-1.18%; n=12) for control cells (FIG. 23H). Furthermore, long-term engraftment with SALL4A- or B-transduced cells was also evident by detecting human CD45+ cells in the mouse peripheral blood at 14 weeks (n=6) or 19 weeks (n=3).
To quantitatively measure the effects of SALL4-transduced CD34+ cells, we conducted limiting-dilution experiments to determine the NOD/SCID mice repopulating cell (SRC) frequency. At 7 weeks after injection, the SRC frequency increased from 1 in 19,200 CD34+ cells (range defined by +/−s.e.: 14,100-25,900) to, respectively, 1 in 7,100 (range defined by +/−s.e.: 5,200-9,800) for SALL4A and 1 in 9,100 (range defined by +/−s.e.: 6,700-12,400) for SALL4B. The total SRC content was expanded by 1080 fold for SALL4A and 844 fold for SALL4B (n=72) compared to uncultured cells by taking into account the increase in the SRC frequencies and total cell numbers (FIG. 23I). Without wishing to be bound by any scientific theory, these results may suggest that overexpression of SALL4 solely in HSCs does not override the regulatory mechanisms involved in the control of stem cell output in vivo.
Example 9
TAT-SALL4B Protein Induced CD34+ Cell Expansion
Lentiviral expression of SALL4 is very efficient, but its clinical application is not ideal due to difficulties in controlling the level and duration of expression of the transgene in vivo as well as the potential for insertional leukemogenesis. In order to use a different approach to demonstrate the role of SALL4 in HSC expansion, a TAT-6×His-SALL4B protein expressed in E. coli, and purified using Ni-NTA agarose (FIGS. 25A and 25B). The recombinant protein of TAT-SALL4B was confirmed by a Western blot with a anti-6×His tag mouse monoclonal antibody and mass spectrometry analysis (FIGS. 25C and 25D). SALL4B was focused on because it is a shorter form and expressed a high level of protein in E. coli. After 3 days of TAT-SALL4B treatment, the CD34+ cells expanded rapidly (FIG. 26A). Human CD34+ cells cultured 3 to 4 days with SALL4 fusion protein (200 nM) along with TPO, SCF and Flt-3 ligand showed more than 10 and 8 fold increases of total mononuclear cells and CD34+ cells, respectively (FIGS. 26B and 26C). TAT-SALL4B protein (200 nM) was added twice a day and appeared to be sufficient to expand the cells. In addition, CFU assays demonstrated that these cells could form various colonies including CFU-GM, CFU-GEMM, and BFU-E (FIG. 26D). By taking the fold increase of the TAT-SALL4B treated cells versus control times the CFU numbers, it was noted that the overall CFU number increased by approximately ten fold.
Example 10
Expression and Purification of TAT-SALL4B Fusion Protein in SF9 Insect Cells
Visual inspection of the SF9 cells at 4 days showed the presence of polyhedrins within the cells (FIG. 30), indicating virus production. The expression of hSALL4B protein was confirmed by Western blotting (FIG. 29). The blot also confirmed the presence of His-tagged SALL4B in the first elute and second elute from Ni-NTA beads.
Example 11
In vitro Expansion of Whole Mouse Bone Marrow Cells by TAT-SALL4B Protein
Mouse whole bone marrow cells were isolated as previously described. Cells starting at 0.4×105 were cultured in 20 ng/ml TAT-SALL4B protein or 20 ng/ml BSA. The numbers of cells were average at 1.16×105, 2.04×105 and 3.16×105 in BSA group and 1.89×105, 7.28×105 and 10.1×105 in SALL4B group on day 4, 7 and 10 (FIG. 31), showing that TAT-SALL4B can promote the proliferation of whole bone marrow cells in vitro.
Example 12
TAT-SALL4B Protein Promotes Marrow Cell Expansion and the Recovery of Bone Marrow
TAT-SALL4B protein, G-CSF or PBS was intraperitoneally injected into mice for 7 consecutive days 24 hours after lethal irradiation. The dose of the lethal irradiation (7Gy, gamma-ray) is able to kill more than 99% of mouse bone marrow cells within one week. An average of 2×107 whole bone marrow nucleated cells could be obtained from flushing out tibia and femur of both sides in one wide type mouse. In the PBS group, the number of whole bone marrow cells was 1.32×105 (+/−0.13×105; n=6) at day 8 after irradiation. In comparison, G-CSF animals had 4.51×105 (+/−0.43×105; n=6) cells and the SALL4B treated group had 7.91×105 (+/−0.75×105; n=7) cells. As consistent with previous reports, G-CSF could increase the number of the cells by 3.42 fold. The fold increases were 6.00 and 1.75 in SALL4B group as compared to PBS control and G-CSF group, respectively, suggesting SALL4B is even better than G-CSF regarding to boosting the proliferation of bone marrow cells after irradiation.
The histological sections from different group at day 8 after irradiation were analyzed. In contrast to PBS group in which only very few cells, mainly marrow stromal cells, left in mouse bone marrow cavity, the cellularization of the bone marrow was dramatically enhanced by G-CSF or SALL4B treatment (FIGS. 32-34). In addition, the majority of cells are identified as of hematopoietic cells. These data demonstrate that SALL4B is efficient in promoting the recovery of bone marrow by increasing the proliferation of bone marrow cells.
Example 13
SALL4B Increases Expansion of Hematopoietic Stem and Progenitor Cells in Mouse Bone Marrow
With flow cytometry, the hematopoietic stem and progenitor cell content with a combination of Lin, c-Kit and Scal-1 staining for the whole bone marrow cells was detected. The percentage of HPCs (Lin-/c-Kit+Scal−) was increased to 14.7% in G-CSF group and 9.82% in SALL4B group as compared to 5.1% control. These results were correlated well with CFC (colony forming cell) assays (FIG. 35). CFC assays are well characterized assays that can detect an increase or decrease in the frequency of hematopoietic progenitor proliferation in response to stimulatory or inhibitory agents.
In addition, compared to control (1.24%), hematopoietic stem cells (HSCs) (Lin-/c-Kit+/Scal-1+) percentage were also significantly higher in GCSF group (FIG. 36). Importantly, the HSC percentage in SALL4B group was even higher than that in G-CSF group (approximately 2.7 fold increase). The total fold increases (vs. control) of HSCs number in mouse bone marrow were 11.8 (n=6) fold and 32.2 (n=7) fold in G-CSF and SALL4B, respectively.
Example 14
Enhanced Long-Term Engraftment of Cord Blood Stem Cells and Progenitor Cells by TAT-SALL4B Protein
The ability of TAT-SALL4B to increase the efficiency of bone marrow transplantation was tested using Umbilical Cord Blood (UCB) cells. 20,000 CD34+ UCB cells were transplanted into sub-lethally irradiated NOD/SCID mice and treated with 2 ug/day SALL4B protein for 7 days and then 2 ug/day every other day for an additional week (FIG. 37). Animals treated with TAT-SALL4B protein isolated from SF9 cells showed an 8.5 fold increase in the long-term engraftment of CD45+ cells (UCB cells) in the peripheral blood 16 weeks post-transplant compared to PBS treated controls. CD45 cells (UCB cells) 16 weeks post-transplant compared to PBS treated controls. The transplanted UCB cells in the marrow was further examined. As shown in FIG. 38, the level of donor cells, UCB in mice administrated with TAT-SALL4B, was increased by 10 fold compared with that of control mice injected with PBS and was measured four months post-transplant, demonstrating an achievement of long-term engraftment. These studies indicate that TAT-SALL4 protein is a robust factor in the promotion of stem cell engraftment.
Example 15
TAT-SALL4 Increases Yield of Stem and Progenitor Cells
Enumeration of hematopoietic colony-forming progenitor cells (CFC) is used to evaluate peripheral blood progenitor cell collections. CFC association with the day of neutrophils recovery, measured as the coefficient of correlation, is stronger than that of the total nuclear cells. SALL4B protein was intraperitoneally injected to wild type mice and then the peripheral blood was collected from injected mice to evaluate the number of CFC. As shown in FIG. 39, the CFC numbers in the peripheral blood from mice injected with SALL4B protein were increased by threefold compared to that of mice injected with PBS. This study indicated that TAT-SALL4 is able to increase the peripheral blood yield of stem and progenitor cells when TAT-SALL4 is administrated.
Discussion
As demonstrated herein, SALL4A and SALL4B are strong positive regulators of hematopoetic stem cell expansion. While previous attempts to expand HSCs using hematopoietic growth factors such as fetal liver tyrosine kinase (Flt3) ligand, stem cell factor, interleukins 6 and 11, HOXB4, OCT4 and Nanog show only a limited expansion of HSCs, HSCs receiving expression of SALL4A or SALL4B are able to achieve a high-level of ex vivo expansion. Cultures of SALL4-transduced cells results in extensive HSC expansion with over 1000-fold higher levels than controls within 2 to 3 weeks and expanded HSCs show no or very little maturation. Moreover, the expansion occurs quite rapidly with significant HSC growth in just a few days. In addition, SALL4-induced HSC expansion exhibits no impairment of hematopoietic cell differentiation. SALL4 appears to function in the maintenance of an undifferentiated proliferation state and block cell differentiation for HSCs.
A new therapeutic strategy is described herein, which in some embodiments uses cytokine-dependent SALL4 technology for the dramatic 10,000 to 15,000-fold ex vivo expansion of human HSCs without significant differentiation over 4 weeks. In some experiments, even after 8 weeks of cell culture, 37% of the CD34+ cells were still CD34+/CD38− (data not shown). In xenotransplantation models, the stem cell frequency of cells that had been induced by SALL4 for 4 weeks ex vivo was only 2-2.5-fold higher than fresh CD34+ cells (FIG. 26H). Without wishing to be bound by any scientific theory, the in vivo growth of SALL4-induced HSCs might be dissimilar to those in cell culture conditions (ex vivo) where an excess of special cytokines is present.
In some embodiments described herein the magnitude of HSC expansion is unprecedentedly high with 10,000 fold for CD34+/CD38− and CD34+/CD38+ populations. In addition, the expansion of engraftable long-term HSCs by the SALL4 approach described herein is achievable in embodiments of the invention and is supported by evidence of the secondary and tertiary transplantation studies described herein.
Massive ex vivo expansion of CD34+ cells can be achieved without differentiation using materials and methods described herein. These expanded cells retain long-term engraftment properties similar to those of un-manipulated cells in vivo. In experimental examples described herein, the SALL4-expanded cells sustained a long-term engraftment demonstrated by serial xenotransplant models and repopulation assays. Most critically, after transplantation they do not override the niche-induced regulatory controls, allowing these expanded stem cells to avoid leukemic formation. No evidence of leukemia was evident in transplanted mice in either serially xenotransplanted animals or by more than 10 months post-transplantation (data not shown). In addition, no leukemic formation was exhibited for 12 months post syngeneic transplantation when either SALL4A or B was expressed and introduced into mouse stem/progenitor hematopoietic cells (n=6).
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## Claims

1. A method for expanding a hematopoietic stem cell population, the method comprising providing to the stem cell population a Sal-like 4 (SALL4) polypeptide attached to a transport moiety capable of crossing a cell membrane, in an amount effective to expand the stem cell population.

2. The method of claim 1, wherein the hematopoietic stem cell is an adult hematopoietic stem cell.

3. The method of claim 1, wherein the hematopoietic stem cell is in or derived from umbilical cord blood, peripheral blood, bone marrow, or spleen.

4. The method of claim 1, wherein the hematopoietic stem cell is a human stem cell.

5. The method of claim 1, wherein the transport moiety is a HIV-1transactivator of transcription (TAT) peptide, a Chariot protein, an arginine-rich peptide, an Antennapedia-derived penetratin peptide, a herpes simplex virus type 1 VP22 protein, or a +36 GFP.

6. The method of claim 1, wherein the SALL4 polypeptide comprises amino acids in the sequence set forth as SEQ ID No: 11 or 12.

7. The method of claim 1, wherein the stem cell population is expanded 10-fold, 20-fold, 50-fold, 100-fold, or 1000-fold.

8. A method for expanding a hematopoietic stem cell population ex vivo, the method comprising providing to the ex vivo stem cell population Sal-like 4 (SALL4) polypeptide in an amount effective to expand the stem cell population.

9. The method of claim 8, wherein the cell population is cultured in media comprising 50 ng/ml FMS-like tyrosine kinase-3 (FLT-3), 50 ng/ml Thrombopoietin (TPO), and/or 50 ng/ml Stem cell factor (SCF) or in media comprising 25 ng/ml FMS-like tyrosine kinase-3 (FLT-3), 25 ng/ml Thrombopoietin (TPO), and/or 25 ng/ml Stem cell factor (SCF).

10. The method of claim 8, wherein the SALL4 polypeptide is encoded by a nucleotide sequence comprising the sequence set forth as SEQ ID No: 5 or 6.

11. The method of claim 8, wherein a stem cell in the population is transduced with a viral vector comprising nucleotides encoding the SALL4 polypeptide, thereby providing the SALL4 polypeptide to the stem cell population.

12. The method of claim 11, wherein expression of said SALL4 polypeptide is under the control of an inducible promoter.

13. The method of claim 8, wherein the hematopoietic stem cell population is an adult hematopoietic stem cell population.

14. The method of claim 8, wherein the hematopoietic stem cell population is in or derived from umbilical cord blood, peripheral blood, bone marrow, or spleen.

15. A method for treatment of a disorder in a subject requiring a hematopoietic stem cell or an expanded hematopoietic stem cell, the method comprising:
a) obtaining a hematopoietic stem cell population,
b) providing to the stem cell population a composition comprising a Sal-like 4 (SALL4) polypeptide in an effective amount for the expansion of the stem cell population, and
c) transplanting the expanded stem cell population to the subject in an amount effective for the treatment of said disorder.