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  • C12N2740/15041—Use of virus, viral particle or viral elements as a vector
  • C12N2740/15043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

• the present invention relates to methods and compositions for expanding a cell population, and particularly stem cell populations such as a hematopoietic stem cell population.
• HSCs Hematopoietic stem cells
• HSCs are clonogenic cells, which possess the properties of both self-renewal (expansion) and multilineage potential giving rise to all types of mature blood cells.
• HSCs are responsible for hematopoiesis and undergo proliferation and differentiation to produce mature blood cells of various lineages while still maintaining their capacity for self-renewal.
• the ability to self- renew maintains the HSC population for the lifespan of an animal and also allows HSCs to repopulate the bone marrow of lethally irradiated congenic hosts.
• MPP multipotent progenitors
• HSCs located in bone marrow niches must achieve a balance between quiescence and activation so that immediate demands for hematopoiesis are fulfilled, while long-term stem cell maintenance is also assured.
• HSCs are responsible for life-long hematopoiesis under homeostatic and stress conditions, which relies on an extraordinary between stem cell self- renewal and differentiation (Li et al. Science, 327: 542-545, 2010; Weissman et al. Cell, 100: 157-168, 2000).
• HSC transplantation is a life-saving therapy for a broad spectrum of disorders, including hematologic, immune, and genetic diseases, as well as cancers (Walasek et al. Annals of the New York Academy of Sciences 1266: 138-150, 2012).
• HSC-based treatment can be limited primarily by the lack of HLA-matched donor bone marrow (BM).
• graft vs host disease GvHD
• graft vs host disease GvHD
• immune suppression medicine has numerous side effects, such as delayed immunological recovery, thrombotic microangiopathy (Sung et al. Stem Cells Translational Medicine, 2: 25-32 (2013) ;Shlomchik et al. Nature Reviews. Immunology, 7: 340-352, 2007).
• Transplantation of HSCs from hUCB reduces the risk of GvHD; however, the lower number of HSCs in hUCB than in BM or mobilized peripheral blood limits its application (Walasek et al. Annals of the New York Academy of Sciences, 1266: 138-150, 2012).
• m 6 A is a prevalent internal modification in mRNAs that regulates the outcome of gene expression by modulating RNA processing, localization, translation, and eventual decay, which is modulated by "writers,” “erasers” and “readers” of the mark (Roundtree et al.
• mESCs mouse embryonic stem cells
• NSCs embryonic neuronal stem cells
• stem cells mouse embryonic stem cells
• m 6 A modifications regulate stem cell fate determination by m 6 A-mediated decay of mRNAs encoding stem cell fate determinant (Batista et al. Cell Stem Cell, 15: 707-719, 2014; Yoon et al.
• Mettl3 and Mettl14 promote leukemogenesis as m 6 A modifications stabilize the mRNAs of oncogenes and/or increase their translation (Vu et al. Nature Medicine, 2017; Barbieri et al. Nature, 2017; Weng et al. Cell Stem Cell, 22: 191 -205 e199, 2018). Furthermore, previous studies have reported that the leukemogenic functions of FTO and Mettl14 are independent of YTHDF reader proteins (Li et al. Cancer Cell, 31 : 127-141 , 2017; Weng et al. Cell Stem Cell, 22: 191 -205 e199, 2018).
• RNA modification is modulated by "writers,” “erasers” and “readers” of the mark (Wang et al. Nature, 505(7481 ): 117-120, 2014), processes that install, recognize and remove this and other marks may have various implications for cellular, developmental, and disease processes. For example, studies have shown that the m 6 A mark may act as a key post-transcriptional modification to promote initiation of microRNA (miRNA) biogenesis (Alarcon et al. Nature, 519(7544): 482-485, 2015).
• miRNA microRNA
• RNA modifications possibly being involved in the differentiation of stem cells to specific lineages (Batista, Cell stem Cell, 15(6): 707-719, 2014; Zhang et al. Nature, 549(7671 ): 273- 276, 2017), and in regulating gene expression (Dominissini et al., Nature 485(7397):201 -206, 2012; Haussmann et al, Nature 540(7632): 301 -304, 2016).
• a m 6 A transferase METTL3 has been identified as a regulator for terminating murine naive pluripotency (Geula et al. Science, 347(6225): 1002-1006, 2015).
• m 6 A "writer" protein METTL3 has also been demonstrated in mouse T cells to disrupt T cell homeostasis and differentiation (Li et al. Nature, 548(7667): 338-342, 2017), and m 6 A RNA methylation has been found to promote XIST-mediated transcriptional repression (Patil et al. Nature, 537(7620): 369-373, 2016). M 6 A RNA modifications have also been shown to regulate the ultraviolet-induced DNA damage response (Xiang et al. Nature, 543(7646): 573-576, 2017).
• HSCs Hematopoietic stem cells
• BM bone marrow
• Sparescent HSCs perform superiorly to proliferative HSCs in lethally irradiated mice, which largely attributes to the quiescent state that protects HSCs from DNA damage (Arai et al., 2004; Fleming et al., 1993; Wilson et al., 2008) (Walter et al., 2015).
• HSCs are preserved in complex BM niches for their maintenance and regeneration (Li and Clevers, 2010; Mendelson and Frenette, 2014; Morrison and Scadden, 2014; Scadden, 2014; Schofield, 1978).
• endosteal (inner bone surface) cells fCalvi et al., 2003; Zhang et al., 2003J, sinusoidal endothelial cells (Hooper et al., 2009; Kiel et al., 2005), Cxcl12 abundant reticular (CAR) cells (Sugiyama et al., 2006), Nestin + and NG2 + perivascular cells (Kunisaki et al., 2013; Mendez-Ferrer et al., 2010), LepR + and Prx- 1 + mesenchymal stem and progenitor cells (Ding and Morrison, 2013; Ding et al., 2012; Green
• the first HSC niche was initially identified as the spindle shaped N-Cadherin + (N-cad + ) pre-osteoblastic cells in the endosteum of the trabecular bone region (Calvi et al., 2003; Xie et al., 2009; Zhang et al., 2003), but the nature and function of N-cad + niche cells in BM remain unclear.
• a method for expanding a population of stem cells is provided, the population of stem cells being obtained from a tissue selected from the group consisting of peripheral blood, cord blood and bone marrow.
• the method includes modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the population of stem cells, to expand the number of stem cells.
• m 6 A N 6 -Methyladenosine
• a method for ex vivo expansion of a substantially undifferentiated stem cell population comprising modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the undifferentiated stem cell population to expand the number of undifferentiated stem cells without significant differentiation of the stem cell population.
• m 6 A N 6 -Methyladenosine
• a method for ex vivo expansion of an hematopoietic stem cell (HSC) population comprising modulating a ⁇ / 6 - Methyladenosine (m 6 A) mRNA modification pathway in the HSC population to expand the HSC population to a sufficient quantity while maintaining a multilineage differentiation potential in the HSC population, which is sufficient for subsequent transplantation into a subject in need thereof.
• HSC hematopoietic stem cell
• a method for ex vivo expansion of hematopoietic stem cells (HSCs) by at least 2-fold comprising introducing a mutation into the stem cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of HSCs in a suitable culture medium.
• kits for expanding an hematopoietic stem cell population (HSC) population for subsequent transplantation into a subject in need thereof comprising a system for introducing a mutation into the HSC population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• HSC hematopoietic stem cell population
• kits for expanding an hematopoietic stem cell population (HSC) population for subsequent transplantation into a subject in need thereof comprising an inhibitor of a m 6 A mRNA modification reader, and instructions for use thereof.
• a method for administering an hematopoietic stem cell (HSC) to a subject in need thereof comprising: (a) introducing, into a sample containing an HSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the HSCs to the subject.
• a method for administering an hematopoietic stem cell (HSC) to a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing an HSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the HSCs to the subject.
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) introducing, into a sample containing an HSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the HSCs to the subject.
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing an HSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the HSCs to the subject.
• a method for expanding a population of hematopoietic cells comprising culturing the population of HSCs under conditions sufficient to result in an expansion of the HSC population by at least 2-fold is provided, wherein the expanded population of HSCs is suitable for transplantation into a mammal in need thereof.
• a method for expanding a population of hematopoietic stem cells comprising: (a) obtaining from a mammal a tissue sample comprising an HSC population; (b) expanding, in vitro, the HSC population from the sample, wherein: (i) the HSC population expands by at least 2-fold; and (ii) the expanded HSC population has at least a 5-fold increase in total colony-forming units.
• a method for reconstituting a hematopoietic stem cell lineage in a subject in need thereof comprising: (a) obtaining from a mammal a tissue sample comprising an HSC population; (b) expanding, in vitro, the HSC population from the sample, wherein: (i) the HSC population expands by at least 2-fold; and (ii) the expanded HSC population has at least a 5-fold increase in total colony-forming units; and (c) transplanting the expanded HSC population into a subject in need thereof.
• a method for expanding a hematopoietic stem cell population in a mammal in need of such expansion comprising administering to the mammal a therapeutically effective amount of a modulator of a N 6 -Methyladenosine (m 6 A) mRNA modification pathway for a period of time sufficient to expand the HSC population by at least 2-fold with HSCs that possess the ability to reconstitute a hematopoietic lineage in the mammal.
• m 6 A N 6 -Methyladenosine
• a method for ex vivo expansion of a mesenchymal stem cell (MSC) population comprising modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the MSC population to expand the MSC population to a sufficient quantity while maintaining a multilineage differentiation potential in the MSC population, which is sufficient for subsequent transplantation into a subject in need thereof.
• MSC mesenchymal stem cell
• a method for ex vivo expansion of mesenchymal stem cells (MSCs) by at least 2-fold comprising introducing a mutation into the stem cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of MSCs in a suitable culture medium.
• kits for expanding a mesenchymal stem cell population (MSC) population for subsequent transplantation into a subject in need thereof comprising a system for introducing a mutation into the MSC population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• MSC mesenchymal stem cell population
• kits for expanding an mesenchymal stem cell population (MSC) population for subsequent transplantation into a subject in need thereof comprising an inhibitor of a m 6 A mRNA modification reader, and instructions for use thereof.
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprising: (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• MSC mesenchymal stem cell
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing a MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• MSC mesenchymal stem cell
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing a MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• a method for expanding a population of mesenchymal cells comprising culturing the population of MSCs under conditions sufficient to result in an expansion of the MSC population by at least 2- fold is provided, wherein the expanded population of MSCs is suitable for transplantation into a mammal in need thereof.
• a method for expanding a population of mesenchymal stem cells comprising: (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein: (i) the MSC population expands by at least 2-fold; and (ii) the expanded MSC population has at least a 5-fold increase in total colony-forming units.
• a method for reconstituting a mesenchymal stem cell lineage in a subject in need thereof comprising: (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein: (i) the MSC population expands by at least 2-fold; and (ii) the expanded MSC population has at least a 5-fold increase in total colony-forming units; and (c) transplanting the expanded MSC population into a subject in need thereof.
• a method for expanding a mesenchymal stem cell population in a mammal in need of such expansion comprising administering to the mammal a therapeutically effective amount of a modulator of a N 6 -Methyladenosine (m 6 A) mRNA modification pathway for a period of time sufficient to expand the MSC population by at least 2-fold with HSCs that possess the ability to reconstitute a mesenchymal lineage in the mammal.
• m 6 A N 6 -Methyladenosine
• a method for ex vivo expansion of a mesenchymal stem cell (MSC) population is provided, the MSC population being obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow, the method comprising modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the MSC population to expand the MSC population to a sufficient quantity while maintaining a multilineage differentiation potential in the MSC population, which is sufficient for subsequent transplantation into a subject in need thereof.
• MSC mesenchymal stem cell
• a method for ex vivo expansion of mesenchymal stem cells (MSCs) by at least 2-fold comprising introducing a mutation into the stem cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of MSCs in a suitable culture medium.
• kits for expanding a mesenchymal stem cell population (MSC) population for subsequent transplantation into a subject in need thereof comprising a system for introducing a mutation into the MSC population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• MSC mesenchymal stem cell population
• kits for expanding an mesenchymal stem cell population (MSC) population for subsequent transplantation into a subject in need thereof comprising an inhibitor of a m 6 A mRNA modification reader, and instructions for use thereof.
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprising: (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• MSC mesenchymal stem cell
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing a MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• MSC mesenchymal stem cell
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• a method for reconstituting bone marrow in a subject in need thereof comprising: (a) culturing, in a suitable culture media, a sample containing a MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• a method for expanding a population of mesenchymal cells comprising culturing the population of MSCs under conditions sufficient to result in an expansion of the HSC population by at least 2-fold is provided, wherein the expanded population of MSCs is suitable for transplantation into a mammal in need thereof.
• a method for expanding a population of mesenchymal stem cells comprising: (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein: (i) the MSC population expands by at least 2-fold.
• a method for reconstituting a mesenchymal stem cell lineage in a subject in need thereof comprising: (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein: (i) the MSC population expands by at least 2-fold; and (c) transplanting the expanded MSC population into a subject in need thereof.
• a method for expanding a mesenchymal stem cell population in a mammal in need of such expansion comprising administering to the mammal a therapeutically effective amount of a modulator of a N 6 -Methyladenosine (m 6 A) mRNA modification pathway for a period of time sufficient to expand the MSC population by at least 2-fold with MSCs that possess the ability to reconstitute a mesenchymal lineage in the mammal.
• m 6 A N 6 -Methyladenosine
• a method of isolating mesenchymal stem cells (MSCs) from a biological sample comprising contacting the biological sample having a population of MSCs with one or more N-cadherin antibodies.
• an isolated population of mesenchymal stem cells is provided, as made by any of the processes described herein.
• an expanded, isolated population of mesenchymal stem cells is provided, as made by any of the processes described herein.
• a kit for isolating a mesenchymal stem cell (MSC) population for subsequent transplantation into a subject in need thereof comprises a system for contacting a biological sample comprising MSCs with one or more N-cadherin antibodies, and instructions for use thereof.
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprises: (a) isolating MSCs from a biological sample comprising a population of MSCs, by contacting the biological sample with one or more N-cadherin antibodies, and (b) administering the isolated MSCs to the subject.
• MSC mesenchymal stem cell
• a method for reconstituting bone marrow in a subject in need thereof comprises: (a) isolating mesenchymal stem cells (MSCs) from a biological sample comprising a population of MSCs, by contacting the biological sample with one or more N-cadherin antibodies; and (b) administering the isolated MSCs to the subject.
• MSCs mesenchymal stem cells
• a method for treating a subject in need of a transplant selected from the group consisting of a bone marrow transplant, a peripheral blood transplant and an umbilical cord blood transplant, is provided.
• the method comprises administering to the subject a population of isolated MSCs obtained by any of the methods described herein.
• a method for expanding a population of chimeric antigen receptor (CAR) T-cells prepared by modifying T-cells obtained from a tissue selected from the group consisting of peripheral blood, cord blood and bone marrow comprises modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the population of CAR T-cells, to expand the number of CAR-T cells.
• CAR chimeric antigen receptor
• a method for ex vivo expansion of a chimeric antigen receptor (CAR) T-cell population comprises modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the CAR T- cell population to expand the number of CAR T-cells.
• CAR chimeric antigen receptor
• a method for ex vivo expansion of a chimeric antigen receptor (CAR) T-cell population prepared by modifying T-cells obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow comprises modulating a ⁇ / 6 - Methyladenosine (m 6 A) mRNA modification pathway in the CAR T-cell population to expand the CAR T-cell population to a sufficient quantity which is sufficient for subsequent transplantation into a subject in need thereof.
• CAR chimeric antigen receptor
• a method for ex vivo expansion of chimeric antigen receptor (CAR) T-cells comprising introducing a mutation into the CAR T-cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of CAR T-cells in a suitable culture medium.
• CAR chimeric antigen receptor
• kits for expanding a chimeric antigen receptor (CAR) T-cell (HSC) population for subsequent transplantation into a subject in need thereof comprises a system for introducing a mutation into the CAR T-cell population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• CAR chimeric antigen receptor
• HSC chimeric antigen receptor
• a method for administering chimeric antigen receptor (CAR) T-cell to a subject in need thereof comprises: (a) introducing, into a sample containing CAR T-cell population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; and (c) administering the CAR T-cells to the subject.
• CAR chimeric antigen receptor
• a method for administering a CAR T-cell to a subject in need thereof comprises: (a) culturing, in a suitable culture media, a sample containing a CAR T-cell population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the CAR T-cells to the subject.
• a method for treating cancer and/or a blood disorder in a subject in need thereof comprises: (a) introducing, into a sample containing a CAR T-cell population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; and (c) administering the CAR T-cells to the subject.
• a method for treating cancer and/or a blood disorder in a subject in need thereof is provided.
• the method comprises: (a) culturing, in a suitable culture media, a sample containing a CAR T-cell population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the CAR T-cells to the subject.
• a method for expanding a population of chimeric antigen receptor (CAR) T-cells comprises culturing the population of CAR T-cells under conditions sufficient to result in an expansion of the CAR T-cell population by at least 2-fold, wherein the expanded population of CAR T- cells is suitable for transplantation into a mammal in need thereof.
• CAR chimeric antigen receptor
• a method for expanding a population of chimeric antigen receptor (CAR) T-cells comprises: (a) obtaining from a mammal a tissue sample comprising a T-cell population; (b) modifying the T-cell population with chimeric antigen receptors to provide CAR T- cell population; and (c) expanding, in vitro, the CAR T-cell population from the sample, wherein: (i) the CAR T-cell population expands by at least 2-fold.
• CAR chimeric antigen receptor
• a method for treating a subject suffering from cancer and/or a blood disorder comprises: (a) obtaining from a mammal a tissue sample comprising a T-cell population; (b) modifying the T- cell population with a chimeric antigen receptor (CAR) to form a CAR T-cell population; (c) expanding, in vitro, the CAR T-cell population from the sample, wherein: (i) the CAR T-cell population expands by at least 2-fold; and (d) transplanting the expanded CAR T-cell population into the subject.
• CAR chimeric antigen receptor
• a method for expanding a chimeric antigen receptor (CAR) T-cell population in a mammal in need of such expansion comprises administering to the mammal a therapeutically effective amount of a modulator of a N 6 -Methyladenosine (m 6 A) mRNA modification pathway for a period of time sufficient to expand the CAR T-cell population by at least 2-fold with CAR T-cells that possess the ability to treat cancer and/or a blood disorder in the mammal.
• m 6 A N 6 -Methyladenosine
• a method of treating a subject suffering from a blood disorder comprises (a) obtaining a population of cells selected from the group consisting of stem cells and T-cells, from a tissue selected from the group consisting of peripheral blood, cord blood and bone marrow; (b) optionally, in a case where the population of cells comprises T-cells, modifying the T-cells with a chimeric antigen receptor (CAR) to provide CAR T-cells; (c) expanding the population of cells by modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the cells, to expand the number of cells; and (d) transplanting the expanded cells to the subject to treat the blood disorder.
• CAR chimeric antigen receptor
• Figs 1A-1 H Ythdf2 KO leads to increase in phenotypic HSCs in mice.
• Fig. 1A is a shematic showing a deletion of Ythdf2 in the HSPCs of Mx1- cre;Ythdf2 f/f conditional KO (cKO) mice;
• Fig. 1 B shows a Western blot (left) and histogram (right) showing intracellular flow validation of knockout Ythdf2 in mouse HSPCs; Fig.
• FIG. 2A-2J Ythdf2 KO results in expansion of functional HSCs in mice.
• FIG. 2A depicts an experimental scheme for limiting dilution transplantation assay (LDA) to determine the frequency of functional HSCs;
• Fig. 2A-2J Ythdf2 KO results in expansion of functional HSCs in mice.
• FIG. 2A depicts an experimental scheme for limiting dilution transplantation assay (LDA) to determine the frequency of functional HSCs
• FIGs. 2I and 2J are, respectively, a bar graph showing quantification of functional mouse hematopoietic stem cells (HSCs) by transplantation assay with peripheral blood analysis for total engrafted donor cells at 4 weeks after transplantation (2I), and a bar graph showing quantification of functional mouse HSCs by transplantation assay with the percentage of B, T and myeloid lineage cells at 4 weeks after transplantation (2J). Data shown as mean ⁇ s.e.m. Unpaired t-test. n.s., nonsignificant.
• Figs. 3A-3I Ythdf2 functions as an m 6 A reader and regulates HSC gene expression by mediating mRNA decay.
• Fig. 3A is a schematic of irCLIP-seq workflow;
• Fig. 3B is a schematic showing Ythdf2 binding motif identified by MEME with all irCLIP peaks found in all three replicates;
• Fig. 3C is a pie chart depicting the fraction of Ythdf2 binding peaks in each of five transcript segments;
• Fig. 3D is a chart showing a GO enrichment analysis of Ythdf2 targets from intersect genes of three Ythdf2 irCLIP-seq replicates;
• FIG. 3E shows representative tracks of Tall harboring m 6 A peaks and Ythdf2 irCLIP peaks, with coverage of m 6 A immunoprecipitation and input fragments indicated in red and grey, respectively, and Ythdf2 irCLIP reads highlighted in yellow;
• Fig. 3H shows images depicting fluorescence in situ hybridization of Tall mRNA (red) and fluorescence immunostaining of Dcpl a (P-body marker) (magenta), Ythdf2 (green) in wt and Ythdf2 KO HSPCs, where arrows indicate co-localized staining. Scale bars, 5 ⁇ m; Fig.
• Figs. 4A-4I Role of YTHDF2 in human cord blood HSCs by m 6 A- seq and RNA-seq analysis.
• Fig. 4A shows metagene profiles depicting sequence coverage in windows surrounding the TSS (left) and stop codon (right), where coverage of m 6 A IP and control (input) fragments indicated in red and grey, respectively;
• Fig. 4B depicts pie charts presenting the fraction of m 6 A peaks in each of five non-overlapping transcript segments;
• Fig. 4C depicts a Venn diagram showing shared and unique m 6 A-tagged genes in mouse and hUCB HSPCs;
• Fig. 4A-4I Role of YTHDF2 in human cord blood HSCs by m 6 A- seq and RNA-seq analysis.
• Fig. 4A shows metagene profiles depicting sequence coverage in windows surrounding the TSS (left) and stop codon (right), where coverage of m 6 A IP and control (input) fragments
• FIG. 4D depicts a chart with a GO enrichment analysis of m 6 A-tagged transcripts shared in both mouse and hUCB HSPCs;
• Fig. 4E shows representative tracks of HOXB4 harboring m 6 A peaks, where color codes are the same as in Fig 4A;
• Fig. 4F depicts a schematic of lentivirus mediated YTHDF2 KD in hUCB CD34 + HSPCs for RNA-seq;
• Fig. 4G is a plot of a cumulative distribution of log2 (fold change) for m 6 A-marked genes (purple line) and non-m 6 A-marked genes (black line), with control and YTHDF2 KD hUCB CD34 + cells;
• FIG. 4H shows representative coverage plots from the RNA-seq analysis, showing increased reads of m 6 A-tagged gene HOXB4 but not a non-m 6 A-tagged gene ACTB in YTHDF2 KD compared to control hUCB CD34 + cells; and
• Fig. 4I is a bar graph showing relative mRNA expression levels of non-m 6 A labeled ACTB (as control) and m 6 A-marked transcription factor related to stem cell self-renewal in control and YTHDF2 KD hUCB CD34 + cells.
• RPKM from RNA-seq analysis were normalized to controls. Adjusted P value were indicated, n.s., nonsignificant.
• Figs 5A-5F YTHDF2 KD facilitates expansion of human cord blood HSCs ex vivo.
• Figs. 5A-5B are bar graphs depicting the fold change of frequency (5A) and absolute number (5B) of indicated cells in YTHDF2 KD over control cells after 7 days culture;
• Fig. 5C shows a bar graph depicting CFU output from transduced CD34 + CD38 " hUCB cells and images of CFU-granulocyte erythrocyte monocyte megakaryocyte (GEMMs) (scale bar, 200 ⁇ m);
• GEMMs CFU-granulocyte erythrocyte monocyte megakaryocyte
• 5D includes images of burst forming unit-erythroid (BFU-E) (left) and colony-forming unit- granulocyte/macrophage (CFU-GM) (right) from 7-days cultured control or YTHDF2 KD hUCB cells (scale bar, 200 ⁇ m), where independent cord blood samples were used and repeated twice for the panels;
• Figs. 6A-6G YTHDF2 KD facilitates expansion of human cord blood functional long-term HSCs.
• Fig. 6A is an image showing an experimental scheme for measuring frequency of HSCs after in vivo expansion
• Fig. 6B includes representative flow plots of hCD45 + GFP + reconstitution from primary recipient mice receiving the highest two cell doses.
• hCD45 human CD45
• Fig. 6D is a plot showing HSC frequency determined by primary LDA. Dashed lines indicate 95% confidence intervals;
• Fig. 6A-6G YTHDF2 KD facilitates expansion of human cord blood functional long-term HSCs.
• Fig. 6A is an image showing an experimental scheme for measuring frequency of HSCs after in vivo expansion
• Fig. 6B includes representative flow plots of hCD45 + G
• FIG. 6E includes representative flow plots of hCD45 + GFP + reconstitution from secondary recipient mice receiving the highest two cell doses;
• Fig. 6D is a graph showing HSC frequency determined by secondary LDA. Dashed lines indicate 95% confidence intervals. Data shown as mean ⁇ s.e.m. Unpaired t-test. n.s., nonsignificant.
• Figs. 7A-7I Ythd ⁇ 2 KO HSCs show no signs of lineage bias or differences in quiescence and homing ability but exhibit lower apoptotic rate.
• Fig. 7B
• FIG. 7D shows images and the weight of spleens from wt and Ythdf2 KO mice
• Figs. 8A-8F Transplantation recipient mice of Ythd ⁇ 2 KO BM display no lineage changes or defects 16 weeks post transplantation.
• Figs. 9A-9K Ythdf2 KO has long-term effect on mouse HSC expansion in vivo without inducing lineage bias.
• Fig 9A is a schematic showing BM and spleen collected from wt and Ythdf2 KO mice were analyzed by flow cytometry at 5-7 months post pl:pC inductions;
• Fig. 9A is a schematic showing BM and spleen collected from wt and Ythdf2 KO mice were analyzed by flow cytometry at 5-7 months post pl:pC inductions
• Figs. 9B to 9E are bar
• FIG. 10A shows plots of metagene profiles depicting sequence coverage in windows surrounding the TSS (up) and stop codon (down), where coverage of m 6 A IP and control (input) fragments indicated in red and grey, respectively;
• Fig. 10B shows pie charts presenting the fraction of m 6 A peaks in each of five transcript segments;
• Fig. 10C shows plots of the fraction of genes in mouse HPSCs with m 6 A peaks in each of the segments as a function of expression level;
• Fig. 10D shows graphs of m 6 A-tagged and non-m 6 A-tagged mRNA degradation rates as determined by analysis of the expression level at 0 hour and 4 hours post actinomycin D treatment in HSPCs.
• Figs 11A-11 E Define Ythdf2 functionality in mouse HSPCs by irCLIP-seq.
• Fig. 11A is an image showing immunoprecipitation of Ythdf2 in control or Flag-Ythdf2 overexpressed HPC7 cells;
• Fig. 11 B is an irCLIP membrane image showing IR800 labeled RNA-Ythdf2 complex, where red box indicate the RNA- Ythdf2 complex collected for library construction, and with samples without UV crosslinking serve as controls;
• Fig. 11 C is a Venn diagram showing intersection genes identified in three independent Ythdf2 irCLIP-seq experiments; Fig.
• FIG. 11 D is a Venn diagram showing overlap of Ythdf2 binding targets and m 6 A labeled mRNAs;
• FIG. 11 E shows representative tracks of Gata2 harboring m 6 A peaks and Ythdf2 irCLIP peaks, where coverage of m 6 A immunoprecipitation and input fragments are indicated in red and grey, respectively, and Ythdf2 irCLIP reads are highlighted in yellow.
• Figures 12A-12F Ythd ⁇ 2 KO increased m 6 A-tagged mRNA expression, contributing to HSC expansion.
• Fig. 12A is a bar graph showing total RNA was extracted from 15,000 sorted BM LSK Flk2 " cells;
• Fig. 12A is a bar graph showing total RNA was extracted from 15,000 sorted BM LSK Flk2 " cells;
• Fig. 12B shows quantification of m 6 A RNA methylation in wt and Ythdf2 KO Lin "
• Figures 13A-13G YTHDF2 regulates expression of transcription factors related to stem cell self-renewal in human cord blood stem cells.
• Fig. 13A is a Venn diagram showing intersection genes identified in three independent m 6 A-seq experiments, using three independent cord blood samples;
• Fig. 13B shows pie charts with the percentage of mRNAs and non-coding RNAs containing m 6 A peaks;
• Fig. 13C is a bar graph showing GO enrichment analysis of the transcription factors harboring m 6 A modifications in hUCB CD34 + cells;
• Fig. 13A is a Venn diagram showing intersection genes identified in three independent m 6 A-seq experiments, using three independent cord blood samples;
• Fig. 13B shows pie charts with the percentage of mRNAs and non-coding RNAs containing m 6 A peaks;
• Fig. 13C is a bar graph showing GO enrichment analysis of the transcription factors harboring m 6 A modifications in hUCB CD34 + cells;
• FIG. 13D shows images of Western blotting of YTHDF2 (up) and ⁇ -Actin (down) in sorted GFP + control and YTHDF2 KD hUCB cells, showing knockdown efficiency of YTHDF2;
• Fig. 13E shows a bar graph with expression level (left) and representative track plots (right) of YTHDF2 from RNA-seq analysis of control and YTHDF2 KD hUCB CD34 + cells, showing knockdown efficiency of YTHDF2.
• Figs. 13F through 13G are representative track plots of indicated transcription factors harboring m 6 A peaks (up) and their representative coverage plots from the RNA-seq analysis (bottom). Adjusted P values are indicated.
• Figs. 14A-14C YTHDF2 KD in hUCB cells resulted in HSC expansion without changing lineage output.
• Fig. 14A depicts representative flow plots of GFP + CD34 + CD38 " CD45RA " EPCR + HSCs in control and YTHDF2 KD hUCB cells post 7 days culture;
• Fig. 14B depicts confirmation of YTHDF2 protein knockdown and overexpression in transduced Hela cells;
• Figs. 15A-15D YTHDF2 KD in hUCB cells resulted in HSC expansion without changing lineage output.
• Fig. 15A includes representative flow plots of hCD45 + GFP + monocyte, megakaryocyte (MK cell), B cell and erythrocyte in primary NSG recipient BM.
• Fig. 15A includes representative flow plots of hCD45 + GFP + monocyte, megakaryocyte (MK cell), B cell and erythrocyte in primary NSG recipient BM.
• Figs. 15B and 15C are bar graphs depicting the percentage of lineage cells in hCD45 + GFP + (Fig. 15B) and in total CD45 + (Fig. 15C) BM
• FIG. 16 expansion of mesenchymal stem cells in vivo.
• Fig. 16 is a bar graph showing the frequency of N-Cad+ CD105+ in TNC with both wt Ythdf2 and a Ythdf2 knockout (KO).
• Figs. 17A-17J functional identification of rHSC population.
• Fig. 17A is a schematic representation of FACS sorting for rHSCs, pHSCs, ST-HSCs and MPPs;
• Fig. 17B shows a quantification of rHSCs and pHSCs function by transplantation assay.
• Fig. 17C shows donor derived cells from rHSCs or pHSCs transplanted mice at 40 weeks post transplantation;
• Fig. 17F shows rHSCs and pHSCs transplanted recipients received 5FU injection at 4 weeks post transplantation as indicated.
• Figs 18A-18I rHSCs located by endosteal region in BM niche.
• Fig. 18A shows representative whole-mount images of mouse sternal bone marrow (BM), with bone (white, generated by second harmonic generation, SHG), MKs (yellow, distinguished by size, morphology and CD41 expression).
• Green arrowheads denoted phenotypic Lin " CD48 ⁇ CD41 ⁇ CD150 + CD49b ⁇ rHSCs
• White arrowheads denoted phenotypic Lin " CD48 " CD41 " CD150 + CD49b + pHSCs
• Fig. 18B shows representative image of rHSCs, pHSCs and 5FU rHSCs.
• FIG. 18F shows absolute number of healthy, apoptotic and dead VE-Cad + CD31 + vessel cells in control mice and mice at 1 day post 5FU treatment
• Figs. 18F-G show absolute number of AnnexinV 4" SytoxG- apoptotic Ve-Cad + CD31 + endothelial cells in central marrow (CM) or N-cad- tomato 4" cells in both CM and bone from control mice and mice 1 day post 5FU treatment.
• N 3 in each group.
• Figs. 18H-I show representative image of N-cad- tomato + and Ve-Cad + CD31 + vessels in control mice and in mice at 3 days post 5FU treatment.
• Figs. 19A-19J N-cad + cells maintain functional HSCs in BM niche.
• Fig. 19A shows a scheme for DT administration to N-cad-CreER T ;iDTR mice used for the experiments shown in B-G. D indicated day (e.g., DO indicates day 0);
• Fig. 19B shows N-cad + cell ablation efficiency as indicated by Tomato 4" cells in N-cad- CreER T ;iDTR mice;
• Figs. 19A shows a scheme for DT administration to N-cad-CreER T ;iDTR mice used for the experiments shown in B-G. D indicated day (e.g., DO indicates day 0);
• Fig. 19B shows N-cad + cell ablation efficiency as indicated by Tomato 4"
• 19E-H show quantification of functional HSCs by transplantation assay in primary 1 ° and secondary 2 ° transplantation.
• Total BM cells from PB analysis for total engrafted donor cells at the indicated number of weeks post transplantation and the percentage of donor-derived B, T and myeloid lineage cells at 16 weeks post transplantation (n 10 mice per group); Figs.
• Figs 20A-20K transcriptome analysis for hematopoietic cells and niche cells.
• Figs. 20A-B shows pearson distance tree and PCA analysis for hematopoietic stem and progenitor cells (HSPCs);
• Figs. 20C-D show pearson distance tree and PCA analysis for BM niche cells;
• Fig. 20E shows HSC signature gene expression in hematopoietic stem and progenitor cells;
• Fig. 20F shows BM niche signature gene expression in niche cells;
• Fig. 20G shows term analysis for BM niche cells;
• Fig. 20H shows stromal cell development gene expression in niche cells from endosteal and perivascular zones;
• FIG. 20I shows lineage tracing for N-cad- CreER T ; R26-tdT; Nestin-GFP mice after 3 TMX injections, and N-cad-CreER T ; R26- ZsG; Cxcl12-DsR mice after 3 TMX injections;
• Fig. 20J shows enzymatically digested bone marrow cells from N-cad-CreERT; R26-tdT mice post TMX injections. LepR and PDFgra stained by antibodies shown as red peak. Isotype control shown as gray peak; Fig. 20K shows CFU-F activity in niche cells from endosteal and perivascular zones.
• Fig. 21A-21G in vitro differentiation potential and localization of N-cad + derived cells.
• Fig. 21 A shows experimental design;
• Fig. 21 B shows live CFU-F colonies cultured from enzymatically digested bone marrow, stained with Cell TraceTM and Tomato 4" cells in one colony in high magnification;
• Figs. 21A-21G in vitro differentiation potential and localization of N-cad + derived cells.
• Fig. 21 A shows experimental design
• Fig. 21 B shows live CFU-F colonies cultured from enzymatically digested bone marrow, stained with Cell TraceTM and Tomato 4" cells in one colony in high magnification;
• Figs. 21A-21G in vitro differentiation potential and localization of N-cad + derived cells.
• 21 C-E show in vitro differentiation of stromal cells derived from N-cad-CreER T ; R26-tdT mice: live tdTomato 4" cells and Alkaline Phosphatase staining of culture 21 days after osteo- differentiation (21 C); live Tomato 4" cells and Oil Red O lipid staining 21 days after adipo-differentiation (21 D); aggrecan antibody stained and toluidine blue stained chondrocytes at 21 days after chondro-differentiation of Tomato 4" cells (21 E); Figs. 21 F-G show(F-G) experimental design; Fig.
• 21 H shows localization of cells derived from N-cad-CreERT; R26-tdT mice post TMX injection at 6 hours, 14 hours, 24 hours, 1 week and 4 weeks;
• Figs. 22A-22K N-cad + stromal cells give rise to osteoblasts and adipocytes in adult mice.
• Fig. 22A shows representative femur sections from N- cad-CreER T ; R26-tdT; Col2.3-GFP mice of different time points post TMX injection showing the anatomical distribution and increasing generation of Tomato + Col2.3- GFP 4" osteoblasts. Scale bar, 100 ⁇ m; Figs.
• 22B-C show higher-power images of N- cad-CreER T ; R26-tdT; Col2.3-GFP mice at early time points post TMX in region i, ii, iii, iv, v and vi shown in 6hr (22B) and 14hr (22C).
• Hollow arrowheads show Tomato + Col2.3GFP + osteoblasts (yellow cells) at 6 hours and 14 hours post TMX, whereas solid arrowheads indicate the N-cad recombined both in the trabecular (ii, iv, v) and cortical (iii, vi) region (green). These cells are potentially undifferentiated as shown by the absence of Col2.3-GFP.
• Figs. 22D-E show image quantification showing percentage of Tomato 4' Col2.3-GFP 4' and Tomato + Col2.3- GFP ⁇ cells in trabecular (22D) and compact bone (22E) at 6 hours, 14 hours, 24 hours, 2 weeks and 4 weeks post TMX injection
• Fig. 22F shows image quantification comparing percentage of potential undifferentiated Tomato + Col2.3- GFP ⁇ between trabecular and compact bone. * P ⁇ 0.05, ** P ⁇ 0.01 , *** P ⁇ 0.001 . Error bars, s.e.m; Fig.
• FIG. 22G shows representative image of trabecular bone (TB) and cortical bone (CB) in N-cad-CreER T ; R26-tdT; Col2.3-GFP mice at 4 weeks post TMX injection.
• Scale bar 20 ⁇ m
• Fig. 22H shows representative low and high-power image of femur section from N-cad-CreER T ; R26-tdT mice with Perilipin staining at 4 weeks post TMX injection.
• periosteal region (i) bone marrow near trabecular region (ii) and central marrow(iii), solid arrowheads showed Tomato + Perilipin + derived from N-cad + MSCs; Fig.
• FIG. 22I shows BODIPY staining showed the lipid droplet (green) inside the Tomato 4" Perilipin 4" adipocyte (arrowheads). Scale bar, 20 ⁇ m; Figs. 22J-K show image quantification of Tomato " " " Perilipin 4" adipocytes in trabecular bone (22J) and periosteal region (22K) at 6 hours, 14 hours, 24 hours, 2 weeks and 4 weeks post TMX injection. ( * P ⁇ 0.05, ** P ⁇ 0.01 , *** P ⁇ 0.001. Error bars, s.e.m.).
• Figs. 23A-23J N-cad + MSCs give rise to chondrocytes during development and post injury.
• Fig. 23A shows experimental design;
• Fig. 23B shows tomato 4" partially colocalized with Aggrecan 4" chondrocytes in rib at E14.5(2 days post TMX induction);
• Fig. 23C shows an Illustration of chondrocyte development in femur;
• Fig. 23D shows a representative femur section from 2-day-old N-cad-CreER T ; R26-tdT mice with TMX induction at E12.5.
• Tomato 4" cells gave rise to Aggrecan 4" cartilage cells in articular surface (i) and the developing secondary ossification center (ii). Arrowheads indicated Tomato 4" Aggrecan 4" cells; Fig. 23E shows a representative femur section from 10-month-old N-cad-CreER T ; R26-tdT mice with TMX induction at E12.5. Tomato 4" cells from early embryonic stage differentiated to Perilipin 4" adipocytes; Fig. 23F shows a representative femur section from 2-month-old N-cad-CreER T ; R26-tdT m ⁇ ce with TMX induction at E12.5.
• Tomato 4" cells from early embryonic stage differentiated to Osteopontin+ hypertrophic chondrocytes (i and ii) and osteoblasts (iii, iv, v and vi);
• Fig. 23G shows an experimental design for femoral groove injury to N-cad-CreER T ; R26-tdT mice with TMX induction at E12.5;
• Fig. 23H shows quantification of Tomato 4" chondrocytes in control mice and in mice 3 weeks after knee cartilage injury.
• Fig. 23J shows AHO staining of the sections in Figure 6H showing the Alcian blue positive chondrocytes in control (i) and in the location of cartilage injury(ii).
• Figs. 24A-24K BrdU assay and N-cad reporter mouse line post 5FU.
• Figs. 24A-F show representative images showing BrdU 4" cells in femur of mice at day 0, 2, 3, 4 and 6 post 5FU treatment. Note that BrdU 4" cells reduced at day 2 post 5FU, and reactivated from day 3 to day 6 post 5FU near bone (red dotted line) or vessel/adipose structure (green dotted line);
• Fig. 24G shows a model of dynamic of BrdU 4" cells;
• Fig. 24H shows a ratio of BrdU 4" cells in bone marrow to bone surface from day 3 to 6 post 5FU treatment; Fig.
• 24I shows a percentage of BrdU 4" cells near bone surface and near vessel/adipose structures from day 3 to 6 post 5FU treatment
• Fig. 24J shows representative whole bone section showing N-cad driven tomato 4" cells in both bone surface and central marrow
• Fig. 24K shows absolute number of N-cad driven tomato 4" cells in central marrow (CM) and in bone of N-cad- TdT mice of control group and mice 3 days post 5FU treatment.
• N 3 in each group. * P ⁇ 0.05, ** P ⁇ 0.01 , *** P ⁇ 0.001. Error bars, s.e.m.
• FIGs. 25A-25B generation of N-cad-CreER T mouse strain.
• Fig 25A shows a generation of N-cad-CreER T mouse strain;
• Fig. 25B shows lineage tracing for N-cad-CreER T , R26-tdT;
• Col2.3-GFP mice after three TMX injections; blood vessels stained by CD31 and Ve-cadherin antibodies.
• FIG. 26A-26E sorting strategy and signature gene expression of niche cells.
• Fig. 26A shows niche cells in endosteal zone harvested from digested bone cells;
• Fig. 26 B shows niche cells from Perivascular and sinusoid zones harvested from digested bone marrow cells;
• Fig. 26C shows localization of NG2- RFP + cells in endosteal and peri-arterial regions;
• Figs 26D-E show heatmaps of osteo-chondrogenic progenitor gene and adipogenic progenitor gene expression in niche cells.
• Figs. 27A-27E lineage tracing in N-cad-CreERT; R26-tdT mice at early time point post TMX induction.
• Figs. 27A-B show representative images of trabecular bone (TB) and cortical bone(CB) in N-cad-CreERT; R26-tdT; Col2.3-GFP mice at 24 hours and 2 weeks post TMX induction.
• Scale bar 20 ⁇ ;
• Figs. 27C-E show representative femur section with high power images of N-cad-CreERT; R26- tdT mice at 6 hours, 14 hours and 24 hours post TMX induction.
• Adipocytes shown with perilipin antibody staining.
• FIGs. 28A-28D characterization of N-cad + MSCs from early development and in injury repair.
• Fig. 28A shows representative images of femur section showing N-cad + MSCs with Aggrecan staining in N-cad-CreER T ; R26-tdT 24 hours post TMX induction at postnatal D2;
• Fig. 28B shows a representative femur section from 2-month-old N-cad-CreER T ; R26-tdT m ce with TMX induction at E12.5.
• Adipocytes shown with Perilipin antibody staining;
• FIG. 28C shows a representative femur section from 2-day-old N-cad-CreER T ; R26-tdT mice with TMX induction at E12.5. Developing bone cells shown with Osteopontin antibody staining; Fig. 28D shows a representative sagittal knee sections in E12.5 TMX induced N-cad-CreER T ; R26-tdT mice of control group and 2 weeks after knee cartilage injury. Scale bar, 1 mm.
• Fig. 29 Image of surviving rHSCs (green, CD150 + Lin- CD49b ⁇ ) at day 3 post 5FU treatment were often detected as single cells adjacent to the bone surface (white, SHG), and proliferating HSCs were often associated with MKs (CD150 + Lin + ) or near the vessels (red, CD31 +).
• Fig. 30 Plot showing production of human Thpo by 10K ncad+ hMSCs and 1000k total hMSCs in vivo.
• One embodiment of the invention is a method for expanding a population of stem cells obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow. This method comprises modulating a N6-methyladenosine (m 6 A) mRNA modification pathway in the population of stem cells to expand the number of stem cells.
• m 6 A N6-methyladenosine
• Another embodiment of the invention is a method for expanding a population of chimeric antigen receptor (CAR) T-cells cells obtained by modifying T- cells obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow.
• This method comprises modulating a N6- methyladenosine (m 6 A) mRNA modification pathway in the population of CAR T-cells to expand the number of stem cells.
• m 6 A N6- methyladenosine
• the population of stem cells and/or T-cells may be obtained from any mammal, such as, e.g., a human, and from any tissue that contains stem cells and/or progenitor cells and/or T-cells.
• tissue may be peripheral blood, cord blood or bone marrow.
• expansion means to increase the number of stem cells and/or CAR-T cells in the population relative to the number of stem cells and/or CAR T-cells in the original population either in vivo or ex vivo using any of the methods disclosed herein.
• the expansion may be at least 40- fold compared to the original number of stem cells and/or CAR T-cells in the population. More preferably, the expansion is at least 2-fold, 4-fold, 5-fold, 8-fold, 10-fold, 15-fold, 20-fold or more compared to the original number of stem cells.
• a population of stem cells means a group of substantially undifferentiated cells that possess the ability to give rise to many different types of cells and which have the ability to self-renew.
• Representative, non- limiting examples of stem cells according to the present invention include bronchioalveolar stem cells (BASCs), bulge epithelial stem cells (bESCs), corneal epithelial stem cells (CESCs), cardiac stem cells (CSCs), epidermal neural crest stem cells (eNCSCs), embryonic stem cells (ESCs), endothelial progenitor cells (EPCs), hepatic oval cells (HOCs), hematopoetic stem cells (HSCs), hematopoietic stem and progenitor cells (HSPCs), keratinocyte stem cells (KSCs), mesenchymal stem cells (MSCs), neuronal stem cells (NSCs), pancreatic stem cells (PSCs), retinal stem cells (RSCs), and skin-derived precursors (SK
• BASCs
• Hematopoietic stem cells have the ability to self-renew (i.e., expand) and can give rise to all the types of progenitor cells (such as, e.g., CMP, GMP, MEP and CLP) and ultimately all the types of blood cells (such as e.g., red blood cells, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, basophils, eosinophils, monocytes, macrophages, and platelets) in the hematopoietic system.
• progenitor cells such as, e.g., CMP, GMP, MEP and CLP
• blood cells such as e.g., red blood cells, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, basophils, eosinophils, monocytes, macrophages, and platelets
• Mesenchymal stem cells are multipotent stromal cells that can differentiate into a variety of cell types (such as, e
• a population of chimeric antigen receptor (CAR) T-cells means a group of T-cells that have been modified with chimeric antigen receptors capable of binding specific antigens, such as antigens on the surface of cancer cells, and may possess the ability to target and kill such cancer cells.
• the CAR T-cells can be prepared by modifying T-cells with the chimeric antigen receptors, such as by introducing DNA coding for the chimeric antigen receptors into the T-cells, to express the chimeric antigen receptors on the surface of the T-cells (Davila et al. Sci TransI Med 6(224), 224ra25 (2014); Tasian et al. Ther Adv Hematol 6(5), 228-241 (2015).
• modulating means altering the signal transduction pathway, e.g., a protein in the m 6 A mRNA modification pathway, including but not limited to lowering or increasing the expression level of a protein, altering the sequence of such a protein (by mutation, pre-translational or post-translational modification or otherwise), or inhibiting or activating such a protein (whether by binding, phosphorylation, glycosylation, translocation or otherwise).
• modulation may be achieved genetically or pharmacologically.
• modulating the m 6 A mRNA modification pathway comprises introducing a mutation into a population of stem cells and/or CAR-T cells, which mutation results in modulation of a molecule in the m 6 A mRNA modification pathway.
• modulation of the m 6 A mRNA modification pathway also includes contacting the stem cells and/or CAR T-cells with a modulator of a molecule in the m 6 A mRNA pathway.
• modulators include a small molecule, a biologic, an antisense RNA, a small interfering RNA (siRNA), and combinations thereof.
• the phrase "modulation of a molecule in the m 6 A mRNA modification pathway” means altering the function of a member of the m 6 A mRNA modification pathway, which altered function may have an effect similar to inhibiting or decreasing the function of a molecule involved in a process upstream and/or downstream of m 6 A modification of mRNA.
• Non-limiting examples of such "modulation” include increasing or decreasing the expression or function of proteins involved in any of the incorporation of N 6 -methyladenosine modifications in mRNA, removal of N 6 -methyladenosine mRNA modifications to mRNA, and/or the recognizing and processing of /V 6 -methyladenosine modified mRNA.
• the modulation may include increasing or decreasing N 6 -methyladenosine modifications in mRNA, and/or that affecting the type and/or distributions of such modifications in mRNA, such as by modulating the activity of one or more of a m 6 A writer (e.g. methyltransferase) and m 6 A eraser (e.g. demethylase).
• the modulation may increase or decreases expression or function of proteins that recognize N 6 -methyladenosine modifications to mRNA to mediate m 6 A- dependent functions, such as by modulating the activity of a m 6 A reader (e.g., an RNA binding protein that recognizes methylated adenosine).
• modulation of the molecule in the m 6 A mRNA modification pathway modulator may result in modulation of the activity and/or expression of a molecule upstream or downstream of an m 6 A mRNA modification process.
• the modulation of the m 6 A mRNA modification pathway involves modulation of a molecule selected from the group consisting of m 6 A mRNA modification readers, m 6 A mRNA modification writers, m 6 A mRNA modification erasers and combinations thereof.
• Non-limiting examples of m 6 A modification writers include methyltransferases that are capable of post-transcriptionally installing the m 6 A modification in messenger RNA, and can include any selected from the group consisting of METTL3, METTL14, WTAP, KIAA1429 and combinations thereof.
• Non-limiting examples of m 6 A modification erasers include demethylases that are capable of reversing the methylation, and can include any selected from the group consisting of FTI, ALKBH5 and combinations thereof.
• M 6 A modification readers include proteins that are capable of selectively binding m 6 A-methylated mRNA to exert regulatory functions through selective recognition of methylated mRNA.
• Suitable m 6 A modification readers can include any selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2, HNRNPC, HNRNPA2B1 , elF3 and combinations thereof.
• the m 6 A modification readers comprise proteins of the YTH domain family of proteins, which includes Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2 and combinations thereof, ⁇ see, e.g., Wang et al. Nature, 505(7481 ): 117-120, 2014; Frayling et al.
• introducing a mutation means any conventional method for producing an alteration in the genetic makeup of the stem cell population and/or CAR T-cell population.
• Non-limiting examples for introducing a mutation into a stem cell population and/or CAR T-cell population include mutagenesis via ultraviolet light irradiation, chemical mutagenesis, targeted mutagenesis such as site directed mutagenesis of a stem cell and/or CAR T-cell, and creation of a transgenic mouse.
• a mutation may be introduced into the stem cell and/or CAR T-cell to delete, replace or reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway, such as a molecule selected from the group consisting of a m 6 A mRNA modification reader, a m 6 A mRNA modification writer, a m 6 A mRNA modification eraser and combinations thereof.
• the mutation is introduced to delete, replace or reduce expression of a gene that expresses a m 6 A mRNA modification reader, such as any selected from the group consisting of Ythdf 1 , Ythdf2, Ythdf3, Ythdc1 , Ythdc2, HNRNPC, HNRNPA2B1 , elF3 and combinations thereof.
• a mutation is introduced to delete, replace or reduce expression of a gene that expresses Ythdf2.
• the mutation is introduced to delete, replace or reduce expression of a gene that expresses a m 6 A mRNA modification writer, such as any selected from the group consisting of METTL3, METTL14, WTAP, KIAA1429 and combinations thereof.
• the mutation is introduced to delete, replace or reduce expression of a gene that expresses a m 6 A mRNA modification eraser, such as any selected from the group consisting of FTI, ALKBH5 and combinations thereof.
• the mutation can be introduced by exposing the stem cells and/or CAR T-cells to a Mx1 -Cre targeting system (see, e.g., Kuhn et al. Science, 269(5229): 1427-1429, 1995) that inactivates or deletes at least a portion of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• a mutation is introduced that incorporates short hairpin RNA (shRNA) into the stem cells and/or CAR T-cells to reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• shRNA short hairpin RNA
• the shRNA may be introduced by exposing the stem cells and/or CAR T-cells to a vector to deliver shRNA, which may be a viral vector such as lentivirus (see, e.g., Chira et al. Oncotarget, 6(31 ): 30675-30703, 2015).
• the shRNA may be capable of triggering gene silencing to regulate gene expression (see, e.g., Paddison et al. Genes Dev. , 16(8): 948-958, 2002).
• a modulator of a N 6 -Methyladenosine mRNA modification pathway is any agent that regulates the activity of any member of the m 6 A mRNA modification pathway, which results in, e.g., an increase or decrease in N 6 -methyladenosine modifications in mRNA, and/or a change in the types and/or distributions of such modifications in mRNA, such as by modulating the activity of one or more of a m 6 A writer (e.g. methyltransferase) and m 6 A eraser (e.g. demethylase).
• a m 6 A writer e.g. methyltransferase
• m 6 A eraser e.g. demethylase
• the agent may be one that increases or decreases activity of proteins that recognize ⁇ / 6 - methyladenosine modifications to mRNA to mediate m 6 A-dependent functions, such as by modulating the activity of a m 6 A reader (e.g., an RNA binding protein that recognizes methylated adenosine).
• a m 6 A reader e.g., an RNA binding protein that recognizes methylated adenosine.
• the m 6 A mRNA modification pathway modulator may act on, or upstream of, or downstream of, an agent that affects the m 6 A modification to mRNA.
• the m 6 A mRNA modification pathway may be modulated by down-regulating and/or inhibiting a member of the m 6 A mRNA modification pathway, such as down-regulating and/or inhibiting a m 6 A mRNA modification reader.
• down-regulating means inhibiting or reducing the amount of or inhibiting or decreasing the activity of a member of the m 6 A mRNA modification pathway.
• Such down-regulation may be accomplished using, e.g. antisense RNA, siRNA, antibodies, or small molecules.
• the m 6 A mRNA modification reader may be down-regulated by contacting the stem cells and/or CAR T-cells with an inhibitor of an m 6 A mRNA reader, to inhibit binding and/or recognizing of the m 6 A modified mRNA by the m 6 A mRNA reader.
• the m 6 A mRNA modification reader that is down-regulated is selected from the group consisting of Ythdf 1 , Ythdf2, Ythdf3, Ythdc1 , Ythdc2, HNRNPC, HNRNPA2B1 , elF3 and combinations thereof.
• the m 6 A mRNA modification reader that is down-regulated is Ythdf2.
• Inhibitors of the m 6 A mRNA modification reader may be any selected from the group consisting of: (inhibitors of HNRNPC) hsa-let-7e-5p (MIRT051596), hsa-mir-455-3p (MIRT037890), hsa-mir-30c-5p (MIRT047904), hsa-mir-186-5p (MIRT045150), hsa- mir-744-5p (MIRT037494), hsa-mir-18a-3p (MIRT040851 ), hsa-mir-484 (MIRT042196), hsa-mir-505-5p (MIRT037959), hsa-mir-615-3p (MIRT039991 ), hsa- mir-342-3p (MIRT043694), hsa-miR-3607-3p, hsa-miR-30d, hsa-miR-3916, hsa-miR- 3162-5
• HNRNPA2B1 hsa-mir-92a-3p
• MIRT049721 hsa-mir- 30c-5p
• MIRT048009 hsa-mir-191 -5p
• MIRT045809 hsa-let-7f-5p
• MIRT051404 hsa-mir-27b-3p
• MIRT046213 hsa-mir-877-3p
• MIRT037116 MIRT037116
• MIRT040278 hsa-mir-1260b
• MIRT052680 hsa-mir-103a-3p
• MIRT027027 hsa- mir-16-5p
• MIRT031508 hsa-mir-1296-5p
• MIRT036075 hsa-mir-197
• MIRT040974 hsa-mir-155-5p (MIRT020771 ), hsa-mir-484 (MIRT042324), hsa-let- 7c-5p (MIRT051776), hsa-miR-3910, hsa-miR-148b, hsa-miR-136, hsa-miR-15a, hsa-miR-488, hsa-miR-500a, hsa-miR-1297, hsa-miR-3159, hsa-miR-374c, hsa- miR-424, hsa-miR-7-1 , hsa-miR-186, hsa-miR-195, hsa-miR-15b, hsa-miR-26b, hsa- miR-505, hsa-miR-1206, hsa-miR
• small molecule includes any chemical or other moiety, other than polypeptides and nucleic acids, that can act to affect biological processes, particularly to modulate members of the m 6 A mRNA modification pathway.
• Small molecules can include any number of therapeutic agents presently known and used, or that can be synthesized in a library of such molecules for the purpose of screening for biological function(s).
• Small molecules are distinguished from macromolecules by size.
• the small molecules of the present invention usually have a molecular weight less than about 5,000 daltons (Da), preferably less than about 2,500 Da, more preferably less than 1 ,000 Da, most preferably less than about 500 Da.
• Small molecules include without limitation organic compounds, peptidomimetics and conjugates thereof.
• organic compound refers to any carbon-based compound other than macromolecules such as nucleic acids and polypeptides.
• organic compounds may contain calcium, chlorine, fluorine, copper, hydrogen, iron, potassium, nitrogen, oxygen, sulfur and other elements.
• An organic compound may be in an aromatic or aliphatic form.
• Non-limiting examples of organic compounds include acetones, alcohols, anilines, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, amino acids, nucleosides, nucleotides, lipids, retinoids, steroids, proteoglycans, ketones, aldehydes, saturated, unsaturated and polyunsaturated fats, oils and waxes, alkenes, esters, ethers, thiols, sulfides, cyclic compounds, heterocyclic compounds, imidizoles, and phenols.
• An organic compound as used herein also includes nitrated organic compounds and halogenated (e.g., chlorinated) organic compounds.
• Preferred small molecules are relatively easier and less expensively manufactured, formulated or otherwise prepared. Preferred small molecules are stable under a variety of storage conditions. Preferred small molecules may be placed in tight association with macromolecules to form molecules that are biologically active and that have improved pharmaceutical properties. Improved pharmaceutical properties include changes in circulation time, distribution, metabolism, modification, excretion, secretion, elimination, and stability that are favorable to the desired biological activity. Improved pharmaceutical properties include changes in the toxicological and efficacy characteristics of the chemical entity.
• a polypeptide mimetic is a molecule that mimics the biological activity of a polypeptide, but that is not peptidic in chemical nature. While, in certain embodiments, a peptidomimetic is a molecule that contains no peptide bonds (that is, amide bonds between amino acids), the term peptidomimetic may include molecules that are not completely peptidic in character, such as pseudo-peptides, semi-peptides, and peptoids.
• biological means products derived from living sources as opposed to a chemical process.
• Non-limiting examples of a “biologic” include proteins, conditioned media, and partially purified products from tissues.
• peptide means a linked sequence of amino acids, which may be natural, synthetic, or a modification or combination of natural and synthetic.
• the term includes antibodies, antibody mimetics, domain antibodies, lipocalins, and targeted proteases.
• the term also includes vaccines containing a peptide or peptide fragment intended to raise antibodies against the peptide or peptide fragment.
• Antibody as used herein includes an antibody of classes IgG, IgM, IgA, IgD, or IgE, or fragments or derivatives thereof, including Fab, F(ab')2, Fd, and single chain antibodies, diabodies, bispecific antibodies, and bifunctional antibodies.
• the antibody may be a monoclonal antibody, polyclonal antibody, affinity purified antibody, or mixtures thereof, which exhibits sufficient binding specificity to a desired epitope or a sequence derived therefrom.
• the antibody may also be a chimeric antibody.
• the antibody may be derivatized by the attachment of one or more chemical, peptide, or polypeptide moieties known in the art.
• the antibody may be conjugated with a chemical moiety.
• the antibody may be a human or humanized antibody.
• antibody-like molecules are also within the scope of the present invention.
• Such antibody-like molecules include, e.g., receptor traps (such as entanercept), antibody mimetics (such as adnectins, fibronectin based "addressable” therapeutic binding molecules from, e.g., Compound Therapeutics, Inc.), domain antibodies (the smallest functional fragment of a naturally occurring single-domain antibody (such as, e.g., nanobodies; see, e.g., Cortez-Retamozo et al., Cancer Res. 2004 Apr 15;64(8):2853-7)).
• receptor traps such as entanercept
• antibody mimetics such as adnectins, fibronectin based "addressable” therapeutic binding molecules from, e.g., Compound Therapeutics, Inc.
• domain antibodies the smallest functional fragment of a naturally occurring single-domain antibody (such as, e.g., nanobodies; see, e.g., Cortez
• Suitable antibody mimetics generally can be used as surrogates for the antibodies and antibody fragments described herein. Such antibody mimetics may be associated with advantageous properties (e.g., they may be water soluble, resistant to proteolysis, and/or be nonimmunogenic). For example, peptides comprising a synthetic beta-loop structure that mimics the second complementarity- determining region (CDR) of monoclonal antibodies have been proposed and generated. See, e.g., Saragovi et al., Science. Aug. 16, 1991 ;253(5021 ):792-5.
• CDR complementarity- determining region
• Peptide antibody mimetics also have been generated by use of peptide mapping to determine "active" antigen recognition residues, molecular modeling, and a molecular dynamics trajectory analysis, so as to design a peptide mimic containing antigen contact residues from multiple CDRs. See, e.g., Cassett et al., Biochem Biophys Res Commun. Jul. 18, 2003;307(1 ): 198-205. Additional discussion of related principles, methods, etc., that may be applicable in the context of this invention are provided in, e.g., Fassina, Immunomethods. October 1994;5(2): 121 -9.
• peptide includes targeted proteases, which are capable of, e.g., substrate-targeted inhibition of post-translational modification such as disclosed in, e.g., U.S. Patent Application Publication No. 20060275823.
• Antisense molecules as used herein include antisense or sense oligonucleotides comprising a single-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA (antisense) sequences.
• RNA or DNA single-stranded nucleic acid sequence
• the ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, for example, Stein and Cohen, Cancer Res. 48:2659, (1988) and van der Krol et al., BioTechniques 6:958, (1988).
• Antisense molecules can be modified or unmodified RNA, DNA, or mixed polymer oligonucleotides. These molecules function by specifically binding to matching sequences resulting in inhibition of peptide synthesis (Wu-Pong, November 1994, BioPharm, 20-33) either by steric blocking or by activating an RNase H enzyme. Antisense molecules can also alter protein synthesis by interfering with RNA processing or transport from the nucleus into the cytoplasm (Mukhopadhyay & Roth, 1996, Crit. Rev. in Oncogenesis 7, 151 -190). In addition, binding of single stranded DNA to RNA can result in nuclease-mediated degradation of the heteroduplex (Wu-Pong, supra).
• Backbone modified DNA chemistry which have thus far been shown to act as substrates for RNase H are phosphorothioates, phosphorodithioates, borontrifluoridates, and 2'-arabino and 2'-fluoro arabino- containing oligonucleotides.
• Antisense molecules may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described, e.g., in WO 91/04753.
• Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors.
• conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell.
• a sense or an antisense oligonucleotide may be introduced into a cell containing the target nucleic acid sequence by formation of an oligonucleotide-lipid complex, as described, e.g., in WO 90/10448.
• RNAi small interfering RNA
• siRNA small interfering RNA
• RNAi RNA interference pathway
• siRNA has unpaired overhanging bases on the 5' or 3' end of the sense strand and/or the antisense strand.
• the term "siRNA” includes duplexes of two separate strands, as well as single strands that can form hairpin structures comprising a duplex region.
• siRNA molecules are not limited to RNA molecules but further encompass chemically modified nucleotides and non-nucleotides. siRNA gene-targeting may be carried out by transient siRNA transfer into cells (achieved by such classic methods as liposome-mediated transfection, electroporation, or microinjection).
• the number of stem cells and/or CAR T-cells is increased by a factor of at least 2-fold.
• the number of stem cells and/or CAR T-cells is increased by a factor of at least 2.5 fold, at least 3 fold, at least 3.5 fold, at least 4-fold, such as at least 5-fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold, or more.
• Surprisingly and unexpectedly such levels of stem cell and/or CAR T-cell expansion are achieved using the methods of the present invention.
• the methods of the present invention may be used to expand any population of stem cells.
• the stem cells that may be expanded according to the methods of the present invention may selected from hematopoietic stem cells (HSCs), hematopoietic stem and progenitor cells (HSPCs), endothelial progenitor cells (EPCs), mesenchymal stem cells (MSCs), cardiac stem cells (CSCs), neuronal stem cells (NSCs), and combinations thereof.
• the stem cells are HSCs.
• the stem cells are MSCs.
• the methods of the present invention may also be capable of expanding stem cells such that the expanded cells have at least a 5-fold increase in total colony-forming units (CFU), such as an 8-fold, 10-fold, and even 15-fold or more increase. Further, the methods may be capable of providing an increase in CFU-granulocyte erythrocyte monocyte megakaryocyte (GEMM) colonies of at least 3.8-fold, such as at least 4-fold, 5-fold, and even at least 8-fold or more.
• CFU total colony-forming units
• Another embodiment of the invention is a method for ex vivo expansion of a substantially undifferentiated stem cell population. This method comprises modulating a /V 6 -methyladenosine mRNA modification pathway in the undifferentiated stem cell population to expand the number of undifferentiated stem cells without significant differentiation of the stem cell population.
• a stem cell population is "substantially undifferentiated” if a sufficient number of cells in that population retain the ability to self-renew and can give rise to various differentiated cell types when transplanted into a recipient, for example, in the case of an HSC population, repopulating the HSC lineage when transplanted (or in the case of an MSC population, repopulating the MSC lineage when transplanted).
• "without significant differentiation” means the expanded stem cell population has a sufficient number of cells that maintain a multi-lineage differentiation potential so that the full scope of a target stem lineage may be regenerated upon transplantation of the expanded stem cell population into a recipient.
• the expanded HSC population when transplanted into a recipient, is capable of regenerating the entire hematopoietic cell lineage.
• the expanded MSC population when transplanted into a recipient, is capable of regenerating the entire mesenchymal cell lineage.
• Another embodiment is a method for ex vivo expansion of a chimeric antigen receptor (CAR) T-cell population.
• This method comprises modulating a ⁇ / 6 - Methyladenosine (m 6 A) mRNA modification pathway in the CAR T-cell population to expand the number of CAR T-cells.
• m 6 A Methyladenosine
• a further embodiment of the invention is a method for ex vivo expansion of an hematopoietic stem cell (HSC) population obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow.
• This method comprises modulating a N 6 -methyladenosine mRNA modification pathway in the HSC population to expand the HSC population to a sufficient quantity while maintaining a multilineage differentiation potential in the HSC population, which is sufficient for subsequent transplantation into a subject in need thereof.
• HSC hematopoietic stem cell
• a further embodiment of the invention is a method for ex vivo expansion of a mesenchymal stem cell (MSC) population obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow.
• This method comprises modulating a N 6 -methyladenosine mRNA modification pathway in the MSC population to expand the MSC population to a sufficient quantity while maintaining a multilineage differentiation potential in the MSC population, which is sufficient for subsequent transplantation into a subject in need thereof.
• MSC mesenchymal stem cell
• a further embodiment of the invention is a method for ex vivo expansion of a chimeric antigen receptor (CAR) T-cell population prepared by modifying T-cells obtained from a tissue selected from the group consisting of peripheral blood, cord blood, and bone marrow.
• the method comprising modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the CAR T-cell population to expand the CAR T-cell population to a sufficient quantity which is sufficient for subsequent transplantation into a subject in need thereof.
• CAR chimeric antigen receptor
• tissue obtained from a tissue means any conventional method of harvesting or partitioning tissue from a donor.
• the tissue may be any tissue that contains a stem cell such as an HSC and/or MSC, and/or a T-cell that is capable of being modified with chimeric antigen receptors.
• the tissue may be obtained from a blood sample, such as a peripheral or cord blood sample, or harvested from bone marrow. Methods for obtaining such samples are well known to the artisan.
• the samples may be fresh, i.e., obtained from the donor without freezing.
• the samples may be further manipulated to remove extraneous or unwanted components prior to expansion.
• the samples may also be obtained from a preserved stock.
• the samples may be withdrawn from a cryogenically or otherwise preserved bank of such blood.
• Such samples may be obtained from any suitable donor.
• the donor is a mammal, for example, a primate, such as a human.
• the sample may be obtained from an autologous or allogeneic donor or source.
• the sample is obtained from an autologous source.
• “maintaining a multilineage differentiation potential” means that the expanded HSC and/or MSC population has the ability, when transplanted into a subject in need of such a transplant, to regenerate all the types of progenitor cells e.g., CMP, GMP, MEP, and CLP, and ultimately all the types of blood cells including, e.g., red blood cells, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, basophils, eosinophils, monocytes, macrophages, and platelets in the hematopoietic system.
• progenitor cells e.g., CMP, GMP, MEP, and CLP
• blood cells e.g., red blood cells, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, basophils, eosinophils, monocytes, macrophages, and platelets in the hematopoietic system.
• that quantity of expanded HSCs and/or MSCs and/or CAR T-cells, which is "sufficient for subsequent transplantation" generally corresponds to that number of HSCs and/or MSCs and/or CAR T-cells, which would result in greater than about 1 % engraftment after transplantation.
• This is one accepted measure of a successful transplant.
• any conventional method may be used to determine the % engraftment, including the one set forth in the Examples. Such a measure may be carried out with or without competitor cells, typically and preferably, without competitor cells. (Zhang, C.C., et a/., Nat Med, 12(2): 240-5, 2006. Zhang, C.C. and H.F. Lodish, Blood, 105(11): 4314-20, 2005).
• modulating the ⁇ / 6 - methyladenosine mRNA modification pathway may be achieved as previously set forth.
• Modulating the N 6 -methyladenosine mRNA modification pathway may include introducing a mutation into the stem cells and/or CAR T-cells that results in modulation of a molecule in the m 6 A mRNA modification pathway, or contacting the stem cells and/or CAR T-cells with a modulator of a molecule in the m 6 A mRNA modification pathway selected from the group consisting of a small molecule, a biologic, an antisense RNA, a small interfering RNA (siRNA), and combinations thereof.
• siRNA small interfering RNA
• the modulation of the m 6 A mRNA modification pathway involves modulation of a molecule selected from the group consisting of m 6 A mRNA modification readers, m 6 A mRNA modification writers, m 6 A mRNA modification erasers, and combinations thereof.
• m 6 A modification writers include methyltransferases that are capable of post-transcriptionally installing the m 6 A modification in messenger RNA, and can include any selected from the group consisting of METTL3, METTL14, WTAP, KIAA1429 and combinations thereof.
• Non-limiting examples of m 6 A modification erasers include demethylases that are capable of reversing the methylation, and can include any selected from the group consisting of FTI, ALKBH5 and combinations thereof.
• M 6 A modification readers include proteins that are capable of selectively binding m 6 A-methylated mRNA to exert regulatory functions through selective recognition of methylated mRNA.
• Suitable m 6 A modification readers can include any selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2, HNRNPC, HNRNPA2B1 , elF3 and combinations thereof.
• the m 6 A modification readers comprise proteins of the YTH domain family of proteins, which includes Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2 and combinations thereof, ⁇ see, e.g., Wang et al. Nature, 505(7481 ): 117-120, 2014; Frayling et al. Science, 316: 889-894, 2007; Zheng et al. Mol. Cell., 49: 18-29, 2012; Cao et al. Open Biol., 6(4): 160003, 2016; Maity et al. The FEBS Journal, 283(9): 1607-1630, 2016).
• modulating the m 6 A mRNA modification pathway comprises introducing a mutation into the stem cells and/or CAR-T cells to delete, replace, or reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• the mutation deletes, replaces or reduces expression of a gene that expresses a molecule selected from the group consisting of a m 6 A mRNA modification reader, a m 6 A mRNA modification writer, a m 6 A mRNA eraser, and combinations thereof.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification reader, such as a m 6 A mRNA modification reader selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, HNRNPC, HNRNPA2B1 , elF3, and combinations thereof.
• a m 6 A mRNA modification reader selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, HNRNPC, HNRNPA2B1 , elF3, and combinations thereof.
• the mutation deletes, replaces or reduces expression of a gene that expresses Ythdf2.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification eraser, such as a m 6 A mRNA modification eraser selected from the group consisting of FTO, ALKBH5 and combinations thereof.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification writer, such as a m 6 A mRNA modification writer selected from the group consisting of METTL3, METTL14, WTAP, KIAA1429 and combinations thereof.
• the mutation can be introduced by any of the methods previously disclosed herein.
• the mutation can be introduced by exposing the stem cells and/or CAR T-cells to a Mx1 - Cre targeting system ⁇ see, e.g., Kuhn et al. Science, 269(5229): 1427-1429, 1995) that inactivates or deletes at least a portion of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• a mutation is introduced that incorporates short hairpin RNA (shRNA) into the stem cells and/or CAR T-cells to reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• shRNA short hairpin RNA
• the shRNA may be introduced by exposing the stem cells and/or CAR-T cells to a vector to deliver shRNA, which may be a viral vector such as lentivirus (see, e.g., Chira et al. Oncotarget, 6(31 ): 30675- 30703, 2015).
• the shRNA may be capable of triggering gene silencing to regulate gene expression (see, e.g., Paddison et al. Genes Dev., 16(8): 948-958, 2002).
• modulating of the m 6 A mRNA modification pathway comprises down-regulating and/or inhibiting a member of the m 6 A mRNA modification pathway, such as down- regulating and/or inhibiting a m 6 A mRNA modification reader.
• down-regulating means inhibiting or reducing the amount of or inhibiting or decreasing the activity of a member of the m 6 A mRNA modification pathway.
• Such down-regulation may be accomplished using, e.g. antisense RNA, siRNA, antibodies, or small molecules.
• the m 6 A mRNA modification reader may be down-regulated by contacting the stem cells and/or CAR T-cells with an inhibitor of an m 6 A mRNA reader, to inhibit binding and/or recognizing of the m 6 A modified mRNA by the m 6 A mRNA reader.
• the m 6 A mRNA modification reader that is down-regulated is selected from the group consisting of Ythdf 1 , Ythdf2, Ythdf3, Ythdc1 , Ythdc2, HNRNPC, HNRNPA2B1 , elF3 and combinations thereof.
• the m 6 A mRNA modification reader that is down-regulated is Ythdf2.
• Inhibitors of the m 6 A mRNA modification reader may be any selected from the group consisting of: (inhibitors of HNRNPC) hsa-let-7e-5p (MIRT051596), hsa-mir-455-3p (MIRT037890), hsa-mir-30c-5p (MIRT047904), hsa-mir-186-5p (MIRT045150), hsa- mir-744-5p (MIRT037494), hsa-mir-18a-3p (MIRT040851 ), hsa-mir-484 (MIRT042196), hsa-mir-505-5p (MIRT037959), hsa-mir-615-3p (MIRT039991 ), hsa- mir-342-3p (MIRT043694),
• HNRNPA2B1 hsa-mir-92a-3p
• MIRT049721 hsa-mir- 30c-5p
• MIRT048009 hsa-mir-191 -5p
• MIRT045809 hsa-let-7f-5p
• MIRT051404 hsa-mir-27b-3p
• MIRT046213 hsa-mir-877-3p
• MIRT037116 MIRT037116
• MIRT040278 hsa-mir-1260b
• MIRT052680 hsa-mir-103a-3p
• MIRT027027 hsa- mir-16-5p
• MIRT031508 hsa-mir-1296-5p
• MIRT036075 hsa-mir-197
• MIRT040974 hsa-mir-155-5p (MIRT020771 ), hsa-mir-484 (MIRT042324), hsa-let- 7c-5p (MIRT051776), hsa-miR-3910, hsa-miR-148b, hsa-miR-136, hsa-miR-15a, hsa-miR-488, hsa-miR-500a, hsa-miR-1297, hsa-miR-3159, hsa-miR-374c, hsa- miR-424, hsa-miR-7-1 , hsa-miR-186, hsa-miR-195, hsa-miR-15b, hsa-miR-26b, hsa- miR-505, hsa-miR-1206, hsa-miR
• the stem cell is selected from HSCs, hematopoietic stem and progenitor cells (HSPCs), endothelial progenitor cells, (EPCs), mesenchymal stem cells (MSCs), cardiac stem cells (CSCs), neuronal stem cells (NSCs), and combinations thereof.
• the stem cell is an HSC.
• the stem cell is a MSC.
• the ex vivo expansion methods can also use a population of cells comprising CAR T-cells.
• the HSC and/or MSC is obtained from a mammalian, e.g., primate or human, tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, although any HSC and/or MSC- containing tissue may be used.
• a mammalian e.g., primate or human
• tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, although any HSC and/or MSC- containing tissue may be used.
• the expansion of the number of stem cells is by at least 2-fold, such as e.g., by at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, and including at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, or at least 20-fold or more.
• the expansion of the number of stem cells is by at least 2-fold, such as e.g., by at least 2.5-fold, at least 3-fold, at least 3.5 fold, at least 4-fold, and including at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, or at least 20-fold or more.
• the expansion of the number of CAR T-cells is by at least 2-fold, such as e.g., by at least 2.5-fold, at least 3-fold, at least 3.5 fold, at least 4-fold, and including at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, or at least 20-fold or more.
• Yet another embodiment of the present invention is an expanded, substantially undifferentiated stem cell population made by a method of the present invention, such as, e.g., the method for ex vivo expansion of a substantially undifferentiated stem cell population or the method for ex vivo expansion of an hematopoietic stem cell (HSC) population.
• a method of the present invention such as, e.g., the method for ex vivo expansion of a substantially undifferentiated stem cell population or the method for ex vivo expansion of an hematopoietic stem cell (HSC) population.
• HSC hematopoietic stem cell
• Yet another embodiment of the present invention is an expanded, substantially undifferentiated stem cell population made by a method of the present invention, such as, e.g., the method for ex vivo expansion of a substantially undifferentiated stem cell population or the method for ex vivo expansion of an mesenchymal stem cell (MSC) population.
• a method of the present invention such as, e.g., the method for ex vivo expansion of a substantially undifferentiated stem cell population or the method for ex vivo expansion of an mesenchymal stem cell (MSC) population.
• MSC mesenchymal stem cell
• Yet another embodiment of the present invention is an expanded, CAR T-cell population made by a method of the present invention, such as, e.g., the method for ex vivo expansion of a CAR T-cell population.
• An additional embodiment of the present invention is a method for ex vivo expansion of hematopoietic stem cells (HSCs) by at least 2-fold, wherein the expanded HSCs, are competent to reconstitute an HSC lineage upon transplantation into a mammalian subject in need thereof.
• This method comprises introducing a mutation into the stem cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of HSCs in a suitable culture medium.
• An additional embodiment of the present invention is a method for ex vivo expansion of mesenchymal stem cells (MSCs) by at least 2-fold, wherein the expanded MSCs, are competent to reconstitute a MSC lineage upon transplantation into a mammalian subject in need thereof.
• This method comprises introducing a mutation into the stem cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of HSCs in a suitable culture medium.
• An additional embodiment of the present invention is a method for ex vivo expansion of chimeric antigen receptor (CAR) T-cells by at least 2-fold, wherein the expanded CAR T-cells are competent to treat a cancer and/or blood disorder upon transplantation into a mammalian subject in need thereof.
• This method comprises introducing a mutation into the CAR T-cells that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader and culturing the population of CAR T-cells in a suitable culture medium.
• “competent to reconstitute an HSC lineage” means that the expanded HSCs, when transplanted into a suitable mammalian subject, result in greater than 1 % engraftment in the recipient, which engrafted cells are able to differentiate into the cell lineages necessary to have a normal functioning hematopoietic system.
• “competent to reconstitute a MSC lineage” means that the expanded MSCs, when transplanted into a suitable mammalian subject, result in greater than 1 % engraftment in the recipient, which engrafted cells are able to differentiate into the cell lineages necessary to have a normal functioning hematopoietic system.
• competent to treat a cancer and/or blood disorder means that the expanded CAR T-cells, when transplanted into a suitable mammalian subject, are capable of providing treatment of a cancer and/or blood disorder from which the mammalian subject is suffering, such as for example at least one of leukemia and lymphoma.
• a "suitable culture medium”, “fluid media” and “media” mean physiologically balanced salt solutions that can maintain a stem cell population and/or CAR T-cell population for a required period of time, which solution may optionally be supplemented with suitable m 6 A mRNA modification pathway modulators of the present invention.
• Such base culture media are well known in the arts.
• a non-limiting example of a suitable base culture medium for HSCs is StemSpan Media (Stem Cell Technologies; Cat. No. 09600), which is supplemented with 10ug/ml Heparin, 5X Penicillin/Streptomycin, 10 ng/ml recombinant mouse (rm) Stem Cell Factor, and 20 ng/ml rm-Thrombopoietin.
• the ex vivo expansion of HSCs and/or MSCs and/or CAR T-cells by at least 2-fold can be performed by any of the methods that have been described herein.
• the method may involve introducing a mutation that deletes, replaces or reduces expression of a gene expressing a m 6 A mRNA modification reader, such as Ythdf2.
• the mutation may be introduced by any of the methods described herein, such as by exposing the stem cells and/or CAR T-cells to a Mx1 -Cre targeting system that inactivates or deletes at least a portion of a gene that expresses a m 6 A mRNA modification reader.
• the mutation may also be introduced by incorporating shRNA into the stem cells and/or CAR-T cells to reduce expression of a gene that expresses a m 6 A mRNA modification reader.
• Other methods of introducing a mutation, and mutations that target other m 6 A mRNA modification readers that are described herein may also be provided.
• the HSCs and/or MSCs and/or CAR T-cells are obtained from a mammalian tissue, preferably primate or human tissue, which is selected from cord blood, peripheral blood, and bone marrow.
• the number of HSCs and/or MSCs and/or CAR T-cells is expanded by a factor of at least 2-fold, such as at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, and including at least 5-fold, at least 8-fold, at least 10-fold, at least 15- fold, at least 20-fold or more.
• kits for expanding an hematopoietic stem cell (HSC) population, mesenchymal stem cell (MSC) population, and/or CAR T-cell population for subsequent transplantation into a subject in need thereof comprises a system for introducing a mutation into the HSC, MSC and/or CAR T-cell population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• the system for introducing a mutation into the HSC, MSC and/or CAR-T cell population includes one or more reagents capable of introducing a mutation into the HSC, MSC and/or CAR-T cell population that results in deletion, replacement or reduced expression of a gene expressing Ythdf2.
• the kit can include a system for introducing a mutation into the HSC, MSC and/or CAR-T cell population that comprises a Mx1 -Cre targeting system that inactivates or deletes at least a portion of a gene that expresses a m 6 A mRNA modification reader.
• the kit can also include a system for introducing a mutation into the HSC, MSC and/or CAR T-cell population that comprises reagents for delivering a lentivirus that incorporates shRNA into the HSC, MSC and/or CAR T-cell population to reduce expression of a gene that expresses a m 6 A mRNA modification reader.
• the kit may further comprise other systems/methods set forth herein for introducing the mutation to modulate a m 6 A mRNA modification pathway, such as by deleting, replacing, or reducing expression of a gene expressing a m 6 A mRNA modification reader, including Ythdf2.
• the kit and the components therein may be packaged in any suitable manner for distribution and/or storage.
• kits for expanding an hematopoietic stem cell population (HSC) population and/or mesenchymal stem cell (MSC) population and/or CAR-T cell population for subsequent transplantation into a subject in need thereof comprises an inhibitor of a m 6 A mRNA modification reader, and instructions for use thereof, where the inhibitor may be any of the inhibitors disclosed herein, such as, e.g., an inhibitor of Ythdf2.
• kits may be able to provide an expansion of the number of stem cells and/or CAR T-cells by a factor selected from the group consisting of at least 2-fold, at least 2.5 fold, at least 3-fold, at least 3.5- fold, at least 4-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• a further embodiment of the present invention is a method for administering an hematopoietic stem cell (HSC) to a subject in need thereof.
• the method comprises (a) introducing, into a sample containing an HSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the HSCs to the subject.
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the HSC population that reduces expression of a gene expressing Ythdf2.
• the HSCs may be obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof.
• the method comprises (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• MSC mesenchymal stem cell
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the MSC population that reduces expression of a gene expressing Ythdf2.
• the MSCs may be obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for administering a chimeric antigen receptor (CAR) T-cell to a subject in need thereof.
• the method comprises (a) introducing, into a sample containing a CAR T-cell population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of CAR T- cells in the sample to a number sufficient to transplant into the subject; and (c) administering the CAR T-cells to the subject.
• CAR chimeric antigen receptor
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the CAR T-cell population that reduces expression of a gene expressing Ythdf2.
• the CAR T-cells may be obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for administering an hematopoietic stem cell (HSC) to a subject in need thereof.
• the method comprises: (a) culturing, in a suitable culture media, a sample containing an HSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the HSCs to the subject.
• the inhibitor is as previously disclosed, such as, e.g., an inhibitor of Ythdf2.
• the HSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof.
• the method comprises: (a) culturing, in a suitable culture media, a sample containing an MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• the inhibitor is as previously disclosed, such as, e.g., an inhibitor of Ythdf2.
• the MSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for administering a chimeric antigen receptor (CAR) T-cell to a subject in need thereof.
• the method comprises: (a) culturing, in a suitable culture media, a sample containing an CAR T-cell population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of CAR T- cells in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the CAR T-cells to the subject.
• the inhibitor is as previously disclosed, such as, e.g., an inhibitor of Ythdf2.
• the CAR T- cells may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow
• the subject may be a mammal, such as a human.
• An additional embodiment of the present invention is a method for reconstituting bone marrow in a subject in need thereof.
• the method comprises (a) introducing, into a sample containing an HSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the HSCs to the subject.
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the HSC population that reduces expression of a gene expressing Ythdf2.
• the HSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• An additional embodiment of the present invention is a method for reconstituting bone marrow in a subject in need thereof.
• the method comprises (a) introducing, into a sample containing a MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; and (c) administering the MSCs to the subject.
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the MSC population that reduces expression of a gene expressing Ythdf2.
• the MSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• An additional embodiment of the present invention is a method for treating cancer and/or a blood disorder in a subject in need thereof.
• the method comprises (a) introducing, into a sample containing a CAR T-cell population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader; (b) culturing the sample in a suitable culture media for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; and (c) administering the CAR T-cells to the subject.
• the method of introducing the mutation, and the mutation targeted at the m 6 A mRNA modification reader are as previously disclosed, such as, for example, a mutation that results in deletion of a gene expressing Ythdf2, or a mutation that results in incorporation of shRNA into the CAR T-cell population that reduces expression of a gene expressing Ythdf2.
• the CAR T-cells may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• a method for reconstituting bone marrow in a subject in need thereof comprises (a) culturing, in a suitable culture media, a sample containing an HSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of HSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the HSCs to the subject.
• the inhibitor is as previously disclosed, such as an inhibitor of Ythdf2.
• the HSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• this method comprises (a) culturing, in a suitable culture media, a sample containing an MSC population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the MSCs to the subject.
• the inhibitor is as previously disclosed, such as an inhibitor of Ythdf2.
• the MSCs may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• “reconstituting bone marrow” means restoration of all or a portion of the bone marrow in a subject suffering from a disease in which normal bone marrow function has been compromised.
• diseases include blood disorders such as aplastic anemia, myelodysplastic syndromes (MDS), paroxysmal nocturnal hemoglobinuria (PNH), and blood cancers, such as leukemia.
• reconstituted means that the transplanted HSCs and/or MSCs are able to successfully engraft in the host and differentiate into all the cell lineages typically found in or derived from bone marrow.
• aspects of the methods herein may involve transplantation of HSCs and/or MSCs obtained from tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, to the subject, for the treatment of blood disorders such as leukemia and lymphoma.
• transplantation of HSCs and/or MSCs obtained from tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow to the subject, for the treatment of blood disorders such as leukemia and lymphoma.
• This method comprises (a) culturing, in a suitable culture media, a sample containing a chimeric antigen receptor (CAR) T-cell population in the presence of an inhibitor of a m 6 A mRNA modification reader, for a period of time sufficient to expand the number of CAR T-cells in the sample to a number sufficient to transplant into the subject; (b) removing from the culture the inhibitor of the m 6 A mRNA modification reader; and (c) administering the CAR T-cells to the subject.
• the inhibitor is as previously disclosed, such as an inhibitor of Ythdf2.
• the T-cells that are modified to prepare the CAR T-cells may be obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow, and the subject may be a mammal, such as a human.
• tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow
• the subject may be a mammal, such as a human.
• treating cancer and/or a blood disorder in a subject means eradicating cancer cells, alleviating symptoms, or otherwise reducing a disease state in a subject suffering from the cancer and/or blood disorder.
• cancers and/or blood disorders include blood disorders such as aplastic anemia, myelodysplastic syndromes (MDS), paroxysmal nocturnal hemoglobinuria (PNH), and blood cancers, such as leukemia and lymphoma.
• a period of time sufficient to expand the number of HSCs means the minimum amount of time to expand the HSCs in culture to a point where there is a sufficient number of HSCs for one or more transplantations
• a period of time sufficient to expand the number of MSCs means the minimum amount of time to expand the MSCs in culture to a point where there is a sufficient number of MSCs for one or more transplantations
• a period of time sufficient to expand the number of CAR T-cells means the minimum amount of time to expand the CAR T-cells in culture to a point where there is a sufficient number of CAR T-cells for one or more transplantations.
• such a period of time may be at least about 10 days in culture.
• the excess cells may be preserved for later use by any conventional method, such as e.g., by cryo- preservation.
• a number sufficient to transplant means the minimum number of stem cells, e.g., HSCs and/or MSCs and/or CAR T-cells, necessary to achieve greater than 1 % engraftment in a recipient.
• administering the HSCs to the subject means conventional methods for delivering HSCs to the subject, including but not limited to, delivering the HSCs surgically and/or intravenously.
• administering the MSCs to the subject means conventional methods for delivering MSCs to the subject, including but not limited to, delivering the MSCs surgically and/or intravenously.
• administering the CAR T-cells to the subject means conventional methods for delivering CAR T-cells to the subject, including but not limited to, delivering the MSCs surgically and/or intravenously.
• the tissue the HSCs and/or MSCs and/or T-cells are obtained from, and the m 6 A mRNA modification reader inhibitors are as previously disclosed.
• An additional embodiment of the present invention is a method for expanding a population of hematopoietic stem cells (HSCs). This method comprises culturing a population of HSCs under conditions sufficient to result in an expansion of the HSC population by at least 2-fold, wherein the expanded population of HSCs is suitable for transplantation into a mammal in need thereof.
• HSCs hematopoietic stem cells
• the "conditions sufficient to result in an expansion of the HSC population” are those conditions that can result in expansion of HSCs in culture by, e.g., at least 2-fold, such as, e.g., by at least 2.5-fold, at least 3-fold, at least 3.5 fold, at least 4-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• "Suitable for transplantation into a mammal” means that the number and quality of HSCs is sufficient to support greater than 1 % engraftment in a mammalian recipient, such as, e.g., a primate recipient, including an human recipient, in need thereof.
• An additional embodiment of the present invention is a method for expanding a population of mesenchymal stem cells (MSCs). This method comprises culturing a population of MSCs under conditions sufficient to result in an expansion of the MSC population by at least 2-fold, wherein the expanded population of MSCs is suitable for transplantation into a mammal in need thereof.
• MSCs mesenchymal stem cells
• the "conditions sufficient to result in an expansion of the MSC population” are those conditions that can result in expansion of MSCs in culture by, e.g., at least 2-fold, such as, e.g., by at least 2.5-fold, at least 3-fold, at least 3.5 fold, at least 4-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• "Suitable for transplantation into a mammal” means that the number and quality of MSCs is sufficient to support greater than 1 % engraftment in a mammalian recipient, such as, e.g., a primate recipient, including an human recipient, in need thereof.
• An additional embodiment of the present invention is a method for expanding a population of chimeric antigen receptor (CAR) T-cells. This method comprises culturing a population of CAR T-cells under conditions sufficient to result in an expansion of the CAR T-cell population by at least 2-fold, wherein the expanded population of CAR T-cells is suitable for transplantation into a mammal in need thereof.
• CAR chimeric antigen receptor
• the "conditions sufficient to result in an expansion of the CAR T-cell population” are those conditions that can result in expansion of CAR T-cells in culture by, e.g., at least 2-fold, such as, e.g., by at least 2.5-fold, at least 3-fold, at least 3.5 fold, at least 4-fold, at least 5-fold, at least 8-fold, at least 10- fold, at least 15-fold, at least 20-fold or more.
• Suitable for transplantation into a mammal means that the number and quality of CAR T-cells is sufficient to support greater than 1 % engraftment in a mammalian recipient, such as, e.g., a primate recipient, including an human recipient, in need thereof.
• Yet another embodiment of the present invention is a method for treating a subject in need of a bone marrow transplant, a peripheral blood transplant, or a cord blood transplant comprising administering to the subject a population of HSCs obtained by a method disclosed herein, particularly the methods for expanding a population of hematopoietic stem cells (HSCs).
• the subject may be a mammal, such as a human.
• Yet another embodiment of the present invention is a method for treating a subject in need of a bone marrow transplant, a peripheral blood transplant, or a cord blood transplant comprising administering to the subject a population of MSCs obtained by a method disclosed herein, particularly the methods for expanding a population of mesenchymal stem cells (MSCs).
• the subject may be a mammal, such as a human.
• Yet another embodiment of the present invention is a method for treating a subject suffering from cancer and/or a blood disorder, comprising administering to the subject a population of CAR T-cells obtained by a method disclosed herein, particularly the methods for expanding a population of CAR T-cells.
• the subject may be a mammal, such as a human.
• a further embodiment of the present invention is a method for expanding a population of hematopoietic stem cells (HSCs).
• the method comprises (a) obtaining from a mammal a tissue sample comprising an HSC population; (b) expanding, in vitro, the HSC population from the sample, wherein (i) the HSC population expands by at least 2-fold; and (ii) the expanded HSC population has at least a 5-fold increase in total colony forming units.
• the HSC population expands by at least 4-fold, such as e.g., at least 5- fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• the mammal is a primate, including a human.
• the human requires a peripheral blood transplant, a cord blood transplant, or a bone marrow transplant.
• the tissue sample is obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• a further embodiment of the present invention is a method for expanding a population of mesenchylam stem cells (MSCs).
• the method comprises (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein (i) the MSC population expands by at least 2-fold.
• the MSC population expands by at least 2.5-fold, such as at least 3-fold, at least 3.5 fold, at least 4-fold, such as e.g., at least 5-fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• the mammal is a primate, including a human.
• the human requires a peripheral blood transplant, a cord blood transplant, or a bone marrow transplant.
• the tissue sample is obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• a further embodiment of the present invention is a method for expanding a population of chimeric antigen receptor (CAR) T-cells.
• the method comprises (a) obtaining from a mammal a tissue sample comprising a T-cell population; (b) modifying the T-cell population with chimeric antigen receptors to provide CAR T-cell population; (c) expanding, in vitro, the CAR T-cell population from the sample, wherein (i) the CAR T-cell population expands by at least 2-fold.
• CAR chimeric antigen receptor
• the CAR T-cell population expands by at least 2.5- fold, such as at least 3-fold, at least 3.5 fold, at least 4-fold, such as e.g., at least 5- fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more.
• the mammal is a primate, including a human.
• the human is suffering from a cancer and/or a blood disorder.
• the tissue sample is obtained from any appropriate tissue, such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• An additional embodiment of the present invention is a method for reconstituting an hematopoietic stem cell lineage in a recipient in need thereof.
• the method comprises (a) obtaining from a mammal a tissue sample comprising an HSC population; (b) expanding, in vitro, the HSC population from the sample, wherein: (i) the HSC population expands by at least 2-fold, such as for example, by at least 4- fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more, and (ii) the expanded HSC population has at least at 5-fold increase in total colony forming units; and (c) transplanting the expanded HSC population into a subject in need thereof, such as a mammal, including a primate or human.
• the human recipient requires a peripheral blood transplant, a cord blood transplant or a bone marrow transplant.
• the tissue sample is obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• the sample may be obtained from an autologous or allogeneic source.
• the sample is obtained from an autologous source.
• An additional embodiment of the present invention is a method for reconstituting a mesenchymal stem cell (MSC) lineage in a recipient in need thereof.
• the method comprises (a) obtaining from a mammal a tissue sample comprising a MSC population; (b) expanding, in vitro, the MSC population from the sample, wherein: (i) the MSC population expands by at least 2-fold, such as for example, by at least 4-fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20- fold or more; and (c) transplanting the expanded MSC population into a subject in need thereof, such as a mammal, including a primate or human.
• MSC mesenchymal stem cell
• the human recipient requires a peripheral blood transplant, a cord blood transplant or a bone marrow transplant.
• the tissue sample is obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• the sample may be obtained from an autologous or allogeneic source.
• the sample is obtained from an autologous source.
• An additional embodiment of the present invention is a method for treating a subject suffering from cancer and/or a blood disorder.
• the method comprises (a) obtaining from a mammal a tissue sample comprising a T-cell population; (b) modifying the T-cell population with a chimeric antigen receptor (CAR) to form a CAR T-cell population; (c) expanding, in vitro, the CAR T-cell population from the sample, wherein: (i) the CAR T-cell population expands by at least 2-fold, such as for example, by at least 4-fold, including at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold or more; and (c) transplanting the expanded CAR-T cell population into a subject in need thereof, such as a mammal, including a primate or human.
• CAR chimeric antigen receptor
• the human recipient may be suffering from, e.g., leukemia and/or lymphoma.
• the tissue sample is obtained from any appropriate tissue such as, e.g., a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• the sample may be obtained from an autologous or allogeneic source.
• the sample is obtained from an autologous source.
• the expanded HSC population comprises HSCs that have a phenotype selected from the group consisting of CD34 " or CD34 + /CD38 "/low /Thy-1 + /CD90 + /Kit "/lo /Lin7CD133 + VEGFR2 + , which are markers for the most primitive and long-term undifferentiated human HSCs; CD150 + /CD487CD244 " , which is a marker for human HSCs and their progenitors; and/or CD1507CD487CD244 + and CD1507CD48 + /CD244 + , which are markers for non-self-renewing multipotent hematopoietic progenitors, and combinations thereof.
• a phenotype selected from the group consisting of CD34 " or CD34 + /CD38 "/low /Thy-1 + /CD90 + /Kit "/lo /Lin7CD133 + VEGFR2 + , which are markers for the most primitive and long-
• the expanded MSC population and/or MSC population subject to expansion comprises MSCs that have a phenotype selected from the group consisting of N- cadherin+ and CD105+, and combinations thereof. That is, the MSC population of any of the embodiments described herein can comprise at least one MSC selected from the group consisting of N-cadherin+ MSCs and CD105+ MSCs. In one embodiment, the MSC population comprises N-cadherin+ MSCs.
• HSCs and/or MSCs having these markers in the population is not critical, so long as the expanded HSC and/or MSC population as a whole is sufficient to result in at least 1 % engraftment in a recipient.
• the invention is a method for expanding a hematopoietic stem cell population in a mammal in need of such expansion.
• This method comprises administering to the mammal a therapeutically effective amount of a modulator of a N 6 -methyladenosine (m 6 A) mRNA modification pathway, for a period of time sufficient to expand the HSC population by at least 2-fold with HSCs that possess the ability to reconstitute an hematopoietic lineage in the mammal.
• m 6 A N 6 -methyladenosine
• the invention is a method for expanding a mesenchymal stem cell population in a mammal in need of such expansion.
• This method comprises administering to the mammal a therapeutically effective amount of a modulator of a N 6 -methyladenosine (m 6 A) mRNA modification pathway, for a period of time sufficient to expand the MSC population by at least 2-fold with MSCs that possess the ability to reconstitute a mesenchymal lineage in the mammal.
• m 6 A N 6 -methyladenosine
• the invention is a method for expanding a chimeric antigen receptor (CAR) T-cell population in a mammal in need of such expansion.
• This method comprises administering to the mammal a therapeutically effective amount of a modulator of a N 6 -methyladenosine (m 6 A) mRNA modification pathway, for a period of time sufficient to expand the CAR T-cell population by at least 2-fold with CAR T-cells that possess the ability to treat cancer and/or a blood disorder in the mammal.
• the modulators may be as previously disclosed herein, and/or modulation may be performed by any method disclosed herein.
• the modulator may comprise a system for introducing a mutation into the HSC and/or MSC and/or CAR T-cell population that deletes, replaces or reduces expression of a gene expressing a N 6 -methyladenosine (m 6 A) mRNA modification reader, such as Ythdf2.
• the modulator may comprise an inhibitor of a N6-methyladenosine (m6A) mRNA modification reader, such as an inhibitor of Ythdf2.
• the mammal in need of expansion may be a human.
• the invention includes a method of isolating mesenchymal stem cells (MSCs) from a biological sample, the method comprising contacting the biological sample having a population of MSCs with one or more N- cadherin antibodies.
• MSCs mesenchymal stem cells
• the biological sample comprises a tissue selected from the group consisting of peripheral blood, cord blood and bone marrow.
• the method of isolating the MSCs can further comprise one or more steps of expanding the population of MSCs from the biological sample, by modulating a N 6 -Methyladenosine (m 6 A) mRNA modification pathway in the population of MSCs, to expand the number of mesenchymal stem cells, such as by any of the methods described herein.
• the population of MSCs is expanded after isolating from the biological sample.
• the population of MSCs in the biological sample is expanded before isolation of the MSCs from the biological sample.
• the MSC population is expanded to a sufficient quantity while maintaining a multilineage differentiation potential in the MSC population, which is sufficient for subsequent transplantation into a subject in need thereof, such that the MSCs isolated by the method can be used for such transplantation.
• the isolated MSCs may be transplanted into a human subject.
• the MSCs may be further isolated from the biological sample by contacting with CD105 antibodies, either in addition to or as an alternative to the N-cadherin antibodies.
• the N-cadherin antibodies may be used to identify the MSCs in the biological sample, by contacting the biological sample with the N-cadherin antibodies and detecting those cells that bind to the N- cadherin antibodies.
• the method of isolating the MSCs comprises expanding the MSC population, by modulating the m 6 A mRNA modification pathway by introducing a mutation into the stem cells that results in modulation of a molecule in the m 6 A mRNA modification pathway or contacting the stem cell with a modulator of a molecule in the m 6 A mRNA modification pathway selected from the group consisting of a small molecule, a biologic, an antisense RNA, a small interfering RNA (siRNA), and combinations thereof, such as by any of the modulation methods described herein.
• a modulator of a molecule in the m 6 A mRNA modification pathway selected from the group consisting of a small molecule, a biologic, an antisense RNA, a small interfering RNA (siRNA), and combinations thereof, such as by any of the modulation methods described herein.
• modulating the m 6 A mRNA modification pathway comprises introducing a mutation into the stem cells to delete, replace, or reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• the mutation deletes, replaces or reduces expression of a gene that expresses a molecule selected from the group consisting of a m 6 A mRNA modification reader, a m 6 A mRNA modification writer, and a m 6 A mRNA eraser.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification reader.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification reader selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2, HNRNPC, HNRNPA2B1 , and elF3.
• the mutation deletes, replaces or reduces expression of a gene that expresses Ythdf2.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification eraser.
• the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification eraser selected from the group consisting of FTO and ALKBH5. In another embodiment, the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification writer. In one embodiment, the mutation deletes, replaces or reduces expression of a gene that expresses a m 6 A mRNA modification writer selected from the group consisting of METTL3, METTL14, WTAP and KIAA1429.
• the method of isolating MSCs comprises expanding the population of MSCS by modulating the m 6 A mRNA modification pathway, by exposing the stem cells to a Mx1 -Cre targeting system that inactivates or deletes at least a portion of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• modulating the m 6 A mRNA modification pathway comprises introducing a mutation that incorporates shRNA into the stem cells to reduce expression of a gene that expresses a molecule in the m 6 A mRNA modification pathway.
• the shRNA is introduced by exposing the stem cells to a lentivirus to deliver the shRNA.
• modulating the m 6 A mRNA modification pathway comprises down-regulating a m 6 A mRNA modification reader.
• the m 6 A mRNA modification reader is selected from the group consisting of Ythdfl , Ythdf2, Ythdf3, Ythdc1, Ythdc2, HNRNPC, HNRNPA2B1 , and elF3.
• the m 6 A mRNA modification reader comprises Ythdf2.
• the method of isolating MSCs further comprise expanding the population of MSCs by down-regulating the m 6 A mRNA modification reader, by contacting the stem cells with an inhibitor of the m 6 A mRNA modification reader that is any of those described herein, such as any of those selected from the group consisting of: (inhibitors of HNRNPC) hsa-let-7e-5p (MIRT051596), hsa-mir- 455-3p (MIRT037890), hsa-mir-30c-5p (MIRT047904), hsa-mir-186-5p (MIRT045150), hsa-mir-744-5p (MIRT037494), hsa-mir-18a-3p (MIRT040851 ), hsa- mir-484 (MIRT042196), hsa-mir-505-5p (MIRT037959), hsa-mir-615-3p (MIRT039991 ), hsa-mir-3
• the invention comprises an isolated population of mesenchymal stem cells made by any of the processes described herein.
• the invention in certain embodiments can comprise an expanded, isolated population of mesenchymal stem cells made by any of the expansion and/or isolation processes described herein.
• kits for isolating a mesenchymal stem cell (MSC) population for subsequent transplantation into a subject in need thereof comprises a system for contacting a biological sample comprising MSCs with one or more N-cadherin antibodies, and instructions for use thereof.
• the kit further comprises a system for expanding the population of MSCs by introducing a mutation into the MSC population that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and instructions for use thereof.
• the system for introducing a mutation into the MSC population includes one or more reagents capable of introducing a mutation into the MSC population that results in deletion, replacement or reduced expression of a gene expressing Ythdf2.
• the system for introducing a mutation into the MSC population comprises a Mx1 -Cre targeting system that inactivates or deletes at least a portion of a gene that expresses a m 6 A mRNA modification reader.
• the system for introducing a mutation into the MSC population comprises reagents for delivering a lentivirus that incorporates shRNA into the MSC population to reduce expression of a gene that expresses a m 6 A mRNA modification reader.
• a method for administering a mesenchymal stem cell (MSC) to a subject in need thereof comprises isolating MSCs from a biological sample comprising a population of MSCs, by contacting the biological sample with one or more N-cadherin antibodies, and administering the isolated MSCs to the subject.
• MSC mesenchymal stem cell
• the method further comprises introducing, into the biological sample containing the MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and culturing the biological sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject.
• the mutation results in deletion a gene expressing Ythdf2.
• the mutation results in incorporation of shRNA into the HSC population that reduces expression of a gene expressing Ythdf2.
• the MSCs are obtained from a biological sample comprising a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• a method for reconstituting bone marrow in a subject in need thereof comprises isolating mesenchymal stem cells (MSCs) from a biological sample comprising a population of MSCs, by contacting the biological sample with one or more N-cadherin antibodies, and administering the isolated MSCs to the subject.
• MSCs mesenchymal stem cells
• the method further comprises introducing, into the biological sample containing the MSC population, a mutation that results in deletion, replacement or reduced expression of a gene expressing a m 6 A mRNA modification reader, and culturing the sample in a suitable culture media for a period of time sufficient to expand the number of MSCs in the sample to a number sufficient to transplant into the subject.
• the MSCs are obtained from a biological sample comprising a tissue selected from the group consisting of cord blood, peripheral blood, and bone marrow.
• a method for treating a subject in need of a transplant selected from the group consisting of a bone marrow transplant, a peripheral blood transplant and an umbilical cord blood transplant comprising administering to the subject a population of isolated MSCs obtained by any of the methods described herein.
• the sample is from an autologous or allogeneic source.
• the sample is from an autologous source.
• a “therapeutically effective amount” is an amount sufficient to effect beneficial or desired results.
• a “therapeutically effective amount” of a modulator and/or expanded cells is an amount sufficient to treat, manage, palliate, ameliorate, or stabilize a condition, such as a bone marrow disease, in the mammal.
• a therapeutically effective amount can be administered in one or more doses.
• the therapeutically effective amount is generally determined by a physician on a case-by-case basis and is within the skill of one in the art. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the subject, the condition being treated, the severity of the condition and the form of the drug being administered.
• Effective dosage forms, modes of administration, and dosage amounts may be determined empirically, and making such determinations is within the skill of the art. It is understood by those skilled in the art that the dosage amount will vary with the route of administration, the rate of excretion, the duration of the treatment, the identity of any other drugs being administered, the age, size, and species of animal, and like factors well known in the arts of medicine and veterinary medicine.
• a suitable dose of a modulator according to the invention will be that amount of the modulator, which is the lowest dose effective to produce the desired effect.
• the effective dose of a modulator maybe administered as two, three, four, five, six or more sub-doses, administered separately at appropriate intervals throughout the day.
• a modulator may be administered in any desired and effective manner: as pharmaceutical compositions for oral ingestion, or for parenteral or other administration in any appropriate manner such as intraperitoneal, subcutaneous, topical, intradermal, inhalation, intrapulmonary, rectal, vaginal, sublingual, intramuscular, intravenous, intraarterial, intrathecal, or intralymphatic. Further, a modulator of the present invention may be administered in conjunction with other treatments. A modulator of the present invention maybe encapsulated or otherwise protected against gastric or other secretions, if desired.
• a modulator of the invention While it is possible for a modulator of the invention to be administered alone, it is preferable to administer the modulator as a pharmaceutical formulation (composition).
• Such pharmaceutical formulations typically comprise one or more modulators as an active ingredient in admixture with one or more pharmaceutically- acceptable carriers and, optionally, one or more other compounds, drugs, ingredients and/or materials.
• the modulator of the present invention may be formulated into pharmaceutically- acceptable dosage forms by conventional methods known to those of skill in the art. See, e.g., Remington's Pharmaceutical Sciences (Mack Publishing Co., Easton, Pa.).
• Pharmaceutically acceptable carriers are well known in the art (see, e.g., Remington's Pharmaceutical Sciences (Mack Publishing Co., Easton, Pa.) and The National Formulary (American Pharmaceutical Association, Washington, D.C.)) and include sugars ⁇ e.g., lactose, sucrose, mannitol, and sorbitol), starches, cellulose preparations, calcium phosphates (e.g. , dicalcium phosphate, tricalcium phosphate and calcium hydrogen phosphate), sodium citrate, water, aqueous solutions (e.g.
• saline sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection
• alcohols e.g. , ethyl alcohol, propyl alcohol, and benzyl alcohol
• polyols e.g., glycerol, propylene glycol, and polyethylene glycol
• organic esters e.g. , ethyl oleate and triglycerides
• biodegradable polymers e.g. , polylactide-polyglycolide, poly(orthoesters), and poly(anhydrides)
• elastomeric matrices e.g., liposomes, microspheres, oils (e.g.
• Each pharmaceutically acceptable carrier used in a pharmaceutical composition comprising a modulator of the invention must be "acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject.
• Carriers suitable for a selected dosage form and intended route of administration are well known in the art, and acceptable carriers for a chosen dosage form and method of administration can be determined using ordinary skill in the art.
• compositions comprising a modulator of the invention may, optionally, contain additional ingredients and/or materials commonly used in pharmaceutical compositions.
• these ingredients and materials are well known in the art and include (1 ) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and silicic acid; (2) binders, such as carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, hydroxypropylm ethyl cellulose, sucrose and acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, sodium starch glycolate, cross-linked sodium carboxymethyl cellulose and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as cetyl alcohol and
• compositions suitable for oral administration may be in the form of capsules, cachets, pills, tablets, powders, granules, a solution or a suspension in an aqueous or non-aqueous liquid, an oil-in-water or water-in-oil liquid emulsion, an elixir or syrup, a pastille, a bolus, an electuary or a paste.
• These formulations may be prepared by methods known in the art, e.g., by means of conventional pan-coating, mixing, granulation or lyophilization processes.
• Solid dosage forms for oral administration may be prepared by mixing the active ingredient(s) with one or more pharmaceutically-acceptable carriers and, optionally, one or more fillers, extenders, binders, humectants, disintegrating agents, solution retarding agents, absorption accelerators, wetting agents, absorbents, lubricants, and/or coloring agents.
• Solid compositions of a similar type maybe employed as fillers in soft and hard-filled gelatin capsules using a suitable excipient.
• a tablet may be made by compression or molding, optionally with one or more accessory ingredients.
• Compressed tablets may be prepared using a suitable binder, lubricant, inert diluent, preservative, disintegrant, surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine.
• the tablets, and other solid dosage forms, such as dragees, capsules, pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein. They may be sterilized by, for example, filtration through a bacteria-retaining filter.
• compositions may also optionally contain opacifying agents and may be of a composition such that they release the active ingredient only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner.
• the active ingredient can also be in microencapsulated form.
• Liquid dosage forms for oral administration include pharmaceutically- acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
• the liquid dosage forms may contain suitable inert diluents commonly used in the art.
• the oral compositions may also include adjuvants, such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.
• Suspensions may contain suspending agents.
• compositions for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more active ingredient(s) with one or more suitable nonirritating carriers which are solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.
• Pharmaceutical compositions which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such pharmaceutically-acceptable carriers as are known in the art to be appropriate.
• Dosage forms for the topical or transdermal administration include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches, drops and inhalants.
• the active compound may be mixed under sterile conditions with a suitable pharmaceutically-acceptable carrier.
• the ointments, pastes, creams and gels may contain excipients.
• Powders and sprays may contain excipients and propellants.
• compositions suitable for parenteral administrations comprise one or more modulator in combination with one or more pharmaceutically- acceptable sterile isotonic aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain suitable antioxidants, buffers, solutes which render the formulation isotonic with the blood of the intended recipient, or suspending or thickening agents.
• Proper fluidity can be maintained, for example, by the use of coating materials, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
• compositions may also contain suitable adjuvants, such as wetting agents, emulsifying agents and dispersing agents. It may also be desirable to include isotonic agents. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption.
• the rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form.
• delayed absorption of a parenterally-administered drug may be accomplished by dissolving or suspending the drug in an oil vehicle.
• injectable depot forms may be made by forming microencapsule matrices of the active ingredient in biodegradable polymers. Depending on the ratio of the active ingredient to polymer, and the nature of the particular polymer employed, the rate of active ingredient release can be controlled. Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue. The injectable materials can be sterilized for example, by filtration through a bacterial-retaining filter.
• the formulations may be presented in unit-dose or multi-dose sealed containers, for example, ampules and vials, and may be stored in a lyophilized condition requiring only the addition of the sterile liquid carrier, for example water for injection, immediately prior to use.
• sterile liquid carrier for example water for injection
• Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the type described above.
• Ythdf2 a well-recognized m 6 A reader promoting targeted mRNA decay (Wang et al. Blood, 505: 17-120, 2014), at least partly with the purpose of investigating its role in the context of HSC maintenance. Without being limited to any particular theory, it is believed that manipulation of Ythdf2 might potentially influence the life span of a great number m 6 A-marked mRNAs, thus impacting adult HSC self-renewal versus differentiation and facilitating HSC expansion. As shown in the examples below, Ythdf2 depletion specifically expands mouse and human HSCs without skewing lineage fate. Accordingly, it is believed that Ythdf2 may play an essential role in regulating HSC self-renewal, and provide a novel approach to enhance hUCB HSCs ex vivo expansion, including in clinical applications.
• the exmaples also show functional definition of the drug-resistant rHSC population, and a finding that rHSCs are maintained in the endosteal niche largely by N-cad + cells during homeostasis and under chemotherapeutic stress. It is further shown that N-cad + cells in endosteal zone are mesenchymal stem cells and contribute to rHSC maintenance.
• mice were generated by Chuan He and Bin Shen group. Mice were housed in the animal facility at Stowers Institute for Medical Research (SIMR) and handled according to Institute and NIH guidelines. All procedures were approved by the IACUC of SIMR.
• SIMR Stowers Institute for Medical Research
• Mouse HSPCs, progenitors, and lineage cells were harvested from BM (femur and tibia) and spleen. Red blood cells were lysed using a 0.16 M ammonium chloride solution, and the cells were filtered with 70 ⁇ m strainers to generate single cell suspensions.
• mice HSC identification cells were stained with antibodies against Sca-1 (D7), c-Kit (2B8), CD34 (RAM34), Flk2 (A2F10), CD48 (HM48-1 ), CD150 (TC15-12F12.2), together with lineage cocktail including CD3 (145-2C11), CD4 (RM4-5), CD8 (53-6.7), Mac-1 (M1/70), Gr1 (RB6-8C5), CD45R (B220, RA3-6B2), IgM (11-41 ) and Ter119 (TER- 119).
• progenitors and lineage cells cells were stained with antibodies as previously described (Qian, P. et al. Cell Stem Cell, 18:214-228, 2016, doi: 10.1016/j. stem.2015.11.001 ).
• 7-aminoactinomycin D (A1310, Life technologies) was used to exclude dead cells.
• Human cord blood samples were acquired from the St. Louis Cord Blood Bank. Mononuclear cells were isolated with LymphoprepTM (StemCell technologies), followed by isolation of human CD34 + cord blood cells by human CD34 MicroBead Kit UltraPure (Miltenyi Biotec).
• LymphoprepTM StemCell technologies
• CD34 MicroBead Kit UltraPure Miltenyi Biotec
• To quantify human HSPCs cells were stained with antibodies against CD34 (581 ), CD38 (HIT2), CD45RA (HI100), CD90 (5E10), CD49f (GoH3), EPCR/CD201 (RCR-401 ). Cell sorting and analyses were performed on MoFlo (Dako), InFlux Cell Sorter (BD Biosciences), and/or MACSQuant (Miltenyi Biotec). Data analysis was performed using FlowJo software.
• Baytril water was given to recipient mice three days before irradiation and continued for another two weeks after irradiation.
• Primary and secondary CRU frequencies were measured using ELDA software (Hu et al. Journal of Immunological Methods, 347: 70-78, 2009), in which successful engraftment was defined as the presence of a distinct CD45.2 + CD45.1 " population >5% and >1 % of total hematopoietic cells in peripheral blood, respectively (Purton et al. Cell Stem Cell, 1 : 263-270, 2007).
• the secondary transplantation recipient mice that died before 16 weeks post transplantation were counted for failed engraftment.
• Cell cycle and apoptosis assays were performed with FITC mouse anti-human Ki67 set (BD Pharmingen) according to the manufacturer's instructions. Briefly, 5x 10 6 BM cells were isolated and stained with HSC antibodies as described above. Cells were fixed by 4% paraformaldehyde at 4 ° C overnight or room temperature (RT) for 1 hour, and then permeabilized with 0.2% triton X-100 on ice for 1 5 mins.
• FITC mouse anti-human Ki67 set BD Pharmingen
• RNA-IP-seq Two replicates of 10 5 LT-HSC, ST-HSC (LSK CD34 + FLK2 " ) and MPP (LSK CD34 + FLK2 + ) from C57BL/6J mouse were sorted into TRIzol (Invitrogen), and total RNA was isolated according to the manufacturer's instructions. RNA was fragmented to ⁇ 100 nucleotide fragments with Ambion fragmentation reagent (2 mins incubation at 70 C). The samples were then subjected to Turbo DNase treatment (Ambion), followed by a phenol-chloroform extraction, and resuspension in 85 ⁇ of nuclease-free water, and 5 ⁇ was saved as input.
• TRIzol Invitrogen
• RNA fragments were diluted into IPP buffer (150 mM NaCI, 0.1 % NP- 40, 10 mM Tris-HCI, pH 7.5). RNA was incubated with 25 ⁇ of protein-G magnetic beads, previously bound to 3 g of anti-m 6 A plyclonal antibody (Synaptic Systems), for 3 hours at 4 ° C in IPP buffer.
• IPP buffer 150 mM NaCI, 0.1 % NP- 40, 10 mM Tris-HCI, pH 7.5.
• Beads were washed twice with 200 ⁇ IPP buffer, twice with 200 ⁇ low-salt buffer (50 mM NaCI, 0.1 % NP-40, 10 mM Tris-HCI, pH 7.5) and twice with 200 ⁇ high-salt buffer (500 mM NaCI, 0.1 % NP-40, 10 mM Tris-HCI, pH 7.5). Beads were then treated with 300 ⁇ Elution Buffer (5 mM Tris-HCL pH 7.5, 1 mM EDTA pH 8.0, 0.05% SDS, 4.2 ⁇ Proteinase K (20 mg/ml)) for 1 .5 hours at 50 ° C, and RNA was recovered with phenol:chloroform extraction followed by ethanol precipitation.
• 300 ⁇ Elution Buffer 5 mM Tris-HCL pH 7.5, 1 mM EDTA pH 8.0, 0.05% SDS, 4.2 ⁇ Proteinase K (20 mg/ml)
• RNA IP was performed with EpiMark® N6- Methyladenosine Enrichment Kit following manufacturer's instructions.
• RNAseq libraries were assessed on Agilent 2100 Bioanalyzer, and 1 ng (mouse) or 10 ng (human) RNA was used to generate RNAseq libraries according to the manufacturer's directions for the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio Inc) using 16 cycles (mouse) or 13 cycles (human) PCR2 amplification.
• the method uses random priming and a template switching oligo to generate complimentary DNA, followed by the ligation of barcoded adapters; ribosomal-derived cDNA is then removed through probe-directed enzyme cleavage and subsequent enrichment of un-cleaved fragments.
• lllumina Primary Analysis version RTA 1 .18.64 and Secondary Analysis version bcl2fastq2 v2.18 were run to demultiplex reads for all libraries and generate FASTQ files.
• libraries were sequenced as 75 bp single read on the lllumina NextSeq instrument using NextSeq Control Software 2.1 .2.
• lllumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.18 were run to demultiplex reads for all libraries and generate FASTQ files.
• Mouse Ythdf2 (mYthdf2) was cloned from commercial cDNA clone (ORIGENE # MC200730) into vector pcDNA5/FRT/Flag plasmid using primers listed: mYthdf2 ORF Clone Bamhl F: 5'-CGC GGA TCC TCG GCC AGC AGC CTC TTG GA-3' and mYthdf2 ORF Clone Notl R: 5'-ATA AGA ATG CGG CCG CCT ATT TCC CAC GAC CTT GAC GT-3'.
• Flag-mYthdf2 was subcloned under EF1 a promoter in pSicoR-EF1 a-IRES-EGFP lentiviral construct (Gibson Assembly ® , forward primer: 5'- GTC GAC GGT ACC GCG GGC CCA TGG ATT ACA AGG ATG ACG ACG-3' and reverse primer: 5'-GAG GGA GAG GGG CGG ATC CCC TAT TTC CCA CGA CCT TGA CGT-3').
• hYthdf2 Human Ythdf2 was cloned from plasmid provided by the Chuan He lab using primers indicated: Forward 5'-CGT TCG AAA TGT CGG CCA GCA GCC TCT-3'; Reverse 5'-TCC CCC GGG TTA TTT CCC ACG ACC TT-3'. Then hYthdf2 was cloned into pSicoR-EF1 a-IRES-EGFP constructs under EF1 a promoter by BstBI and Xmal restriction digestions and ligation.
• lentiviruses were generated by transfection of pSicoR-EF1 a-Flag-mYthdf2-IRES-EGFP constructs together with the psPAX2 and pMD2.G plasmids at a ratio of 10:7.5:2.5 into 293T cells using calcium phosphate transfection.
• the virus particles were harvested 48, 72, and 96 hours post transfection, filtered by 0.45 micrometers filter unit (Millipore), and then centrifuged at 18,000 RPM, 4 C for 2 hours.
• HPC7 cells were infected with recombinant lentivirus- transducing units in the presence of 4pg/ml_ polybrene (Sigma). 48 hours after infection, GFP + cells were sorted and cultured for experiments.
• irCLIP-seq and data analysis.
• irCLIP-seq the procedure was modified from the previously reported methods (Zarneger et al. Nature Methods, 13: 489-492, 2016); Simsek et al. Cell, 169: 1051 -1065 e1018, 2017).
• irCLIP was performed on -3*10 8 Flag-Ythdf2 HPC7 cells by UV crosslinking cells at 0.4J/cm 2 for 3 times.
• lysis buffer 150mM KCI, 10mM HEPES pH 7.6, 2mM EDTA, 0.5% NP-40, 0.5mM DTT, 1 : 100 protease inhibitor cocktail, 400U/ml RNase inhibitor; 1 ml cell pellet and 2ml lysis buffer. Pipetted up and down several times, and then the mRNP lysate was incubated on ice for 5 mins and shock-frozen at -80 C with liquid nitrogen. The mRNP lysate was thawed on ice and centrifuged at 15,000g for 15 mins to clear the lysate.
• Flag- Ythdf2 was isolated with 30 ⁇ of protein-G magnetic beads per 1 ml lysate, previously bound to 2pg of anti-Flag monoclonal antibody (Sigma) for 2 hours at 4 ° C on rotation. The beads were collected, washed eight times with 1 ml ice-cold NT2 buffer (200mM NaCI, 50mM HEPES pH 7.6, 2mM EDTA, 0.05% NP-40, 0.5mM DTT, 200U/ml RNase inhibitor) and one time with 200 ⁇ irCLIP NT2 buffer (50mM Tris, pH 7.5; 150mM NaCI; 1 mM MgCI 2 ; 0.0005% NP-40).
• 1 ml ice-cold NT2 buffer 200mM NaCI, 50mM HEPES pH 7.6, 2mM EDTA, 0.05% NP-40, 0.5mM DTT, 200U/ml RNase inhibitor
• 200 ⁇ irCLIP NT2 buffer 50mM
• mRNP complex was digested with RNase 1 (Thermo Fisher #AM2294) at 0.41 ⁇ / ⁇ in irCLIP NT2 buffer (aqueous volume of 30 ⁇ and supplemented with 6 ⁇ of PEG400 (16.7% final)).
• the nuclease reaction was incubated at 30 C for 15 mins in an Eppendorf Thermomixer, 15 s 1 ,400 r.p.m., 90 s rest. Nuclease digestions were stopped by addition of 0.5mL of ice-cold high- stringency buffer (20mM Tris, pH 7.5; 120mM NaCI; 25mM KCI; 5mM EDTA; 1 % Trition-X100; 1 % Na-deoxycholate).
• Immunoprecipitates were then quickly rinsed with 0.25m L then with 0.05mL of ice-cold irCLIP NT2 buffer.
• the irCLIP adaptor ligation and library construction followed previously reported protocol (Zarneger et al. Nature Methods, 13: 489-492, 2016).
• Enriched motifs were identified by taking midpoints of each binding site found in all three replicates, adding 20 bases up and downstream, and running MEME (4.11.1 ) with parameters "-dna -mod zoops -revcomp -minw 5 -maxw 10 -nmotifs 10 -maxsize 1000000". After motifs were identified, we ran tomtom (4.11.1 ) against transfac (1 -2017) to identify known binding sites. GO enrichment analysis was performed using a hypergeometric test in R. GO terms were considered enriched if they had a BH-adjusted p-value less than 0.05. Selected terms of interest are shown in the bar plot.
• Bars in the bar plot indicate percentage of genes in the list being tested having the term divided by the percentage of genes in the genome having the term. Peaks found by FAST-iCLIP in all three replicates were assigned to various features in the genome. Promoters were defined as upstream 150 bases from the TSS. "trans_stop” was defined as upstream and downstream 200 bases from the transcript start site.
• Cord blood transduction was conducted as described previously (Rentas, S. et al. Nature, 532:508-511, 2016, doi: 10.1038/nature17665). Briefly, fresh CD34 + cord blood cells or flow-sorted CD34 + CD38 " cells were prestimulated for 12-18h in StemSpan medium (StemCell Technologies) supplemented with growth factors interleukin 6(IL-6; 20ng/ml, Peprotech), stem cell factor (SCF; l OOng/ml, Peprotech), Flt3 ligand (FLT3-L; 100ng/ml, Peprotech) and thrombopoietin (TPO; 20ng/ml, Peprotech).
• IL-6 interleukin 6
• SCF stem cell factor
• Flt3 ligand Flt3 ligand
• TPO thrombopoietin
• Lentiviruses were then added in the same medium at a multiplicity of infection (MOI) of 50-200 for 24 hours. Cells were then given 2 days after transduction before in vitro or in vivo assays.
• Human YTHDF2 was targeted for knockdown by shRNA targeting 5'- AAG G AC GTTC C C AATAG C C AA-3' near the N terminus of CDS, as used in a previous report (Wang, X. et al. Nature 505:117-120, 2014, doi: 10.1038/nature12730).
• Scramble shRNA seed sequence 5'- G C G C G ATAG C G CTAATAAT-3' ) were used as control.
• Three doses, 50K, 20K and 10K, of sorted GFP + cells were transplanted into sublethally irradiated (3.25Gy) NSG mice, respectively.
• the cut-off for HSC engraftment was an exhibition of more than 1 % human CD45 + GFP + cells out of total CD45 + cells in BM of primary transplantation recipients.
• BM cells from highest two doses primary recipients were collected and mixed together at 10 weeks post transplantation.
• Three doses, 1.2 ⁇ 10 7 , 8 x 10 6 , 4 x 10 6 , of BM cells were transplanted into sublethally irradiated (3.25Gy) NSG mice, respectively.
• HSC engraftment was an exhibition of more than 0.2% human CD45 + GFP + cells out of total CD45 + cells in BM of secondary transplantation recipients.
• HSC frequency was assessed using ELDA software (Hu et al. Journal of Immunological Methods, 347: 70-78, 2009).
• ELDA software Human et al. Journal of Immunological Methods, 347: 70-78, 2009.
• female NSG mice aged 6-8 weeks were used.
• Regions smaller than 100 bp were discarded, and regions over 200 bp were divided into 100 to 200 bp sub-regions; m 6 A signal over control was calculated at each region; and regions with at least 2-fold enrichment in all replicates were identified as m 6 A peaks.
• m 6 A peaks distribution and m 6 A marked genes were determined by overlapping all m 6 A peaks with hg19 and mm10 RefGene annotation.
• m 6 A marked genes were identified by overlapping m 6 A peaks with hg19 RefGene.
• genes marked by m 6 A in all three samples were compared against human transcription factor database http://fantom.gsc.riken.jP/5/sstar/Browse_Transcription_Factors_hg19.
• GO term analysis was then performed using R package enrich GO.
• m 6 A marked human transcription factors were used as searching list, and all the expressed genes were used as background. Hemopoiesis related BP terms with significant enrichment were used to generate Figure 3C.
• RNA-seq Human cord blood CD34 + cells were transduced with control or human YTHDF2 KD lentivirus and sorted out for GFP + CD34 + 10 days later. Three replicates of 12,000 GFP + CD34 + cells were sorted for each group and were used to extract total RNA. Four nanograms of high quality total RNA was used for cDNA synthesis and library preparation according to the manufacturer's directions with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, 634891 ) and Nextera XT (lllumina, FC-131 -1096).
• Resulting short fragment libraries were checked for quality and quantity using an Agilent 2100 Bioanalyzer and Invitrogen Qubit Fluorometer. Equal molar libraries were pooled, requantified, and sequenced as 75 base pair single reads on a High Output flow cell on the lllumina NextSeq 500 instrument. Following sequencing, lllumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 2.18 were run to demultiplex reads for all libraries and generate FASTQ files.
• RNA-seq analysis For RNA-seq analysis, reads were aligned to UCSC genome hg38 with Tophat version 2.0.13 with default parameters, using Ensembl 87 gene models. Read counts were generated using HTSeq-count with -m intersection-nonempty. Reads were also aligned to ERCC control sequences and counts tabulated. A scaling factor was calculated based on the median of the ERCC counts for each sample and used for normalization. Differentially expressed genes were found using the edgeR package (3.18.1 ) in R (3.4.1 ). Differentially expressed genes were required to have a BH-adjusted p-value ⁇ .05 and a 2-fold change in expression.
• RNA stability assay 15,000 sorted LT-, ST-HSCs and MPPs were cultured in StemSpan SFEM medium (Stem Cell Technologies) supplemented with 10pg/mL heparin (Sigma), 0.5* penicillin/streptomycin (Sigma), 10ng/ml_ recombinant mouse (rm) SCF (Biovision, Inc.), and 20ng/ml_ Tpo (Cell Sciences, Inc.) (Perry et al. Genes and Development, 25: 1928-1942 (2011)) at 37°C 5% CO2 5% O2. Sorted cells were treated with 5 ⁇ actinomycin D (Sigma) for inhibition of mRNA transcription. Cells were harvested at 0 hour or 4 hours post treatment, and total RNA was extracted and used for RNA-seq. [00246] m 6 A RNA methylation quantification
• Mouse BM Lineage negative cells from wt and Ythdf2 KO mice were enriched with mouse Lineage Cell Depletion Kit (Miltenyi Biotec), followed by total RNA extraction with TRIzol (Invitrogen). The quantification of m 6 A RNA methylation in Lin " cells were performed with m 6 A RNA Methylation Quantification Kit (Abeam ab185912) following manufacturer's protocol. 200ng total RNA were used per replicates for either group.
• IRDye 800CW Goat anti- Mouse IgG and IRDye 800CW Goat anti-Rabbit IgG antibodies were used for intracellular staining.
• BM cells from wt and Ythdf2 KO mice were stained with HSC markers as above, then fixed with the Cytofix/Cytoperm kit (BD Biosciences) according to the manufacturer's instructions.
• RNA in situ hybridization was performed using RNAscope multiplex fluorescent detection kit according to the manufacturer's instructions (Advanced Cell Diagnostics) with a couple of modifications: Antigen retrieval was unnecessary, and digestion was performed with 1 :15 diluted proteinase III solution for 10 mins at RT. RNAscope probes targeting mouse Tall and Gata2 were designed and produced by ACDbio. After the in situ hybridization was completed, slides were rinsed twice with PBST and directly processed with background blocking (Background buster solution, Innovex, cat. no. NB306) and primary antibody incubation.
• background buster solution Innovex, cat. no. NB306
• Anti-YTHDF2 (MBL, 1 : 500) and anti-Dcpl a (Santa Cruz, SC100706, 1 :200) antibodies were diluted with antibody diluent reagent buffer (Life technologies, cat. no. 003118) and incubated at 4°C overnight.
• Donkey anti- rabbit Alexa Fluor 488 (Invitrogen, 1 :500) and donkey anti- mouse Alexa Fluor 633 (Invitrogen, 1 :500) were used for protein target multiplexing.
• Ythdf2 KO leads to increase in phenotypic HSCs in primary mice.
• Crispr-Cas9 technology was utilized to generate Ythdf2 f/f conditional knockout mice, and then crossed with Mx1-Cre mice to specifically reduce Ythdf2 expression in hematopoietic cells (hereafter Ythdf2 KO mice) (Fig. 1A and B).
• BM HSPCs showed no discernible difference at the absence of pl:pC ( Figure 7A).
• a short- term homing assay was initially perfomed by transplanting 1 ⁇ 10 6 carboxyfluorescein diacetate succinimidyl ester (CFDA SE)-labelled BM cells from KO mice or their control littermates into lethally irradiated recipient mice, and no significant difference was found in their homing capacity between mutant and wt controls (Fig. 7I).
• CFDA SE carboxyfluorescein diacetate succinimidyl ester
• Ythdf2 regulates HSC self-renewal gene expression by m 6 A- mediated mRNA decay.
• mapping was performed of the m 6 A methylome by methylated RNA immunoprecipitation combined with high-throughput sequencing (MeRIP-seq or m 6 A- seq) in LT-HSCs, ST-HSCs, and MPPs sorted from adult C57BL/6J mice (Meyer et al. Cell, 149: 1635-1646, 2012; Schwartz et al. Cell, 155: 1409-1421 , 2013; Dominissini et al. Nature, 485: 201 -206, 2012).
• m 6 A peaks were selected by identifying significantly enriched overlapping peaks from two independent replicates.
• Ythdf2 is a well- recognized m 6 A "reader" that mediates mRNA decay (Wang et al. Nature, 505: 117- 120, 2014)
• the targets of Ythdf2 were further determined by performing infrared UV- crosslinking immunoprecipitation sequencing (irCLIP-seq) in the mouse multipotent hematopoietic precursor cell line HPC-7 (Pinto do et al. The EMBO Journal, 17: 5744-5756, 1998; Zarnegar et al.
• Ythdf2 bound to transcription factor mRNAs such as that of Tall and Gata2, on sites largely overlapping with m 6 A peaks (Fig. 3E; Fig. 5E and Table S2, Ythdf2 targeted mRNAs from three irCLIP-seq replicates).
• Ythdf2 KO HSPCs Single cell immunofluorescence staining and intracellular flow cytometry further revealed that Ythdf2 KO HSPCs exhibited significant increases in the intensities of rri6A-labeled transcription factors involved in stem cell self-renewal, such as TAL1 , GATA2, RUNX1 and STAT5, indicative of a suppressive role of Ythdf2 in HSC self-renewal (Fig. 3G; Fig. 12C).
• TAL1 , GATA2, RUNX1 and STAT5 indicative of a suppressive role of Ythdf2 in HSC self-renewal
• FISH fluorescence in situ hybridization
• m 6 A modifications predominantly occurred in mRNAs ( ⁇ 95%), preferential in mRNA ORF regions, 3'UTRs, and near the stop codon, as expected (-90%) (Figs. 4A and 4B; Fig. 13B).
• m 6 A landscapes in mouse and hUCB HSPCs were compared, and it was found that 2,239 genes were commonly m 6 A tagged (Fig. 4C). These commonly m 6 A-tagged transcripts were enriched for genes related to hematopoiesis and stem cell maintenance (Fig. 4D).
• m 6 A-labeled transcription factor transcripts in hUCB CD34 + cells were next characterized by performing GO term analysis.
• major GO terms were related to cell fate commitment and stem cell maintenance (Fig. 13C).
• HOXB4 overexpression of which has been reported to expand human and mouse HSCs ex vivo (Amsellem et al. Nature Medicine, 9: 1423-1427, 2003; Antonchuck et al. Cell, 109: 39-45, 2002), was marked by m 6 A in hUCB CD34 + cells (Fig.
• transcripts marked by m 6 A including HOXB4 and other HSC self-renewal related transcription factors, showed significant increases of input mRNA reads in the YTHDF2 KD cells compared to the control, without noticeable changes for non-m 6 A labelled genes (Figs. 4G to 41; Figs. 13F and 13G). These results support the role of YTHDF2 in regulating hUCB HSC self-renewal through RNA degradation.
• RNA-induced YTHDF2 KD in hUCB HSPCs was performed as above (Fig. 4F).
• lentiviral knockdown of YTHDF2 resulted in an average 14.3-fold and 13.6-fold increase, respectively, in the frequency and absolute number of CD34 + CD38 " CD45RA " EPCR + phenotypic HSCs and a 5.1 -fold increase in CFUs relative to control cells, especially the most primitive CFU-granulocyte erythrocyte monocyte megakaryocyte (GEMM) colony type and burst forming unit-erythroid (BFU-E), reflecting higher expression level of key transcription factors for hematopoiesis, such as TAL1, in YTHDF2 KD hUCB cells (Figs.
• GEMM CFU-granulocyte erythrocyte monocyte megakaryocyte
• BFU-E burst forming unit-erythroid
• YTHDF2 KD was performed by transplanting GFP + cells sorted from hUCB CD34 + cells infected with control and YTHDF2 shRNA at day 4 post infection (Fig. 6A).
• BM cells were analyzed from recipient NOD/SCID //2rg nu " (NSG) mice and measured the functional HSC frequency after in vivo expansion.
• NSG recipient NOD/SCID //2rg nu " mice
• recipients of YTHDF2 KD cells displayed a 9-fold increase in human hematopoietic cell (hCD45 + GFP + ) engraftment in BM without changes in the proportions of each lineage (Figs.
• YTHDF2 KD significantly increased the percentage of myeloid, megakaryocyte and erythrocyte in the BM of primary recipients (Figs 15C). Accordingly, it was found that the HSC frequency in YTHDF2 KD cells was increased 4.4-fold relative to that in control cells (Fig. 6D).
• Hematopoietic (CD45, Ter119) and endothelial cells (CD31 ) were excluded using specific markers.
• Mesenchymal stem cell present within the total bone marrow stromal cells were further purified by inclusion of N-Cadherin and CD105 antibodies.
• Mesenchymal stem cells marking both N-Cadherin + and CD105 + were quantitated.
• Conditional deletion of Ythdf2 led to 3.6-fold expansion in frequency of mesenchymal stem cells (Fig. 16).
• embodiments herein identify Ythdf2 as an important regulator of human and mouse HSC self-renewal by coupling the post- transcriptional m 6 A modification to the degradation of mRNAs encoding key transcription factors for self-renewal.
• Ythdf2 Repression of Ythdf2 in mouse HSPCs and hUCB HSCs can lead to increased expression of multiple key TFs critical for self- renewal, thereby facilitating ex vivo expansion of both phenotypic and functional HSCs without noticeable lineage bias and leukemia potential.
• stem cell niches may contribute to Ythdf2 suppression-mediated mouse HSC expansion as Mx1-cre can be activated in mesenchyme stromal cells. It would be interesting to study the function of Ythdf2 on mesenchymal stem cells (MSCs) and how repression of Ythdf2 in both HSCs and MSCs may synergistically expand HSCs in vivo.
• MSCs mesenchymal stem cells
• Mettl3 and Mettl14 Given the broad and complicated impact of m 6 A writer complex Mettl3 and Mettl14 on mRNA splicing, translation, and pri-miRNA processing (Barbieri et al. Nature,, 2017; Alarcon et al. Nature, 519: 482-485, 2015; Liu et al. Nature, 518: 560- 564, 2015), Mettl3 or Mettl14 depletion results in distinct outcomes in normal stem cells and leukemia. Recent studies have demonstrated that Mettl3 and Mettl14 play essential roles in leukemia development and leukemia stem cell maintenance (Vu et al. Nature Medicine, 2017; Barbieri et al. Nature, 2017; Weng et al.
• Ythdf2 is believed to be mainly involved in m 6 A-mediated mRNA decay (Batista et al. Cell Stem Cell, 15: 707-719, 2014; Yoon et al. Cell, 2017; Zhang et al. Nature, 549: 273-276, 2017; Wang et al. Nature, 505: 117-120, 2014). According to certain embodiments herein, it is believed that manipulating Ythdf2 may extend the half-life of specific m 6 A-marked mRNAs encoding TFs critical for stem cell self-renewal without affecting other aspects of mRNA processing.
• a major limitation in using hUCB HSC transplantation is the insufficient number of HSCs in one hUCB unit.
• Dlk1 , SR1 , Musashi2 and UM171 can expand hUCB HSCs by targeting Notch, AHR signaling or other unknown pathway (Boitano et al. Science, 329: 1345-1348, 2010; Fares et al. Science, 345: 1509-1512, 2014; Rentas et al. Nature, 532: 508-511, 2016; Chou et al. Experimental Hematology!, 41 : 479-490 e474, 2013).
• embodiments herein provide a novel and potent way to target multiple key TFs critical for HSC self-renewal and to enhance the expansion of HSCs. For example, reducing Ythdf2 level and function during in vitro culture via small chemicals or AAV- mediated KD may allow the Ythdf2 level and function to restore after transplantation in vivo, and thus not affect normal HSC maintenance and function in human patients. Furthermore, in certain embodiments, methods described herein may be combined with other methods to facilitate the expansion of not only human HSCs, but also other stem cells, rendering an approach for stem cell-based therapies.
• N-cad-CreER T mice were generated by Applied StemCell, Inc.
• tamoxifen Sigma
• TMX intraperitoneally
• mice To induce N-Cad + cells ablation in N-cad-CreER T ;iDTR mice, DT (Sigma) was injected intraperitoneally every other day at a dose of 50ng per g body as indicated. 5FU (Sigma-Aldrich) was injected once in the tail vein at 150pg per g body weight. After 5FU injection, mice were analyzed as described in the text. All mouse strains used in this study had a C57BL/6J genetic background. Animals were randomly included in the experiments according to genotyping results. Animal experiments were conducted in a blinded fashion with respect to the investigator. The numbers of animals used per experiment are stated in the figure legends.
• mice used in this study were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and were handled according to SIMR and National Institutes of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of the SIMR.
• SIMR Stowers Institute for Medical Research
• NASH National Institutes of Health
• hematopoietic cells were harvested from bone marrow (femur and tibia). Red blood cells were lysed using a 0.16 M ammonium chloride solution.
• a lineage cocktail (Lin, phycoerythrin (PE)-Cy5) was used, including anti-CD3 (145-2C11), anti-CD4 (RM4-5), anti-CD8 (53-6.7), anti-Mac-1 (M1/70), anti-Gr1 (RB6-8C5), anti-B220 (RA3-6B2), anti-lgM (11/41 ) and anti-TER119 (TER-119) (100 ng antibody cocktail per million bone marrow cells, eBioscience).
• Monoclonal antibodies to SCA1 (D7, eBioscience), c-KIT (2B8, eBioscience), FLK2 (A2F10, eBioscience), CD34 (RAM34, eBioscience), CD48 (HM48-1 , eBioscience), CD150 (TC15-12F12.2, BioLegend) and CD49b (HMa2, Biolegend) (all used as 50 ng per million bone marrow cells) were also used where indicated.
• monoclonal antibodies to CD45.1 (A20, eBioscience), CD45.2 (104, eBioscience), CD3, B220, Mac-1 and Gr1 were used.
• 7-aminoactinomycin D (A1310, Life technologies) was used to exclude dead cells.
• CD45 (30-F11, eBioscience), CD31 (390, eBioscience), PDGFRa-biotin (APB5, eBioscience), LepR-Bio (R&D), CD51 (clone RM7-V, Biolegend). Samples stained with biotin conjugated antibodies were washed with staining medium, then incubated with streptavidin brilliant violet 421 TM (Biolegend, 1 :500).
• Fluorescence imaging was performed on a spinning-disk confocal microscope (UltraVIEW; PerkinElmer), including an inverted microscope (Axiovert 200 M; Carl Zeiss Microimaging, Jena, Germany), attached to a spinning-disk confocal system (CSU-X1 ; Yokogawa Corporation of America) and Orca-R2 camera (Hamamatsu) with Volocity acquisition software (PerkinElmer) and a 20x/0.8 Plan-Apochromat objective (Carl Zeiss). Images were collected as a series of optical sections, with a step size of 4 ⁇ m. Images were collected in a tile pattern (overlap 10%) sufficient to cover the entire sample. Channels were collected sequentially.
• Blue dye was excited using 405 nm light (50 mW diode laser, OEM) and (red dye) was excited using 561 nm light (50 mW solid state laser, OEM), and each was collected using a multibandpass emission filter with 415nm-775nm 580nm-650nm bands.
• Green dye was excited using 488 nm light (50 mW solid state laser, OEM) and collected using a multibandpass emission filter of 500nm-550nm
• far red dye was excited using 640 nm light (50 mW solid state laser, OEM) and collected using a multibandpass emission filter with 455nm-515nm and 660nm-750nm. Exposure times and laser powers were adjusted to compensate for variations in staining.
• Second Harmonic Generation (SHG) imaging was performed immediately following fluorescence imaging.
• SHG images were collected on a LSM- 780 laser scanning confocal microscope (Carl Zeiss) equipped with a QUASAR detection unit, a 10x 0.45 Plan-Apochromat objective (Carl Zeiss), and Zen 2012 acquisition software (v8.1 .3, Carl Zeiss). Images were collected as a series of optical sections, with a step size of 8 ⁇ m and a pixel size (1 .32 ⁇ m/pixel) an integer multiple of four times the fluorescence pixel size. SHG images were taken with a laser light wavelength of 900 nm and collected at 371 -420 nm.
• images of Cd150-PE were taken using the 561 nm line of a DPSS laser (Melles Griot) and collected at 566-735 nm concurrently with the SHG images. Images were collected in a tile pattern (no overlap) sufficient to cover the entire sample. Tiles were stitched into a complete 3D image using Zen software.
• HSCs were identified by eye. Cells were considered negative for staining if the shape of the cell could not be discerned by eye, or if the shape of the cell formed a dark region in a field of positive signal.
• Distance measurements to niche components were made using Fiji and Microsoft Excel software. The locations of the HSC and nearest point of each of the three niche components were marked using point ROIs in Fiji and locations were transferred to excel, where distances in 3D were then calculated using the 3D Pythagorean Theorem. To calculate distances for randomly distributed HSCs, random point ROIs were generated using a custom plugin in FIJI in the same images analyzed for observed HSCs.
• RNA sequencing and analysis RNA sequencing and analysis. cDNA was generated from 1000 purified cells using SMARTer Ultra Low Input RNA kit (Clonetech) and library was generated by the Nextera XT DNA Library Preparation Kit (lllumina), followed by sequencing on an lllumina HiSeq2500 for 50bp single reads. Raw reads were demultiplexed into Fastq format allowing up to one mismatch using lllumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome mm 10 with TopHat v2.0.13, default parameters. FPKM values were generated using Cufflinks v2.2.1 with "-u - max-bundle-frags 100000000".
• Ncad- CreER T driven Tomato 4" BM/Bone stromal cells were isolated from CFU-F cultures by digesting with 0.25% Trypsin/EDTA, split into 3 aliquots, and seeded into separate cultures permissive for differentiation: StemPro Osteogenesis kit Gibco A10072-01 , Adipogenesis kit A10070-01 and Chondrogenesis differentiation kit A10071 -01 .
• the osteoblastic differentiation was assessed by VECTOR Red Alkaline Phosphatase; the adipogenic differentiation was detected by Oil Red O (Sigma); and the chondrogenic differentiation was detected by Toluidine blue (Sigma, 0.1 g T Blue/1 OOmL distilled water).
• Sections were blocked with Power BlockTM Universal Blocking Reagent for 30 minutes to 1 hour and then stained overnight with rabbit-anti- Aggrecan (Millipore, 1 :300), rabbit-anti-Perilipin (Cell Signaling, 1 :300) and goat-anti- Osteopontin (R&D, 1 :300).
• Donkey-anti-goat Alexa Fluor 488 and Donkey-anti-goat Alexa Fluor 647 were used as secondary antibodies (all from Invitrogen, 1 :300).
• Antibodies were diluted with Antibody Diluent Solution (Invitrogen 00-3218). Slides were mounted with FLUORO-GEL (Electron Microscopy Science 1798510), and images were acquired with an Olympus slide scanner.
• CD48 " CD49b ⁇ subpopulation which exists only in conventional LT-HSCs (CD34 ⁇ Flk2 ⁇ Lineage ⁇ Sca-1 + c-Kit + (LSK) cells) but not in short-term HSCs (ST-HSCs; CD34 + FLK2 " LSK) or multipotent progenitor cells (MPPs; CD34 + FLK2 + LSK). It was proposed that the CD48- CD49b ⁇ LT-HSCs subpopulation enriches rHSCs and that the CD48 ⁇ CD49b + LT-HSCs subpopulation enriches primed HSCs (hereafter pHSC(s)) (Fig.
• rHSCs or pHSCs were transplanted into recipient mice and the mice were challenged with 5FU at 4 weeks post transplantation. As shown in Figure 17F, rHSCs were insensitive to 5FU treatment; however, pHSCs dramatically reduced their reconstitution ability (44% reduction at 20 weeks post transplantation). Taken together, the data indicated that CD48 " CD49b " LT-HSC indeed enriched rHSCs that were resistant to chemotherapeutic treatment, whereas CD48 ⁇ CD49b + LT-HSC enriched pHSCs that were sensitive to chemotherapy; furthermore, the former gave rise to the latter but not vice versa in the transplantation assay.
• Drug-resistant rHSCs predominantly localize in the endosteal region of bone marrow
• N-cad + pre-osteoblastic cells in bone surface have been found resistant, whereas Osx + osteoblasts have been found to be sensitive to 5FU treatment and N-cad + stromal cells have been found to give rise to Osx + osteoblasts during recovery post 5FU treatment (Sugimura et al., 2012).
• a recent study showed dramatic depletion of LepR + stromal cells in central marrow due to cell death 1 day following irradiation (Zhou et al., 2017). To track the early changes in vascular and endosteal niches, an apoptotic assay was performed at day 1 post 5FU treatment.
• N-Cad driven Tomato 4" cells in central marrow as well as in bone surface increased by 2.2-fold and 1 .7-fold respectively (Fig. 18H, Fig. 24K).
• the number of CD31 4" vessel cells also increased but showed a dilated and damaged architecture (Fig. 181).
• Previous reports and this data showed that vessels and associated stromal cells in the perivascular niche, including LepR 4" and N-cad + cells, suffered immediate damage and were sensitive to 5FU stress, whereas N-cad + endosteal stromal cells remained stable.
• N-Cad + niche cells maintain functional HSCs including rHSCs in bone marrow
• N-cad + stromal cells were the first identified HSC niche cells, and though N-cad + stromal cells at the endosteal niche were resistant while Osx + osteoblasts were sensitive to chemotherapy, a direct evidence for N-cad + functionally supporting HSCs was still missing due to lack of proper genetic mouse lines. According to aspects herein, the N-cad-CreER T line was generated (Fig. 25A) and showed that N-cad + stromal cells gave rise to both Col2.3-GFP + osteoblastic cells and perivascular cells (Fig. 25B).
• N-cad-CreER T induced DTR encoding diphtheria toxin receptor line (N-cad-CreER T ;iDTR) was generated, in which N-cad + niche cells were rendered sensitive to diphtheria toxin (DT).
• Three tamoxifen (TMX) injections were administered and followed with intraperitoneal injections of DT (one injection every other day) to the N-cad- CreER T ;iDTR mice and analyzed them on the first day after the last injection (Fig. 19A).
• a transplantation assay was also performed to test the functional HSC numbers in N-cad + stromal cell ablated mice. It was found that bone marrow cells from N-cad + stromal cell ablated mice gave significantly lower levels of donor cell reconstitution (28.3% reduction at 20 weeks) (Fig. 19E) with reduced myeloid cell production (24.5% to 17.1 %) (Fig. 19F). To further investigate whether N-cad + niche cells contributed to maintaining the long-term self-renewal of HSCs, a secondary transplantation was conducted at 20 weeks post the primary transplantation.
• BM cells from the N-cad + stromal cell ablated mice had deeper reduction of donor cell reconstitution capacity in the secondary transplantation (40.5% reduction at 16 weeks) (Fig. 19G), although they were capable of multilineage reconstitution (Fig. 19H).
• HSPCs hematopoietic stem and progenitor cells
• M central bone marrow
• PCA principal component analysis
• vWF in rHSCs were 6.1 -fold higher than in pHSCs, suggesting that rHSCs enriched most of the vWF + HSCs which reside at the apex of the HSC hierarchy (Sanjuan-Pla et al., 2013).
• progenitor signature genes such as CD34, CD48, and Flt3(Flk2) and Itga2 (CD49b) had low expression in rHSCs (Acar et al., 2015; Chen et al., 2016; Gazit et al., 2014).
• rHSCs post 5FU had high expression levels of CXCR4, Ctnnall (a-Catulin)(Park et al., 2002), Esam (Endothelial cell-selective adhesion molecule) and CD150 (encoding Slamfl, signaling lymphocytic activated molecule), consistent with their functions associated with the converted primed state (Fig. 20E).
• N-cad driven tdTomato N-cad- TdT
• M mesenchymal stem cell
• MSC mesenchymal stem cell
• Fig. 20C pearson distance tree
• Fig. 20D PCA analysis
• NG2-RFP cells had a very similar transcriptome profile to Col2.3-GFP + osteoblasts (Fig. 20C-D). It was also found that NG2-RFP cells were predominantly restricted to endosteum in the epiphysis or diaphysis, though they were also detected in the peri-arterial region (Fig. 26C).
• Pecam CD31
• CDH5 VE-cadherin
• PF4 and Adgrel were enriched in MKs and macrophages (Macs).
• Cspg4 was enriched in NG2-RFP cells.
• Nestin-GFP cells did not have endogenous Nestin (Nes) expression, consistent with previous reports (Ding et al.,2012; Greenbaum et al., 2013).
• N-cad-TdT(B) cells isolated from the endosteal zone also had high levels of SCF, Cxcl12, LepR and Pdgfra expression compared to other cells from the endosteal zone, such as Col2.3-GFP and NG2-RFP cells (Fig. 20F).
• Col2.3-GFP cells enriched osteoblast gene Col1 a and progenitor cell gene Ly6a ⁇ SCA1) (Yang et al., 2014).
• N-Cad-TdT(B) cells from the endosteal region enriched chondrocyte genes Spockl, Col2a1 and Col1a2 and bone development genes such as Tnc.
• both N-Cad-TdT(B) and N-Cad- TdT(M) enriched most of the mesenchymal stem and progenitor cell (MSPC) genes such as Prrxl, Pdgfre, Pdgfra, Sp7, Sox9 and Greml.
• MSPC mesenchymal stem and progenitor cell
• Marrow harvested NG2-RFP cells also had higher levels of MSPC gene expression, such as Alcam, Sp7, Mcam, Sox9 and GH1, but with high level osteoblast and chondrocyte related genes such as Col1a1, Col2a1, and Col1a2. It was also found that among all perivascular niche cells, LepR + cells exclusively enriched Gla as well as several osteoblast and chondrocyte markers such as Atf4 and Tnc. Cxcl12-RFP cells significantly enriched MSPC gene Itgav. Furthermore, Greml was enriched in N-Cad-TdT(B) and in all perivascular niche cells but not in NG2-RFP cells.
• Col2.3-GFP cells were enriched for more mature osteo-lineage genes (Dmp1, Col1a1, Spp1, Bglap).
• Nestin-GFP, Cxcl12- RFP and LepR were consistent with their known role in enriching MSC genes (Prrxl, Pdgfra, Itgb l, Greml (Fig. 20H).
• N-Cad-TdT(M) and N-Cad-TdT(B) were enriched for chondrogenic (Sox9, Col2a1 and Tnc), adipogenic (Cebpct, Ppary, Adipoq) and osteogenic (Col1a1, Runx2) genes, suggesting a tri-potential nature of N-Cad + stromal cells.
• NG2-RFP was enriched for both bone development genes (Dmp1, Bglap, Sp7, Runx2, Col1a1) and chondrogenic genes (Sox9, Col2a1 and Tnc), suggesting an osteo-chondrogenic role (Fig. 26D-E).
• N-cad-CreER T induced reporter cells largely overlap with LepR + and Cxcl12 + stem/stromal cells
• N-cad in vivo lineage tracing was performed using the TdT or ZsG reporter, and found that, at day 3 post induction, N-cad-CreER T lineage traced cells partially overlapped with Cxcl12-RFP and Nestin-GFP cells (Fig. 20I). Moreover, 98.3% and 97.9% N-cad-CreER T derived cells were positive for LepR and Pdgfra expression respectively (Fig. 20J). This result further supported that N-cad + stromal cells have MSC potential as suggested by the transcriptome analysis.
• CFU-F colony-forming unit-fibroblasts
• Example B-6 N-cad + stromal cells give rise to osteoblasts, chondrocytes, and adipocytes in vitro and in vivo
• N-cad + cells To test the MSC potential of N-cad + cells, in vitro differentiation assay was performed by splitting cells obtained from individual CFU-F colonies formed by N-cad + cells into three aliquots and sub-cloned them into cultures permissive for bone, fat, or cartilage cell differentiation. It was found that Tomato 4" cells underwent multilineage differentiation, giving rising to Alkaline phosphate-positive osteoblastic cells, Oil-red-O-positive adipocytes, and Aggrecan-stained and Toluidine-blue- positive chondrocytes (Fig. 21 C-E).
• N-cad + stromal cells To characterize in vivo function of N-cad + stromal cells, the dynamic anatomical distribution of N-cad derived cells was analyzed after one dose of TMX treatment (Fig. 21 F, G). Interestingly, detected N-cad derived cells were detected in metaphysis of trabecular as early as 6 hours post TMX, but only very few cells were seen in central marrow, suggesting that a large portion of N-cad + cells originated from the endosteal region (Fig. 21 H).
• N-cad derived cells increased by 2.2 ⁇ 0.2-fold in trabecular bone region from 1 to 2 weeks post TMX treatment and remained stable afterwards; in cortical bone region, the cell number increased by 2.95 ⁇ 0.2-fold at 2 weeks post TMX, but then declined at 6 weeks post TMX, suggesting that N-cad + cells in trabecular bone region were more quiescent compared to cortical bone region.
• N-cad derived cells continuously increased in central marrow up to 6 weeks, suggesting that N-cad derived cells might be proliferating and differentiating within this area (Fig. 211).
• N-cad + cells generated Col2.3-GFP + osteoblasts (Dacic et al., 2001 ) in a time dependent manner (Fig. 22A, Fig. 27A-B).
• N-cad-derived osteoblasts were detected in the peri-trabecular region as early as 6 hours post TMX induction (Fig. 22B) and in the compact bone region at 14 hours post TMX induction (Fig. 22C).
• N-cad + stromal cells generated adipocytes in the trabecular bone region, particularly the endosteal cells, (Fig. 22H), and this was further confirmed by BODIPY lipid probe staining (Fig. 22I).
• the frequency of N-cad + derived adipocytes increased quickly initially and declined later on, as evidenced by the quantification that 39.3% ⁇ 4.5%, 77.1 % ⁇ 6.7% and 17.2% ⁇ 3% of N-cad + derived cells were observed at 6, 14 and 24 hours respectively after TMX induction, suggesting that adipocytes might have a frequent turnover rate (Fig. 22J-K, Fig. 27C-E).
• Ncad+ MSCs were enriched > 10-fold as compared to other markers.
• just 10K Ncad+ hMSCs produced even higher human thrombopoietin (THPO or TPO) than total hMSCs in vivo.
• THPO or TPO human thrombopoietin
• Ncad- hMSCs exhibited a function similar to the total hMSCs. Accordingly, isolating MSC with N-cadherin antibodies can provide for enrichment of the MSC population.
• N-cad + stromal cells give rise to chondrocytes during development and post injury
• N-cad-CreER T After N-cad-CreER T ; R26-tdT mice were induced with TMX at 1 or 2 weeks when the growth plate develops, Tomato 4" chondrocytes in cartilages of femur or tibia remained undetectable (data not shown).
• TMX induction was started to N-cad- CreER T ; R26-tdT mice at embryonic stage E12.5, when MSCs were undergoing condensation and chondrocyte differentiation in the fetal bone (Fig. 23A).
• N-cad derived tdT + cells were located peripherally, with differentiated N-cad derived Tomato 4" chondrocytes located in the central region of the rib at E14.5 embryos (Fig. 23B).
• N-cad derived chondrocytes were detected in both the columnar zone where the secondary ossification center forms, and in the superficial zone, which is imperative to resist the sheer force for deeper layer protection (Fig. 23C, D).
• N-cad + cells contributed to early and long-term adipogenesis during development.
• N- cad 4" cells derived Osteopontin 4" osteoblast and osteocyte were detected at 2 months after birth but not at early P2 (Fig. 23F, Fig. 28C).
• HSCs have been widely studied. HSCs can be maintained in either active, quiescent or deeply quiescent states. It is well known that the quiescence characterization of HSCs is functionally related to their long-term self-renewal potential (Foudi et al., 2008; Wilson et al., 2008). However, how the quiescent HSC population overcomes the consequence of myeloablation in vivo is an unanswered question. In spite of their quiescence, the majority of HSCs cannot survive chemotherapeutic stress such as 5FU (Longley et al., 2003).
• HSCs quiescent but chemotherapeutic sensitive HSC subpopulations
• pHSCs quiescent but chemotherapeutic sensitive HSC subpopulations
• rHSCs have an attenuated DNA repair system compared to pHSCs during homeostasis, but rHSCs can quickly activate their DNA repair pathways and the stress-response program to survive chemotherapeutic stress, and support subsequent hematopoiesis to overcome the consequence of myeloablation.
• HSC quiescence also correlated with their low metabolic state, which may be considered analogous to 'sleeping', and was termed as HSC dormancy or hibernation (Takubo et al., 2013; Wilson et al., 2008; Yamazaki et al., 2011).
• quiescence was not the only mechanism underlying drug resistance; instead, both the intrinsic stress-response program and the extrinsic niche protection contributed to drug resistance.
• N-cad + stromal cells were the first identified HSC niche cells (Zhang et al., 2003) and confirmed by subsequent studies (Arai et al., 2004; Sugiyama et al., 2006). N-cad + cells were initially proposed as osteoblastic progenitor cells based on their endosteal location. According to apects herein, by using two reporter lines, it was found that N-cad + stromal cells were distributed in both endosteal region and perivascular sites. More intriguingly, it was found that the majority of N-cad + cells overlapped with LepR + cells and Pdgfra 4" cells.
• N-Cad + stromal cells generated 72% ⁇ 6% Col2.3-GFP + cells; however, 9.3% ⁇ 4.7% N-cad + Col2.3GFP " cells were also detected in the endosteal region. These immature cells accounted for the primitive MSCs, which could explain the insufficient efficiency of Col2.3-Cre genetic model in HSC niche function studies (Ding and Morrison, 2013; Ding et al., 2012; Greenbaum et al., 2013).
• N-Cad-TdT + and Nestin-GFP + were enriched in the trabecular region
• N-Cad- TdT + was concentrated in the trabecular region where engraftment of transplanted HSCs was detected as previously reported (Nilsson et al., 2001 ; Xie et al., 2009) and survived after stress as observed here. All these data indicated that although N-cad + cells share a similar transcriptome profile with other MSCs, their anatomic distribution may indicate their unique HSC niche function; indeed, it was shown that the N-cad + endosteal niche cell plays a critical role in preserving rHSCs.
• N-cad + cells eliminated both pHSCs and rHSCs in BM. This could be explained by the anatomical distribution of N-cad + niche cell in both endosteal and perivascular zones. Furthermore, it was shown that N-cad expression could be detected in a subset of HSCs; however, the N-cad-TdT reporter mouse lines did not support this observation (data not shown).
• N-cad + stromal cells function as MSCs and support primitive HSC maintenance, especially under stress.
• HSCs hematopoietic stem cells
• hUCB human umbilical cord blood
• Ythdf2 is well recognized to promote the targeted mRNA decay.
• the physiological functions of Ythdf2 on adult stem cells are still elusive.
• Embodiments herein demonstrate that conditional knockout (KO) mouse Ythdf2 increased phenotypic and functional HSC numbers, but neither skewed lineage differentiation nor led to hematopoietic malignancies.
• knockdown (KD) of human YTHDF2 led to over 10-fold increase in ex vivo expansion of hUCB HSCs, 5-fold increase in colony-forming units (CFUs), and more than 8-fold increase in functional hUCB HSCs in the 2 rounds of limiting dilution transplantation assay.
• m 6 A mapping of RNAs from mouse hematopoietic stem and progenitor cells (HSPCs) as well as from hUCB HSCs revealed m 6 A enrichment on mRNAs encoding transcription factors critical for stem cell self-renewal. These m 6 A-marked mRNAs were recognized by Ythdf2 and underwent mRNA decay. In Ythdf2 KO HSPCs and YTHDF2 KD hUCB HSCs, these mRNAs were stabilized, leading to an increase in protein levels and facilitating HSC expansion which can be rescued by knockdown the mRNA, such as Tall mRNA.
• embodiments show the function of Ythdf2 in adult stem cells maintenance and identify an important role of Ythdf2 in regulating HSC ex vivo expansion via the mechanism of controlling the stability of multiple mRNAs critical for HSC self- renewal, thus having a strong potential for future clinical applications.
• HSCs hematopoietic stem cells
• BM niches bone marrow (BM) niches
• rHSCs reserve HSCs
• pHSCs primed HSCs
• pHSCs and rHSCs could support long-term hematopoiesis under homeostasis; however, pHSCs were sensitive to chemotherapy, whereas rHSCs survived chemotherapy and supported subsequent regeneration after myeloablation.
• N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nature medicine 23, 1369-1376 (2017).
• ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Molecular cell 49, 18-29 (2013).
• RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency.
• RNA m6A Reader YTHDF2 Is Essential for the Post- transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence. Molecular cell 67 , 1059-1067 e1054 (2017).
• Hematopoietic stem cell subtypes expand differentially during development and display distinct lymphopoietic programs.
• Osteoblast ablation reduces normal long-term hematopoietic stem cell self-renewal but accelerates leukemia development. Blood 125, 2678-2688. 82 Bruns, I., Lucas, D., Pinho, S., Ahmed, J., Lambert, M.P., Kunisaki, Y., Scheiermann, C, Schiff, L, Poncz, M., Bergman, A., et a!. (2014). Megakaryocytes regulate hematopoietic stem cell quiescence through CXCL4 secretion. Nat Med 20, 1315-1320.
• Osteoblastic cells regulate the haematopoietic stem cell niche. Nature 425, 841-846.
• Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche. Nature 530, 223-227.
• N-cadherin expression level distinguishes reserved versus primed states of hematopoietic stem cells.
• Engraftment and reconstitution of hematopoiesis is dependent on VEGFR2-mediated regeneration of sinusoidal endothelial cells.
• SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121, 1109-1121.
• the epichaperome is an integrated chaperome network that facilitates tumour survival. Nature 538, 397-401.
• Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy. Nature.
• Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF. Nature cell biology 19, 891-903.

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