# Patent

## Title
Nuclear reprogramming factor comprising miRNA and a protein factor

## Abstract

A method of preparing induced pluripotent stem cells, comprising a nuclear reprogramming step with a nuclear reprogramming factor in the presence of miRNA, wherein said miRNA has a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof.

## Background
PRIOR RELATED APPLICATIONS
This application is a continuation application of U.S. patent application Ser. No. 12/292,717, filed Nov. 25, 2008, which is a continuation-in-part application of PCT/JP2008/59586, filed May 23, 2008, which claims priority to U.S. provisional patent application No. 60/996,893, filed Dec. 10, 2007. U.S. patent application Ser. No. 12/292,717 also relies on and claims direct benefit of U.S. provisional patent application No. 60/996,893, filed Dec. 10, 2007. The entire disclosures of all of these applications are hereby incorporated herein in their entireties.


FIELD OF THE INVENTION
The present invention relates to efficient methods for preparing induced pluripotent stem cells through reprogramming of somatic cells, to induced pluripotent stem cells, to uses of induced pluripotent stem cells and to somatic cells derived by inducing differentiation of said pluripotent cells. The present invention also relates to nuclear reprogramming factors and to miRNAs involved in generating induced pluripotent stem cells. The present invention also relates to screening methods, treatments, and therapies involving the use of induced pluripotent stem cells.
BACKGROUND OF THE INVENTION
Embryonic stem cells (ES cells) are stem cells established from human or mouse early embryos which have a characteristic feature that they can be cultured over a long period of time while maintaining pluripotent ability to differentiate into all kinds of cells existing in living bodies. Human embryonic stem cells are expected for use as resources for cell transplantation therapies for various diseases such as Parkinson's disease, juvenile diabetes, and leukemia, taking advantage of the aforementioned properties. However, transplantation of ES cells has a problem of causing rejection in the same manner as organ transplantation. Moreover, from an ethical viewpoint, there are many dissenting opinions against the use of ES cells which are established by destroying human embryos.
If dedifferentiation of patients' own differentiated somatic cells could be induced to establish cells having pluripotency and growth ability similar to those of ES cells (these cells are referred herein to as “induced pluripotent stem cells” or “iPS cells,” though they are sometimes called “embryonic stem cell-like cells” or “ES-like cells”), it is expected that such cells would be useful as ideal pluripotent cells, free from rejection or ethical difficulties. Recently, it has been reported that such iPS cells can be produced from differentiated cells of mouse or human, which has created a great sensation (International Publication No. WO2007/069666 A1; Takahashi et al., Cell 126:663-76, 2006; Takahashi et al., Cell 131:861-72, 2007; Yu et al., Science 318:1917-20, 2007; and Park et al., Nature 451:141-46, 2008, herein incorporated by reference in their entireties). Thus, the term “induced pluripotent stem cells (iPS cells)” refers to cells having similar properties to those of ES cells, and more specifically the term includes undifferentiated cells which are reprogrammed from somatic cells and have pluripotency and proliferation potency. However, this term is not to be construed as limiting in any sense, and should be construed to have its broadest meaning.
These methods include a reprogramming step through introduction of a plurality of specific factors (for example, four factors of Oct3/4, Sox2, Klf4, and c-Myc can be used in Takahashi et al., Cell 126:663-76, 2006), and the introduction of these factors is mediated by viral vectors such as retroviral or lentiviral vectors. However, all previously reported nuclear reprogramming methods mediated by the introduction of genes involve a problem of low efficiency in which only a small number of induced pluripotent stem cells can be obtained. In particular, there is a problem in that, if reprogramming is carried out in somatic cells through the introduction of three factors (namely, Oct3/4, Sox2, and Klf4) excluding c-Myc, then the production efficiency of induced pluripotent stem cells becomes low. Nevertheless, the efficient production of iPS cells without the use of c-Myc would provide certain advantages, as c-Myc is suspected to cause tumorigenesis in tissues and in chimeric mice generated from induced pluripotent stem cells.
It is known that various small RNAs are expressed in cells. Examples of small RNA include RNA molecules of about 18-25 nucleotides in length which can be cleaved out with a dicer, an RNase specific to double-stranded RNA. Small RNA is mainly classified into siRNA (small interfering RNA) and miRNA (microRNA, hereinafter abbreviated as “miRNA”). Small RNA is known to function as a guide molecule for finding target sequences in processes such as translational suppression, mRNA degradation, or alteration of chromatin structure. Small RNAs function via RNA interference (RNAi) or miRNA molecular mechanisms. In addition, small RNA is also known to play an important role in the regulation of developmental processes (for example, as general remarks, refer to Jikken Igaku (Experimental Medicine), 24, pp. 814-819, 2006; and microRNA Jikken Purotokoru (microRNA Experimental Protocol), pp. 20-35, 2008, YODOSHA CO., LTD., herein incorporated by reference in their entireties).
ES cell-specific microRNAs have been identified (Houbaviy et al., Developmental Cell 5:351-58, 2003). In particular, ES cell-specific expression of a microRNA cluster, which includes several types of miRNAs in mouse ES cells, has been reported (Houbaviy et al., Developmental Cell 5:351-58, 2003, herein incorporated by reference in its entirety). It has also been reported that miRNA-295 suppressed the expression of Rb12, a member of the Rb tumor suppressor gene family, and increased the expression of methylase to be thereby associated with DNA methylation (Sinkkonen et al., Nature Structural & Molecular Biology 15:259-267, 2008; Benetti et al., Nature Structural & Molecular Biology 15:268-279, 2008, herein incorporated by reference in their entireties). However, these documents do not disclose any role of small RNA in the nuclear reprogramming of somatic cells.
SUMMARY OF THE INVENTION
The present invention relates to methods for efficiently preparing induced pluripotent stem cells. The present invention provides methods for achieving efficient preparation of induced pluripotent stem cells in the presence of miRNA. The present invention also provides methods for efficient preparation of induced pluripotent stem cells with a nuclear reprogramming factor. The present invention also provides methods for efficient preparation of induced pluripotent stem cells with a nuclear reprogramming factor in the presence of increased miRNA as compared to the level present in the somatic cell prior to nuclear reprogramming. The present invention also provides such methods wherein the nuclear reprogramming factor does not include c-Myc and/or Sox2.
The invention provides a method of preparing induced pluripotent stem cells, comprising nuclear reprogramming at least one somatic cell with nuclear reprogramming factor and at least one miRNA, wherein the at least one miRNA increases efficiency of the nuclear reprogramming of the at least one somatic cell compared to nuclear reprogramming of the at least one somatic cell with the nuclear reprogramming factor in the absence of the at least one miRNA.
The invention also provides such a method, wherein the at least one miRNA is expressed in embryonic stem cells at a higher level than in somatic cells.
The invention also provides such a method, wherein a gene encoding the nuclear reprogramming factor and/or the at least one miRNA is introduced into the at least one somatic cell.
The invention also provides such a method, wherein a vector comprising the gene and/or a vector encoding the at least one miRNA is introduced into the at least one somatic cell.
The invention also provides such a method, wherein the vector comprising the gene or encoding the at least one miRNA is a retroviral vector.
The invention also provides such a method, wherein the gene is selected from an Oct family gene, a Klf family gene, and a Sox family gene.
The invention also provides such a method, wherein the gene is selected from Oct3/4, Klf4, and Sox2.
The invention also provides such a method, wherein the nuclear reprogramming factor comprises Oct3/4, Klf4, and Sox2.
The invention also provides such a method, wherein the at least one miRNA is introduced into the at least one somatic cell as primary miRNA.
The invention also provides such a method, wherein the at least one miRNA is introduced into the at least one somatic cell as pre-miRNA.
The invention also provides such a method, wherein the at least one miRNA comprises at least one miRNA represented by SEQ ID NOs: 1 to 14.
The invention also provides such a method, wherein the at least one miRNA comprises at least one miRNA contained in miRNA cluster hsa-miR-302-367 cluster.
The invention also provides such a method, wherein the at least one miRNA regulates DNA methylation.
The invention also provides such a method, wherein the at least one miRNA regulates de novo DNA methylation.
The invention also provides such a method, wherein the at least one miRNA down-regulates DNA methylation.
The invention also provides such a method, wherein the at least one miRNA comprises at least 10 contiguous nucleotides of at least one miRNA represented by SEQ ID NOs: 1 to 14.
The invention also provides such a method, wherein the at least one miRNA comprises at least 30 contiguous nucleotides of at least one miRNA represented by SEQ ID NOs: 1 to 14.
The invention also provides such a method, wherein the at least one miRNA comprises at least 60 contiguous nucleotides of at least one miRNA represented by SEQ ID NOs: 1 to 14.
The invention also provides such a method, wherein the nuclear reprogramming factor does not include c-Myc and/or Sox2.
The invention also provides such a method, wherein the at least one miRNA comprises hsa-miR-302-367 cluster miRNA.
The invention also provides such a method, wherein the nuclear reprogramming factor comprises an Oct family gene member, a Sox family gene member, and a Klf family gene member.
The invention also provides such a method, wherein the at least one miRNA comprises mmu-miR-295/295* and mmu-miR-294/294*.
The invention also provides such a method, wherein the at least one miRNA comprises hsa-miR-302-367 cluster, hsa-miR-371-373 cluster and hsa-miR-520c miRNA.
The invention also provides such a method, wherein the nuclear reprogramming factor comprises a Klf family gene, and an Oct family gene.
The invention also provides such a method, wherein the nuclear reprogramming factor further comprises a Myc family gene.
The invention also provides such a method, wherein the nuclear reprogramming factor further comprises a Sox family gene.
The invention also provides such a method, wherein the nuclear reprogramming factor further comprises a Sox family gene.
The invention also provides such a method, wherein the nuclear reprogramming factor comprises KLF4 and OCT3/4.
The invention also provides such a method, wherein the nuclear reprogramming factor excludes a Sox family gene.
The invention also provides such a method, wherein the nuclear reprogramming factor excludes a Myc family gene.
The invention also provides such a method, where the at least one somatic cell comprises a plurality of somatic cells.
The invention also provides a method of increasing the efficiency of nuclear reprogramming comprising: adding a nuclear reprogramming factor and at least one miRNA to at least one somatic cell so that the number of induced pluripotent stem cells produced is greater than in the absence of the added miRNA.
The invention also provides an induced pluripotent stem cell induced by reprogramming a somatic cell, wherein the reprogramming is performed by adding at least one miRNA and in the absence of eggs, embryos, or embryonic stem (ES) cells.
The invention also provides such an induced pluripotent stem cell, wherein the induced pluripotent stem cell is a human cell.
The invention also provides an induced pluripotent stem cell obtained by a method of preparing induced pluripotent stem cells, comprising nuclear reprogramming at least one somatic cell with nuclear reprogramming factor and at least one miRNA, wherein the at least one miRNA increases efficiency of the nuclear reprogramming of the at least one somatic cell compared to nuclear reprogramming of the at least one somatic cell with the nuclear reprogramming factor in the absence of the at least one miRNA.
The invention also provides an pluripotent stem cell obtained by a method of increasing the efficiency of nuclear reprogramming comprising: adding a nuclear reprogramming factor and at least one miRNA to at least one somatic cell so that the number of induced pluripotent stem cells produced is greater than in the absence of the added miRNA.
The invention also provides somatic cell derived by inducing differentiation of any of the above pluripotent stem cells.



BRIEF DESCRIPTION OF THE DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee.
FIG. 1 shows the results of confirmation on the production efficiency of induced pluripotent stem cells through induction of nuclear reprogramming in mouse embryonic fibroblasts with a combination of three genes comprising Oct3/4, Klf4, and Sox2 (this combination—represented as “3f”, “c-Myc(−)”, or OSK”—means that c-Myc was omitted from a combination of four genes comprising Oct3/4, Klf4, Sox2 and c-Myc, which is highly efficient for nuclear reprogramming), in the presence of various miRNAs. 3f+DsRed represents a combination where DsRed (Discosoma sp. red fluorescent protein) as a control was added to the combination of the aforementioned three genes. The results of three independent experiments are shown. The graph shows the number of ES-like colonies in the cells transduced with OSK with or without DsRed, or with various miRNAs.
FIG. 2 shows the production efficiency of induced pluripotent stem cells. The top row of images shows the results of nuclear reprogramming in mouse tail tip fibroblasts (TTFs) when DsRed was added, as a control, to the combination of three genes comprising Oct3/4, Klf4, and Sox2 (a combination of three genes in which c-Myc was omitted from the combination of four genes). The bottom row of images shows the results of induction of nuclear reprogramming in mouse TTFs with the combination of three genes comprising Oct3/4, Klf4, and Sox2 in the presence of mmu-miR-295. The number in the figure indicates the number of Nanog GFP positive colonies/the number of total colonies on days 7, 21, and 28 after drug selection was started.
FIG. 3 shows the results of confirmation on the production efficiency of induced pluripotent stem cells through induction of nuclear reprogramming in adult human dermal fibroblasts expressing the mouse ecotropic virus receptor Slc7a1 gene using lentivirus (aHDF-Slc-7a1) with the combination of three genes comprising Oct3/4, Klf4, and Sox2 (Myc(−)3f: a combination of three genes in which c-Myc was omitted from the combination of four genes comprising Oct3/4, Klf4, Sox2, and c-Myc), or the combination of four genes comprising Oct3/4, Klf4, Sox2, and c-Myc (Y4f), in the presence of various miRNAs.
FIGS. 4A-B shows the results of ES-like colonies produced after transduction with 4 factors, i.e., OCT3/4, SOX2, KLF4, and c-MYC (OSMK), as well as with 3 factors, i.e., OCT3/4, SOX2, KLF4 in the presence of various miRNAs (OSK+). FIG. 4A shows the number of human ES-like colonies obtained by transduction with 4 factors (OSMK), and with 3 factors without c-MYC plus miRNAs (OSK+). FIG. 4B shows the morphology of ES-like colonies from a subset of the samples counted in FIG. 4A.
FIG. 5 shows expression of ES cell markers in iPS cells produced by nuclear reprogramming of mouse Tail Tip Fibroblasts (TTFs) with 4 factors (OCT3/4, SOX2, c-MYC, and KLF4) and with 3 factors (OCT3/4, SOX2, and KLF4, i.e. “Myc(−)3f”)+mmu-miR-295/295* or DsRed.
FIGS. 6A-B show the results of MEFs infected with 3 factors (Oct3/4, c-MycWT, and Klf4, i.e., “Sox(−)”) with mmu-miR-290-295 cluster, 290-5p/290-3p(mmu-miR-290), 291a-5p/291a-3p(mmu-miR-291a), 292-5p/292-3p(mmu-miR-292), 293/293*(mmu-miR-293), 294/294*(mmu-miR-294) or 295/295*(mmu-miR-295). FIG. 6A shows the number of Nanog GFP positive colonies. FIG. 6B shows expression of ES marker genes in iPS cells checked with RT-PCR.
FIGS. 7A-C show the results of iPS induction with Fb-Ng MEFs (MEFs derived from Fbx15-β geo/Nanog-IRES-Puror reporter mouse) over-expressing Oct3/4, c-Myc, and Klf4 (“Sox(−)”)+mmu-miR-295/295* or hsa-miR-302-367 cluster miRNAs. FIG. 7A shows cell morphology of MEFs transduced with Oct3/4, c-Myc, and Klf4 (“Sox(−)”)+mmu-miR-295/295*. FIG. 7B shows chimeras derived from iPS cells induced with Sox(−)3f+mmu-miR-295/295*. FIG. 7C shows embryoid body (EB)-mediated in vitro differentiation by human iPS cells. Human iPS cells (61B1, 61N2) were established by transduction of 4 genes (OCT3/4, KLF4, SOX2, and c-MYC, i.e., “OSMK”) or 3 genes (OCT3/4, KLF4, and c-MYC, i.e., “OMK(SOX(−)”) in the presence of hsa-miR-302-367 cluster miRNA. After culturing for 16 days, immunohistochemistry analysis was performed in the cells by using an antibody against each of α-fetoprotein (AFP) which is a differentiation marker for endodermal cells, α-smooth muscle actin (a-SMA) which is a differentiation marker for mesodermal cells, and GFAP (DAKO) which is a differentiation marker for ectodermal cells. Nuclei were stained with Hoechst 33342 (Invitrogen).
FIG. 8 shows cell morphology of iPS cells induced with OSMK; SOX(−) (OKM)+hsa-miR-302-367 cluster miRNA; and OCT3/4+KLF4+hsa-miR-302-367 cluster miRNA.



TABLE 3 shows iPS induction by transduction with 4 factors (OCT3/4, SOX2, MYC, KLF4, i.e., “OSMK”), with 3 factors (SOX(−)3factors, i.e., “OMK”) plus various miRNAs (OMK:mock or miRNAs=2.5:1.5), and with 2 factors (OCT3/4+KLF4, i.e., “OK”) plus various miRNAs. Transduction with DsRed was performed as a as control. On Day 40 after infection, the number of ES-like colonies was counted. TABLE 3 shows the results of six independent experiments (Exp. 54, 61, 63, 114, 130 and 133).
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides methods for efficiently preparing induced pluripotent stem cells through reprogramming of one or more somatic cells. In particular, the present invention provides efficient preparation of induced pluripotent stem cells in the presence of miRNA. The present invention also provides efficient preparation with or without using a suspected tumorigenic factor: c-Myc. The present invention also provides efficient preparation with or without using Sox2. The nuclear reprogramming is preferably performed without c-Myc and/or Sox2.
The inventors of the present invention have conducted intensive studies, and as a result, they have found that induced pluripotent stem cells can be efficiently prepared by introduction of nuclear reprogramming-inducing gene(s) into somatic cells in the presence of specific miRNA. The present invention was achieved on the basis of the above findings.
The present invention thus provides a method of preparing induced pluripotent stem cells, comprising nuclear reprogramming with a nuclear reprogramming factor in the presence of miRNA, wherein said miRNA has a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof.
A preferred embodiment of the present invention provides the aforementioned method wherein: (a) said miRNA is expressed in embryonic stem cells at a higher level than in somatic cells; and/or (b) said miRNA has a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof and/or (c) said nuclear reprogramming is performed in the presence of increased levels of one or more miRNAs as compared to the level(s) present in the somatic cell prior to nuclear reprogramming.
Another preferred embodiment of the present invention provides: the aforementioned method wherein the nuclear reprogramming factor is either a single substance, or a combination of a plurality of substances, which is/are positive in the screening method of nuclear reprogramming factor described in International Publication No. WO2005/80598 A1, incorporated by reference herein in its entirety; the aforementioned method wherein the nuclear reprogramming factor is either a gene product of a single gene, or a combination of gene products of a plurality of genes, which is/are positive in the screening method of nuclear reprogramming factor described in International Publication No. WO2005/80598 A1, incorporated by reference herein in its entirety; the aforementioned method wherein the nuclear reprogramming with the nuclear reprogramming factor is carried out by introduction of the aforementioned gene(s) and/or substance(s) into somatic cells; the aforementioned method wherein introduction of the aforementioned gene(s) into somatic cells is carried out with a recombinant vector; and the aforementioned method wherein the nuclear reprogramming with the nuclear reprogramming factor is carried out by introduction of gene product(s) of the aforementioned gene(s) into somatic cells.
Yet another preferred embodiment of the present invention provides the aforementioned method wherein: the gene encoding the reprogramming factor comprises one or more gene(s) selected from an Oct family gene, a Klf family gene, a Sox family gene, a Myc family gene, a Lin family gene, and a Nanog gene, preferably a combination of two genes selected from the aforementioned genes except for the Myc family genes of Sox family genes, more preferably a combination of three genes, and particularly preferably a combination four or more genes. In a preferred embodiment, the combination can be any combination of factors which does not comprise c-Myc or Sox2.
More preferable combinations are: (a) a combination of two genes comprising of an Oct family gene and a Sox family gene; (b) a combination of three genes comprising an Oct family gene, a Klf family gene, and a Sox family gene; and (c) a combination of four genes comprising an Oct family gene, a Sox family gene, a Lin family gene, and a Nanog gene. Further, it is also preferable to combine any of the above genes with a TERT gene and/or a SV40 Large T antigen gene. It may be preferable to omit Klf family genes depending on the situation. The Myc family genes may or may not be included in these combinations. Combinations without the Myc family gene can be suitably used according to the present invention.
Among these embodiments, particularly preferable combinations are: a combination of two genes comprising Oct3/4 and Sox2; a combination of three genes comprising Oct3/4, Klf4, and Sox2; and a combination of four genes comprising Oct3/4, Sox2, Lin28, and Nanog. It is also preferable to combine any of the above genes with a TERT gene and/or a SV40 Large T antigen gene. It may be preferable to omit Klf4 depending on the situation. c-Myc may be included in these combinations. However, combinations without c-Myc can be suitably used in the present invention.
Other preferable combinations are: (a) a combination of two genes comprising of an Oct family gene and a Klf family gene; (b) a combination of three genes comprising an Oct family gene, a Klf family gene, and a Myc family gene. Yet another preferred embodiment of the present invention provides: the aforementioned method wherein the somatic cells are those derived from mammals including human, mouse, rat, cattle, sheep, horse, monkey, and hamster, preferably somatic cells from human or mouse, and most preferably somatic cells from human; the aforementioned method wherein the somatic cells are human embryonic cells, or adult human-derived somatic cells; and the aforementioned method wherein the somatic cells are somatic cells collected from a patient.
Yet another preferred embodiment of the present invention provides the aforementioned method wherein the miRNA comprises one or more miRNA(s) included in the RNA sequences specified by the registration names of the miRBase database or the accession numbers shown in Table 1 or Table 2; the aforementioned method wherein the RNA sequences specified by the registration names of the miRBase database (and the accession numbers) shown in Table 1 or Table 2 comprise one or more RNA(s) selected from hsa-miR-372 (MI0000780), hsa-miR-373 (MI0000781), hsa-miR-302b (MI0000772), hsa-miR-302c (MI0000773), hsa-miR-302a (MI0000738), hsa-miR-302d (MI0000774), hsa-miR-367 (MI0000775), hsa-miR-520c (MI0003158), mmu-miR-290 (MI0000388), mmu-miR-291a (MI0000389), mmu-miR-294 (MI0000392), and mmu-miR-295 (MI0000393); the aforementioned method wherein the miRNA comprises miRNA included in RNA specified by hsa-miR-302-367; and the aforementioned method wherein the miRNA comprises one or more miRNA(s) included in one or more RNA sequence(s) selected from the RNA sequences represented by SEQ IDS: 1 to 14 in the Sequence Listing.
The present invention provides an oligonucleotide comprising at least 10 contiguous nucleotides in the nucleotide sequence of the miRNA of the present invention, and an antisense oligonucleotide having a sequence that is complementary to that of the above oligonucleotide. The present invention also provides an oligonucleotide comprising at least 15, at least 20, at least 30, at least 50, or at least 60 contiguous nucleotides in the nucleotide sequence of the miRNA of the present invention. The present invention also provides an oligonucleotide comprising at least 70, at least 80, at least 100, at least 150, at least 200, at least 300, at least 400, at least 600, or at least 800 contiguous nucleotides in the nucleotide sequence of the miRNA of the present invention.
The present invention also provides induced pluripotent stem cells that can be obtained by the aforementioned method. In addition, the present invention also provides somatic cells obtained by inducing differentiation from the abovementioned induced pluripotent stem cells.
Further, the present invention provides a stem cell therapy comprising transplanting somatic cells into a patient, wherein the somatic cells are obtained by inducing differentiation from induced pluripotent stem cells that are obtained according to the aforementioned method by using somatic cells isolated and collected from a patient.
In addition, the present invention provides a method for evaluation of physiological effect or toxicity of a compound, a drug, or a toxic agent, with use of various cells obtained by inducing differentiation from induced pluripotent stem cells that are obtained by the aforementioned method.
Further, the present invention provides: a method for preparing induced pluripotent stem cells which uses miRNA expressed in embryonic stem cells at a higher level than in somatic cells, and having a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof; and a nuclear reprogramming method of somatic cells which uses miRNA expressed in embryonic stem cells at a higher level than in somatic cells, and having a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof.
In addition, the present invention provides methods comprising the use of miRNA expressed in embryonic stem cells at a higher level than in somatic cells (e.g., the miRNA may be expressed at levels which are higher in the ES cell as compared to the ES cell which has differentiated or which has begun differentiating such as determined by RT-PCR or Northern blot analysis), and having a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof, for preparation of induced pluripotent stem cells; and methods relating to the use of miRNA expressed in embryonic stem cells at a higher level than in somatic cells, and having a property of providing a higher nuclear reprogramming efficiency in the presence of the miRNA than in the absence thereof, for nuclear reprogramming of somatic cells. In other words, nuclear reprogramming, and thus, induced pluripotent stem cell production, can be performed in the presence of miRNA and in the absence of miRNA. The nuclear reprogramming may also be performed in the presence of various amounts and/or kinds of miRNA, such that, for example, the efficiency of the nuclear reprogramming is increased when the level of the miRNA is increased in the somatic cell prior to nuclear reprogramming.
In addition, the present invention provides methods comprising the use of miRNA having a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof, for preparation of induced pluripotent stem cells. For example, the presence of added miRNA can provide the formation of an induced pluripotent stem cell as compared to the lack of formation in the absence of the miRNA. Also, for example when nuclear reprogramming is performed on the same number of somatic cells in the presence of a nuclear reprogramming factor containing the same components in the same concentrations with and without addition of miRNA, increased efficiency can be observed when a greater number of induced pluripotent stem cells are generated in the sample which comprises the addition of miRNA than in the sample without the addition of miRNA. In another embodiment, increased efficiency of induced pluripotent stems cell production can also be achieved with increased amounts of miRNA as compared to miRNA amounts present in the somatic cell prior to nuclear reprogramming.
BEST MODE FOR CARRYING OUT THE INVENTION
The methods of the present invention relate to, e.g., a method for preparing induced pluripotent stem cells, comprising nuclear reprogramming with a nuclear reprogramming factor in the presence of miRNA, wherein said miRNA has a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof. In a preferred embodiment of the present invention, (a) said miRNA is expressed in embryonic stem cells at a higher level than in somatic cells; and (b) said RNA has a property of providing a higher nuclear reprogramming efficiency in the presence of said miRNA than in the absence thereof.
As for the miRNA, for example, its classification and in vivo functions are described in Jikken Igaku (Experimental Medicine), 24, pp. 814-819, 2006; microRNA Jikken Purotokoru (microRNA Experimental Protocol), pp. 20-35, 2008, YODOSHA CO., LTD. The number of nucleotides of miRNA is for example 18 to 25, and preferably about 19 to 23. At present, a database storing data relating to about 1,000 miRNA sequences is available (for example, miRBase, Griffiths-Jones et al. Nucleic Acids Research 36:D154-D158, 2008 (published online Nov. 8, 2007), see also microrna sanger.ac.uk/sequences/index.shtml [online]), and it is possible for those skilled in the art to obtain any miRNA data therefrom, and to readily extract miRNA expressed in embryonic stem cells at a higher level than in somatic cells. In addition, it is also possible to readily specify miRNA expressed in embryonic stem cells at a higher level than in somatic cells by confirming the difference in miRNA expression between embryonic stem cells and somatic cells with use of available techniques for those skilled in the art such as miRNA microarray and real-time PCR analyses.
The difference in the nuclear reprogramming efficiency with and without miRNA can be understood by the following manner, as specifically described in Examples of this application: transgenic mice are generated by insertion of sequences encoding Enhanced Green Fluorescent Protein (EGFP) and a puromycin resistance gene downstream of a Nanog gene promoter region, the expression of which is specific to ES cells; then, three genes, for example, Oct3/4, Sox2, and Klf4, and various miRNAs are introduced into embryonic fibroblasts derived from these transgenic mice to induce nuclear reprogramming, followed by confirmation of the production efficiency of induced pluripotent stem cells. The production efficiency can be determined, for example, by counting the number of colonies. More specifically, the number of colonies can be compared by the following manner: drug selection is started from the 21st day after introduction of the above genes and miRNA; and the number of total colonies and the number of Nanog GFP positive colonies (GFP, the expression of which is induced by the Nanog gene promoter region, is observable under fluorescent microscopy) are counted on the 28th day. It should be understood, however, that: the confirmation of the nuclear reprogramming efficiency is not limited to the above method; appropriate modification and alteration can be made in the above method; and any appropriate method can be employed by those skilled in the art.
As for the miRNA, it is preferable to use miRNA derived from the same animal species as the target animal whose somatic cells are to be reprogrammed. Usable miRNA includes wild type miRNA as well as miRNAs in which one to several nucleotides (for example 1 to 6 nucleotides, preferably 1 to 4 nucleotides, more preferably 1 to 3 nucleotides, yet more preferably 1 or 2 nucleotides, and most preferably 1 nucleotide) are substituted, inserted, and/or deleted, and which are capable of exerting equivalent functions to those of the wild type miRNA in vivo. For example, the miRNA of the present invention includes miRNAs in which one to several nucleotides are substituted, inserted, and/or deleted, and which increase the efficiency of iPS cell production. The miRNA of the present invention also includes miRNAs in which one to several nucleotides are substituted, inserted, and/or deleted, and which improve the efficiency of nuclear reprogramming. The miRNA of the present invention also includes miRNAs in which one to several nucleotides are substituted, inserted, and/or deleted, and which regulate DNA methylation. The present invention also includes such miRNAs wherein the DNA methylation is down-regulated. The present invention also includes such miRNAs wherein the DNA methylation is de novo DNA methylation.
Examples of the miRNA preferably used in the methods of the present invention can include, but are not limited to, one or more miRNA(s) included in the following RNA sequences registered in the miRBase: hsa-miR-372 (MI0000780), hsa-miR-373 (MI0000781), hsa-miR-302b (MI0000772), hsa-miR-302c (MI0000773), hsa-miR-302a (MI0000738), hsa-miR-302d (MI0000774), hsa-miR-367 (MI0000775), hsa-miR-520c (MI0003158), mmu-miR-290 (MI0000388), mmu-miR-291a (MI0000389), mmu-miR-294 (MI0000392), and mmu-miR-295 (MI0000393) (Numbers in the brackets respectively indicate miRBase accession numbers. The symbol “hsa-miR-” represents human miRNA, and the symbol “mmu-miR-” represents mouse miRNA).
In the method of the present invention, miRNAs that have been confirmed to improve the nuclear reprogramming efficiency in the above manner can be used either alone or in combinations of two or more types. In addition, a plurality of miRNAs forming a cluster may also be used. For example, hsa-miR-302-367 which is available as a miRNA cluster, or individual miRNAs from the hsa-miR-302-367 cluster, and the like may be used. Examples of RNA sequences for use in the present invention are shown in SEQ ID NOS: 1 to 14 in the Sequence Listing. SEQ ID NO: 1: mmu-miR-294 (MI0000392); SEQ ID NO: 2: mmu-miR-295 (MI0000393); SEQ ID NO: 3: hsa-miR-372 (MI0000780); SEQ ID NO: 4: hsa-miR-373 (MI0000781); SEQ ID NO: 5: hsa-miR-302b (MI0000772); SEQ ID NO: 6: hsa-miR-302c (MI0000773); SEQ ID NO: 7: hsa-miR-302a (MI0000738); SEQ ID NO: 8: hsa-miR-302d (MI0000774); SEQ ID NO: 9: hsa-miR-367 (MI0000775); SEQ ID NO: 10: hsa-miR-520c (MI0003158); SEQ ID NO: 11: mmu-miR-291a (MI0000389); SEQ ID NO:13: has-miR-371-373 cluster, and SEQ ID NO:14: mmu-miR-290 (MI0000388). In addition, RNA represented by SEQ ID NO: 12: hsa-miR-302-367 cluster can also be preferably used. Among these RNA sequences, some RNA sequences may include a plurality of miRNAs within one sequence. Use of such an RNA sequence may achieve efficient production of iPS cells. Further, an RNA sequence including a plurality of miRNAs within one sequence and one or more other RNA sequence(s) including one or more miRNA(s) can also be used in combination.
miRNA is non-coding RNA which is not translated into a protein. miRNA is first transcribed as pri-miRNA from a corresponding gene, then this pri-miRNA generates pre-miRNA having a characteristic hairpin structure of about 70 nucleotides, and this pre-miRNA is further processed into mature miRNA, which is mediated by Dicer. In the present invention, not only mature miRNA but also pri-miRNA or pre-miRNA can be used as long as the effect of the present invention is not impaired. In addition, miRNA for use in the present invention may be either natural type or non-natural type. Thus, any small RNA or RNA precursor may be used as long as the effect of the present invention is not impaired.
The production method of miRNA for use in the present invention is not specifically limited, although the production can be achieved, for example, by a chemical synthetic method or a method using genetic recombination technique. When the production is carried out by a method using genetic recombination technique, miRNA for use in the present invention can, for example, be produced through transcription reaction with use of a DNA template and a RNA polymerase obtained by means of gene recombination. Examples of usable RNA polymerase include a T7 RNA polymerase, a T3 RNA polymerase, and a SP6 RNA polymerase.
Alternatively, a recombinant vector capable of expressing miRNA can be produced by insertion of miRNA-encoding DNA into an appropriate vector under the regulation of expression control sequences (promoter and enhancer sequences and the like). The type of vector used herein is not specifically limited, although DNA vectors are preferred. Examples thereof can include viral vectors and plasmid vectors. The viral vector is not specifically limited, although retroviral vectors, adenoviral vectors, adeno-associated viral vectors, and the like can be employed. In addition, as to the above plasmids, mammalian expression plasmids well known to those skilled in the art can be employed.
Methods for using a retrovirus as a vector are disclosed in WO 2007/69666 A1; Takahashi et al., Cell 126:663-676, 2006; and Takahashi et al., Cell 131:861-872, 2007, which are herein incorporated by reference in their entireties. Methods for using a lentivirus as a vector are disclosed in Yu et al., Science 318:1917-1920, 2007, which is herein incorporated by reference in its entirety. Methods for using adenovirus as a vector are disclosed in Stadtfeld et al., Science 322:945-949, 2008, which is herein incorporated by reference in its entirety. Methods for using a plasmid as a non-viral vector are disclosed in U.S. Provisional Application No. 61/071,508; U.S. Provisional Application No. 61/136,246; U.S. Provisional Application No. 61/136,615; and U.S. Provisional Application No. 61/193,363 entitled “Method for Nuclear Reprogramming” filed Nov. 21, 2008; and Okita et al., Science 322:949-953, 2008, which are herein incorporated by reference in their entireties. One of ordinary skill in the art could choose and use an appropriate method from among the above known methods, or from any of the other known methods or vectors available in the prior art.
Nuclear reprogramming can be performed in the presence of miRNA in any number of ways. The manner of providing the miRNA is not specifically limited, although examples thereof can include a method for directly injecting miRNA into nuclei of somatic cells, and a method for introducing an appropriate recombinant vector capable of expressing miRNA into somatic cells. However, these methods are not to be considered as limiting.
The method for introducing a recombinant vector into somatic cells is not specifically limited, and can be carried out by any method well known to those skilled in the art. Examples of the employable methods can include transient transfection, microinjection, a calcium phosphate precipitation method, liposome-mediated transfection, DEAE dextran-mediated transfection, electroporation, and methods comprising the use of a gene gun.
As to confirming a nuclear reprogramming factor, for example, the screening method of nuclear reprogramming factor described in International Publication No. WO2005/80598 A1, incorporated by reference herein in its entirety, can be used. Those skilled in the art are able to screen a nuclear reprogramming factor for use in the method of the present invention by referring to the above publication. In addition, the nuclear reprogramming factor can also be confirmed by using a method in which appropriate modification or alteration has been made in the above screening method.
Examples of the combination of genes encoding reprogramming factors are disclosed in International Publication No. WO2007/069666 A1 and its family member U.S. patent application Ser. No. 12/213,035 and U.S. patent application Ser. No. 12/289,873, filed Nov. 6, 2008, entitled “Nuclear Reprogramming Factor and Induced Pluripotent Stem Cells” which are incorporated by reference herein in their entireties. Those skilled in the art are able to appropriately select a gene that can be preferably used for the method of the present invention by referring to the above publication. In addition, other examples of the combinations of genes encoding reprogramming factors are disclosed, for example, in Yu et al., Science 318:1917-20, 2007, incorporated by reference herein in its entirety. Accordingly, those skilled in the art are able to understand the variety of the combination of genes encoding reprogramming factors, and are able to employ an appropriate combination of genes in the method of the present invention, which combination is not disclosed in International Publication No. WO2007/069666 A1 or Yu et al., Science 318:1917-20, 2007, by using the screening method of nuclear reprogramming factor described in International Publication No. WO2005/80598 A1.
Examples of the gene encoding a reprogramming factor that can be used for the method of the present invention can include: one or more gene(s) selected from an Oct family gene, a Klf family gene, a Sox family gene, a Myc family gene, a Lin family gene, and a Nanog gene; preferably one or more gene(s) selected from an Oct family gene, a Klf family gene, a Sox family gene, a Lin family gene, and a Nanog gene, and excluding a Myc family gene; one or more gene(s) selected from an Oct family gene, a Klf family gene, a Myc family gene, a Lin family gene, and a Nanog gene, and excluding a Sox family gene; more preferably a combination of two genes; yet more preferably a combination of three genes; and most preferably a combination of four genes.
Regarding the Oct family gene, Klf family gene, Sox family gene, and Myc family gene, specific examples of these family genes are described in International Publication No. WO2007/069666 A1. Regarding the Lin family gene, those skilled in the art are able to extract the family gene in a similar way. Examples of the Lin family genes include, for example, Lin28 and Lin28b. The NCBI accession numbers of Lin28 are NM—145833 (mouse) and NM—024674 (human). The NCBI accession numbers of Lin28b are NM—001031772 (mouse) and NM—001004317 (human).
In addition, reprogramming factor(s) encoded by one or more gene(s) selected from an Oct family gene, a Klf family gene, a Sox family gene, a Myc family gene, a Lin family gene, and a Nanog gene, may be substituted by, for example a cytokine, or one or more other low molecular weight compound(s) in some cases. Examples of such low molecular weight compound(s) can include low molecular weight compounds having an enhancing action on the expression of one or more gene(s) selected from an Oct family gene, a Klf family gene, a Sox family gene, a Myc family gene, a Lin family gene, and a Nanog gene. Those skilled in the art are able to readily screen such low molecular weight compound(s).
More preferable combinations of genes are as follows:
(a) a combination of two genes comprising an Oct family gene and a Sox family gene;
(b) a combination of three genes comprising an Oct family gene, a Klf family gene, and a Sox family gene;
(c) a combination of four genes comprising an Oct family gene, a Sox family gene, a Lin family gene, and a Nanog gene;
(d) a combination of two genes comprising an Oct family gene and a Klf family gene; and
(e) a combination of three genes comprising an Oct family gene, a Klf family gene, and a Myc family gene.
However, these combinations are not to be considered as limiting.
All of these genes are commonly present in mammals, including human. In order to use the above genes according to the present invention, genes derived from any mammal (for example, derived from a mammal such as human, mouse, rat, cattle, sheep, horse, and monkey) can be employed. In addition, it is also possible to use a wild type gene product, as well as mutant gene products in which several amino acids (for example 1 to 10 amino acids, preferably 1 to 6 amino acids, more preferably 1 to 4 amino acids, yet more preferably 1 to 3 amino acids, and most preferably 1 or 2 amino acids) have been substituted, inserted, and/or deleted, and which have comparable equivalent functions to those of the wild type gene product. For example, as to the c-Myc gene product, a stable type variant, e.g., (T58A) and the like may also be used as well as the wild type. The same principle can be applied to other gene products.
In addition to the above genes, a gene encoding a factor which induces immortalization of cells may also be combined. As disclosed in International Publication No. WO2007/069666 A1, for example, one or more gene(s) selected from a TERT gene, and following genes: SV40 Large T antigen, HPV16 E6, HPV16 E7, and Bmil, can be either solely used or jointly used in an appropriate combination.
Preferable combinations are as follows, for example:
(e) a combination of four genes comprising an Oct family gene, a Klf family gene, a Sox family gene, and a TERT gene;
(f) a combination of four genes comprising an Oct family gene, a Klf family gene, a Sox family gene, and a SV40 Large T antigen gene; and
(g) a combination of five genes comprising an Oct family gene, a Klf family gene, a Sox family gene, a TERT gene, and a SV40 Large T antigen gene.
The Klf family gene may be omitted from the above combinations.
Further, in addition to the above genes, one or more gene(s) selected from Fbx15, ERas, ECAT15-2, Tcl1, and β-catenin may be combined, and/or one or more gene(s) selected from ECAT1, Esg1, Dnmt3L, ECAT8, Gdf3, Sox15, ECAT15-1, Fthl17, Sall4, Rex1, UTF1, Stella, Stat3, and Grb2 may also be combined. These combinations are specifically described in International Publication No. WO2007/069666 A1.
Particularly preferable combinations of genes are as follows:
(1) a combination of two genes comprising Oct3/4 and Sox2;
(2) a combination of three genes comprising Oct3/4, Klf4, and Sox2;
(3) a combination of four genes comprising Oct3/4, Sox2, Lin28, and Nanog;
(4) a combination of four genes comprising Oct3/4, Sox2, TERT, and SV40 Large T antigen gene;
(5) a combination of five genes comprising Oct3/4, Klf4, Sox2, TERT, and SV40 Large T antigen gene;
(6) a combination of two genes comprising Oct3/4 and Klf4;
(7) a combination of three genes comprising Oct3/4, Klf4, and c-Myc; and
(8) a combination of four genes comprising Oct3/4, Sox2, Klf4, and c-Myc.
However, these combinations are not to be considered as limiting.
The factors including the gene products as mentioned above may also be combined with one or more gene product(s) of gene(s) selected from: Fbx15, Nanog, ERas, ECAT15-2, Tcl1, and β-catenin. Further, these factors may also be combined with one or more gene product(s) of gene(s) selected from: ECAT1, Esg1, Dnmt3L, ECAT8, Gdf3, Sox15, ECAT15-1, Fth117, Sall4, Rex1, UTF1, Stella, Stat3, and Grb2, for example. These gene products are disclosed in International Publication No. WO2007/069666 A1. However, gene products that can be included in the nuclear reprogramming factors of the present invention are not limited to the gene products of genes specifically described above. The nuclear reprogramming factors of the present invention can include other gene products which can function as a nuclear reprogramming factor, as well as one or more factors involving differentiation, development, or proliferation, and factors having other physiological activities. It should be understood that the aforementioned aspect may also be included within the scope of the present invention.
Among these genes, if one or more gene product(s) is/are already expressed in somatic cells to be reprogrammed, such gene products can be excluded from the factors to be introduced. For example, one or more gene(s) besides the already-expressed gene(s) can be introduced into somatic cells by an appropriate gene introduction method, for example, a method using a recombinant vector. Alternatively, among these genes, if one or more gene product(s) is/are introduced into nuclei by a technique such as addition of an HIV virus-derived TAT peptide and/or nuclear localization signal to form a fusion protein or by a technique such as nuclear microinjection, or simply by addition of a small molecule capable of diffusing across the plasma membrane, the other one or more gene(s) can be introduced by an appropriate gene introduction method, for example, a method using a recombinant vector.
In addition, a gene product serving as a nuclear reprogramming factor may be either a protein itself produced from the abovementioned gene, or in the form of a fusion gene product between such a protein and another protein, a peptide, or the like. For example, a fusion protein having Green Fluorescent Protein (GFP) and a fusion gene product having a peptide such as a histidine tag may also be used. Further, use of a prepared fusion protein having a HIV virus-derived TAT peptide enables the promotion of endocytosis of a nuclear reprogramming factor through cell membrane, and also enables the induction of reprogramming by simply adding such a fusion protein into the medium while avoiding complicated manipulations such as gene introduction. The preparation method of the aforementioned fusion gene product is well known to those skilled in the art, and therefore those skilled in the art are able to readily design and prepare an appropriate fusion gene product according to the purpose.
In this application, the term “induced pluripotent stem cells (iPS cells)” refers to cells having similar properties to those of ES cells, and more specifically the term includes undifferentiated cells which are reprogrammed from somatic cells and have pluripotency and proliferation potency. However, this term is not to be construed as limiting in any sense, and should be construed to have its broadest meaning. The preparation method of induced pluripotent stem cells with the use of a nuclear reprogramming factor is described in International Publication No. WO2005/80598 A 1 (the term “ES-like cell” is used in this publication), and methods for isolating induced pluripotent stem cells are also specifically described. In addition, specific examples of the reprogramming factor and specific examples of the reprogramming method of somatic cells with use of such a reprogramming factor are disclosed in International Publication No. WO2007/069666 A1. Accordingly, it is desirable for those skilled in the art to refer to these publications for carrying out the present invention.
The preparation method of induced pluripotent stem cells from somatic cells by the method of the present invention is not specifically limited, and any method can be employed as long as the method enables nuclear reprogramming of somatic cells with a nuclear reprogramming factor in the presence of miRNA in an environment where somatic cells and induced pluripotent stem cells can grow. For example, a vector comprising a gene which can express a nuclear reprogramming factor can be used to introduce such a gene into somatic cells, and at either the same or different timing, a recombinant vector which can express miRNA can be introduced into the somatic cells. If such vectors are used, two or more genes may be incorporated into a vector to effect simultaneous expression of respective gene products in somatic cells.
When gene(s) and/or miRNA are introduced into somatic cells with use of a vector which can express the above gene(s), the expression vector may be introduced into somatic cells that have been cultured on feeder cells, or the expression vector may also be introduced into somatic cells alone. The latter method is sometimes more suitable in order to improve the introduction efficiency of the expression vector. As to the feeder cells, there may be appropriately used feeder cells for use in culture of embryonic stem cells. Examples thereof can include primary culture cells of 14 or 15 day-mouse embryonic fibroblasts and STO cells of fibroblast cell line, which are treated with either radiation or a drug such as mitomycin C.
The culture of somatic cells introduced with a nuclear reprogramming factor under an appropriate condition leads to autonomous nuclear reprogramming, as a result of which induced pluripotent stem cells can be produced from somatic cells. The process for introducing a gene encoding a nuclear reprogramming factor and/or miRNA into somatic cells with use of an expression vector to thereby obtain induced pluripotent stem cells can be performed in accordance with, for example, a method using a retrovirus. Examples of such method include methods described in publications such as Takahashi et al., Cell 126:663-76, 2006; Takahashi et al., Cell 131:861-72, 2007; Yu et al., Science 318:1917-20, 2007. When human induced pluripotent stem cells are to be produced, it is desirable to set the cell culture density after the introduction of an expression vector to be lower than normal cases for culturing animal cells. For example, it is preferable to keep culturing at a density of 1×104 to 1×105 cells/10 cm dish, and more preferably about 5×104 cells/10 cm dish. The medium for use in culture is not specifically limited, and can be appropriately selected by those skilled in the art, although for example it is sometimes preferable to use a medium suitable for human ES cell culture for the production of human induced pluripotent stem cells. The medium selection and culture condition can be referred to the above publications.
Thus produced induced pluripotent stem cells can be checked with various markers specific to undifferentiated cells, and the means therefor is described in the above publications specifically in detail. For example, some pluripotent cell markers include: alkaline phosphatase (AP); ABCG2; stage specific embryonic antigen-1 (SSEA-1); SSEA-3; SSEA-4; TRA-1-60; TRA-1-81; Tra-2-49/6E; ERas/ECAT5, E-cadherin; βIII-tubulin; α-smooth muscle actin (α-SMA); fibroblast growth factor 4 (Fgf4), Cripto, Dax1; zinc finger protein 296 (Zfp296); N-acetyltransferase-1 (Nat1); (ES cell associated transcript 1 (ECAT1); ESG1/DPPA5/ECAT2; ECAT3; ECAT6; ECAT7; ECAT8; ECAT9; ECAT10; ECAT15-1; ECAT15-2; Fth117; Sall4; undifferentiated embryonic cell transcription factor (Utf1); Rex1; p53; G3PDH; telomerase, including TERT; silent X chromosome genes; Dnmt3a; Dnmt3b; TRIM28; F-box containing protein 15 (Fbx15); Nanog/ECAT4; Oct3/4; Sox2; Klf4; c-Myc; Esrrb; TDGF1; GABRB3; Zfp42, FoxD3; GDF3; CYP25A1; developmental pluripotency-associated 2 (DPPA2); and T-cell lymphoma breakpoint 1 (Tcl1); DPPA3/Stella; DPPA4. Other markers can include Dnmt3L; Sox15; Stat3; Grb2; SV40 Large T Antigen; HPV16 E6; HPV16 E7, β-catenin, and Bmi1. Such cells can also be characterized by the down-regulation of markers characteristic of the differentiated cell from which the iPS cell is induced. For example, iPS cells derived from fibroblasts may be characterized by down-regulation of the fibroblast cell marker Thy1 and/or up-regulation of SSEA-3 and 4. It is understood that the present invention is not limited to those markers listed herein, and encompasses markers such as cell surface markers, antigens, and other gene products including ESTs, RNA (including microRNAs and antisense RNA), DNA (including genes and cDNAs), and portions thereof.
Various media capable of retaining undifferentiation property and pluripotency of ES cells and various media incapable of retaining these properties are known in the art, and appropriate combination of these media enables efficient isolation of induced pluripotent stem cells. The differentiation ability and proliferation potency of thus isolated induced pluripotent stem cells can be readily checked by those skilled in the art, with use of general checking means for ES cells. In addition, colonies of induced pluripotent stem cells can be obtained by growing thus produced induced pluripotent stem cells under an appropriate condition, and the presence of these induced pluripotent stem cells can be identified with reference to the shape of their colonies. For example, it is known that mouse induced pluripotent stem cells form raised colonies, while human induced pluripotent stem cells form flat colonies. These colony shapes are respectively very similar to those of mouse ES cells and human ES cells, and those skilled in the art are thus able to identify these produced induced pluripotent stem cells with reference to the shape of their colonies.
The type of somatic cell to be reprogrammed by the method of the present invention is not specifically limited, and any somatic cell can be used. For example, somatic cells derived from any mammal (for example, derived from a mammal such as human, mouse, rat, cattle, sheep, horse, and monkey) can be employed. Not only embryonic somatic cells but also neonatal somatic cells, matured somatic cells, and tissue stem cells may also be used. In addition, various somatic cells such as skin cells, liver cells, and gastric mucosa cells can be reprogrammed. For use of induced pluripotent stem cells in therapies against diseases, it is desirable to use somatic cells isolated from the patient. For example, somatic cells involved in a disease and somatic cells associated with a therapy for a disease can be used.
The application of induced pluripotent stem cells produced by the method of the present invention is not specifically limited, and these cells can be used for every examination/study to be performed with use of ES cells, and for any disease therapy which utilizes ES cells. For example, induced pluripotent stem cells obtained by the method of the present invention can be induced into desired differentiated cells (such as nerve cells, myocardial cells, blood cells and insulin-producing cells) by treatment with retinoic acid, a growth factor such as EGF, or glucocorticoid, so that appropriate tissue can be formed. Stem cell therapies through autologous cell transplantation can be achieved by returning these differentiated cells or tissue obtained in the above manner, into the patient. However, the application of the induced pluripotent stem cells of the present invention is not to be limited to the abovementioned specific aspects.
EXAMPLES
The present invention will be explained more specifically with reference to the following examples. However, the scope of the present invention is not limited to these examples.
Example 1
Preparation of Induced Pluripotent Stem Cells Through Nuclear Reprogramming of Mouse Embryonic Fibroblasts
pMXs-based retroviral vectors, which respectively encode each of three genes of mouse-derived Oct3/4, Sox2, and Klf4, control DsRed or each miRNA of 18 types of miRNAs, were transfected into PLAT-E cells using FuGENE 6 reagent (Roche) to get retroviruses. On the next day, embryonic fibroblasts (Nanog GFP MEF, WO2007/069666 A 1) derived from transgenic mice generated by insertion of sequences encoding EGFP gene and puromycin resistance gene downstream of a Nanog gene promoter region, were seeded at 1×105 cells/well in 6-well plates. On the next day, these cells were infected with retroviruses expressing Oct3/4, Sox2, Klf4, and each type of miRNA selected from 18 types of miRNAs, at a ratio of 1 ml of virus mixture expressing these three factors to 1 ml of virus solution expressing miRNA or DsRed, so as to prepare induced pluripotent stem cells through nuclear reprogramming.









TABLE 1





miRNA
miRNA sequence (other name(s)
miRBase


number
indicated in parentheses)
accession number

















1
mmu-miR-150
MI0000172


2
mmu-miR-182
MI0000224


3
mmu-miR-126
MI0000153


4
mmu-miR-290-295 cluster


5
mmu-miR-290
MI0000388



(mmu-miR-290-5p/290-3p)


6
mmu-miR-291a
MI0000389



(mmu-miR-291a-5p/291a-3p)


7
mmu-miR-292
MI0000390



(mmu-miR-292-5p/292-3p)


8
mmu-miR-294
MI0000392



(mmu-miR-294/294*)


X(9)
mmu-miR-295
MI0000393



(mmu-miR-295/295*)


10
mmu-miR-17-92 cluster


11
mmu-miR-323
MI0000592


12
mmu-miR-130b
MI0000408


13
mmu-miR-7a-1
MI0000728


14
mmu-miR-7a-2
MI0000729


15
mmu-miR-205
MI0000248


16
mmu-miR-200a
MI0000554


17
mmu-miR-200c
MI0000694


18
mmu-miR-mix





*indicates star form of miRNA.






From the third day after infection, the cells were cultured in an ES cell medium containing LIF. On the fourth day after infection, the cells were harvested by trypsinization, and the whole amount thereof was spread over mytomicin-C treated STO cells as feeder cells. Every other day thereafter, the ES cell medium containing LIF was replaced. From the 21st day after infection, drug selection was started with addition of puromycin at a final concentration of 1.5 μg/ml. On the 28th day, the number of Nanog GFP positive colonies (GFP, the expression of which is induced by a Nanog gene promoter region, can be observed with the use of fluorescent microscopy) was counted. As a control, DsRed was used in place of miRNA. The results are shown in FIG. 1. It was found that mmu-miR-294 and mmu-miR-295 could respectively improve the nuclear reprogramming efficiency when introduced into mouse embryonic fibroblasts together with three factors of Oct3/4, Sox2, and Klf4, and could enable efficient establishment of induced pluripotent stem cells.
Example 2
Preparation of Induced Pluripotent Stem Cells Through Nuclear Reprogramming of Mouse Tail Tip Fibroblasts
pMXs-based retroviral vectors, which respectively encode each of three genes of mouse-derived Oct3/4, Sox2, and Klf4, DsRed (control), or mmu-miR-295, were transfected into PLAT-E cells using FuGENE 6 reagent (Roche) to get retroviruses. On the next day, tail tip fibroblasts (Nanog GFP tailtip fibroblasts) derived from transgenic mice generated by insertion of sequences encoding EGFP gene and puromycin resistance gene downstream of a Nanog gene promoter region, were seeded at 1×105 cells/well in 6-well plates. On the next day, these cells were infected with retroviruses expressing three factors of Oct3/4, Sox2, and Klf4, and either DsRed or mmu-miR-295, at a ratio of 1:1:1:1, so as to prepare induced pluripotent stem cells through nuclear reprogramming.
Since the third day after infection, the cells were cultured in an ES cell medium containing LIF. On the fourth day after infection, the cells were harvested by trypsinization and the whole amount thereof was spread over mytomicin-C treated STO cells as feeder cells. Every other day thereafter, the ES cell medium containing LIF was replaced. From the 7th, 21st, or 28th day after infection, drug selection was started with addition of puromycin at a final concentration of 1.5 μg/ml. On the 39th day, the number of total colonies and the number of Nanog GFP positive colonies (GFP, the expression of which is induced by Nanog promoter region, can be observed with fluorescent microscopy) were counted. The results are shown in FIG. 2. It was found that mmu-miR-295 could improve the nuclear reprogramming efficiency when introduced into mouse tail tip fibroblasts together with three factors of Oct3/4, Sox2, and Klf4, and could accelerate the reprogramming speed and enable efficient establishment of induced pluripotent stem cells.
Example 3
Preparation of Induced Pluripotent Stem Cells Through Nuclear Reprogramming of Adult Human Dermal Fibroblasts
pMXs-based retroviral vectors, which encode three genes of human-derived OCT3/4, SOX2, and KLF4, and control DsRed or either 23 types of miRNAs or an miRNA cluster, were transfected into PLAT-E cells using FuGENE 6 reagent (Roche) to get retroviruses. On the next day, adult human dermal fibroblasts (aHDF) which were generated to express a rodent ecotropic virus receptor Slc7a1 (aHDF-Slc7a1), were seeded at 3×105 cells/well in 6-cm dishes. On the next day, the cells were infected with retroviruses expressing three genes of OCT3/4, SOX2, KLF4, and various types of miRNAs, at a ratio of 1:1:1:1, so as to produce induced pluripotent stem cells through nuclear reprogramming.









TABLE 2





miRNA
miRNA sequence (othername(s)
miRBase


number
indicated in parentheses)
accession number

















1
hsa-miR-371
MI0000779



(hsa-miR-371-5p/371-3p)


2
hsa-miR-372
MI0000780


3
hsa-miR-373
MI0000781



(hsa-miR-373/373*)


4
hsa-miR-371-373 cluster


5
hsa-miR-93
MI0000095



(hsa-miR-93/93*)


6
hsa-miR-302a
M I0000738



(hsa-miR-302a/302a*)


7
hsa-miR-302b
MI0000772



(hsa-miR-302b/302b*)


8
hsa-miR-302c
MI0000773



(hsa-miR-302c/302c*)


9
hsa-miR-302d
MI0000774



(hsa-miR-302d/302d*)


10
hsa-miR-367
MI0000775



(hsa-miR-367/367*)


11
hsa-miR-302-367 cluster


12
hsa-miR-520a
MI0003149



(hsa-miR-520a-5p/520a-3p)


13
hsa-miR-520b
MI0003155


14
hsa-miR-520c
MI0003158



(hsa-miR-520c-5p/520c-3p)


15
hsa-miR-520d
MI0003164



(hsa-miR-520d-5p/520d-3p)


16
hsa-miR-520e
MI0003143


17
mmu-miR-290-295 cluster


18
mmu-miR-290
MI0000388



(mmu-miR-290-5p/290-3p)


19
mmu-miR-291a
MI0000389



(mmu-miR-291a-5p/291a-3p)


20
mmu-miR-292
MI0000390



(mmu-miR-292-5p/292-3p)


21
mmu-miR-293
MI0000391



(mmu-miR-293/293*)


22
mmu-miR-294
MI0000392



(mmu-miR-294/294*)


23
mmu-miR-295
MI0000393



(mmu-miR-295/295*)









On the sixth day after infection, the cells were harvested by trypsinization and the whole amount of 5×105 cells was spread over on mytomicin-C treated STO cells as feeder cells. Every other day thereafter, human ES cell medium containing bFGF (ReproCELL) was replaced. On the 24th, 32nd, and 40th day, the number of total colonies and the number of colonies having morphology of human ES-like cells were counted. As a control, DsRed was used in place of miRNA. The results are shown in FIG. 3. It was found that the number of colonies of induced pluripotent stem cells increased twice or more, as compared to the control, by introduction of three genes in the presence of hsa-miR-372, 373, 302b, 302-367 cluster (including 302b, 302c, 302a, 302d, and 367), 520c, mmu-miR-291a, 294, or 295.
Example 4
Preparation of Induced Pluripotent Stem Cells Through Nuclear Reprogramming of Adult Human Dermal Fibroblasts
3×105 aHDF-S1c7a1 cells were plated on 60 mm gelatin coated dishes and infected with retrovirus to express DsRed, 4 factors (OCT3/4, SOX2, c-MYC, and KLF4), or 3 factors (OCT3/4, SOX2, KLF4) in the presence of various miRNAs independently. Six days after infection, 5×105 aHDF-S1c7a1 cells were reseeded on mytomicin-C treated STO cells. Forty days after infection, the number of human ES-like colonies was counted. The same experiment was repeated three times.
FIG. 4A shows the results of three independent experiments. It was found that the number of colonies of induced pluripotent stem cells increased, as compared to the control, by introduction of three genes in the presence of hsa-miR-372, 373/373* (hsa-miR-373), 371-373 cluster (including 371, 372, and 373), 302b/302b* (hsa-miR-302b), 302-367 cluster (including 302b, 302c, 302a, 302d, and 367), 520c-5p/520c-3p (hsa-miR-520c), mmu-mir-290-5p/290-3p (mmu-mir-290), mmu-mir-291a-5p/291a-3p (mmu-mir-291a), 294/294* (mmu-mir-294), or 295/295* (mmu-mir-295).
FIG. 4B shows the morphology of ES-like colonies of iPS cells by using microscopy.
Example 5
Expression of ES Cell Markers in iPS Cells Produced by Nuclear Reprogramming of Mouse Tail Tip Fibroblasts (TTFs) with 4 Factors (OCT3/4, SOX2, c-MYC, and KLF4) and with 3 Factors (OCT3/4, SOX2, and KLF4)+mmu-miR-295/295*
5×104 FbNg TTFs (TTFs derived from Fbx15-β geo/Nanog-IRES-Puror reporter mouse) cells were plated on gelatin coated 6-well plates and infected with retrovirus to express 3 factors (Oct3/4, Sox2, Klf4) plus either DsRed (Myc(−)3f+DsRed), mmu-miR-295/295* (Myc(−)3f+mmu-miR-295/295*), or c-Myc (4 factor). On Day 4 after infection, all the cells (Myc( ) f+DsRed; Myc(−)3f+mmu-miR-295/295*) or 20 times diluted cells (4 factors) were reseeded on Puromycin and Hygromycin-resistant-MSTO (PH-MSTO) cells. Puromycin selection was started on Day 7, 14, 21, 28.
RT-PCR analysis using the Rever Tra Ace Kit (Takara) showed that the iPS cells transfected with 4 factors (OCT3/4, SOX2, c-MYC, and KLF4), or with 3 factors (OCT3/4, SOX2, and KLF4)+mmu-miR-295/295* expressed the ES cell specific marker genes Oct3/4, Sox2, Nanog, and that the amounts of expression thereof were equivalent to those obtained with mouse ES cells(ES) and mouse iPS cells (Fbx iPS) (FIG. 5).
Example 6
Preparation of Induced Pluripotent Stem Cells Through Nuclear Reprogramming of Mouse Embryonic Fibroblasts with 3 Factors (Oct3/4, Klf4, and c-Myc) with miRNAs
1×105 Nanog MEFs (MEFs derived from Nanog-IRES-Puror reporter mouse) were plated on gelatin coated 6-well plates and infected with retrovirus to express 3 factors (Oct3/4, c-MycWT(wild type), and Klf4) with mmu-miR-290-295 cluster, 290-5p/290-3p (mmu-miR-290), 291a-5p/291a-3p (mmu-miR-291), 292-5p/292-3p (mmu-miR-292), 293/293* (mmu-miR-293), 294/294* (mmu-miR-294) or 295/295* (mmu-miR-295) miRNAs (1:1). On day 4 after infection, half of the cells were reseeded on Puromycin and Hygromycin-resistant-MSTO (PH-MSTO) cells. Puromycin selection was started from 14 days after infection.
FIG. 6A shows the number of Nanog GFP positive colonies. The results of three independent experiments are shown with different colors. “DsRed” indicates the combination of Oct3/4, Klf4, c-Myc and DsRed.
FIG. 6B shows the results of RT-PCR analysis. RT-PCR analysis using the Rever Tra Ace Kit (Takara) showed that the iPS cells transfected with 4 factors (OCT3/4, SOX2, c-MYC, and KLF4), or with 3 factors (OCT3/4, SOX2, and KLF4)+mmu-miR-290-295 cluster, 291a-5p/291a-3p, 294/294* and 295/295* expressed the ES cell specific marker genes Oct3/4, Sox2, Nanog, and that the amounts of expression thereof were equivalent to those obtained with mouse ES cells (ES) and mouse iPS cells (Fbx iPS).
Example 7
iPS Induction with Fb-Ng MEFs (MEFs Derived from Fbx15-β geo/Nanog-IRES-Puror reporter mouse) over-expressing Oct3/4, c-Myc, and Klf4 (“Sox(−)”)+mmu-miR-295/295* or hsa-miR-302-367 Cluster miRNAs
1×105 Fb-Ng MEFs (MEFs derived from Fbx15-β geo/Nanog-IRES-Puror reporter mouse) were plated on gelatin coated 6-well plates and infected with retrovirus to express 3 factors (Oct3/4, c-MycWT(wild type), Klf4)+miR-295/295*or hsa-miR-302-367 cluster. On day 4 after infection, cells were reseeded on Puromycin and Hygromycin resistant mytomycin-C treated STO cells (PH-MSTO) by in 6-well or 10 cm dishes. Puromycin selection was started from 7 days after infection.
FIG. 7A shows cell morphology of MEFs transduced with Oct3/4, c-Myc, and Klf4 (“Sox(−)”)+mmu-miR-295/295*. The colonies showed morphology similar to that of ES cells. FIG. 7B shows chimeras derived from iPS cells induced with Sox(−)3f+mmu-miR-295/295*.
FIG. 7C shows embryoid body (EB)-mediated in vitro differentiation by human iPS cells. Human iPS cells (61B1, 61N2) which were established by transduction of 4 genes (OCT3/4, KLF4, SOX2, and c-MYC, i.e. “OSMK”) or 3 genes (OCT3/4, KLF4, and c-MYC, i.e., “OMK(SOX(−)”)+hsa-miR-302-367 cluster miRNA were plated on a low-binding dish, and embryoid bodies were formed on 100 mm dishes in accordance with the method described in Takahashi et al., Cell 131:861-872, 2007. After culturing for 2 weeks, the cells were stained using an antibody against each of α-fetoprotein (R&D systems) which is a differentiation marker for endodermal cells, α-smooth muscle actin (DAKO) which is a differentiation marker for mesodermal cells, and Glial Fibrillary Astrocytic Protein (GFAP) (DAKO) which is a differentiation marker for ectodermal cells. The expression of each marker was confirmed by staining. Nuclei were stained with Hoechst 33342 (Invitrogen).
Example 8
iPS Induction with 4 factors (OCT3/4, SOX2, MYC, KLF4) or 3 factors (OCT3/4, MYC, KLF4, i.e., “SOX(−)3”) with and without Various miRNAs
3×105 cells of aHDF-Slc7a1 cells were plated on 60 mm gelatin coated dishes and infected with retrovirus to express 4 factors: OCT3/4, SOX2, c-MYC, KLF4 (OSMK) or 3 factors: SOX(−)3factors (OMK) in the presence of miRNAs as indicated (OMK:mock or miRNAs=2.5:1.5), or with 2 factors: OCT3/4+KLF4 (OK) in the presence of miRNAs as indicated. Cells were infected with DsRed as control. Six days after infection, 5×105 aHDF-Slc7a1 cells were reseeded on mytomicin-C treated STO cells (MSTOcells). On Day 40 after infection, the number of ES-like colonies was counted.
TABLE 3 shows the number of human ES(hES)-like colonies in aHDF-Slc7a1 cells tranduced with OSMK, OMK with or without miRNAs, and with OK with or without miRNAs. The hES-like colonies showed in cells transduced with OSMK, OMK+miRNAs (hsa-miR-371-373 cluster, hsa-miR-302-367 cluster, or hsa-miR-371-373 cluster+302-367 cluster) were detected by six independent experiments (Exp. 54, 61, 63, 114, 130, and 133).













TABLE 3





Number of hES-like colonies
Exp. 54
Exp. 61
Exp. 63
Exp. 114
Exp. 130
Exp. 133























A
control
DsRed
0
0
0
0
0
0


B
OSMK
Y4f (O:S:M:K = 1:1:1:1)
5
41
54
37
39
100


G

Y4f (OMK:S = 2.5:1.5)


13
7
4
22


H
OMK + mock
Sox(−)Y3f + mock
0
0
0
0
0
0


I
or miRNA
Sox(−)Y3f + h-miR-371-373 cluster
0
0
1
0
0
0


J

Sox(−)Y3f + h-miR-302-367 cluster
0
2
3
0
8
5


K

Sox(−)Y3f + h-mir-371-373 cluster + 302-367 cluster



0
0
6


M
OK + mock
OK + mock



0
0
0


N
or miRNA
OK + h-miR-371-373 cluster



0
0
0


O

OK + h-miR-302-367 cluster



0
0
4


P

OK + h-miR-371-373 cluster + 302-367 cluster



1
0
0









FIG. 8 shows cell morphology of iPS cells induced with OSMK (61B1); OMK (SOX(−))+hsa-miR-302-367 cluster miRNA (61N2); and OK+hsa-miR-302-367 cluster miRNA (13301).
INDUSTRIAL APPLICABILITY
The present invention provides an efficient method for preparing induced pluripotent stem cells. The method of the present invention has higher nuclear reprogramming efficiency as compared to conventional methods. For example, safe induced pluripotent stem cells can be efficiently produced without using c-Myc or gene products thereof. Accordingly, the method of the present invention enables efficient production of highly safe induced pluripotent stem cells from a patient's own somatic cells. Cells differentiated from such pluripotent stem cells (for example, myocardial cells, insulin-producing cells, or nerve cells) can be safely utilized in stem cell transplantation therapies for treatment of various diseases, such as heart failure, insulin dependent diabetes mellitus, Parkinson's diseases, and spinal cord injury.
Although the present invention has been described in considerable detail with regard to certain versions thereof, other versions are possible, and alterations, permutations, and equivalents of the versions shown will become apparent to those skilled in the art upon a reading of the specification and study of the drawings. Also, the various features of the versions herein can be combined in various ways to provide additional versions of the present invention. Furthermore, certain terminology has been used for the purposes of descriptive clarity, and not to limit the present invention. Therefore, any appended claims should not be limited to the description of the preferred versions contained herein and should include all such alterations, permutations, and equivalents as fall within the true spirit and scope of the present invention.
Having now fully described this invention, it will be understood to those of ordinary skill in the art that the methods of the present invention can be carried out with a wide and equivalent range of conditions, formulations, and other parameters without departing from the scope of the invention or any embodiments thereof.
All the disclosures of the above publication are incorporated herein by reference.
The attached Sequence Listing includes SEQ ID NOs: 13 and 14, as well as those sequences disclosed in PCT/JP2008/59586, which is incorporated by reference herein in its entirety.

## Claims

1. A nuclear reprogramming factor for a somatic cell, which comprises isolated miRNA comprising at least 15 contiguous nucleotides in the nucleotide sequence selected from the group consisting of: hsa-miR-372, hsa-miR-373, hsa-miR-371-373 cluster, hsa-miR-302b, hsa-miR-302c, hsa-miR-302a, hsa-miR-302d, hsa-miR-367, hsa-miR-302-367 cluster, hsa-miR-520c, mmu-miR-290, mmu-miR-291a, mmu-miR-294, and mmu-miR-295, and isolated genes selected from the group consisting of an Oct family gene and a Klf family gene.

2. The nuclear reprogramming factor according to claim 1, wherein the nucleotide sequence is selected from the group consisting of SEQ ID NOs: 1 to 14.

3. The nuclear reprogramming factor according to claim 1, wherein the miRNA is selected from the group consisting of: hsa-miR-372; hsa-miR-373 or hsa-miR-373/373*; hsa-miR-371-373 cluster; hsa-miR-302b or hsa-miR-302b/302b*; hsa-miR-302-367 cluster; hsa-miR-520c or hsa-miR-520c-5p/520c-3p; mmu-miR-291a or mmu-miR-291a-5p/291a-3p; mmu-miR-294 or mmu-miR-294/294*; and mmu-miR-295 or mmu-miR-295/295*.

4. The nuclear reprogramming factor according to claim 3, wherein the miRNA consists of hsa-miR-302-367 cluster.

5. The nuclear reprogramming factor according to claim 3, wherein the miRNA consists of mmu-miR-295/295* or 294/294*.

6. The nuclear reprogramming factor according to claim 1, wherein the Oct family gene and the Klf family gene is selected from Oct3/4 and Klf4.

7. The nuclear reprogramming factor according to claim 1, wherein the nuclear reprogramming factor further comprises a Sox family gene.

8. The nuclear reprogramming factor according to claim 7, wherein the Sox family gene is Sox2.