# Patent

## Title
Constructs for making induced pluripotent stem cells

## Abstract

Systems, constructs, and methods for reprogramming cells are provided. In one aspect, for example, a transformation construct for generating iPS cells can include an expression vector having a plurality of reprogramming factors, each reprogramming factor being under control of a separate promoter.

## Background
PRIORITY DATA
This application is a continuation-in-part of U.S. patent application Ser. No. 13/960,305, filed on Aug. 6, 2013, which is a continuation of Patent Cooperation Treaty Patent Application Serial No. PCT/US2012/025117, filed on Feb. 14, 2012, which claims the benefit of U.S. Provisional Patent Application Ser. No. 61/442,695, filed on Feb. 14, 2011, all of which are incorporated herein by reference.


GOVERNMENT INTEREST
This invention was made with government support under grant numbers R01 NS033123 and NS073009 awarded by National Institutes of Health. The government has certain rights in this invention.


BACKGROUND
Current protocols for the generation of induced pluripotent stem (iPS) cells from somatic cells are slow (e.g. 30-45 days) and are inefficient (<0.1% of cells are reprogrammed). Additionally, the generation of iPS cells from somatic cells achieved by simultaneous viral transduction of defined reprogramming transcription factors using Lenti- or Retro- or Adeno-viruses requires multiple viral vectors for gene delivery. Lenti- or Retro-viruses can also result in insertional mutagenesis and can present significant barriers to research, clinical, and therapeutic application of iPS cells. A single gene delivery system does not ensure the infectivity and co-expression of all genes in one cell which is critical for reprogramming. Despite the progress in embryonic stem (ES) cells research in recent years, feeder cells such as inactivated mouse embryonic fibroblasts (iMEF) are still required to generate iPS cells from human or mouse fibroblasts. Feeder cells provide the essential support and nutrients to allow ES/iPS cells to grow, attach, and proliferate. The risk of contamination of viruses or other macromolecules from the mouse cells limits the use of such iPS cells for therapeutic purposes.
SUMMARY
The present disclosure provides systems, constructs, and methods for reprogramming cells. In one aspect, for example, a transformation construct for generating iPS cells can include an expression vector having a plurality of reprogramming factors, where each reprogramming factor is under control of a separate promoter. In one aspect, the expression vector can be selected from plasmids, viruses, and combinations thereof. In another aspect, the expression vector can be selected from adenoviral vectors, episomal vectors, retroviral vectors, and lentiviral vectors. In one specific aspect the expression vector can be an episomal vector.
Various reprogramming factors are contemplated for use in aspects of the present invention. In one aspect, for example, the plurality of reprogramming factors can include OCT3/4, SOX2, and at least one member selected from KLF4, c-Myc, NANOG, or LIN28. In another aspect, the plurality of reprogramming factors can include OCT3/4, SOX2, KLF4, and c-Myc. In yet another aspect, the plurality of reprogramming factors can consist of OCT3/4, SOX2, and KLF4. In a further aspect, the plurality of reprogramming factors includes OCT3/4, SOX2, NANOG, and LIN28. Furthermore, in one aspect, the expression vector can have a sequence that is at least 80% homologous to SEQ ID 72. In yet another aspect, the expression vector has a sequence that is at least 95% homologous to SEQ ID 72. In a further aspect, the expression vector has the sequence of SEQ ID 72.
Various promoters and/or sets of promoters are contemplated, and any appropriate promoter is considered to be within the present scope. In one aspect, for example, at least one of the reprogramming factors is under the control of a CMV promoter. In another aspect, the CMV promoter is a weak CMV promoter. Furthermore, in various aspects the expression vector can further include a reporter sequence under control of a separate promoter.
The present disclosure additionally provides methods of generating iPS cells. In one aspect such a method can include separately cloning a plurality of reprogramming factors including OCT3/4, SOX2, and at least one member selected from the group consisting of KLF4, c-Myc, NANOG, or LIN28 into separate vectors, where each reprogramming factor is controlled by a separate promoter. The method can further include consecutively cloning each of the reprogramming factors including each promoter into a single shuttle vector, linearizing the shuttle vector and recombining in bacterial cells to create an expression vector, infecting transformable cells with the expression vector, and growing the transformable cells for a period of time to generate iPS cells. In one specific aspect, the reprogramming factors can be cloned into separate vectors using blunt end ligation. In some aspects, the present method can further include generating the iPS cells in the absence of feeder cells, in the absence of a matrigel matrix, or in the absence of feeder cells and a matrigel matrix.
Furthermore, in one aspect an iPS cell is provided that is generated according to the methods and techniques of the present disclosure. In another aspect, a subsequent generation cell ultimately obtained from the iPS cell according to the present disclosure is provided. In yet another aspect, the differentiated cell derived from the iPS cell according to the present disclosure is provided. Non-limiting examples of such differentiated cell types can include endoderm, ectoderm, mesoderm, or an appropriate combination thereof. In some aspects, the differentiated cell can be a neuron.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic view of a vector system in accordance with one aspect of the present disclosure;
FIG. 2A is a schematic view of a vector system in accordance with another aspect of the present disclosure;
FIG. 2B shows data demonstrating protein expression of multiple reprogramming factors in accordance with another aspect of the present disclosure;
FIG. 3A is a schematic view of an adenoviral construct in accordance with yet another aspect of the present disclosure;
FIG. 3B shows iPS cells generated with adenoviral constructs without feeder cells, IMR90 cells transduced with Ad-GFP, and iPS cell colonies in IMR90 cells transduced with Ad-SOK in accordance with another aspect of the present disclosure;
FIG. 4A shows IMR90 cells transduced with adenoviruses, either Ad-GFP (a) or Ad-SOK (b) in accordance with a further aspect of the present disclosure; and
FIG. 4B shows RT-PCR data of EX cell marker genesin accordance with yet a further aspect of the present disclosure;
FIG. 5A shows a timeline for transformation in accordance with another aspect of the present disclosure;
FIG. 5B shows cells tested for ALP staining in accordance with another aspect of the present disclosure;
FIG. 5C shows a Western blot analyses in accordance with another aspect of the present disclosure;
FIG. 6A shows real-time PCR and Western blot data in accordance with another aspect of the present disclosure;
FIG. 6B shows real-time PCR and Western blot data in accordance with another aspect of the present disclosure;
FIG. 7A shows data demonstrating expression of markers in iPS cells in accordance with another aspect of the present disclosure;
FIG. 7B shows data demonstrating expression of markers in iPS cells in accordance with another aspect of the present disclosure;
FIG. 8A shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 8B shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 8C shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 8D shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 8E shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 8F shows data representing isolated RNA from iPS cells that demonstrate high expression of undifferentiated ES cell-marker genes in accordance with another aspect of the present disclosure;
FIG. 9 shows images of cells undergoing morphological changes in accordance with another aspect of the present disclosure;
FIG. 10A shows data from SkMC-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 10B shows data from SkMC-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 10C shows data from SkMC-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 10D shows data from SkMC-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 10E shows data from SkMC-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 11A shows data from SCA2 skin fibroblast-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 11B shows data from SCA2 skin fibroblast-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 11C shows data from SCA2 skin fibroblast-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 11D shows data from SCA2 skin fibroblast-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 11E shows data from SCA2 skin fibroblast-derived iPS cells in accordance with another aspect of the present disclosure;
FIG. 12 shows immunohistochemistry data from differentiated iPS cells in accordance with another aspect of the present disclosure;
FIG. 13 shows histological data revealing development of muscle and adipose tissues in accordance with another aspect of the present disclosure;
FIG. 14 shows an illustration of an experimental time line in accordance with another aspect of the present disclosure;
FIG. 15A shows a heat-map of a gene expression profile in accordance with another aspect of the present disclosure;
FIG. 15B shows a heat-map of a gene expression profile in accordance with another aspect of the present disclosure;
FIG. 16 shows the construction of a CMV weak promoter in accordance with another aspect of the present disclosure;
FIG. 17 shows the validation of the CMV weak promoter in accordance with another aspect of the present disclosure;
FIG. 18A shows the generation of iPS cells using the CMV weak promoter in accordance with another aspect of the present disclosure;
FIG. 18B shows the generation of iPS cells using the CMV weak promoter in accordance with another aspect of the present disclosure;
FIG. 18C shows the generation of iPS cells using the CMV weak promoter in accordance with another aspect of the present disclosure; and
FIG. 19 shows a schematic view of an exemplary expression construct in accordance with another aspect of the present disclosure.



DETAILED DESCRIPTION
Before the present disclosure is described herein, it is to be understood that this disclosure is not limited to the particular structures, process steps, or materials disclosed herein, but is extended to equivalents thereof as would be recognized by those ordinarily skilled in the relevant arts. It should also be understood that terminology employed herein is used for the purpose of describing particular embodiments only and is not intended to be limiting.
Definitions
The following terminology will be used in accordance with the definitions set forth below.
It should be noted that, as used in this specification and the appended claims, the singular forms “a,” and, “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” includes one or more of such cells and reference to “the flask” includes reference to one or more of such flasks.
As used herein, the term “substantially” refers to the complete or nearly complete extent or degree of an action, characteristic, property, state, structure, item, or result. For example, an object that is “substantially” enclosed would mean that the object is either completely enclosed or nearly completely enclosed. The exact allowable degree of deviation from absolute completeness may in some cases depend on the specific context. However, generally speaking the nearness of completion will be so as to have the same overall result as if absolute and total completion were obtained. The use of “substantially” is equally applicable when used in a negative connotation to refer to the complete or near complete lack of an action, characteristic, property, state, structure, item, or result. For example, a composition that is “substantially free of” particles would either completely lack particles, or so nearly completely lack particles that the effect would be the same as if it completely lacked particles. In other words, a composition that is “substantially free of” an ingredient or element may still actually contain such item as long as there is no measurable effect thereof.
As used herein, the term “about” is used to provide flexibility to a numerical range endpoint by providing that a given value may be “a little above” or “a little below” the endpoint.
As used herein, a plurality of items, structural elements, compositional elements, and/or materials may be presented in a common list for convenience. However, these lists should be construed as though each member of the list is individually identified as a separate and unique member. Thus, no individual member of such list should be construed as a de facto equivalent of any other member of the same list solely based on their presentation in a common group without indications to the contrary.
Concentrations, amounts, and other numerical data may be expressed or presented herein in a range format. It is to be understood that such a range format is used merely for convenience and brevity and thus should be interpreted flexibly to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited. As an illustration, a numerical range of “about 1 to about 5” should be interpreted to include not only the explicitly recited values of about 1 to about 5, but also include individual values and sub-ranges within the indicated range. Thus, included in this numerical range are individual values such as 2, 3, and 4 and sub-ranges such as from 1-3, from 2-4, and from 3-5, etc., as well as 1, 2, 3, 4, and 5, individually.
This same principle applies to ranges reciting only one numerical value as a minimum or a maximum. Furthermore, such an interpretation should apply regardless of the breadth of the range or the characteristics being described.
The Disclosure
The inventors have developed a non-integrating vector system where multiple reprogramming factors are cloned in a single cassette in an expression vector. In some aspects, all defined reprogramming factors that are sufficient for the generation of iPS cells are cloned in a single cassette in an expression vector. Additionally, each gene corresponding to each reprogramming factor is expressed under the control of its own independent promoter that allows the balanced expression of all genes in one cell. In contrast to single expression of reprogramming factors in individual vectors, cells are reprogrammed into iPS cells in about 2-14 days with greater than about 80% efficiency without the need for feeder cells. These iPS cells show human ES cell morphology, and express ES cell surface markers and pluripotent cell-specific genes. The iPS cells can also be differentiated into cells of the three germ layers. Furthermore, iPS cells can be generated from a variety of cells, including, without limitation, human skeletal muscle cells and skin fibroblasts.
Several different standards to demonstrate pluripotency have traditionally been used. Except for the ability to generate normal embryos, iPS cells generated by the present invention in as little as 2-3 days without feeder cells meet all the reported criteria seen in iPS cells generated by other methods. Cells reprogrammed using the present techniques display features typical of human ES cells, including the presence of an unmethylated NANOG promoter, early initiation of mesenchymal to epithelial transition, expression of ES cell-marker genes and cell surface markers, as well as differentiation into germ layers in vitro and in vivo, including neurons.
Balanced expression of reprogramming factors under the control of individual promoters leads to a qualitative change in reprogramming and obviates the use of feeder cells. The short and reproducible time course of reprogramming can facilitate the study of these pathways and identify novel proteins important in the reprogramming process. This is particularly true for those proteins and lincRNAs that show overall little expression changes between the initial and final time points, but actually experience a change in between these time points. Initial pathway analysis highlights the importance of genes involved in cytokine-receptor pathways, with later upregulation of genes involved in hedgehog signaling, whereas genes involved in cell cycle and DNA replication are down-regulated at intermediate and late stages, as is described more fully herein. The more complete and coordinated activation of reprogramming pathways as a result of balanced expression of reprogramming factors can allow further detailed dissection of these pathways and their timing as well as analysis of the role of linc- and other non-coding RNAs in human reprogramming.
It should also be noted that the methods for vector construction, gene expression, generation of iPS cells, cell lines utilized, and other specific protocol details are shown as non-limiting examples in the following discussion. Furthermore, the techniques described herein can be utilized in a variety of contemplated transformation systems, and should not be seen as being limited to the iPS transformation system disclosed herein. Variation in the number of reprogramming factors included in the cassette and the specific types of reprogramming factors can vary, both within the iPS system and in other transformation systems.
A variety of promoters are contemplated, and any promoter that can be utilized as described herein is considered to be within the present scope. In some cases the selection of a given promoter or set of promoters can be a design choice that takes into account the particular expression vector utilized, any size requirements or limitations established by the promoter/vector combination, and the like. In one non-limiting aspect, however, the promoter can be a cytomegalovirus (CMV) promoter, and in some aspects a human CMV promoter. Additionally, in some aspects each reprogramming factor in the expression vector can have a separate promoter of the same promoter type, e.g. each reprogramming factor can have a separate CMV promoter. In other aspects, each reprogramming factor can have a separate promoter, but all of the promoters in the expression vector may not be of the same promoter type. Thus, in some cases different promoters can be utilized to affect the balance of expression of the reprogramming factors in a cell. In some aspects, each reprogramming factor may have a different type of promoter. It is also noted that a promoter can be modified to increase or decrease expression of a reprogramming factor if desired.
In some aspects it is contemplated that a promoter-driven reporter can be included in the cassette to, among other things, track transgene expression. Any reporter that can be loaded into the cassette with the reprogramming factors is considered to be within the present scope. In one specific example, the reporter can be a promoter driven GFP marker. Thus in some aspects a reporter can be expressed using a dedicated reporter promoter, while in other aspects a reporter can be expressed using one or more of the reprogramming factor promoters.
Furthermore, numerous expression vectors are contemplated, and any such vector that is capable of receiving and expressing multiple reprogramming factors each from dedicated promoters is considered to be within the present scope. Non-limiting examples can include adenoviral vectors, episomal vectors, retroviral vectors, lentiviral vectors, and the like.
As has been described, in one aspect the present disclosure provides a transformation construct for generating iPS cells that can include a vector backbone having a plurality of reprogramming factors, where each reprogramming factor is under control of a separate promoter. The vector backbone can be contained in a suitable delivery package such as, for example, an adenovirus particle, an episomal expression vehicle, etc.
As one specific example, and without using feeder cells and/or matrigel systems, the inventors have successfully created human induced pluripotent stem (iPS) cells from human embryonic fibroblast IMR90 cells by producing an adenoviral vector containing multi-reprogramming factors in a single cassette. It is noted that the use of IMR90 fibroblasts should not be seen as limiting, and any cell type capable of reprogramming is considered to be within the present scope. Non-limiting examples of cells and cell-types can include human fibroblasts, human fibroblasts from patients with SCA2, skeletal muscle (e.g. SKMC), and the like. Additionally, the present scope includes all fibroblast cell lines as well as other cells such as muscle and blood cells, as well as cell lines derived therefrom.
This adenoviral construct allows balanced expression of all reprogramming factors in single cell, and greatly speeds up the reprogramming efficiency of cells in a short period of time over conventional iPS cell generation methods. For example, traditional iPS cell generation methods can take about 30-45 days, whereas the present methods can generate iPS cells in 10 days or less. In one aspect, iPS cells can be generated in from about 2 to about 10 days. In another aspect, iPS cells can be generated in from about 2 to about 6 days. In yet another aspect, iPS cells can be generated in from about 2 to about 3 days. The time period for the generation of iPS cells is measured from the time of transfection with a viral cassette until the observable appearance of stem cell-like colonies.
As has been described, the current methods allow iPS cells to be generated without the use of feeder cells and/or matrigel systems. While not intending to be bound to any scientific theory, this may be due to a more rapid transformation of the cells into iPS cells. Because the multiple reprogramming factors are introduced simultaneously into recipient cells under the control of separate promoters, regardless of the expression vector utilized, this may allow a more rapid transformation into iPS cells that more quickly forms colonies of cells that have increased surface area compared to, for example, adhered fibroblasts. Such increased surface area also results in increased access to nutrients in the culture medium, thus rendering feeder cells unnecessary. Furthermore, the simultaneous or near simultaneous transformation into iPS cells may promote survival of iPS cells through secreted factors. Additionally, cells that are just about to transform into iPS cells, or that have just undergone this transition, begin to migrate towards each other to form colonies. This also suggests the presence of secretable factors to indicate location and initiate locomotion toward iPS cell colonies. Various classes of such secretable factors are contemplated, including, without limitation, peptides, proteins, lipoproteins, glycoproteins, glycolipids, and the like, and may be co-expressed with receptor molecules at the cell surface.
Numerous methods and techniques for generating an expression vector are contemplated, and can vary depending on the vector utilized, the cell system, the preferences of the technician, etc. As such, the following description is not considered to be limiting. In one aspect, reprogramming factors can be cloned separately into separate vectors, where each reprogramming factor is under the control of a separate promoter, such as, for example, a cytomegalovirus (CMV) promoter. One example of such a vector is pAdTrack-CMV. It is noted that the present scope includes any promoter that is capable of being separately associated with a set of reprogramming factors and loaded into a vector. Non-limiting examples can include the CAG-promoter, a combination of CMV early enhancer elements, chicken beta-actin promoter, and the like. Additionally, a mutated promoter, such as a mutated CMV promoter, can be utilized to alter the expression of the associated reprogramming factor.
Subsequently, multiple reprogramming factors along with the associated promoters can be consecutively subcloned into a shuttle vector. One non-limiting example can be using blunt end ligation. Any number of reprogramming factors can be subcloned into the shuttle vector. In one aspect, at least two reprogramming factors can be subcloned therein. In another aspect, at least three reprogramming factors can be subcloned therein. In another aspect, at least four reprogramming factors can be subcloned therein.
A variety of reprogramming factors and reprogramming factor combinations are contemplated, and any such factor or factor combination capable of generating iPS cells is considered to be within the present scope. Non-liming examples of reprogramming factors include OCT3/4, SOX2, KLF4, c-Myc, NANOG, LIN28, and the like, including combinations thereof. In one aspect, the reprogramming factors can include OCT3/4, SOX2 and at least one factor selected from KLF4, c-Myc, NANOG, or LIN28. In another aspect, the reprogramming factors can include OCT3/4, SOX2, and at least two factors selected from, KLF4, c-Myc, NANOG, or LIN28. In one specific aspect, the reprogramming factors include OCT3/4, SOX2, KLF4, and c-Myc. In one aspect, one example of an OCT3/4, SOX2, KLF4, and c-Myc construct is at least 80% homologous to SEQ ID 1. In another aspect, the construct can be at least 95% homologous, or 100% homologous to SEQ ID 1. Furthermore, in one aspect, the expression vector can have a sequence that is at least 80% homologous to SEQ ID 72. In yet another aspect, the expression vector has a sequence that is at least 95% homologous to SEQ ID 72. In a further aspect, the expression vector has the sequence of SEQ ID 72. In some aspects, SEQ ID 72 may be otherwise referred to as pAd-GFP-KcMOS. It should be noted that the order of the reprogramming factors as recited herein may not be limiting, but can be used in specific order when so specified. For example, pAd-GFP-KcMOS can be referred to in some aspects as pAd-SocMK. As such, the present scope includes sequences similar to SEQ ID 72 where the reprogramming factors have been inserted in a different order. A schematic representation of an exemplary expression construct pAd-GFP-KcMOS is shown in FIG. 19.
In another specific aspect, the reprogramming factors include or consist of OCT3/4, SOX2, and KLF4. In one aspect, one example of an OCT3/4, SOX2, and KLF4 construct is at least 80% homologous to SEQ ID 4. In another aspect, the construct can be at least 95% homologous, or 100% homologous to SEQ ID 4. In yet another specific aspect, the reprogramming factors include or consist of OCT3/4, SOX2, NANOG, and LIN28. In a further specific aspect, the reprogramming factors include OCT3/4, SOX2, NANOG, and LIN28. In yet another aspect, other members of the OCT, SOC, NANOG, and LIN families can be utilized.
In another aspect, at least one reprogramming factor can be selected from AIRE, CBFA2T3, CEBPE, CRABP2, EGR4, HIC2, IRX4, IRF7, KCNH2, KLF3, KLF4, KLF9, LIN28B, LHX6, LHX1, NFATC1, NFATC2, PEG3, POLR3G, PAX8, RAX2, RUNX3, SFRS17A, SOX8, TAF4B, ZNF57, and the like. In yet another aspect, at least one reprogramming factor can be selected from ETS1, FOXM1, HEY1, HOXA4, HOXA3, KLF6, KLF2, LZTS1, LBX2, MYBL1, MYBL2, MITF, POGK, RUNX1, SALL2, SOX6, SP140, SMAD6, SMAD9, TCF19, TOP2A, VGLL3, ZNF641, ZNF671, ZNF70, and the like.
Other non-limiting examples of reprogramming factors can include on or more selected from DBP, ZNF33B, CREB3L2, ZSCAN16, AHR, ZNF138, HSF4, HMX2, HEY1, ZNF192, PITX2, MAX, CIR1, PBX3, ZNF3, PRDM2, HOXC9, NFKB2, NRL, BATF3, SOX4, BARHL1, TSC22D3, MEF2D, GATAD2B, ZNF33A, KLF7, NR1D2, AHR, ZNF639, ETV6, IKZF4, NR1D2, ZNF217, HOXC8, GLIS3, HOXC6, ZNF397, ARID4A, ZNF496, MLLT10, ZFP36L1, NRL, PKNOX1, MTA3, PAX7, DMTF1, MZF1, RUNX1, HOXA2, HHEX, MLLT10, NFE2L1, PBX3, YEATS4, TAF6, SREBF2, RFX5, HCLS1, TP53, BACH1, TP53, ADNP, NFIL3, LMO4, KLF2, SCAND2, HOXA6, LMO4, SNAPC5, FOXC1, PCGF6, TAF5L, HOXB4, ETV6, HOXA4, ZNF256, ZNF449, ZNF193, RUNX1, ZBTB17, MYOG, NFIC, TBX5, HOXA5, CUX1, GLI3, CNOT7, TCF25, CNOT7, NPAT, SP4, MSC, IRF2, TBX5, RUNX1, ZBTB38, CREM, ZNF397, NR2F1, ZNF217, KLF5, RFXAP, HMGB2, CBL, ZNF93, ZSCAN12, MYST2, EGR2, SATB1, E2F1, PLAG1, PFDN1, E2F3, ZNF18, ENST00000300681, HLX, E2F2, SALL2, L3 MBTL1, RCAN1, ARNT2, RERE, GTF2I, HIF1A, RUNX1, SMAD9, ZNF211, SMAD6, HOXB7, MLL, CREB3L4, GLI2, HOXB8, TBX3, IRF9, NR2F2, CREB3L4, NCOR1, SMAD9, ARNTL, CITED2, ZNF213, CITED2, LZTR1, RFX5, MEIS1, BCL6, TAF5L, RB1, ATF6B, CBFA2T2, ZNF219, SCAND1, ZFP36L1, MYPOP, PBX2, SHOX2, TBX3, STAT2, EBF1, LZTS1, EPAS1, TCF7L2, ZNF236, DLX1, PBX1, ZNF75D, ETS2, TCF25, CSRNP2, TADA2A, ZFHX2, JUN, MMP14, ZBTB16, TFDP3, ZNF19, ZSCAN21, MYC, SOX6, GATAD1, ZFHX3, RUNX2, CREBBP, ELK1, ZNF187, HIF1A, NOBOX, ZSCAN20, ELK1, JDP2, FOXD1, HCFC1, BRD8, TCF21, SIM2, ZKSCAN4, HOXA7, ZNF174, MLLT10, ADNP, TFDP1, CREB3L2, FLI1, SMAD3, ZBTB25, TSC22D2, TCF19, TFDP1, EBF1, STAT1, ETV3, RUNX1, ZNF117, TGIF1, RXRB, USF2, PKNOX2, TFE3, ETV5, SP1, ZKSCAN3, TEAD2, RUNX2, SMAD5, ZNF71, RBPJ, ZNF85, TCF7L1, AR, CREB3L1, PBX1, UHRF1, CREBL2, NR2E3, MSRB2, NFKB1, THRA, NFATC4, NME2, ETS1, TCEAL1, KLF12, USF2, ELF2, CLOCK, NR3C1, UHRF1, ZNF45, ZKSCAN4, ZNF135, HOXB2, ARNT, NFYC, UBP1, MEIS2, GLI2, TBX2, ZFHX4, CTBP1, ZKSCAN2, KLF6, STAT5B, ZFP37, LASS2, TEAD1, NR2C2, CUX1, THRA, RUNX1T1, SP140, HMG20A, STAT3, MYBL2, ZSCAN18, MTA2, TOP2B, SCMH1, HOXB2, ZNF3, ZNF281, ZXDC, ARNTL2, EBF1, STATE, FOXO3, NR3C1, ZNF500, VAX2, MSRB2, PPARG, TCF4, CTBP1, HOXB3, DMTF1, SOX13, TADA3, HDAC1, ZKSCAN5, HOXB5, TARDBP, ZNF91, FOXC2, ZNF498, PTTG1, SUPT6H, GLI2, YY1, TAF12, FUBP1, STAT3, CREB1, ZEB2, ZNF175, PURA, CREM, ZNF268, ZNF132, SLC2A4RG, POU6F1, SMAD2, ZNF70, FOXO3, ATF1, RELA, TOP2A, TCF12, SP140, FUBP1, ZEB2, MSL3, BLZF1, MECOM, NFIC, PRRX1, KLF6, FOXM1, RELA, EGR1, CLOCK, ZNF202, TSHZ3, BACH1, PPARG, ZNF189, ZNF45, PHTF1, GTF2H4, PHTF1, SRF, FOXL1, ATF2, HOPX, NR2C1, ZNF69, SIX4, ELK3, ZNF167, MECOM, HMGB1, NFYB, ZNF148, ZEB1, RFXANK, PCGF2, STRN3, HOMEZ, ZNF498, NFAT5, SATB2, CTNNB1, ADNP2, TCF7L2, HOXB6, HIC1, ATF2, ZHX3, MTA1, GTF21RD1, CTNNB1, E2F7, TRERF1, FOXF2, TFCP2, HDX, PITX1, ZNF207, E2F7, PRDM2, LCOR, PITX1, ZNF155, CUX1, FOXO3, MEF2C, TFE3, ZEB1, ZNF197, and the like.
Furthermore, additional non-limiting examples of reprogramming factors can include on or more selected from SLC30A9, ZFP36L2, ELK4, ZHX3, TCFL5, GABPB1, NKX3-1, BLZF1, BLZF1, ZSCAN2, ZNF134, AFF1, NFYA, NCOR1, TRPS1, PLAGL2, PURB, GTF2H3, TAF7, CBFB, TRPS1, ATF6, ZSCAN30, FOXN2, CTCF, CREB3, SOX9, SIX1, E2F3, BHLHE41, FOSL1, TEAD3, ZHX3, TWIST1, BUD31, AFF1, NPAS1, TFCP2, TAF1B, TFEB, AFF4, ZNF174, ETV1, ZSCAN30, ZNF35, SOX5, ETV1, NFYC, ETV1, TRIM22, NFE2L3, TSHZ1, ZNF83, ENO1, AFF4, FOXN2, TCF7L2, SMAD4, BNC1, ETV1, FOS, GAS7, TRIM28, NCOR1, ZSCAN22, ELK4, SALL1, GATAD2A, DRAP1, TFAM, MEIS3, NFIX, MSX2, SMAD1, EGR3, POU2F2, GABPB1, ELF1, NFYC, IRF3, ZNF215, MAFK, ENST00000445531, KLF10, BHLHE40, TFAM, TSC22D1, MEF2B, CSRNP1, HR, CSRNP1, JUND, TARDBP, RARG, ATF5, TCF3, BCL3, PRDM1, ELF1, JUNB, GCFC1, MAFF, TULP4, USF1, IRF1, RBCK1, NOTCH1, AHCTF1, ZNF134, PPARD, ZNF274, TGIF2, UBN1, PRDM1, KLF3, MEF2B, ZNF444, DRGX, RAX2, MNT, PPARA, ZNF41, ZNF215, HMGA1, ZNF169, RBCK1, ZNF169, MBD1, MYCL1, TARDBP, C2orf3, ZNF81, FOXO4, MAX, MYNN, PLAGL2, FOSB, MSX1, KLF16, ZNF197, SOLH, ELF4, ZHX1, NFIA, IRF3, GCFC1, TEAD4, ZHX2, TFEB, E2F5, NKX1-1, AATF, GATA2, HNRNPAB, NFATC2, ZNF92, MAX, ZNF628, KLF4, RXRA, ZNF232, CSDA, PA2G4, YBX1, XBP1, MLL, NPAS2, SCML2, CSDA, SOX13, MYOD1, PPARD, NOTCH1, CNBP, TFIP11, IRF7, ZSCAN29, NKX2-3, ZNF24, HNF1B, C11orf9, FBXW7, MEF2D, REXO4, NFATC3, SOX8, ZNF207, SPEN, MGA, SNAPC4, ZRANB2, PA2G4, AHCTF1, MNT, ARID3A, RNF4, ERF, ETV4, DLX2, KLF9, ESRRA, YBX1, GATAD2A, ESRRA, TP73, KLF17, NKX6-3, MXD1, NFYC, HOXA9, TBP, TP73, HSF1, MBD1, TSC22D4, CEBPB, MTF1, RARA, BTAF1, MBD1, TLX2, TAF13, MRRF, CITED1, NFATC1, MLL, FOXL2, LASS5, NR1H3, NFATC1, LEF1, ZNF81, POU3F1, MXD1, PAX8, NOLC1, MGA, TBX1, SCML1, GABPA, NR1D1, MEF2A, POU2F1, HMBOX1, MAFG, HMX1, ZGPAT, IRX4, MBD1, MAFG, GRHL2, SPDEF, ATF3, PRRX2, NR1H2, E2F6, MAFB, MRRF, KLF11, HR, HEYL, CNBP, SNAPC2, MLX, FOXA3, ATF3, PITX3, ZNF24, ZSCANSA, AEBP1, E2F6, ZNF37A, LHX1, E2F6, HMBOX1, ETV2, FOXK2, ATF3, MAFB, RUNX3, ZGLP1, FOXK2, ZNF394, SPIB, ETV2, ZNF394, VDR, HMBOX1, HMG20B, LASS6, MYNN, ZGLP1, FOXK2, NR6A1, ARGFX, HIRA, CDX1, KLF1, ESR1, EN2, ZKSCAN1, HMG20B, TCF15, TPRX1, HMG20B, RARA, NFYA, ZNF263, RORA, PURB, TAF5, GSX1, HNF1A, UNCX, SEBOX, LASS6, FOXE3, IRX2, BATF2, DUXA, MAF, E2F4, MLL, ZNF148, MAFA, ZNF165, SIX2, LHX6, ECSIT, DUX4, HES6, TAF4, TFAP2E, SIX3, NR4A2, RELB, IRX2, LHX3, NFE2, NR4A2, MLL4, HOXA10, SPEN, E4F1, NKX1-2, SREBF1, NKX2-5, HES6, ZNF169, CCRN4L, RFX3, TBX19, RBCK1, FOXH1, HOXB9, HES6, MESP1, LBX1, STAT4, DUX4, NFX1, NR2F6, HES6, HES1, HMX1, PPARA, ZNF445, DUX4L4, SOX11, EVX1, PBX4, ZXDC, ZNF131, LMO1, ZNF3, KDM5B, STATSA, DUX4, PHFSA, REL, ZNF446, MLL4, ZNF157, IRF5, HOXA9, TAF10, HSF1, ZNF133, TRERF1, NR113, ISL2, LMX1B, SIM1, SCAND2, MYNN, ARX, TBX6, VSX1, TBX10, NR5A2, GATA6, PAX6, TFDP2, KDM5B, SNAPC5, HAND1, PAX4, DUX4, NFX1, ZNF277, SNAPC5, ZBTB48, POU5F1, ESRRG, HOXD9, CBFA2T2, FOXD2, TEF, PHF1, DDIT3, SUPT4H1, LASS3, ZNF33A, RORB, POU5F1, DMRT1, HINFP, EDF1, CDX1, ATF4, ZNF323, CNOT8, POU4F2, VPS72, FOSL2, ATF3, NFXL1, ZIC1, SPI1, CREB5, CEBPD, C5orf41, HSF1, DUX4, ZNF33A, NEUROG3, TRIM25, SREBF1, GCM1, EMX1, LASS4, PRDM2, HMX3, ONECUT2, SIX5, HOPX, ESRRB, HSF2, HOXC4, PROP1, ZNF33A, ZSCAN2, SHOX, HOXA3, NR4A3, MESP2, and the like.
Additionally, it should be noted that any one or more of the above reprogramming factors can be utilized with any other reprogramming factor described herein or in any combination with any other reprogramming factor described herein.
Turning now to FIG. 1, a schematic outline of one non-limiting example of an expression system (e.g. AdEasy-1) is provided. Reprogramming factors of interest, such as, and without limitation, OCT3/4, SOX2, KLF4, and c-Myc, can be first cloned separately into a vector under separate promoters 102 (e.g. pAdTrack-CMV). Then, each reprogramming factor along with the promoter can be consecutively subcloned into a shuttle vector 104 (e.g. pAdTrack) using a technique such as, for example, blunt end ligation. The resultant plasmid can be linearized by digesting with a restriction endonuclease such as PmeI, and recombination can be carried out using high competence bacterial cells, such as E. coli BJ5183 cells, by homologous recombination. In some cases, high competence bacterial cells can allow for more efficient recombination. In cases where an adenoviral vector is to be used, the recombinant adenoviral plasmid 106 (e.g. pSOKcM-AdEasy-1) can then be linearized 108 with an enzyme such as Pad and transfected into an adenovirus packaging cell line for virus production. One non-limiting example of such a cell line is HEK 293A. The “left arm” and “right arm” shown in FIG. 1 represent the regions mediating homologous recombination between the shuttle vector 104 and the adenoviral backbone vector 106. The recombination can be confirmed by multiple restriction endonuclease analyses, and the production of recombinant adenoviruses can be followed by GFP expression.
Validation of protein expression can be accomplished using any of a number of known methods, such as western blotting, and the like. As one example, FIG. 2A shows a schematic representation of an adenoviral vector containing multi-reprogramming factors in a single cassette, pSOKcM-AdEAsy-1 102. FIG. 2B shows SH5Y cells that were transiently transfected with pSOKcM-AdEasy-1 and pSOKcM-AdShuttle constructs. Protein extracts from harvested cells at 40-54 hrs post-transfection were probed by Western blot analysis using the antibodies indicated. Blots were re-probed for Actin as an internal loading control. These results indicate that the recombinant adenoviral construct expresses all proteins from the adenoviral vector in cells tested.
iPS cells can thus be generated using an expression vector containing multi-reprogramming factors. iPS cells can be generated from a variety of transfectable cell types, and any type of cell capable of transfection is considered to be within the present scope. One specific example of such a transfectable cell type includes IMR90 human fetal fibroblasts. As is shown in FIG. 3, iPS cells can be generated with an adenoviral vector without feeder cells or a matrigel matrix. In FIG. 3A, adenoviral constructs (AdEasy-1): Ad-GFP or Ad-SOK are shown. In FIG. 3B a timeline of experimental design is shown. IMR90 cells were transduced with adenoviruses, Ad-GFP or Ad-SOK on day 2. Culture medium was changed every day with regular cell culture medium. Colonies appeared at days 4-7 in culture dishes. The top of FIG. 3B shows photomicrographs of IMR90 cells transduced with Ad-GFP on day 7; phase contrast in the top left image and GFP expression in the top right image. FIG. 3B middle and bottom images show iPS cell-like colonies appearing in IMR90 cells transduced with Ad-SOK on days 4-7, as shown by phase contrast (FIG. 3B middle and bottom left). GFP expression in fluorescence microscopy of the same colony is shown in FIG. 3B bottom right. Thus by days 4-7, several colonies showing ES cell-like morphology emerged and all colonies looked identical. The resultant colonies (iPS cells) can be further expanded or subjected to characterization.
Following generation, iPS cells can be further characterized. The undifferentiated state of human ES cells/iPS cells express high levels of membrane alkaline phosphatase (AP), and AP staining can be used to characterize such stem cells. For AP staining, iPS cells are generated from iMR90 cells in 24 well plates using the methods as described. At day 7, iPS cells are fixed with 4% paraformaldehyde for 2 minutes, followed by 15-minute incubation with staining solution (Alkaline Phosphatase Detection Kit; Millipore). AP staining data demonstrate the positive staining for iPS cells, as shown in FIG. 4A. In this case, IMR90 cells are transduced with adenoviruses, Ad-GFP or Ad-SOK for 7 days. Human iPS cells generated from Ad-SOK are positive for alkaline phosphatase (AP) staining. FIG. 4B shows RT-PCR analyses of ES cell marker genes, IMR90 cells are transduced with adenoviruses. Ad-GFP or Ad-SOK for 7 days. Total RNA is isolated from harvested cells and synthesized cDNAs (150 ng) are used for RT-PCR analyses. Human iPS cells express many undifferentiated ES cell marker genes including telomerase reverse transcriptase (hTERT) and growth and differentiation factor 3 (GDF3). FIG. 4B shows an expression profile by RT-PCR analyses, demonstrating that iPS cells derived from IMR90 cells highly express the hTERT and GDF3 genes.
In another aspect of the present disclosure, somatic cell reprogramming was tested using the adenovirus containing OCT3/4, SOX2, KLF4, and c-Myc (Ad-SOcMK) shown in FIG. 1. IMR90 cells were transduced with the adenovirus, and the timeline for transformation is shown in FIG. 5A. Briefly, the IMR90 cells were transduced with Ad-SOcMK or Ad-GFP for 12 or 21 hrs, after which the medium was replaced with human ES cell medium. Within 1 day, Ad-SOcMK-transduced cells took on a different appearance and began to form small cell clusters. By day 2 or 3, several colonies of cells showing ES cell-like morphology emerged in the dish (FIG. 1B, top right and middle right). Cells were also tested for ALP staining, as is shown in FIG. 5B, bottom right. The ALP assay reveals strong staining of IMR90-derived iPS cells indicating pluripotency, while no ALP staining is observed in the GFP-transduced cells (FIG. 5B, lower left). The expression of exogenous individual protein factors in protein extracts from harvested cells was also investigated by Western blot analyses, as is shown in FIG. 5C. The results demonstrate that all RFs in the adenovirus are highly expressed in transduced IMR90 cells but not in Ad-GFP-transduced cells.
Gene expression changes during the reprogramming process have traditionally been difficult to study. One reason for this difficulty in human cells may be due to the fact that currently known methods of reprogramming occur at low frequency and take such long periods of time to occur. This is particularly true for a new class of regulatory RNAs, called long inter-spersed non-coding (line) RNAs. The short and synchronized reprogramming process of the present disclosure can facilitate the study of global transcription changes. To pursue these issues, the inventors have studied global gene expression changes during reprogramming to determine the correlation between gene expression changes and reprogramming. Using singular value decomposition, for example, regulated functional pathways in early and intermediate stages of reprogramming of human cells have been identified, including a set of novel lincRNAs.
Without intending to be bound to any scientific theory, mesenchymal-to-epithelial transition (MET) is a key regulatory event during reprogramming of somatic cells to the pluripotent state. Expression of exogenous reprogramming factors effectively activate the epithelial program and shut down key mesenchymal genes to favor the MET transition of somatic cells toward induced pluripotency. These events are associated with depletion of the mesenchymal marker THY1, and upregulation of the epithelial marker CDH122-24. To investigate this, the steady-state levels of THY1 and CDH1 in iPS cells generated with Ad-SOcMK are measured, RT PCR and Western blot analyses reveals upregulation of CDH1 and concomitant reduction of THY1 in iPSCs when compared with control (See FIG. 6A). As THY1 is exclusively expressed in fibroblasts and fibroblast cells dramatically switched the state in a short period of time, the expression level of THY1 by real-time PCR can be determined as a function of reprogramming efficiency, Real-time PCR and Western blot data reveals a decrease in levels of THY1 by  ̃80% in Ad-SOcMK transduced cells as cells are reprogrammed (See FIG. 6A lower panel, and FIG. 6B).
It was next examined whether iPS cells generated with Ad-SOcMK express human ES cell-marker genes such as NANOG, Telomerase reverse transcriptase (TERT), LIN28, stage specific embryonic antigens (SSEA-1, -3, and -4), and tumor-related antigens (TRA1-60 and -81). Expression of each marker in iPS cells was studied by immunofluorescence using antibodies against endogenous proteins (FIGS. 7A-B). The corresponding secondary antibodies were conjugated with Dylight variants. Immunostaining data revealed expression of ES cell markers in iPS cells generated with Ad-SOcMK from IMR90 cells.
To measure steady state levels of undifferentiated ES cell-marker genes, real-time RT-PCR, semi-quantitative PCR, and Western blot analyses can be performed. Real-time and semi-quantitative PCR analysis of isolated RNA from iPS cells demonstrate high expression of undifferentiated ES cell-marker genes, including NANOG, TERT, L1N28, ALPL, growth and differentiation factor 3 (GDF3), fibroblast growth factor 4 (FGF4), developmental pluripotency-associated 5 (DPPA5), interferon induced transmembrane protein 1 (IFITM1), galanin prepropeptide (GAL), gamma-aminobutyric acid (GABA) A receptor, beta 3 (GABRB3), teratocarcinoma-derived growth factor 1 (TDGF1), Nodal homolog (NODAL) and podocalyxin-like 2 (PODXL2) (See FIGS. 8A-F). Western blot analyses in protein extracts from harvested iPS cells confirmed protein expression of NANOG in iPS cells generated with Ad-SOcMK (FIG. 8B, bottom panel).
One of the prominent morphological changes during MET is the transformation of elongated fibroblasts into tightly packed clusters of rounded cells. Ad-SOcMK transduced cells undergo progressive epithelial-like morphological changes from elongated fibroblasts (FIG. 9, panels a, h) to packed clusters of rounded cells as visualized by phase contrast microscopy (FIG. 9, panels d, f, h), Morphological changes occur in close association with expression of ALP. ALP-positive cells appeared as early as day 1 in Ad-SOcMK transduced cells and ALP positive cells progressively increased as reprogramming time increased (FIG. 9, panels l, n, p). Cells transduced with Ad-GFP showed neither morphological changes (FIG. 9, panels c, e, g) nor staining for ALP (FIG. 9, panels k, m, o). Thus, reprogramming of IMR90 cells by Ad-SOcMK results in rapid and specific mesenchymal to epithelial transition with very high efficiency.
Such reprogramming of somatic cells is also accompanied by significant epigenetic changes. As one example, the NANOG promoter changes from a highly methylated state in somatic cells to being unmethylated and active in iPS cells. In one aspect, bisulfite genomic sequence analysis can be used to evaluate the methylation status of cytosine guanine dinucleotides (CpGs) in the NANOG promoter. CpGs are highly unmethylated iPS cells when compared with the highly methylated CpGs in parent IMR90 cells. This indicates that the NANOG promoter is active in iPS cells derived from IMR90 cells resulting in increased steady-state levels (FIG. 8B, lower panel). In order to exclude the possibility of viral DNA integration into genomic DNA, Southern blot analysis can be performed by digesting genomic DNA from iPS cells generated with Ad-SOcMk with BamHI and AscI for KLF4 and c-MYC probes, respectively. Notably, Southern blot analyses does not detect genomic integration of the adenoviral transgene into iPS cells derived from IMR90 cells (data not shown). In addition, chromosomal G-band analyses showed that iPS cells generated with Ad-SOcMK had a normal karyotype of 46XX (data not shown).
As has been described, a variety of cell types can be utilized to generate iPS cells according to aspects of the present disclosure, and any such capable cell is considered to be within the present scope. As examples, human skeletal muscle cells (SkMCs) and spinocerebellar ataxia 2 (SCA2) patient skin fibroblasts can be used. When SkMCs and SCA2 skin fibroblasts are transduced, several iPS cell colonies resembling ES cell-like morphology emerge in the dishes as early as day 3. The SkMC and SCA2 skin fibroblast-derived iPS cells positively stain for ALP, and immunofluorescence and RT-PCR analysis data reveals that these iPS cells express many undifferentiated ES cell-marker genes and followed the MET process (For SkMCs see FIG. 10, panels a-e; for SCA2 see FIG. 11, panels a-e). These findings demonstrate that the expression vectors of the present disclosure can be used to generate iPS cells rapidly and efficiently from a number of somatic cells in a short period of time.
One of the useful characteristics of pluripotency is the ability of iPS cells to differentiate into all three germ layers. The following non-limiting example is provided to show such differentiation. For example, for in vitro differentiation, freshly prepared iPS cells with Ad-SOcMK as have been described were cultured in ES cell medium without basic fibroblast growth factor (bFGF) for 8-9 days. The resultant embryoid bodies (EBs) in suspension cultures (see FIG. 12, panels c-j) are allowed to differentiate further in chamber slides. After 9-10 days in adherent culture, attached cells show various types of morphologies. Immunocytochemistry reveals the detection of Nestin (ectoderm, FIG. 12, panel d), smooth muscle actin (SMA) (mesoderm, FIG. 12, panel e), and alpha-fetoprotein (AFP) (endoderm, FIG. 12, panel f). To test whether iPS cells could be differentiated into neurons, iPS cells are seeded on inactivated MEF cells and cultured for 22-25 days. Morphological and immunostaining data revealed that the iPS cells were differentiated into neurons with a subpopulation of neurons staining with the dopaminergic marker tyrosine hydroxylase (TH) (FIG. 12, panels g, h).
To examine developmental potential in vivo, iPS cells generated with Ad-SOcMK are injected into NOD/SCID mice subcutaneously. After 9-10 weeks, teratomas develop and histological data reveals development of muscle and adipose tissues (mesoderm) (FIG. 13, panels I, j). Thus, iPS cells generated according to aspects of the present disclosure show pluripotency with the potential of differentiating into germ layers in vitro and in vivo.
As has been described, traditional methods for reprogramming of human primary somatic cells have low efficiency, making the molecular characterization of reprogramming difficult. Given the rapid time course and absence of feeder cell contamination, the techniques according to aspects of the present disclosure can allow monitoring of expression changes at multiple time points during the reprogramming process as compared to just the beginning (fibroblasts) and final (iPS cells) time points. In one aspect, therefore, RNAs are isolated from Ad-SOcMK and Ad-GFP transduced IMR90 cells at 0, 24, 48 and 72 hrs post-transduction and queried for global gene expression changes by hybridization to oligonucleotide arrays representing 27,958 protein coding genes and 7,419 lincRNAs. Differential expression analyses (>2 fold change) shows changes in 6,852 genes for 0/24 hr, 12,945 for 0/48 hr, and 14,158 for 0/72 hr (data not shown). Based on the significant and rapid changes in global gene expression, the experiment is repeated and RNA expression is analyzed at 6 hr intervals for 84 hrs after Ad-SOcMK transduction, FIG. 14 shows an illustration of the experimental time line. To identify temporal waves of gene expression across time points, the entire data set is analyzed, including Ad-GFP-transduced control cells (>1.5-fold differential expression) by using singular value decomposition (SVD)25.
FIG. 15A shows a heat-map of the gene expression profile for this data set including lincRNAs (21,372 genes). As can be seen in FIG. 15A, a large class of RNAs is highly expressed in IMR90 cells with rapid reduction in the following 12-24 hrs. A second class of RNAs shows little change initially, and then exhibits increased expression with a return to or below initial levels by 72-84 hrs. Additionally, genes in a third group have low expression in the first 24-48 hrs, but then become highly expressed from that time on. Similar clustering of lincRNA expression can be observed (>four-fold differential expression, 1059 lincRNAs, FIG. 15B). Of note, changes in a large number of genes would have remained undetectable as the expression levels were similar at 0/12 hrs compared with 74/82 hrs, while expression greatly changed at the intervening time points.
Gene ontology and KEGG annotation can then be used to examine pathway-wide changes (Table 1). To do this, the heat-map of gene expression (FIG. 15A) is broken down into an early wave: 10%-40% percentile genes, an intermediate wave: 40%-75% percentile genes, and a late wave: 75%-95% percentile genes: Genes related to cytokine-cytokine receptor interactions are up-regulated in the early wave and remain no through 72 hrs (z-score >4.1 at all time points). Genes related to hedgehog signaling show increased expression in the intermediate and late waves (z-score >4.3). Genes involved in DNA replication and cell cycle genes are down-regulated in the intermediate and late wave (z-score >6.2). Additionally, it was validated that various randomly selected genes are specifically enriched or down regulated in ES cells from the two microarray data sets by real-time PCR. For all genes, expression changes are in the same direction within the same order of magnitude (data not shown).







TABLE 1







KEGG pathway genes
















Number
Number







of
of
z-
z-




Gene
Genes
Genes
score
score


Wave
KEGG Pathway
Set
Up
Down
(Up)
(Down)
















Early
Cytokine-cytokine
265
13

4.14




receptor interaction


Inter-
Hedgehog signaling
56
14

4.89


mediate
pathway



Cytokine-cytokine
265
41

4.88



receptor interaction



Protein digestion
78
16

4.29



and absorption


Late
Cytokine-cytokine
265
57

5.87



receptor interaction



Gastric acid
74
20

4.6



secretion



Malaria
49
15

4.55



Hedgehog signaling
56
16

4.37



pathway



Neuroactive ligand-
311
55

4.14



receptor interaction


Inter-
Cell cycle
122

27

7.21


mediate
DNA replication
35

12

6.78



Oocyte meiosis
111

19

4.68



TGF-beta signaling
83

15

4.4



pathway


Late
DNA replication
35

16

6.98



Cell cycle
122

33

6.23



Homologous
27

11

5.27



recombination



Systemic lupus
122

27

4.42



erythematosus



Pathways in cancer
325

56

4.34



Pancreatic cancer
70

18

4.33



TGF-beta signaling
83

20

4.23



pathway









As has been described, in some aspects an altered promoter can be utilized to alter the expression of a particular reprogramming factor. The expression of the reprogramming factor can be increased or decreased, depending on the desired results. In one specific aspect, a weakened CMV promoter (CMVWP) can be utilized. It should be understood that the discussion of the CMVWP should not be seen as limiting, and is merely exemplary. Because of strong promoter activity, CMV promoter (589 bp) has previously been used in mammalian system to express a protein in order to study protein functionality. Decreasing the expression of a reprogramming factor can be beneficial in the reprogramming process. In some cases, overexpression of a protein may actually hamper the reprogramming process. As such, in some cases factors can be tuned to more beneficial rates of expression. Additionally, by decreasing the size of the CMV promoter without interruption of promoter activity, a greater sequence size can be loaded into the expression vector. To this end, CMVWP has been developed to, among other reasons, regulate protein expression and allow a higher amount of genetic material to be cloned into a single cassette.
The inventors have constructed a series of mutant CMV promoters by deleting 200 or 322 bp from original CMV promoter (CMV589bp) sequence of pEGFPN1 (Clontech Inc., USA) plasmid using either PCR or restriction digestion methods. The resultant mutant CMV promoters are tested for promoter activity by Western blot analyses expressing in HEK293 or SH-SY5Y cells. Of these, CMVΔ(121-443)bp-GFP construct, designated as CMV weak promoter-GFP (CMVWP-GFP) results in the significant reduction of the GFP protein expression by >60% when compared with CMV589bp-GFP or CMVΔ(1-200)bp-GFP. As is shown in FIG. 16, construction of CMV promoter variants is shown. 200 bp deleted from the 5′ end through PCR or 322 bp deleted by AatII digestion from the CMV promoter region of pEGFPN1 is shown in the upper panel of FIG. 16. Validation of promoter activity is shown in the lower panel of FIG. 16. Protein extracts from HEK293 or SH-SY5Y cells transfected with CMV promoter variants were subjected to Western blot analyses using the antibodies indicated. The blots were re-probed for Actin as an internal loading control. CMVΔ(121-443)bp promoter [CMV weak promoter (CMVWP)] results in significant reduction of GFP protein expression.
In order to validate this CMVWP activity further, reprogramming factors OCT3/4, SOX2, KLF4 and c-MYC genes were cloned separately into pre-GFP deleted CMVWP-GFP plasmid at NheI site and tested for promoter activity by Western blot analyses expressing in HEK293 or SH-SY5Y cells. The Western blot data revealed the reduction of promoter activity of CMVWP by >70% when compared with CMV589bp promoter (See FIG. 17).
iPS cells are then generated using the CMVWP in the viral cassette as has previously been disclosed for the CMV promoter. In short, IMR90 cells are plated at a density of 1.5 ̃2.5×106 cells per 10 cm tissue culture dish without feeder cells. The next day (day 2), IMR90 cells are about 60-70% confluent and the cells are transduced with medium (DMEM, 5% FBS, 1% NEAA, 0.5% penicillin-streptomycin) containing adenoviruses, Ad-GFP (control) or Ad(CMVWP)-GFP-cMKSO viruses. From day 3 onward, the culture medium is replaced with human ES cell medium including DMEM/F12, 20% Knockout Serum Replacement (KSR), 1× nonessential amino acids, 1× sodium pyruvate, 1× L-glutamine, 0.1 mM b-mercaptoethanol, 25 ng/ml basic fibroblast growth factor (bFGF), and 0.5% penicillin-streptomycin. The medium is changed every day and incubated for 7-8 days. By days 4-7, several colonies showing ES cell-like morphology emerge and all colonies look identical, as shown in FIG. 18B. The resultant colonies (iPSCs) can be further expanded or subjected to characterization. SEQ ID 2, SEQ ID 3, and SEQ ID 4 are examples of adenovirus cassettes utilizing CMVWP.
Additionally, as has been described, the undifferentiated state of human ES/iPS cells express high levels of membrane alkaline phosphatase (ALP) and ALP staining can be used to characterize the stem cells. For ALP staining, iPS cells are generated from iMR90 cells in 12 wells plate using the methods described. An experimental timeline is shown in FIG. 18A. At day 4, iPS cells are fixed with 4% paraformaldehyde for 2 minutes, followed by 15-minute incubation with staining solution (Alkaline Phosphatase Detection Kit; Millipore). ALP staining data demonstrates the positive staining for iPS cells, as is shown in FIG. 18C. As such, the CMVWP promoter can be utilized to generate iPS cells according to the methods and techniques described herein.
EXAMPLES
Materials
Reprogramming factors: OCT3/4, SOX2, GKLF4 and c-Myc. Plasmids containing the reprogramming factors (pEP4 E02S ET2K, pCEP4-M2L, pEP4 E02S EN2K, pEP4 E02S CK2M EN2L) are purchased from Addgene Inc., USA.
Each of the reprogramming factors was PCR amplified from the plasmids with NheI restriction sites. The authenticity of each gene was verified by NheI restriction digestion analyses and DNA sequencing.
Plasmid, pEGP-N1 (4.7 kb) is purchased from Clontech Inc., USA.
Adenoviral plasmid (pAdEasy-1, 33.4 kb), Shuttle vectors (pAdTrack and pAdTrack-CMV), Competent cells (AdEasier cells: E. coli BJ5183 containing pAdEasy-1 backbone), and Packaging cells (HEK 293A) were generous gift from CoraliePoizet, Larry Kedes Lab, University of Southern California, Los Angeles, Calif., USA.
All enzymes related to cloning experiments are purchased from New England Biolabs Inc., USA.
Human embryonic fibroblast IMR90 cells were obtained from the American Type Culture Collection (ATCC), Catalog No. CCL-186. IMR90 cells were maintained in DMEM medium containing 10% fetal bovine serum (FBS).
Human skeletal muscle cells (SkMCs) were obtained from Lonza Inc., USA, Catalog NO. CC-2661. SkMCs were maintained in SkGM medium (catalog #3160, Lonza Inc., USA), containing 10% FBS.
Human spinocerebellar ataxia 2 (SCA2) skin fibroblasts containing (CAG)57 were obtained from Coriell Cell Repositories, USA Catalog No. # GM04319. SCA2 skin fibroblasts were cultured in MEM medium containing 15% FBS.
DMEM (Invitrogen, cat. no. 11965-092)
Fetal bovine serum, FBS (Hyclone, Thermo Scientific)
KO serum replacement (KOSR; Invitrogen, cat. no. 10828-028)
PBS without Ca/Mg (Hyclone, Thermo Scientific)
L-Gin, 100× (Invitrogen Inc.,)
Nonessential amino acid solution (NEAA) (Invitrogen Inc.,)
2-Mercaptoethanol, 1000×, 55 mM (Invitrogen Inc.,)
Sodium Pyruvate, 100× (Invitrogen Inc.,)
Basic fibroblast growth factor (bFGF; Invitrogen, cat. no. 13256-029)
7.5% BSA solution (wt/vol; Invitrogen, cat. no. 15260-037)
Penicillin/streptomycin, 100× (Invitrogen Inc.,)
0.25% Trypsin/EDTA (Invitrogen, cat. no. 25200-056)
0.05% Trypsin/EDTA (Invitrogen, cat. no. 25300-054)
Collagenase type IV (Invitrogen, cat. no. 17104-019)
Attachment factor, AF 1×, (Invitrogen, cat. no. 17104-019)
Equipment
Inverted tissue culture microscope with phase contrast microscope, Nikon Eclipse, TS100 (5×, 10×, 20×, 40× objectives)
Stereomicroscope (Nikon; SMZ-1500 or similar)
Incubator, Hera cell 240i, Thermo Scientific
Biosafety cabinet with aspirator for tissue culture
Biosafety cabinet with aspirator for tissue culture, fitted for stereomicroscope
Tissue culture centrifuge, Sorvall, Legend X1 Centrifuge, Thermo Scientific.
Tissue culture dishes and Flasks, 100 mm, 150 mm and T-25
Tissue culture plates, 4, 6 and 12-well
Filter unit: Millex-HV, PVDF, 0.45 nm, 33 mm, Millipore Inc.,
Conical tubes, 15 and 50 ml
Water bath Isotemp (Fisher Scientific, USA)
Plastic disposable transfer pipettes, 1, 5, 10 and 25 ml
Glass disposable transfer pipettes, 5 ml
Disposable sterile filter system (0.22 μm, 250 ml and 500 ml)
Disposable syringes, 60, 30, 10 and 1 ml
Hypodermic needle, 27-30G
Freezing container (Nalgene Labware, cat. no. 5100)
Cell lifter (Corning, cat. no. 3008)
Reagent Setup
Culture medium 1 (CM-1): DMEM, 10% FBS, and 1% penicillin-streptomycin
Transduction medium: culture medium 2 (CM-2): DMEM, 5% FBS, 1% NEAA, and 0.5% penicillin-streptomycin.
Culture medium 3 (CM-3): DMEM, 10% FBS, 1% NEAA, and 0.5% penicillin-streptomycin.
Mouse embryo fibroblast (MEF) medium: DMEM, 10% FBS, 1% NEAA, and 0.5% penicillin-streptomycin.
hiPS cell medium: DMEM/F12 containing 20% KOSR (vol/vol), 50 ng/ml bFGF, 1× L-GIn, 1×NEAA, 1× Sodium Pyruvate, 100 μM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin.
2× cell-freezing medium: DMEM, 20% DMSO (vol/vol), 40% FBS (vol/vol), and 1% penicillin-streptomycin
2× iPS cell-freezing medium: DMEM/F12, 20% DMSO (vol/vol), 60% FBS (vol/vol), and 20% hiPS medium (vol/vol).
Example 1
Cloning of Reprogramming Factors
Cloning techniques follow methods published in Molecular cloning (A laboratory manual by Tom Maniatis, J. Sambrook, and E. F. Fritsch), which is incorporated herein by reference.
pEGFP-N1 plasmid (4.7 kb; purchased from Clontech Inc., USA.) is digested with BglII and NotI to remove the GFP open reading frame (ORF) from the plasmid backbone. The digestion reaction mix is as follows:
















pEGFP-N1 Plasmid DNA (1 μg/ul)
10 μl



10X Buffer
 5 μl



BglII (10 U/μl)
 1 μl



NotI(10 U/μl)
 1 μl



H2O
33 μl



Total
50 μl










The digestion reaction mix is incubated at 37° C. for 3-4 hrs. Heat inactivation is performed at 65° C. for 30 min. The digested product is then electrophoresed on a 0.8% agarose gel and the plasmid back bone (3.9 kb) is purified using a gel extraction kit (Qiagen).
Each of the reprogramming factors (OCT3/4, SOX2, GKLF4 and c-Myc) are PCR amplified from pEP4 E02S ET2K or pCEP4-M2L or pEP4 E02S EN2K or pEP4 E02S CK2M EN2L plasmids (Addgene) with NheI restriction sites. The PCR products are cloned into pEGFP N1 (GFP deletion) at NheI site from the above digestion reaction. The ligation reaction mix is as follows:
















Vector DNA (10 ng/μl)
 1 μl



Insert DNA (PCR product)
 5 μl



10X Buffer
 2 μl



T4 DNA ligase (3 U/μl)
 1 μl



H2O
11 μl



Total
20 μl










The ligation reaction mix is incubated at 16° C. for 18-24 hrs. The DNA is mixed with DH5α competent cells (New England Biolabs Inc.) and the transformation is performed. The cell suspension is inoculated onto 10 cm petri dishes containing LB-agar plus 50 μg/ml of kanamycin. The agar plates are incubated at 37° C. for 20-24 hrs. The positive clones of each gene are verified by NheI restriction digestion analyses and DNA sequencing.
In order to clone the four reprogramming factors into the pAdTrack shuttle vector, each cassette from the above reaction is consecutively subcloned into the shuttle vector (Sox2 cassette at HindIII site, OCT3/4 cassette at EcoRV site, KLF4 cassette at SalI site, and c-Myc cassette at NotI site), designated as pAdSOcMK shuttle vector, as is shown in FIG. 1. The ligation reaction mix is as follows:
















pShuttle Vector DNA (10 ng/μl)
 1 μl



Insert DNA (CMV-SOX2-SV40PA) (10 ng/μl)
 5 μl



10X Buffer
 2 μl



T4 DNA ligase (3 U/μl)
 1 μl



H2O
11 μl



Total
20 μl










The ligation reaction mix is incubated at 16° C. for 18-24 hrs. The DNA is mixed with DH5α competent cells and the transformation is performed. The cell suspension is inoculated onto 10 cm petri dishes containing LB-agar plus 50 μg/ml of kanamycin. The agar plates are incubated at 37° C. for 20-24 hrs. The positive clones of each gene are verified by restriction digestion analyses and DNA sequencing.
Example 2
Generation of Recombinant Adenoviral Plasmids by Homologous Recombination in E. Coli (FIG. 1)
High competence bacterial cells (E. coli BJ5183) are utilized in the following methods to achieve efficient recombination.
Recombinant pAdShuttle plasmid clones containing the reprogramming factors (pAdSOcMK) from Example 1 are grown in 4.0 ml LB/kanamycin in a 5-ml conical tube, and shaken overnight in a 37° C. orbital shaker. The plasmid DNA is purified by an alkaline lysis procedure. It has been found that efficient homologous recombination in AdEasiercells is improved by maintaining the integrity of the shuttle vector DNAs. Plasmids purified with commercial DNA minipreparation kits can contain significant numbers of nicked DNA molecules that may be detrimental to efficient and faithful recombination. The conventional alkaline lysis procedure can provide consistent and reliable results.
The recombinant shuttle vector plasmid is linearized by digesting with the restriction endonuclease PmeI, and purified using a gel extraction kit (Qiagen). The digestion reaction mix is as follows:
















Recombinant shuttle vector DNA (1 μg/μl)
10 μl



10X Buffer
 5 μl



PmeI (10 U/μl)
 1 μl



100X BSA
0.5 μl 



H2O
33.5 μl  



Total
50 μl










The digestion reaction is incubated at 37° C. for 3-4 hrs. Heat inactivation is performed at 65° C. for 30 min. The digested product is electrophoresed on a 0.8% agarose gel and the plasmid back bone is purified using a gel extraction kit (Qiagen).
10 μl (100 ng/μl) of the linearized plasmid is mixed with 50-100 μl of E. coli BJ5183 cells and incubated on ice for 40-60 min. The bacteria/DNA mix is then heat shocked at 42° C. for 1.5-2 min and immediately incubated on ice for 0.5-1 min. The cells are immediately placed in 250-300 μl of LB-Broth and grown at 37° C. for 1.5-2 hrs.
100 μl of the cell suspension is inoculated onto each of three 10 cm petri dishes containing LB-agar plus 50 μg/ml of kanamycin. The agar plates are incubated at 24-30° C. for 2-3 days until colonies appear. Each colony is isolated and grown in 4 ml LB medium containing 50 μg/ml of kanamycin at 24-30° C. for 2 days in an orbital shaker.
Plasmid DNA is isolated using the conventional alkaline lysis method. Pact restriction digestion is performed on candidate clones. Correct recombinants usually yield a large fragment ( ̃30 kb) and a smaller fragment of 4.5 kb.1-3 μl of correct recombinant plasmids (pAdSOcMK adenoviral vector) are retransformed into DH10B competent cells. The correct clones are subjected to restriction enzyme and/or PCR analysis to verify authenticity. The plasmids are purified with Pure Link Maxi Kit (Invitrogen Inc.,) in order to transfect into the packaging cells (HEK 293A cells) for virus production.
Example 3
Adenovirus Production in Packaging Cells (HEK 293A)
Day 1: HEK 293A cells (E1-transformed human embryonic kidney cells) are plated at a density of 1−2×106 cells per T-25 flask in cell culture medium containing DMEM, 10% FBS, and 1% penicillin-streptomycin. The cells are incubated at 37° C., 5% CO2 for 24 hr.
Day 2: The confluency can be about 50-70% at the time of transfection. The recombinant adenoviral plasmids (pAdSOcMK) are digested with PacI (often 5 μg DNA is needed for one transfection). The digested plasmids are ethanol precipitated and resuspended in 25-30 μl of sterile H20. A standard lipofectamine transfection is performed according to manufacturer's protocol (Invitrogen Inc.). Mix 5 μg of PacI-digested plasmid and 25 μl of Lipofectamine in 500 μl of OptiMem I medium, and incubate at room temperature for 15-30 min. While waiting, medium from the recipient cells can be removed and the cells can be wash once with a serum-free medium (DMEM).2.5-3.0 ml Opti-Mem I is added to a T-25 flask containing the cells. Incubate the cells (37° C., 5% CO2) for 10-15 min. The lipofectamine-DNA mix is added to the flasks with the cells and returned to the incubator for 5-6 hrs. The lipofectamine/DNA medium is removed and 5-7 ml of fresh cell culture medium is added, and the cells are incubated at 37° C., 5% CO2.
Incubation continues until  ̃90% of the cells detach (die) from the flask surface. This often takes approximately 20-30 days. Transfections and viral production can be monitored by GFP expression. The cells are scraped off the flask with a scrapper at 20-30 days post-transfection and the medium with the cells is collected in 15/50 ml conical tubes. The tubes are spun in a benchtop centrifuge, and supernatant (sup 1) is collected and the pellet is resuspended in 2-3 ml sterile PBS. The cells are frozen in a dry ice/methanol bath or a −80° C. freezer, thawed in a 37° C. water bath, and vortexed vigorously. This procedure of freeze/thaw/vortex is repeated for 3-4 more cycles. The samples are spun briefly, and the supernatant (sup 2) is collected. Sup 1 and sup 2 are mixed (hereinafter “adenovirus particles”). The adenovirus particles are filtered with a 0.45 μm syringe filter and stored at −20/−80° C. until use.
Example 4
Amplification of Adenoviruses
Two 50-70% confluent T-25 flasks of HEK 293A cells are infected using 40-50% of the viral supernatant containing the adenovirus particles from Example 3 for each flask. Cytopathic effect (CPE) or cell lysis should appear at 7-10 days post infection. Effective production of adenoviruses can be monitored by GFP expression. When >90% of the cells die, the cells are scraped off and adenoviral supernatant is prepared as described in Example 3. Authenticity of recombinant adenovirus can be confirmed by infecting the viral supernatant to any infectable cells and Western blot and/or PCR analyses of target genes. Multiple rounds of infection cycles in HEK 293A cells can be carried out to harvest adenoviral particles.
Example 5
Generation of iPS Cells by Adenoviral Vector Containing Multi-Reprogramming Factors from IMR90 Human Fetal Fibroblasts without Using Feeder Cells
Human embryonic fibroblast IMR90 cells are purchased from the American Type Culture Collection (ATCC) (Manassas, Va., http://www.atcc.org; Catalog No. CCL-186). IMR90 cells are cultured and maintained in culture medium 1 (CM-1) containing DMEM, 10% FBS, and 1% penicillin-streptomycin according to manufacturer's protocol.
The fibroblasts IMR90 are thawed as follows:

    
    
        1. Prepare 9 ml of CM-1 in a 15 ml conical tube.
        2. A vial of frozen fibroblasts is removed from the liquid nitrogen tank and placed into a 37° C. water bath until most (but not all) cells are thawed.
        3. The vial is wiped with ethanol, the cap is opened, and the cell suspension is transferred to the tube prepared in step 1.
        4. The tube is centrifuged at 1100 rpm for 3 minutes, and the supernatant is discarded.
        5. The cells are re-suspended in 10 ml of CM-1, and transferred to a 100 mm dish (0.5-1×105 cells/dish). The cells are incubated in a 37° C., 5% CO2 incubator until the cells become 80 ̃90% confluent. The medium is changed every other day.
    
    


The fibroblasts are passaged as follows:

    
    
        1. The medium is discarded the cells are washed once with PBS.
        2. The PBS is aspirated, and 1.5 ml per dish of 0.05% trypsin/0.53 mM EDTA is added, and the cells are incubated for 1-2 minutes at 37° C.
        3. 8.5 ml of CM-1 is added, and the cells are separated into a single cell suspension by pipetting up and down several times.
        4. The cell suspension is adjusted to 40 ml by the addition of CM-1 medium, and transferred to dishes (10 ml per 10 mm dish). Thus the cells are divided up in a 1:4 ratio. The cells are incubated at 37° C., 5% CO2 until the cells become 80-90% confluent. This commonly takes 4-5 days after passage.
    
    


Adenoviral transduction is accomplished as follows:

    
    
        Day 1: IMR90 cells are plated at a density of 1.5 ̃2.5×106 cells per 10 cm tissue culture dish in CM-1 without feeder cells and incubated at 37° C., 5% CO2 for 24 hr.
        Day 2: When IMR90 cells are about 60-70% confluent, the culture medium is removed and the cells are transduced with culture medium 2 (CM-2) including DMEM, 5% FBS, 1% NEAA, 0.5% penicillin-streptomycin and also containing adenovirus particles as generated in either of Examples 3 and 4, Ad-GFP or Ad-SOK or Ad-SOcMK at 100-500 pfu/cell. The cells are incubated at 37° C., 5% CO2 for 24 hr.
        Day 3: The culture medium is changed with culture medium 3 (CM-3) including of DMEM, 10% FBS, 1% NEAA, 0.5% penicillin-streptomycin. The cells are incubated at 37° C., 5% CO2 for 24 hr.
        Day 4: Incubation continues. The medium is changed every day with CM-3 and incubated for more 3-4 days.
        By days 4-7, several colonies showing ES cell-like morphology emerge and all colonies look identical, as shown in FIG. 3.
    
    


Example 6
Adenovirus Transduction and iPSC Generation
IMR90 cells (1.0-1.5×106) are cultured overnight on 100 mm dishes without feeder cells. On the following day, cells are transduced with Ad-SOcMK or Ad-GFP (control). Adenoviruses are removed at 24 hrs post-transduction (day 1), and replaced with human ES cell medium consisting of DMEM/F12 (#11330-32, Invitrogen Inc., USA), 20% Knockout Serum Replacement (KSR) (#10828-028, Invitrogen Inc., USA), 1× nonessential amino acids, 1× sodium pyruvate, 1× L-glutamine, 0.1 mM β-mercaptoethanol, 25 ng/ml basic fibroblast growth factor (bFGF) (#PHG0263, Invitrogen Inc., USA), and 0.5% penicillin-streptomycin. The medium is changed every day and by days 2-3, several colonies showing ES cell-like morphology emerged on the dish. The same protocol is used to generate iPSCs from SkMCs and SCA2 patient skin fibroblasts. Feeder cells are not used.
Example 7
Western Blot Analysis 
Protein extracts are resolved by SDS-PAGE and transferred to Hybond P membranes (Amersham Bioscience Inc., USA). After blocking with 5% skim milk in 0.1% Tween 20/PBS, the membranes are incubated with primary antibodies in 5% skim milk in 0.1% Tween 20/PBS for 2 hrs at room temperature or overnight at 4° C. After several washes with 0.1% Tween 20/PBS, the membranes are incubated with the corresponding secondary antibodies conjugated with HRP in 5% skim milk in 0.1% Tween 20/PBS for 2 hrs at room temperature. Following three additional washes with 0.1% Tween 20/PBS, signals are detected by using the Immobilon Western Chemiluminescent HRP Substrate (#WBKLSO100, Millipore Inc., USA) according to the manufacturer's protocol. The antibodies with their sources and dilutions are listed in Table 2.







TABLE 2







Antibodies












Dilutions
Dilutions





(Western
(Immuno-

Catalog


Antibodies
blot)
fluorescence)
Vendors name
#














Primary Antibodies:






Monoclonal antibodies






(mAb):






OCT-3/4 (C-10)
1:5000

Santa Cruz Inc., USA
sc-5279 


GKLF (B-9)
1:7000

′′
sc-166100


c-MYC (9E10)
1:5000

′′
sc-40  


SSEA-1

1:500
Millipore Inc., USA
MAB4301-20


SSEA-3

1:500
′′
MAB4303-20


SSEA-4

1:500
′′
MAB4304-20


TRA-1-60

1:500
′′
MAB4360-20


TRA-1-81

1:500
′′
MAB4381-20


Smooth Muscle Actin (SMA)

1:500
′′
CBL171


Alpha Feto Protein (AFP)

1:500
′′
2004189


Polyclonal antibodies






(pAb):






Host: Rabbit






SOX-2 (H-65)
1:4000

Santa Cruz Inc., USA
sc-20088 


LIN-28 (H-44)

1:500
′′
sc-67266 


TERT (H-231)

1:500
′′
sc-7212 


NANOG
1:3000
1:500
Cell Signaling Tech.,
3580





USA



THY1
1:4000

Cell Signaling Tech.,
9798





USA



Nestin

1:500
Millipore Inc., USA
AB5922


mAb conjugated with HRP:






Beta-Actin (AC-15)
1:10000

Sigma Inc., USA
A3854


Secondary Antibodies:






Conjugation: HRP


Sigma Inc., USA
A2304


anti-mouse IgG
1:5000





anti-rabbit IgG
1:5000

Santa Cruz Inc., USA
sc-2077 


Conjugation: Dylight 549






anti-mouse IgG

1:2000
Fisher Scientific, USA
35507


anti-rabbit IgG

1:2000
′′
35557









Example 8
Alkaline Phosphatase Staining and Immunocytochemistry
ALP staining was performed using the Alkaline Phosphatase Detection Kit (#SCR004, Millipore Inc., USA). Briefly, iPS cells are fixed with 4% paraformaldehyde/PBS for 2 min, followed by 15 min incubation with staining solution according to the manufacturer's protocol. For immunocytochemistry, cells are fixed in 4% paraformaldehyde/PBS for 20 min at room temperature. The cells are then permeabilized with 70% ethanol and stored at 4° C. After washing with PBS, cells were blocked with 10% BSA/PBS for 2 hrs at room temperature. Slides were incubated with primary antibodies in 10% BSA/PBS for 2 hrs at room temperature or overnight at 4° C., washed three times with PBS and incubated with the corresponding secondary antibodies conjugated with Dylight variants. Following incubation, cells are washed three times with PBS and nuclei stained with 4′,6-diamidino-2-phenylindole (DAPI) (Sigma Inc., USA). The slides are mounted with mounting medium, Vectashield (Vector Inc., USA) and cells visualized using confocal microscopy (Nikon Eclipse Ti microscopy). The antibodies with their sources and dilutions are listed in Table 2.
Example 9
PCR Analysis
Total RNA is prepared from harvested cells using the RNAeasy Kit (Qiagen Inc., USA). cDNA is synthesized from 5 μg of total RNA using MMLV reverse transcriptase and random hexanucleotide primers (New England Biolab Inc., USA) according to the manufacturer's protocol. To study gene expression of iPS cells, cDNAs (150 ng for semi-quantitative and 5 ng for real-time PCR) derived from the total RNA is subjected to PCR analysis. In regular PCR, the PCR products are cloned and verified by sequencing. Primer sequences used for semi-quantitative and real-time PCR are listed in Tables 3 and 4.







TABLE 3





Primers

















CDH1



Forward: SEQ ID 5



5′-AGCCATGGGCCCTTGGAGCCGCAG-3′



Reverse: SEQ ID 6



5′-GGAATAACCCAGTCTCTCTTCTGTC-3′



 



GAL



Forward: SEQ ID 7



5′-TGCGGCCCGAAGATGACATGAAACC-3′



Forward: SEQ ID 8



5′-CCCAGGAGGCTCTCAGGACCGCTC-3′



 



THY1



Forward: SEQ ID 9



5′-GAGGAGGCTGCAGCAGCGGAAGAC-3′



Forward: SEQ ID 10



5′-GAGCCAGCAGGCTGATGCCCTCAC-3′



 



GABRB3



Forward: SEQ ID 11



5′-CCTTGCCCAAAATCCCCTATGTCAAAGC-3′



Reverse: SEQ ID 12



5′-GTATCGCCAATGCCGCCTGAGACCTC-3′



 



NANOG



Forward: SEQ ID 13



5′-ATTATAAATCTAGAGACTCCAGG-3′



Reverse: SEQ ID 14



5′-CATGGAGGAAGGAAGAGGAGAGAC-3′



 



TDGF1



Forward: SEQ ID 15



5′-CTGCTGCCTGAATGGGGGAACCTGC-3′



Reverse: SEQ ID 16



5′-GCCACGAGGTGCTCATCCATCACAAGG-3′



 



ALPL



Forward: SEQ ID 17



5′-TTATAAGGCGGCGGGGGTGGTGGC-3′



Reverse: SEQ ID 18



5′-CGAAGGGGAACTTGTCCATCTCCAG-3′



 



NODAL



Forward: SEQ ID 19



5′-ATCATCCGCAGCCTACAGGCAG-3′



Reverse: SEQ ID 20



5′-CTGTCCCTCCTGGGCCCGCCAGG-3′



 



TERT



Forward: SEQ ID 21



5′-CCTGCTCAAGCTGACTCGACACCGTG-3′



Reverse: SEQ ID 22



5′-GGAAAAGCTGGCCCTGGGGTGGAGC-3′



 



PODXL2



Forward: SEQ ID 23



5′-CTCAACCAGCAGCTCCTAGAAGGG-3′



Reverse: SEQ ID 24



5′-GCTGGCCCGCGCCTGGCAGCTGC-3′



 



GDF3



Forward: SEQ ID 25



5′-CTTATGCTACGTAAAGGAGCTGGG-3′



Reverse: SEQ ID 26



5′-GTGCCAACCCAGGTCCCGGAAGTT-3′



 



GAPDH



Forward: SEQ ID 27



5′-TGAAGGTCGGAGTCAACGGATTTGG-3′



Reverse: SEQ ID 28



5′-GGAGGCCATGTGGGCCATGAG-3′



 



FGF4



Forward: SEQ ID 29



5′-CTACAACGCCTACGAGTCCTACAAG-3′



Reverse: SEQ ID 30



5′GTTGCACCAGAAAAGTCAGAGTTG-3′



 



OCT3/4*



Forward: SEQ ID 31



5′-AGGAGTCCCAGGACATCAAAGCTCTG-3′



 



SOX2*



Forward: SEQ ID 32



5′-CCGGCGGCAATAGCATGGCGAGCGG-3′



 



DPPA4



Forward: SEQ ID 33



5′-ATATCCCGCCGTGGGTGAAAGTTC-3′



Reverse: SEQ ID 34



5′-ACTCAGCCATGGACTGGAGCATCC-3′



 



KLF4*



Forward: SEQ ID 35



5′-TCCAATTCGCTGACCCATCCTCCG-3′



 



IFITM1



Forward: SEQ ID 36



5′-



CCCCAAAGCCAGAAGATGCACAAGGAGG-



3′



Reverse: SEQ ID 37



5′-CGTCGCCAACCATCTTCCTGTCCCTAG-3′



 



c-MYC*



Forward: SEQ ID 38



5′-ATGGTGACCGAGCTGCTGGGAGGAG-3′



 



Poly A*



Reverse: SEQ ID 39



5′-ATACATTGATGAGTTTGGACAAAC-3′







*Primers used for exogenous gene.













TABLE 4





Primers
















THY1
TDGF1


Forward: SEQ ID 40
Forward: SEQ ID 42


5′-GAGGAGGCTGCAGCAGCGGAAGAC-3′
5′-GGATACAGCACAGTAAGGAGC-3′


Reverse: SEQ ID 41
Reverse: SEQ ID 43


5′-CCACTAGGCAGGCCGTTAGGCTGG-3′
5′-GCACAGACCCACAGTTCTC-3′


 


OCT3/4
GDF3


Forward: SEQ ID 44
Forward: SEQ ID 46


5′-TCTCCCATGCATTCAAACTGAG-3′
5′-CCCGAGACTTATGCTACGTAAAG-3′


Reverse: SEQ ID 45
Reverse: SEQ ID 47


5′-CCTTTGTGTTCCCAATTCCTTC-3′
5′-GGCAGACAGGTTAAAGTAGAGG-3′


 


NANOG
ALPL


Forward: SEQ ID 48
Forward: SEQ ID 50


5′-AGCTACAAACAGGTGAAGACC-3′
5′-GATGTGGAGTATGAGAGTGACG-3′


Reverse: SEQ ID 49
Reverse: SEQ ID 51


5′-GTGGTAGGAAGAGTAAAGGCTG-3′
5′-GGTCAAGGGTCAGGAGTTC-3′


 


TERT
GABRB3


Forward: SEQ ID 52
Forward: SEQ ID 54


5′-GCACGGCTTTTGTTCAGATG-3′
5′-CAAGGCAAAGAATGACCGTTC-3′


Reverse: SEQ ID 53
Reverse: SEQ ID 55


5′-CGGTTGAAGGTGAGACTGGC-3′
5′-TGCTGAATTCCTGGTATCGC-3′


 


LIN28
NODAL


Forward: SEQ ID 56
Forward: SEQ ID 58


5′-GCAGAAGCGCAGATCAAAAG-3′
5′-AGGAGTTTCATCCGACCAAC-3′


Reverse: SEQ ID 57
Reverse: SEQ ID 59


5′-CGGACATGAGGCTACCATATG-3′
5′-TCTGCCATTATCCACATACAGC-3′


 


IFITM4
FGF4


Forward: SEQ ID 60
Forward: SEQ ID 62


5′-ATCAACATCCACAGCGAGAC-3′
5′-CCATGAAGGTCACCCACTTC-3′


Reverse: SEQ ID 61
Reverse: SEQ ID 63


5′-CAACCATCTTCCTGTCCCTAG-3′
5′-CTCTTGCATTAAACTCTTCATCCG-3′


 


PODXL2
CDH1


Forward: SEQ ID 64
Forward: SEQ ID 66


5′-CCCAGCGAAGAGAATGAAGAG-3′
5′-CCCAATACATCTCCCTTCACAG-3′


Reverse: SEQ ID 65
Reverse: SEQ ID 67


5′-AATGGAACCTGCCTTCTCAG-3′
5′-CCACCTCTAAGGCCATCTTTG-3′


 


GAL
GAPDH


Forward: SEQ ID 68
Forward: SEQ ID 70


5′-GCGCACAATCATTGAGTTTCTG-3′
5′-GAAGGTGAAGGTCGGAGTCAACG-3′


Reverse: SEQ ID 69
Reverse: SEQ ID 71


5′-AGACAAACATGCCCAGGAGG-3′
5′-GAAGATGGTGATGGGATTTCC-3′









Example 10
Bisulfite Sequencing
To assess the methylation status of CpGs in the promoter region of NANOG, genomic DNA is purified from IMR90 cells transduced with Ad-GFP or Ad-SOcMK using the DNeasy Kit (Qiagen Inc., USA). Purified genomic DNA (1 μg) is used to convert unmethylated cytosines (C) to uracil (U) using EZ DNA methylation kit (#D5001, Zymo Research Inc., USA), according to the manufacturer's protocol. Treated DNA is purified with QIAquick column (Qiagen Inc., USA) and purified DNA (150 ng) from each sample is subjected to PCR analyses for the promoter region of NANOG using the following primers: forward 5′-CACCATGCGTGGCTAATTTTTGTA-3′, reverse 5′-TTAAAATCCTGGAGTCTCTAGATTT-3′. The resulting PCR products are subcloned into the pCR2.1-TOPO vector (Invitrogen Inc., USA). Ten clones of each sample are verified by sequencing.
Example 11
In Vitro Differentiation
To determine the differentiation ability of iPS cells in vitro, the floating culture method is used to form Embryoid bodies (EBs). Briefly, IMR90 cells are transduced with Ad-SOcMK. On day 3, the resultant iPS cells are mechanically dissociated and cultured in ES cell medium (without bFGF) in non-coated T25 flasks. The medium is changed every other day. After 7 days in floating culture, ball-shaped structures typical for EBs are formed. EBs are then transferred to 0.1% gelatin-coated chamber slides using the same medium. The medium is changed every other day once EBs are attached to the slide. Differentiated cells are fixed after 8 days in adherent culture and stained with antibodies recognizing marker proteins for each germ layer.
Example 12
Teratoma Formation 
To examine the in vivo development potential of iPS cells, IMR90 cells are transduced with Ad-SOcMK. On day 3, the resultant iPSCs are injected subcutaneously to 4 of 6-week-old male nonobese diabetic severe combined immunodeficient (NOD/SCID) mice (Charles River Laboratories) (3×106 iPSCs for each mouse). For control experiment, IMR90 cells (3×106 cells) are also injected into one mouse. After 9-10 weeks, tumors are dissected and fixed in 4% paraformaldehyde. Teratoma experiments are conducted in Comparative Oncology Resource Core at the University of Utah. Samples are embedded in paraffin and stained with hematoxylin and eosin in the Tissue Resource and Application Core (TRAC) at the University of Utah. All procedures are performed in accordance with protocols approved by the University of Utah Animal Research Committee guidelines.
Example 12
Microarray Analyses
IMR90 cells are transduced with Ad-SOcMK or Ad-GFP. Adenoviruses are removed at 12 hrs post-transduction and cells are sampled at every 6 hrs. Total RNA is prepared from each sample using Qiagen RNeasy kit according to manufacturer's protocol. Human genome SurePrintG3 8×60K carrying 27,958 genes and 7,419 LincRNA targets (Agilent Technologies, Inc.) are used for microarray hybridization to examine the global gene expression. Approximately 1 μg of RNA from each sample is labeled using Agilent Two-Color Quick Amp Labeling Kit following manufacturer's instructions. All arrays are hybridized at 65° C. for 17 hrs and scanned using an Agilent scanner G2505C. The gene expression raw data is extracted using Agilent Feature Extraction Software version 10.5. Quality control is done on the basis of Agilent quality control metrics. Singular value decomposition (SVD) of the qualified data, with gene expression centered at its time average, identified several “eigengenes,” i.e., significant patterns of expression variation across time. Sorting the data according to the two most significant eigengenes gives a global picture of the dynamics of gene expression, in which individual genes appear to be classified into groups of similar regulation and function25. Array experiments are performed in Microarray Core Facility at the University of Utah.
Of course, it is to be understood that the above-described arrangements are only illustrative of the application of the principles of the present disclosure. Numerous modifications and alternative arrangements may be devised by those skilled in the art without departing from the spirit and scope of the present disclosure and the appended claims are intended to cover such modifications and arrangements. Thus, while the present disclosure has been described above with particularity and detail in connection with what is presently deemed to be the most practical embodiments of the disclosure, it will be apparent to those of ordinary skill in the art that numerous modifications, including, but not limited to, variations in size, materials, shape, form, function and manner of operation, assembly and use may be made without departing from the principles and concepts set forth herein.

## Claims

1. A transformation construct for generating induced pluripotent stem (iPS) cells, comprising:
an expression vector including a plurality of reprogramming factors, each reprogramming factor being under control of a separate promoter, wherein the plurality of reprogramming factors includes OCT3/4, SOX2, and at least one member selected from the group consisting of KLF4, c-Myc, NANOG, and LIN28.

2. The construct of claim 1, wherein the expression vector is selected from the group consisting of plasmids, viruses, and combinations thereof.

3. The construct of claim 1, wherein the expression vector is selected from the group consisting of adenoviral vectors, episomal vectors, retroviral vectors, and lentiviral vectors.

4. The construct of claim 1, wherein the expression vector is an episomal vector.

5. The construct of claim 1, wherein the plurality of reprogramming factors includes OCT3/4, SOX2, KLF4, and c-Myc.

6. The construct of claim 1, wherein the plurality of reprogramming factors consists of OCT3/4, SOX2, and KLF4.

7. The construct of claim 1, wherein the plurality of reprogramming factors includes OCT3/4, SOX2, NANOG, and LIN28.

8. The construct of claim 1, wherein the expression vector has a sequence that is at least 80% homologous to SEQ ID 72.

9. The construct of claim 1, wherein the expression vector has a sequence that is at least 95% homologous to SEQ ID 72.

10. The construct of claim 1, wherein at least one of reprogramming factor is under the control of a CMV promoter.

11. The construct of claim 10, wherein the CMV promoter is a weak CMV promoter.

12. The construct of claim 1, wherein the expression vector further includes a reporter sequence under control of a separate promoter.