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  • C12N2510/00—Genetically modified cells

Definitions

• the present disclosure relates generally to novel methods and compositions for using engineered reprogramming factor(s) for the creation of induced pluripotent stem cells (iPSCs) through a controlled process.
• this disclosure relates to establishing combinations of reprogramming factors, including fusions between conventional reprogramming factors with trans activation domains, optimized for reprogramming of various cell types.
• the exemplary methods disclosed herein can be used for creating induced pluripotent stem cells from various mammalian cell types, including non-human primate cells.
• Exemplary methods of feeder-free derivation of human induced pluripotent stem cells using synthetic messenger RNA are also disclosed.
• iPSCs induced pluripotent stem cells
• the therapeutic potential of induced pluripotent stem cells (iPSCs) has spurred efforts to develop reprogramming methods that sidestep the need to genetically modify somatic cells to effect reprogramming to the pluripotent state.
• mRNA messenger RNA
• RNA transfection is in principle the most attractive of these methods as it affords precise control over the reprogramming factor (RF) expression time course, while completely obviating any requirement for "clean up" of the reprogrammed cells to purge residual traces of the vector.
• Current protocols for mRNA-based reprogramming are relatively labor- intensive, however, owing to the need to retransfect daily for the ⁇ 2 weeks required for the induction of pluripotency in human cells. These procedures also rely on the use of feeder cells, adding complexity and technical variability to the process while introducing a potential source of contamination with non-human-derived (“xeno”) biological material.
• iPSCs induced pluripotent stem cells
• M30 mouse embryonic fibroblasts
• Sox2, Klf4 and c- Myc SMM
• the present disclosure provides methods and compositions for generating stem cells capable of producing all the different tissues of the body.
• the methods disclosed herein can be used to reprogram non- human fibroblasts into induced pluripotent stem cells (iPSCs).
• iPSCs induced pluripotent stem cells
• RF reprogramming factors
• engineered variants of conventional reprogramming factors such as Oct4 (also referred to as Oct3/4), Sox 2, etc., incorporating transactivation domains of known, strong transcription factors, such as VP16 and MyoD.
• the methods and compositions disclosed herein results in a feeder-freeprotocol which dramatically reduces the time, cost and effort involved in mRNA-based reprogramming.
• the present disclosure provides a method for dedifferentiating or reprogramming somatic cell comprising: a) transfecting the isolated somatic cell with a composition comprising an effective amount of a fusion product between any one or more of a synthetic mRNA reprogramming factor selected from Oct4, Sox2, Klf4, cMyc, Nanog, and Lin28 and a transactivation domains whereby the somatic cell is reprogrammed or dedifferentiated.
• a method of claim 1, wherein the composition comprises Oct4 fused to an N-terminal MyoD transactivation domain is provided.
• the Oct4 is fused to an N-terminal MyoD transactivation domain in tandem triplicates.
• a method for reprogramming mammalian cells by using any one or more of the synthetic mRNA of reprogramming factor of claim 1 said method
• target cells at a density of 15 k to 500 k cells/well of a standard 6- well plate in a feeder-free surface; b) transfecting cells with varying doses of 50 ng to 800 ng/ml mRNA each time during reprogramming is provided.
• the target cells are grown at a density of 30 k, 75 k, 100 k, or 150 k cells/well of a standard 6-well plate in a feeder-free surface; b) transfecting cells with varying doses of 50 ng to 800 ng/ml mRNA each time during reprogramming, whereas lower doses are used at earlier time points than later time points; c) attaining iPSCs without passaging.
• the target cells are grown at a density of 15 k, 75 k, 100 k, or 150 k cells/well of a standard 6-well plate in a feeder-free surface, whereas the volume of each well is adjusted to be as between 0.5 ml to 5 ml of appropriate medium; transfecting cells with varying doses of 50 ng to 800 ng/ml mRNA each time during reprogramming, whereas lower doses are used at earlier time points than later time points; attaining iPSCs without passaging.
• the mammalian cells are human cells. In one embodiment, the mammalian cells are human cells. In one
• the method is Xeno-free.
• the mammalian cells are non- human primate cells.
• the non-human primate cells are cynomolgus monkey cells.
• the one or more factors are selected from the group consisting of mRNAs, regulatory RNAs, siRNA miRNA, and combinations thereof.
• the somatic cells are transfected with at least two different RNAs.
• the somatic cells are selected from the group consisting of unipotent, multipotent, pluripotent, and differentiated cells.
• the one or more RNAs induces de-differentiation of the somatic cells to unipotent, multipotent, or pluripotent cells.
• the at least one of the factors is selected from the group consisting of OCT4, SOX2, NANOG, LIN28, KLF4 and MYC mRNA.
• the OCT4, SOX2, NANOG, and LIN28 mRNA are administered in combination.
• the OCT4, SOX2, KLF4 and MYC mRNA are administered in combination.
• the transfected cells are maintained in culture as induced pluripotent stem (iPS) cells.
• the transfected cells form induced pluripotent stem cells, further comprising inducing the iPS cells to form differentiated cells.
• a method for treating or inhibiting one or more symptoms of a disease or disorder in a patient comprising de-differentiating cells in vitro and administering the cells to the patient.
• the composition further comprises Rarg and LrH-l transaction activation domains.
• the composition comprises OCT4 fused to a VP16 transactivation domain.
• the disclosure provides iPSCs derived from non-human primate cells which were used to establish disease model systems because they can produce in-integration-free, feeder-free testing environment without other animal products.
• the non-human iPSCs described herein are useful for preclinical testing.
• FIG. 1 hESC-Like Colonies in an HDF-a Feeder-Free Reprogramming Culture. lOx bright-field images of emergent hESC-like colonies at day 9 of a feeder-free derivation from 75K HDF-a adult fibroblasts, treated for 9 days with 400 ng/ml mRNA cocktail (M30+ c-Myc + Nanog + ) delivered as a media supplement using Stemfect transfection reagent.
• M30+ c-Myc + Nanog + 400 ng/ml mRNA cocktail
• FIG. 1 Schematic summarizing the procedure for making mRNA reprogramming cocktails.
• Figure 6 Generation of synthetic mRNA Cocktails using 2-Thio-Uracil for reprogramming cocktails. Synthetic mRNAs encoding a number of RFs on a SYBR E- gel. The mRNAs have 10% of then Uracil bases replaced by 2-Thio-Uracils. 100 ng of RNA was loaded per lane.
• Figure 7 Human iPSCs created using mRNA cocktails with mRNAs modified with 2-Thio-Uracil. Populations of human iPSCs after (A) 7 days or (B) 11 days of reprogramming during different reprogramming runs in Pluriton (A) or Allele
• Figure 8 Cynomolgus Monkey iPSC colonies created using mRNA cocktail in feeder-free reprogramming culture. Shown in the pictures are lOx bright-field images of emergent hESC-like colonies on day 10 and day 13. In the day 10 panel, the cells near the center exhibit morphology changes from fibroblast to stem cells. In the day 13 panel, the cells formed a large colony of fully transformed monkey iPSCs.
• Differentiated cells can be reverted to a pluripotent state by the expression of a select group of transcription factors opened up the prospect that patient-specific cells might be used to generate cells of any desired type for the study of genetic disease in vitro and ultimately for cell-replacement therapy.
• Expression of the reprogramming factors can be achieved through the application of viral vectors which integrate into the genome, and iPSC derivations are still usually performed with integrating retrovirus or lentivirus.
• the attendant modification of the genome represents an important hurdle to therapeutic application of iPSCs, while the possibility of reactivated expression from integrated viral cassettes is a concern even for in vitro studies.
• Lentiviral vectors which encode the multiple factors required for iPSC induction in a single polycistronic cassette flanked by lox recombination sites, which allows for almost-seamless excision of the transgene after reprogramming through transient expression of Cre recombinase.
• Transgene insertion with subsequent excision can also be effected by using a transposon vector followed by brief expression of transposase.
• Non-integrating DNA vector which can transiently express reprogramming factors for enough time to induce pluripotency, including adenovirus, plasmid and episomal DNA. It has also proved possible to generate iPSC by repeated transduction of cells with recombinant RF proteins incorporating cell-penetrating peptides, albeit with low efficiency. Relatively efficient iPSC conversion can now be achieved using Sendai virus, which has a completely RNA-based reproductive cycle, and by sustained transfection of synthetic mRNA transcripts encoding the Yamanaka factors.
• feeder cells buffer the population density of the culture as the target cells grow out from a low starting density over the extended time course required for iPSC induction, evening out the delivered dose of RNA and transfection reagent (both of which have associated toxicities) and supporting the viability of the target cells in the face of the pro-apoptotic and cytostatic forces engendered by the reprogramming process.
• This requirement adds complexity and hands-on time to the procedure and introduces an important source of technical variability, especially given that the feeders are themselves subject to transfection.
• feeder layer also impedes monitoring and analysis of the reprogramming process.
• human feeder cells are currently the standard for mRNA reprogramming, even these cells are a potential source of xeno-biological contamination when non-human animal products are used in their derivation and expansion.
• novel methods, materials, and protocols are provided herein to produce iPSCs with improved efficiency of reprogramming and improved quality of the resultant cells.
• the current invention embodiments were used successfully to achieve significant surprising and unexpected improvements through potentiation of the RF cocktail delivered to the cells.
• the current invention embodiments also provide a novel protocol(s) which compresses and streamlines the mRNA reprogramming process, and which support the production of footprint-free iPSCs from human fibroblasts without the use of feeder cells or any other potentially xeno-contaminated reagents.
• the novel methods and compositions provided herein will extend the benefits of the previously known mRNA method and help clear remaining roadblocks to the therapeutic application of iPSC technology.
• the present disclosure relates generally to methods of using engineered reprogramming factor(s) for the creation of induced pluripotent stem cells (iPSCs) through a kinetically controlled process. More specifically, this invention relates to establishing combinations of reprogramming factors, including fusions between conventional
• reprogramming factors with transactivation domains optimized for reprogramming different types of cells; introducing these factors as synthetic messenger RNA (mRNA) into cultured mammalian cells at the preferred density by methods that result in appropriate levels of transgene expression; maintaining cell under defined conditions to result in previously unattainable efficiency of reprogramming.
• mRNA synthetic messenger RNA
• the current invention dramatically reduces the time, cost and effort involved in reprogramming, with the options to be completely feeder-free and Xeno-free, and without passaging.
• the materials and procedures disclosed herein are useful for creating induced pluripotent stem cells from different types of mammalian cells, including human fibroblasts.
• aspects of the disclosure also provide methods for generating stem cells capable of producing variety of different tissues of the human body by using messenger RNA molecules without the need of viral vectors, animal products or feeder cells.
• the novel methods disclosed herein can be used to reprogram human fibroblasts into induced pluripotent stem cells (iPSCs) with surprising and unexpected efficiency under optimal conditions.
• iPSCs induced pluripotent stem cells
• the present disclosure provides useful processes and compositions for treating non-human mammalian cells (e.g. fibroblasts) with cocktails of "cleaned-up" mRNAs encoding exemplary reprogramming factors described herein,
• the mRNA composition can be used without causing the treated cells to undergo cell death associated with introduction of the mRNA molecules.
• the non-human mammalian cells are cynomolgus monkey cells.
• the cynomolgus monkey cells are seeded in a gradient in a well so that cells grow at varying local densities.
• cells suitable for use with the method include, but are not limited to, primary cells and established cell lines, embryonic cells, immune cells, stem cells, and differentiated cells including, but not limited to, cells derived from ectoderm, endoderm, and mesoderm, including fibroblasts, parenchymal cells, hematopoietic cells, and epithelial cells.
• stem cells include unipotent cells, multipotent cells, and pluripotent cells; embryonic stem cells, and adult stem cells such as hematopoietic stem cells, mesenchymal stem cells, epithelial stem cells, and muscle satellite cells.
• somatic cells are de-differentiated or reprogrammed.
• somatic cells include fibroblasts, keratinocytes, adipocytes, muscle cells, organ and tissue cells, and various blood cells including, but not limited to, hematopoietic cells including hematopoietic stem cells, and cells that provide short- or long-term hematopoietic engraftment.
• the most preferred cell types include, but are not limited to, human fibroblasts, keratinocytes and hematopoietic stem cells. The methods are particularly useful for de-differentiating and optionally re- differentiating cells, without permanent alteration of cell genomes.
• RNAs useful in the disclosed method include mRNAs, regulatory RNAs, or small RNAs such as siRNA or miRNA wherein the one or more mRNAs encode polypeptides that function to de-differentiate or reprogram the cell.
• the efficiency of transfection is high. Typically more than 90% of the transfected cell population will express the introduced RNA. Therefore, it is possible to transfect cells with one or more distinct RNAs.
• the population of cells can be transfected with one or more distinct mRNAs, one or more distinct siRNAs, one or more distinct miRNAs, or combinations thereof.
• the population of cells can be transfected with multiple RNAs simultaneously in a single administration, or multiple administrations can be staggered minutes, hours, days, or weeks apart. Transfection of multiple distinct RNAs may be staggered. For example, if it is desirable for a first RNA to be expressed prior to expression of one or more additional RNAs.
• the level of expression of the transfected RNA can be manipulated over a wide range by changing the amount of input RNA, making it possible to individually regulate the expression level of each transfected RNA.
• the effective amount of input RNA is determined based on the desired result.
• the PCR-based technique of mRNA production facilitates the design of mRNAs with different structures and domain
• RNAs useful in the disclosed methods are known in the art, and will be selected based on the target host cell type as well as the pathway or cellular activity to be manipulated, or the therapeutic application.
• Constructs useful for de- differentiating cells for example, converting adult, differentiated somatic cells into stem cells, can be constructed based on known genes, mRNAs, or other nucleotide or protein sequences.
• polynucleotide and nucleic acid used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or
• deoxyribonucleotides include, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
• Oligonucleotides generally refers to polynucleotides of between about 5 and about 100 nucleotides of single- or double-stranded DNA. However, for the purposes of this disclosure, there is no upper limit to the length of an oligonucleotide. Oligonucleotides are also known as oligomers or oligos and may be isolated from genes, or chemically synthesized by methods known in the art.
• microRNA refers to any type of interfering RNAs, including but not limited to, endogenous microRNAs and artificial microRNAs (e.g., synthetic miRNAs). Endogenous microRNAs are small RNAs naturally encoded in the genome which are capable of modulating the productive utilization of mRNA.
• An artificial microRNA can be any type of RNA sequence, other than endogenous microRNA, which is capable of modulating the activity of an mRNA.
• a microRNA sequence can be an RNA molecule composed of any one or more of these sequences.
• a "microRNA precursor” refers to a nucleic acid having a stem-loop structure with a microRNA sequence incorporated therein.
• a “mature microRNA” includes a microRNA that has been cleaved from a microRNA precursor (a "pre-miRNA”), or that has been synthesized (e.g., synthesized in a laboratory by cell-free synthesis), and has a length of from about 19 nucleotides to about 27 nucleotides, e.g., a mature microRNA can have a length of 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, 26 nt, or 27 nt.
• a mature microRNA can bind to a target mRNA and inhibit translation of the target mRNA.
• OCT4 genomic, mRNA (cDNA), and protein sequences for OCT4 are known in the art, see, for example, (OCT4) POU5F1 POU class 5 homeobox
• Gene ID: 5460 which provides mRNA (cDNA) sequences Genbank accession no. NM— 001173531.1 entitled Homo sapiens POU class 5 homeobox 1 (POU5F1), transcript variant 3, mRNA; Genbank accession no. NM— 002701.4 entitled Homo sapiens POU class 5 homeobox 1 (POU5F1) transcript variant 1, mRNA; and Genbank accession no.
• Exemplary genomic, mRNA (cDNA), and protein sequences for SOX2 are also known in the art, see, for example, SOX2 SRY (sex determining region Y)-box 2 [Homo sapiens], Gene ID: 6657, which provides mRNA (cDNA) sequence Genbank Accession no. NM— 003106.2 entitled mRNA sequence Homo sapiens SRY (sex determining region Y)- box 2 (SOX2), mRNA.
• Exemplary genomic, mRNA (cDNA), and protein sequences for NANOG are also known in the art, see for example NANOG Nanog homeobox [Homo sapiens], Gene ID: 79923, which provides the mRNA (cDNA) sequence Genbank accession no. NM— 024865.2 entitled Homo sapiens Nanog homeobox (NANOG), mRNA.
• Exemplary genomic, mRNA (cDNA), and protein sequences for LIN28 are also known in the art, see for example LIN28A homolog A (C. elegans) [Homo sapiens], Gene ID: 79727, which provides the mRNA (cDNA) sequence Genbank accession no.
• Exemplary genomic, mRNA (cDNA), and protein sequences for KLF4 are known in the art, see, for example, KLF4 Kruppel- like factor 4 (gut) [Homo sapiens], Gene ID: 9314, which provides the mRNA (cDNA) sequence Genbank accession no. NM— 004235.4 entitled Homo sapiens Kruppel-like factor 4 (gut) (KLF4), mRNA.
• MYC v-myc myelocytomatosis viral oncogene homolog
• avian Homo sapiens
• Gene ID: 4609 which provides the mRNA (cDNA) sequence Genbank accession no. NM— 002467.4 entitled Homo sapiens v-myc myelocytomatosis viral oncogene homolog avian) (MYC), mRNA.
• a "stem-loop structure” refers to a nucleic acid having a secondary structure that includes a region of nucleotides which are known or predicted to form a double strand (step portion) that is linked on one side by a region of predominantly single-stranded nucleotides (loop portion).
• the terms “hairpin” and “fold-back” structures are also used herein to refer to stem-loop structures. Such structures are well known in the art and these terms are used consistently with their known meanings in the art.
• the actual primary sequence of nucleotides within the stem-loop structure is not critical to the practice of the invention as long as the secondary structure is present.
• the secondary structure does not require exact base-pairing.
• the stem may include one or more base mismatches.
• the base-pairing may be exact, i.e. not include any mismatches.
• stem cell refers to an undifferentiated cell that can be induced to proliferate.
• the stem cell is capable of self -maintenance, meaning that with each cell division, one daughter cell will also be a stem cell.
• Stem cells can be obtained from embryonic, fetal, post-natal, juvenile or adult tissue.
• progenitor cell refers to an undifferentiated cell derived from a stem cell, and is not itself a stem cell. Some progenitor cells can produce progeny that are capable of differentiating into more than one cell type.
• induced pluripotent stem cell refers to a stem cell induced from a somatic cell, e.g., a differentiated somatic cell, and that has a higher potency than said somatic cell.
• iPS cells are capable of self-renewal and differentiation into mature cells, e.g., smooth muscle cells. iPS may also be capable of differentiation into smooth muscle progenitor cells.
• isolated refers to a cell that is in an environment different from that in which the cell naturally occurs, e.g., where the cell naturally occurs in a multicellular organism, and the cell is removed from the multicellular organism, the cell is "isolated.”
• An isolated genetically modified host cell can be present in a mixed population of genetically modified host cells, or in a mixed population comprising genetically modified host cells and host cells that are not genetically modified.
• an isolated genetically modified host cell can be present in a mixed population of genetically modified host cells in vitro, or in a mixed in vitro population comprising genetically modified host cells and host cells that are not genetically modified.
• a "host cell,” as used herein, denotes an in vivo or in vitro cell (e.g., a eukaryotic cell cultured as a unicellular entity), which eukaryotic cell can be, or has been, used as recipients for a nucleic acid (e.g., an exogenous nucleic acid), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
• genetic modification refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (i.e., nucleic acid exogenous to the cell). Genetic change (“modification”) can be accomplished by incorporation of the new nucleic acid into the genome of the host cell, or by transient or stable maintenance of the new nucleic acid as an extrachromosomal element. Where the cell is a eukaryotic cell, a permanent genetic change can be achieved by introduction of the nucleic acid into the genome of the cell. Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like.
• exogenous nucleic acid refers to a nucleic acid that is not normally or naturally found in and/or produced by a cell in nature, and/or that is introduced into the cell (e.g., by electroporation, transfection, infection, lipofection, or any other means of introducing a nucleic acid into a cell).
• treatment refers to obtaining a desired pharmacologic and/or physiologic effect.
• the effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse affect attributable to the disease.
• Treatment covers any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occuning in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.
• a mammal refers to a mammal, including, but not limited to, a human, a non- human primate, a rodent (e.g., a mouse, a rat, etc.), an ungulate, a canine, a lagomorph, a feline, etc.
• a subject of interest is a human.
• a subject is a non-human animal such as a monkey, rodent, or a lagomorph.
• a “therapeutically effective amount” or “efficacious amount” means the amount of a compound, a nucleic acid, or a number of cells that, when administered to a subject for treating a disease, is sufficient to effect such treatment for the disease.
• the “therapeutically effective amount” will vary depending on the compound or the cell, the disease and its severity and the age, weight, etc., of the subject to be treated.
• mRNA-based reprogramming could be enhanced through the use of engineered variants of Oct4 or Sox 2 incorporating an N- terminal MyoD transactivation domain (Hirai et al, Stem Cells, 2011) or a C-terminal triple repeat of the VP16 transactivation domain (Wang et al, EMBO Reports, 2011 ; in which synthetic reprogramming factors were prepared by fusing the VP16 transactivation domain to OCT4 (also known as Pou5f 1), NANOG and SOX2, respectively, these synthetic factors could reprogram both mouse and human fibroblasts with enhanced efficiency and accelerated kinetics), or by augmenting the "standard" RF cocktail with two additional factors, Rarg and Lrh-1 (Wang et al, PNAS, 2011).
• the method can also be widely used for re-differentiating or reprogramming of cells, for example, to produce iPS cells that can be further modulated to form
• hematopoietic stem cells mesenchymal stem cells, epithelial stem cells, and muscle satellite cells, or differentiated cells of human tissues, including, but not limited to, red blood cells, white blood cells including lymphocytes, platelets, stromal cells, fat cells, bone cells including osteoclasts, epithelial tissue including skin cells, muscle tissue including smooth muscle, skeletal muscle, and cardiac muscle, vascular tissue including endothelial cells, liver tissue including hepatocytes, and nervous tissue including neurons.
• Methods of inducing differentiation of iPS cells into various differentiated cells types including, but not limited to, cardiomyocytes, hematopoietic stem cells, bone cells such as, osteoclasts, hepatocytes, retinal cells, and neurons, stem cells including, but not limited to, isolated embryonic stem cells, hematopoietic stem cells, and induced pluripotent stem cells can be induced to differentiate by transient transfection with RNAs that induce differentiation. Additionally, or
• cells can be re-differentiated by culturing the cells under cell type-specific conditions.
• iPS cells can be maintained on CF-1 feeders and subsequently adapted to feeder-free conditions.
• iPS cells can be induced to form differentiated retinal cells by culturing the cells in the presences of noggin, Dkk-1, and IGF-1
• Previously reported methodologies relied on integrating vectors, i.e. viruses or plasmids, to carry the modified factors.
• a reprogramming trial was performed comparing the performance of six different mRNA combination cocktails comprising transcripts for five factors for mRNA reprogramming (Oct4, Sox2, Klf4, cMyc- T58A and Lin28), or a 7-reprogram factor RF cocktail including Rarg and Lrh-1, each combination was tested in three variations based on wild-type Oct4 and the MyoD- and VP16-Oct4 fusion constructs (designated M3O and VPx3, respectively).
• BJ fibroblasts were transfected in feeder-based reprogramming cultures for 11 days, by which time advanced morphologies were apparent in several of the wells. Over the next few days, colonies with characteristic hESC morphologies emerged in wells transfected with the cocktails based on wild-type Oct4 and M30. The target cells in the VPx3-transfected cultures retained a fibroblastic morphology, albeit while showing accelerated growth and some tendency to aggregate into foci, and no colonies emerged.
• the 5-factor and 7-factor embodiments of the wild type Oct4 and M30-based cocktails showed similar colony productivity, hence no advantage accrued from the inclusion of Rarg and Lrh-1 in the cocktails. However, the M3O cocktail gave several times the number of colonies produced with wild-type Oct4. In light of this result, colonies were picked from the M3O 5-factor well for expansion and further analysis ( Figure 1). Pluripotency of M30-derived colonies was confirmed by
• the method can also be widely used for re-differentiating or reprogramming of cells, for example, to produce iPS cells that can be further modulated to form
• hematopoietic stem cells mesenchymal stem cells, epithelial stem cells, and muscle satellite cells, or differentiated cells of human tissues, including, but not limited to, red blood cells, white blood cells including lymphocytes, platelets, stromal cells, fat cells, bone cells including osteoclasts, epithelial tissue including skin cells, muscle tissue including smooth muscle, skeletal muscle, and cardiac muscle, vascular tissue including endothelial cells, liver tissue including hepatocytes, and nervous tissue including neurons.
• iPS cells Methods of inducing differentiation of iPS cells into various differentiated cells types, including, but not limited to, cardiomyocytes, hematopoietic stem cells, bone cells such as, osteoclasts, hepatocytes, retinal cells, and neurons, are known in the art (Song at al., Cell Res., 19(11): 1233-42 (2009), Lamba et al., PLoS One, 5(l):e8763 (2010), Gai et al, Cell Biol Int. 200933(11): 1184-93 (2009).
• Stem cells including, but not limited to, isolated embryonic stem cells, hematopoietic stem cells, and induced pluripotent stem cells can be induced to differentiate by transient transfection with RNAs that induce
• cells can be re-differentiated by culturing the cells under cell type-specific conditions.
• iPS cells can be maintained on CF-1 feeders and subsequently adapted to feeder-free conditions.
• iPS cells can be induced to form differentiated retinal cells by culturing the cells in the presences of noggin, Dkk-1, and IGF- lln another aspect, the potency of the mRNA cocktail could be further enhanced by the inclusion of Nanog ti'anscripts.
• the efficacy of the M30-based 5-factor or 6-factor cocktails was confirmed in additional feeder-based experiments using three additional human fibroblast lines (HDF-f, HDF-n and XFF). Reprogrammmg kinetics and efficiency were markedly improved with all three of these low-passage lines, which displayed faster native population doubling times than BJs in normal expansion culture. In some cases, we obtained hESC-like colonies from as little as six days of transfection, although the yields were much higher in experiments where transfection was continued for a few more days. Experiments involving periodic reinforcement of the feeder layer by addition of fresh cells suggested that while this strategy might give some benefits, they would be offset by the complexity of the resulting protocol. We therefore decided to focus on applying the more potent cocktails to development of a streamlined, feeder- free protocol.
• the current disclosure relates to creation of feeder-free iPSCs.
• Feeder- independent iPSC derivation has generally proved somewhat challenging regardless of the reprogramming technology employed, but raises special difficulties in the context of a sustained transfection regime.
• the propensity of cells to undergo mitotic arrest or apoptosis in sparse cultures is exacerbated when the cells are stressed by transfection and by ectopic expression of reprogramming factors.
• RNA doses which are well tolerated at the high cell densities characteristic of feeder-based reprogramming produce more severe cytotoxic effects when distributed among fewer cells.
• MET mesenchymal-to-epithelial transition
• MET mesenchymal-to-epithelial transition
• the ⁇ 7 days typically required for human fibroblasts to reach MET when using current mRNA cocktails makes it hard to head off the problem of fibroblastic overgrowth even if cells are plated at the lowest survivable initial densities.
• Cells can be thinned by passaging to postpone this fate, but the plating efficiency of highly stressed reprogramming intermediates is hard to predict and, in any case, a passaging-based derivation protocol would sacrifice convenience and scale poorly to high-throughput applications.
• cells can also be seeded at a gradient in a well so that different local cell density can facilitate the repeated transfection,
• the current disclosure relates to phenotypic indications of MET (involution of fibroblastic process, and the emergence of foci and cobblestone morphologies).
• MET was accelerated by our invention using enhanced cocktails, enabling feeder-free reprogramming using the 6-factor M3O cocktail without passaging, seeding target cells at a variety of low densities (50K vs. 100K vs. 150K per well).
• the cells are seeded at a density gradient with a total cell number ranging from about 15K to 500K cells per well.
• One aspect of the current invention relates to the fate of these reprogramming cultures, which proved highly sensitive to the seeding density, presumably because the effects of excessive cytotoxicity and of fibroblastic overgrowth are both self -reinforcing over the course of the transfection regime.
• RNA dosing 1200 ng per well
• dozens of hESC-like colonies were obtained from HDF-n and XFF fibroblasts plated at 100K per well, while the corresponding 50K and 150K cultures gave only a few colonies after succumbing to a population crash and to fibroblastic overgrowth, respectively.
• BJ and HDF-a even the most promising (150K) cultures became virtually quiescent shortly after reaching confluence, subsequently yielding only sporadic colonies with delayed kinetics.
• One aspect of the current invention relates to purify the in vitro transcribed mRNAs through size exclusion chromatography to remove aberrant RNA species that may form dsRNA structures, either by themselves or with mRNAs, and provoke cellular immune responses.
• RNA species that may form dsRNA structures, either by themselves or with mRNAs, and provoke cellular immune responses.
• Using such "cleaned-up" mRNAs - mRNA with reduced cellular immunogenicity effectively allowed reprogramming of non-human primate cells grown in gradient densities.
• RNA dosing was scaled down in "24-hour transfection" wells to compensate for an expected increase in cytotoxicity, and two different transfection reagents were tested (RNAiMAX and Stemfect).
• XFF cells were plated at 50K per well and transfected for 9 days.
• the conventional "4-hour transfection" regime gave on the order of a hundred TRA-l-60 + colonies per well with the c-Myc -based cocktail, while the L-Myc cocktail performed comparatively poorly ( Figure 2). Results from the "24-hour transfection" cultures were still more impressive.
• optimization of the factor stoichiometry can also enhance the pace of reprogramming—the mRNA method provide the opportunity of defining cocktails which address early and late phases of ipPSC induction independently.
• the gains obtained from using M30 provide validation for the recent application of novel, engineered repiOgramming factors to iPSC generation.
• engineered reprogramming factors include fusing SOX2, KLF4, CMYC, LMYC, LI 28, NANOG, etc. to transactivation domains from factors other than VP16 OR MYOD, SUCH AS GAL4, GATAl, P53, etc.
• reagents and methodology used to deliver mRNA can also be used to co-transfect siRNA and miRNA, which have already proven their worth in iPSC generation. Nonetheless, the feeder-free protocol disclosed herein represents a substantial advance over current protocols, reducing the time required for reprogramming by as much as a half with an equal or greater reduction in labor and materials costs, taking troublesome steps out of the procedure, and allowing mRNA to be delivered to cells with almost the same ease as growth factors or cytokines— i.e., as a media supplement.
• cells are reprogrammed to modulate the immune response.
• lymphocytes can be reprogrammed into regulatory T cells which can be administered to a patient in need thereof to increase or transfer immune tolerance, especially self-tolerance.
• the induction or administration of Foxp3 positive T cells may be useful in reducing autoimmune responses such graft rejection, and/or reducing, inhibiting or mitigating one or more symptoms of an autoimmune diseases or disorder such as diabetes, multiple sclerosis, asthma, inflammatory bowel disease, thyroiditis, renal disease, rheumatoid arthritis, systemic lupus erythematosus, alopecia greata, anklosing spondylitis,
• autoimmune Addison's disease autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune inner ear disease, autoimmune lymphoproliferative syndrome (ALPS), autoimmune thrombocytopenic purpura (ATP), Behcet's disease, bullous pemphigoid, cardiomyopathy, celiac sprue-dermatitis, chronic fatigue syndrome immune deficiency syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, cicatricial pemphigoid, cold agglutinin disease, Crest syndrome, Crohn's disease, Dego's disease, dermatomyositis, dermatomyositis— juvenile, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia— fibromyositis, Grave's disease, Guillain-Barre, Hashimoto's thyroiditis, idiopathic pulmonary fibrosis, idiopathic thro
• the methods can be used to generate cells which may be useful in the treatment of a variety of diseases and disorders, including, but not limited to, diseases such as Parkinson's, Alzheimer disease, wound healing, and multiple sclerosis.
• the methods are also useful for organ regeneration, and for restoration or supplementation of the immune system.
• cells at different stages of differentiation such as iPS cells, hematopoietic stem cells, multipotent cells or unipotent cells such as precursor cells, for example, epithelial precursor cells, and others can be administered intravenously or by local surgery.
• the methods can be used in combination with other conventional methods, such as a prescription medication regime, surgeiy, hormone therapy, chemotherapy and/or radiotherapy.
• a kit includes RNAs, cells, and a means for transfecting the RNA into the cells.
• the RNAs can be lyophilized or in solution. Kits may optionally include other materials such as cell culture reagents.
• a kit provides re-differentiated, dedifferentiated, or reprogrammed cells prepared according to the disclosed methods, and stored and/or shipped refrigerated or frozen for later use. Cells are typically stored in a solution maintaining viability. Kits containing cells should be stored or shipped using a method consistent with viability such as in a cooler containing dry ice so that cells are maintained below 4° C, and preferably below - 20° C.
• kits optionally include one or more of the following: bioactive agents, media, excipients and one or more of: a syringe, a needle, thread, gauze, a bandage, a disinfectant, an antibiotic, a local anesthetic, an analgesic agent, surgical thread, scissors, a scalpel, a sterile fluid, and a sterile vessel.
• Components of the kit may be packaged individually and can be sterile.
• the kits are generally provided in a container, e.g., a plastic, cardboard, or metal container suitable for commercial sale. Any of the kits can include instructions for use.
• the methods can be used to generate cells which may be useful in the treatment of a variety of diseases and disorders, including, but not limited to,
• neurodegenerative diseases such as Parkinson's, Alzheimer disease, and multiple sclerosis.
• the methods disclosed herein are also useful for organ regeneration, and for restoration or supplementation of the immune system. For example, cells at different stages of
• iPS cells hematopoietic stem cells
• multipotent cells unipotent cells
• precursor cells for example, epithelial precursor cells
• the methods can be used in combination with other conventional methods, such as a prescription medication regime, surgery, hormone therapy, chemotherapy and/or radiotherapy.
• aspects of the disclosure provide culturing systems of stem cells and differentiation methods for producing skin tissue cells for wound treatment, and stem cell therapy for the treatment of arthritis, Lupus, and other autoimmune-related diseases.
• Plasmid constructs for generating linear PCR-product in vitro transcription (F T) templates were constructed using Ligation Independent Cloning (LIC).
• LIC Ligation Independent Cloning
• pTVT parental plasmid
• UTRs 5' and 3' untranslated regions
• ORF open reading frame
• a linearized version of the ⁇ vector bearing 5' overhangs was produced by reannealing of two PCR products amplified from the plasmid using tailed primers.
• ORF PCR products with complementary overhangs were produced by an analogous procedure, pooled with the vector PCR products and
• Cap analog and modified NTPs were purchased from Trilink Biotechnologies.
• a 2.5x NTP mix was prepared (ARCA: ATP :5m- CTP:GTP:Pseudo- UTP at 15: 15:3.75:3.75:3.75 mM) to replace the standard NTPs provided with the
• MEGAscript T7 Kit (Ambion) used to perform ⁇ reactions.
• Each 40 uL IVT reaction comprised 16 uL NTP mix, 4 uL lOx T7 Buffer, 16 uL DNA template and 4 uL T7 enzyme. Reactions were incubated 4-6 hours at 37°C and then treated with 2 uL TURBO DNase for a further 15 minutes at 37°C before being purified on MEGAclear (Ambion) spin columns, the RNA products being eluted in a volume of 100 uL.
• RNA yield was quantitated by Nanodrop (Thermo Scientific), and the preps were consequently adjusted to a standardized working concentration of 100 ng/uL by addition of TE pH 7.0 (Ambion). RNA cocktails were assembled by pooling preps representing the various RFs in the desired stoichiometric ratios.
• the fraction of each RF used took into account the predicted molecular weight of the respective transcript, all RFs being equimolar except for Oct4 and its derivatives, which were included at 3x molar concentration.
• a 10% spike of mRNA encoding a short-lived nuclearized monomeric LanYFP fluorescent protein was added to the cocktails to facilitate monitoring of transfection efficacy during reprogramming trials.
• mRNAs were also produced by using 2-Thio-Uracil at 25% or 10% of total Uracil (see Figure 6).
• Cells targeted for reprogramming included BJ neonatal fibroblasts (ATCC), HDF-f fetal fibroblasts, HDF-n neonatal fibroblasts and HDF-a adult fibroblasts (ScienCell), and XFF xeno-free neonatal fibroblasts (Millipore).
• BJ medium DMEM + 10% FBS
• ScienCell Fibroblast Medium DMEM + 10% FBS
• FibroGRO Xeno-Free Human Fibroblast Expansion Medium (Millipore) for the BJ, HDF and XFF cells respectively.
• Feeder cells used were 3001G irradiated neonatal human foreskin fibroblasts (GlobalStem) and FibroGRO mitomycin C-inactivated xeno-free human neonatal fibroblasts (Millipore). Cell passaging steps pertinent to xeno-free feeder-based and feeder-free reprogramming trials were performed using TrypLE Select (Gibco), an animal product-free cell dissociation reagent.
• Target cells were plated in Pluriton serum-free media (Stemgent) plus antibiotics, Pluriton Supplement and 200 ng/ml B 18R interferon inhibitor (eBioscience). Media was replaced daily during and after reprogramming, with B 18R supplementation being discontinued the day after the final transfection. In experiments in which cells were split onto fresh feeders during Pluriton serum-free media (Stemgent) plus antibiotics, Pluriton Supplement and 200 ng/ml B 18R interferon inhibitor (eBioscience). Media was replaced daily during and after reprogramming, with B 18R supplementation being discontinued the day after the final transfection. In experiments in which cells were split onto fresh feeders during
• RNAiMAX Invitrogen
• RNAiMAX-based transfection cocktails were made up by diluting 100 ng/uL RNA 5x in calcium/magnesium-free DPBS and 5 uL of RNAiMAX per ug of RNA lOx in the same diluent, pooling to produce a 10 ng/uL RNA/vehicle suspension and dispensing to culture media after a 15-minute room temperature incubation.
• RNA and Stemfect (4 uL per ug of RNA) were mixed in Stemfect buffer to give an RNA concentration of 10 ng/uL. The mixture was incubated for 15 minutes, then delivered to culture media or refrigerated for later use.
• reprogramming of human fibroblasts were also performed in media other than pluriton, e.g. Allele's Reprogramming media (see Figure 7).
• Allele's Reprogramming media see Figure 7
• B18R was not used at all, in other experiments, it was used only in some of the transfections.
• a novel method for highly efficient reprogramming of non- stem cells into pluripotent stem cells by contacting target cells with combinations of engineered reprogramming factors and non-engineered reprogramming factors in such a way that iPSCs can be produced in about 9 days, sometimes as short of 6, or even 5 days. These iPS cells can be produced as feeder-free, xeno-free, and footprint-free iPSCs.
• the novel technology also differs from all previously known technologies in that the iPSCs so created are "clean" in that they have not been in contact with any virus or vector.

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