High-Efficiency RNA Interference in Human Embryonic Stem Cells
http://www.100md.com
《干细胞学杂志》
a Harvard Stem Cell Institute and Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology and Division of Hematology/Oncology, Children’s Hospital, Boston, Massachusetts, USA;
b Washington University School of Medicine, St. Louis, Missouri, USA;
c Technion, Rambam Medical Center, Haifa, Israel
Key Words. Human embryonic stem cells ? RNA interference ? Transgene expression ? Retroviral and lentiviral vectors ? Oct4 ? Nanog ? Self-renewal
Correspondence: George Q. Daley, M.D., Ph.D., Harvard Stem Cell Institute and Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology and Division of Hematology/Oncology, Children’s Hospital, Boston, Massachusetts 02115, USA. Telephone: 617-919-2013; Fax: 617-730-0222; e-mail: george.daley@childrens.harvard.edu
ABSTRACT
Human embryonic stem (hES) cells are able to differentiate along all embryonic and adult cell lineages, making them valuable tools in the study of early developmental processes and a promising source of cells for gene and tissue replacement therapies. Vectors for efficient transgene expression in hES cells and their progeny are necessary to evaluate hES cell self-renewal and directed differentiation into specified lineages. Lentiviral vectors are emerging as an efficient tool for transgenesis because they escape much of the transgene silencing that is observed with oncoretrovirus-based vectors in hematopoietic and ES cells .
Recently, the use of lentiviral vectors has been described for transgene expression in hES cells . In this study, we extend the use of lentiviral gene transfer to achieve high-efficiency loss of function in hES cells. Classical strategies to knockout genes in mouse ES cells rely on gene targeting by homologous recombination. This technique was successfully applied to hES cells . Stable expression of small interfering RNAs (siRNAs) provides a faster and more convenient method to knockdown gene expression, but high-efficiency RNA interference is required to approximate gene knockout. siRNA duplexes have been successfully used to suppress multiple genes in mammalian cells , but to date RNA Interference (RNAi) has not been exploited with high efficiency in hES cells. Retroviral and lentiviral vectors have been described that stably express stem-loop cassettes under the control of RNA polymerase III U6 promoters that give rise to inhibitory RNAs after intracellular processing. Using these vectors, we have produced concentrated viral stocks that enable highly efficient transduction of siRNA in hES cells to effect gene silencing. We demonstrate high-efficiency silencing of a green fluorescent protein (GFP) transgene and the stem cell–specific transcription factors Oct4/POU5F1 and Nanog in hES cells.
MATERIAL AND METHODS
We first modified a hES cell line to stably express an enhanced GFP (eGFP) transgene. We transfected 293T cells with a lentiviral vector expressing eGFP under the control of the human phosphoglycerate kinase promoter and a plasmid encoding the VSV-G protein to produce a pseudotyped viral supernatant. We then used this virus at a MOI of 50 to infect the human H9 hES cell line to produce a population that expressed GFP in 50% of cells (49.8% ± 4.4% ; n = 5). We next transduced the H9-GFP cells with increasing MOIs of the VSV-G pseudotyped vectors Retro-hair (RH) and Lentihair (LH) encoding stem-loop structures targeting the GFP gene (Fig. 1A). Infection of H9-GFP with the vectors RH-GFPi and LH-GFPi reduces GFP expression up to fivefold after 2 days and up to 140-fold after 7 days (measured by fluorescence-activated cell sorter histogram statistics) (Figs. 1B, 1C). Infected colonies maintained viability, and the reduction in GFP expression could be appreciated by fluorescence and phase-contrast microscopy, respectively (Fig. 1D). These data demonstrate that highly efficient gene silencing can be achieved when retroviral and lentiviral vectors are used to deliver interfering RNAs in hES cells.
Figure 1. Retroviral delivery of RNA interference mediates gene silencing in human embryonic stem cells. Small interfering RNA molecules against the GFP transcript were introduced as stem-loop structures by retroviral and lentiviral vectors into a human embryonic stem cell line (WA09/H9) in which the GFP gene had been stably integrated. (A): Retroviral vector (RH)-GFPi and lentiviral vector (LH)-GFPi used to deliver the interfering RNA molecules to silence GFP expression. (B): Fluorescence-activated cell sorter histograms of H9-GFP cells 48 hours after transduction with increasing doses of the retroviruses RH-GFPi and LH-GFPi. The upper histogram represents the H9-GFP–expressing cell line before infection with the siRNA retroviruses. (C): Histogram statistics reveal reduction in GFP expression up to fivefold after 2 days and up to 140-fold after 7 days. Data are means ± standard error for two experiments. (D): Phase contrast (upper) and fluorescence (lower) microscopy of individual H9-GFP colonies before (left) and after (right) transduction (day 4) with the retrovirus LH-GFPi. Abbreviations: GFP, green fluorescent protein; LH, lentihair; RH, retrohair.
To demonstrate a biological effect of gene knockdown in hES cells, we targeted two genes implicated in maintenance of pluripotency in mouse ES cells: Oct4 , a developmentally regulated gene belonging to the POU class of helix-turn-helix transcription factors, and Nanog , a homeodomain transcription factor. We developed lentiviral vectors with two oligonucleotides encoding stem-loop structures targeting the human Oct4/POU5F1 gene and one oligonucleotide targeting the human Nanog gene (Fig. 2A). We then transduced H9 hES cells with VSV-G pseudotyped and concentrated viruses by a single round of infection for 24 hours. The control Lentilox vector expressing eGFP from the cytomegalovirus promoter gave robust transduction efficiencies of 85% at a MOI of 50 (84.7% ± 3.1% ; n = 10) GFP-positive H9 cells. Infected cell cultures were maintained in MEF-conditioned media , conditions that would otherwise maintain the self-renewal of hES cells. After RNAi application, Western blot analysis showed complete extinction of the Oct4 protein (Fig. 2B). We interrogated the levels of expression of the TRA-1-60 antigen associated with undifferentiated ES cells at different time points after RNAi application. TRA-1-60 levels fell, achieving a nadir by day 7, when TRA-1-60 was markedly reduced from 80% in the control population to 28% in the population infected with the Oct4-RNAi knockdown vectors. TRA-1-60 reduction was even greater (to 3%) in cells infected with the Nanog-RNAi knockdown vector (Fig. 2C). The differentiated cell populations transduced by the RNAi vector (GFP positive and TRA-1-60 negative) represent most cells at this time point. They are no longer refractile and assume a flattened morphology, typical of differentiating cultures of hES cells. After 10 days, however, nontransduced, undifferentiated hES cells overgrow the slower growing differentiated cells, suggesting that a selection strategy would be required to obtain pure, stable populations of differentiated cells after RNAi treatment. TRA-1-60 antigen expression remained stable and high when H9 hES cells were infected with the GFP knockdown vector LH-GFPi, demonstrating that siRNA expression per se does not promote hES cell differentiation.
Figure 2. Small interfering RNA molecules against the human Oct4 and Nanog transcripts were introduced as stem-loop structures by lentiviral vectors in the human embryonic stem cell line WA09/H9. (A): Lentiviral vectors LL-OCT4i and LL-NANOGi used to deliver the interfering RNAs targeting Oct4 and Nanog. (B): Western blot analysis of the Oct4 protein in cells after RNAi application at a MOI of 10, 50, and 100 at day 6. The blot was stripped and reprobed with actin as a loading control. (C): FACS histograms of TRA1-60–stained H9 at day 7 after transduction with the Lentilox37 control vector (right), the two lentiviral Oct4 RNAi vectors (middle), and the lentiviral Nanog RNAi vector (left) at a MOI of 50. Cells were stained with the primary antibody TRA-1-60 and detected with PE secondary antibody in the FL2 chanel (y-axis). The GFP positivity in the FL1 chanel (x-axis) marks the vector-transduced cell populations. The percentages indicate the cell populations in each of the four quadrants. (D): Quantitative real-time reverse transcription polymerase chain reaction analysis of human Oct4 and Nanog at days 4 and 7 (upper panel) and the trophectodermal lineage markers chorionic gonadotropin alpha and beta, the endodermal marker albumin, the mesodermal marker cardiac actin, and the ectodermal markers nestin and neuro-filament heavy chain at day 7 after transduction (lower panel). Data are means ± standard error for three experiments, each carried out in triplicate (upper panel), and a single representative experiment carried out in triplicate (lower panel). Abbreviations: MOI, multiplicity of infection; PE, phycoerythrin.
As assessed by QRT-PCR, application of the Oct4 knockdown vectors reduced Oct4 expression to 31% on day 4 and 15% on day 7, whereas the Nanog knockdown reduced Nanog expression to 14% on day 4 and 13% on day 7 (Fig. 2D). We also observed that Oct4-RNAi reduced Nanog expression and Nanog-RNAi reduced Oct4 expression. This reciprocal effect occurred already at day 4, when the culture shift into differentiation was just at its beginning, suggesting coordinate gene regulation of Oct4 and Nanog in hES cells. Decreased Oct4 expression has been shown to redirect mouse ES cells into the trophectodermal lineage , whereas Nanog expression seems to prevent differentiation into primitive endoderm . Although undifferentiated H9 cells have been reported to express low levels of some trophoblastic markers , QRT-PCR analysis of Oct4-RNAi–treated H9 showed twofold to fourfold upregulation of the trophoblastic markers human chorionic gonadotropin alpha (hCG) and beta (Fig. 2D). In the case of the Nanog knockdown, the endodermal marker albumin was upregulated 13-fold, confirming a role for Nanog in antagonizing endodermal differentiation. Interestingly, the most striking effect was 47-fold upregulation of hCG, suggesting a role for Nanog in modulating trophectodermal differentiation as well. The expression of the mesodermal marker cardiac actin was modestly decreased, whereas we did not detect significant changes in the ectodermal markers nestin and neurofilament heavy chain for either of the knockdowns.
Our data indicate that Oct4 and Nanog are central to hES cell maintenance and play functionally conserved roles in hES and mouse ES cells . The profound consequence of the Nanog knockdown on loss of self-renewal supports a central role for Nanog in the transcription factor hierarchy that maintains the pluripotency of hES cells. Furthermore, our data demonstrate that downregulation of Oct4 and Nanog promotes hES cell differentiation under conditions that would otherwise foster self-renewal.
We have demonstrated that RNA interference is effective at inducing gene silencing in hES cells, both for the GFP transgene as well as the endogenous genes Oct4 and Nanog. Recent reports used transfection of chemically synthesized siRNAs against a GFP transgene and Oct4 in hES cells. Comparison of these data with our results concerning GFP and Oct4 silencing, TRA-1-60 downregulation, as well as upregulation of trophectodermal and endodermal markers highlights the greater efficiency of viral delivery of siRNAs, whose effects at higher MOIs approximate gene knockout. A report targeting mouse ES cell pluripotency genes of the Src kinase families describes difficulties isolating stable siRNA-expressing clones . Given the high titers that can be generated and corresponding high infection rates in cell populations, lentiviral vector–delivered RNAi allows evaluation of silencing of genes involved in self-renewal, differentiation, or apoptosis without having to select stable ES cell clones. When combined with large-scale libraries of interfering RNAs or the recently available lentiviral conditional RNA interference systems , our rapid and convenient approach should be applicable to genome-wide screening experiments and conditional loss-of-function analysis in hES cells and their progeny.
ACKNOWLEDGMENTS
Lois C, Hong EJ, Pease S et al. Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors. Science 2002;295:868–872.
Pfeifer A, Ikawa M, Dayn Y et al. Transgenesis by lentiviral vectors: lack of gene silencing in mammalian embryonic stem cells and preimplantation embryos. Proc Natl Acad Sci U S A 2002;99:2140–2145.
Cherry SR, Biniszkiewicz D, van Parijs L et al. Retroviral expression in embryonic stem cells and hematopoietic stem cells. Mol Cell Biol 2000;20:7419–7426.
Ma Y, Ramezani A, Lewis R et al. High-level sustained transgene expression in human embryonic stem cells using lentiviral vectors. STEM CELLS 2003;21:111–117.
Gropp M, Itsykson P, Singer O et al. Stable genetic modification of human embryonic stem cells by lentiviral vectors. Mol Ther 2003;7:281–287.
Zwaka TP, Thomson JA. Homologous recombination in human embryonic stem cells. Nat Biotechnol 2003;21:319–321.
Elbashir SM, Harborth J, Lendeckel W et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001;411:494–498.
McManus MT, Sharp PA. Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 2002;3:737–747.
Stewart SA, Dykxhoorn DM, Palliser D et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 2003;9:493–501.
Rubinson DA, Dillon CP, Kwiatkowski AV et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 2003;33:401–406.
Thomson JA, Itskovitz-Eldor J, Shapiro SS et al. Embryonic stem cell lines derived from human blastocysts. Science 1998;282:1145–1147.
Daheron L, Opitz SL, Zaehres H et al. LIF/STAT3 Signaling fails to maintain self-renewal of human embryonic stem cells. STEM CELLS 2004;22:770–778.
Xu C, Inokuma MS, Denham J et al. Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol 2001;19:971–974.
Yuan B, Latek R, Hossbach M et al. siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 2004;32:W130–W134.
Burns JC, Friedmann T, Driever W et al. Vesicular stomatitis virus G glycoprotein pseudotyped retroviral vectors: concentration to very high titer and efficient gene transfer into mammalian and nonmammalian cells. Proc Natl Acad Sci U S A 1993;90:8033–8037.
Draper JS, Pigott C, Thomson JA et al. Surface antigens of human embryonic stem cells: changes upon differentiation in culture. J Anat 2002;200:249–258.
Zufferey R, Dull T, Mandel RJ et al. Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J Virol 1998;72:9873–9880.
Pesce M, Scholer HR. Oct-4: gatekeeper in the beginnings of mammalian development. STEM CELLS 2001;19:271–278.
Chambers I, Colby D, Robertson M et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 2003;113:643–655.
Mitsui K, Tokuzawa Y, Itoh H et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 2003;113:631–642.
Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 2000;24:372–376.
Xu RH, Chen X, Li DS et al. BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nat Biotechnol 2002;20:1261–1264.
Vallier L, Rugg-Gunn PJ, Bouhon IA et al. Enhancing and diminishing gene function in human embryonic stem cells. STEM CELLS 2004;22:2–11.
Hay DC, Sutherland L, Clark J et al. Oct-4 knockdown induces similar patterns of endoderm and trophoblast differentiation markers in human and mouse embryonic stem cells. STEM CELLS 2004;22:225–235.
Matin MM, Walsh JR, Gokhale PJ et al. Specific knockdown of Oct4 and ?2-microglobulin expression by RNA interference in human embryonic stem cells and embryonic carcinoma cells. STEM CELLS 2004;22:659–668.
Anneren C, Cowan CA, Melton DA. The Src family of tyrosine kinases is important for embryonic stem cell self-renewal. J Biol Chem 2004;279:31590–31598.
Berns K, Hijmans EM, Mullenders J et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004;428:431–437.
Paddison PJ, Silva JM, Conklin DS et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004;428:427–431.
Wiznerowicz M, Trono D. Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference. J Virol 2003;77:8957–8961.
Ventura A, Meissner A, Dillon CP et al. Crelox-regulated conditional RNA interference from transgenes. Proc Natl Acad Sci U S A 2004;101:10380–10385.(Holm Zaehresa, M. William)
b Washington University School of Medicine, St. Louis, Missouri, USA;
c Technion, Rambam Medical Center, Haifa, Israel
Key Words. Human embryonic stem cells ? RNA interference ? Transgene expression ? Retroviral and lentiviral vectors ? Oct4 ? Nanog ? Self-renewal
Correspondence: George Q. Daley, M.D., Ph.D., Harvard Stem Cell Institute and Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology and Division of Hematology/Oncology, Children’s Hospital, Boston, Massachusetts 02115, USA. Telephone: 617-919-2013; Fax: 617-730-0222; e-mail: george.daley@childrens.harvard.edu
ABSTRACT
Human embryonic stem (hES) cells are able to differentiate along all embryonic and adult cell lineages, making them valuable tools in the study of early developmental processes and a promising source of cells for gene and tissue replacement therapies. Vectors for efficient transgene expression in hES cells and their progeny are necessary to evaluate hES cell self-renewal and directed differentiation into specified lineages. Lentiviral vectors are emerging as an efficient tool for transgenesis because they escape much of the transgene silencing that is observed with oncoretrovirus-based vectors in hematopoietic and ES cells .
Recently, the use of lentiviral vectors has been described for transgene expression in hES cells . In this study, we extend the use of lentiviral gene transfer to achieve high-efficiency loss of function in hES cells. Classical strategies to knockout genes in mouse ES cells rely on gene targeting by homologous recombination. This technique was successfully applied to hES cells . Stable expression of small interfering RNAs (siRNAs) provides a faster and more convenient method to knockdown gene expression, but high-efficiency RNA interference is required to approximate gene knockout. siRNA duplexes have been successfully used to suppress multiple genes in mammalian cells , but to date RNA Interference (RNAi) has not been exploited with high efficiency in hES cells. Retroviral and lentiviral vectors have been described that stably express stem-loop cassettes under the control of RNA polymerase III U6 promoters that give rise to inhibitory RNAs after intracellular processing. Using these vectors, we have produced concentrated viral stocks that enable highly efficient transduction of siRNA in hES cells to effect gene silencing. We demonstrate high-efficiency silencing of a green fluorescent protein (GFP) transgene and the stem cell–specific transcription factors Oct4/POU5F1 and Nanog in hES cells.
MATERIAL AND METHODS
We first modified a hES cell line to stably express an enhanced GFP (eGFP) transgene. We transfected 293T cells with a lentiviral vector expressing eGFP under the control of the human phosphoglycerate kinase promoter and a plasmid encoding the VSV-G protein to produce a pseudotyped viral supernatant. We then used this virus at a MOI of 50 to infect the human H9 hES cell line to produce a population that expressed GFP in 50% of cells (49.8% ± 4.4% ; n = 5). We next transduced the H9-GFP cells with increasing MOIs of the VSV-G pseudotyped vectors Retro-hair (RH) and Lentihair (LH) encoding stem-loop structures targeting the GFP gene (Fig. 1A). Infection of H9-GFP with the vectors RH-GFPi and LH-GFPi reduces GFP expression up to fivefold after 2 days and up to 140-fold after 7 days (measured by fluorescence-activated cell sorter histogram statistics) (Figs. 1B, 1C). Infected colonies maintained viability, and the reduction in GFP expression could be appreciated by fluorescence and phase-contrast microscopy, respectively (Fig. 1D). These data demonstrate that highly efficient gene silencing can be achieved when retroviral and lentiviral vectors are used to deliver interfering RNAs in hES cells.
Figure 1. Retroviral delivery of RNA interference mediates gene silencing in human embryonic stem cells. Small interfering RNA molecules against the GFP transcript were introduced as stem-loop structures by retroviral and lentiviral vectors into a human embryonic stem cell line (WA09/H9) in which the GFP gene had been stably integrated. (A): Retroviral vector (RH)-GFPi and lentiviral vector (LH)-GFPi used to deliver the interfering RNA molecules to silence GFP expression. (B): Fluorescence-activated cell sorter histograms of H9-GFP cells 48 hours after transduction with increasing doses of the retroviruses RH-GFPi and LH-GFPi. The upper histogram represents the H9-GFP–expressing cell line before infection with the siRNA retroviruses. (C): Histogram statistics reveal reduction in GFP expression up to fivefold after 2 days and up to 140-fold after 7 days. Data are means ± standard error for two experiments. (D): Phase contrast (upper) and fluorescence (lower) microscopy of individual H9-GFP colonies before (left) and after (right) transduction (day 4) with the retrovirus LH-GFPi. Abbreviations: GFP, green fluorescent protein; LH, lentihair; RH, retrohair.
To demonstrate a biological effect of gene knockdown in hES cells, we targeted two genes implicated in maintenance of pluripotency in mouse ES cells: Oct4 , a developmentally regulated gene belonging to the POU class of helix-turn-helix transcription factors, and Nanog , a homeodomain transcription factor. We developed lentiviral vectors with two oligonucleotides encoding stem-loop structures targeting the human Oct4/POU5F1 gene and one oligonucleotide targeting the human Nanog gene (Fig. 2A). We then transduced H9 hES cells with VSV-G pseudotyped and concentrated viruses by a single round of infection for 24 hours. The control Lentilox vector expressing eGFP from the cytomegalovirus promoter gave robust transduction efficiencies of 85% at a MOI of 50 (84.7% ± 3.1% ; n = 10) GFP-positive H9 cells. Infected cell cultures were maintained in MEF-conditioned media , conditions that would otherwise maintain the self-renewal of hES cells. After RNAi application, Western blot analysis showed complete extinction of the Oct4 protein (Fig. 2B). We interrogated the levels of expression of the TRA-1-60 antigen associated with undifferentiated ES cells at different time points after RNAi application. TRA-1-60 levels fell, achieving a nadir by day 7, when TRA-1-60 was markedly reduced from 80% in the control population to 28% in the population infected with the Oct4-RNAi knockdown vectors. TRA-1-60 reduction was even greater (to 3%) in cells infected with the Nanog-RNAi knockdown vector (Fig. 2C). The differentiated cell populations transduced by the RNAi vector (GFP positive and TRA-1-60 negative) represent most cells at this time point. They are no longer refractile and assume a flattened morphology, typical of differentiating cultures of hES cells. After 10 days, however, nontransduced, undifferentiated hES cells overgrow the slower growing differentiated cells, suggesting that a selection strategy would be required to obtain pure, stable populations of differentiated cells after RNAi treatment. TRA-1-60 antigen expression remained stable and high when H9 hES cells were infected with the GFP knockdown vector LH-GFPi, demonstrating that siRNA expression per se does not promote hES cell differentiation.
Figure 2. Small interfering RNA molecules against the human Oct4 and Nanog transcripts were introduced as stem-loop structures by lentiviral vectors in the human embryonic stem cell line WA09/H9. (A): Lentiviral vectors LL-OCT4i and LL-NANOGi used to deliver the interfering RNAs targeting Oct4 and Nanog. (B): Western blot analysis of the Oct4 protein in cells after RNAi application at a MOI of 10, 50, and 100 at day 6. The blot was stripped and reprobed with actin as a loading control. (C): FACS histograms of TRA1-60–stained H9 at day 7 after transduction with the Lentilox37 control vector (right), the two lentiviral Oct4 RNAi vectors (middle), and the lentiviral Nanog RNAi vector (left) at a MOI of 50. Cells were stained with the primary antibody TRA-1-60 and detected with PE secondary antibody in the FL2 chanel (y-axis). The GFP positivity in the FL1 chanel (x-axis) marks the vector-transduced cell populations. The percentages indicate the cell populations in each of the four quadrants. (D): Quantitative real-time reverse transcription polymerase chain reaction analysis of human Oct4 and Nanog at days 4 and 7 (upper panel) and the trophectodermal lineage markers chorionic gonadotropin alpha and beta, the endodermal marker albumin, the mesodermal marker cardiac actin, and the ectodermal markers nestin and neuro-filament heavy chain at day 7 after transduction (lower panel). Data are means ± standard error for three experiments, each carried out in triplicate (upper panel), and a single representative experiment carried out in triplicate (lower panel). Abbreviations: MOI, multiplicity of infection; PE, phycoerythrin.
As assessed by QRT-PCR, application of the Oct4 knockdown vectors reduced Oct4 expression to 31% on day 4 and 15% on day 7, whereas the Nanog knockdown reduced Nanog expression to 14% on day 4 and 13% on day 7 (Fig. 2D). We also observed that Oct4-RNAi reduced Nanog expression and Nanog-RNAi reduced Oct4 expression. This reciprocal effect occurred already at day 4, when the culture shift into differentiation was just at its beginning, suggesting coordinate gene regulation of Oct4 and Nanog in hES cells. Decreased Oct4 expression has been shown to redirect mouse ES cells into the trophectodermal lineage , whereas Nanog expression seems to prevent differentiation into primitive endoderm . Although undifferentiated H9 cells have been reported to express low levels of some trophoblastic markers , QRT-PCR analysis of Oct4-RNAi–treated H9 showed twofold to fourfold upregulation of the trophoblastic markers human chorionic gonadotropin alpha (hCG) and beta (Fig. 2D). In the case of the Nanog knockdown, the endodermal marker albumin was upregulated 13-fold, confirming a role for Nanog in antagonizing endodermal differentiation. Interestingly, the most striking effect was 47-fold upregulation of hCG, suggesting a role for Nanog in modulating trophectodermal differentiation as well. The expression of the mesodermal marker cardiac actin was modestly decreased, whereas we did not detect significant changes in the ectodermal markers nestin and neurofilament heavy chain for either of the knockdowns.
Our data indicate that Oct4 and Nanog are central to hES cell maintenance and play functionally conserved roles in hES and mouse ES cells . The profound consequence of the Nanog knockdown on loss of self-renewal supports a central role for Nanog in the transcription factor hierarchy that maintains the pluripotency of hES cells. Furthermore, our data demonstrate that downregulation of Oct4 and Nanog promotes hES cell differentiation under conditions that would otherwise foster self-renewal.
We have demonstrated that RNA interference is effective at inducing gene silencing in hES cells, both for the GFP transgene as well as the endogenous genes Oct4 and Nanog. Recent reports used transfection of chemically synthesized siRNAs against a GFP transgene and Oct4 in hES cells. Comparison of these data with our results concerning GFP and Oct4 silencing, TRA-1-60 downregulation, as well as upregulation of trophectodermal and endodermal markers highlights the greater efficiency of viral delivery of siRNAs, whose effects at higher MOIs approximate gene knockout. A report targeting mouse ES cell pluripotency genes of the Src kinase families describes difficulties isolating stable siRNA-expressing clones . Given the high titers that can be generated and corresponding high infection rates in cell populations, lentiviral vector–delivered RNAi allows evaluation of silencing of genes involved in self-renewal, differentiation, or apoptosis without having to select stable ES cell clones. When combined with large-scale libraries of interfering RNAs or the recently available lentiviral conditional RNA interference systems , our rapid and convenient approach should be applicable to genome-wide screening experiments and conditional loss-of-function analysis in hES cells and their progeny.
ACKNOWLEDGMENTS
Lois C, Hong EJ, Pease S et al. Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors. Science 2002;295:868–872.
Pfeifer A, Ikawa M, Dayn Y et al. Transgenesis by lentiviral vectors: lack of gene silencing in mammalian embryonic stem cells and preimplantation embryos. Proc Natl Acad Sci U S A 2002;99:2140–2145.
Cherry SR, Biniszkiewicz D, van Parijs L et al. Retroviral expression in embryonic stem cells and hematopoietic stem cells. Mol Cell Biol 2000;20:7419–7426.
Ma Y, Ramezani A, Lewis R et al. High-level sustained transgene expression in human embryonic stem cells using lentiviral vectors. STEM CELLS 2003;21:111–117.
Gropp M, Itsykson P, Singer O et al. Stable genetic modification of human embryonic stem cells by lentiviral vectors. Mol Ther 2003;7:281–287.
Zwaka TP, Thomson JA. Homologous recombination in human embryonic stem cells. Nat Biotechnol 2003;21:319–321.
Elbashir SM, Harborth J, Lendeckel W et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001;411:494–498.
McManus MT, Sharp PA. Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 2002;3:737–747.
Stewart SA, Dykxhoorn DM, Palliser D et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 2003;9:493–501.
Rubinson DA, Dillon CP, Kwiatkowski AV et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 2003;33:401–406.
Thomson JA, Itskovitz-Eldor J, Shapiro SS et al. Embryonic stem cell lines derived from human blastocysts. Science 1998;282:1145–1147.
Daheron L, Opitz SL, Zaehres H et al. LIF/STAT3 Signaling fails to maintain self-renewal of human embryonic stem cells. STEM CELLS 2004;22:770–778.
Xu C, Inokuma MS, Denham J et al. Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol 2001;19:971–974.
Yuan B, Latek R, Hossbach M et al. siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 2004;32:W130–W134.
Burns JC, Friedmann T, Driever W et al. Vesicular stomatitis virus G glycoprotein pseudotyped retroviral vectors: concentration to very high titer and efficient gene transfer into mammalian and nonmammalian cells. Proc Natl Acad Sci U S A 1993;90:8033–8037.
Draper JS, Pigott C, Thomson JA et al. Surface antigens of human embryonic stem cells: changes upon differentiation in culture. J Anat 2002;200:249–258.
Zufferey R, Dull T, Mandel RJ et al. Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J Virol 1998;72:9873–9880.
Pesce M, Scholer HR. Oct-4: gatekeeper in the beginnings of mammalian development. STEM CELLS 2001;19:271–278.
Chambers I, Colby D, Robertson M et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 2003;113:643–655.
Mitsui K, Tokuzawa Y, Itoh H et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 2003;113:631–642.
Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 2000;24:372–376.
Xu RH, Chen X, Li DS et al. BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nat Biotechnol 2002;20:1261–1264.
Vallier L, Rugg-Gunn PJ, Bouhon IA et al. Enhancing and diminishing gene function in human embryonic stem cells. STEM CELLS 2004;22:2–11.
Hay DC, Sutherland L, Clark J et al. Oct-4 knockdown induces similar patterns of endoderm and trophoblast differentiation markers in human and mouse embryonic stem cells. STEM CELLS 2004;22:225–235.
Matin MM, Walsh JR, Gokhale PJ et al. Specific knockdown of Oct4 and ?2-microglobulin expression by RNA interference in human embryonic stem cells and embryonic carcinoma cells. STEM CELLS 2004;22:659–668.
Anneren C, Cowan CA, Melton DA. The Src family of tyrosine kinases is important for embryonic stem cell self-renewal. J Biol Chem 2004;279:31590–31598.
Berns K, Hijmans EM, Mullenders J et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004;428:431–437.
Paddison PJ, Silva JM, Conklin DS et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004;428:427–431.
Wiznerowicz M, Trono D. Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference. J Virol 2003;77:8957–8961.
Ventura A, Meissner A, Dillon CP et al. Crelox-regulated conditional RNA interference from transgenes. Proc Natl Acad Sci U S A 2004;101:10380–10385.(Holm Zaehresa, M. William)