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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number ι (43) International Publication Date ¾ ί t 2 6 April 2012 (26.04.2012) WO 2012/054896 Al (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, C12N 5/00 (2006.01) C12N 15/00 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, C12N 5/02 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (21) International Application Number: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, PCT/US201 1/057387 ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (22) International Filing Date: NO, NZ, OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, 2 1 October 201 1 (21 .10.201 1) RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, (25) Filing Language: English ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 61/406,064 22 October 2010 (22.10.2010) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, 61/415,244 18 November 2010 (18.1 1.2010) US UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, (71) Applicant (for all designated States except US): BIO- DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, TIME INC. [US/US]; 1301 Harbor Bay Parkway, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, Alameda, California 94502 (US). SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, ML, MR, NE, SN, TD, TG). (72) Inventors; and (75) Inventors/Applicants (for US only): WEST, Michael D. Published: [US/US]; 308 Ashton Lane, Mill Valley, California — with international search report (Art. 21(3)) 9494 1 (US). CHAPMAN, Karen B. [US/US]; 308 A sh ton Lane, Mill Valley, California 94941 (US). — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of (74) Agent: SCHERER, David C ; Bozicevic, Field & Fran amendments (Rule 48.2(h)) cis LLP, 1900 University Avenue, Suite 200, East Palo Alto, California 94303 (US). — with sequence listing part of description (Rule 5.2(a)) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, 0 0 © © (54) Title: METHODS OF MODIFYING TRANSCRIPTIONAL REGULATORY NETWORKS IN STEM CELLS (57) Abstract: A method of generating an isolated progenitor cell line is disclosed which involves modulating the activity of a ¾ transcriptional regulator in a pluripotent stem cell and inducing the differentiation of said pluripotent stem cell in vitro to generate a progenitor cell line. METHODS OF MODIFYING TRANSCRIPTIONAL REGULATORY NETWORKS IN STEM CELLS INTRODUCTION The comprehensive differentiation potential of human pluripotent stem cells such as human embryonic stem (hES) and human induced pluripotent stem (hiPS) cells opens new opportunities in research and cell-based therapy. Their potential to cascade through all of the somatic cell lineages and to display all of the transcriptional pathways of development has generated interest in the use of these cells to map the precise structure of the human transcriptional regulatory network and to generate cell-based therapies for a potential wide array of disorders. However, many in vitro differentiation technologies yield only partially purified cell formulations that may pose the risk of ectopic tissue formation at engraftment sites. Embryoid bodies, or other similar differentiation modalities in vitro contain dozens or hundreds of discrete cell types in a mixture. The clonal isolation and propagation of progenitors greatly facilitates the generation of highly purified and identified formulations for research and therapeutic purposes (see, e.g., West et al, 2008. Regen. Med. 3(3): 287-308; U.S. Patent applications 11/604,047, filed on November 21, 2006 (US Patent Pub. No. 2008/0070303) and 12/504,630, filed on July 16, 2009 (US Patent Pub. No. 2010/0184033), all of which are incorporated herein by reference). Nevertheless, other cell types have yet to be isolated and propagated from normal pluripotent and multipotent cells. Thus, methods of isolating such novel cell types, as well as methods for introducing perturbations into the transcriptional regulatory network in stem cells in order to construct a computer model of the entire human transcriptional regulatory network, would greatly benefit basic research as well as manufacturing technology for cell-based therapies. SUMMARY We have demonstrated that the long initial telomere length of hES cells, together with the robust proliferative capacity of primitive hES-derived progenitor cell types facilitates the industrial expansion and characterization of >140 diverse and scalable clonal lineages with diverse site and temporal-specific homeobox gene expression (West et al, 2008. Regen. Med. 3(3): 287-308; see also U.S. Patent application 11/604,047, filed on November 2 1, 2006 (US Patent Pub. No. 2008/0070303); U.S. Patent application 12/504,630, filed on July 16, 2009 (US Patent Pub. No. 2010/0184033); PCT Patent application serial no. PCT/US201 1/037969, filed on May 25, 2011 titled "Improved Methods of Screening Embryonic Progenitor Cell Lines"; and U.S. Provisional application 61/496,436, filed on June 13, 2011 titled "Methods and Compositions for Producing Endothelial Progenitor Cells From Pluripotent Stem Cells", each of which is incorporated herein by reference). We describe a technology to generate such novel and scalable cell lines through the exogenous or endogenous up or down-regulation of the activity of transcriptional regulators. Such exogenously or endogenously-introduced modifications to the activity of transcriptional regulators may include transcription factors constitutively expressed in pluripotent stem cells such as hES cells or somatic cells reprogrammed to pluripotency such as hiPS cells. Such transcriptional regulators can be introduced in a manner that allows the precise regulation of the level and timing of their expression including but not limited to the use of an inducible promoter driving the expression or inhibition of expression of a number of transcription factors. The exogenously-administered transcriptional regulators with precise control of level and timing of expression are introduced in pluripotent stem cells which also have inducible levels of expression of a gene capable of forcing cell proliferation (cell cycle driver). Also described herein are computer algorithms useful in assembling a computer model of the transcriptional regulatory network of human and other animal species. BRIEF DESCRIPTION OF THE DRAWINGS Figure 1: Constitutive expression of the transcription factor OCT4 in clonal iPS-derived progenitorprogenitor cell lines compared to normal hES-derived diverse clonal progenitorprogenitors and normal hES cells. Figure 2 : Graph of microarray data for LHX3 isoform 1 and RESP18 transcript levels in diverse clonal progenitorprogenitors, cultured somatic cell types, hES cells, and hiPS cells as well as clonal progenitors made from hiPS cells constitutively expressing the transcriptional regulator OCT4. Figure 3: Microarray gene expression analysis of the expression of IL19 (Accession number NM_013371.2) in diverse normal cultured cell types, diverse normal clonal progenitor cell lines derived from hES cells, hES and iPS cells, and select cell lines of the present invention including 14SM008X, 14PEND11X, and 14PEND20X. Figure 4 : Microarray gene expression analysis of the expression of Gastrin-releasing peptide (GRP) (Accession number NM_001012513.1) in diverse normal cultured cell types, diverse normal clonal progenitor cell lines derived from hES cells, hES and iPS cells, and select cell lines of the present invention including 14SKEL14Z, 14SKEL15Z, 14SKEL20Z, 14SKEL24Z, and 14PEND20X. Figure 5 : Microarray gene expression analysis of the expression of paraoxonase 3 (PON3) (Accession number NM_000940.1) in diverse normal cultured cell types, diverse normal clonal progenitor cell lines derived from hES cells, hES and iPS cells, and the select cell lines of the present invention 14PEND2X. DETAILED DESCRIPTION OF THE INVENTION Abbreviations AFP - Alpha fetoprotein BMP - Bone Morphogenic Protein BRL Buffalo rat liver BSA Bovine serum albumin CD Cluster Designation cGMP Current Good Manufacturing Processes CNS Central Nervous System DMEM Dulbecco's modified Eagle's medium DMSO Dimethyl sulphoxide DPBS Dulbecco's Phosphate Buffered Saline EBs Embryoid bodies EC Embryonal carcinoma EC Cells Embryonal carcinoma cells; hEC cells are human embryonal carcinoma cells ECAPCs Embryonic cutaneous adipocyte progenitor cells ECM Extracellular Matrix ED Cells Embryo-derived cells; hED cells are human ED cells EDTA Ethylenediamine tetraacetic acid EG Cells Embryonic germ cells; hEG cells are human EG cells EP Cells Embryonic progenitor cells are cells derived from primordial stem cells that are more differentiated than primordial stem cells, in that they no longer display markers such as SSEA4, TRAl-60 or TRA-1-81 seropositivity in the case of the human species, but have not fully differentiated. Embryonic progenitor cells correspond to the embryonic stages as opposed to the postnatal stage of development. ES Cells Embryonic stem cells; hES cells are human ES cells FACS Fluorescence activated cell sorting FBS Fetal bovine serum FCS Fetal calf serum FGF Fibroblast Growth Factor GFP Green Fluorescent Protein GMP Good Manufacturing Practices hED Cells Human embryo-derived cells hEG Cells Human embryonic germ cells are stem cells derived from the primordial germ cells of fetal tissue. hEP Cells Human embryonic progenitor cells are embryonic progenitor cells from the human species. hiPS Cells Human induced pluripotent stem cells. HSE Human skin equivalents are mixtures of cells and biological or synthetic matrices manufactured for testing purposes or for therapeutic application in promoting wound repair.
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    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
  • 22 Ultra-Conserved Elements in Vertebrate and Fly Genomes Mathias Drton Nicholas Eriksson Garmay Leung

    22 Ultra-Conserved Elements in Vertebrate and Fly Genomes Mathias Drton Nicholas Eriksson Garmay Leung

    22 Ultra-Conserved Elements in Vertebrate and Fly Genomes Mathias Drton Nicholas Eriksson Garmay Leung Ultra-conserved elements in an alignment of multiple genomes are consecutive nucleotides that are in perfect agreement across all the genomes. For aligned vertebrate and fly genomes, we give descriptive statistics of ultra-conserved elements, explain their biological relevance, and show that the existence of ultra-conserved elements is highly improbable in neutrally evolving regions. 22.1 The data Our analyses of ultra-conserved elements are based on multiple sequence align- ments produced by MAVID [Bray and Pachter, 2004]. Prior to the alignment of multiple genomes, homology mappings (from Mercator [Dewey, 2005]) group into bins genomic regions that are anchored together by neighboring homolo- gous exons. A multiple sequence alignment is then produced for each of these alignment bins. MAVID is a global multiple alignment program, and therefore homologous regions with more than one homologous hit to another genome may not be found aligned together. Table 22.1 shows an example of Merca- tor’s output for a single region along with the beginning of the resulting MAVID multiple sequence alignment. Species Chrom. Start End Alignment Dog chrX 752057 864487 + A----AACCAAA--------- Chicken chr1 122119382 122708162 − TGCTGAGCTAAAGATCAGGCT Zebrafish chr9 19018916 19198136 + ------ATGCAACATGCTTCT Pufferfish chr2 7428614 7525502 + ---TAGATGGCAGACGATGCT Fugufish asm1287 21187 82482 + ---TCAAGGG----------- Table 22.1. Mercator output for a single bin, giving the position and orientation on the chromosome. Notice that the Fugu fish genome has not been fully assembled into chromosomes (cf. Section 4.2). The vertebrate dataset consists of 10,279 bins over 9 genomes (Table 22.2).