Search

Purpose: To develop therapeutics to treat metastasis of solid tumor cancers. To overcome obstacles to developing anti-metastasis treatments by: 1) developing an animal model that reproducibly mimics cancer metastasis and does so within a reasonable timeframe; and 2) figuring out the basic science that drives metastasis. Experimental: We discovered that all pluripotent human stem cells express a MUC1 cleavage product called MUC1* (muk 1 star). All MUC1 cleavage stops with the onset of differentiation and MUC1 goes back to its quiescent state. Over 75% of solid tumor cancers also express MUC1*. Overexpression of MUC1*, as well as enzymes that cleave MUC1 to MUC1* are predictors of poor prognosis. NME1 is a ligand of MUC1* that is secreted by both embryonic stem cells and cancer cells. As a dimer, NME1 dimerizes the MUC1* extra cellular domain to activate the MAP kinase growth pathway. In an embryo, the more stem cells there are, the more NME1 is secreted and it goes from the active dimer to an inactive hexamer (doesn’t bind MUC1*). The paradox was, “How do stem cells limit self-replication, but cancer cells do not?” Answer: A primitive growth factor, NME7AB, looks like a single chain dimer of NME1, so is always active, is expressed in the earliest, naïve stem cells and in metastatic cancer cells. Unpublished Results: Growing cancer cells in recombinant NME7AB for 10 days transforms them into metastatic cells: 1) become non-adherent; 2) enter dormancy; 3) upregulate metastatic markers by 200-fold; 4) form sub-cu tumors in mice from as few as 50 cells; iv injection leads to total metastasis in 10 days; 5) the percent of injected tumor cells that were first grown in NME7AB determines the growth of the entire tumor. We developed a monoclonal antibody that blocks interaction of NME7AB and MUC1*. This antibody reverses established metastasis of breast cancers in animals. NME7AB should be turned off early in embryogenesis, but is aberrantly re-activated in metastatic cancers. Yamanaka factors OCT4, SOX2 and NANOG bind to the promoters of NME7, MUC1 and MMP16, an enzyme that cleaves MUC1 to MUC1* and exposes the cryptic binding site for NME7AB. Conclusions: Primitive growth factor, NME7AB, drives metastasis of solid tumor cancers. Antibody that disrupts NME7AB-MUC1* interaction reverses metastasis in animals. Citation Format: Cynthia C. Bamdad, Benoit J. Smagghe, Mark G. Carter, Trevor J. Grant, Laura M. Reale, Michael J. Nash, Danica M. Walkley, Jac-Leen S. Nash, Kevin R. Yi, Andrew K. Stewart. Metastasis: Cancer cells that have turned on a Yamanaka-like pluripotency program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2487.

Purpose: To develop an antibody therapeutic that disrupts interaction between onco-embryonic growth factor NME7AB and its cognate growth factor receptor, MUC1*, for the treatment of solid tumors and inhibition of their metastases. Normally, NME7 is only expressed and secreted by cells of a Day 3 to Day 5 human blastocyst. NME7 expression is then turned off and expression of self-regulating, adult forms of NME proteins is turned on. However, we found that NME7 expression is mistakenly turned on again in cancer cells. Cleavage of NME7 to NME7AB enables secretion from the cell, where it then binds to and dimerizes the MUC1* extracellular domain, which activates the MAP kinase signaling cascade. Methods: Because NME7AB shares homology to other adult forms of NME proteins, which are required for normal cellular function, we needed to develop a monoclonal antibody that binds to NME7AB, but not to other NME proteins, and disrupts its interaction with the MUC1* growth factor receptor as well. To investigate the effects of NME7AB on cancer growth and metastasis, we generated populations of cancer cells that had been cultured in a serum-free media to which was added a recombinant NME7AB. The parent cells, the NME7AB grown progeny, or mixed populations were implanted into NSG mice to test the effect of novel anti-NME7AB antibodies on tumor growth and metastasis. Parent tumor cells and the NME7AB-grown cells were engineered to emit light at different wavelengths so that growth of each population could be separately tracked in live animals. Results: Cancer cells that were cultured in a serum-free media containing recombinant NME7AB for 10 days acquired characteristics of more metastatic cells, often called cancer stem cells (referred to here as NME7AB-CSCs). They upregulated metastatic markers by up to 100-fold, became non-adherent, entered dormancy and formed tumors from injection of as few as 10,000 cells. The addition of an anti-NME7AB antibody during the 10-day culture period blocked this transition. NME7AB-CSCs that were injected into the tail vein of NSG mice induced widespread metastasis in 6-10 days, after which an anti-NME7AB antibody was i.v. administered. The anti-NME7AB antibody greatly reduced or cleared the metastasis. Animals implanted sub-cutaneously with NME7AB-CSCs, then administered anti-NME7AB antibody, showed a significant reduction in the spread of breast cancer cells to the liver. Mixed populations of parent cells plus NME7AB-CSCs, which emitted light at different wavelengths, were implanted sub-cutaneously and allowed to become established. The percent of the implanted tumor that was NME7AB-CSCs determined the growth rate of the entire tumor. An anti-NME7AB antibody inhibited growth of the parent cells as well as the NME7AB-CSCs. Conclusion: These data support further pre-clinical development to allow for a clinical candidate to be tested in a metastatic as well as an adjuvant setting. Citation Format: Cynthia Carol Bamdad, Benoit J. Smagghe, Mark G. Carter, Trevor J. Grant, Danica M. Page, Laura M. Reale, Michael J. Nash, Jac-Leen S. Nash, Andrew K. Stewart. Novel anti-NME7antibody inhibits metastasis of solid tumor cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3458.

TPS1130 Background: Metastatic breast cancer (MBC) remains incurable and novel immunotherapy for durable response remains an unmet need. Chimeric antigen receptor (CAR) T-cell therapy, an innovative form of immunotherapy wherein autologous T-cells are genetically modified to target tumor specific cell-surface markers, has been developed for treatment of solid tumors. huMNC2-CAR44 recognizes the growth factor receptor form of MUC1, which is the transmembrane cleavage product called MUC1*. MUC1* is a Class I growth factor receptor that is activated by ligand-induced dimerization of its truncated extra cellular domain, which activates the MAP kinase signaling pathway as well as survival pathways. Onco-embryonic growth factor NME7AB binds to an ectopic site on MUC1* that is only unmasked after MUC1 is cleaved and the tandem repeat domain is shed from the cell surface. The targeting head of the CAR, huMNC2, competes with NME7AB for binding to this ectopic site. huMNC2 does not bind to full-length MUC1, hence highly tumor-selective. 70% of solid tumor cancers express a huMNC2 reactive MUC1* and huMNC2-scFv bound robustly to 93% of the breast cancers with minimal staining of normal tissues. huMNC2-CAR44 T cells completely obliterated a variety of MUC1* positive solid tumors in NSG mice in vivo. IND enabling animal studies demonstrated that huMNC2-CAR44 T potently inhibited MUC1* positive tumors xenografted into female NSG mice, whether the tumor cells were MUC1 negative cells stably transduced with MUC1* or breast cancer cells such as T47D that naturally express MUC1*. In one study, huMNC2-CAR44 T treated mice survived tumor-free for over 12 weeks, whereas control group had to be sacrificed at 3 weeks due to disease progression. Methods: This is a first-in human, phase I/II trial evaluating the safety and efficacy of huMNC2-CAR44 T in patients with MBC. Key inclusion criteria include age ≥18 years, ECOGPS 0-1, available FFPE tumor sample, tumor IHC ≥30% MUC1* and preserved organ function. Dose escalation is standard 3+3 design with dosing levels ranging from 3.3x10^5 to 1.0x10^7 CAR+ cells/kg, and fludarabine/cyclophosphamide lymphodepletion pre-treatment. Phase I accepts patients with MBC that has progressed through at least 3 previous lines of therapy. The primary objective of Phase I is to determine safety and determine a recommended Phase II dose (RPIID), with the exploratory objectives of assessing CAR T cell expansion, persistence, tumor penetration and potential tumor escape. Six (6) patients have been enrolled and five (5) patients have been treated to date. Phase II will be comprised of 3 cohorts of 15 patients in each arm of luminal, HER2+ and triple negative breast cancers for a total of 45 patients in Phase II. Clinical trial information: NCT04020575.

Background Minerva Biotechnologies has opened a Phase I 1st-in-human CAR T clinical trial, NCT-04020575, for metastatic breast cancers at the Fred Hutchinson Cancer Research Center. huMNC2-CAR44 targets the truncated extra cellular domain of MUC1* (muk 1 star), which is the transmembrane cleavage product that remains after MUC1 is cleaved and the tandem repeat domain is shed from the cancer cells. No therapeutic that targets MUC1* has ever been tested in humans. All previous, failed attempts to therapeutically target MUC1 have targeted the tandem repeat domains, which are cleaved and shed from the surface of cancer cells. MUC1 cleavage increases as tumor stage increases. Cleavage and shedding of the tandem repeat domain unmasks an ectopic binding site for onco-embryonic growth factor NME7AB. The antibody fragment that targets the CAR to the tumor competes with NME7AB for binding to this same ectopic site. MUC1* growth factor receptor is activated when onco-embryonic growth factor NME7AB dimerizes its truncated extra cellular domain. Methods Autologous huMNC2-CAR44 T cells undergo a short 11-day manufacturing process, which includes an antigen stimulation step and preserves many of the cells in the naive and central memory state. Patients are pre-treated with standard Cy-Flu lymphodepletion. Dose escalation phase is standard 3 × 3 with a starting dose 3.3 × 10e5 CAR T cells and going up to 1.0 × 10e7 cells. Patients are eligible if biopsy is greater than or equal to 30% reactive with MNC2 in a CLIA validated diagnostic assay. Results In vitro, huMNC2-CAR44 T cells killed cancer cells, but not non-cancer cells even if they expressed MUC1 or a normal form of cleaved MUC1. In NSG mice (n>300), huMNC2-CAR44 T cells eliminated MUC1* positive tumors from implanted breast cancer cells. A single CAR T cell injection eliminated tumors for 100 days; control animals had to be sacrificed at Day 20. Further, huMNC2-CAR44 T cell mediated killing increased as MUC1* density increased. In tissue micro array studies, huMNC2-scFv recognized 95% of breast cancers, across all subtypes, 83% ovarian, 78% pancreatic and 71% of lung cancers. huMNC2-scFv showed almost no binding to normal tissues and no staining of critical organs. Although patient recruitment has been slowed by COVID-19, preliminary results indicate CAR T cell expansion and possible efficacy. Conclusions Preliminary results show that patients experienced robust CAR T cell expansion with CAR-positive T cells persisting at Day 60 post huMNC2-CAR44 T cell treatment. Possible signs of efficacy were measured. Trial Registration NCT04020575

The efficiency of embryonic stem (ES) cell derivation relies on an optimized culture medium and techniques for treating preimplantation stage embryos. Recently, ES cell derivation from the preblastocyst developmental stage was reported by removing the zona pellucida from embryos of the most efficient strain for ES cell derivation (129Sv) during early preimplantation. Here, we showed that ES cells can be efficiently derived and maintained in a modified medium (MEMα), from preblastocysts of a low-efficiency mouse strain (a hybrid consisting of 50% B6, 25% CBA, and 25% DBA). Preblastocyst-derived ES cell lines were normal in terms of pluripotency-related protein expression, and chromosome number. Also, preblastocyst-derived ES cell lines from various culture conditions showed pluripotency in vivo through teratoma analysis. Interestingly, ES cell lines produced from preblastocysts and blastocysts, regardless of the derivation culture conditions, are nearly indistinguishable by their global gene expression profiles.

We demonstrate the qualitative and quantitative power of single-cell transcript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC's). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency. Using single-cell analysis of H9 hESC's differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers. Our single-cell profiles reveal mixed populations of cell types, with both transcriptional and temporal heterogeneity marking differentiation under all conditions. Interestingly, we also observe extensive and prolonged co-expression of markers regulating both pluripotency and lineage differentiation in all culture conditions, and we find that pluripotency marker transcripts remain detectable in the majority of cells for many days. Finally, we show that cells derived from undifferentiated hESC colonies display consistent gene expression profiles characterized by three cohorts of transcripts: uniform, absent and sporadically detected messages, and that a striking correlation exists between genes' membership in these cohorts and their hESC promoter chromatin state, with bivalent promoters dominating the sporadic transcripts.

This study was designed to examine the effect of the age of rabbit oocytes on the developmental potential of cloned embryos. The metaphase II oocytes used for nuclear transfer (NT) were collected at 10, 12, 14, and 16 h post-hCG injection (hpi). The total number of oocytes collected per donor (21.4–23.7) at 12 to 16 hpi was similar, but significantly higher than that collected at 10 hpi (16.2). Additionally, a significant improvement in blastocyst development was achieved with embryos generated by electrically mediated cell fusion (56.0%), compared to those from nuclear injection (13.1 %) (Experiment 1). Markedly higher blastocyst development (45.8–54.5%) was also achieved with oocytes collected at 10–12 hpi than from those collected 14–16 hpi (8.3–14.3%) (Experiment 2). In Experiment 3, the blastocyst rates of NT embryos derived from oocytes harvested 12 hpi (39.2–42.8 %) were significantly higher than from those collected at 16 hpi (6.8–8.4 %) (p

Although the first mouse embryonic stem (ES) cell lines were derived 2 decades ago, and standard protocols for ES cell derivation are widely used today, the technical difficulty of these protocols still pose a challenge for many investigators attempting to produce large numbers of ES cell lines, and are limited to only a few mouse strains. Recently, glucose concentration was shown to have a significant effect on the efficiency of ES cell derivation, but the mechanism(s) mediating this effect are still the subject of debate. In this report, we investigated the effect of glucose concentration on ES cell derivation efficiency from blastocysts in the context of a new medium, Minimum Essential Medium alpha (MEMalpha). Furthermore, we propose novel methods to improve mouse ES cell derivation efficiency using in vitro epigenetic modifications during early passages, combined with detection of Oct4-expressing cells. Based on the results reported here, modified MEMalpha containing high glucose improves the efficiency of ES cell derivation remarkably, compared with Knockout Dulbecco's-Modified Eagle Media (KDMEM). Epigenetic modifications are able to improve the efficiency even further.

Scientists have generated human stem cells that in some respects mimic mouse naïve cells, but their dependence on the addition of several extrinsic agents, and their propensity to develop abnormal karyotype calls into question their resemblance to a naturally occurring “naïve” state in humans. Here, we report that a recombinant, truncated human NME7, referred to as NME7AB here, induces a stable naïve-like state in human embryonic stem cells and induced pluripotent stem cells without the use of inhibitors, transgenes, leukemia inhibitory factor (LIF), fibroblast growth factor 2 (FGF2), feeder cells, or their conditioned media. Evidence of a naïve state includes reactivation of the second X chromosome in female source cells, increased expression of naïve markers and decreased expression of primed state markers, ability to be clonally expanded and increased differentiation potential. RNA-seq analysis shows vast differences between the parent FGF2 grown, primed state cells, and NME7AB converted cells, but similarities to altered gene expression patterns reported by others generating naïve-like stem cells via the use of biochemical inhibitors. Experiments presented here, in combination with our previous work, suggest a mechanistic model of how human stem cells regulate self-replication: an early naïve state driven by NME7, which cannot itself limit self-replication and a later naïve state regulated by NME1, which limits self-replication when its multimerization state shifts from the active dimer to the inactive hexamer.

Delayed implantation (embryonic diapause) occurs when the embryo at the blastocyst stage achieves a state of suspended animation. During this period, blastocyst growth is very slow, with minimal or no cell division. Nearly 100 mammals in seven different orders undergo delayed implantation, but the underlying molecular mechanisms that direct this process remain largely unknown. In mice, ovariectomy before preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which normally lasts for 1–2 weeks by continued progesterone treatment, although blastocyst survival decreases with time. An estrogen injection rapidly activates blastocysts and initiates their implantation in the progesterone-primed uterus. Using this model, here we show that among ≈20,000 genes examined, only 229 are differentially expressed between dormant and activated blastocysts. The major functional categories of altered genes include the cell cycle, cell signaling, and energy metabolic pathways, particularly highlighting the importance of heparin-binding epidermal growth factor-like signaling in blastocyst–uterine crosstalk in implantation. The results provide evidence that the two different physiological states of the blastocyst, dormancy and activation, are molecularly distinguishable in a global perspective and underscore the importance of specific molecular pathways in these processes. This study has identified candidate genes that provide a scope for in-depth analysis of their functions and an opportunity for examining their relevance to blastocyst dormancy and activation in numerous other species for which microarray analysis is not available or possible due to very limited availability of blastocysts.

A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells was assembled, including 250000 ESTs, representing approximately 39000 unique transcripts. The cDNA libraries, enriched in full-length clones, were condensed into the NIA 15 and 7.4K clone sets, freely distributed to the research community, providing a standard platform for expression studies using microarrays. They are essential tools for studying mammalian development and stem cell biology, and to provide hints about the differential nature of embryonic and adult stem cells.

A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from embryonic and newborn organ libraries consisting of ∼120,000 cDNA clones, which were initially re-arrayed into a set of ∼11,000 unique cDNA clones. A set of tubes was constructed from the racks in this set to prevent contamination and potential mishandling errors in all further re-arrays. Sequences from this set (11K) were analyzed further for quality and clone identity, and high-quality clones with verified identity were re-arrayed into the final set (7.4K). The set is freely available, and a corresponding database was built to provide comprehensive annotation for those clones with known identity or homology, and has been made available through an extensive Web site that includes many link-outs to external databases and analysis servers.[The sequence data from this study have been submitted to GenBank under accession nos. BQ550036–BQ563104.]

HIC1 is a candidate tumor suppressor gene which is frequently hypermethylated in human tumors, and its location within the Miller-Dieker syndrome's critical deletion region at chromosome 17p13.3 makes it a candidate gene for involvement in this gene deletion syndrome. To study the function of murine Hic1 in development, we have created Hic1 -deficient mice. These animals die perinatally and exhibit varying combinations of gross developmental defects throughout the second half of development, including acrania, exencephaly, cleft palate, limb abnormalities and omphalocele. These findings demonstrate a role for Hic1 in the development of structures affected in the Miller-Dieker syndrome, and provide functional evidence to strengthen its candidacy as a gene involved in this disorder.

Loss of imprinting (LOI) of the insulin-like growth factor II gene ( IGF2 ) is an epigenetic alteration that results in a modest increase in IGF2 expression, and it is present in the normal colonic mucosa of about 30% of patients with colorectal cancer. To investigate its role in intestinal tumorigenesis, we created a mouse model of Igf2 LOI by crossing female H19 +/– mice with male Apc +/Min mice. Mice with LOI developed twice as many intestinal tumors as did control littermates. Notably, these mice also showed a shift toward a less differentiated normal intestinal epithelium, reflected by an increase in crypt length and increased staining with progenitor cell markers. A similar shift in differentiation was seen in the normal colonic mucosa of humans with LOI. Thus, altered maturation of nonneoplastic tissue may be one mechanism by which epigenetic changes affect cancer risk.

Although leukemia inhibitory factor (LIF) maintains the ground state pluripotency of mouse embryonic stem cells and induced pluripotent stem cells (iPSCs) by activating the Janus kinase/signal transducer and activator of transcription 3 (Jak/Stat3) pathway, the mechanism remained unclear. Stat3 has only been shown to promote complete reprogramming of epiblast and neural stem cells and partially reprogrammed cells (pre-iPSCs). We investigated if and how Jak/Stat3 activation promotes reprogramming of terminally differentiated mouse embryonic fibroblasts (MEFs). We demonstrated that activated Stat3 not only promotes but also is essential for the pluripotency establishment of MEFs during reprogramming. We further demonstrated that during this process, inhibiting Jak/Stat3 activity blocks demethylation of Oct4 and Nanog regulatory elements in induced cells, which are marked by suppressed endogenous pluripotent gene expression. These are correlated with the significant upregulation of DNA methyltransferase (Dnmt) 1 and histone deacetylases (HDACs) expression as well as the increased expression of lysine-specific histone demethylase 2 and methyl CpG binding protein 2. Inhibiting Jak/Stat3 also blocks the expression of Dnmt3L, which is correlated with the failure of retroviral transgene silencing. Furthermore, Dnmt or HDAC inhibitor but not overexpression of Nanog significantly rescues the reprogramming arrested by Jak/Stat3 inhibition or LIF deprivation. Finally, we demonstrated that LIF/Stat3 signal also represents the prerequisite for complete reprogramming of pre-iPSCs. We conclude that Jak/Stat3 activity plays a fundamental role to promote pluripotency establishment at the epigenetic level, by facilitating DNA demethylation/de novo methylation, and open-chromatin formation during late-stage reprogramming.

Stem cells are found in all multicellular organisms, including two broadly defined cell types: embryonic stem cells (ESC) (C. Y. Cheong and T. Lufkin; and N. Lifantseva et al.) that are derived from the inner cell mass of blastocyst-stage embryos and adult stem cells that are present in adult tissues (C. M. Teven et al., R. Chung et al., and A. C. Wilber et al.). Nuclear reprogramming refers to the erasure and remodeling of epigenetic marks, which is a part of normal mammalian development. This reprogramming is likely required for totipotency of the newly formed embryo and erasure of acquired epigenetic changes (Felici). Advances in stem cells including induced pluripotent stem (IPS) cells (D. Dey and G. R. D. Evans; and P. Noisa and R. Parnpai) and nuclear reprogramming (C. M. Teven et al.) will provide new insights into the mechanisms of cellular differentiation, during embryonic development (N. Lifantsevaa et al.) as well as in adult tissues (C. M. Teven et al.), and their pluripotency (A. C. Wilber et al.), which may lead to cell-based therapies (R. Eggenschwiler et al.) for several human diseases (R. Chung et al.). Fuliang Du Mark G. Carter Giorgio A. Presicce Shinn-Chih Wu Perng-Chih Shen

The objective was to determine cryotolerance of in vitro cultured rabbit embryos to the open-pulled straw (OPS) method. Overall, 844 rabbit embryos at pronuclear, 2- to 4-cell, 8-cell, and morula/blastocyst stages were vitrified, and ≥ 1 mo later, were sequentially warmed, rehydrated, and subjected to continuous culture (n = 691) or embryo transfer (ET, n = 153). Embryos vitrified at the 8-cell stage or beyond had greater survival, expanded blastocyst and hatched blastocyst rates in vitro, and better term development than those vitrified at earlier stages. The 8-cell group had 70.1% expanded blastocysts, 63.7% hatched blastocysts, and 25.7% term development, as compared to 1.5-17.7%, 1.5-4.3% and 2.8-3.7% in the pronuclear, 2-cell and 4-cell embryos, respectively (P0.05). The expanded and hatched blastocyst rates in vitrified morula/blastocyst post-warming were higher than that in the 8-cell group; however, their term development after ET was similar (8-cell vs morula/blastocyst: 25.7 vs 19.4%, P0.05). Development after ET was comparable between vitrified-warmed embryos and fresh controls at 8-cell and morula/blastocyst stages (19.4-25.7 vs 13.7-26.6%, P0.05). For embryos at pronuclear or 2- to 4-cell stages, however, term rates were lower in the vitrified-warmed (2.8-3.7%) than in fresh controls (28.6-35.6%, P0.05). Therefore, cultured rabbit embryos at various developmental stages had differential crytolerance. Under the present experimental conditions, the 8-cell stage appeared to be the critical point for acquiring cryotolerance. We inferred that for this OPS cryopreservation protocol, rabbit embryos should be vitrified no earlier than the 8-cell stage, and stage-specific protocols may be needed to maximize embryo survival after vitrification and re-warming.

We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures.

Large-scale systematic gene expression analyses of early embryos and stem cells provide useful information to identify genes expressed differentially or uniquely in these cells. We review the current status of various approaches applied to preimplantation embryos and stem cells: expressed sequence tag, serial analysis of gene expression, differential display, massively parallel signature sequencing, DNA microarray (DNA chip) analysis, and chromatin-immunoprecipitation microarrays. We also discuss the biological questions that can only be addressed by the analysis of global gene expression patterns, such as so-called stemness and developmental potency. As the emphasis now shifts from expression profiling to functional studies, we review the genome-scale functional studies of genes: expression cloning, gene trapping, RNA interference, and gene disruptions. Finally, we discuss the future clinical application of such methodologies.

To understand global features of gene expression changes during in vitro neural differentiation, we carried out the microarray analysis of embryonic stem cells (ESCs), embryonal carcinoma cells, and adult neural stem/progenitor (NS) cells. Expression profiling of ESCs during differentiation in monolayer culture revealed three distinct phases: undifferentiated ESCs, primitive ectoderm-like cells, and neural progenitor cells. Principal component (PC) analysis revealed that these cells were aligned on PC1 over the course of 6 days. This PC1 represents approximately 4,000 genes, the expression of which increased with neural commitment/differentiation. Furthermore, NS cells derived from adult brain and their differentiated cells were positioned along this PC axis further away from undifferentiated ESCs than embryonic stem–derived neural progenitors. We suggest that this PC1 defines a path to neural fate, providing a scale for the degree of commitment/differentiation.

Thyroid hormone (TH) controlled gene expression profiles have been studied in the tail, hind limb and brain tissues during TH-induced and spontaneous Xenopus laevis metamorphosis. Amplified cRNA probes mixed with a universal standard were hybridized to a set of 21,807-sense strand 60-mer oligonucleotides on each slide representing the entries in X. laevis UniGene Build 48. Most of the up-regulated genes in hind limb and brain are the same. This reflects in part the fact that the initial response to TH induction in both tissues is cell proliferation. A large number of up-regulated genes in the limb and brain programs encode common components of the cell cycle, DNA and RNA metabolism, transcription and translation. Notch is one of the few genes that is differentially expressed exclusively in the brain in the first 48 h of TH induction studied in these experiments. The TH-induced gene expression changes in the tail are different from the limb and brain programs. Distinct muscle and fibroblast programs were identified in the tail. Dying muscle fibers in tail (marked by active caspase-3) up-regulate a group of genes that include proteolytic enzymes. At the climax of metamorphosis, tail muscle down-regulates more than half of the genes that encode the glycolytic enzymes in the cytoplasm and the tricarboxylic acid pathway and all five complexes of the electron transport system in mitochondria. These changes in gene expression precede the activation of caspase-3. Some of these same energy metabolism-related genes are up-regulated in the limb and brain programs by TH. A prominent feature of the tail fibroblasts is the down-regulation of several collagen and other extra cellular matrix genes and the up-regulation of hydrolytic enzymes that are responsible for dissolving the notochord and resorbing the tail.

Mammalian preimplantation embryos provide an excellent opportunity to study temporal and spatial gene expression in whole mount in situ hybridization (WISH). However, large-scale studies are made difficult by the size of the embryos ( approximately 60mum diameter) and their fragility. We have developed a chamber system that allows parallel processing of embryos without the aid of a microscope. We first selected 91 candidate genes that were transcription factors highly expressed in blastocysts, and more highly expressed in embryonic (ES) than in trophoblast (TS) stem cells. We then used the WISH to identify 48 genes expressed predominantly in the inner cell mass (ICM) and to follow several of these genes in all seven preimplantation stages. The ICM-predominant expressions of these genes suggest their involvement in the pluripotency of embryonic cells. This system provides a useful tool to a systematic genome-scale analysis of preimplantation embryos.

An in-situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes is presented. Exogenous RNA controls derived from yeast allow quantitative estimation of absolute endogenous transcript abundance, The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

This chapter discusses some technical aspects of genomic approaches such as complementary DNA (cDNA) analyses and expression profiling. It presents two examples of such applications: expression profiling and comparison among various types of stem cells; and expression profiling between cloned mice and normal mice. The fundamental information required for genomics approaches are the sequences and structures of the genes under study. This information is provided by Expressed Sequence Tag projects, in which cDNA libraries are first made from a variety of tissues and randomly selected individual cDNA clones are sequenced from their 5'- or 3'-ends. Two forms of microarrays are currently available: cDNA microarrays and oligonucleotide microarrays. Various bioinformatics and statistical analysis tools have been developed and utilized for the analysis of expression profiles of a large number of genes. In particular, hierarchical clustering, self-organizing map and k-means clustering analyses have been widely used.

Decreasing oocyte competence with maternal aging is a major factor in human infertility. To investigate the age-dependent molecular changes in a mouse model, we compared the expression profiles of metaphase II oocytes collected from 5- to 6-week-old mice with those collected from 42- to 45-week-old mice using the NIA 22K 60-mer oligo microarray. Among approximately 11 000 genes whose transcripts were detected in oocytes, about 5% (530) showed statistically significant expression changes, excluding the possibility of global decline in transcript abundance. Consistent with the generally accepted view of aging, the differentially expressed genes included ones involved in mitochondrial function and oxidative stress. However, the expression of other genes involved in chromatin structure, DNA methylation, genome stability and RNA helicases was also altered, suggesting the existence of additional mechanisms for aging. Among the transcripts decreased with aging, we identified and characterized a group of new oocyte-specific genes, members of the human NACHT, leucine-rich repeat and PYD-containing (NALP) gene family. These results have implications for aging research as well as for clinical ooplasmic donation to rejuvenate aging oocytes. © Oxford University Press 2004; all rights reserved.

A defect in klotho gene expression in the mouse results in a syndrome that resembles human aging, with greatly shortened lifespan, arteriosclerosis, and defective hearing. In an effort to find functional murine variants of klotho, we sequenced the gene and examined renal expression of the secreted and membrane-bound Klotho isoforms from 16 laboratory-derived and 4 wild-derived inbred strains. Among the laboratory-derived strains, no sequence variation was found in any of the exons or intron-exon boundaries. Among the wild-derived strains, we found 45 sequence variants with six resulting in amino acid substitutions. One wild-derived strain, SPRET/Ei, had four amino acid substitutions and higher levels of the membrane form and total klotho mRNA. In addition, the membrane to secreted klotho expression ratio was elevated in three wild-derived strains with amino acid substitutions. Interestingly, SPRET/Ei mice have longer lifespans, decreased atherosclerosis risk factors, and better hearing than almost all other mouse strains.

Applications of microarray technologies to mouse embryology/genetics have been limited, due to the nonavailability of microarrays containing large numbers of embryonic genes and the gap between microgram quantities of RNA required by typical microarray methods and the miniscule amounts of tissue available to researchers. To overcome these problems, we have developed a microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 22,000 unique mouse transcripts, assembled primarily from sequences of stem cell and embryo cDNA libraries. We have optimized RNA labeling protocols and experimental designs to use as little as 2 ng total RNA reliably and reproducibly. At least 98% of the probes contained in the microarray correspond to clones in our publicly available collections, making cDNAs readily available for further experimentation on genes of interest. These characteristics, combined with the ability to profile very small samples, make this system a resource for stem cell and embryogenomics research.[Supplemental material is available online atwww.genome.org and at the NIA Mouse cDNA Project Web site,http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html.]

The gene hypermethylated in cancer-1 (HIC1) encodes a zinc-finger transcription factor1 that belongs to a group of proteins known as the POZ family2. HIC1 is hypermethylated and transcriptionally silent in several types of human cancer1,3,4,5. Homozygous disruption of Hic1 impairs development and results in embryonic and perinatal lethality in mice6. Here we show that mice disrupted in the germ line for only one allele of Hic1 develop many different spontaneous malignant tumors, including a predominance of epithelial cancers in males and lymphomas and sarcomas in females. The complete loss of Hic1 function in the heterozygous mice seems to involve dense methylation of the promoter of the remaining wild-type allele. We conclude that HIC1 is a candidate tumor-suppressor gene for which loss of function in both mouse and human cancers is associated only with epigenetic modifications.

Dangerous organophosphorus (OP) compounds have been used as insecticides in agriculture and in chemical warfare. Because exposure to OP could create a danger for humans in the future, butyrylcholinesterase (BChE) has been developed for prophylaxis to these chemicals. Because it is impractical to obtain sufficient quantities of plasma BChE to treat humans exposed to OP agents, the production of recombinant BChE (rBChE) in milk of transgenic animals was investigated. Transgenic mice and goats were generated with human BChE cDNA under control of the goat β-casein promoter. Milk from transgenic animals contained 0.1–5 g/liter of active rBChE. The plasma half-life of PEGylated, goat-derived, purified rBChE in guinea pigs was 7-fold longer than non-PEGylated dimers. The rBChE from transgenic mice was inhibited by nerve agents at a 1:1 molar ratio. Transgenic goats produced active rBChE in milk sufficient for prophylaxis of humans at risk for exposure to OP agents.

Cystic fibrosis (CF) is a lethal inherited disease that results from abnormal chloride conduction in epithelial tissues. ClC-2 chloride channels are expressed in epithelia affected by CF and may provide a key “alternative” target for pharmacotherapy of this disease. To explore this possibility, the expression level of ClC-2 channels was genetically manipulated in airway epithelial cells derived from a cystic fibrosis patient (IB3-1). Whole-cell patch-clamp analysis of cells overexpressing ClC-2 identified hyperpolarization-activated Cl − currents (HACCs) that displayed time- and voltage-dependent activation, and an inwardly rectifying steady-state current–voltage relationship. Reduction of extracellular pH to 5.0 caused significant increases in HACCs in overexpressing cells, and the appearance of robust currents in parental IB3-1 cells. IB3-1 cells stably transfected with the antisense ClC-2 cDNA showed reduced expression of ClC-2 compared with parental cells by Western blotting, and a significant reduction in the magnitude of pH-dependent HACCs. To determine whether changes in extracellular pH alone could initiate chloride transport via ClC-2 channels, we performed 36 Cl − efflux studies on overexpressing cells and cells with endogenous expression of ClC-2. Acidic extracellular pH increased 36 Cl − efflux rates in both cell types, although the ClC-2 overexpressing cells had significantly greater chloride conduction and a longer duration of efflux than the parental cells. Compounds that exploit the pH mechanism of activating endogenous ClC-2 channels may provide a pharmacologic option for increasing chloride conductance in the airways of CF patients.

Trichostatin A (TSA) is a potent inhibitor of histone deacetylases and has been shown to improve cloned embryo pre-implantation and term development. We examined the effects of TSA treatment on cloned mouse embryonic gene expression using microarrays. Cloned mouse embryos were generated using long-term haematopoietic stem cells (LT-HSC) and terminally differentiated granulocytes (Gr-1) as nuclear donors, which have been shown to have significantly different cloning efficiencies (Sung et al. 2006 Nat. Gen. 38, 1323–1328). Late 2-cell and blastocyst stage cloned embryos and control, BDF1 in vivo and IVF embryos (n = 10 from each embryo type and stage, except LT-HSC blastocysts, where n = 5) were snap frozen in liquid nitrogen. Total RNA was isolated from individual embryos and amplified using the TargetAmp 2 round Aminoallyl aRNA amplification kit (Epicentre Biotechnologies, Madison, WI, USA). Amplified RNA from each embryo and a standard reference was labelled with Cy3 or Cy5 and hybridized to the mouse exonic evidence based oligonucleotide (MEEBO) microarray allowing for the interrogation of ~25 000 genes. After Loess normalization, ANOVA with false discovery rate (P

Although leukemia inhibitory factor (LIF) maintains the ground state pluripotency of mouse embryonic stem cells and induced pluripotent stem cells (iPSC) by activating the Janus kinase/signal transducer and activator of transcription 3 (Jak/Stat3) pathway, the mechanism remains unclear. Stat3 has only been shown to promote complete reprogramming of epiblast and neural stem cells, and the partially reprogrammed cells (pre-iPSC). We investigated if and how Jak/Stat3 activation promotes reprogramming of terminally differentiated mouse embryonic fibroblasts (MEF). We demonstrated that activated Stat3 not only promotes but is essential for the pluripotency establishment in MEF cell reprogramming. We further demonstrated that, during reprogramming, inhibiting Jak/Stat3 activity blocks demethylation of Oct4 and Nanog regulatory DNA sequences in induced cells, which are marked by suppressed endogenous pluripotent gene expression. These are correlated with significant upregulation of DNA methyltransferase (Dnmt) 1 and histone deacetylases (HDAC) expression, as well as the increased expression of lysine-specific histone demethylase 2 and methyl-CpG binding protein 2. Inhibiting Jak/Stat3 also blocks the expression of Dnmt3L, which is correlated with the failure of retroviral transgene silencing. Furthermore, Dnmt or HDAC inhibitor but not overexpression of Nanog rescues the reprogramming arrested by Jak/Stat3 inhibition or LIF deprivation. Finally, we demonstrated that LIF/Stat3 signal also represents the prerequisite for complete reprogramming of pre-iPSC. We conclude that Jak/Stat3 activity plays a fundamental role in promoting the establishment of pluripotency at the epigenetic level, by facilitating DNA demethylation/de novo methylation and open-chromatin formation during late stage reprogramming.

The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

Understanding preimplantation development is important both for basic reproductive biology and for practical applications including regenerative medicine and livestock breeding. Global expression profiles revealed and characterized the distinctive patterns of maternal RNA degradation and zygotic gene activation, including two major transient waves of de novo transcription. The first wave corresponds to zygotic genome activation (ZGA); the second wave, named mid-preimplantation gene activation (MGA), precedes the dynamic morphological and functional changes from the morula to blastocyst stage. Further expression profiling of embryos treated with inhibitors of transcription, translation, and DNA replication revealed that the translation of maternal RNAs is required for the initiation of ZGA. We propose a cascade of gene activation from maternal RNA/protein sets to ZGA gene sets and thence to MGA gene sets. The large number of genes identified as involved in each phase is a first step toward analysis of the complex gene regulatory networks.