Paul S. Knoepfler

Sin meets NuRD and other tails of repression.

Why are there multiple HDAC corepressor complexes? Although the mSin3 and Mi-2/NuRD complexes could be redundant, it is difficult to imagine the high degree of evolutionary conservation of two such multicomponent systems unless some aspects of their function are unique. Indeed both the chromatin remodeling activity associated with Mi-2/NuRD as well as the distinct transcription factors present in both corepressor complexes point toward specialization. Perhaps Mi-2/NuRD target genes are predominantly localized in relatively closed regions of chromatin, thus requiring a nucleosome remodeling step for access of Mi-2/NuRD to histones and subsequent or concomitant deacetylation (see Tyler and Kadonaga 1999xTyler, J.K and Kadonaga, J.T. Cell. 1999; 99: 443–446Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesTyler and Kadonaga 1999). Such genes might be resistant to Sin3-mediated repression, which would be reserved for previously remodeled actively transcribed genes that may not require further chromatin remodeling for deacetylation such as HO in yeast (8xKrebs, J.E, Kuo, M.H, Allis, C.D, and Peterson, C.L. Genes Dev. 1999; 13: 1412–1421Crossref | PubMedSee all References, 3xCosma, M.P, Tanaka, T, and Nasmyth, K. Cell. 1999; 97: 299–311Abstract | Full Text | Full Text PDF | PubMed | Scopus (548)See all References). There is also compelling evidence that certain silenced regions of chromatin may occupy nuclear compartments distinct from those in which active genes reside. Therefore, it is possible that the Mi-2/NuRD (or, for that matter, any of the other corepressors mentioned above) may possess activities that facilitate relocalization of targeted genetic regions to specific nuclear domains (see Sun and Elgin 1999xSun, F.L and Elgin, S.C.R. Cell. 1999; 99: 459–462Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesSun and Elgin 1999 [this issue of Cell]).In a general sense, the mechanism of repression is likely to have gene-specific aspects even though much of the regulatory machinery involved is common to all genes. Different corepressors may be thought of as acting to unleash HDAC activities at the target site in distinct ways. For example, some corepressors may tether HDAC to the complex while others may release HDAC in the vicinity of the gene target. The interplay between different types of chromatin modifications including deacetylation, methylation, and chromatin remodeling may be coordinated through the functions of corepressors (see Bird and Wolffe 1999xBird, A.P and Wolffe, A.P. Cell. 1999; 99: 451–454Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesBird and Wolffe 1999 and Tyler and Kadonaga 1999xTyler, J.K and Kadonaga, J.T. Cell. 1999; 99: 443–446Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesTyler and Kadonaga 1999). Moreover, the recent work on corepressors has illuminated a profound connection between transcriptional repression and fundamental aspects of cell biology including proliferation, differentiation, and cancer.*To whom correspondence should be addressed (e-mail: eisenman@fhcrc.org).

Deconstructing stem cell tumorigenicity: A roadmap to safe regenerative medicine

Many of the earliest stem cell studies were conducted on cells isolated from tumors rather than from embryos. Of particular interest was research on embryonic carcinoma cells (EC), a type of stem cell derived from teratocarcinoma. The EC research laid the foundation for the later discovery of and subsequent work on embryonic stem cells (ESC). Both ESC isolated from the mouse (mESC) and then later from humans (hESC) shared not only pluripotency with their EC cousins, but also robust tumorigenicity as each readily form teratoma. Surprisingly, decades after the discovery of mESC, the question of what drives ESC to form tumors remains largely an open one. This gap in the field is particularly serious as stem cell tumorigenicity represents the key obstacle to the safe use of stem cell‐based regenerative medicine therapies. Although some adult stem cell therapies appear to be safe, they have only a very narrow range of uses in human disease. Our understanding of the tumorigenicity of human induced pluripotent stem cells (IPSC), perhaps the most promising modality for future patient‐specific regenerative medicine therapies, is rudimentary. However, IPSC are predicted to possess tumorigenic potential equal to or greater than that of ESC. Here, the links between pluripotency and tumorigenicity are explored. New methods for more accurately testing the tumorigenic potential of IPSC and of other stem cells applicable to regenerative medicine are proposed. Finally, the most promising emerging approaches for overcoming the challenges of stem cell tumorigenicity are highlighted. Stem Cells 2009;27:1050–1056

Myc influences global chromatin structure.

The family of myc proto‐oncogenes encodes transcription factors (c‐, N‐, and L‐Myc) that regulate cell growth and proliferation and are involved in the etiology of diverse cancers. Myc proteins are thought to function by binding and regulating specific target genes. Here we report that Myc proteins are required for the widespread maintenance of active chromatin. Disruption of N‐myc in neuronal progenitors and other cell types leads to nuclear condensation accompanied by large‐scale changes in histone modifications associated with chromatin inactivation, including hypoacetylation and altered methylation. These effects are largely reversed by exogenous Myc as well as by differentiation and are mimicked by the Myc antagonist Mad1. The first chromatin changes are evident within 6 h of Myc loss and lead to changes in chromatin structure. Myc widely influences chromatin in part through upregulation of the histone acetyltransferase GCN5. This study provides the first evidence for regulation of global chromatin structure by an oncoprotein and may explain the broad effects of Myc on cell behavior and tumorigenesis.

Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential.

Skeletal muscle differentiation is initiated by the transcription factor MyoD, which binds directly to the regulatory regions of genes expressed during skeletal muscle differentiation and initiates chromatin remodeling at specific promoters. It is not known, however, how MyoD initially recognizes its binding site in a chromatin context. Here we show that the H/C and helix III domains, two domains of MyoD that are necessary for the initiation of chromatin remodeling at the myogenin locus, together regulate a restricted subset of genes, including myogenin. These domains are necessary for the stable binding of MyoD to the myogenin promoter through an interaction with an adjacent protein complex containing the homeodomain protein Pbx, which appears to be constitutively bound at this site. This demonstrates a specific mechanism of targeting MyoD to loci in inactive chromatin and reveals a critical role of homeodomain proteins in marking specific genes for activation in the muscle lineage.

Nmyc plays an essential role during lung development as a dosage- sensitive regulator of progenitor cell proliferation and differentiation

Understanding how lung progenitor cells balance proliferation against differentiation is relevant to clinical disorders such as bronchopulmonary dysplasia of premature babies and lung cancer. Previous studies have established that lung development is severely disrupted in mouse mutants with reduced levels of the proto-oncogene Nmyc, but the precise mechanisms involved have not been explored. We show here that Nmyc expression in the embryonic lung is normally restricted to a distal population of undifferentiated epithelial cells, a high proportion of which are in the S phase of the cell cycle. Overexpression of NmycEGFP in the epithelium under the control of surfactant protein C (Sftpc) regulatory elements expands the domain of S phase cells and upregulates numerous genes associated with growth and metabolism, as shown by transcriptional microarray. In addition, there is marked inhibition of differentiation, coupled with an expanded domain of expression of Sox9 protein, which is also normally restricted to the distal epithelial compartment. By contrast, conditional deletion of Nmyc leads to reduced proliferation, epithelial differentiation and high levels of apoptosis in both epithelium and mesenchyme. Unexpectedly, about 50% of embryos in which only one copy of Nmyc is deleted die perinatally, with similarly abnormal lungs. We propose a model in which Nmyc is essential in the developing lung for maintaining a distal population of undifferentiated, proliferating progenitor cells.

Hematopoietic Stem Cell Function and Survival Depend on c-Myc and N-Myc Activity

Myc activity is emerging as a key element in acquisition and maintenance of stem cell properties. We have previously shown that c-Myc deficiency results in accumulation of defective hematopoietic stem cells (HSCs) due to niche-dependent differentiation defects. Here we report that immature HSCs coexpress c-myc and N-myc mRNA at similar levels. Although conditional deletion of N-myc in the bone marrow does not affect hematopoiesis, combined deficiency of c-Myc and N-Myc (dKO) results in pancytopenia and rapid lethality. Interestingly, proliferation of HSCs depends on both myc genes during homeostasis, but is c-Myc/N-Myc independent during bone marrow repair after injury. Strikingly, while most dKO hematopoietic cells undergo apoptosis, only self-renewing HSCs accumulate the cytotoxic molecule Granzyme B, normally employed by the innate immune system, thereby revealing an unexpected mechanism of stem cell apoptosis. Collectively, Myc activity (c-Myc and N-Myc) controls crucial aspects of HSC function including proliferation, differentiation, and survival.

myc maintains embryonic stem cell pluripotency and self-renewal

While endogenous Myc (c-myc) and Mycn (N-myc) have been reported to be separately dispensable for murine embryonic stem cell (mESC) function, myc greatly enhances induced pluripotent stem (iPS) cell formation and overexpressed c-myc confers LIF-independence upon mESC. To address the role of myc genes in ESC and in pluripotency generally, we conditionally knocked out both c- and N-myc using myc doubly homozygously floxed mESC lines (cDKO). Both lines of myc cDKO mESC exhibited severely disrupted self-renewal, pluripotency, and survival along with enhanced differentiation. Chimeric embryos injected with DKO mESC most often completely failed to develop or in rare cases survived but with severe defects. The essential nature of myc for self-renewal and pluripotency is at least in part mediated through orchestrating pluripotency-related cell cycle and metabolic programs. This study demonstrates that endogenous myc genes are essential for mESC pluripotency and self-renewal as well as providing the first evidence that myc genes are required for early embryogenesis, suggesting potential mechanisms of myc contribution to iPS cell formation.

Division and apoptosis of E2f-deficient retinal progenitors

The activating E2f transcription factors (E2f1, E2f2 and E2f3) induce transcription and are widely viewed as essential positive cell cycle regulators. Indeed, they drive cells out of quiescence, and the ‘cancer cell cycle’ in Rb1 null cells is E2f-dependent. Absence of activating E2fs in flies or mammalian fibroblasts causes cell cycle arrest, but this block is alleviated by removing repressive E2f or the tumour suppressor p53, respectively. Thus, whether activating E2fs are indispensable for normal division is an area of debate. Activating E2fs are also well known pro-apoptotic factors, providing a defence against oncogenesis, yet E2f1 can limit irradiation-induced apoptosis. In flies this occurs through repression of hid (also called Wrinkled; Smac/Diablo in mammals). However, in mammals the mechanism is unclear because Smac/Diablo is induced, not repressed, by E2f1, and in keratinocytes survival is promoted indirectly through induction of DNA repair targets. Thus, a direct pro-survival function for E2f1–3 and/or its relevance beyond irradiation has not been established. To address E2f1–3 function in normal cells in vivo we focused on the mouse retina, which is a relatively simple central nervous system component that can be manipulated genetically without compromising viability and has provided considerable insight into development and cancer. Here we show that unlike fibroblasts, E2f1–3 null retinal progenitor cells or activated Müller glia can divide. We attribute this effect to functional interchangeability with Mycn. However, loss of activating E2fs caused downregulation of the p53 deacetylase Sirt1, p53 hyperacetylation and elevated apoptosis, establishing a novel E2f–Sirt1–p53 survival axis in vivo. Thus, activating E2fs are not universally required for normal mammalian cell division, but have an unexpected pro-survival role in development.

N-myc Is an Essential Downstream Effector of Shh Signaling during both Normal and Neoplastic Cerebellar Growth

We examined the genetic requirements for the Myc family of oncogenes in normal Sonic hedgehog (Shh)-mediated cerebellar granule neuronal precursor (GNP) expansion and in Shh pathway-induced medulloblastoma formation. In GNP-enriched cultures derived from N-myc(Fl/Fl) and c-myc(Fl/Fl) mice, disruption of N-myc, but not c-myc, inhibited the proliferative response to Shh. Conditional deletion of c-myc revealed that, although it is necessary for the general regulation of brain growth, it is less important for cerebellar development and GNP expansion than N-myc. In vivo analysis of compound mutants carrying the conditional N-myc null and the activated Smoothened (ND2:SmoA1) alleles showed, that although granule cells expressing the ND2:SmoA1 transgene are present in the N-myc null cerebellum, no hyperproliferation or tumor formation was detected. Taken together, these findings provide in vivo evidence that N-myc acts downstream of Shh/Smo signaling during GNP proliferation and that N-myc is required for medulloblastoma genesis even in the presence of constitutively active signaling from the Shh pathway.

Why Myc? An Unexpected Ingredient in the Stem Cell Cocktail

Screening cocktails of candidate genes for induction of pluripotency and self-renewal in nonstem cells has identified a surprising new embryonic stem cell regulator, the myc proto-oncogene. Here the possible mechanisms by which myc controls self-renewal and pluripotency are discussed.