Christopher J. Bowman

Genome-wide remodeling of the epigenetic landscape during myogenic differentiation

We have examined changes in the chromatin landscape during muscle differentiation by mapping the genome-wide location of ten key histone marks and transcription factors in mouse myoblasts and terminally differentiated myotubes, providing an exceptionally rich dataset that has enabled discovery of key epigenetic changes underlying myogenesis. Using this compendium, we focused on a well-known repressive mark, histone H3 lysine 27 trimethylation, and identified novel regulatory elements flanking the myogenin gene that function as a key differentiation-dependent switch during myogenesis. Next, we examined the role of Polycomb-mediated H3K27 methylation in gene repression by systematically ablating components of both PRC1 and PRC2 complexes. Surprisingly, we found mechanistic differences between transient and permanent repression of muscle differentiation and lineage commitment genes and observed that the loss of PRC1 and PRC2 components produced opposing differentiation defects. These phenotypes illustrate striking differences as compared to embryonic stem cell differentiation and suggest that PRC1 and PRC2 do not operate sequentially in muscle cells. Our studies of PRC1 occupancy also suggested a “fail-safe” mechanism, whereby PRC1/Bmi1 concentrates at genes specifying nonmuscle lineages, helping to retain H3K27me3 in the face of declining Ezh2-mediated methyltransferase activity in differentiated cells.

A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers

Monomethylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and promoters, although its function is unknown. Here, we uncover roles for H3K4me1 in diverse cell types. Remarkably, we find that MLL3/4 provokes monomethylation of promoter regions and the conditional repression of muscle and inflammatory response genes in myoblasts. During myogenesis, muscle genes are activated, lose MLL3 occupancy, and become H3K4-trimethylated through an alternative COMPASS complex. Monomethylation-mediated repression was not restricted to skeletal muscle. Together with H3K27me3 and H4K20me1, H3K4me1 was associated with transcriptional silencing in embryonic fibroblasts, macrophages, and human embryonic stem cells (ESCs). On promoters of active genes, we find that H3K4me1 spatially demarcates the recruitment of factors that interact with H3K4me3, including ING1, which, in turn, recruits Sin3A. Our findings point to a unique role for H3K4 monomethylation in establishing boundaries that restrict the recruitment of chromatin-modifying enzymes to defined regions within promoters.

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

To identify the compendium of distal regulatory elements that govern myogenic differentiation, we generated chromatin state maps based on histone modifications and recruitment of factors that typify enhancers in myoblasts and myotubes. We found a striking concordance between the locations of these newly defined enhancers, MyoD1-binding events, and noncoding RNA transcripts. These enhancers recruit several sequence-specific transcription factors in a spatially constrained manner around MyoD1-binding sites. Remarkably, MyoD1-null myoblasts show a wholesale loss of recruitment of these factors as well as diminished monomethylation of H3K4 (H3K4me1) and acetylation of H3K27 (H3K27ac) and reduced recruitment of Set7, an H3K4 monomethylase. Surprisingly, we found that H3K4me1, but not H3K27ac, could be restored by re-expression of MyoD1 in MyoD1(-/-) myoblasts, although re-expression of this factor in MyoD1-null myotubes restored both histone modifications. Our studies identified a role for MyoD1 in condition-specific enhancer assembly through recruitment of transcription factors and histone-modifying enzymes that shape muscle differentiation.

Loss of Metal Ions, Disulfide Reduction and Mutations Related to Familial ALS Promote Formation of Amyloid-Like Aggregates from Superoxide Dismutase

Mutations in the gene encoding Cu-Zn superoxide dismutase (SOD1) are one of the causes of familial amyotrophic lateral sclerosis (FALS). Fibrillar inclusions containing SOD1 and SOD1 inclusions that bind the amyloid-specific dye thioflavin S have been found in neurons of transgenic mice expressing mutant SOD1. Therefore, the formation of amyloid fibrils from human SOD1 was investigated. When agitated at acidic pH in the presence of low concentrations of guanidine or acetonitrile, metalated SOD1 formed fibrillar material which bound both thioflavin T and Congo red and had circular dichroism and infrared spectra characteristic of amyloid. While metalated SOD1 did not form amyloid-like aggregates at neutral pH, either removing metals from SOD1 with its intramolecular disulfide bond intact or reducing the intramolecular disulfide bond of metalated SOD1 was sufficient to promote formation of these aggregates. SOD1 formed amyloid-like aggregates both with and without intermolecular disulfide bonds, depending on the incubation conditions, and a mutant SOD1 lacking free sulfhydryl groups (AS-SOD1) formed amyloid-like aggregates at neutral pH under reducing conditions. ALS mutations enhanced the ability of disulfide-reduced SOD1 to form amyloid-like aggregates, and apo-AS-SOD1 formed amyloid-like aggregates at pH 7 only when an ALS mutation was also present. These results indicate that some mutations related to ALS promote formation of amyloid-like aggregates by facilitating the loss of metals and/or by making the intramolecular disulfide bond more susceptible to reduction, thus allowing the conversion of SOD1 to a form that aggregates to form resembling amyloid. Furthermore, the occurrence of amyloid-like aggregates per se does not depend on forming intermolecular disulfide bonds, and multiple forms of such aggregates can be produced from SOD1.

The placenta, transfer of immunoglobulins, and safety assessment of biopharmaceuticals in pregnancy

Anatomical and developmental differences of the parental–offspring interface among experimental animals and humans throughout gestation are reviewed focusing on biodistribution of immunoglobulins (IgG). The formation of the extraembryonic membranes, uteroplacental circulation, and characteristics of the placenta (gross shape, modes of implantation, surface modifications that increase surface area, and extent of embryonic invasion into maternal tissue) are reviewed. Placental physiology and function are covered with attention to transfer of xenobiotics. Placental transfer of immunoglobulins in the human, non-human primate (NHP), rodent, and rabbit is discussed and the transfer of human fragment crystallizable (Fc)-containing biopharmaceuticals and potential impact on developmental toxicity risk assessment are specifically addressed. Safety assessment is often limited to the NHP as the only pharmacologically relevant model, despite poor statistical power as employed in current experimental designs. Although data are limited, the gestational timing of placental IgG transfer in rabbits appears to be more consistent with that of humans (i.e. occurring at the very end and after completion of organogenesis) than that of rodents, making the rabbit a reasonable choice assuming it is pharmacologically relevant. The rodent is not considered the most appropriate model for human placental transfer of Fc-containing biopharmaceuticals because it is currently believed to overestimate exposure during organogenesis. Nevertheless, the rodent may provide a conservative approach for hazard identification. It is clear that additional experimentation is needed to further clarify the timing of prenatal transfer of Fc-containing biopharmaceuticals in various species.

The mammalian Sin3 proteins are required for muscle development and sarcomere specification.

ABSTRACT The highly related mammalian Sin3A and Sin3B proteins provide a versatile platform for chromatin-modifying activities. Sin3-containing complexes play a role in gene repression through deacetylation of nucleosomes. Here, we explore a role for Sin3 in myogenesis by examining the phenotypes resulting from acute somatic deletion of both isoforms in vivo and from primary myotubes in vitro. Myotubes ablated for Sin3A alone, but not Sin3B, displayed gross defects in sarcomere structure that were considerably enhanced upon simultaneous ablation of both isoforms. Massively parallel sequencing of Sin3A- and Sin3B-bound genomic loci revealed a subset of target genes directly involved in sarcomere function that are positively regulated by Sin3A and Sin3B proteins. Both proteins were coordinately recruited to a substantial number of genes. Interestingly, depletion of Sin3B led to compensatory increases in Sin3A recruitment at certain target loci, but Sin3B was never found to compensate for Sin3A loss. Thus, our analyses describe a novel transcriptional role for Sin3A and Sin3B proteins associated with maintenance of differentiated muscle cells.

The design of chronic toxicology studies of monoclonal antibodies: implications for the reduction in use of non-human primates.

The changing environment of monoclonal antibody (mAb) development is impacting on the cost of drug development and the use of experimental animals, particularly non-human primates (NHPs). The drive to reduce these costs is huge and involves rethinking and improving nonclinical studies to make them more efficient and more predictive of man. While NHP use might be unavoidable in many cases because of the exquisite specificity and consequent species selectivity of mAbs, our increasing knowledge base can be used to improve drug development and maximise the output of experimental data. Data on GLP regulatory toxicology studies for 58mAbs were obtained from 10 companies across a wide range of therapeutic indications. These data have been used to investigate current practice and identify study designs that minimise NHP use. Our analysis shows that there is variation in the number of animals used for similar studies. This information has been used to develop practical guidance and make recommendations on the use of science-based rationale to design studies using fewer animals taking into account the current regulatory guidance. There are eight recommendations intended to highlight areas for consideration. They include guidance on the main group size, the inclusion of recovery groups and the number of dose groups used in short and long term chronic toxicology studies.

Dynamic Loss of H2B Ubiquitylation without Corresponding Changes in H3K4 Trimethylation during Myogenic Differentiation

ABSTRACT Ubiquitylation of H2B on lysine 120 (H2Bub) is associated with active transcriptional elongation. H2Bub has been implicated in histone cross talk and is generally regarded to be a prerequisite for trimethylation of histone 3 lysine 4 (H3K4me3) and H3K79 in both yeast and mammalian cells. We performed a genome-wide analysis of epigenetic marks during muscle differentiation, and strikingly, we observed a near-complete loss of H2Bub in the differentiated state. We examined the basis for global loss of this mark and found that the H2B ubiquitin E3 ligase, RNF20, was depleted from chromatin in differentiated myotubes, indicating that recruitment of this protein to genes substantially decreases upon differentiation. Remarkably, during the course of myogenic differentiation, we observed retention and acquisition of H3K4 trimethylation on a large number of genes in the absence of detectable H2Bub. The Set1 H3K4 trimethylase complex was efficiently recruited to a subset of genes in myotubes in the absence of detectable H2Bub, accounting in part for H3K4 trimethylation in myotubes. Our studies suggest that H3K4me3 deposition in the absence of detectable H2Bub in myotubes is mediated via Set1 and, perhaps, MLL complexes, whose recruitment does not require H2Bub. Thus, muscle cells represent a novel setting in which to explore mechanisms that regulate histone cross talk.

Neonatal Fc Receptor and its Role in the Absorption, Distribution, Metabolism and Excretion of Immunoglobulin G-Based Biotherapeutics

The neonatal Fc receptor (FcRn) is a heterodimeric membrane associated protein expressed in a variety of endothelial, epithelial and hematopoietic cells. FcRn regulates pH dependent intracellular trafficking of immunoglobulin G (IgG) and albumin, resulting in enhanced serum persistence and transcellular permeability of these proteins compared to other proteins of similar size. FcRn confers passive immunity during the early stages of life by facilitating maternal transmission of antibodies during gestation, and in some species during the neonatal period. The receptor continues to contribute to immunity beyond the perinatal period and throughout life by providing immunosurveillance in intestinal, pulmonary and genitourinary mucosa. In this capacity, FcRn facilitates bidirectional transport of IgG across mucosa and intracellular trafficking of antigen-antibody complexes in antigen presenting cells. Based on the functional roles of FcRn in regulating serum persistence and transcellular permeability, protein engineers have sought to exploit this receptor as a means of enhancing the absorption, distribution, metabolism and excretion (ADME) of IgG-based therapeutics. In this review, the current state of knowledge regarding the structural, mechanistic and functional properties of FcRn, as they relate to the ADME of IgG-based therapeutics, are discussed.

Maternal‐placental insulin‐like growth factor (IGF) signaling and its importance to normal embryo‐fetal development

As background for an antibody-based therapeutic program against the IGF receptor, we undertook a review of available information on the early pregnancy-specific regulation and localization of IGFs, IGF-binding proteins (BPs), IGFBP-specific proteases, and the type 1 IGF receptor relative to placental maintenance, function of placental nutrient transporters, placental cellular differentiation/turnover/apoptosis, and critical hormone signaling needed to maintain pregnancy. Possible adverse outcomes of altered IGF signaling include prenatal loss, fetal growth retardation, and maldevelopment are also discussed. It appears that the IGF axes in both the conceptus and mother are important for normal embryo-fetal growth. Thus, all molecules (i.e., both small and large) that disrupt the IGF axis could be expected to have some degree of fetal consequences.