PPARalpha /gamma ragaglitazar eliminates fatty liver and enhances insulin action in fat-fed rats in the absence of hepatomegaly

Peroxisome proliferator-activated receptor (PPAR)alpha and PPARgamma agonists lower lipid accumulation in muscle and liver by different mechanisms. We investigated whether benefits could be achieved on insulin sensitivity and lipid metabolism by the dual PPARalpha/gamma agonist ragaglitazar in high fat-fed rats. Ragaglitazar completely eliminated high-fat feeding-induced liver triglyceride accumulation and visceral adiposity, like the PPARalpha agonist Wy-14643 but without causing hepatomegaly. In contrast, the PPARgamma agonist rosiglitazone only slightly lessened liver triglyceride without affecting visceral adiposity. Compared with rosiglitazone or Wy-14643, ragaglitazar showed a much greater effect (79%, P < 0.05) to enhance insulin's suppression of hepatic glucose output. Whereas all three PPAR agonists lowered plasma triglyceride levels and lessened muscle long-chain acyl-CoAs, ragaglitazar and rosiglitazone had greater insulin-sensitizing action in muscle than Wy-14643, associated with a threefold increase in plasma adiponectin levels. There was a significant correlation of lipid content and insulin action in liver and particularly muscle with adiponectin levels (P < 0.01). We conclude that the PPARalpha/gamma agonist ragaglitazar has a therapeutic potential for insulin-resistant states as a PPARgamma ligand, with possible involvement of adiponectin. Additionally, it can counteract fatty liver, hepatic insulin resistance, and visceral adiposity generally associated with PPARalpha activation, but without hepatomegaly.     

Alternating Planarity/Nonplanarity in n-Doped Odd-Membered, All-Trans Polyenes: Molecular Structures of NaCnHn+2 (n = 3, 5, 7, and 9)

The electronic structures of small, odd-membered, all-trans polyenes doped with one Na atom at various positions have been investigated using Hartree-Fock and density functional (B3LYP) theory with a 6-31G(d) basis set. Two distinctly different structural motifs have been identified. In one motif, the dopant atom interacts with an allylic polyene unit in a 4-electron interaction that results in a planar polyene backbone. The other motif has the dopant atom interacting with a pentadienyl polyene unit in a 6-electron interaction, which produces a significantly warped polyene backbone. Independent of structural motif at the doping site, the portion of the polyene structure outside the interaction region remains largely undisturbed in terms of planarity and bond length alternation. For a particular formula unit and potential energy surface, the stationary points corresponding to minima and transition states are remarkably close in energy despite the pronounced changes that occur in the dihedral angles of the polyene backbone at the dopant sites. Whereas internal and external instabilities are found in the Hartree-Fock wavefunctions for NaC₇H₉ and NaC₉H₁₁ structures, the restricted B3LYP wavefunctions are stable for all structures investigated.Electronic Supplementary Material available.     

The Endogenous and Cell Cycle-dependent Phosphorylation of tau Protein in Living Cells: Implications for Alzheimer’s Disease

In Alzheimer’s disease the neuronal microtubule-associated protein tau becomes highly phosphorylated, loses its binding properties, and aggregates into paired helical filaments. There is increasing evidence that the events leading to this hyperphosphorylation are related to mitotic mechanisms. Hence, we have analyzed the physiological phosphorylation of endogenous tau protein in metabolically labeled human neuroblastoma cells and in Chinese hamster ovary cells stably transfected with tau. In nonsynchronized cultures the phosphorylation pattern was remarkably similar in both cell lines, suggesting a similar balance of kinases and phosphatases with respect to tau. Using phosphopeptide mapping and sequencing we identified 17 phosphorylation sites comprising 80–90% of the total phosphate incorporated. Most of these are in SP or TP motifs, except S214 and S262. Since phosphorylation of microtubule-associated proteins increases during mitosis, concomitant with increased microtubule dynamics, we analyzed cells mitotically arrested with nocodazole. This revealed that S214 is a prominent phosphorylation site in metaphase, but not in interphase. Phosphorylation of this residue strongly decreases the tau–microtubule interaction in vitro, suppresses microtubule assembly, and may be a key factor in the observed detachment of tau from microtubules during mitosis. Since S214 is also phosphorylated in Alzheimer’s disease tau, our results support the view that reactivation of the cell cycle machinery is involved in tau hyperphosphorylation.     

High-performance liquid chromatographic analysis of melatonin in human plasma and rabbit serum with on-line column enrichment

This paper describes the development of a simple and sensitive analytical method for the quantification of melatonin in human plasma and rabbit serum, using standard analytical equipment and on-line column enrichment without prior extraction, clean-up or derivatization. The analytical procedure was found to be accurate, precise and linear. For human plasma, the accuracy was 101% (range 89–106%), and the mean precision was 5% (range 2–9%) for all concentrations (0, 2, 10, 50 and 200 ng/ml) tested (n=6). The accuracy in rabbit serum was 101% (range 90–112%), and the mean precision was 13% (range 8–19%) for all concentrations (0, 2, 10, 50, 200 and 500 ng/ml) tested (n=6). The retention time of melatonin was about 8 min and the total recoveries were found to be approximately 65 and 85%, respectively, for human plasma and rabbit serum. The limit of detection was found to be lower than 1 ng/ml for human plasma and around 2 ng/ml for rabbit serum. The method is, therefore, found to be suitable for melatonin bioavailability studies in rabbits and presumably also in humans.     

Characterization of HTT Inclusion Size,Location, and Timing in the zQ175 Mouse Model of Huntington′s Disease: An In Vivo High-Content Imaging Study

Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin gene. Major pathological hallmarks of HD include inclusions of mutant huntingtin (mHTT) protein, loss of neurons predominantly in the caudate nucleus, and atrophy of multiple brain regions. However, the early sequence of histological events that manifest in region- and cell-specific manner has not been well characterized. Here we use a high-content histological approach to precisely monitor changes in HTT expression and characterize deposition dynamics of mHTT protein inclusion bodies in the recently characterized zQ175 knock-in mouse line. We carried out an automated multi-parameter quantitative analysis of individual cortical and striatal cells in tissue slices from mice aged 2–12 months and confirmed biochemical reports of an age-associated increase in mHTT inclusions in this model. We also found distinct regional and subregional dynamics for inclusion number, size and distribution with subcellular resolution. We used viral-mediated suppression of total HTT in the striatum of zQ175 mice as an example of a therapeutically-relevant but heterogeneously transducing strategy to demonstrate successful application of this platform to quantitatively assess target engagement and outcome on a cellular basis.     

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

HLA class I molecules reflect the health state of cells to cytotoxic T cells by presenting a repertoire of endogenously derived peptides. However, the extent to which the proteome shapes the peptidome is still largely unknown. Here we present a high-throughput mass-spectrometry-based workflow that allows stringent and accurate identification of thousands of such peptides and direct determination of binding motifs. Applying the workflow to seven cancer cell lines and primary cells, yielded more than 22,000 unique HLA peptides across different allelic binding specificities. By computing a score representing the HLA-I sampling density, we show a strong link between protein abundance and HLA-presentation (p < 0.0001). When analyzing overpresented proteins – those with at least fivefold higher density score than expected for their abundance – we noticed that they are degraded almost 3 h faster than similar but nonpresented proteins (top 20% abundance class; median half-life 20.8h versus 23.6h, p < 0.0001). This validates protein degradation as an important factor for HLA presentation. Ribosomal, mitochondrial respiratory chain, and nucleosomal proteins are particularly well presented. Taking a set of proteins associated with cancer, we compared the predicted immunogenicity of previously validated T-cell epitopes with other peptides from these proteins in our data set. The validated epitopes indeed tend to have higher immunogenic scores than the other detected HLA peptides. Remarkably, we identified five mutated peptides from a human colon cancer cell line, which have very recently been predicted to be HLA-I binders. Altogether, we demonstrate the usefulness of combining MS-analysis with immunogenesis prediction for identifying, ranking, and selecting peptides for therapeutic use.The highly polymorphic Human Leukocyte Antigen class I (HLA-I)¹ genes are encoded by three loci (HLA-A, B, and C) in a gene-rich region on chromosome 6. They produce up to six unique cell surface receptors that bind and present the so-called HLA class I peptidome, which consists of peptides derived from proteolysis of intracellular proteins. Their function is to reflect the health state of the body''s cells to CD8+ cytotoxic T cells. During thymic maturation T cells that react to self-peptides are eliminated (1), leaving T cells with the capability to recognize peptides from viruses and bacteria. This recognition is interpreted as a danger signal, leading to removal of infected cells. Transformed, preneoplastic and cancer cells also tend to display atypical self-peptides from mutated or excessively expressed self-proteins, known as tumor associated antigens (TAAs). Although HLA-I molecules are indispensable in prevention of disease, they also pose a substantial health problem by causing allergies (2), life-threatening autoimmune diseases (3), and the often fatal rejection of donor organs because of recognition of both major and minor histocompatibility antigens (4).Finding the rules for peptide generation and selection is regarded as the most important open issue in the field of HLA-I biology by leading experts (5). Although the antigen presentation pathway is well characterized, it is still unclear how basic properties such as protein abundance, turnover, and subcellular localization influence and shape the HLA-I presented peptidome (6–10). One expectation is that protein abundance should correlate with presentation (11), but previous studies have reported conflicting and contradicting results that mostly argue against a strong link (6, 7, 10, 12, 13). It is also not fully understood why only some HLA-sampled self-peptides from cancer antigens spontaneously activate T cells, whereas others do not.The majority of HLA-I peptides are derived from proteasomal degradation (5). Although the proteasome generates an excess of peptides, only some have the required sequence motifs for HLA binding, resulting in a selective sampling of available peptides (14). The presented peptides are typically nine amino acids long, but the length can range from eight to 15. The high degree of genetic variance of HLA-I receptors translates into allele-specific peptide-binding motifs defined by anchor positions, which are usually the second and the last positions in a peptide (15). Each cell has around 200,000 cell-surface-expressed HLA complexes, which bind about 10,000 unique peptide sequences (16). The affinity of a peptide toward the presenting HLA molecule does not correlate strongly with its immunogenicity, and neither does the number of presented HLA complexes (17). Instead, the most robust predictor of peptide immunogenicity appears to be the number of potential reactive T-cell clones (17–19).The longer the source protein, the higher the chances it will contain sequences that fit to a certain HLA motif, which would inflate the representation of longer proteins regardless of biological role. Furthermore, some HLA-I peptide sequences can be mapped to multiple proteins, potentially causing a problem in determining the number of observed HLA peptides per protein (13). This illustrates that careful accounting of the potentially and actually presented HLA peptides is important in properly delineating trends in propensity of peptide presentation.In cancer immunotherapy, T cells can be directed against tumors, based on the pattern of cancer associated HLA peptides. Therefore, there is great interest in determining the identity of these immunogenic peptides. Bioinformatic methods that attempt to predict HLA peptides of cancer proteins of interest are easily accessible and most commonly used. They typically score sequences with respect to proteasomal degradation, transport into the ER via the transporter associate with antigen processing (TAP) and binding to different HLA-I alleles (20). However, their precision success is modest (21, 22). The second approach is to directly capture the naturally presented peptides using mass spectrometry; however, this requires the relevant biological sample and sophisticated instruments and workflows, which have become accessible only recently for large-scale work (23–28). Although identification of cancer associated HLA peptides by MS, if performed stringently, establish the in vivo existence of the peptide, it still does not guarantee that it will elicit a potent T-cell response, which is required for further development into therapeutics (29). Therefore, like in the case of in silico predicted peptides, the immunogenicity of the peptides must in any case be tested empirically.We here present a rich and high confidence HLA-I peptidome, established by applying state-of-the-art mass-spectrometric techniques on a collection of seven cell lines. We investigate how abundance affects the propensity of proteins to be presented as measurable HLA peptides and whether or not there are specific protein classes that are overrepresented even independent of abundance. Likewise, we explore how to use in silico immunogenicity tools on the set of identified HLA peptides from cancer-associated proteins, with a view to select vaccine candidates.     

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.