Triple helix-targeted DNA methylation with DNA methyltransferase-oligodeoxynucleotide conjugates

In this work, three bacterial DNA methyltransferases (MTases), that methylate cytosine within the CpG recognition sequence, were coupled to a triple helix-forming oligodeoxynucleotide (TFO) to create constructs for targeted DNA methylation. The constructs were designed to target and methylate a single CpG site located in the promoter region of the epithelial cell adhesion molecule (EpCAM), of which the overexpression has been found in many carcinomas and is correlated to the methylation status within the promoter region (van der Gun et al., 2008). The coupling strategy was based on the SNAP-tag technology, with which the benzylic carbon of a para-substituted benzylguanine (BG) is connected to a variant of O6-alkylguanine DNA alkyltransferase (hAGT) that is fused with a DNA MTase. The BG modification of the TFO occurred in two steps and BG-PEG35-TFO was obtained with an overall yield of 65%. SNAP-tag fusion proteins of M.SssI, M.MpeI and the low DNA affinity mutant M.MpeI(Q142L) were then coupled to the BG-modified TFO. The purification of M.SssI-TFO by anion exchange chromatography proved to be challenging and the product that was obtained with a yield of less than 5% was contaminated with BG-PEG35-TFO, which could not be removed from the product. M.SssI-TFO was therefore not further investigated. The conjugates M.MpeI-TFO and M.MpeI(Q142L)-TFO could be purified by anion exchange chromatography with a yield of 55% and 16%, respectively. The DNA methylation specificity of M.MpeI-TFO was tested in vitro with a modification-restriction assay using Litcon54 DNA, a plasmid that was designed for the TFO to bind near a CpG site, and Litcon47, a similar plasmid lacking the triple helix-forming site (TFS). The methylation status of the challenged CpG sites was verified by incubation with the CpG methylation-sensitive restriction endonuclease R.Psp1406I. The experiment was carried out on supercoiled, open-circular, and linear plasmid. Specificity towards the target site was observed with all three forms of Litcon54. Non-specific methylation was also observed and derived from methylation by both unbound and bound M.MpeI-TFO. The latter could be suppressed in linear Litcon54, which led to a higher specificity towards the target site compared to the supercoiled and open-circular forms. Preincubation of M.MpeI-TFO with linear Litcon54 did not affect the specificity. Higher amounts of NaCl in the reaction buffer, that would decrease the affinity of M.MpeI-TFO with the DNA, possibly also reduced the stability of the triple helix and therefore did not increase the specificity towards the targeted site. The highest specificity towards the targeted site was achieved with 20 eq. of M.MpeI(Q142L)-TFO and linear Litcon54. Not only was non-specific methylation by bound conjugate suppressed due to the use of linear plasmid, but also the reduced DNA binding affinity of the DNA MTase led to minimal non-specific methylation by free M.MpeI(Q142L)-TFO

Acylcarnitine Profiles in Plasma and Tissues of Hyperglycemic NZO Mice Correlate with Metabolite Changes of Human Diabetes

The New Zealand obese (NZO) mouse is a polygenic model for obesity and diabetes with obese females and obese, diabetes-prone males, used to study traits of the metabolic syndrome like type 2 diabetes mellitus (T2DM), obesity, and dyslipidaemia. By using LC-MS/MS, we here examine the suitability of this model to mirror tissue-specific changes in acylcarnitine (AC) and amino acid (AA) species preceding T2DM which may reflect patterns investigated in human metabolism. We observed high concentrations of fatty acid-derived ACs in 11 female mice, high abundance of branched-chain amino acid- (BCAA-) derived ACs in 6 male mice, and slight increases in BCAA-derived ACs in the remaining 6 males. Principal component analysis (PCA) including all ACs and AAs confirmed our hypothesis especially in plasma samples by clustering females, males with high BCAA-derived ACs, and males with slight increases in BCAA-derived ACs. Concentrations of insulin, blood glucose, NEFAs, and triacylglycerols (TAGs) further supported the hypothesis of high BCAA-derived ACs being able to mirror the onset of diabetic traits in male individuals. In conclusion, alterations in AC and AA profiles overlap with observations from human studies indicating the suitability of NZO mice to study metabolic changes preceding human T2DM

ACYLCARNITINE AND AMINO ACID PROFILING IN PLASMA AND TISSUES OF NZO MICE AS A MODEL FOR OBESITY-INDUCED TYPE 2 DIABETES

Metabolomics has identified biomarkers in human plasma with a predictive quality for type 2 diabetes (T2D) development. Amongst these markers are various acylcarnitine species, most prominently those derived from branched-chain amino acid (BCAA) breakdown. The metabolic perturbations in tissues underlying these changes in plasma are often unknown and hard to assess in humans. Thus, animal models are used to have access to the different tissues. In contrast to diet-induced obesity models or monogenetic mouse models of obesity and diabetes, the New Zealand Obese (NZO) mouse is a prototypical polygenic model for obesity, with a male-specific susceptibility to developing diabetes. We have used this model to study the metabolic alterations in obesity-induced diabetes for changes in tissue-specific acylcarnitine and amino acid profiles. Twelve male and 11 female NZO mice at an age of 8 weeks were fed a chemically-defined high carbohydrate diet for 12 weeks. Acylcarnitine and amino acid profiles were obtained from plasma, skeletal muscle, heart muscle, liver, kidney and adipose tissues, using a high-resolution LC-MS/MS method. This method covered around 35 amino acids and 43 acylcarnitine species originating from fatty acids and amino acids, as well as odd-numbered and dicarboxylic acylcarnitines. Furthermore, blood glucose, plasma insulin, non-esterified fatty acids (NEFA), triglyceride and urea concentrations were measured. Hierarchical cluster analysis of principle components derived from plasma samples revealed a grouping of normoglycemic females, normoglycemic males and hyperglycemic males and this originated mainly from differences in concentrations of acylcarnitines derived from BCAAs and odd-numbered short- and medium-chain fatty acids. Hyperglycemic males were characterized by high insulin levels and low levels of NEFAs. These findings largely match with findings in humans. Comparison of metabolite profiles in diabetic and non-diabetic male mice revealed the largest overlap of significant metabolite changes between plasma and liver, including longer-chain odd-numbered acylcarnitine species. In conclusion, the alterations in acylcarnitine and amino acid profiles in NZO mice largely overlap with findings in humans, suggesting similar underlying metabolic perturbations in this diabetes model as compared to humans. The metabolite profiling of individual tissues in this model suggests a specific role of the liver in the generation of odd-numbered fatty acylcarnitines

Approximate energy functionals for one-body reduced density matrix functional theory from many-body perturbation theory

We develop a systematic approach to construct energy functionals of the one-particle reduced density matrix (1RDM) for equilibrium systems at finite temperature. The starting point of our formulation is the grand potential Ω[G] regarded as variational functional of the Green’s function G based on diagrammatic many-body perturbation theory and for which we consider either the Klein or Luttinger–Ward form. By restricting the input Green’s function to be one-to-one related to a set on one-particle reduced density matrices (1RDM) this functional becomes a functional of the 1RDM. To establish the one-to-one mapping we use that, at any finite temperature and for a given 1RDM γ in a finite basis, there exists a non-interacting system with a spatially non-local potential v[γ] which reproduces the given 1RDM. The corresponding set of non-interacting Green’s functions defines the variational domain of the functional Ω. In the zero temperature limit we obtain an energy functional E[γ] which by minimisation yields an approximate ground state 1RDM and energy. As an application of the formalism we use the Klein and Luttinger–Ward functionals in the GW-approximation to compute the binding curve of a model hydrogen molecule using an extended Hubbard Hamiltonian. We compare further to the case in which we evaluate the functionals on a Hartree–Fock and a Kohn–Sham Green’s function. We find that the Luttinger–Ward version of the functionals performs the best and is able to reproduce energies close to the GW energy which corresponds to the stationary point.peerReviewe

Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause

International audienceEmbryonic diapause in mammals leads to a reversible developmental arrest. While completely halted in many species, European roe deer ( Capreolus capreolus ) embryos display a continuous deceleration of proliferation. During a 4-mo period, the cell doubling time is 2 to 3 wk. During this period, the preimplantation blastocyst reaches a diameter of 4 mm, after which it resumes a fast developmental pace to subsequently implant. The mechanisms regulating this notable deceleration and reacceleration upon developmental resumption are unclear. We propose that amino acids of maternal origin drive the embryonic developmental pace. A pronounced change in the abundance of uterine fluid mTORC1-activating amino acids coincided with an increase in embryonic mTORC1 activity prior to the resumption of development. Concurrently, genes related to the glycolytic and phosphate pentose pathway, the TCA cycle, and one carbon metabolism were up-regulated. Furthermore, the uterine luminal epithelial transcriptome indicated increased estradiol-17β signaling, which likely regulates the endometrial secretions adapting to the embryonic needs. While mTORC1 was predicted to be inactive during diapause, the residual embryonic mTORC2 activity may indicate its involvement in maintaining the low yet continuous proliferation rate during diapause. Collectively, we emphasize the role of nutrient signaling in preimplantation embryo development. We propose selective mTORC1 inhibition via uterine catecholestrogens and let-7 as a mechanism regulating slow stem cell cycle progression