A distinctive epigenetic ageing profile in human granulosa cells.

STUDY QUESTION: Does women's age affect the DNA methylation (DNAm) profile differently in mural granulosa cells (MGCs) from other somatic cells? SUMMARY ANSWER: Accumulation of epimutations by age and a higher number of age-related differentially methylated regions (DMR) in MGCs were found compared to leukocytes from the same woman, suggesting that the MGCs have a distinctive epigenetic profile. WHAT IS KNOWN ALREADY: The mechanisms underlying the decline in women's fertility from the mid-30s remain to be fully elucidated. The DNAm age of many healthy tissues changes predictably with and follows chronological age, but DNAm age in some reproductive tissues has been shown to depart from chronological age (older: endometrium; younger: cumulus cells, spermatozoa). STUDY DESIGN, SIZE, DURATION: This study is a multicenter cohort study based on retrospective analysis of prospectively collected data and material derived from healthy women undergoing IVF or ICSI treatment following ovarian stimulation with antagonist protocol. One hundred and nineteen women were included from September 2016 to June 2018 from four clinics in Denmark and Sweden. PARTICIPANTS/MATERIALS, SETTING, METHODS: Blood samples were obtained from 118 healthy women with varying ovarian reserve status. MGCs were collected from 63 of the 119 women by isolation from pooled follicles immediately after oocyte retrieval. DNA from leukocytes and MGCs was extracted and analysed with a genome-wide methylation array. Data from the methylation array were processed using the ENmix package. Subsequently, DNAm age was calculated using established and tailored age predictors and DMRs were analysed with the DMRcate package. MAIN RESULTS AND ROLE OF CHANCE: Using established age predictors, DNAm age in MGCs was found to be considerable younger and constant (average: 2.7 years) compared to chronological age (average: 33.9 years). A Granulosa Cell clock able to predict the age of both MGCs (average: 32.4 years) and leukocytes (average: 38.8 years) was successfully developed. MGCs differed from leukocytes in having a higher number of epimutations (P = 0.003) but predicted telomere lengths unaffected by age (Pearson's correlation coefficient = -0.1, P = 0.47). DMRs associated with age (age-DMRs) were identified in MGCs (n = 335) and in leukocytes (n = 1) with a significant enrichment in MGCs for genes involved in RNA processing (45 genes, P = 3.96 × 10-08) and gene expression (152 genes, P = 2.3 × 10-06). The top age-DMRs included the metastable epiallele VTRNA2-1, the DNAm regulator ZFP57 and the anti-Müllerian hormone (AMH) gene. The apparent discordance between different epigenetic measures of age in MGCs suggests that they reflect difference stages in the MGC life cycle. LARGE SCALE DATA: N/A. LIMITATIONS, REASONS FOR CAUTION: No gene expression data were available to associate with the epigenetic findings. The MGCs are collected during ovarian stimulation, which may influence DNAm; however, no correlation between FSH dose and number of epimutations was found. WIDER IMPLICATIONS OF THE FINDINGS: Our findings underline that the somatic compartment of the follicle follows a different methylation trajectory with age than other somatic cells. The higher number of epimutations and age-DMRs in MGCs suggest that their function is affected by age. STUDY FUNDING/COMPETING INTEREST(S): This project is part of ReproUnion collaborative study, co-financed by the European Union, Interreg V ÖKS, the Danish National Research Foundation and the European Research Council. The authors declare no conflict of interest.

Rare genetic variants suggest dysregulation of signaling pathways in low- and high-risk patients developing severe ovarian hyperstimulation syndrome.

PURPOSE: To investigate if rare gene variants in women with severe ovarian hyperstimulation syndrome (OHSS) provide clues to the mechanisms involved in the syndrome. METHODS: Among participants in a prospective randomized study (Toftager et al. 2016), six women with predicted low and six women with predicted high risk of OHSS developing severe OHSS (grades 4 and 5, Golan classification) were selected. In the same cohort, six plus six matched controls developing no signs of OHSS (Golan grade 0) were selected. Whole-exome sequencing was performed. Analysis using a predefined in silico OHSS gene panel, variant filtering, and pathway analyses was done. RESULTS: We found no convincing monogenetic association with the development of OHSS using the in silico gene panel. Pathway analysis of OHSS variant lists showed substantial overlap in highly enriched top pathways (p value range p < 0.0001 and p > 9.8E-17) between the low- and high-risk group developing severe OHSS, i.e., "the integrin-linked kinase (ILK) signaling pathway" and the "axonal guidance signaling pathway," both being connected to vasoactive endothelial growth factor (VEGF) and endothelial function. CONCLUSION: Rare variants in OHSS cases with two distinct risk profiles enrich the same signaling pathways linked to VEGF and endothelial function. Clarification of the mechanism as well as potentially defining genetic predisposition of the high vascular permeability is important for future targeted treatment and prevention of OHSS; the potential roles of ILK signaling and the axonal guidance signaling need to be validated by functional studies.

Prediction of three-dimensional structure of plant lectins from the domains of concanavalin A.

The circularly permuted sequence homology that relates concanavalin A to the other leguminous plant lectins can be explained by an evolutionary model that requires three exons. The identification of these potential exons from the amino acid sequence data allows the prediction of three domains in the lectin structure. The predicted domains are reasonable, functional and structural units in concanavalin A, demonstrating the correspondence of exons and domains. In addition, slight modifications to the three-dimensional structure of concanavalin A produced a model which was consistent with the sequence data for the other plant lectins.

Internal residue criteria for predicting three-dimensional protein structures.

The internal amino acid residues of proteins are almost always non-polar since the hydrophobic effect is very important in stabilizing the three-dimensional structure. This fact suggests several new criteria for judging the correctness of structures predicted from sequence data. The dinucleotide binding domain has been used as a test structure for these criteria. The percentage of ionic residues, mutation data, hydrophobicity, dipole moments, and internal preferences of the residues on the interiors of the known dinucleotide binding folds are consistent with expectations. On the other hand, the values of these parameters for predicted domains in glutamate dehydrogenase (Wootton, J.C. (1974) Nature 252, 542--546) and aldolase (Stellwagen, E. (1976) J. Mol. Biol. 106, 903--911) differ significantly from the expected values indicating that these predictions are not entirely correct. The internal residue criteria can then be used to test modifications of the predictions for a better correlation with the internal residue pattern of the domain.

Crystal structure of Lysbeta(1)82-Lysbeta(2)82 crosslinked hemoglobin: a possible allosteric intermediate.

The crystal structure of human hemoglobin crosslinked between the Lysbeta82 residues has been determined at 2.30 A resolution. The crosslinking reaction was performed under oxy conditions using bis(3, 5-dibromosalicyl) fumarate; the modified hemoglobin has increased oxygen affinity and lacks cooperativity. Since the crystallization occurred under deoxy conditions, the resulting structure displays conformational characteristics of both the (oxy) R and the (deoxy) T-states. beta82XLHbA does not fully reach its T-state conformation due to the presence of the crosslink. The R-state-like characteristics of deoxy beta82XLHbA include the position of the distal Hisbeta63 (E7) residue, indicating a possible reason for the high oxygen affinity of this derivative. Other areas of the molecule, particularly those thought to be important in the allosteric transition, such as Tyrbeta145 (HC2) and the switch region involving Proalpha(1)44 (CD2), Thralpha(1)41 (C6) and Hisbeta(2)97 (FG4), are in intermediate positions between the R and T-states. Thus, the structure may represent a stabilized intermediate in the allosteric transition of hemoglobin.

Crystallization and preliminary X-ray analysis of peanut agglutinin-N6-benzylaminopurine complex.

Preliminary diffraction data collected on peanut agglutinin (PNA) crystals grown in the presence of N6-benzylaminopurine (BAP) indicate a monoclinic cell (P2) with a = 67.0 A, b = 35.2 A, c = 65.8 A and beta = 68.6 degrees. This is the first example of a legume lectin crystallized with a bound phytohormone. Crystals of PNA grown previously in the presence of lactose had an orthorhombic space group (P2(1)2(1)2) with a = 128.8 A, b = 126.0 A and c = 76.1 A and one tetramer per asymmetric unit. The Vm value for the PNA-BAP crystals is 2.62 A3/Da, assuming one monomer of PNA per asymmetric unit. Thus, while the PNA-lactose complex crystallized as tetramers, the PNA-BAP complex has, at most, dimers in the crystal. These results indicate that BAP, a naturally occurring phytohormone, can modify the quaternary structure of PNA by dissociation and change its carbohydrate valence.

A spectrophotometric assay for the degradation of the siderophore deferrioxamine B.

A spectrophotometric assay using ferric perchlorate in a perchloric acid solution has been developed to monitor the degradation of the trihydroxamate siderophore deferrioxamine B to monohydroxamates. Using the ferric perchlorate solution and employing various concentrations of acetohydroxamic acid (as the model monohydroxamic acid) while maintaining a constant amount of deferrioxamine B resulted in the shifting of the absorption maximum from that of ferrioxamine B to longer wavelengths and toward that of a pure ferri-acetomonohydroxamic acid solution. A similar result was noted when a cell-free extract, from a bacterium capable of using deferrioxamine B as its sole carbon source, was given the siderophore in a phosphate buffer and aliquots of the enzyme-deferrioxamine B solution were removed for analysis. The assay may thus be used to monitor the formation of the monohydroxamic acid degradation products of the siderophore by the enzyme(s) in the cell-free extract.

Structural basis for the thermal stability of glyceraldehyde-3-phosphate dehydrogenases.

The amino acid sequences of two thermophilic and five mesophilic glyceraldehyde-3-phosphate dehydrogenases have been compared with the known three-dimensional structure of this enzyme to determine the factors responsible for thermal stability. The changes are greatest in the S-loop regions at the center of the tetramer, which show a quantitative increase in hydrophobicity and polarity that can strengthen subunit interactions in a complementary manner. The S-loops also show increases in residue volume and bulk that may indicate a tighter packing at the molecular center. In addition, there are changes in the secondary structural parameters indicating that the helices, in particular, may be more stable in the thermophilic proteins. Increases in the hydrophobicity of domain and subunit contacts for the Thermus aquaticus glyceraldehyde-3-phosphate dehydrogenase may explain why it is the most thermostable protein in this series.

Enzymatic protection from autoxidation for crosslinked hemoglobins.

The autoxidation rates of hemoglobins crosslinked between the alpha subunits (alpha 99XLHb A) and between the beta subunits (beta 82XLHb A) were reduced in the presence of catalase and/or superoxide dismutase. In the presence of catalase the rate for alpha 99XLHb A decreased 2.3 fold and for beta 82XLHb A, 1.9 fold. Superoxide dismutase reduced the rate 1.6 fold for alpha 99XLHb A and 1.8 fold for beta 82XLHb A. In the presence of both catalase and superoxide dismutase the rate of autoxidation decreased by 3.0 fold in alpha 99XLHb A and 4.0 fold in beta 82XLHb A. The presence of catalase and superoxide dismutase or both in the crosslinked hemoglobin samples increases the autoxidation half-life of oxyhemoglobins. This suggests that crosslinked hemoglobins to be used as blood substitutes could be protected from oxidation in storage by these enzymes.

Thermal stabilities of hemoglobins crosslinked with different length reagents.

Bis(3,5-dibromosalicyl) succinate and glutarate were used to crosslink met-, oxy- and deoxyhemoglobins. The added flexibility of these reagents compared to the fumarate analog resulted in a more heterogeneous product but did not greatly affect the maximum thermal stability of the crosslinked hemoglobins.

The modification of hemoglobin by a long crosslinking reagent: bis(3,5-dibromosalicyl) sebacate.

Bis(3,5-dibromosalicyl) sebacate is a bifunctional protein crosslinking reagent. It reacts with oxy form of human hemoglobin A to produce a crosslinked hemoglobin between two beta chains in the 2,3-bisphosphoglycerate binding cleft, decreasing the oxygen affinity. The oxygen binding curve of crosslinked hemoglobin had a P50 of 18.5 mmHg compared to a P50 of 11.0 mmHg for native hemoglobin and remains highly cooperative, n = 2.2. Crosslinking hemoglobin between the two beta chains also results in a 12.5 degrees C increase in the thermal denaturation temperature. The crosslinked hemoglobin is oxidized more rapidly to methemoglobin. Its autoxidation rate in 0.01 M MOPS, pH 7.4, at 37 degrees C was 1.4 times as fast as that of Hb A.

Thermal stability of hemoglobin crosslinked in the T-state by bis(3,5-dibromosalicyl) fumarate.

Bis(3,5-dibromosalicyl) fumarate was used to crosslink oxyhemoglobin between Lys 82 beta 1 and Lys 82 beta 2 (Walder, J. A., et al. (1979) Biochemistry 18, 4265) and deoxyhemoglobin between Lys 99 alpha 1 and Lys 99 alpha 2 (Chatterjee R.Y., et al. (1986) J. Biol. Chem. 261, 9929). Thermal denaturations demonstrated that alpha crosslinked hemoglobin (alpha 99XLHb A) has the same stability as the beta crosslinked one (beta 82XLHb A). Both alpha and beta crosslinked methemoglobins have a denaturation temperature in 0.9 M guanidine of 57 degrees C compared to 41 degrees C of Hb A. The second product from the T-state crosslinking reaction was found to be crosslinked between the beta chains by chain separation and amino acid analysis. The possible positions for this crosslink are limited to the bisphosphoglycerate binding site in the three-dimensional structure. Its stability is comparable to that of the alpha 99XLHb A or beta 82XLHb A. These modified hemoglobins are potential blood substitutes.

Effects of crosslinking on the thermal stability of hemoglobin. I. The use of bis(3,5-dibromosalicyl) fumarate.

The double-headed aspirin, bis(3,5-dibromosalicyl) fumarate, has been used to crosslink hemoglobin A between Lys 82 beta 1 and Lys 82 beta 2 (J. A. Walder et al. (1979) Biochemistry 18,4265). Denaturation experiments were used to compare the stability of this crosslinked protein to that of hemoglobin A. Thermal denaturations, done in 0.01 M 4-morpholine-propanesulfonic acid, pH 7, containing 0.9 M guanidine to prevent precipitation at high temperatures, were monitored by changes in absorbance between 190 and 650 nm using a diode array spectrophotometer. The sample was heated from 25 to 70 degrees C at 0.3 degrees C/min. The data were analyzed by using both a two-state model and a novel first derivative method. As expected, methemoglobin A had a single, broad transition with a midpoint of 40.7 degrees C. The crosslinked methemoglobin showed a transition at 57.1 degrees C. Two minor transitions, one of which was apparently due to residual unmodified hemoglobin, were also observed in the crosslinked sample. Thus, a single crosslink between only two of the four subunits can lead to a significantly more stable molecule. These results can be explained by Le Chatelier's principle, since crosslinking prevents dissociation of the beta-subunits and, thereby, holds the entire tetramer together.