Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis

To better understand the compositional and structural dynamics of the human spliceosome during its activation, we set out to isolate spliceosomal complexes formed after precatalytic B but prior to catalytically active C complexes. By shortening the polypyrimidine tract of the PM5 pre-mRNA, which lacks a 3' splice site and 3' exon, we stalled spliceosome assembly at the activation stage. We subsequently affinity purified human B(act) complexes under the same conditions previously used to isolate B and C complexes, and analyzed their protein composition by mass spectrometry. A comparison of the protein composition of these complexes allowed a fine dissection of compositional changes during the B to B(act) and B(act) to C transitions, and comparisons with the Saccharomyces cerevisiae B(act) complex revealed that the compositional dynamics of the spliceosome during activation are largely conserved between lower and higher eukaryotes. Human SF3b155 and CDC5L were shown to be phosphorylated specifically during the B to B(act) and B(act) to C transition, respectively, suggesting these modifications function at these stages of splicing. The two-dimensional structure of the human B(act) complex was determined by electron microscopy, and a comparison with the B complex revealed that the morphology of the human spliceosome changes significantly during its activation. The overall architecture of the human and S. cerevisiae B(act) complex is similar, suggesting that many of the higher order interactions among spliceosomal components, as well as their dynamics, are also largely conserved.

Exon definition complexes contain the tri-snRNP and can be directly converted into B-like precatalytic splicing complexes

The first step in splicing of pre-mRNAs with long introns is exon definition, where U1 and U2 snRNPs bind at opposite ends of an exon. After exon definition, these snRNPs must form a complex across the upstream intron to allow splicing catalysis. Exon definition and conversion of cross-exon to cross-intron spliceosomal complexes are poorly understood. Here we demonstrate that, in addition to U1 and U2 snRNPs, cross-exon complexes contain U4, U5, and U6 (which form the tri-snRNP). Tri-snRNP docking involves the formation of U2/U6 helix II. This interaction is stabilized by a 5' splice site (SS)-containing oligonucleotide, which can bind the tri-snRNP and convert the cross-exon complex into a cross-intron, B-like complex. Our data suggest that the switch from cross-exon to cross-intron complexes can occur directly when an exon-bound tri-snRNP interacts with an upstream 5'SS, without prior formation of a cross-intron A complex, revealing an alternative spliceosome assembly pathway.

RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core

Although U snRNAs play essential roles in splicing, little is known about the 3D arrangement of U2, U6, and U5 snRNAs and the pre-mRNA in active spliceosomes. To elucidate their relative spatial organization and dynamic rearrangement, we examined the RNA structure of affinity-purified, human spliceosomes before and after catalytic step 1 by chemical RNA structure probing. We found a stable 3-way junction of the U2/U6 snRNA duplex in active spliceosomes that persists minimally through step 1. Moreover, the formation of alternating, mutually exclusive, U2 snRNA conformations, as observed in yeast, was not detected in different assembly stages of human spliceosomal complexes (that is, B, B(act), or C complexes). Psoralen crosslinking revealed an interaction during/after step 1 between internal loop 1 of the U5 snRNA, and intron nucleotides immediately downstream of the branchpoint. Using the experimentally derived structural constraints, we generated a model of the RNA network of the step 1 spliceosome, based on the crystal structure of a group II intron through homology modelling. The model is topologically consistent with current genetic, biochemical, and structural data.

Thermodynamic Analysis of the Impact of the Surfactant−Protein Interactions on the Molecular Parameters and Surface Behavior of Food Proteins

This paper reports on the thermodynamics of the interactions between surfactants (anionic, CITREM, SSL; nonionic, PGE; zwitterionic, phospholipids) and food proteins (sodium caseinate, legumin) depending on the chemical structure and molecular state (individual molecules, micelles) of the surfactants and the molecular parameters (conformation, molar mass, charge) of the proteins under changes of pH in the range from 7.2 to 5.0 and temperature from 293 to 323 K. The marked effect of the protein-surfactant interactions on the molecular parameters (the weight-average molar mass, the gyration and hydrodynamic radii) and the thermodynamic affinity of the proteins for an aqueous medium were determined by a combination of static and dynamic laser light scattering. Thermodynamically justified schematic sketches of the molecular mechanisms of the complex formation between like-charged proteins and surfactants have been proposed. In response to the complex formation between the proteins and the surfactants, the more stable and fine foams have been detected generally.

A case of HHV-8-associated HIV-negative primary effusion lymphoma in Moscow

Primary effusion lymphoma is a rare tumor of B-cell derivation which is associated with human herpes virus type 8 (HHV-8) in 100% and with human immunodeficiency virus (HIV) in most of cases. The paper describes the first case in Russia of HIV(-) HHV-8(+) Epstein-Barr virus (EBV)(+) primary effusion lymphoma in a male patient aged 56 years. The tumor was located in the pleural cavity. Interestingly, the patient was HIV-negative while having a positive tumor HHV-8 test. There are only 22 similar cases described worldwide.

The relationship between the structure and functionality of essential PUFA delivery systems based on sodium caseinate with phosphatidylcholine liposomes without and with a plant antioxidant: an in vitro and in vivo study

The aim of this work was to establish the main relationship between the structure and functionality of supramolecular complexes formed by sodium caseinate (SC) with phosphatidylcholine (PC) liposomes filled with fish oil (FO) to an equal mass ratio of n-3 to n-6 polyunsaturated fatty acids (PUFA) in the absence and presence of one of the most effective plant antioxidants, namely the essential oil of clove buds (EOC). The functionality of the supramolecular complexes (SC-PC-FO and SC-PC-FO-EOC) was considered from the point of view of the possibility of their use as effective delivery systems for long-chain n-3 PUFAs (eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids from FO). The laser light scattering method was used in the static, dynamic and electrophoretic modes to characterize the structure and thermodynamic parameters of the supramolecular complexes in an aqueous medium. It was found that the SC-PC-FO and SC-PC-FO-EOC complex particles had the following similar properties: nanosize; a spherical shape; 100% solubility in an aqueous medium (pH 7.0, ionic strength = 0.001 M); a high encapsulating ability of SC (up to 70%) in relation to the studied liposomes; and a high protective ability relative to lipid autooxidation (up to 96% on the 20th day of storage at room temperature in light). In addition, a sequential transformation of both the structural and thermodynamic parameters has been observed for the complex particles under in vitro simulated gastrointestinal (GI) conditions in accordance with the INFOGEST protocol. A greater release of the encapsulated lipids from the enzymatically hydrolyzed complex particles was observed at the small intestine stage compared to their release at the gastric stage. These data were in good agreement with those on the assessment of the bioavailability of the target PUFAs in in vivo experiments based on the chronic intake of aqueous solutions of the complexes (both SC-PC-FO and SC-PC-FO-EOC) by experimental mice for 92 days. Liver lipid profiles of the mice, obtained by gas-liquid chromatography, showed the following: (i) an almost twofold increase in the DHA content as compared with that of the control; (ii) an almost threefold decrease in the mass ratio of arachidonic acid (AA) (C20:4 n-6) to DHA (C22:6 n-3) compared to that of the control due to both a significant decrease in the AA content and a simultaneous pronounced increase in the DHA content; and (iii) an almost twofold decrease in the mass ratio of the total amounts of n-6 to n-3 PUFAs compared to that of the control.

Key structural factors and intermolecular interactions underlying the formation, functional properties and behaviour in the gastrointestinal tract in vitro of the liposomal form of nutraceuticals coated with whey proteins and chitosan

The aim of this study was to gain a better understanding of the key structural factors and intermolecular interactions underlying the formation, functionality, and in vitro gastrointestinal behaviour of the liposomal form of nutraceuticals coated with whey proteins (WPI) and chitosan (CHIT). Phosphatidylcholine (PC) liposomes were used to encapsulate a combination of hydrophobic and hydrophilic nutraceuticals. The hydrophobic constituents were long-chain (LC) n-3 PUFAs (DHA and EPA) from fish oil (FO), vitamin D3, and clove essential oil (CEO), while the hydrophilic component was γ-aminobutyric acid (GABA). A combination of physicochemical methods was used to achieve this goal, including electron paramagnetic resonance spectroscopy (EPRS), laser light scattering in dynamic, static, and electrophoretic modes, transmission electron microscopy, spectrophotometry and tensiometry. The efficiency of encapsulating the nutraceuticals in PC liposomes simultaneously was as follows: 100 ± 1% for both FO triglycerides and CEO, 82 ± 2% for vitamin D3, and 50 ± 1% for GABA. According to EPRS data, encapsulating LC PUFA reduced microviscosity at a depth of 20 Å in the PC bilayer. The co-encapsulation of other nutraceuticals in PC liposomes at selected concentrations did not alter this effect. The upper part (8 Å) of PC liposome bilayers showed an increase in rigidity parameter S, indicating the presence of D3, CEO, and partially GABA. The liposome layer-by-layer encapsulation efficiency (EE%) was achieved by using WPI to form the binary complex [WPI-(PC-FO-D3-GABA-CEO)] (EE = 50% at pH 7.0 and I = 0.001 M), followed by coating with chitosan to form the ternary complex [WPI-(PC-FO-D3-GABA-CEO)]-CHIT (EE = 80% at pH 5.1 and I = 0.001 M). The biopolymer-coated liposomes displayed high water solubility owing to their submicron sizes, thermodynamic affinity for the aqueous medium, and 20 mV ζ-potential values. The chitosan shell regulated the release of liposomes from the ternary complex during in vitro gastrointestinal digestion. In the stomach, the hydrolysis of chitosan by pepsin resulted in a 40% release of liposomes. In the small intestine, chitosan was separated from the WPI-liposome core, facilitatig its hydrolysis and resulting in a 60% release of liposomes. The bioavailability of nutraceuticals encapsulated in PC liposomes in the small intestine may be enhanced by the interactions of both non-hydrolysed and hydrolysed liposomes with bile salts and mucin.

Added prognostic value of sentinel lymph node mapping in endometrial cancer to molecular subgroups

OBJECTIVE

Treatment approaches for endometrial cancer became more personalized in the last decade, mainly due to two key advancements - sentinel lymph node (SLN) mapping and molecular classification. However, their prognostic interaction remains relatively unexplored.

METHODS

This retrospective cohort study included patients with endometrial cancer, who underwent surgical treatment including SLN mapping at the Bern University Hospital, Switzerland. Ultrastaging of the SLNs and a molecular analysis on the primary tumor was performed.

RESULTS

The study cohort included 206 patients, of which 197 tumor samples underwent molecular classification. 11.2 % were classified as POLEmut, 25.9 % as MMRd, 46.2 % as NSMP, and 16.8 % as p53abn. Overall, 834 SLN were removed. SLN macrometastasis were most prevalent in patients with p53abn tumors (24.2 %), followed by MMRd (13.7 %), NSMP (5.5 %), and POLEmut (0 %) tumors (p = .006). Mean follow-up time was 70.9 months. SLN macrometastasis was significantly associated with a higher risk of recurrence in the entire study cohort (p > .001) and the NSMP subgroup (p > .001). In the MMRd subgroup, SLN macrometastasis remained a significant predictor of recurrence (p = .030) and disease-specific death (p = .047) in multivariate Cox regression analysis. For patients with p53abn endometrial cancer, there was no association between SLN macrometastasis and risk of recurrence (p = .618) or disease specific death (p = .798).

CONCLUSIONS

SLN macrometastasis is an independent predictor of recurrence and disease-specific death in patients with MMRd endometrial cancer. In the subgroup of p53abn endometrial cancers, SLN macrometastasis did not have an added impact on oncological outcome.