Myelin basic protein has lectin-like properties

Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies

Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework. By integrating DE and GSE analyses, iDEA can improve the power and consistency of DE analysis and the accuracy of GSE analysis. Importantly, iDEA uses only DE summary statistics as input, enabling effective data modeling through complementing and pairing with various existing DE methods. We illustrate the benefits of iDEA with extensive simulations. We also apply iDEA to analyze three scRNA-seq data sets, where iDEA achieves up to five-fold power gain over existing GSE methods and up to 64% power gain over existing DE methods. The power gain brought by iDEA allows us to identify many pathways that would not be identified by existing approaches in these data.

Differential expression (DE) and gene set enrichment (GSE) analysis tend to be carried out separately. Here, the authors present iDEA (integrative Differential expression and gene set Enrichment Analysis) for the analysis of scRNAseq data which uses a Baysian approach to jointly model DE and GSE for improved power in both tasks.

Interaction between oligodendroglia and immune cells: mitogenic effect of an oligodendrocyte precursor cell line on syngeneic T lymphocytes

We analyzed cellular interactions between T lymphocytes and a recently established immortal glial line, L3 that retains several properties of immature oligodendrocytes (Aloisi et al., J Neurosci Res 27:16-24, 1990). L3 oligodendrocytes (L3-OL) cannot be induced to express class II antigens, nor do they specifically present antigen to syngeneic specific T lymphocyte. However, L3-OL strongly enhance the proliferation of freshly activated, interleukin-2(IL-2)-dependent T-line lymphocytes and concanavalin A (ConA)-activated lymphoblasts, irrespective of their antigen specificity or surface phenotype (CD4+ or CD8+). Resting and some activated T cells were susceptible to the mitogenic effect of L3-OL only in the presence of exogenous IL-2, not of other cytokines. The mitogenic effect of L3-OL did not depend on cell viability. It was observed in paraformaldehyde-fixed L3-OL cells and in membrane preparations, but not in culture supernatant. Neither intact L3-OL cells nor membrane preparations had direct IL-2 activity. The conclusion that the mitogenic effect of L3-OL cells is exerted by membrane structures acting as a costimulatory factor(s) of IL-2 is supported by the finding that it is largely blocked by a monoclonal anti-IL-2 receptor antibody. The effect is distinct from membrane-bound IL-1, membrane-bound tumor necrosis factor-alpha (TNF-alpha), IL-3, or IL-6 and cannot be reconstituted by these cytokines.

On the spontaneous adherence of myelin basic protein to T lymphocytes

We have applied a double tagging system in order to study whether purified myelin basic protein is able to adhere to normal human peripheral T lymphocytes without the need to purify cells. Evaluation of myelin basic protein adherence to peripheral blood mononuclear cells was determined with biotinylated myelin basic protein and fluoresceinated avidin, and lymphocyte population was identified by the corresponding phycoerythrinated monoclonal antibody. The observed adherence of myelin basic protein to T lymphocytes was found to depend on protein conformation.

Folding and function of the myelin proteins from primary sequence data

To explain how the myelin proteins are involved in the organization and function of the myelin sheath requires knowing their molecular structures. Except for P2 basic protein of PNS myelin, however, their structures are not yet known. As an aid to predicting their molecular folding and possible functions, we have developed a FORTRAN program to analyze the primary sequence data for proteins, and have applied this to the myelin proteins in particular. In this program, propensities for the secondary structure conformations as well as physical-chemical parameters are assigned to the amino acids and the pattern of these parameters is examined by calculating their average values, autocorrelation functions and Fourier transforms. To compare two proteins, their sequences are aligned using a unitary scoring matrix, and homologies are searched by plotting a two-dimensional map of the correlation coefficients. Comparison of the corresponding myelin basic proteins (MBP) and P0 glycoproteins (P0) for rodent and shark showed that the conserved residues included most of the amino acids which were predicted to form the alpha or beta conformations, while the altered residues were mainly in the hydrophilic and turn or coil regions. In both rodent and shark the putative extracellular domain of P0 glycoprotein displayed consecutive peaks of beta propensity similar to that for the immunoglobulins, while the cytoplasmic domain showed alpha-beta-alpha folding. To trace the immunoglobulin fold along the P0 sequence, we compared the beta propensity curve of P0 with that of the immunoglobulin M603, whose three-dimensional structure has been determined. We propose that the flat beta-sheets of P0 are orientated parallel to the membrane surface to facilitate their homotypic interaction in the extracellular space. An extra beta-fold in the extracellular domain of shark P0 compared with rodent P0 was found, and this may result in a greater attraction between the apposed extracellular surfaces and may account for a smaller extracellular space as measured by x-ray diffraction. A computer search of the myelin protein sequences for functional motifs revealed sites for N-glycosylation, phosphorylation, nucleotide binding, and certain enzyme activities. We note especially that there are potential nucleotide binding sites in proteolipid protein (PLP), MBP and 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). This is consistent with the experimental observations that PLP acts like an ionophore or proton channel when reconstituted into planar lipid bilayers, MBP binds GTP, and CNP catalyzes in vitro the hydrolysis of 2',3'-nucleotides into corresponding 2'-nucleotides.

Detection and mapping of endogenous receptors for carrier-immobilized constituents of glycoconjugates (lectins) by labelled (neo)glycoproteins and by affinity chromatography in human adult mesencephalon, pons, medulla oblongata and cerebellum

Different carrier-immobilized carbohydrate moieties were employed as tools to detect respective binding sites glycohistochemically and glycobiochemically. Besides ascertaining their presence the pattern of endogenous sugar receptors (lectins) in different regions of the human central nervous system was mapped to reveal any non-uniform expression. A strong and specific staining with biotinylated neoglycoproteins, exposing different sugar moieties as ligands, indicated the presence of sugar receptors in the nuclei, neuronal pathways and accessory structures such as ependyma cells, plexus chorioideus, intra- and extracerebral vessels and leptomeninges localized in the mesencephalon, in the pons, in the medulla oblongata and in the cerebellum. Significant differences were seen for various neuroanatomical regions like nerve cells in the basal and central regions of the nuclei pontis in the glycohistochemically detected level of expression of endogenous sugar receptors (lectins). The used approach with carbohydrate constituents of cellular glycoconjugates as ligands in search of specific receptors complemented studies on the localization of glycoconjugates with sugar-specific tools like plant lectins. Exemplary glycobiochemical investigations on the medulla oblongata and cerebellum were performed to investigate the molecular nature of sugar receptors detected glycohistochemically. Despite notable overall similarities, carbohydrate-binding proteins of differing molecular weight can be isolated from these two regions of the central nervous system, namely in the case of receptors with specificity to beta-galactoside termini, to N-acetyl-D-galactosamine and N-acetyl-D-glucosamine and to D-xylose. These combined glycohistochemical and glycobiochemical results serve as a guideline for exploring the physiological relevance of the detected regional differences.

Regional differences in the distribution of endogenous receptors for carbohydrate constituents of cellular glycoconjugates, especially lectins, in cortex, hippocampus, basal ganglia and thalamus of adult human brain

Ten different types of labelled neoglycoproteins, exposing glycohistochemically pivotal carbohydrate moieties that mostly are constituents of naturally occurring glycoconjugates with an aromatic spacer, were synthesized. The panel was applied to fixed, paraffin-embedded sections of different cortical regions and white matter, of hippocampal gyrus, basal ganglia, thalamus nuclei and adjacent areas of adult human brain to comprehensively map the presence of respective binding sites in these parts. Compliance with accepted criteria for specificity of binding was routinely ascertained. Overall, not a uniform binding pattern, but a distinct distribution with regional differences on the level of specific cytoplasmic and nuclear staining in nerve cells was determined, fiber structures being generally labelled with medium or strong intensity. For example, among the neurons localized in the five cortical laminae the binding of N-acetyl-D-galactosamine varied from strong to undetectable. Biochemical analysis, employing carbohydrate residues as affinity ligands in chromatography, proved that the neuroanatomically different regions exhibited a pattern of receptors with notable similarities. These results on endogenous binding sites for glycoconjugates, especially lectins, are complementary to assessment of localization of cellular glycoconjugates by plant lectins and carbohydrate-specific monoclonal antibodies. They are thus a further obligatory step to substantiate the physiological roles of recognitive protein-carbohydrate interactions in the central nervous system.

Lactose- and heparin-inhibitable agglutinin from human fetal brain

An agglutinin activity which was sensitive to lactose and heparin was estimated during prenatal brain development. The agglutinin showed higher specific activities in cerebral cortex and midbrain. There was an increase in lectin specific activity in all the brain regions with development. In addition to brain, other fetal organs also showed the presence of developmentally regulated agglutinin. Cerebral cortical agglutinin was purified by Sepharose CL-6B gel filtration and asialofetuin- and heparin-Sepharose affinity chromatography. Purified agglutinin was strongly inhibited by lactose, asialofetuin, and heparin. It showed no requirement for divalent cations and was maximally active at pH 8.0. Electrophoretic characterization showed the aggregate nature of the agglutinin, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave subunit molecular weights of 58,000, 45,000, and 24,000.

Endogenous sugar receptor pattern in human glioblastomas and gangliocytomas studied by histochemical application of biotinylated (neo)glycoproteins and affinity chromatography

Biotinylation of chemically glycosylated bovine serum albumin, yielding a panel of neoglycoproteins, and of desialylated, naturally occurring glycoproteins allowed to systematically evaluate presence and distribution of various types of endogenous sugar receptors in the sections of human glioblastomas and gangliocytomas by a routine histochemical procedure. Pronounced cytoplasmic staining with markers, carrying constituents of natural glycoconjugates, e.g. for beta-galactoside-specific receptors, contrasted with the different intensities, noticed for alpha- and beta-glucoside-specific receptors. Significant qualitative differences between the two tumor types were detected with N-acetyl-D-galactosamine- and sialic acid-carrying probes. Nuclear staining with only a part of the applied panel underscored the specificity of the protein-carbohydrate interaction. Fine structural features of the synthetic neoglycoproteins, e.g. the mode of coupling of the carbohydrate moiety to the protein, were found to exert a significant influence on their suitability as histochemical markers. On the basis of the histochemical results, exemplary biochemical analysis of certain classes of endogenous sugar receptors by affinity chromatography and subsequent gel electrophoresis, namely of beta-galactoside-, alpha-fucoside-, alpha-mannoside- and alpha-glucoside-specific proteins, revealed presence and characteristics of respective sugar receptors that can contribute to the histochemical staining. Similar extent of histochemical staining with the respective probes notwithstanding, the different tumor types exhibited qualitative differences in the expression of individual endogenous sugar receptors. The combined histochemical and biochemical analysis is supposed to be of conspicuous value for biological and clinical investigations on endogenous sugar receptors.

Comparative histochemical and biochemical analysis of endogenous receptors for glycoproteins in human and pig peripheral nerve

Endogenous sugar-binding proteins were localized in sections of human and pig peripheral nerves by the application of two types of labelled ligands: neoglycoproteins (chemically glycosylated carrier proteins that had proven to be histochemically inert) and desialylated, naturally occurring glycoproteins. These proteins allowed evaluation of the presence and distribution of endogenous receptors for carbohydrates, commonly present in cellular glycoconjugates. (Neo)glycoprotein binding was similar, but not identical, for the two types of mammalian peripheral nerves. The pig nerve differed from the human nerve in more pronounced staining when using different types of beta-galactoside-terminated (neo)glycoproteins and charge-carrying neoglycoproteins, such as bovine serum albumin, bearing galactose-6-phosphate residues, glucuronic acid residues, and sialic acid residues. Comparative biochemical analysis of certain classes of sugar receptors by affinity chromatography and gel electrophoresis revealed the presence of sugar receptors that can contribute to the histochemical staining in a pattern with certain significant differences among rather similar expression for the two species. The assessment of sugar receptor distribution by application of (neo)glycoprotein binding among morphologically defined regions in nerves may hold promise in detecting developmental regulation and changes during nerve degeneration and subsequent regeneration after trauma or pathological states. Correlation of these results to changes in the structure and abundance of glycoconjugates, which are the potential physiological ligands of endogenous sugar receptors commonly detected by plant lectins, may help to infer functional relationships.

Induction of experimental autoimmune encephalomyelitis in guinea pigs using myelin basic protein and myelin glycolipids

Strain 13 guinea pigs were immunized with galactocerebroside, asialo-GM1 (GA1) or GM4 ganglioside in association with myelin basic protein (MBP) in complete Freund's adjuvant (CFA) to produce experimental autoimmune encephalomyelitis (EAE). The clinical and pathological features, serum antibodies, and lipid compositions of affected brains and spinal cords were compared with those of guinea pigs immunized with MBP, in CFA, alone. Perivascular demyelination was seen in brains from all guinea pigs immunized with GA1/MBP. The incidence and degree of demyelination in this group were significantly higher than in the group immunized with only MBP. The onset of EAE was slightly, but significantly, retarded in groups of animals immunized with GM4/MBP and there was no detectable demyelination. Otherwise, no significant differences were detected between groups. Augmentation of EAE by myelin glycolipids may provide some important clues in understanding the mechanism of demyelinating diseases.