Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing.

BACKGROUND: Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA sequencing for fresh frozen samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples. RESULTS: Our results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In addition, both techniques showed that the immune landscape was heterogeneous in the 6 ependymoma samples used for this study. CONCLUSIONS: The low-abundant genes were detected in higher quantities using the NanoString technique, even when FFPE samples were used. RNA sequencing is better suited for biomarker discovery, fusion gene detection, and getting a broader overview of the TIME. The technique that was used to measure the samples had a considerable effect on the type of immune cells that were identified. The limited number of tumor-infiltrating immune cells compared to the high density of tumor cells in ependymoma can limit the sensitivity of RNA expression techniques regarding the identification of the infiltrating immune cells.

Impact of atopic dermatitis and loss-of-function mutations in the filaggrin gene on the development of occupational irritant contact dermatitis.

BACKGROUND: Atopic dermatitis (AD) and loss-of-function mutations in the filaggrin gene (FLG) are both associated with chronic irritant contact dermatitis (ICD). As FLG mutations also are a major risk factor for AD, it is not clear whether FLG mutations are an independent risk factor for ICD or whether the risk is mediated by AD. OBJECTIVES: To investigate the relative contribution and interaction of FLG mutations and AD in German patients with occupational ICD and controls (vocational school apprentices). METHODS: A total of 634 patients and 393 controls were genotyped for R501X, 2282del4, R2447X and S3247X. Current or past flexural eczema was used as an indicator of AD. RESULTS: FLG mutations were found in 15·9% of the patients with ICD and 8·3% of the controls, with a crude odds ratio (OR) of 2·09 [95% confidence interval (CI) 1·33-3·28] for the combined genotype. The adjusted OR for FLG mutations, corrected for AD, was 1·62 (95% CI 1·01-2·58). Subjects with AD were at approximately three times higher risk of developing ICD than controls (OR 2·89; 95% CI 2·09-3·99). There was no evidence of an interaction between these two risk factors. CONCLUSIONS: Our results indicate that both FLG mutations and AD increase the risk of ICD. Individuals with concurrent FLG mutations and AD are at the highest risk of developing ICD.

Natural moisturizing factor components in the stratum corneum as biomarkers of filaggrin genotype: evaluation of minimally invasive methods.

BACKGROUND: The carriers of loss-of-function mutations in the filaggrin gene (FLG) have reduced levels of natural moisturizing factor (NMF) in the stratum corneum. The concentration of NMF components which are formed by filaggrin protein breakdown in the stratum corneum might therefore be useful as a biomarker of the FLG genotype. OBJECTIVES To investigate the feasibility of different sampling methods for the determination of two NMF components, 2-pyrrolidone-5-carboxylic acid (PCA) and urocanic acid (UCA), in the stratum corneum as biomarkers for the FLG genotype. METHODS: PCA and UCA from the stratum corneum were sampled by using a tape stripping technique and an extraction technique using skin patches containing potassium hydroxide (KOH). The concentrations of PCA and UCA were measured by high-performance liquid chromatography. Eleven carriers of an FLG mutation and 10 individuals wild type for the two most common FLG mutations (R501X and R2447X) [corrected] were included in the study. RESULTS: The most significant difference between the FLG genotypes was found for PCA sampled by the tape stripping technique. The mean values of PCA obtained by the tape stripping technique were, respectively, 0.18, 0.50 and 1.64 mmol g(-1) protein in homozygous (or compound heterozygous), heterozygous and wild-type genotypes (P < 0.005 homozygous vs. heterozygous; P < 0.0001 heterozygous vs. wild type). The tape stripping technique showed less intrasubject variation compared with the KOH patches, in particular when the concentrations of UCA and PCA on the tape strips were normalized for protein amount. CONCLUSIONS: The concentration of PCA in the stratum corneum collected by tape stripping showed it to be a feasible biomarker of the FLG genotype.

Loss-of-function polymorphisms in the filaggrin gene are associated with an increased susceptibility to chronic irritant contact dermatitis: a case-control study.

BACKGROUND: Polymorphisms in the filaggrin (FLG) gene, which result in loss of filaggrin production, may alter the skin barrier and are a well-known predisposing factor for atopic dermatitis. OBJECTIVES: As a compromised skin barrier and atopic dermatitis are risk factors for chronic irritant contact dermatitis (CICD), our objective was to determine whether polymorphisms in the FLG gene contribute towards susceptibility to occupational CICD. METHODS: In a case-control study, the FLG polymorphisms R501X and 2282del4 were determined in 296 patients with CICD. Two hundred and seventeen apprentices in vocational training for high-risk occupations for CICD were chosen as controls. Data on skin diseases and conditions were collected by dermatologists from patients and by means of questionnaires from controls. RESULTS: Heterozygotes for R501X and 2282del4, FLG null alleles, were more frequent among patients with CICD (12.5%) compared with controls (6.9%), resulting in an odds ratio of 1.91 (95% confidence interval 1.02-3.59). Among patients who were carriers of a FLG null allele, we found a higher lifetime prevalence of flexural eczema (62% vs. 46%; P = 0.04) and a higher atopy score (13 vs. 10 points; P = 0.05) compared with noncarriers. In the apprentice group, signs of dermatitis before the start of the vocational training were four times more prevalent in carriers (43%) than in noncarriers (10%; P < 0.001). CONCLUSIONS: Our study shows that FLG null alleles are associated with increased susceptibility to CICD; whether or not the FLG null allele is an independent risk factor needs further study.

Despite differential gene expression profiles pediatric MDS derived mesenchymal stromal cells display functionality in vitro.

Pediatric myelodysplastic syndrome (MDS) is a heterogeneous disease covering a spectrum ranging from aplasia (RCC) to myeloproliferation (RAEB(t)). In adult-type MDS there is increasing evidence for abnormal function of the bone-marrow microenvironment. Here, we extensively studied the mesenchymal stromal cells (MSCs) derived from children with MDS. MSCs were expanded from the bone-marrow of 17 MDS patients (RCC: n=10 and advanced MDS: n=7) and pediatric controls (n=10). No differences were observed with respect to phenotype, differentiation capacity, immunomodulatory capacity or hematopoietic support. mRNA expression analysis by Deep-SAGE revealed increased IL-6 expression in RCC- and RAEB(t)-MDS. RCC-MDS MSC expressed increased levels of DKK3, a protein associated with decreased apoptosis. RAEB(t)-MDS revealed increased CRLF1 and decreased DAPK1 expressions. This pattern has been associated with transformation in hematopoietic malignancies. Genes reported to be differentially expressed in adult MDS-MSC did not differ between MSC of pediatric MDS and controls. An altered mRNA expression profile, associated with cell survival and malignant transformation, of MSC derived from children with MDS strengthens the hypothesis that the micro-environment is of importance in this disease. Our data support the understanding that pediatric and adult MDS are two different diseases. Further evaluation of the pathways involved might reveal additional therapy targets.

The distribution of GABA in lumbar motoneuronal cell groups. A quantitative ultrastructural study in rat.

gamma-Aminobutyric acid (GABA)-containing profiles were identified at the ultrastructural level in rat lumbar motoneuronal cell groups by means of the postembedding immunogold technique, which is assumed to give very accurate quantitative results. It was found that 84.5% of the GABA-labeled terminals were of the F-type (containing many flattened vesicles), whereas P-type terminals (presynaptic to other terminals) constituted 9.2% of the GABAergic terminal profiles. A few of the GABA-labeled terminal profiles (1.7%) were G-type (containing many granular vesicles and presumed serotonergic), possibly indicating co-existence of GABA and serotonin. It is concluded that in spinal motoneuronal cell groups the large majority of the GABAergic terminal profiles were involved in postsynaptic inhibition of motoneurons, while only a minority was engaged in presynaptic inhibition.

A new combination of WGA-HRP anterograde tracing and GABA immunocytochemistry applied to afferents of the cat inferior olive at the ultrastructural level.

In order to identify cerebellar terminals in the cat inferior olive which contain gamma-aminobutyric acid (GABA), a technique was developed combining anterograde transport of wheatgerm agglutinine-conjugated horseradish peroxidase (WGA-HRP) with gold-immunocytochemistry. With this technique both the HRP reaction product and the immunogold labelling can be visualized in a single ultrathin section. Our results suggest that most, if not all of the WGA-HRP-labelled cerebellar terminals in the rostral medial accessory olive (MAO) and the rostral principal olive (PO) are GABAergic. In an additional experiment the GABAergic innervation of the rostral MAO was studied in combination with WGA-HRP anterograde tracing from the rostral mesencephalon. In this case the WGA-HRP-labelled terminals were never found to be GABA-positive.

Determination of polyethylene glycols of different molecular weight in the stratum corneum.

We developed a sensitive method for determination of polyethylene glycols (PEGs) of different molecular weight (MW) in the human stratum corneum (SC) obtained by tape stripping. The analysis is based on derivatization with pentafluoropropionic anhydride (PFPA) and gas chromatography-electron capture detection (GC-ECD). The identification and quantification of PEGs was done using individual oligomers. The method showed to be suitable for studying permeability in normal and impaired skin with respect to MW in the range of 150-600 Da.

Multiple types of association of photosystem II and its light-harvesting antenna in partially solubilized photosystem II membranes.

Photosystem II is a multisubunit pigment-protein complex embedded in the thylakoid membranes of chloroplasts. It utilizes light for photochemical energy conversion, and is heavily involved in the regulation of the energy flow. We investigated the structural organization of photosystem II and its associated light-harvesting antenna by electron microscopy, multivariate statistical analysis, and classification procedures on partially solubilized photosystem II membranes from spinach. Observation by electron microscopy shortly after a mild disruption of freshly prepared membranes with the detergent n-dodecyl-alpha,D-maltoside revealed the presence of several large supramolecular complexes. In addition to the previously reported supercomplexes [Boekema, E. J., van Roon, H., and Dekker, J. P. (1998) FEBS Lett. 424, 95-99], we observed complexes with the major trimeric chlorophyll a/b protein (LHCII) in a third, L-type of binding position (C2S2M0-2L1-2), and two different types of megacomplexes, both identified as dimeric associations of supercomplexes with LHCII in two types of binding sites (C4S4M2-4). We conclude that the association of photosystem II and its associated light-harvesting antenna is intrinsically heterogeneous, and that the minor CP26 and CP24 proteins play a crucial role in the supramolecular organization of the complete photosystem. We suggest that different types of organization form the structural basis for photosystem II to specifically react to changing light and stress conditions, by providing different routes of excitation energy transfer.

Energy transfer in LHCII monomers at 77K studied by sub-picosecond transient absorption spectroscopy.

Energy transfer from chlorophyll b (Chl b) to chlorophyll a (Chl a) in monomeric preparations of light-harvesting complex II (LHCII) from spinach was studied at 77 K using pump-probe experiments. Sub-picosecond excitation pulses centered at 650 nm were used to excite preferentially Chl b and difference absorption spectra were detected from 630 to 700 nm. Two distinct Chl b to Chl a transfer times, approximately 200 fs and 3 ps, were found. A clearly distinguishable energy transfer process between Chl a molecules occurred with a time constant of 18 ps. The LHCII monomer data are compared to previously obtained LHCII trimer data, and both data sets are fitted simultaneously using a global analysis fitting routine. Both sets could be described with the following time constants: 140 fs, 600 fs, 8 ps, 20 ps, and 2.9 ns. In both monomers and trimers 50% of the Chl b to Chl a transfer is ultrafast (<200 fs). However, for monomers this transfer occurs to Chl a molecules that absorb significantly more toward shorter wavelengths than for trimers. Part of the transfer from Chl b to Chl a that occurs with a time constant of 600 fs in trimers is slowed down to several picoseconds in monomers. However, it is argued that observed differences between monomers and trimers should be ascribed to the loss of some Chl a upon monomerization or a shift of the absorption maximum of one or several Chl a molecules. It is concluded that Chl b to Chl a transfer occurs only within monomeric subunits of the trimers and not between different subunits.

Xanthophylls in light-harvesting complex II of higher plants: light harvesting and triplet quenching.

A spectral and functional assignment of the xanthophylls in monomeric and trimeric light-harvesting complex II of green plants has been obtained using HPLC analysis of the pigment composition, laser-flash induced triplet-minus-singlet, fluorescence excitation, and absorption spectra. It is shown that violaxanthin is not present in monomeric preparations, that it has most likely a red-most absorption maximum at 510 nm in the trimeric complex, and that it is involved in both light-harvesting and Chl-triplet quenching. Two xanthophylls (per monomer) have an absorption maximum at 494 nm. These play a major role in both singlet and triplet transfer. These two are most probably the two xanthophylls resolved in the crystal structure, tentatively assigned to lutein, that are close to several chlorophyll molecules [Kühlbrandt, W., Wang, N. D., & Fujiyoshi, Y. (1994) Nature 367, 614-621]. A last xanthophyll contribution, with an absorption maximum at 486 nm, does not seem to play a significant role in light-harvesting or in Chl-triplet quenching. On the basis of the assumption that the two structurally resolved xanthophylls are lutein, this 486 nm absorbing xanthophyll should be neoxanthin. The measurements demonstrate that violaxanthin is connected to at least one chlorophyll a with an absorption maximum near 670 nm, whereas the xanthophylls absorbing at 494 nm are connected to at least one chlorophyll a with a peak near 675 nm.

Spectroscopic characterization of the spinach Lhcb4 protein (CP29), a minor light-harvesting complex of photosystem II.

A spectroscopic characterization is presented of the minor photosystem II chlorophyll a/b-binding protein CP29 (or the Lhcb4 protein) from spinach, prepared by a modified form of a published protocol [Henrysson, T., Schroder, W. P., Spangfort, M. & Akerlund, H.-E. (1989) Biochim. Biophys. Acta 977, 301-308]. The isolation procedure represents a quicker, cheaper means of isolating this minor antenna protein to an equally high level of purity to that published previously. The pigment-binding protein shows similarities to other related light-harvesting complexes (LHCs), including the bulk complex LHCIIb but more particularly another minor antenna protein CP26 (Lhcb5). It is also, in the main, similar to other preparations of CP29, although some significant differences are discussed. In common with CP26, the protein binds about six chlorophyll a and two chlorophyll b molecules. Two chlorophyll b absorption bands are present at 638 and 650 nm and they are somewhat more pronounced than in a recent report [Giuffra, E., Zucchelli, G., Sandonà, D., Croce, R., Cugini, D., Garlaschi, F.M., Bassi, R. & Jennings, R.C. (1997) Biochem. 36, 12984-12993]. The bands give rise to positive and negative linear dichroism, respectively; both show negative CD bands (cf. bands with similar properties at 637 and 650 nm in CP26). Chlorophyll a absorption is dominated by a large contribution at 674 nm which also shows similarities to the major band in LHCIIb and CP26, while (as for CP26) a reduction in absorption around 670 nm is observed relative to the bulk complex. Principal differences from LHCIIb and CP26, and from other CP29 preparations, occur in the carotenoid region.

Decreasing the chlorophyll a/b ratio in reconstituted LHCII: structural and functional consequences.

Trimeric (bT) and monomeric (bM) light-harvesting complex II (LHCII) with a chlorophyll a/b ratio of 0.03 were reconstituted from the apoprotein overexpressed in Escherichia coli. Chlorophyll/xanthophyll and chlorophyll/protein ratios of bT complexes and 'native' LHCII are rather similar, namely, 0.28 vs 0. 27 and 10.5 +/- 1.5 vs 12, respectively, indicating the replacement of most chlorophyll a molecules with chlorophyll b, leaving one chlorophyll a per trimeric complex. The LD spectrum of the bT complexes strongly suggests that the chlorophyll b molecules adopt orientations similar to those of the chlorophylls a that they replace. The circular dichroism (CD) spectra of bM and bT complexes indicate structural arrangements resembling those of 'native' LHCII. Thermolysin digestion patterns demonstrate that bT complexes are folded and organized like 'native' trimeric LHCII. Surprisingly, in the bT complexes at 77 K, half of the excitations that are created on either chlorophyll b or xanthophyll are transferred to chlorophyll a. No or very limited triplet transfer from chlorophyll b to xanthophyll appears to take place. However, the efficiency of triplet transfer from chlorophyll a to xanthophyll is close to 100%, even higher than in 'native' LHCII at 77 K. It is concluded from the triplet-minus-singlet and CD results that the single chlorophyll a molecule that on the average is present in each bT complex binds preferably next to a xanthophyll molecule at the interface between the monomers.