An association between chronic widespread pain and the gut microbiome

OBJECTIVES

Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP.

METHODS

CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterized using 16S rRNA amplicon sequencing and amplicon sequence variants, and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors.

RESULTS

Alpha diversity was significantly lower in CWP cases than controls (Mann-Whitney test, P-values 2.3e-04 and 1.2e-02, for Shannon and Simpson indices respectively). The species Coprococcus comes was significantly depleted in CWP cases (Padj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, P = 7.4e-8). A Mendelian randomization study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP.

CONCLUSIONS

We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.

Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips

Background: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.

Results: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript.

Conclusions: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras.

Using surveys of Affymetrix GeneChips to study antisense expression

We have used large surveys of Affymetrix GeneChip HG-U133_Plus_2 data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription.

We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA.

In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts.

Using surveys of Affymetrix GeneChips to study antisense expression

We have used large surveys of Affymetrix GeneChip data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription. We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA. In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts.

On the causes of outliers in Affymetrix GeneChip data

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips.

Hybridization and cell uptake studies with radiolabelled antisense oligonucleotides

BACKGROUND

Radiolabelled antisense oligonucleotides have been proposed as radiopharmaceuticals for imaging changes in the level of gene expression in vivo. This paper describes a study of the uptake of radiolabelled oligonucleotides in cell lines expressing different levels of the target mRNA.

METHODS

A 15-mer phosphorodiester deoxyoligonucleotide antisense to c-myc was labelled with 99mTc and 32P. Hybridization and stability studies were performed in vitro. Cell uptake studies were carried out in a c-myc expressing transformed rat embryonic fibroblast cell-line, TGR-1, and a knock-out cell line HO15.19 which does not express c-myc.

RESULTS

The oligonucleotides were efficiently labelled with both radionuclides and retained their ability to hybridize with their complementary mRNA when extracted from cell lines. The radiolabelled oligonucleotides were stable for a few hours in human serum. No statistically significant difference was found between the uptake of radioactivity by the two cell lines.

CONCLUSIONS

Although able to bind efficiently to their target in cell-free systems, radiolabelled oligonucleotides may be prevented from performing effectively as radiopharmaceutical vectors by the barriers imposed by cell membranes and/or intracellular metabolism.

Photoreduction of monoclonal antibodies for conjugation and fragmentation

The conjugation of enzymes, fluorescent or radioactive labels, cross-linkers and other moieties to antibodies is a commonly performed procedure in biochemical research. Using reduced disulphides, conjugation can be an inconvenient, multistep, time- and material-consuming process. We have developed a reduction technique based on UV irradiation, which lacks these drawbacks. Antibodies are irradiated in a sealed vial for a few minutes by a common laboratory UV source in the presence of stannous ions, following the depletion of atmospheric oxygen. The preparation may subsequently be conjugated with thiol-reactive probes such as maleimide derivatives, with no need for any prior purification or concentration. This simple, rapid and effective reduction and conjugation process results in a fully functional immunoglobulin conjugate that can be used for a variety of biochemical applications.

Comparison of the stability of technetium-labeled peptides to challenge with cysteine

We have labeled a series of short peptides with technetium-99m either by direct labeling at pH 11 or by exchange from [99mTc]technetium glucoheptonate. Typical labeling yields obtained were as follows: N-acetyl-Gly-Cys(S-Acm)-Gly-Cys(S-Acm)-Gly-NH2 (Acm = acetamidomethyl) 99%, S-benzoyl-mercaptoacetyltriglycine (S-Benzoyl-MAG3) 95%, mercaptoacetyldiglycine-NH2 (MAG2-NH2) 94%, MAG3 92%, N-acetyl-Aib-Aib-Cys-NH2 (Aib = aminoisobutyric acid) 91%, Gly-Gly-Gly-Gly 90%, N-acetyl-Gly-Gly-Cys-Gly 87%, cyclo-1, 4-(Gly-Gly-Gly-Gln) 40%, S-methyl-MAG2-NH2 0%. In the absence of cysteine, all of the labeled peptides were quite stable in solution, with at least 80-90% of the labeled peptide remaining at 24 h. The order of stability of the labeled peptides to challenge with cysteine was found to be MAG3 > S-benzoyl-MAG3 > N-acetyl-Gly-Cys(S-Acm)-Gly-Cys(S-Acm)-Gly-NH2 >N-acetyl-Aib-Aib-Cys-NH2 > MAG2-NH2 > N-acetyl-Gly-Gly-Cys-Gly > cyclo-1,4-(Gly-Gly-Gly-Gln) > Gly-Gly-Gly-Gly. The peptides without a sulfur donor were least stable to challenge with cysteine.

Uptake of 99Tcm-nitrido dithiocarbamate complexes by tumour cells

Uptake of radiopharmaceuticals by tumour cells may provide useful information on the biochemical characteristics of the cell, such as its drug resistance status. We have prepared a series of 99Tcm-nitrido dithiocarbamate complexes of the type [99TcmN(dtc)2] (dtc = N-R1-N-R2-dithiocarbamato, R1, R2 = Me, Me; Et, Et; Et, n-Bu; Me, CH2CH2NMe2; Me, CH2CH2NMe3+; Me, CH2COOMe), and investigated the kinetics of uptake of these complexes in several tumour cell lines. The 99Tcm-nitrido dithiocarbamate complexes were prepared by stannous reduction of [99Tcm]pertechnetate in a solution of DPTA and succinic dihydrazide followed by addition of the appropriate dithiocarbamate. The complexes were analysed by reverse-phase HPLC. The complexes were incubated with the human tumour cell lines MKN-45, H-69, H-348 and MCF-7 and with normal mixed leukocytes and erythrocytes, and the uptake and washout of the various complexes were determined at various time points. Uptake was rapid, high in some cell lines and lower in others. In general, the more lipophilic complexes showed high uptake, but the most lipophilic did not show the greatest uptake. Uptake was temperature-independent. Most of the bound activity was retained by the cells after removal of unbound tracer. The mechanism of uptake is different to that of 99Tcm-MIBI. The high and stable uptake of these complexes suggests that they may have application for in vivo tumour imaging and characterization, and further studies are required to establish their mechanisms of uptake.

Site-specific conjugation and labelling of prostate antibody 7E11C5.3 (CYT-351) with technetium-99m

Attachment of chelating agents to the sugar residues of antibodies for subsequent radiolabelling is an attractive approach since it may have less effect on the immunoreactivity than attachment through lysine residues, which are distributed throughout the antibody and may be present near the antigen binding site. We have attached a new hydrazide-linked chelator CYT-395 (Cytogen Corp., Princeton, N.J.) to the sugar residues of the anti-prostate monoclonal antibody 7E11C5.3 and optimised the conditions for labelling the conjugate with technetium-99m in order to compare the conjugate to 7E11C5.3 antibody labelled directly with technetium using a mercaptoethanol reduction technique. Labelling yields of 70%-90% were obtained at specific activities up to 2000 MBq/mg antibody. The stability of the technetium-labelled conjugate in plasma or to a challenge with 0.1 or 1.0 mM cysteine was similar to that of direct-labelled antibody. In nine patients with prostate cancer, the plasma clearance of the labelled conjugate followed a two-compartment model, with an average beta-phase half-life of 31.4+/-3.9 h. The average urinary clearance at 24 h was 15.3+/-5.0% of the injected dose. In this group of patients there was no significant difference between the blood and urine clearance of the labelled conjugate, and the clearances of the direct-labelled antibody.

Technetium-99m labelling of the anti-tumour antibody PR1A3 by photoactivation

Irradiation of antibody with ultraviolet light leads to reduction of disulphide bonds. Thus irradiation can be used to generate free thiols prior to direct labelling of antibody with technetium-99m, and has a potential advantage over methods using chemical reducing agents such as mercaptoethanol or tin, in that no purification step is needed to remove excess reducing agent. We have used the photoactivation method developed by Sykes et al. to label the anti-tumour antibody PR1A3 with 99mTc. The antibody was irradiated at 300 nm using a Rayonet photochemical reactor with eight RMR3000 lamps. In a typical experiment, the antibody solution was injected into a nitrogen-filled borosilicate glass vial and purged with nitrogen. A degassed solution containing stannous fluoride and methylene diphosphonate was then added to the antibody and the vial was irradiated. Following the irradiation, [99mTc]pertechnetate was injected into the vial and the reaction mixture was incubated for 30 min at room temperature before being analysed by size-exclusion high-pressure liquid chromatography and instant thin-layer chromatography. Labelling yields greater than 95% were obtained using antibody concentrations ranging from 0.5mg/ml to 5mg/ml. Irradiation times as short as 5 min and tin to antibody ratios in the range between 11 and 32 microg tin per mg antibody gave high labelling yields. Labelling yields greater than 95% were obtained after storage of the photoactivated antibody at -70 degrees C for several weeks. The stability of the 99mTc-labelled photoactivated PR1A3 was similar to that of 99mTc-labelled mercaptoethanol-reduced PR1A3. The mean immunoreactive fraction was 77% for the photoactivation-labelled PR1A3, compared to 93% for PR1A3 labelled by mercaptoethanol reduction. Biodistribution studies were carried out using 99mTc-photoactivation-labelled PR1A3 or PR1A3 labelled by mercaptoethanol reduction in Balb/c mice and in nude mice with MKN-45 human tumour xenografts. There was no significant difference in tumour uptake between the mice that received photoactivated PR1A3 and those that received mercaptoethanol-reduced PR1A3. There was also no significant difference in uptake in most organs in Balb/c mice; however, the photoactivated antibody cleared more rapidly from the blood, and whole-body clearance was also faster for the photoactivated PR1A3. In conclusion, the photoactivation technique provides a very convenient "one-pot" method for labelling antibodies with 99mTc.

A cross-linked monoclonal antibody fragment for improved tumor targeting

Cross-linked F(ab')2 fragments derived from PR1A3, a murine monoclonal antibody used in radioimmunoscintigraphy of colorectal tumors, were produced using the bifunctional reagent bismaleimidohexane (BMH) as follows: Digestion of PR1A3 with pepsin gave F(ab')2 fragments which were purified by ion-exchange chromatography. Fab' was produced by reduction of F(ab')2 with cysteine. Following reaction with BMH, cross-linked F(ab')2 fragments, XL-F(ab')2, were isolated by preparative size-exclusion HPLC. Analysis by HPLC and SDS-PAGE demonstrated the presence of a molecule of approximately 100 kDa containing a nonreducible 50,000 MWt chain. Competitive and direct radioligand binding assays demonstrated that the XL-F(ab')2 had a capacity to bind to antigen similar to that of unmodified F(ab')2. The biodistribution of 125I-labeled XL-F(ab')2 and unmodified F(ab')2 was compared in a nude mouse human tumor xenograft model at 4, 24, and 48 h after injection. Differences between the two preparations were most significant after 24 or 48 h. Tumor uptake of the XL-F(ab')2 was greater and normal tissue retention less than with the unmodified fragment. Tumor to normal tissue ratios at 48 h ranged from 6.2 to 35.2 for XL-F(ab')2 while for the normal F(ab')2 they ranged from 1.5 to 14.2. These results suggest that cross-linked antibody fragments may produce better tumor targeting in clinical application.

HPLC assay of melatonin in plasma with fluorescence detection

We report an HPLC assay for melatonin that incorporates automated injection, methanol/water mobile phase, and fluorescence detection. Plasma samples were extracted by solid and liquid phases. Recovery was > 70% for 1-10 mL of plasma extracted, approximately 40 pg-250 ng of melatonin. Samples were dried and reconstituted in 100 mL/L methanol. Injections were 25 microL or 150 microL, depending on sample concentration, and the melatonin peak was eluted in 380 mL/L methanol. The detection limit of the assay was 6 pg on the column, allowing a practical sensitivity in plasma of 11 pmol/L for 8-mL samples and 34 pmol/L for 2-mL samples. More than 100 plasma samples from volunteers and patients were assayed and the results compared with an established RIA. The mean daytime concentration of melatonin was 20.7 pmol/L (SEM = 1.2) and 18.5 pmol/L (SEM = 1.6) for HPLC and RIA, respectively, and the mean nighttime concentration was 82.4 pmol/L (SEM = 6.5) and 82.2 (SEM = 7.3), respectively.

HPLC assay of melatonin in plasma with fluorescence detection

We report an HPLC assay for melatonin that incorporates automated injection, methanol/water mobile phase, and fluorescence detection. Plasma samples were extracted by solid and liquid phases. Recovery was > 70% for 1-10 mL of plasma extracted, approximately 40 pg-250 ng of melatonin. Samples were dried and reconstituted in 100 mL/L methanol. Injections were 25 microL or 150 microL, depending on sample concentration, and the melatonin peak was eluted in 380 mL/L methanol. The detection limit of the assay was 6 pg on the column, allowing a practical sensitivity in plasma of 11 pmol/L for 8-mL samples and 34 pmol/L for 2-mL samples. More than 100 plasma samples from volunteers and patients were assayed and the results compared with an established RIA. The mean daytime concentration of melatonin was 20.7 pmol/L (SEM = 1.2) and 18.5 pmol/L (SEM = 1.6) for HPLC and RIA, respectively, and the mean nighttime concentration was 82.4 pmol/L (SEM = 6.5) and 82.2 (SEM = 7.3), respectively.