Abstract
A nationwide tuberculosis outbreak linked to a viable bone allograft product contaminated with Mycobacterium tuberculosis was identified in June 2021. Our subsequent investigation identified ...73 healthcare personnel with new latent tuberculosis infection following exposure to the contaminated product, product recipients, surgical instruments, or medical waste.
BackgroundFaecal calprotectin (FCAL) rises rapidly in children with Crohn’s disease (CD) following treatment with exclusive enteral nutrition (EEN). We aimed to identify clinical, dietary and ...diet-related microbial metabolites which associate with the recurrence of FCAL above 250 mg/kg after 21 days of food reintroduction.MethodsChildren with CD (age 6–17 years), clinically responding to EEN, were recruited, prospectively, from 11 UK hospitals (January 2020-May 2023, NCT04225689). They provided a single faecal sample before EEN completion (timepoint A) and 6 serial samples (timepoints B-G; 3, 6, 9, 12, 15, 21 days) in the first 21 days of food reintroduction. Faecal short (SCFA) and branched (BCFA) chain fatty acids were measured as proxies of fibre and protein bacterial fermentation, respectively. In faeces, pH, water content (%), Bristol stool score, total microbial load (qPCR) and starch output were measured. Clinical parameters, medications, CRP, ESR, albumin and anthropometry were recorded at EEN completion. Nutrient and food group intake was analysed with Nutritics®. Relationships with FCAL levels were explored.Results Thirty children provided 209/210 (99%) of expected faecal samples. FCAL (median Q1, Q3, mg/kg) increased within 12 days of food reintroduction (EEN completion: 328 154, 2370 vs 12 days post-EEN: 1123 (451, 2073), p<0.01) and remained high throughout follow-up. Negative correlations were observed between FCAL with acetate, whereas positive correlations were noted with BCFA (isovalerate and isobutyrate) and their ratio over acetate; the latter remained significant at all 7 timepoints (figure 1A). Use of immunosuppressants, blood inflammatory markers, clinical and anthropometry at EEN completion were not predictive of FCAL increase post-EEN.In a subset of patients with FCAL<250 mg/kg at EEN completion, (n=13/30), subset regression using ‘end of EEN’ diet-related microbial data, generated a model with 91% accuracy to predict FCAL increase over 250 mg/kg at 21 days of food reintroduction, with isovalerate being the sole predictor of FCAL recurrence (figure 1B). Average intake of cereal products (median Q1, Q3, g/day) over 21 days was lower in patients who experienced an FCAL recurrence (FCAL<250mg/kg: 313 (223, 370) vs FCAL>250mg/kg: 186 (167, 217), p=0.013). Positive correlations were observed between the 21-day average intake of cereal products and concentration of SCFA at 21 days post-EEN; acetate (rho=0.38, p=0.041), butyrate (rho=0.46, p=0.0.01) and total SCFA (rho=0.41, p=0.026).ConclusionsThis study suggests that early FCAL rebound, following treatment with EEN, is related to an increased ratio of dietary protein to fibre bacterial fermentation and a lower intake of cereal products.Abstract OC2 Figure 1(A): Correlations between faecal parameters and FCAL at EEN completion (Time-point A) and food reintroduction (Time-points B-G) after adjustment for multiple comparisons (Benjamini-Hochberg). (B): Subset regression analysis using end-of-EEN data to predict FCAL recurrence (FCAL>250mg/kg at day 21)
BackgroundExclusive enteral nutrition (EEN) is a main therapy for active Crohn’s disease (CD) in children, but normalisation of faecal calprotectin (FCAL) varies among patients, even in those who ...enter clinical remission. To better understand disease characteristics related to EEN efficacy and its mechanism of action, we compared clinical and microbial parameters between patients whose FCAL normalised against those who did not at EEN completion.MethodsChildren with CD, clinically responding to EEN, were recruited from 11 UK hospitals (January 2020- May 2023, NCT04225689) and provided a single faecal sample before EEN completion. Patients were divided in two groups according to levels of FCAL at EEN completion (FCAL<250 and FCAL>250 mg/kg). Levels of faecal short chain fatty acids (SCFA), faecal sample characteristics (pH, water content (%), bristol stool score) and total microbial load (qPCR) were compared between the two groups. Anthropometric and clinical parameters (blood inflammatory markers, use of immunosuppressants, disease duration, disease location) were also compared. Machine learning using feature elimination with data imputation for missing data was performed to identify associations between clinical, anthropometry, microbial parameters and FCAL normalisation.ResultsAt EEN completion, 84 children (female, 35%) were recruited age, median (IQR): 13.2 (11.8, 14.9 years) with a median (Q1, Q3) FCAL of 643 (146, 2033) mg/kg. Out of 84 patients, 35 (42%) had an FCAL<250 mg/kg. Total microbial load and SCFA were measured in a subset of patients (n=44). Patients with FCAL<250mg/kg had a higher faecal pH and lower microbial load compared to those with FCAL>250mg/kg faecal pH; FCAL<250 mg/kg: 8.3 (8.1, 8.6) vs FCAL>250 mg/kg; 7.95 (7.6, 8.3), p=0.001; microbial load (log10 16S rRNA gene copies/g): FCAL<250mg/kg: 10.7 (10.4, 10.9) vs FCAL>250mg/kg: 11.0 (10.5, 11.2), p=0.02. Median BMI z-score was also non-significantly (p=0.052) higher in patients with FCAL<250mg/kg. The use of immunosuppressants at EEN completion, disease duration, disease location and other faecal parameters were not different between the two groups. A multicomponent random forest model (clinical, blood inflammatory markers, anthropometry, faecal parameters) predicted normalisation of FCAL with 71% accuracy (sensitivity: 69%, specificity: 71%, p=<0.001, figure 1). Higher faecal pH, BMI z-scores and lower total microbial load were the most influential parameters relating to FCAL<250mg/kg.ConclusionsWe showed that the efficacy of EEN in reducing gut inflammation might be, at least in part, mediated via reducing gut bacterial biomass and modulating luminal pH and the downstream effects this may have on inflammatory members of the microbial community.Abstract OC1 Figure 1(A) Random forest (RF) classification between FCAL responders and non-responders using clinical, anthropometry and microbial data. (B): Area under the curve of the best RF model. (C): Barplots of categorical variables included in RF model
Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic ...responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.
The hepatitis C virus (HCV) infects nearly 3% of the World's population, causing severe liver disease in many. Standard of care therapy is currently pegylated interferon alpha and ribavirin ...(PegIFN/R), which is effective in less than half of those infected with the most common viral genotype. Two IL28B single nucleotide polymorphisms (SNPs), rs8099917 and rs12979860, predict response to (PegIFN/R) therapy in treatment of HCV infection. These SNPs were identified in genome wide analyses using Illumina genotyping chips. In people of European ancestry, there are 6 common (more than 1%) haplotypes for IL28B, one tagged by the rs8099917 minor allele, four tagged by rs12979860.
We used massively parallel sequencing of the IL28B and IL28A gene regions generated by polymerase chain reaction (PCR) from pooled DNA samples from 100 responders and 99 non-responders to therapy, to identify common variants. Variants that had high odds ratios and were validated were then genotyped in a cohort of 905 responders and non-responders. Their predictive power was assessed, alone and in combination with HLA-C.
Only SNPs in the IL28B linkage disequilibrium block predicted drug response. Eighteen SNPs were identified with evidence for association with drug response, and with a high degree of confidence in the sequence call. We found that two SNPs, rs4803221 (homozygote minor allele positive predictive value (PPV) of 77%) and rs7248668 (PPV 78%), predicted failure to respond better than the current best, rs8099917 (PPV 73%) and rs12979860 (PPV 68%) in this cross-sectional cohort. The best SNPs tagged a single common haplotype, haplotype 2. Genotypes predicted lack of response better than alleles. However, combination of IL28B haplotype 2 carrier status with the HLA-C C2C2 genotype, which has previously been reported to improve prediction in combination with IL28B, provides the highest PPV (80%). The haplotypes present alternative putative transcription factor binding and methylation sites.
Massively parallel sequencing allowed identification and comparison of the best common SNPs for identifying treatment failure in therapy for HCV. SNPs tagging a single haplotype have the highest PPV, especially in combination with HLA-C. The functional basis for the association may be due to altered regulation of the gene. These approaches have utility in improving diagnostic testing and identifying causal haplotypes or SNPs.
Three-dimensional epithelial culture models are widely used to emulate a more physiologically relevant microenvironment for the study of genes and signaling pathways. Prostate epithelial cells can ...grow into solid cell masses or acinus-like spheroids in Matrigel. To test if the ability to form acinus-like spheroids in Matrigel is dependent on how undifferentiated a cell is or whether it is tumor or nontumor, we established six novel epithelial cell lines. Primary prostate epithelial cells were immortalized using HPV16 E6 gene transduction and were named Shmac 2, 3, and 6 (nontumor); Shmac 4, Shmac 5, and P4E6 (tumor). All cell lines were phenotyped in monolayer culture, and their ability to form acinus-like spheroids in Matrigel investigated. The cell lines exhibited a wide range of population doubling times and all showed an intermediate phenotype in monolayer culture (luminalCK+/basalCK+/CD44+/PSA+/AR−). Only Shmac 5 cells formed acinus-like spheroids when cultured in Matrigel. Co-culture of the spheroids with fibroblasts advanced differentiation by inducing androgen receptor expression and epithelial polarization. Our findings indicate that tumor cells can form acinus-like spheroids in Matrigel.
Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease.
We carried out meta-analyses of exome ...array data and three lung function measures: forced expiratory volume in one second (FEV
), forced vital capacity (FVC) and the ratio of FEV
to FVC (FEV
/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals.
We identified significant (P<2·8x10
) associations with six SNPs: a nonsynonymous variant in
, which is predicted to be damaging, three intronic SNPs (
and
) and two intergenic SNPs near to
and
Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including
and
.
Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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