A quarter of patients with type 1 diabetes have co-existing non-islet autoimmunity: the findings of a UK population-based family study

Individuals with type 1 diabetes (T1D) are at increased risk of coeliac disease (CD), autoimmune thyroiditis and autoimmune gastritis, but the absolute risks are unclear. The aim of this study was to investigate the prevalence of autoantibodies to tissue transglutaminase (TGA), thyroid peroxidase (TPOA) and gastric H⁺ /K⁺ -ATPase (ATPA) and their genetic associations in a well-characterized population-based cohort of individuals with T1D from the Bart's-Oxford family study for whom islet autoantibody prevalence data were already available. Autoantibodies in sera from 1072 patients (males/females 604/468; median age 11·8 years, median T1D duration 2·7 months) were measured by radioimmunoassays; HLA class II risk genotype was analysed in 973 (91%) using polymerase chain reaction with sequence specific primers (PCR-SSP). The prevalence of TGA (and/or history of CD), TPOA and ATPA in patients was 9·0, 9·6 and 8·2%, respectively; 3·1% had two or more autoantibodies. Females were at higher risk of multiple autoimmunity; TGA/CD were associated with younger age and TPOA with older age. ATPA were uncommon in patients under 5 years, and more common in older patients. Anti-glutamate decarboxylase autoantibodies were predictive of co-existing TPOA/ATPA. TGA/CD were associated with human leucocyte antigen (HLA) DR3-DQ2, with the DR3-DQ2/DR3-DQ2 genotype conferring the highest risk, followed by DR4-DQ8/DR4-DQ8. ATPA were associated with DR3-DQ2, DRB1*0404 (in males) and the DR3-DQ2/DR4-DQ8 genotype. TPOA were associated with the DR3-DQ2/DR3-DQ2 genotype. Almost one-quarter of patients diagnosed with T1D aged under 21 years have at least one other organ-specific autoantibody. HLA class II genetic profiling may be useful in identifying those at risk of multiple autoimmunity.

Abstract PD8-10: APOBEC mutation signature in breast cancer correlates with tumor mutation burden and poor responses to therapy

Introduction

Mutational processes can be characterized by unique combinations of mutation types in the form of mutational signatures and have been associated with age, known mutagenic exposures, defects in DNA maintenance, or the APOBEC family of cytidine deaminases. We asked whether mutation signatures could be extracted from DNA sequence information in a targeted 434 gene panel covering 297 breast cancer specimens.

Materials and Methods

Targeted whole exome sequencing (Illumina, 2x50bp) of a 434 gene panel was performed on a set of 297 primary and metastatic breast tumor samples. Tissue of origin included breast (56%), liver (15%), lymph node (10%), lung (3%) and others (16%). Alignment was done with BWA against the human reference hg19 and variant calling was performed using VarDict. Germline variants were filtered based on allele frequencies, cohort specific population frequencies, as well as using 1000 Genomes and ExAC population frequencies. For somatic signature inference, only single nucleotide variants were retained. Panel specific trinucleotide frequencies were computed and normalized towards whole genome frequencies and somatic signatures were inferred using deconstructSigs method.

Results

We identified a total of 26 signatures from the set of 30 known signatures in our patient samples. Due to the small panel size, there was only a limited number of mutations available per patient to infer somatic signatures. On average, we identified two somatic signatures per sample. Most common mutation signatures identified were: Signature 1 (90.8%) - result of an endogenous mutational process initiated by spontaneous deamination of 5-methylcytosine; Signature 6 (21.8%) - defective DNA mismatch repair; Signature 15 (15.6%) - defective DNA mismatch repair; Signatue 7 (9.9%) - ultraviolet light exposure; and Signature 10 (6.5%) - altered activity of POLE. An APOBEC specific signature was identified in 20 (7%) samples. APOBEC positive samples showed significantly higher tumor mutational burden (10.7 vs. 5.7 mutations/mb) as compared to APOBEC negative samples (p<=0.001). PIK3CA was found to be mutated in 80% of APOBEC positive samples, compared to 36% of APOBEC negative samples. In addition, we found higher rates of mutations in TP53 (70% vs. 50%), MLL3 (50% vs. 19%) and MLL2 (25% vs 14%) of APOBEC positive patients. Response rates of APOBEC positive patients were significantly worse than of APOBEC negative patients, with 50 percent of patients having progressive disease compared to 25 percent of APOBEC negative patients(p=0.07, borderline).

Conclusions

We demonstrate the feasibility of a targeted sequencing approach to extract somatic mutation signatures from breast tumor samples, and we highlight the potential of using the APOBEC signature to predict therapeutic responses.

Citation Format: Meissner T, Amallraja A, Willis S, Harris R, Leyland-Jones B, Williams C. APOBEC mutation signature in breast cancer correlates with tumor mutation burden and poor responses to therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-10.

Abstract PD4-15: A tale of two pathways: Mutations in PI3K pathway in TNBC patients matter for the oncogenic cooperation with DNA damage repair pathway

Background: Mutations guide targeted therapy in the personalized medicine. In the opening chapter of our recently edited book (Dey et al., 2016), Prof. L. Cantley elegantly elucidated the basic signaling of the PI3K pathway in cancers. Mutations in the PI3K pathway are not only common and subtype-specific in BC but are also contextual. Alterations in DNA damage repair (DDR) pathway involving HRD (Homologous Recombination Defect) genes are one of the important contextual events of the upregulation of the PI3K pathway (De et al., 2016). Aim: Here we interrogated the contextuality of alterations of the PI3K and DDR pathway genes in our Avera patients. The mechanism of contextual cooperation between the pathwayswas experimentally validated. Methods: We examined mutation profile (FoundationOne) of our patients (Avera Cancer Institute) and patients fromthe TCGA data (cBioPortal). We validated the cooperation of the two pathwaysexperimentally by the synergy model of mutation-specific drugs; PI3K-PTEN-mTOR pathway inhibitor(s) and PARP inhibitor(s) using TNBC model.Results: We analyzed alterations of 17 and 12 genes of the PI3K and DDR pathways respectively in subtypes of BC. In luminal A and HER2-enriched (TCGA, Nature 2012), the alteration of PIK3CA reached 49 % and 47% as compared to 37 % in luminal B and 25% in basal-like.In the basal-like/TNBC subtype (cBioPortal) 12 DDR pathway genes (CHEK1/2, RAD51, BRCA1/2, MLH1, MSH2, ATM, ATR, MDC1, PARP1, FANCF) were altered in 90.1 % of cases, and 17 PI3K pathway genes were altered in 88.9 % of cases.Our ER+ve patients presented a diverse variety of PIK3CA mutations (E545K,  E545A, E545G, E542K, E453K, E762K, E365K, N345K, C420R, E81K, Q546R, C420R, E726K, E81K, E970K, H1047R, H1047L P104L, P539R, G106R,G1049R, R93Q,N345T, V105_E109>E, L113del, K111del) as compared to a less diverse type of PIK3CA mutations (Amplification, E542K, H1047R) in our TNBC patients. In our TNBC patients, the predominant type of mutation in PI3K pathway genes was found in PTEN consisting of Y68C, Y180*, loss, loss exons 1-5, and deletion exon1. The other most common mutation found in TNBC patients was in TP53 (>80%) and somatic BRCA1/2 (˜15%) genes. The interaction between the two pathways was evaluated using the mostly altered oncogenes and tumor suppressor genes (PTEN, AKT1/2, TSC1/2, mTOR, RICTOR, RHEB, BRCA1/2, ATM, ATR, FANCF) applying STRING10 to test the association at the highest 0.900 confidence views. Finally, we experimentally validated the contextual synergy of 2 pathways by demonstrating that a node-specific inhibition of the PI3K-mTOR pathway by GDC-0980 in the presence of carboplatin resulted in (1) an enhanced impairment of DSB repair and (2) a subsequent sensitization to PARPi (i). This effect occurred simultaneously with the inhibition of classic PI3K-mTOR survival signal(s) which induced a robust antiproliferative/proapoptotic effect even in BRCA-competent TNBC cells. The absence of PTEN, on the other hand, sensitized TNBC cells to PARPi in the presence of carboplatin, an effect more pronounced in BRCA-loss. Conclusion: Our data showed that the PI3K pathway cooperates with the DDR pathway in the breast oncogenesis especially basal-like and TNBC.

Citation Format: Dey N, Williams C, Krie A, Klein J, Williams K, Carlson JH, De PK, Leyland-Jones B. A tale of two pathways: Mutations in PI3K pathway in TNBC patients matter for the oncogenic cooperation with DNA damage repair pathway [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-15.

Mineral analysis of complete dog and cat foods in the UK and compliance with European guidelines

Mineral content of complete pet food is regulated to ensure health of the companion animal population. Analysis of adherence to these regulatory guidelines has not been conducted. Here, mineral composition of complete wet (n = 97) and dry (n = 80) canine and feline pet food sold in the UK was measured to assess compliance with EU guidelines. A majority of foods complied with ≥8 of 11 guidelines (99% and 83% for dry and wet food, respectively), but many failed to provide nutritional minimum (e.g. Cu, 20% of wet food) or exceeded nutritional maximum (e.g. Se, 76% of wet food). Only 6% (6/97) of wet and 38% (30/80) of dry food were fully compliant. Some foods (20–30% of all analysed) had mineral imbalance, such as not having the recommended ratio of Ca:P (between 1:1 to 2:1). Foods with high fish content had high levels of undesirable metal elements such as arsenic. This study highlights broad non-compliance of a range of popular pet foods sold in the UK with EU guidelines (94% and 61% of wet and dry foods, respectively). If fed exclusively and over an extended period, a number of these pet foods could impact the general health of companion animals.

Precise predictions for V + jets dark matter backgrounds

High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the Z ( ν ν ¯ ) +  jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by Z ( ℓ + ℓ - ) +  jet, W ( ℓ ν ) +  jet and γ +  jet production, and extrapolating to the Z ( ν ν ¯ ) +  jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the-art calculations for all relevant V +  jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different V +  jet processes play a key role. The anticipated theoretical uncertainty in the Z ( ν ν ¯ ) +  jet background is at the few percent level up to the TeV range.

Foetal haemoglobin, blood transfusion, and retinopathy of prematurity in very preterm infants: a pilot prospective cohort study

PurposeTo identify if there is an association between foetal haemoglobin (HbF) concentration and retinopathy of prematurity (ROP) in very preterm infants.Patients and methodsProspective cohort study. Infants born <32 weeks' gestational age or <1501 g in two tertiary neonatal units between January 2012 and May 2013 (n=42) were enrolled. HbF and adult haemoglobin (HbA) concentrations were measured using high-pressure liquid chromatography from blood samples sent as part of routine neonatal care once routinely requested laboratory tests had been performed. Clinical data were obtained from case notes. We calculated odds ratios (ORs) (95% confidence intervals (CIs)) to quantify the relationship between initial and mean %HbF with ROP severity (none, stages 1-3).ResultsA total of 42 infants were recruited: mean gestation 28.0 weeks (SD 1.91); mean birth weight 1042 g (SD 264). Six infants died before ROP screening; 14/36 developed ROP (39%); and 22/36 (61%) did not. Infants who developed ROP had similar initial %HbF (83.3 vs 92.3%, P=0.06), but significantly lower mean %HbF (61.75 vs 91.9%, P=0.0001) during their inpatient stay than those who did not develop ROP. In ordinal logistic regression models adjusted for birth weight, gestation and transfusion volume, mean post-natal %HbF was negatively associated with ROP severity: adjusted OR 0.94 (0.90-0.99), while initial %HbF at birth was not: adjusted OR 1.05 (0.97-1.16).ConclusionReplacing HbF by HbA during transfusion may promote ROP development by rapidly increasing oxygen availability to the retina. Conversely, maintaining a higher %HbF may be a protective factor against ROP.

An international comparison of retinopathy of prematurity grading performance within the Benefits of Oxygen Saturation Targeting II trials

Purpose

To investigate whether the observed international differences in retinopathy of prematurity (ROP) treatment rates within the Benefits of Oxygen Saturation Targeting (BOOST) II trials might have been caused by international variation in ROP disease grading.

Methods

Groups of BOOST II trial ophthalmologists in UK, Australia, and New Zealand (ANZ), and an international reference group (INT) used a web based system to grade a selection of RetCam images of ROP acquired during the BOOST II UK trial. Rates of decisions to treat, plus disease grading, ROP stage grading, ROP zone grading, inter-observer variation within groups and intra-observer variation within groups were measured.

Results

Forty-two eye examinations were graded. UK ophthalmologists diagnosed treat-requiring ROP more frequently than ANZ ophthalmologists, 13.9 (3.49) compared to 9.4 (4.46) eye examinations, P=0.038. UK ophthalmologists diagnosed plus disease more frequently than ANZ ophthalmologists, 14.1 (6.23) compared to 8.5 (3.24) eye examinations, P=0.021. ANZ ophthalmologists diagnosed stage 2 ROP more frequently than UK ophthalmologists, 20.2 (5.8) compared to 12.7 (7.1) eye examinations, P=0.026. There were no other significant differences in the grading of ROP stage or zone. Inter-observer variation was higher within the UK group than within the ANZ group. Intra-observer variation was low in both groups.

Conclusions

We have found evidence of international variation in the diagnosis of treatment-requiring ROP. Improved standardisation of the diagnosis of treatment-requiring ROP is required. Measures might include improved training in the grading of ROP, using an international approach, and further development of ROP image analysis software.

Tolerance of Pseudomonas aeruginosa in in-vitro biofilms to high-level peracetic acid disinfection

BACKGROUND

Biofilm has been suggested as a cause of disinfection failures in flexible endoscopes where no lapses in the decontamination procedure can be identified. To test this theory, the activity of peracetic acid, one of the widely used disinfectants in the reprocessing of flexible endoscopes, was evaluated against both planktonic and sessile communities of Pseudomonas aeruginosa.

AIM

To investigate the ability of P. aeruginosa biofilm to survive high-level peracetic acid disinfection.

METHOD

The susceptibility of planktonic cells of P. aeruginosa and biofilms aged 24, 48, 96, and 192 h to peracetic acid was evaluated by estimating their viability using resazurin viability and plate count methods. The biomass of the P. aeruginosa biofilms was also quantified using Crystal Violet assay. Planktonic cells of P. aeruginosa were treated with 5-30 ppm concentration of peracetic acid in the presence of 3.0 g/L of bovine serum albumin (BSA) for 5 min. Biofilms of P. aeruginosa were also treated with various peracetic acid concentrations (100-3000 ppm) for 5 min.

FINDINGS

Planktonic cells of P. aeruginosa were eradicated by 20 ppm of peracetic acid, whereas biofilms showed an age-dependent tolerance to peracetic acid, and 96 h biofilm was only eradicated at peracetic acid concentration of 2500 ppm.

CONCLUSION

Ninety-six-hour P. aeruginosa biofilm survives 5 min treatment with 2000 ppm of peracetic acid, which is the working concentration used in some endoscope washer-disinfectors. This implies that disinfection failure of flexible endoscopes might occur when biofilms build up in the lumens of endoscopes.