Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk

Linkage and candidate gene studies have identified several breast cancer susceptibility genes, but the overall contribution of coding variation to breast cancer is unclear. To evaluate the role of rare coding variants more comprehensively, we performed a meta-analysis across three large whole-exome sequencing datasets, containing 26,368 female cases and 217,673 female controls. Burden tests were performed for protein-truncating and rare missense variants in 15,616 and 18,601 genes, respectively. Associations between protein-truncating variants and breast cancer were identified for the following six genes at exome-wide significance (P < 2.5 × 10-6): the five known susceptibility genes ATM, BRCA1, BRCA2, CHEK2 and PALB2, together with MAP3K1. Associations were also observed for LZTR1, ATR and BARD1 with P < 1 × 10-4. Associations between predicted deleterious rare missense or protein-truncating variants and breast cancer were additionally identified for CDKN2A at exome-wide significance. The overall contribution of coding variants in genes beyond the previously known genes is estimated to be small.

Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry

Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.

A213 ERCP-RELATED ADVERSE EVENTS IN PRIMARY SCLEROSING CHOLANGITIS: A SYSTEMATIC REVIEW & META-ANALYSIS

Background

Endoscopic retrograde cholangiopancreatography (ERCP) is a valuable diagnostic and therapeutic tool in primary sclerosing cholangitis (PSC). Although the complications of ERCP are well known in the general population, there is conflicting data regarding complications in patients with PSC. Factors that predict ERCP-related adverse events in PSC are also unclear.

Aims

To conduct a systematic review and meta-analyses to 1. compare ERCP-related adverse events in patients with and without PSC and 2. determine risk factors associated with ERCP-related adverse events in PSC.

Methods

A systematic search was conducted in Embase, PubMed and CENTRAL for studies published from January 1, 2000 to May 12, 2021. Eligible studies included adults with PSC undergoing ERCP and reported at least one ERCP-related adverse event (bleeding, perforation, pancreatitis, cholangitis) or risk factor associated with complications. Raw event rates for adverse events and risk factors were used to calculate odds ratios (ORs) which were then pooled using random-effects models.

Results

Four studies contributed to the first meta-analysis. There was a significant three-fold increase in the 30-day odds of cholangitis in PSC compared to those without PSC (4.3% vs. 2.0%; OR 3.26, 95% CI 1.08–9.90; p=0.037; I2=73.0%) (Figure 1). However, there were no significant differences in 30-day pancreatitis (4.2% vs. 3.4%; OR 0.89, 95% CI 0.26–3.07; p=0.851; I2=87.9%), bleeding (0.3% vs. 1.1%; OR 0.36, 95% CI 0.06–2.21; p=0.272; I2=50.3%), or perforation (0.7% vs. 0.5%; OR 1.19, 95% CI 0.40–3.51; p=0.752; I2=28.5%).

In a second meta-analysis, risk factors contributing to post-ERCP pancreatitis (PEP) in PSC were pooled from five studies. While female sex was not associated with PEP, accidental passage of wire into the pancreatic duct (OR 7.44, 95% CI 3.33–16.65; p&lt;0.001; I2=65.0%) and biliary sphincterotomy (OR 4.80, 95% CI 1.92–12.03; p=0.001; I2=73.1%) were associated with higher PEP odds.

Conclusions

In the context of limited comparative data and study heterogeneity, PSC patients have higher odds of post-ERCP cholangitis despite the majority receiving antibiotics. Odds of bleeding, pancreatitis, and perforation were similar between groups. Accidental wire passage and biliary sphincterotomy increased odds of PEP, which helps identify higher-risk groups. Future studies should elucidate ERCP-related risks in PSC and guide preventive strategies.

Funding Agencies

None

Ustekinumab in bio-naïve and bio-failure Crohn's disease patients: Results from a « real-life » monocentric cohort

BACKGROUND

The pivotal clinical trials have largely demonstrated the efficacy and safety of ustekinumab in Crohn's disease. Real-life cohorts published so far only include very few bio-naïve patients. This study assesses effectiveness and safety of ustekinumab in bio-naïve and bio-failure patients treated with ustekinumab in routine practice and look for predictors of response.

METHODS

We performed a retrospective monocentric study. Initial response was assessed by maintenance therapy beyond week 16. Sustained response was assessed by the continuation or cessation of therapy over time for another reason than stopping in sustained remission. Treatment persistence was assessed by Kaplan Meier curves and predictors of treatment persistence were studied by univariate and multivariate Cox model.

RESULTS

Out of 156 recorded patients, three patients were still in their induction phase at time of analysis and 5 patients were lost to follow-up, leaving 148 patients for clinical effectiveness analyses, including 35 bio-naïve when starting ustekinumab. A maintenance therapy was initiated in 79.7%. At one year, the probability to be still treated with ustekinumab was 73.8%. Treatment cessation increased with smoking in multivariate analysis. Previous biologic failure (as a whole), CRP and fecal calprotectin baseline levels did not influence initial response and treatment persistence.

CONCLUSION

A large proportion of CD patients initially respond to ustekinumab and continue this treatment beyond one year. Treatment persistence is as high in bio-failure as in bio-naïve patients.

Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.

[Pharmaceutical analysis of medication orders in health care facilities: A France-Quebec comparison]

OBJECTIVES

The pharmaceutical analysis of drug prescriptions is one of the key steps in the drug circuit. This mandatory regulatory practice in France and Quebec is based on national standards. The main objective of this work was to compare the practical methods of pharmaceutical analysis performed in French and Quebec university hospitals.

METHODS

This is a prospective comparative survey conducted in 2 French and Quebec university hospital centres among pharmacists and pharmacy residents.

RESULTS

The response rate to the survey was 60% (45/75). Between 16 and 22 elements were deemed necessary to structure the centralized, decentralized or mixed pharmaceutical analysis. The chronological ranking of these elements was comparable between the French and Quebec participants. All participants were in favour of the development of initial and continuing training in pharmaceutical analysis. Finally, the majority of participants were against using individual pharmaceutical analysis performance indicators to optimize the process (82%; 37/45).

CONCLUSIONS

The French-Quebec practice of prescription analysis by a ward-pharmacist complies with national standards. The main differences in the practice of pharmaceutical analysis are related to the types of organization, the tools available and the length of time pharmacists have been deployed in care units in France and Quebec.

Transition from pediatric to adult care in adolescents with hereditary metabolic diseases: Specific guidelines from the French network for rare inherited metabolic diseases (G2M)

Inherited metabolic diseases (IMD) form a heterogeneous group of genetic disorders that surface primarily during childhood and result in significant morbidity and mortality. A prevalence of 1 in 2500-5000 live births is often reported. The transfer of adolescents from pediatric care to adult health facilities is often difficult for patients and their families and can lead to a breakdown in medical follow-up and therefore serious complications. Existing recommendations for the successful transition of patients with chronic disorders do not specifically address patients with IMDs associated with dietary treatment. Here, the French network for rare inherited metabolic diseases (G2M) presents its reflections and recommendations for a successful transition. Preparations for the transfer must be made well in advance. The transfer must aim for adolescents gaining autonomy by making them responsible and providing them with the knowledge that will enable them to manage their care themselves, know how to react appropriately if there is any change in their condition, and move comfortably within the adult healthcare system. This requires the active participation of the patient, his or her family, and pediatric and adult care teams. It involves multidisciplinary management plus the production and maintenance of an educational therapy program. Finally, the identification of physicians and dietitians trained in IMDs, relevant subspecialists, and even expert patients could improve the continuum of complete and appropriate care for these patients within adult medicine.

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Dietary practices in propionic acidemia: A European survey

Background

The definitive dietary management of propionic acidaemia (PA) is unknown although natural protein restriction with adequate energy provision is of key importance.

Aim

To describe European dietary practices in the management of patients with PA prior to the publication of the European PA guidelines.

Methods

This was a cross-sectional survey consisting of 27 questions about the dietary practices in PA patients circulated to European IMD dietitians and health professionals in 2014.

Results

Information on protein restricted diets of 186 PA patients from 47 centres, representing 14 European countries was collected. Total protein intake [PA precursor-free L-amino acid supplements (PFAA) and natural protein] met WHO/FAO/UNU (2007) safe protein requirements for age in 36 centres (77%). PFAA were used to supplement natural protein intake in 81% (n = 38) of centres, providing a median of 44% (14–83%) of total protein requirement. Seventy-four per cent of patients were prescribed natural protein intakes below WHO/FAO/UNU (2007) safe levels in one or more of the following age groups: 0–6 m, 7–12 m, 1–10 y, 11–16 y and > 16 y. Sixty-three per cent (n = 117) of patients were tube fed (74% gastrostomy), but only 22% received nocturnal feeds.

Conclusions

There was high use of PFAA with intakes of natural protein commonly below WHO/FAO/UNU (2007) safe levels. Optimal dietary management can only be determined by longitudinal, multi-centre, prospective case controlled studies. The metabolic instability of PA and small patient cohorts in each centre ensure that this is a challenging undertaking.

Neurovascular microcirculatory vasodilation mediated by C-fibers and Transient receptor potential vanilloid-type-1 channels (TRPV 1) is impaired in type 1 diabetes

Microvascular dysfunction may have an early onset in type 1 diabetes (T1D) and can precede major complications. Our objectives were to assess the endothelial-dependent (acetylcholine, ACh; and post-occlusive hyperemia, PORH), non-endothelial-dependent (sodium nitroprusside, SNP) and neurovascular-dependent (local heating, LH and current induced vasodilation, CIV) microcirculatory vasodilation in T1D patients compared with matched control subjects using a laser speckle contrast imager. Seventeen T1D patients - matched with 17 subjects according to age, gender, Body-Mass-Index, and smoking status - underwent macro- and microvascular investigations. The LH early peak assessed the transient receptor potential vanilloid type 1 channels (TRPV1) mediated vasodilation, whereas the plateau assessed the Nitirc-Oxyde (NO) and endothelium-derived hyperpolarizing factor (EDHF) pathways. PORH explored sensory nerves and (EDHF), while CIV assessed sensory nerves (C-fibers) and prostaglandin-mediated vasodilation. Using neurological investigations, we observed that C-fiber and A-delta fiber functions in T1D patients were similar to control subjects. PORH, CIV, LH peak and plateau vasodilations were significantly decreased in T1D patients compared to controls, whereas there was no difference between the two groups for ACh and SNP vasodilations. Neurovascular microcirculatory vasodilations (C-fibers and TRPV 1-mediated vasodilations) are impaired in TD1 patients whereas no abnormalities were found using clinical neurological investigations. Clinicaltrials: No. NCT02538120.

Dietary practices in isovaleric acidemia: A European survey

Background

In Europe, dietary management of isovaleric acidemia (IVA) may vary widely. There is limited collective information about dietetic management.

Aim

To describe European practice regarding the dietary management of IVA, prior to the availability of the E-IMD IVA guidelines (E-IMD 2014).

Methods

A cross-sectional questionnaire was sent to all European dietitians who were either members of the Society for the Study of Inborn Errors of Metabolism Dietitians Group (SSIEM-DG) or whom had responded to previous questionnaires on dietetic practice (n = 53). The questionnaire comprised 27 questions about the dietary management of IVA.

Results

Information on 140 patients with IVA from 39 centres was reported. 133 patients (38 centres) were given a protein restricted diet. Leucine-free amino acid supplements (LFAA) were routinely used to supplement protein intake in 58% of centres. The median total protein intake prescribed achieved the WHO/FAO/UNU [2007] safe levels of protein intake in all age groups. Centres that prescribed LFAA had lower natural protein intakes in most age groups except 1 to 10 y. In contrast, when centres were not using LFAA, the median natural protein intake met WHO/FAO/UNU [2007] safe levels of protein intake in all age groups. Enteral tube feeding was rarely prescribed.

Conclusions

This survey demonstrates wide differences in dietary practice in the management of IVA across European centres. It provides unique dietary data collectively representing European practices in IVA which can be used as a foundation to compare dietary management changes as a consequence of the first E-IMD IVA guidelines availability.

[Selection and optimal sequence of critical elements for medication review: A simulation with hospital pharmacy residents]

OBJECTIVES

The main objective of this study was to compare the responses of pharmacy residents regarding critical steps for medication order review, in the presence or absence of clinical pharmacists on patient care units, to describe the sequence of these steps and to compare them to an optimal sequence. The secondary objectives were to test this sequence in a simulation and to assess the residents' level of agreement on medication order review.

METHODS

Twenty-two validation steps were selected from guidelines. A simulation on order review was organized in three steps: selecting elements judged to be necessary or not for the order review critical path, then organizing this sequence in chronological order, implementation of this critical path on two simulated practical cases, resident perceptions about order review in their training.

RESULTS

Forty-one residents participated in the activity. Responses were heterogeneous regarding the elements' sequence and the time required for the review of a simulated case (3-13minutes). A majority of residents considered that their training was insufficient (29/41), that pharmacists validated differently (27/41), and that it was impossible to review the 22 proposed items for each prescription (30/41).

CONCLUSIONS

This article highlights heterogeneous medication order review practices among pharmacy residents, due to a lack of training in their curriculum according to them. It is essential to acquire medication order review standard both locally and nationally.

Osteoprotegerin levels are associated with liver fat and liver markers in dysmetabolic adults

AIM

This study aimed to determine the association between visceral adipose tissue (VAT), liver fat (LF) content, and other markers of the metabolic syndrome (MetS) and osteoprotegerin (OPG) in dysmetabolic adults.

METHODS

Subjects from the NUMEVOX cohort were included if they fulfilled at least one MetS criterion. They then underwent a thorough metabolic and cardiovascular evaluation, including arterial stiffness, atherosclerotic plaques, homoeostasis model assessment for insulin resistance (HOMA-IR) indices and OPG. VAT and LF content were measured by magnetic resonance imaging (MRI). Ultrasound examination of arteries and arterial stiffness were recorded, and age- and gender-adjusted paired correlations calculated.

RESULTS

Body mass index, waist circumference and MRI-derived VAT correlated with OPG, whereas abdominal subcutaneous fat did not. OPG levels were strongly correlated with LF content (r=0.25, P=0.003), liver markers such as alanine aminotransferase (r=0.39, P<0.001) and HOMA-IR index (r=0.39, P<0.0001). Plasma OPG also correlated with arterial stiffness and the number of atherosclerotic sites.

CONCLUSION

Plasma OPG levels are positively associated with both liver markers and increased LF content, but not with subcutaneous fat in dysmetabolic men. These findings suggest that elevated OPG levels may play a role in the link between fatty liver disease and enhanced cardiovascular risk.

2 × 2 Tables: a note on Campbell's recommendation

For 2 × 2 tables, Egon Pearson's N - 1 chi-squared statistic is theoretically more sound than Karl Pearson's chi-squared statistic, and provides more accurate p values. Moreover, Egon Pearson's N - 1 chi-squared statistic is equal to the Mantel-Haenszel chi-squared statistic for a single 2 × 2 table, and as such, is often available in statistical software packages like SPSS, SAS, Stata, or R, which facilitates compliance with Ian Campbell's recommendations.

Infection control in households of drug-resistant tuberculosis patients co-infected with HIV in Mumbai, India

BACKGROUND

Mumbai has a population of 21 million, and an increasingly recognised epidemic of drug-resistant tuberculosis (DR-TB).

OBJECTIVE

To describe TB infection control (IC) measures implemented in households of DR-TB patients co-infected with the human immunodeficiency virus (HIV) under a Médecins Sans Frontières programme.

METHODS

IC assessments were carried out in patient households between May 2012 and March 2013. A simplified, standardised assessment tool was utilised to assess the risk of TB transmission and guide interventions. Administrative, environmental and personal protective measures were tailored to patient needs.

RESULTS

IC assessments were carried out in 29 houses. Measures included health education, segregating sleeping areas of patients, improving natural ventilation by opening windows, removing curtains and obstacles to air flow, installing fans and air extractors and providing surgical masks to patients for limited periods. Environmental interventions were carried out in 22 houses.

CONCLUSIONS

TB IC could be a beneficial component of a comprehensive TB and HIV care programme in households and communities. Although particularly challenging in slum settings, IC measures that are feasible, affordable and acceptable can be implemented in such settings using simplified and standardised tools. Appropriate IC interventions at household level may prevent new cases of DR-TB, especially in households of patients with a lower chance of cure.

Practices in prescribing protein substitutes for PKU in Europe: No uniformity of approach

BACKGROUND

There appears little consensus concerning protein requirements in phenylketonuria (PKU).

METHODS

A questionnaire completed by 63 European and Turkish IMD centres from 18 countries collected data on prescribed total protein intake (natural/intact protein and phenylalanine-free protein substitute [PS]) by age, administration frequency and method, monitoring, and type of protein substitute. Data were analysed by European region using descriptive statistics.

RESULTS

The amount of total protein (from PS and natural/intact protein) varied according to the European region. Higher median amounts of total protein were prescribed in infants and children in Northern Europe (n=24 centres) (infants <1 year, >2-3g/kg/day; 1-3 years of age, >2-3 g/kg/day; 4-10 years of age, >1.5-2.5 g/kg/day) and Southern Europe (n=10 centres) (infants <1 year, 2.5 g/kg/day, 1-3 years of age, 2 g/kg/day; 4-10 years of age, 1.5-2 g/kg/day), than by Eastern Europe (n=4 centres) (infants <1 year, 2.5 g/kg/day, 1-3 years of age, >2-2.5 g/kg/day; 4-10 years of age, >1.5-2 g/kg/day) and with Western Europe (n=25 centres) giving the least (infants <1 year, >2-2.5 g/kg/day, 1-3 years of age, 1.5-2 g/kg/day; 4-10 years of age, 1-1.5 g/kg/day). Total protein prescription was similar in patients aged >10 years (1-1.5 g/kg/day) and maternal patients (1-1.5 g/kg/day).

CONCLUSIONS

The amounts of total protein prescribed varied between European countries and appeared to be influenced by geographical region. In PKU, all gave higher than the recommended 2007 WHO/FAO/UNU safe levels of protein intake for the general population.

The influences of psychotic symptoms on the activities of daily living of individuals with Alzheimer disease: a longitudinal analysis

OBJECTIVES

Psychotic symptoms associated with Alzheimer Disease (AD) contribute to excess functional dependence. Longitudinal studies have generally examined the association between rates of functional decline and the occurrence of psychotic symptoms from either a single evaluation or from multiple evaluations rather than through changes in frequency and severity of symptoms. Although the presence or absence of psychotic symptoms at initial or follow-up examinations may be associated with changes in functional status, the nature of the relationship between changes in these domains cannot be inferred. We examine the association between changes in the frequency of psychotic symptoms and changes in dependence in activities of daily living (ADL) over a period ranging from 1 to 74 months (median = 17.7).

METHOD

Data from a cohort of 234 individuals referred to a memory clinic were analyzed using multilevel linear regression. Information on ADL, behavioral and psychological symptoms, depression, and cognition was collected.

RESULTS

An increase in the frequency of psychotic symptoms had a unique influence on the deterioration of basic ADL, after controlling for demographic variables, changes in cognition, depression, and other behavioral and psychological symptoms (B = -.017, p = .003). However, changes in psychotic symptoms did not significantly contribute to declines in the ability to perform instrumental ADL (B = -.008, p = .439).

CONCLUSION

Changes in psychotic symptoms may influence basic but not instrumental ADL over time. These findings may have ramifications for studies and treatment plans for individuals with AD who demonstrate psychotic symptoms.

Dietary management of urea cycle disorders: European practice

BACKGROUND

There is no published data comparing dietary management of urea cycle disorders (UCD) in different countries.

METHODS

Cross-sectional data from 41 European Inherited Metabolic Disorder (IMD) centres (17 UK, 6 France, 5 Germany, 4 Belgium, 4 Portugal, 2 Netherlands, 1 Denmark, 1 Italy, 1 Sweden) was collected by questionnaire describing management of patients with UCD on prescribed protein restricted diets.

RESULTS

Data for 464 patients: N-acetylglutamate synthase (NAGS) deficiency, n=10; carbamoyl phosphate synthetase (CPS1) deficiency, n=29; ornithine transcarbamoylase (OTC) deficiency, n=214; citrullinaemia, n=108; argininosuccinic aciduria (ASA), n=80; arginase deficiency, n=23 was reported. The majority of patients (70%; n=327) were aged 0-16y and 30% (n=137) >16y. Prescribed median protein intake/kg body weight decreased with age with little variation between disorders. The UK tended to give more total protein than other European countries particularly in infancy. Supplements of essential amino acids (EAA) were prescribed for 38% [n=174] of the patients overall, but were given more commonly in arginase deficiency (74%), CPS (48%) and citrullinaemia (46%). Patients in Germany (64%), Portugal (67%) and Sweden (100%) were the most frequent users of EAA. Only 18% [n=84] of patients were prescribed tube feeds, most commonly for CPS (41%); and 21% [n=97] were prescribed oral energy supplements.

CONCLUSIONS

Dietary treatment for UCD varies significantly between different conditions, and between and within European IMD centres. Further studies examining the outcome of treatment compared with the type of dietary therapy and nutritional support received are required.

Treatment of acute decompensation of maple syrup urine disease in adult patients with a new parenteral amino-acid mixture

BACKGROUND

Acute decompensation of maple syrup urine disease (MSUD) is usually treated by enteral feeding with an amino-acid mixture without leucine (Leu), valine or isoleucine. However, its administration is ineffective in cases of gastric intolerance and some adult patients refuse enteral feeding via a nasogastric tube. We developed a new parenteral amino-acid mixture for patients with MSUD.

METHODS

Seventeen decompensation episodes in four adult patients with MSUD treated with a parenteral amino-acid mixture (group P) were compared to 18 previous episodes in the same patients treated by enteral feeding (group E).

RESULTS

The mean Leu concentration at presentation was similar in the groups P and E (1196.9 μmol/L and 1212.2 μmol/L, respectively). The mean decrease in the Leu concentration during the first 3 days of hospitalisation was significantly higher in group P than group E (p = 0.0026); there were no side effects. The mean duration of hospitalisation was similar (4 vs. 4.5 days, p = NS). No patient in group P deteriorated whereas one patient in group E required dialysis.

CONCLUSION

This new parenteral amino-acid mixture is safe and allows efficient Leu concentration decrease during acute MSUD decompensation episodes in adults. Its use avoids the need for nasogastric tube insertion.

The costimulatory molecule CD70 is regulated by distinct molecular mechanisms and is associated with overall survival in diffuse large B-cell lymphoma

In diffuse large B-cell lymphomas (DLBCL), a recurrent deletion of the 19p13 region has recently been described. CD70 and TNFSF9 genes are suspected tumor suppressor genes, but previous studies suggest an oncogenic role for CD70. Therefore, we studied the consequences of variation in CD70 copy number and epigenetic modifications on CD70 expression. Copy-number variation was investigated in 144 de novo DLBCL tissues by comparative genomic hybridization array and quantitative multiplex PCR. Gene expression was assessed by quantitative RT-PCR, and CD70 promoter methylation was determined by pyrosequencing. The 19p13.3.2 region was deleted in 21 (14.6%) cases, which allowed the minimal commonly deleted region of 57 Kb that exclusively includes the CD70 gene to be defined. Homozygous deletions were observed in four (2.7%) cases, and acquired single-nucleotide variations of CD70 were detected in nine (6.3%) cases. CD70 was highly expressed in both germinal centre B-cell-like (GCB) and activated B-cell-like (ABC) DLBCL compared to normal tissue, with distinct molecular mechanisms of mRNA expression regulation. A gene dosage effect was observed in the GCB subtype, whereas promoter methylation was the predominant mechanism of down regulation in the ABC subtype. However, high CD70 expression levels correlated to shorter overall survival in both the GCB (P = 0.0021) and the ABC (P =0.0158) subtypes. In conclusion, CD70 is targeted by recurrent deletions, somatic mutations and promoter hypermethylation, but its high level of expression is related to an unfavorable outcome, indicating that this molecule may constitute a potential therapeutic target in selected DLBCL.

Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia

BACKGROUND

Congenital multiple intestinal atresia (MIA) is a severe, fatal neonatal disorder, involving the occurrence of obstructions in the small and large intestines ultimately leading to organ failure. Surgical interventions are palliative but do not provide long-term survival. Severe immunodeficiency may be associated with the phenotype. A genetic basis for MIA is likely. We had previously ascertained a cohort of patients of French-Canadian origin, most of whom were deceased as infants or in utero. The goal of the study was to identify the molecular basis for the disease in the patients of this cohort.

METHODS

We performed whole exome sequencing on samples from five patients of four families. Validation of mutations and familial segregation was performed using standard Sanger sequencing in these and three additional families with deceased cases. Exon skipping was assessed by reverse transcription-PCR and Sanger sequencing.

RESULTS

Five patients from four different families were each homozygous for a four base intronic deletion in the gene TTC7A, immediately adjacent to a consensus GT splice donor site. The deletion was demonstrated to have deleterious effects on splicing causing the skipping of the attendant upstream coding exon, thereby leading to a predicted severe protein truncation. Parents were heterozygous carriers of the deletion in these families and in two additional families segregating affected cases. In a seventh family, an affected case was compound heterozygous for the same 4bp deletion and a second missense mutation p.L823P, also predicted as pathogenic. No other sequenced genes possessed deleterious variants explanatory for all patients in the cohort. Neither mutation was seen in a large set of control chromosomes.

CONCLUSIONS

Based on our genetic results, TTC7A is the likely causal gene for MIA.

Effect of thermal heat stress on energy utilization in two lines of pigs divergently selected for residual feed intake

Castrated males from 2 lines of purebred French Large White obtained from a divergent selection experiment for their residual feed intake (RFI) over 7 generations were measured for their energy utilization during thermal acclimation to increased ambient temperature. The RFI(+) line consumed more feed than predicted from its performance, whereas the RFI- line consumed less feed. Each pig was exposed to 24°C for 7 d (P0) and thereafter to a constant temperature of 32°C for 3 consecutive periods of 7 d (P1, P2, P3). Feed intake, feeding behavior parameters, digestibility, components of heat production (HP; measured by indirect calorimetry in respiration chambers), and energy, nitrogen, fat, and water balance were measured in pigs offered feed and water ad libitum and individually housed in respiratory chambers. Two identical respiratory chambers were simultaneously used, and 5 pigs of each line were measured successively. Whatever the trait, the interaction between line and period was not significant (P > 0.10). On average, ADFI was greater in the RFI+ than in the RFI- line (1,945 vs. 1,639 g/d; P = 0.051) in relation to an increase of the mean size of each feeding bout (128 vs. 82 g/visit; P < 0.001). There was no line effect on nutrient and energy digestibility. Total HP tended to be greater in RFI+ than in RFI- lines (1,279 vs. 1,137 kJ·kg BW-0.60·d-1; P = 0.065), which tended to retain more energy (968 vs. 798 kJ·kg BW-0.60·d-1; P = 0.050). The sensible heat loss was greater in RFI+ compared with the RFI- line (644 vs. 560 kJ·kg BW-0.60·d-1; P = 0.020). The RFI+ pigs consumed more water (+981 vs. 657 g·kg BW-0.60·d-1; P = 0.085) and produced more urine (589 vs. 292 g·kg BW-0.60·d-1; P < 0.001) than RFI- pigs, whereas water evaporation was similar for both lines. On average, ME intake and HP declined by about 38% and 20%, respectively, from P0 to P1 (P < 0.001). In contrast to ME intake, HP gradually decreased (P < 0.05) from P1 to P3 in connection with a reduction of the activity related HP. The evaporative heat loss represented 30% on the total heat loss on P0, and this proportion significantly increased on P1 (61%; P < 0.001) and remained constant thereafter. In conclusion, our results suggest that thermal heat acclimation in pigs is mainly related to a biphasic reduction of HP rather than a change in the ability of losing heat, and it did not significantly differ between RFI+ and RFI- lines despite a decreased HP in the latter ones.

Proteinuria in metastatic pheochromocytoma is associated with an increased risk of Acute Respiratory Distress Syndrome, spontaneously or after therapy with 131I-meta-iodobenzylguanidine (131I-MIBG)

Acute Respiratory Distress Syndrome (ARDS) has been reported rarely in pheochromocytoma, occurring spontaneously or after therapy with 131I-meta-iodobenzylguanidine (131I-MIBG). Our objective was to determine whether proteinuria is associated with an increased risk of ARDS. This was a retrospective analysis of a prospective cohort study of 64 patients with metastatic pheochromocytoma or paraganglioma treated with 131I-MIBG on institutional protocols. Proteinuria was defined as at least one urinalysis positive for at least trace protein within 1 month prior to 131I-MIBG or within 1 month prior to spontaneous ARDS. Proportions were compared using Fisher's exact test. Urinalyses within the defined time period were available for 48 patients, 8 of whom had proteinuria. Of the 8 patients with proteinuria, 5 developed ARDS: 3 within 10 days following 131I-MIBG, two 6 months following 131I-MIBG. Both patients who developed ARDS 6 months after 131I-MIBG had proteinuria within 1 month before apparently spontaneous ARDS. None of the 40 patients whose urinalyses were all negative for protein developed ARDS. None of the 16 patients with missing urinalyses developed ARDS. Patients with antecedent proteinuria were more likely to develop ARDS than those without proteinuria (63% vs. 0%; p<0.0001). The following variables were not significantly associated with ARDS: 131I-MIBG activities administered, number of 131I-MIBG administrations, age, hypertension, or secretion of catecholamines or metanephrines. In patients with metastatic pheochromocytoma or paraganglioma, proteinuria is associated with ARDS and urine protein should be examined prior to administering 131I-MIBG.

Co-variation of STI1 and WDR36/UTP21 alters cell proliferation in a glaucoma model

PURPOSE

To investigate the role of multigenic variation in primary open-angle glaucoma (POAG) involving the rRNA processing gene WD repeat domain 36 (WDR36).

METHODS

We examined the heat shock protein 70/90 (HSP70/90)-organizing co-chaperone stress-induced-phosphoprotein 1 (STI1) as a potential co-modifying gene in glaucoma patients found to harbor WDR36 amino acid variation. The STI1 gene was sequenced and its POAG-associated amino acid variant K434R, as well as the single nucleotide polymorphism (SNP) P173T, were tested for functional defects in a yeast model system previously used to characterize WDR36 variants (using the homologous yeast gene U3 protein 21 [UTP21]).

RESULTS

A POAG patient heterozygous for the WDR36 variant L25P was discovered to also carry the STI1 variant K434R in a heterozygous state. Variant K434R, located at an evolutionarily-conserved site, was not found in a pool of clinically-examined individuals lacking WDR36 variation which included 55 normal controls and 20 patients with normal tension glaucoma (NTG). STI1 (K434R) and the homologous yeast variant K470R were able to rescue yeast growth-inhibition by the HSP90-inhibitor radicicol. Double mutant haploid strains expressing human STI1 (K434R) and recombinant yeast UTP21 variants did not have significantly different levels of 18S rRNA from the corresponding hSTI1 (WT) strains. However, specific double mutant K434R strains exhibited significantly slower culture growth at 37 °C. Double mutant P173T strains also displayed altered growth rates at 37 °C.

CONCLUSIONS

STI1 variation does not play a significant direct role in the genetics of POAG. However, as previously found for the STI1 null allele, non-synonymous variants of human STI1 confer growth dysregulation in the context of specific yeast UTP21 mutations and heat stress. Based on the genetic association of two co-heterozygous STI1 and WDR36 variants in a POAG patient and the functional analyses performed in a model system for basic eukaryotic cellular processes, these experiments point to a conserved molecular pathway involving STI1 and WDR36.

Glucose inhibits angiogenesis of isolated human pancreatic islets

Owing to strong interactions between pancreatic islets and the surrounding capillary network, we hypothesized that high glucose concentrations might affect key angiogenesis factors from isolated human islets, thus contributing to beta-cell failure in diabetes. Human islets from eight distinct donors were studied following 96 h in culture in the presence of normal (5.5 mmol/l) or high (16.7 mmol/l) glucose concentrations. Similar studies were performed with HUVECs. Human angiogenesis-related genes and corresponding proteins were studied by real-time quantitative PCR (RT-qPCR) and protein arrays respectively. Angiogenesis and proliferation assays were also performed with HUVECs under the same culture conditions. RT-qPCR and proteome analysis of human islets incubated with 16.7 mM/l glucose revealed a significant decrease in pro-angiogenic factors including vascular endothelial growth factor (VEGF) mRNA by 20% and VEGF protein levels by 42% as well as additional proteins such as fibroblast growth factor-4 by 41%, MMP9 by 18%, monocyte chemoattractant protein-1 by 21%, and prolactin by 25%. In contrast, we observed a 17% increase in thrombospondin-1 (TSP-1, listed as THBS1 in the HUGO database) and a 37% increase in angiotensinogen gene expression levels, but neither angiotensin-converting enzyme nor angiotensin II type 1 receptor gene expression was affected. The amounts of anti-angiogenic proteins such as TSP-1 and serpin B5/maspin were also increased by 70 and 98% respectively as well as endostatin by 63%. Angiogenesis assays of HUVECS in the presence of high glucose concentrations revealed a 30% decrease in tree-like tubular network formation. These data suggest that glucose reduces key factors of islet angiogenesis, which might exacerbate beta-cell failure.

Increased expression of CD44v6 in endocrine pancreatic tumours but not in midgut carcinoid tumours

Aims/background-To analyse the different isoforms of CD44 in various types of endocrine pancreatic and gut carcinoid tumours and to investigate the relation between their expression and tumour dissemination. This study was prompted by the recent observation that inappropriate splicing of the CD44 gene was correlated with tumour progression and metastasis formation in a number of human cancers.Methods-Expression of CD44 isoforms was studied in 38 endocrine pancreatic tumours and gut neuroendocrine tumours using antibodies directed against products of exons v3, v4-v5, v6, v7-v8 as well as against the standard CD44 molecule (CD44H). CD44 gene expression was also analysed by reverse transcription PCR (RT-PCR) in nine endocrine and seven carcinoid tumours.Results-All gastrinomas except one (nine of 10) and about half of the other endocrine pancreatic tumours (seven of 15) expressed CD44v6. Most (10/11) midgut carcinoid tumours were CD44v6 negative, with no detectable immunostaining. CD44v3, CD44v4-v5 and CD44v7-v8 were not expressed in any of these tumours. CD44 mRNA analysis illustrated a complex splice pattern and expression of large CD44 isoforms in CD44v6 positive endocrine tumours, whereas the standard form only was detected in midgut carcinoid tumours. No correlation between CD44 variant expression and tumour metastasis was observed.Conclusions-CD44 variants encoding exon v6 are preferentially expressed both in gastrinomas and in most pancreatic endocrine tumours. In contrast to other tumours, the expression of CD44v6 in pancreatic neuroendocrine tumours does not seem to be correlated with tumour dissemination.

How to translate therapeutic recommendations in clinical practice guidelines into rules for critiquing physician prescriptions? Methods and application to five guidelines

BACKGROUND

Clinical practice guidelines give recommendations about what to do in various medical situations, including therapeutical recommendations for drug prescription. An effective way to computerize these recommendations is to design critiquing decision support systems, i.e. systems that criticize the physician's prescription when it does not conform to the guidelines. These systems are commonly based on a list of "if conditions then criticism" rules. However, writing these rules from the guidelines is not a trivial task. The objective of this article is to propose methods that (1) simplify the implementation of guidelines' therapeutical recommendations in critiquing systems by automatically translating structured therapeutical recommendations into a list of "if conditions then criticize" rules, and (2) can generate an appropriate textual label to explain to the physician why his/her prescription is not recommended.

METHODS

We worked on the therapeutic recommendations in five clinical practice guidelines concerning chronic diseases related to the management of cardiovascular risk. We evaluated the system using a test base of more than 2000 cases.

RESULTS

Algorithms for automatically translating therapeutical recommendations into "if conditions then criticize" rules are presented. Eight generic recommendations are also proposed; they are guideline-independent, and can be used as default behaviour for handling various situations that are usually implicit in the guidelines, such as decreasing the dose of a poorly tolerated drug. Finally, we provide models and methods for generating a human-readable textual critique. The system was successfully evaluated on the test base.

CONCLUSION

We show that it is possible to criticize physicians' prescriptions starting from a structured clinical guideline, and to provide clear explanations. We are now planning a randomized clinical trial to evaluate the impact of the system on practices.