Quantification of drug metabolising enzymes and transporter proteins in the paediatric duodenum via LC-MS/MS proteomics using a QconCAT technique.

Characterising the small intestine absorptive membrane is essential to enable prediction of the systemic exposure of oral formulations. In particular, the ontogeny of key intestinal Drug Metabolising Enzymes and Transporter (DMET) proteins involved in drug disposition needs to be elucidated to allow for accurate prediction of the PK profile of drugs in the paediatric cohort. Using pinch biopsies from the paediatric duodenum (n = 36; aged 11 months to 15 years), the abundance of 21 DMET proteins and two enterocyte markers were quantified via LC-MS/MS. An established LCMS nanoflow method was translated to enable analysis on a microflow LC system, and a new stable-isotope-labelled QconCAT standard developed to enable quantification of these proteins. Villin-1 was used to standardise abundancy values. The observed abundancies and ontogeny profiles, agreed with adult LC-MS/MS-based data, and historic paediatric data obtained via western blotting. A linear trend with age was observed for duodenal CYP3A4 and CES2 only. As this work quantified peptides on a pinch biopsy coupled with a microflow method, future studies using a wider population range are very feasible. Furthermore, this DMET ontogeny data can be used to inform paediatric PBPK modelling and to enhance the understanding of oral drug absorption and gut bioavailability in paediatric populations.

Reviewing the risk of breast cancer recurrence following breast reconstruction.

BACKGROUND: It is widely accepted that both autologous and alloplastic reconstruction are safe. A recent publication reported a significant association between textured implants and metastatic recurrence of breast cancer. This study aims to assess if the published results are reproducible in our cohort and to review the safety of breast reconstruction. METHODS: This is a retrospective cohort study of adult patients undergoing mastectomy and either alloplastic or autologous breast reconstruction at a single quaternary hospital. Outcomes include disease free survival (DFS), local and recurrence free survival (LRRFS) and BIA-ALCL. For time to event endpoints, unadjusted and multivariate adjusted hazard ratios (HRs) were estimated using Cox regression, and penalized Cox regression respectively. RESULTS: Four hundred and twenty-six patients of whom 187 underwent autologous reconstruction and 239 underwent alloplastic. There were 43 cancer recurrences (24 alloplastic and 19 autologous) and 14 local regional recurrences (8 alloplastic and 4 autologous). There were 26 deaths and no instances of BIA-ALCL. Median follow-up time was 4.7 years. No evidence of association was found between breast reconstruction method and DFS (HR 0.87 CI: 0.47-1.58). It is uncertain whether implant texture grade was associated with increased breast cancer recurrence (HR 2.17 CI: 0.65-7.52). CONCLUSION: Both autologous and alloplastic breast reconstruction have been carried out in our cohort and reconstructive modality was not associated with either reduced DFS or LRRFS. The results in this cohort show there is uncertainty between the use of textured breast implants and either local or distant breast cancer recurrence.

Comparing Direct-to-Implant and Two-Stage Breast Reconstruction in the Australian Breast Device Registry.

BACKGROUND: There remains a lack of clarity surrounding the benefits, risks, and outcomes between two-stage expander/implant reconstruction and single-stage direct-to-implant (DTI) reconstruction. This study used a national data set to examine real-world outcomes of two-stage and DTI reconstructions. METHODS: A cohort study was conducted examining patients in the Australian Breast Device Registry (ABDR) from 2015 to 2018 who underwent prosthetic breast reconstruction following mastectomy. DTI and two-stage cohorts after definitive implant insertion were compared. Rate of revision surgery, reasons for revision, and patient-reported outcome measures were recorded. Statistical analysis was undertaken using Fisher exact or chi-square, Wilcoxon rank sum, or t tests; Nelson-Aalen cumulative incidence estimates; and Cox proportional hazards regression. RESULTS: A total of 5152 breast reconstructions were recorded, including 3093 two-stage and 2059 DTI reconstructions. Overall revision surgery rates were 15.6% for DTI (median follow-up, 24.7 months), compared with 9.7% in the two-stage cohort (median follow-up, 26.5 months; P < 0.001). The most common reasons for revision for DTI and two-stage reconstruction were capsular contracture (25.2% versus 26.7%; P = 0.714) and implant malposition (26.7% versus 34.3%; P = 0.045). Multivariate analysis found acellular dermal matrix use ( P = 0.028) was significantly associated with a higher risk of revision. The influence of radiotherapy on revision rates was unable to be studied. Patient satisfaction levels were similar between reconstructive groups; however, patient experience was better in the DTI cohort than in the two-stage cohort. CONCLUSIONS: The ABDR data set demonstrated that DTI reconstruction had a higher revision rate than two-stage, but with comparable patient satisfaction and better patient experience. Capsular contracture and device malposition were leading causes of revision in both cohorts. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, III.

Distinct ecological fitness factors coordinated by a conserved Escherichia coli regulator during systemic bloodstream infection.

The ability of bacterial pathogens to adapt to host niches is driven by the carriage and regulation of genes that benefit pathogenic lifestyles. Genes that encode virulence or fitness-enhancing factors must be regulated in response to changing host environments to allow rapid response to challenges presented by the host. Furthermore, this process can be controlled by preexisting transcription factors (TFs) that acquire new roles in tailoring regulatory networks, specifically in pathogens. However, the mechanisms underlying this process are poorly understood. The highly conserved Escherichia coli TF YhaJ exhibits distinct genome-binding dynamics and transcriptome control in pathotypes that occupy different host niches, such as uropathogenic E. coli (UPEC). Here, we report that this important regulator is required for UPEC systemic survival during murine bloodstream infection (BSI). This advantage is gained through the coordinated regulation of a small regulon comprised of both virulence and metabolic genes. YhaJ coordinates activation of both Type 1 and F1C fimbriae, as well as biosynthesis of the amino acid tryptophan, by both direct and indirect mechanisms. Deletion of yhaJ or the individual genes under its control leads to attenuated survival during BSI. Furthermore, all three systems are up-regulated in response to signals derived from serum or systemic host tissue, but not urine, suggesting a niche-specific regulatory trigger that enhances UPEC fitness via pleiotropic mechanisms. Collectively, our results identify YhaJ as a pathotype-specific regulatory aide, enhancing the expression of key genes that are collectively required for UPEC bloodstream pathogenesis.

An Optimised Monophasic Faecal Extraction Method for LC-MS Analysis and Its Application in Gastrointestinal Disease.

Liquid chromatography coupled with mass spectrometry (LC-MS) metabolomic approaches are widely used to investigate underlying pathogenesis of gastrointestinal disease and mechanism of action of treatments. However, there is an unmet requirement to assess faecal metabolite extraction methods for large-scale metabolomics studies. Current methods often rely on biphasic extractions using harmful halogenated solvents, making automation and large-scale studies challenging. The present study reports an optimised monophasic faecal extraction protocol that is suitable for untargeted and targeted LC-MS analyses. The impact of several experimental parameters, including sample weight, extraction solvent, cellular disruption method, and sample-to-solvent ratio, were investigated. It is suggested that a 50 mg freeze-dried faecal sample should be used in a methanol extraction (1:20) using bead beating as the means of cell disruption. This is revealed by a significant increase in number of metabolites detected, improved signal intensity, and wide metabolic coverage given by each of the above extraction parameters. Finally, we addressed the applicability of the method on faecal samples from patients with Crohn's disease (CD) and coeliac disease (CoD), two distinct chronic gastrointestinal diseases involving metabolic perturbations. Untargeted and targeted metabolomic analysis demonstrated the ability of the developed method to detect and stratify metabolites extracted from patient groups and healthy controls (HC), highlighting characteristic changes in the faecal metabolome according to disease. The method developed is, therefore, suitable for the analysis of patients with gastrointestinal disease and can be used to detect and distinguish differences in the metabolomes of CD, CoD, and HC.

The Differential Metabolic Signature of Breast Cancer Cellular Response to Olaparib Treatment.

Metabolic reprogramming and genomic instability are key hallmarks of cancer, the combined analysis of which has gained recent popularity. Given the emerging evidence indicating the role of oncometabolites in DNA damage repair and its routine use in breast cancer treatment, it is timely to fingerprint the impact of olaparib treatment in cellular metabolism. Here, we report the biomolecular response of breast cancer cell lines with DNA damage repair defects to olaparib exposure. Following evaluation of olaparib sensitivity in breast cancer cell lines, we immunoprobed DNA double strand break foci and evaluated changes in cellular metabolism at various olaparib treatment doses using untargeted mass spectrometry-based metabolomics analysis. Following identification of altered features, we performed pathway enrichment analysis to measure key metabolic changes occurring in response to olaparib treatment. We show a cell-line-dependent response to olaparib exposure, and an increased susceptibility to DNA damage foci accumulation in triple-negative breast cancer cell lines. Metabolic changes in response to olaparib treatment were cell-line and dose-dependent, where we predominantly observed metabolic reprogramming of glutamine-derived amino acids and lipids metabolism. Our work demonstrates the effectiveness of combining molecular biology and metabolomics studies for the comprehensive characterisation of cell lines with different genetic profiles. Follow-on studies are needed to map the baseline metabolism of breast cancer cells and their unique response to drug treatment. Fused with genomic and transcriptomics data, such readout can be used to identify key oncometabolites and inform the rationale for the design of novel drugs or chemotherapy combinations.

Lessons Learned in Implementing Patient-Reported Outcome Measures (PROMs) in the Australian Breast Device Registry (ABDR).

BACKGROUND: The Australian Breast Device Registry (ABDR) is a clinical quality registry which utilizes both surgical data and patient-reported outcome measures (PROMs) to understand device performance. The ABDR is the first national breast device registry utilizing the BREAST-Q Implant Surveillance module to conduct PROMs via text messaging as the primary method of contact for most patients. ABDR PROMs are structured upon a successful acceptability and feasibility study and a pilot study. OBJECTIVES: This aim of this paper was to examine the challenges we faced and consider how lessons learned in implementing PROMs might inform future registry studies and interventions. METHODS: We tracked the number of completed follow-ups and documented feedback between October 2017 and December 2018 from various stakeholders, including sites, surgeons, and patients. RESULTS: In total, 10,617 patients were contacted: 59% of breast augmentation and 77% breast reconstruction patients responded to our PROMs survey. We encountered challenges and developed solutions to overcome several key issues, including database setup; follow-up contact methods; ethics; education of surgeons and patients; associated costs; and ongoing evaluation and modification. The strategies we devised to address these challenges included drawing on experiences from previous studies, greater communication with sites and surgeons, and having the flexibility to improve and modify our PROMs. CONCLUSIONS: The ABDR PROMs experience and lessons learned can inform a growing number of registries seeking to conduct PROMs. We describe our approach, obstacles encountered, and strategies to increase patient participation. As more breast device registries worldwide adopt PROMs, data harmonization is crucial to better understand patient outcomes and device performance.

Identification of Predictive Factors for Patient-Reported Outcomes in the Prospective Australian Breast Device Registry.

BACKGROUND: Patient-reported outcome measures (PROMs) are an important tool for evaluating outcomes following breast device procedures and are used by breast device registries. PROMs can assist with device monitoring through benchmarked outcomes but need to account for demographic and clinical factors that may affect PROM responses. OBJECTIVES: This study aimed to develop appropriate risk-adjustment models for the benchmarking of PROM data to accurately track device outcomes and identify outliers in an equitable manner. METHODS: Data for this study were obtained from the Australian Breast Device Registry, which consists of a large prospective cohort of patients with primary breast implants. The 5-question BREAST-Q implant surveillance module was used to assess PROMs at 1 year following implant insertion. Logistic regression models were used to evaluate associations between demographic and clinical characteristics and PROMs separately by implant indication. Final multivariate risk-adjustment models were built sequentially, assessing the independent significant association of these variables. RESULTS: In total, 2221 reconstructive and 12,045 aesthetic primary breast implants with complete 1-year follow-up PROMs were included in the study. Indication for operation (post-cancer, risk reduction, or developmental deformity) was included in the final model for all reconstructive implant PROMs. Site type (private or public hospital) was included in the final breast reconstruction model for look, rippling, and tightness. Age at operation was included in the reconstruction models for rippling and tightness and in the aesthetic models for look, rippling, pain, and tightness. CONCLUSIONS: These multivariate models will be useful for equitable benchmarking of breast devices by PROMs to help track device performance.

Breast Device Surgery in Australia: Early Results from the Australian Breast Device Registry.

BACKGROUND: The Australian Breast Device Registry (ABDR) is a clinical quality registry designed to monitor the performance of breast devices; and the quality and safety of breast device surgery. OBJECTIVE: To report on breast device surgery characteristics across Australia. METHODS: Participants were registered patients in the ABDR from 2012 to 2018. Results are described using percentages, mean and median. Revision rates were calculated using survival analysis methods. RESULTS: A total of 37,603 patients were registered and had undergone reconstruction (post-cancer 15.1%, risk-reducing mastectomy 3.4% and developmental deformity 2.4%) or cosmetic augmentation (74.7%) procedures. The majority of breast implant devices were silicone filled with textured surface (reconstruction 74.0% and augmentation 64.0%). Sub-pectoral plane was the most common for both reconstruction (60.1%) and augmentation (76.6%) procedures. For reconstruction surgery, the most common surgical incision was previous mastectomy scar (44.0%) and inframammary (31.8%), and for augmentation, it was inframammary (83.4%). Intraoperative/postoperative antibiotic usage for reconstruction was 85.8% and augmentation was 89.4%. Revision incidence due to complication at 12 months post-cancer reconstruction was 5.1%, risk-reducing reconstruction 5.7% and developmental deformity implants 4.5%. Revision incidence due to complication at 12 months after augmentation procedure was 1.1%. Patient-reported outcome measures (PROMs) indicate high levels of satisfaction at 1 year for augmentation and reconstruction procedures. CONCLUSION: We report on early data from the ABDR and reflect on the uptake of the registry by surgeons and patients. The registry also benefits from international collaborative approaches to addressing challenges and is committed to facilitate international post-market surveillance.

NS5A resistance leading to failure of 24-week therapy with sofosbuvir/ledipasvir and ribavirin for the treatment of hepatitis C genotype 1a infection in a HIV-1 co-infected patient.

Herein we report a previously undescribed case of treatment-emergent non-structural protein 5A (NS5A) resistance mutations, Q30H and Y93C, leading to a failure of 24-week course of sofosbuvir/ledipasvir+ribavirin therapy for the treatment of hepatitis C virus (HCV) genotype 1a in interferon-experienced, human immunodeficiency virus type 1 (HIV-1) co-infected patient with cirrhosis.

Dualities of living with HIV/HCV co-infection: patients' perspectives from those who are ineligible for or nonresponsive to treatment.

In Europe, an estimated 33% of HIV-infected individuals are co-infected with the hepatitis C virus (HCV). The aim of this study was to develop an understanding of the experiences of patients ineligible for or not responding to treatment. Patients attending an HIV/HCV clinic were interviewed. A qualitative design using hermeneutic interpretive phenomenology was employed. Transcripts, field notes, and a reflexive journal were analyzed to extract themes and identify commonalities, differences, and hidden meanings. In line with the duality of co-infection, duality was observed in responses. Participants described defining negative moments in their lives that resulted in developing positive health care strategies. Another dichotomy was one of loneliness and of social relationships. Finally, participants described a revival phenomenon, moving from feelings of death to looking forward to unexpected futures. Those working with co-infected patients need to be aware of how duality impacts people who are ineligible for or nonresponsive to treatment.

Variation in both IL28B and KIR2DS3 genes influence pegylated interferon and ribavirin hepatitis C treatment outcome in HIV-1 co-infection.

Pegylated-IFN and ribavirin remains the current treatment for chronic HCV infection in patients co-infected with HIV-1, but this regimen has low efficacy rates, particularly for HCV genotype 1/4 infection, has severe side effects and is extremely costly. Therefore, accurate prediction of treatment response is urgently required. We have recently shown that the NK cell gene, KIR2DS3 and a SNP associated with the IL28B gene synergise to increase the risk of chronic infection in primary HCV mono-infected patients. Identification of SNPs associated with the IL28B gene has also proven very powerful for predicting patient response to treatment. Patients co-infected with HIV-1 are of particular concern given they respond less well to HCV treatment, have more side effects and suffer a more rapid liver disease progression. In this study, we examined both IL28B and KIR2DS3 for their ability to predict treatment response in a cohort of HIV-1/HCV co-infected patients attending two treatment centres in Europe. We found that variation in both host genetic risk factors, IL28B and KIR2DS3, was strongly associated with sustained virological response (SVR) to treatment in our co-infected cohort (n = 149). The majority of patients who achieved a rapid virological response (RVR) achieved a SVR. However, it is currently impossible to predict treatment outcome in patients who fail to achieve an RVR. In our cohort, the presence of host genetic risk factors, IL28B-T and KIR2DS3 alleles, resulted in increased odds of treatment failure in these RVR negative patients (n = 88). Our data suggests that testing for host genetic factors will improve predicting treatment responsiveness in the clinical management of co-infected patients, and provides further evidence of the importance of the innate immune system in the immune response to HCV.

Human immunodeficiency virus type 1 in Ireland: phylogenetic evidence for risk group-specific subepidemics.

HIV genetic diversity may have an impact on viral pathogenesis, transmission, response to treatment, and vaccine development. Public health surveillance that monitors the frequency and variety of HIV subtypes in a particular region or patient group is vital to successfully control the pandemic. We present the first comprehensive report on HIV diversity in Ireland. This study comprised all new HIV-1 diagnoses that were confirmed in the National Virus Reference Laboratory, University College Dublin, from January 2004 to December 2008. HIV 1 protease and reverse transcriptase sequences were generated using the Siemens Trugene HIV 1 Genotyping System. Subtypes were determined using web-based genotyping tools. There were 1579 new diagnoses [615 (39%) female and 964 (61%) male], of which 1060 had HIV-1 RNA specimens available for sequencing. Of sequenced samples, HIV-1 subtype B accounted for 50% overall, decreasing from 55.1% in 2004 to 49.5% in 2008. In addition, subtype B accounted for more than 80% of Irish-born individuals and more than 90% of Irish-born injection drug users and men who have sex with men. Subtype C was the second most prevalent in the overall cohort, accounting for 25%, although it accounted for only 6.1% of Irish-born individuals, with no evidence of in country transmission. The prevalence of non-subtype B HIV-1 infection in Ireland is increasing. However, these appear primarily to be imported infections not yet circulating within traditional Irish risk groups. Enhanced HIV-1 molecular epidemiology surveillance is required to monitor the spread of HIV-1, to inform future public health policy, and to ultimately control the HIV-1 epidemic in Ireland.

Documented prevalence of HIV type 1 antiretroviral transmitted drug resistance in Ireland from 2004 to 2008.

HIV-1-infected individuals with transmitted HIV drug resistance (TDR) begin antiretroviral therapy (ART) with a lower genetic barrier to resistance and a higher risk of both virological failure and of developing further resistance. TDR surveillance informs HIV-1 public health strategies and first line ART. TDR has not been studied nationally in an Irish population. This study includes all new HIV diagnoses from January 2004 to September 2008 from the National Virus Reference Laboratory, University College Dublin. HIV-1 protease and reverse transcriptase sequences were generated, and resistance mutations identified using the Siemens TRUGENE HIV-1 Genotyping System. Subtypes were determined using web-based genotyping tools. The study comprised 1579 patients. There were 305 new diagnoses in 2004 (173 male; 132 female), 298 in 2005 (175M; 123F), 321 in 2006 (197M; 124F), 297 in 2007 (184M; 113F), and 358 (235M; 123F) in 2008. HIV-1 RNA was sequenced from 158/305 patients in 2004, 199/298 in 2005, 225/321 in 2006, 203/297 in 2007, and 275/358 in 2008. The overall TDR rate was 6.3%, peaking in 2006 at 10.4% and declining to 5.3% in 2008. The majority of TDR was seen in Irish born individuals with HIV-1 subtype B infection. The TDR rate in Ireland is comparatively low. Thus, a health technology assessment is required to ascertain the most cost effective use of genotypic antiretroviral resistance testing (GART) in the future: the current approach of performing baseline GART on all new diagnoses, or perhaps a more targeted approach that focuses on patients commencing nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART.

Elevated serum levels of interferon- gamma -inducible protein-10 in patients coinfected with hepatitis C virus and HIV.

Coinfection with hepatitis C virus (HCV) and human immunodeficiency virus (HIV) is associated with an accelerated course of HCV infection and a faster progression to severe liver disease. We have investigated whether the development of liver disease in coinfected patients is associated with specific chemokine and cytokine production. Four cohorts--HCV/HIV-coinfected patients, HCV-monoinfected patients, HIV-monoinfected patients, and healthy control subjects--were studied. Serum levels of the 10-kDa interferon- gamma -inducible protein (IP-10) were higher in all 3 groups of infected patients than in control subjects (P<.0001). HCV/HIV-coinfected patients had significantly higher IP-10 levels than monoinfected patients. In HCV-monoinfected patients, liver fibrosis scores and liver enzyme levels were positively correlated with IP-10 levels. Elevated IP-10 levels are associated with and may contribute to liver damage in both HCV-monoinfected and HCV/HIV-coinfected patients.

The AoPR10 promoter and certain endogenous PR10 genes respond to oxidative signals in Arabidopsis.

SUMMARY The PR10 class of genes has been associated with plant defence. Previous studies with an asparagus PR10 gene (AoPR1) promoter in heterologous plants suggested that the AoPR10-GUS transgene was responsive to oxidative signals/stresses. Arabidopsis thaliana AoPR10-GUS transgenics allowed expression to be compared with that of a close homologue from the large family of PR10 class genes within the Arabidopsis genome. AoPR10-GUS was induced developmentally at sites of phenylpropanoid accumulation and by wounding, pathogen challenge and treatment with H(2)O(2) but not with salicylic acid (SA), ethylene, methyljasmonate or NO donors. Both wound- and pathogen-associated AoPR10-GUS expression could be suppressed by superoxide dismutase and the NADPH oxidase inhibitor, diphenylene iodonium. Northern blotting using an Arabidopsis PR10 homologue as a probe revealed transcript up-regulation by oxidative species generated by glucose oxidase and xanthine oxidase. In Arabidopsis, the AoPR10-GUS transgene was potentiated by SA and expressed systemically following wounding or challenge with avirulent bacteria. AoPR10-GUS x npr1-1 crosses revealed that potentiation and systemic expression was NPR1-independent. Systemic AoPR10-GUS expression following elicitation of a hypersensitive response but not wounding was abolished in NahG crosses, suggesting an SA-mediated potentiating action during SAR (systemic acquired resistance). These data suggest that the AoPR10 promoter reports the expression of reactive oxygen species-responsive PR10 genes and may indicate systemic changes in oxidative status following either wounding and/or the elicitation of a hypersensitive response in Arabidopsis.