A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris.

Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we confirm the previously reported finding that B11220 was missing a 12.8 kb region on chromosome VI. This region contains a gene cluster encoding proteins related to alternative sugar utilization. We show that B11221, which has the gene cluster, readily assimilates and utilizes D-galactose and L-rhamnose as compared to B11220, which harbors the deletion. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both isolates grown on glucose or galactose showed that the gene cluster was upregulated when grown on D-galactose. These findings reinforce growing evidence of a link between metabolism and drug tolerance. B11221 resists phagocytosis by macrophages and exhibits decreased ß-1,3-glucan exposure, a key determinant that allows Candida to evade the host immune system, as compared to B11220. In a transcriptomic analysis of both isolates co-cultured with macrophages, we find upregulation of genes associated with transport and transcription factors in B11221. Our studies show a positive correlation between membrane composition and immune evasion, alternate sugar utilization, and drug tolerance in C. auris.

A Comprehensive Evaluation of the Effects of RNA-Editing Proteins ADAR and ADARB1 on the Expression of the Drug-Metabolizing Enzymes in HepaRG Cells.

Two RNA-editing proteins, the adenosine deaminase acting on RNA, ADAR, and ADARB1, broadly regulate gene expression in editing-dependent and editing-independent manners. Previous studies showed that the expression of the drug-metabolizing cytochrome P450s (P450s) and UDP glucuronosyltransferases (UGTs) changes upon knockdown (KD) of ADAR or ADARB1 in different hepatic cell lines. To systematically survey the effects of these two ADARs on the expression of P450s and UGTs, we used small interfering RNA in HepaRG cells and tested the association between the expression of the P450s and ADARs in a liver sample cohort (n = 246). KD of ADAR increased the expression of the CYP3As and CYP2C9 and reduced the expression of the others, whereas KD of ADARB1 reduced the expression of nearly all genes tested. ADAR KD also suppressed the induction of most P450s, whereas ADARB1 KD had mixed effects depending on the inducer/gene combination. P450 expression was positively associated with both ADARs in liver samples, consistent with the KD results. However, after adjusting for the expression of transcription factors (TFs) known to regulate P450 expression, the associations disappeared, indicating that the effects of ADAR or ADARB1 primarily occur through TFs. Moreover, we found that the expression of normally spliced CYP3A5 transcripts is increased in both KDs, indicating a direct effect of the ADARs on promoting the usage of the cryptic splice site generated by CYP3A5*3. Taken together, our results revealed the nonoverlapping regulatory effects of ADAR and ADARB1 and supported their broad roles in controlling the expression of drug-metabolizing enzymes in the liver. SIGNIFICANCE STATEMENT: Here, this study systematically surveyed the roles of ADAR and ADARB1 in both basal and induced expression of drug-metabolizing enzymes and assessed their coexpression in liver samples. This study's results support that ADAR and ADARB1 regulate the expression of the drug-metabolizing enzymes in the liver, suggesting that factors affecting ADAR expression also have the potential to impact drug metabolism.

Modeling Contraception and Pregnancy in Malawi: A Thanzi La Onse Mathematical Modeling Study.

Malawi has high unmet need for contraception with a costed national plan to increase contraception use. Estimating how such investments might impact future population size in Malawi can help policymakers understand effects and value of policies to increase contraception uptake. We developed a new model of contraception and pregnancy using individual-level data capturing complexities of contraception initiation, switching, discontinuation, and failure by contraception method, accounting for differences by individual characteristics. We modeled contraception scale-up via a population campaign to increase initiation of contraception (Pop) and a postpartum family planning intervention (PPFP). We calibrated the model without new interventions to the UN World Population Prospects 2019 medium variant projection of births for Malawi. Without interventions Malawi's population passes 60 million in 2084; with Pop and PPFP interventions. it peaks below 35 million by 2100. We compare contraception coverage and costs, by method, with and without interventions, from 2023 to 2050. We estimate investments in contraception scale-up correspond to only 0.9 percent of total health expenditure per capita though could result in dramatic reductions of current pressures of very rapid population growth on health services, schools, land, and society, helping Malawi achieve national and global health and development goals.

Regulation of CYP3A4 and CYP3A5 by a lncRNA: a potential underlying mechanism explaining the association between CYP3A4*1G and CYP3A metabolism.

The cytochrome P450 3A4 (CYP3A4) enzyme is the most abundant drug-metabolizing enzyme in the liver, displaying large inter-person variability with unknown causes. In this study, we found that the expression of CYP3A4 is negatively correlated with AC069294.1 (ENSG00000273407, ENST00000608397.1), a lncRNA generated antisense to CYP3A4. Knockdown of AC069294.1 in Huh7 cells increased CYP3A4 mRNA ~3-fold, whereas overexpression of AC069294.1 decreased CYP3A4 mRNA by 89%. We also observed changes in CYP3A5 expression when AC069294.1 was knocked down or overexpressed, indicating dual effects of AC069294.1 on both CYP3A4 and CYP3A5 expression. Consistently, the expression level of CYP3A5 is also negatively correlated with AC069294.1. Previous studies have shown associations between an intronic single nucleotide polymorphism CYP3A4*1G (rs2242480) and CYP3A metabolism, but the results are inconsistent and the underlying mechanism is unclear. We show here that CYP3A4*1G (rs2242480) is associated with 1.26-fold increased expression of AC069294.1 (P < 0.0001), and decreased expression of CYP3A4 by 31% (P = 0.008) and CYP3A5 by 39% (P = 0.004). CYP3A4*1G is located ~2.7 kb upstream of AC069294.1 and has been previously reported to have increased transcriptional activity in reporter gene assays. Taken together, our results demonstrate the regulation of CYP3A4 and CYP3A5 by a novel lncRNA AC069294.1. Our results also indicate that the clinically observed CYP3A4*1G associations may be caused by its effect on the expression of AC069294.1, and thereby altered expression of both CYP3A4 and CYP3A5. Furthermore, because CYP3A4*1G is in high linkage disequilibrium with CYP3A5*1, increased AC069294.1 expression caused by CYP3A4*1G may decrease expression of the normal-functioning CYP3A5*1, explaining additional inter-person variability of CYP3A5.

Transcriptional Regulation of Carboxylesterase 1 in Human Liver: Role of the Nuclear Receptor Subfamily 1 Group H Member 3 and Its Splice Isoforms.

Carboxylesterase 1 (CES1) is the predominant carboxylesterase in the human liver, involved in metabolism of both xenobiotics and endogenous substrates. Genetic or epigenetic factors that alter CES1 activity or expression are associated with changes in drug response, lipid, and glucose homeostasis. However, the transcriptional regulation of CES1 in the human liver remains uncertain. By applying both the random forest and Sobol's Sensitivity Indices (SSI) to analyze existing liver RNA expression microarray data (GSE9588), we identified nuclear receptor subfamily 1 group H member 3 (NR1H3) liver X receptor (LXR)α as a key factor regulating constitutive CES1 expression. This model prediction was validated using small interfering RNA (siRNA) knockdown and CRISPR-mediated transcriptional activation of NR1H3 in Huh7 and HepG2 cells. We found that NR1H3's activation of CES1 is splice isoform-specific, namely that increased expression of the NR1H3-211 isoform increased CES1 expression whereas NR1H3-201 did not. Also, in human liver samples, expression of NR1H3-211 and CES1 are correlated, whereas NR1H3-201 and CES1 are not. This trend also occurs during differentiation of induced pluripotent stem cells (iPSCs) to hepatocytes, where only expression of the NR1H3-211 isoform parallels expression of CES1 Moreover, we found that treatment with the NR1H3 agonist T0901317 in HepG2 cells had no effect on CES1 expression. Overall, our results demonstrate a key role of NR1H3 in maintaining the constitutive expression of CES1 in the human liver. Furthermore, our results support that the effect of NR1H3 is splice isoform-specific and appears to be ligand independent. SIGNIFICANCE STATEMENT: Despite the central role of carboxylesterase 1 (CES1) in metabolism of numerous medications, little is known about its transcriptional regulation. This study identifies nuclear receptor subfamily 1 group H member 3 as a key regulator of constitutive CES1 expression and therefore is a potential target for future studies to understand interperson variabilities in CES1 activity and drug metabolism.

Health-related quality of life impacts upon 5-year survival after coronary artery bypass surgery.

BACKGROUND: Poor preoperative health-related quality of life (HRQoL) has been associated with reduced short-term survival after coronary artery bypass graft (CABG) surgery; however, its impact on long-term mortality is unknown. This study's objective was to determine if baseline HRQoL status predicts 5-year post-CABG mortality. METHODS: This prespecified, randomized on/off bypass follow-up study (ROOBY-FS) subanalysis compared baseline patient characteristics and HRQoL scores, obtained from the Seattle Angina Questionnaire (SAQ) and Veterans RAND Short Form-36 (VR-36), between 5-year post-CABG survivors and nonsurvivors. Standardized subscores were calculated for each questionnaire. Multivariable logistic regression assessed whether HRQoL survey subcomponents independently predicted 5-year mortality (p ≤ .05). RESULTS: Of the 2203 ROOBY-FS enrollees, 2104 (95.5%) completed baseline surveys. Significant differences between 5-year post-CABG deaths (n = 286) and survivors (n = 1818) included age, history of chronic obstructive pulmonary disease, stroke, peripheral vascular disease, renal dysfunction, diabetes, lower left ventricular ejection fraction, atrial fibrillation, depression, non-White race/ethnicity, lower education status, and off-pump CABG. Adjusting for these factors, baseline VR-36 physical component summary score (p = .01), VR-36 mental component summary score (p < .001), and SAQ physical limitation score (p = .003) were all associated with 5-year all-cause mortality. CONCLUSIONS: Pre-CABG HRQoL scores may provide clinically relevant prognostic information beyond traditional risk models and prove useful for patient-provider shared decision-making and enhancing pre-CABG informed consent.

ESR1 ChIP-Seq Identifies Distinct Ligand-Free ESR1 Genomic Binding Sites in Human Hepatocytes and Liver Tissue.

The estrogen receptor alpha (ESR1) is an important gene transcriptional regulator, known to mediate the effects of estrogen. Canonically, ESR1 is activated by its ligand estrogen. However, the role of unliganded ESR1 in transcriptional regulation has been gaining attention. We have recently shown that ligand-free ESR1 is a key regulator of several cytochrome P450 (CYP) genes in the liver, however ligand-free ESR1 has not been characterized genome-wide in the human liver. To address this, ESR1 ChIP-Seq was conducted in human liver samples and in hepatocytes with or without 17beta-estradiol (E2) treatment. We identified both ligand-dependent and ligand-independent binding sites throughout the genome. These two ESR1 binding categories showed different genomic localization, pathway enrichment, and cofactor colocalization, indicating different ESR1 regulatory function depending on ligand availability. By analyzing existing ESR1 data from additional human cell lines, we uncovered a potential ligand-independent ESR1 activity, namely its co-enrichment with the zinc finger protein 143 (ZNF143). Furthermore, we identified ESR1 binding sites near many gene loci related to drug therapy, including the CYPs. Overall, this study shows distinct ligand-free and ligand-bound ESR1 chromatin binding profiles in the liver and suggests the potential broad influence of ESR1 in drug metabolism and drug therapy.

Review: Veratrum californicum Alkaloids.

Veratrum spp. grow throughout the world and are especially prevalent in high mountain meadows of North America. All parts of Veratrum plants have been used for the treatment of ailments including injuries, hypertension, and rheumatic pain since as far back as the 1600s. Of the 17-45 Veratrum spp., Veratrum californicum alkaloids have been proven to possess favorable medicinal properties associated with inhibition of hedgehog (Hh) pathway signaling. Aberrant Hh signaling leads to proliferation of over 20 cancers, including basal cell carcinoma, prostate and colon among others. Six of the most well-studied V. californicum alkaloids are cyclopamine (1), veratramine (2), isorubijervine (3), muldamine (4), cycloposine (5), and veratrosine (6). Recent inspection of the ethanolic extract from V. californicum root and rhizome via liquid chromatography-mass spectrometry has detected up to five additional alkaloids that are proposed to be verazine (7), etioline (8), tetrahydrojervine (9), dihydrojervine (10), 22-keto-26-aminocholesterol (11). For each alkaloid identified or proposed in V. californicum, this review surveys literature precedents for extraction methods, isolation, identification, characterization and bioactivity to guide natural product drug discovery associated with this medicinal plant.

Cis-acting regulatory elements regulating CYP3A4 transcription in human liver.

The CYP3A4 enzyme is the most abundant drug-metabolizing enzyme in the liver, metabolizing ~50% of commonly used medications. CYP3A4 displays large interperson variability in expression and enzyme activity with unknown causes. This study aims to identify cis-acting regulatory elements controlling the transcription of CYP3A4, using chromatin conformation capture (4C and 3C assays), chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR), clustered regularly interspaced short palindromic repeats (CRISPR)-mediated deletions of genomic regions and reporter gene assays in primary culture human hepatocytes and hepatic cell lines. 4C assays identified four regions (R1-R4) interacting with the CYP3A4 promoter, one of which overlaps with the previously identified upstream enhancers CLEM4/XREM (R2) while the other three are novel. ChIP-qPCR, reporter gene assays and CRISPR-mediated deletion experiments indicate regulatory roles for both R2 and R4. Interestingly, the deletion of R4 increased CYP3A4 while decreasing CYP3A43 expression, possibly due to competitive domain-domain interactions within the CYP3A cluster, supported by deletion of R4 increasing interaction between the CYP3A4 promoter and R2. We also identified a single nucleotide polymorphism rs62471956 within R4, with the variant allele A having increased transcriptional activity in a reporter gene assay. The rs62471956 A allele is associated with higher CYP3A43 expression and lower CYP3A4 expression in a cohort of 136 liver samples, further supporting the opposing effects of R4 on CYP3A4 and CYP3A43. rs62471956 is in complete linkage disequilibrium with CYP3A4*22, potentially contributing to reduced expression of CYP3A4*22. These results validate previously identified enhancers (CLEM4 and XREM) of CYP3A4 and demonstrate additional regulatory mechanisms underlying CYP3A4 transcriptional control via competitive domain-domain interactions within the CYP3A cluster.

Five-Year Outcomes after On-Pump and Off-Pump Coronary-Artery Bypass.

BACKGROUND: Coronary-artery bypass grafting (CABG) surgery may be performed either with cardiopulmonary bypass (on pump) or without cardiopulmonary bypass (off pump). We report the 5-year clinical outcomes in patients who had been included in the Veterans Affairs trial of on-pump versus off-pump CABG. METHODS: From February 2002 through June 2007, we randomly assigned 2203 patients at 18 medical centers to undergo either on-pump or off-pump CABG, with 1-year assessments completed by May 2008. The two primary 5-year outcomes were death from any cause and a composite outcome of major adverse cardiovascular events, defined as death from any cause, repeat revascularization (CABG or percutaneous coronary intervention), or nonfatal myocardial infarction. Secondary 5-year outcomes included death from cardiac causes, repeat revascularization, and nonfatal myocardial infarction. Primary outcomes were assessed at a P value of 0.05 or less, and secondary outcomes at a P value of 0.01 or less. RESULTS: The rate of death at 5 years was 15.2% in the off-pump group versus 11.9% in the on-pump group (relative risk, 1.28; 95% confidence interval [CI], 1.03 to 1.58; P=0.02). The rate of major adverse cardiovascular events at 5 years was 31.0% in the off-pump group versus 27.1% in the on-pump group (relative risk, 1.14; 95% CI, 1.00 to 1.30; P=0.046). For the 5-year secondary outcomes, no significant differences were observed: for nonfatal myocardial infarction, the rate was 12.1% in the off-pump group and 9.6% in the on-pump group (P=0.05); for death from cardiac causes, the rate was 6.3% and 5.3%, respectively (P=0.29); for repeat revascularization, the rate was 13.1% and 11.9%, respectively (P=0.39); and for repeat CABG, the rate was 1.4% and 0.5%, respectively (P=0.02). CONCLUSIONS: In this randomized trial, off-pump CABG led to lower rates of 5-year survival and event-free survival than on-pump CABG. (Funded by the Department of Veterans Affairs Office of Research and Development Cooperative Studies Program and others; ROOBY-FS ClinicalTrials.gov number, NCT01924442 .).

Gone Caving: Roles of the Transcriptional Regulators YAP and TAZ in Skeletal Development.

PURPOSE OF REVIEW: The development of the skeleton is controlled by cellular decisions determined by the coordinated activation of multiple transcription factors. Recent evidence suggests that the transcriptional regulator proteins, Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), could have important roles in directing the activity of these transcriptional programs. However, in vitro evidence for the roles of YAP and TAZ in skeletal cells has been hopelessly contradictory. The goals of this review are to provide a cross-sectional view on the state of the field and to synthesize the available data toward a unified perspective. RECENT FINDINGS: YAP and TAZ are regulated by diverse upstream signals and interact downstream with multiple transcription factors involved in skeletal development, positioning YAP and TAZ as important signal integration nodes in an hourglass-shaped signaling pathway. Here, we provide a survey of putative transcriptional co-effectors for YAP and TAZ in skeletal cells. Synthesizing the in vitro data, we conclude that TAZ is consistently pro-osteogenic in function, while YAP can exhibit either pro- or anti-osteogenic activity depending on cell type and context. Synthesizing the in vivo data, we conclude that YAP and TAZ combinatorially promote developmental bone formation, bone matrix homeostasis, and endochondral fracture repair by regulating a variety of transcriptional programs depending on developmental stage. Here, we discuss the current understanding of the roles of the transcriptional regulators YAP and TAZ in skeletal development, and provide recommendations for continued study of molecular mechanisms, mechanotransduction, and therapeutic implications for skeletal disease.

A Randomized Controlled Trial of TELEmedicine for Patients with Inflammatory Bowel Disease (TELE-IBD).

INTRODUCTION: Telemedicine has shown promise in inflammatory bowel disease (IBD). The objective of this study was to compare disease activity and quality of life (QoL) in a 1-year randomized trial of IBD patients receiving telemedicine vs. standard care. METHODS: Patients with worsening symptoms in the prior 2 years were eligible for randomization to telemedicine (monitoring via texts EOW or weekly) or standard care. The primary outcomes were the differences in change in disease activity and QoL between the groups; change in healthcare utilization among groups was a secondary aim. RESULTS: 348 participants were enrolled (117 control group, 115 TELE-IBD EOW, and 116 TELE-IBD weekly). 259 (74.4%) completed the study. Age was 38.9 ± 12.3 years, 56.6% were women, 91.9% were Caucasian, 67.9% had Crohn's disease (CD) and 42.5% had active disease at baseline. In CD, all groups experienced a decrease in disease activity (control -5.2 ± 5.0 to 3.7 ± 3.6, TELE-IBD EOW 4.7 ± 4.1 to 4.2 ± 3.9, and TELE-IBD weekly 4.2 ± 4.2 to 3.2 ± 3.4, p < 0.0001 for each of the groups) In UC, only controls had a significant decrease in disease activity (control 2.9 ± 3.1 to 1.4 ± 1.4, p = 0.01, TELE-IBD EOW 2.7 ± 3.1 to 1.7 ± 1.9, p = 0.35, and TELE-IBD Weekly 2.5 ± 2.5 to 2.0 ± 1.8, p = 0.31). QoL increased in all groups; the increase was significant only in TELE-IBD EOW (control 168.1 ± 34.0 to 179.3 ± 28.2, p = 0.06, TELE-IBD EOW 172.3 ± 33.1 to 181.5 ± 28.2, p = 0.03, and TELE-IBD Weekly 172.3 ± 34.5 to 179.2 ± 32.8, p = 0.10). Unadjusted and adjusted changes in disease activity and QoL were not significantly different among groups. Healthcare utilization increased in all groups. TELE-IBD weekly were less likely to have IBD-related hospitalizations and more likely to have non-invasive diagnostic tests and electronic encounters compared to controls; both TELE-IBD groups had decreased non-IBD related hospitalizations and increased telephone calls compared to controls. DISCUSSION: Disease activity and QoL, although improved in all participants, were not improved further through use of the TELE-IBD system. TELE-IBD participants experienced a decrease in hospitalizations with an associated increase in non-invasive diagnostic tests, telephone calls and electronic encounters. Research is needed to determine if TELE-IBD can be improved through patient engagement and whether it can decrease healthcare utilization by replacing standard care.

Characterization of Individual Human Antibodies That Bind Pertussis Toxin Stimulated by Acellular Immunization.

Despite high vaccination rates, the incidence of whooping cough has steadily been increasing in developing countries for several decades. The current acellular pertussis (aP) vaccines all include the major protective antigen pertussis toxin (PTx) and are safer, but they appear to be less protective than infection or older, whole-cell vaccines. To better understand the attributes of individual antibodies stimulated by aP, we isolated plasmablast clones recognizing PTx after booster immunization of two donors. Five unique antibody sequences recognizing native PTx were recovered and expressed as recombinant human IgG1 antibodies. The antibodies all bind different epitopes on the PTx S1 subunit, B oligomer, or S1-B subunit interface, and just one clone neutralized PTx in an in vitro assay. To better understand the epitopes bound by the nonneutralizing S1-subunit antibodies, comprehensive mutagenesis with yeast display provided a detailed map of the epitope recognized by antibodies A8 and E12. Residue R76 is required for antibody A8 binding and is present on the S1 surface but is only partially exposed in the holotoxin, providing a structural explanation for A8's inability to neutralize holotoxin. The B-subunit-specific antibody D8 inhibited PTx binding to a model receptor and neutralized PTx in vitro as well as in an in vivo leukocytosis assay. This is the first study, to our knowledge, to identify individual human antibodies stimulated by the acellular pertussis vaccine and demonstrates the feasibility of using these approaches to address outstanding issues in pertussis vaccinology, including mechanisms of accelerated waning of protective immunity despite repeated aP immunization.

Preoperative factors associated with worsening in health-related quality of life following coronary artery bypass grafting in the Randomized On/Off Bypass (ROOBY) trial.

For advanced coronary disease, coronary artery bypass graft (CABG) surgery generally improves patients' symptoms and long-term survival. Unfortunately, some patients experience worse health-related quality of life (HRQL) after CABG. The objective of this study is to report the frequency and risk factors associated with 1-year post-CABG HRQL deterioration. METHODS: From 2002 to 2007, 2203 "Randomized On/Off Bypass" (ROOBY) trial patients randomly received either off-pump or on-pump CABG at 18 VA medical centers. Subjects completed both baseline and 1-year Seattle Angina Questionnaire (SAQ) and the Veterans Rand 36 (VR-36) questionnaires to assess HRQL. Using previously published criteria, the rates of clinically significant changes were determined for the SAQ [angina frequency (AF), physical limitation (PL), and quality of life (QoL)] and VR36 [mental component score (MCS) and physical component score (PCS)] subscales. Multivariate regression models were then used to identify pre-CABG patient characteristics associated with worsened 1-year HRQL status for each subscale. RESULTS: Over 80% of patients had an improvement or no change in SAQ and VR-36 subscale scores 1 year after CABG. The HRQL scale-specific deterioration rates were 4.5% SAQ-AF, 16.8% SAQ-PL, 4.9% SAQ-QoL, 19.4% VR36-MCS, and 13.5% VR36-PCS. Predictors of 1-year HRQL deterioration were diabetes and smoking for the SAQ-AF; diabetes, chronic obstructive pulmonary disease (COPD), and peripheral vascular disease (PVD) for SAQ-PL; COPD and depression for the SAQ-QoL; diabetes for VR36-PCS, and history of stroke and depression for VR36-MCS. The baseline score was an independent predictor for worsening in all the subscales studied. CONCLUSIONS: Among VA patients, less than 20% experienced worse HRQL 1 year after CABG. For patients with low symptom burden at baseline, diabetes, smoking, depression, PVD, COPD, and a prior stroke, clinicians should be more cautious in pre-CABG counseling as to their anticipated HRQL improvements.

Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.

Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide and whole transcriptome sequence analyses were performed on tumors from six patients with advanced, sporadic intrahepatic cholangiocarcinoma (SIC) to identify potential therapeutically actionable events. Among the somatic events captured in our analysis, we uncovered two novel therapeutically relevant genomic contexts that when acted upon, resulted in preliminary evidence of anti-tumor activity. Genome-wide structural analysis of sequence data revealed recurrent translocation events involving the FGFR2 locus in three of six assessed patients. These observations and supporting evidence triggered the use of FGFR inhibitors in these patients. In one example, preliminary anti-tumor activity of pazopanib (in vitro FGFR2 IC50≈350 nM) was noted in a patient with an FGFR2-TACC3 fusion. After progression on pazopanib, the same patient also had stable disease on ponatinib, a pan-FGFR inhibitor (in vitro, FGFR2 IC50≈8 nM). In an independent non-FGFR2 translocation patient, exome and transcriptome analysis revealed an allele specific somatic nonsense mutation (E384X) in ERRFI1, a direct negative regulator of EGFR activation. Rapid and robust disease regression was noted in this ERRFI1 inactivated tumor when treated with erlotinib, an EGFR kinase inhibitor. FGFR2 fusions and ERRFI mutations may represent novel targets in sporadic intrahepatic cholangiocarcinoma and trials should be characterized in larger cohorts of patients with these aberrations.

Concordance between administrative data and clinical review for mortality in the randomized on/off bypass follow-up study (ROOBY-FS).

BACKGROUND: The optimal methodology to identify cardiac versus non-cardiac cause of death following cardiac surgery has not been determined. METHODS: The Randomized On/Off Bypass Trial was a multicenter, randomized, controlled clinical trial of 2203 patients (February 2002-May 2008) comparing 1-year cardiac outcomes between off-pump and on-pump bypass surgery. In 2013, the Veterans Affairs (VA) Cooperative Studies Program funded a follow-up study to assess 5-year outcomes including mortality. Deaths were identified and confirmed using the National Death Index (NDI), VA Vital Status file, and medical records. An Endpoints Committee (EC) reviewed patient medical records and classified each cause of death as cardiac, non-cardiac, or unknown. Using pre-determined ICD-10 codes, NDI death certificates were independently used to classify deaths as cardiac or non-cardiac. Cause of death was compared between the NDI and EC classifications and concordance measured, using Kappa statistics. RESULTS: Of the 297 5-year deaths identified by the NDI and/or VA vital status file and confirmed by the EC, 219 had adequate patient records for EC cause of death determination. The EC adjudicated 141 of these deaths as non-cardiac and 78 as cardiac, while the NDI classified 150 as non-cardiac and 69 as cardiac; agreement was 77.6% (kappa 0.500; P < 0.001). CONCLUSIONS: Since concordance between EC and NDI cause of death classifications was only moderate, caution should be exercised in relying exclusively on NDI data to determine cause of death. A hybrid approach, integrating multiple information sources, may provide the most accurate approach to classifying cause of death.

Hormone resuscitation therapy for brain-dead donors - is insulin beneficial or detrimental?

Hormonal replacement therapy to brain-dead potential organ donors remains controversial. A retrospective study was carried out of hormonal therapy on procurement of organs in 63 593 donors in whom information on thyroid hormone therapy (triiodothyronine or levothyroxine [T3 /T4 ]) was available. In 40 124 donors, T3 /T4 and all other hormonal therapy were recorded. The percentage of all organs procured, except livers, was greater when T3 /T4 had been administered. An independent beneficial effect of antidiuretic hormone (ADH) was also clear. Corticosteroids were less consistently beneficial (most frequently when T3 /T4 had not been administered), although never detrimental. Insulin was almost never beneficial and at times was associated with a reduced yield of organs, particularly of the pancreas and intestine, an observation that does not appear to have been reported previously. In addition, there was reduced survival at 12 months of recipients of pancreases from T3 /T4 -treated donors, but not of pancreas grafts. The possibly detrimental effect observed following insulin therapy is discussed.

Difficulty in Identifying Factors Responsible for Pressure Ulcer Healing in Veterans With Spinal Cord Injury.

OBJECTIVE: To identify characteristics associated with pressure ulcer (PrU) healing for individuals with spinal cord injury (SCI). DESIGN: Secondary analysis of a large clinical trial's data for healing PrUs in individuals with SCI; prospective Delphi process was conducted with SCI and/or PrU experts. SETTING: Spinal cord injury centers. PARTICIPANTS: There were 629 screening and 162 treatment participants (N=791); 185 SCI clinicians/national PrU/wound care experts participated in the Delphi process. INTERVENTIONS: None. MAIN OUTCOME MEASURE: PrU healing of 50% and 100% at weeks 4 and 12. RESULTS: Poisson regression models using the top Delphi-recommended factors found that only ulcer stage consistently predicted 50% and 100% healing at weeks 4 and 12. Additionally, ischial/perineal location was associated with 33% higher likelihood of 50% healing at week 4. Patient noncompliance with treatment recommendations, the top-ranked Delphi factor, did not predict healing at week 4 or 12. Expanded models found that at week 4, baseline PrU size, PrU stage IV, PrU pain, and American Spinal Injury Association grade A significantly predicted 100% healing, while at week 12, only PrU stage (IV) significantly predicted 100% healing. Significant predictors of 50% healing at week 4 included baseline PrU size, stage, ischial/perianal location body mass index >30kg/m2, foul odor, and signs of infection. At week 12, PrU duration, paraplegia predicted 50% healing. SCI center identifiers consistently showed 2- to 5-fold variation in predicting 50% PrU healing at weeks 4 and 12. CONCLUSIONS: Delphi panel-recommended factors (eg, patient compliance) did not predict PrU healing. Reducing center-level variability in wound healing by learning from best practices should be a health system goal. PrU healing in SCI is still poorly understood, and future studies should focus on as yet unidentified or underappreciated factors.

Thyroid hormone therapy and procurement of livers from brain-dead donors.

Hormonal therapy to brain-dead potential organ donors remains controversial. A retrospective study was carried out of hormonal therapy on procurement of organs in 63,593 donors in whom information on T3/T4 therapy was available. In 40,124 donors, T3/T4 and all other hormonal therapy was recorded. The percentages of all organs procured, except livers, were greater in T3/T4-treated donors. Nevertheless, if T3/T4 therapy had been administered to the donor, liver transplantation was associated with significantly increased graft and recipient survival at 1 month and 12 months. The potential reasons for the lack of effect of T3/T4 therapy on the number of livers procured are discussed.

An investigation of the equine infectious disease threat represented by the presence of donkeys at mixed equestrian events in Ireland.

BACKGROUND: The number of abandoned or otherwise neglected donkeys has significantly increased in Ireland in the recent past. The real or perceived capacity of the donkey to act as a reservoir of equine infectious disease, and thus pose an increased risk of disease transmission to horses and ponies, may be a factor in this increased abandonment and neglect. The authors here report on a field study exploring the infectious disease transmission threat the donkey poses to the general equine industry in Ireland through an examination of biosecurity standards and the views of horse and donkey exhibitors at nine mixed equestrian events in 2014. Quantitative information was gathered via the organising committee (if any) and through an examination of facilities and procedures. Qualitative information was gathered using a semi-structured questionnaire to ascertain the view of exhibitors regarding the keeping of donkeys and any infectious disease transmission risks posed. RESULTS: At eight of nine events visited there were no entrance controls, no veterinary examinations, no enforcement of legislation regarding equine identification and equine premises registration and no isolation facilities on site for equids. Contact between donkeys and other equids was largely uncontrolled. Exhibitors had travelled from abroad to one event. Exhibitors generally opined that they did not perceive the donkey to represent any additional infectious disease transmission threat above that posed by other equids; there was however a general sense that donkeys were less well regarded for other reasons including nuisance and uselessness. CONCLUSIONS: When biosecurity controls are not in place (or enforced) to actually check passports, verify identification and equine premises registration, mixed equestrian events may unwittingly act as the mechanism of spread of endemic and potentially more seriously exotic equine infectious disease. Donkeys were not generally considered by equine exhibitors at mixed events in Ireland to represent a heightened reservoir of disease or to pose an increased risk of transmission of contagious disease suggesting that other factors should be considered more important when studying the incidence of abandonment and neglect.