IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods

BACKGROUND

Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed standardized bioinformatics pipelines to process IS sequencing data, to generate reports, and/or to perform comparative studies across different GT trials. Keeping up with the technological advances in the field of IS analysis, different computational pipelines have been published over the past decade. These pipelines focus on identifying IS from single-read sequencing or paired-end sequencing data either using read-based or using sonication fragment-based methods, but there is a lack of a bioinformatics tool that automatically includes unique molecular identifiers (UMI) for IS abundance estimations and allows comparing multiple quantification methods in one integrated pipeline.

RESULTS

Here we present IS-Seq a bioinformatics pipeline that can process data from paired-end sequencing of both old restriction sites-based IS collection methods and new sonication-based IS retrieval systems while allowing the selection of different abundance estimation methods, including read-based, Fragment-based and UMI-based systems.

CONCLUSIONS

We validated the performance of IS-Seq by testing it against the most popular  analytical workflow available in the literature (INSPIIRED) and using different scenarios. Lastly, by performing extensive simulation studies and a comprehensive wet-lab assessment of our IS-Seq pipeline we could show that in clinically relevant scenarios, UMI quantification provides better accuracy than the currently most widely used sonication fragment counts as a method for IS abundance estimation.

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

BACKGROUND

Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible "cryptic" epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen.

METHODS

Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution.

RESULTS

Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions.

CONCLUSION

This work provides a molecular basis for the structural "dynamism" of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

LInezolid Monitoring to MInimise Toxicity (LIMMIT1): a multicentre retrospective review of patients receiving linezolid therapy and the impact of therapeutic drug monitoring

BACKGROUND

Linezolid is a broad-spectrum antimicrobial but toxicity limits it use. This study aimed to evaluate linezolid toxicity in a large multicentre cohort. Secondary objectives were to identify factors contributing to toxicity, including the impact of therapeutic drug monitoring (TDM).

METHODS

Patients administered linezolid between January 2017 and December 2019 were reviewed retrospectively. Data was collected on patient characteristics, linezolid therapy and outcomes. Descriptive statistics were performed on all patients, and statistical comparisons were undertaken between patients who did and did not experience linezolid toxicity. A multivariable logistic regression model was constructed to identify any covariates correlated with toxicity.

RESULTS

Linezolid was administered to 1,050 patients. Of these, 381 patients did not meet the inclusion criteria, and 47 patients were excluded as therapy ceased for non-toxicity reasons. There were 105/622 (16.9%) patients assessed to have linezolid toxicity. Those who experienced toxicity displayed a higher baseline creatinine (96.5µmol/L vs 79µmol/L, p=0.025), lower baseline platelet count (225 × 10⁹/L vs 278.5 × 10⁹/L, p=0.002), and received a longer course (median 21 vs 14 days, p<0.001) than patients who did not. Linezolid TDM was performed in 144 patients (23%). The multivariable logistic regression demonstrated that TDM-guided appropriate dose adjustment significantly reduced the odds of linezolid toxicity (aOR=0.45, 95%CI 0.21-0.96, p=0.038), and that treatment duration > 28 days was no longer significantly associated with toxicity.

CONCLUSIONS

This study confirmed linezolid treatment-limiting toxicity remains a problem, and suggests that TDM-guided dose optimisation may reduce the risk of toxicity and facilitate prolonged courses beyond 28 days.

LBODP056 Factors That Associate With Under-diagnosing Prediabetes In Primary Care: A Retrospective Study

Diabetes is the leading risk factor for cardiovascular diseases and other comorbidities that significantly reduce the quality of life. Prediabetes is the preceding condition that increases the risk of Type 2 Diabetes Mellitus (T2DM). The Diabetes Prevention Program Outcomes Study (2002-2014) shows that regression from prediabetes to normoglycemic level is associated with a reduction in cardiovascular risk, while such reduction going from diabetes to normal glucose was not statistically significant. As such, it is critical that patients are screened, diagnosed, and counseled for the treatment of prediabetes. This study investigates how well a large hospital system in suburban San Diego, California diagnoses prediabetes and determines if patient demographics could help explain the missed diagnoses. Patient records from five outpatient clinics under Scripps Health who qualified for the diagnosis of prediabetes determined from either more than one fasting blood glucose (FBG) 100-125 mg/dL, or Hemoglobin A1c (HbA1c) 5.7-6.4% between 2018-2020 were reviewed. Factors such as age, race, sex, body mass index (adjusted for different races), and comorbidities were compared between the correctly diagnosed and missed diagnosed. Only 37% of the qualifying patients were diagnosed with prediabetes or impaired fasting blood glucose; of these patients 93% qualified by HbA1c. Of the factors reviewed, overweight and obesity, female sex, Asian race, comorbidities including lipid disorders, and conditions requiring systemic steroids are positively correlated with a correct diagnosis of prediabetes. Factors like male sex, Black/African American race, comorbidities requiring immunosuppressants, antineoplastics, and iron replacements are negatively correlated with a correct diagnosis. This study demonstrates that prediabetes was grossly underdiagnosed, and the diagnosis seems to be made primarily by HbA1c. These data suggest that the convenience of HbA1c and patients’ BMI, race, gender and comorbidities play a role in healthcare providers’ screening for and making the diagnosis of prediabetes.

Presentation: No date and time listed

High-throughput analysis of hematopoietic stem cell engraftment after intravenous and intracerebroventricular dosing

Hematopoietic stem/progenitor cell gene therapy (HSPC-GT) has shown clear neurological benefit in rare diseases, which is achieved through the engraftment of genetically modified microglia-like cells (MLCs) in the brain. Still, the engraftment dynamics and the nature of engineered MLCs, as well as their potential use in common neurogenerative diseases, have remained largely unexplored. Here, we comprehensively characterized how different routes of administration affect the biodistribution of genetically engineered MLCs and other HSPC derivatives in mice. We generated a high-resolution single-cell transcriptional map of MLCs and discovered that they could clearly be distinguished from macrophages as well as from resident microglia by the expression of a specific gene signature that is reflective of their HSPC ontogeny and irrespective of their long-term engraftment history. Lastly, using murine models of Parkinson's disease and frontotemporal dementia, we demonstrated that MLCs can deliver therapeutically relevant levels of transgenic protein to the brain, thereby opening avenues for the clinical translation of HSPC-GT to the treatment of major neurological diseases.

A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages

The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is needed, especially for cancer immunotherapy development, which requires understanding of molecular mechanisms and discovery of more druggable targets. In this work, we assembled and evaluated an integrated experimental framework and analytical process to enable genome-wide scale discovery of ligand-receptors potentially used for cellular crosstalks, followed by targeted validation. We assessed the complementarity of four different technologies: single-cell RNA sequencing and Spatial transcriptomic (measuring over >20,000 genes), RNA In Situ Hybridization (RNAscope, measuring 4-12 genes) and Opal Polaris multiplex protein staining (4-9 proteins). To utilize the multimodal data, we implemented existing methods and also developed STRISH (Spatial TRanscriptomic In Situ Hybridization), a computational method that can automatically scan across the whole tissue section for local expression of gene (e.g. RNAscope data) and/or protein markers (e.g. Polaris data) to recapitulate an interaction landscape across the whole tissue. We evaluated the approach to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We showed that inference of cell-cell interactions using scRNA-seq data can misdetect or detect false positive interactions. Spatial transcriptomics still suffers from misdetecting lowly expressed ligand-receptor interactions, but reduces false discovery. RNAscope and Polaris are sensitive methods for defining the location of potential ligand receptor interactions, and the STRISH program can determine the probability that local gene co-expression reflects true cell-cell interaction. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors.

POS1165 ASSOCIATION OF LDHD RARE VARIANTS WITH EARLY-ONSET GOUT IN TWO FAMILIES WITH AN ADDITIONAL ASSOCIATION OF RHBG VARIANT IN ONE

Background

Elevated lactate is known to favor urine urate reabsorption by the URAT1 urate/anion exchanger. Autosomal recessive gout caused by pathogenic variant in the LDHD gene encoding for D-lactate deshydrogenase has been recently identified in a large consanguineous Bedouin-Israeli kindred (1).

Objectives

We report here on two families in whom early-onset gout was linked to other variants leading to deficient D-LDH enzymes.

Methods

Studies of the two families were approved by appropriate Ethics committees. Whole exome sequencing (WES) was used to identify the genetic cause of familial gout. Dosages of D-lactate were performed on immediately frozen serum and urine samples by ELISA, using a D-lactate colorimetric assay kit (Abcam ab83429).

Results

Family 1 was Melanesian, living in the Lifou island of New Caledonia. The two index patients were two sisters who developed gout at the age of 13 and 16 years respectively. When seen at the ages of 25 and 27 years, they both had severe gout with frequent polyarticular flares, and multiple tophi and destructive arthropathies in the earliest age of onset one. WES, performed on the 2 affected sisters, their non-consanguine parents, and an unaffected brother, showed that the 2 affected sisters carried homozygous rare variant in DLDH gene (NM_153486.3: c.206 C>T; rs1035398551). This variant was at heterozygote level in both parents and absent in the unaffected brother. It was considered as probably damaging according to in silico prediction software. No association with any other gene was found.

The c.206C>T variant in LDHD was searched by Sanger sequencing method in 13 other extended family members. One 23 year-old brother of the two diseased sisters with atypical MTP flares, high uricemia and double contours at US examination of his MTPs, carried the c.206 C>T variant at the homozygous level. Three other heterozygous patients were found; two of whom were male with late-onset gout, the third one being a non-menopausal female with no gout. No variant carrier was found in the other 9 genotyped family members. The 3 homozygous patients for the c.206 C>T variant had very high hyperuricemia (range 738-834 was searched by Sanger sequencing method in 13 other extended family members. One 23 year-old brother of the two diseased sisters with atypical MTP flares, high uricemia and double contours at US examination of had very low or no D-lactate in plasma and urine. L-lactate blood and urine levels were normal in all subjects.

Family 2 was Vietnamese, living in a remote area of central Vietnam. The two affected children suffered from an extremely severe, destructive gout, which started at the age of 21 years in a daughter and at the age of 9 in her youngest brother, who had developed for the last 3 years, dysarthria, night shakes, memory loss, urine incontinence and an inability to read and count and died at the age of 34, a few months after being seen by us. WES was performed in the two probands, their father and mother (who denied consanguinity), and an unaffected brother. An undescribed variant in LDHD (NM_153486.3: c.1363dupG) was identified in homozygous level in the 2 juvenile gout patients and at the heterozygous level in their 2 parents and unaffected brother. This variant led to a frameshift followed by a stop codon p.(AlaGly432fsTer58). In addition, the two juvenile gout patients were homozygous for an undescribed frameshift (NR_046115.1: c.1064dup) variant of the RHBG gene encoding for a Rhesus Blood Group family ammonium transporter. The two parents carried the heterozygous variant which was not identified in the non-gout brother.

Conclusion

We report on 2 families in whom autosomal recessive juvenile gout was due to rare or undescribed, damaging LDHD gene variants. In addition, we observed in the Vietnamese family, an additional non-described frameshift homozygous variant in RHBG, the pathophysiological role of which deserves to be investigated.

References

[1]Drabkin M et al. Hyperuricemia and gout caused by missense mutation in D-lactate dehydrogenase. J Clin Invest. 2019;129:5163-5168

Disclosure of Interests

Thomas Bardin Consultant of: leo Pharma, Yves-Marie Ducrot: None declared, Quang Nguyen: None declared, Emmanuel Letavernier: None declared, Hang-Korng Ea: None declared, Frederic Touzain: None declared, Duc Minh Do: None declared, Julien Corot: None declared, Yan Barguil: None declared, Antoine Biron: None declared, Pascal Richette: None declared, Corinne Collet: None declared

Investigating SARS-CoV-2 Test Positivity Calculations Across US Jurisdictions

Purpose

Throughout the COVID-19 pandemic, many US epidemiologists and policymakers turned to an indicator called test positivity, or the percent of tests coming back positive for SARS-CoV-2, to contextualize COVID-19 case counts with testing volume. But the nation's patchworked health data infrastructure, composed of 56 systems managed by each state and territory, complicated efforts to calculate the metric in a comparable way across US jurisdictions. We set out to map jurisdictional reporting differences in test positivity and investigate whether they interfered with its effectiveness and comparability as an indicator. Understanding these differences is important because jurisdictional test positivity informed consequential policy and individuals’ understanding of risk in their communities.

Methods & Materials

We surveyed the health department websites of all US states and territories to examine how these jurisdictions were presenting test positivity on COVID-19 dashboards. When details about definitions were unavailable on jurisdictional websites, we reached out to jurisdictional public health officials for clarification. We also scored jurisdictions' presentations against best practices we identified for calculating the metric.

Results

Among the 48 states and territories posting test positivity values, we observed no consensus on how to calculate the metric—jurisdictions used different units, test types, averaging techniques, and dating schemes. By looking at data for jurisdictions that posted multiple test positivity metrics, we observed that these definitional differences could result in variations from 31% to 300%. Only four states were following all ten of the best practices for reporting test positivity.

Conclusion

The sheer number of ways states and territories define test positivity is alarming, given how much the indicator influenced US COVID-19 policy. Based on our survey, we believe the confidence of regulators in the precision and national comparability of test positivity is misplaced: The metric's value reflects state and territorial reporting decisions as much as actual viral prevalence. These findings underscore the need to invest in centralized public health infrastructure and create national reporting standards to improve unity of state reporting.

Evaluating the Quality of Federal SARS-CoV-2 Diagnostic Testing Data

Purpose

In April 2020, the US Department of Health and Human Services (HHS) and the US Centers for Disease Control and Prevention established the COVID-19 Electronic Laboratory Reporting program (CELR) to collect data on SARS-CoV-2 laboratory tests. Over the course of the following year, the federal government, partnering with the Association for Public Health Laboratories, onboarded every state to submit laboratory results to this system—the first of its kind in the US. We set out to evaluate the quality of data collected by CELR.

Methods & Materials

We compared jurisdiction-level data collected through CELR and published by HHS to the testing data published by jurisdictions on their health department webpages. Because jurisdictions define their testing data differently, we anticipated some differences from federal testing data. However, jurisdictions also tend to prioritize their dashboard reporting—since it is what is used for policy decisions like reopening—so we hypothesized that differences from federal data absent a definitional explanation could point to problems with federal data. Where we found differences between jurisdictional and federal data, we conducted interviews with public health officials to understand their cause.

Results

Of the 56 states and territories, as of April 2021 (the first month when all states were onboarded to CELR), 38 had federal total data that diverges from state data by more than 5%. Of those states, the differences of 27 could not be explained by definitional factors. Based on our interviews, we identified three problems: non-electronic reporting streams, out-of-date surveillance systems, and deduplication of laboratory data.

Conclusion

The federal testing dataset displays major unresolved quality problems, and because states present testing data so differently, state-published data forms a poor alternative to federal datasets. The federal government, which is uniquely positioned to provide testing data on infectious diseases, must work to improve the quality of laboratory data submissions by states. To support better national laboratory data, the United States should invest in updating state and laboratory data surveillance infrastructure—including updates to state surveillance systems and laboratory system updates to eliminate outdated reporting methods like faxes—and in creating more national laboratory data infrastructure.

Application of Laser-Induced, Deep UV Raman Spectroscopy and Artificial Intelligence in Real-Time Environmental Monitoring-Solutions and First Results

Environmental monitoring of aquatic systems is the key requirement for sustainable environmental protection and future drinking water supply. The quality of water resources depends on the effectiveness of water treatment plants to reduce chemical pollutants, such as nitrates, pharmaceuticals, or microplastics. Changes in water quality can vary rapidly and must be monitored in real-time, enabling immediate action. In this study, we test the feasibility of a deep UV Raman spectrometer for the detection of nitrate/nitrite, selected pharmaceuticals and the most widespread microplastic polymers. Software utilizing artificial intelligence, such as a convolutional neural network, is trained for recognizing typical spectral patterns of individual pollutants, once processed by mathematical filters and machine learning algorithms. The results of an initial experimental study show that nitrates and nitrites can be detected and quantified. The detection of nitrates poses some challenges due to the noise-to-signal ratio and background and related noise due to water or other materials. Selected pharmaceutical substances could be detected via Raman spectroscopy, but not at concentrations in the µg/l or ng/l range. Microplastic particles are non-soluble substances and can be detected and identified, but the measurements suffer from the heterogeneous distribution of the microparticles in flow experiments.

Chronic lymphoid leukemia metastasis to the gallbladder as a focal mass: A case report

Chronic lymphocytic leukemia (CLL) is the second most common hematologic malignancy, and it is characterized by lymphocytic leukocytosis and secondary hematologic deficiencies. While it most commonly presents as a systemic disease, extramedullary involvement may rarely occur. The literature surrounding CLL metastatic disease to the gallbladder is particularly sparse. Interestingly, we describe a case of a 67-year-old female who presented with painless jaundice and was found to have a rapidly growing gallbladder wall mass which was determined to be CLL metastatic disease after extensive surgical resection. It is important for radiologists to recognize the possibility of CLL metastatic disease to the gallbladder when evaluating potential cases of cholecystitis due to the overlapping spectrum of imaging findings. Cognizant radiologists can potentially save patients from surgical intervention as CLL is classically treated with chemotherapy.

Differential trajectories in LVEF predicts divergent clinical outcomes in HFrEF patients

Background

Recovery or improvement in LVEF is observed in many HFrEF patients following optimal medical management and device therapies, but whether this reflects true myocardial recovery remains controversial and the significance of LVEF decompensation in relation to clinical outcomes is unclear.

Purpose

To elucidate clinical characteristics and assess prognosis of HFrEF patients with differential trajectories in LVEF.

Methods

Heart failure (HF) patients were enrolled in a prospective Heart Function registry from outpatient cardiology clinics at an academic institution between Feb 2018 and Nov 2019. Retrospective analysis was conducted on 2D-echocardiography (echo) performed between Jan 2009 and Nov 2019. In total, 590 patients met the inclusion criteria with ≥2 repeated echo evaluations separated by ≥1 year. Patient demographics and clinical characteristics at enrollment were collected through review of medical records. Cardiovascular and HF specific admissions were captured using the corresponding ICD-10-CA codes. During a median follow-up of 5.9 years (IQR: 3.1 to 8.5 years) from the first echo date, clinical outcomes were assessed through composite mortality and hospitalizations endpoints.

Results

We identified 3 independent cohorts with 279 patients having permanently reduced LVEF (&lt;40%, HFrEF), 236 patients with recovered LVEF (&gt;40% on serial evaluations, HFrecEF) and 75 patients with subsequent decompensation in LVEF (&gt;40%, then &lt;40%, HFdecEF) following initial recovery. Use of ACE inhibitors or ARBs (94% vs. 99% vs. 91%) and beta blockers (88% vs. 87% vs. 87%) at baseline echo was similar amongst HFrEF, HFrecEF and HFdecEF cohorts respectively. HFrecEF cohort had higher usage of MRA (55% vs. 65% vs. 44%, p=0.002) and diuretics (74% vs. 80% vs. 65%, p=0.026). HFdecEF cohort was characterized by a predominance of males (80% vs. 69% vs. 80%, p=0.01), and more patients with ischemic etiology (41% vs. 28% vs. 60%, p&lt;0.001) compared with the HFrecEF cohort and resembled more closely to demographics of the HFrEF cohort. Median LVEF at baseline echo was similar across the cohorts. However, HFdecEF cohort had lower LV end-diastolic diameter (p&lt;0.001), LV end-systolic diameter (p&lt;0.001) and LV mass (p=0.01) compared with the HFrEF cohort sharing similarities with the HFrecEF cohort on baseline echo, suggesting lesser extent of adverse cardiac remodeling in both HFrecEF and HFdecEF cohorts initially. Over a median 5.9 years follow-up, HFdecEF and HFrEF patients had a significantly higher risk (compared to those with HFrecEF) of composite all-cause mortality with all-cause (80% vs. 75% vs. 57%, p=0.004), cardiovascular (48% vs. 50% vs. 29%, p=0.001) and HF hospitalizations (31% vs. 32% vs. 16%, p=0.004).

Conclusion

HFrEF patients who never recover their LVEF and patients with decompensation in LVEF following initial recovery represent a clinically higher risk group than patients who remained recovered during follow-up.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): University of Alberta Hospital Foundation, Canadian Institutes of Health Research

Myocardial iron depletion exacerbates end-stage heart failure by promoting adverse remodeling and worsening mitochondrial function

Background

Heart failure (HF) is highly associated with systemic iron deficiency (ID) yet its association with myocardial iron depletion (MID) remains barely unveiled. Similarly, it has been unclear whether and how MID deteriorates the progression to advanced HF. Furthermore, neither the underlying pathophysiology nor the negative impact of unmet iron availability to the failing heart, at the molecular level, is elucidated.

Purpose

We aim to integrate clinical information and experimental data from human explanted heart tissues: 1) to establish the defining criterion of MID in advanced HF population; 2) to recapitulate the pathophysiological role MID plays in the progression of HF; and 3) to identify novel HF molecular signatures or potential cures to correct MID status underestimated in the failing hearts.

Methods

Adult failing hearts (N=143), including dilated (n=76) and ischemic (n=67) cardiomyopathies, and non-failing control hearts (NFC, N=46) were collected per Human Explanted Heart Program. Iron levels were measured directly from both ventricles, which were re-evaluated by cardiac magnetic resonance imaging (CMR) mapping sequences (e.g. T1, T2*, etc.). Mitochondrial metabolic, reactive oxygen species (ROS) and ROS-scavenging profiles were assessed spectrophotometrically. Tissue remodeling and ultrastructure characteristics were captured by confocal and electron microscopies respectively. Meanwhile, the patients' clinical profiles were integrated into the analysis of molecular regulatory mechanism.

Results

Myocardial iron content in LV was significantly lower in HF versus NFC [121.4 (88.1–150.3) vs. 137.4 (109.2–165.9) μg/g dry weight, p&lt;0.05], while both RVs showed no difference. With a cutoff of 86.1 μg/g iron level in LV, it screened ∼23% HF patients with MID (HF-MID). Compared with non-MID HF patients, depleted iron store weakly correlated with systemic hemoglobin concentration (r=−0.27, p=0.13) but highly with T2* and magnetic susceptibility proving CMR as an exceptional surrogate for non-invasive diagnosis. And it was noted that MID independently predicted ominous endpoints as NYHA grade increased and LV dysfunctions worsened (all p&lt;0.05). Cardiac respiratory chain enzymatic activities from complex I to V (except for COX III) were further suppressed in the iron-deficient failing hearts, indicating altered myocardial metabolism and excessive ROS production. Moreover, the whole anti-ROS defense were severely impaired, consistent with remarkably inverse tissue remodeling and ultrastructure disintegrity in HF-MID. Mechanistically, two iron-regulatory proteins (IRP-1/2) and following iron trafficking pathways were inactivated possibly determine the restricted iron availability to advanced failing hearts.

Conclusions

MID worsens HF progression primarily mediated by mitochondrial dysfunction and collapsed oxidative protection in LV, independently predicting an inferior prognosis. CMR demonstrates clinical potential to monitor MID.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Canadian Institutes for Health Research (CIHR); Heart & Stroke Foundation (HSF)

Discovery and analyses of pathogenic variants in explanted hearts from primary cardiomyopathy patients

Background

Dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) are disorders of the myocardium that affect the structure and function of the heart.

Purpose

The primary aim of this study was to discover damaging genetic variants in myocardial tissue from patients with DCM or HCM, who underwent heart transplantation.

Methods

Whole exome sequencing was performed on myocardial tissue from 103 explanted hearts with diagnosis of cardiomyopathy; 80 DCM and 13 HCM. Sanger sequencing was performed to confirm the loss-of-function variants in genes known to be linked to cardiomyopathy. RNA sequencing was conducted to confirm copy number variation deletions detected in the cohort. Burden analysis was performed by comparing the frequency of variants found in the study cohort to the frequency in the population database gnomAD.

Results

Rare (minor allele frequency &lt;1.0E-04) loss-of-function variants, deleterious missense variants, or copy number variation deletions, collectively described as damaging variants, were identified in cardiomyopathy genes in 42 of all 93 samples (45.2%). Damaging variants were identified in 37 of 80 DCM samples (46.3%) and 5 of 13 HCM samples (38.4%). The mean read depth for normal and variant allele were comparable. All the 28 loss-of-function variants in cardiomyopathy genes found in the cardiomyopathy cases were confirmed by Sanger sequencing. Two copy number variation deletions both in titin (TTN) were also detected and confirmed. Burden analyses showed that the genes TTN and lamin A/C (LMNA) had a higher frequency of loss-of function variants in the DCM cohort (17.5% and 3.75%, respectively) compared to the reference population with genome-wide significance (p=3.45E-22 and 4.34E-07, respectively). Furthermore, our analysis showed that deleterious missense variants in osteoclast-stimulating factor 1 (OSTF1), which previously has not been associated with cardiomyopathy, was highly enriched in the DCM cohort compared to the reference population (p=2.10E-06).

Conclusions

The frequency of damaging variants that are likely pathogenic (46.3%) is higher in DCM cases in this cohort compared to previous studies. These data indicate that patients with end-stage DCM are more likely to have a genetic cause for their disease. As read depth of variant and normal alleles were, these are likely germline and not mosaic variants, and can enable cascade testing in family members. Moreover, our study demonstrates that CNVs in TTN that alter the reading frame can cause DCM.

Funding Acknowledgement

Type of funding source: None

Thermal neutron transmutation doping of GaN semiconductors

High quality Ge doping of GaN is demonstrated using primarily thermal neutrons for the first time. In this study, GaN was doped with Ge to concentrations from 10¹⁶ Ge atoms/cm³ to 10¹⁸ Ge atoms/cm³. The doping concentrations were measured using gamma-ray spectroscopy and confirmed using SIMS analysis. The data from SIMS analysis also show consistent Ge doping concentration throughout the depth of the GaN wafers. After irradiation, the GaN was annealed in a nitrogen environment at 950 °C for 30 min. The neutron doping process turns out to produce spatially uniform doping throughout the whole volume of the GaN substrate.

Universal scaling of adsorption of nonionic surfactants on carbonates using cloud point temperatures

HYPOTHESIS

Nonionic surfactants alter the wettability of oil-wet carbonate surfaces to a water-wet state. The degree of surfactant adsorption is expected to determine the extent of the wettability alteration. Furthermore, the structure of the hydrophobic and hydrophilic units of the surfactant should affect the degree of adsorption and correlate with the wettability alteration.

EXPERIMENTS

The adsorption on Indiana limestone was measured for nonionic surfactants with two different types of hydrophobic units and hydrophilic polyethoxylate units ranging from 15 to 40 mers. Measurements were conducted for several surfactant concentrations and temperatures.

FINDINGS

Adsorption increased with temperature and for surfactants with fewer hydrophilic groups. The adsorption occurs as micelles rather than individual surfactant molecules. An increase in adsorption is observed for the more hydrophobic surfactants at higher temperature and is attributed to the increase in micelle sizes. Adsorption collapses onto a universal curve as a function of the difference between cloud point of the surfactant and system temperature. At the same time wettability alteration was found to have a direct correlation with surfactant adsorption. These findings are critical for judicious selection of nonionic surfactants for analysis and design of wettability alteration for oil reservoirs.

Molecular Dynamics Simulations of Aqueous Nonionic Surfactants on a Carbonate Surface

The interactions and structure of secondary alcohol ethoxylates with 15 and 40 ethoxylate units in water near a calcite surface are studied. It is found that water binds preferentially to the calcite surface. Prediction of the free-energy landscape for surfactant molecules shows that single-surfactant molecules do not adsorb because they cannot get close enough to the surface because of the water layer for attractive ethoxylate-calcite or dispersion interactions to be significant. Micelles can adsorb onto the surface even with the intervening water layer because of the integrative effect of the attractive interactions of all the surfactant molecules. Adsorption is found to increase because of the closer proximity of the micelles to the surface due to a weakened water layer at higher temperatures. The free-energy well and barrier values are used to estimate surface to bulk partition coefficients for different surfactants and temperatures, and qualitative agreement is found with experimental observations. The combined effect of surfactant-water and surfactant-solid interactions is found to be responsible for an increased adsorption for nonionic surfactants as the system approaches the cloud point.

Review of Free Prostate-Specific Antigen Assay Utilization at Danbury Hospital

Introduction

Measuring the concentration of free fraction of prostate-specific antigen (fPSA) present in serum in addition to the total PSA (tPSA) concentration has been shown to enhance specificity over tPSA alone in evaluating male patients with mild-moderate elevations of tPSA in the diagnostic “gray zone” (4.0-10.0 ng/mL) and negative findings on digital rectal exam. The clinical utility of fPSA has not been demonstrated outside the tPSA gray zone, as the probability of prostate cancer is very low at tPSA <4.0 and very high at tPSA >10.0. However, many clinicians order tPSA and fPSA concurrently without first knowing the results of the tPSA. This study was to review orders for fPSA and provide suggestions for improving utilization.

Methods

Paired test results for concurrently ordered tPSA and fPSA tests during the time periods of January to February 2018 and January to February 2019 (before and after laboratory information system upgrade) were extracted for quality assurance purposes. No patient identifiers were included. Data were sorted and the percentage of “appropriate” fPSA orders was calculated for each time period.

Results

The number of concurrent total and fPSA tests ordered was 174 for January-February 2018 and 232 for January-February 2019. The number of tPSA within the 4.0 to 10.0 ng/mL range was 78 for January-February 2018 and 148 for January-February 2019. The percentage of “appropriate” fPSA test orders (tPSA 4.0-10.0 ng/mL) was 44.8% for January-February 2018 and 63.8% for January-February 2019.

Conclusion

A high percentage of inappropriate fPSA orders was found during both time periods. Inappropriate fPSA testing is not only unnecessary and wasteful but can lead to diagnostic errors. Options for driving improved utilization include automatic canceling of fPSA orders when tPSA is not within the diagnostic gray zone and offering fPSA as a “reflex” test that is performed only when tPSA is within the diagnostic gray zone.

Reconstruction and evaluation of changes in hydrologic conditions over a transboundary region by a regional climate model coupled with a physically-based hydrology model: Application to Thao river watershed

The differences among countries in terms of physical features, governmental policies, priorities in short- and long-term water resources management may lead to conflicts in managing and sharing of water resources over the transboundary regions. Due to no formal data sharing agreement between countries, there has been usually no data availability at transboundary regions. In this study, a methodology, in which a physically-based hydrology model was coupled with a regional climate model, is proposed to reconstruct and evaluate hydrologic conditions over transboundary regions. For the case study, Thao river watershed (TRW), within Vietnam and China, was selected. The Watershed Environmental Hydrology (WEHY) model was implemented based on topography, soil, and land use/cover information which was retrieved from global satellite data resources. The watershed model-WEHY was first validated over the TRW, and then was used to reconstruct historical hydrologic conditions during 1950-2007. The results of this study suggest no significant trend in the annual streamflow over the target watershed. In addition, there is a time shift in the wet season between the upstream sector in China and the downstream sector in Vietnam over the TRW. The annual flow contribution from the upstream sector in China to the outlet of TRW is estimated to be around 66%, and the remaining 34% contribution comes from the downstream sector in Vietnam territory. Last but not the least, the annual flow as a function of return period varies not only with the return period but also as a function of the time window, reflecting the effect of the changing regime on the streamflows at the TRW. The evolution of the flow frequency through time is an evidence of the ongoing non-stationarity in the hydrologic conditions over TRW.

Candidaemia and a risk predictive model for overall mortality: a prospective multicentre study

Background

Candidaemia is associated with high mortality. Variables associated with mortality have been published previously, but not developed into a risk predictive model for mortality. We sought to describe the current epidemiology of candidaemia in Australia, analyse predictors of 30-day all-cause mortality, and develop and validate a mortality risk predictive model.

Methods

Adults with candidaemia were studied prospectively over 12 months at eight institutions. Clinical and laboratory variables at time of blood culture-positivity were subject to multivariate analysis for association with 30-day all-cause mortality. A predictive score for mortality was examined by area under receiver operator characteristic curves and a historical data set was used for validation.

Results

The median age of 133 patients with candidaemia was 62 years; 76 (57%) were male and 57 (43%) were female. Co-morbidities included underlying haematologic malignancy (n = 20; 15%), and solid organ malignancy in (n = 25; 19%); 55 (41%) were in an intensive care unit (ICU). Non-albicans Candida spp. accounted for 61% of cases (81/133). All-cause 30-day mortality was 31%. A gastrointestinal or unknown source was associated with higher overall mortality than an intravascular or urologic source (p < 0.01). A risk predictive score based on age > 65 years, ICU admission, chronic organ dysfunction, preceding surgery within 30 days, haematological malignancy, source of candidaemia and antibiotic therapy for ≥10 days stratified patients into < 20% or ≥ 20% predicted mortality. The model retained accuracy when validated against a historical dataset (n = 741).

Conclusions

Mortality in patients with candidaemia remains high. A simple mortality risk predictive score stratifying patients with candidaemia into < 20% and ≥ 20% 30-day mortality is presented. This model uses information available at time of candidaemia diagnosis is easy to incorporate into decision support systems. Further validation of this model is warranted.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4065-5) contains supplementary material, which is available to authorized users.

MON-388 To Cut Or Not To Cut? Cystic Adrenal Lymphangioma Mimicking Pheochromocytoma

Background:Lymphangiomas are rare benign vascular tumors. Adrenal gland lymphangiomas are an even less common occurrence. Although usually non-functional, these tumors may mimic pheochromocytomas [1]. We present a case of a patient with a cystic adrenal lymphangioma with elevated catecholamines in the setting of acute appendicitis. Case presentation:A 30 year-old-man with a history of intermittent anxiety presented with abdominal pain. An abdominal computer tomography (CT) scan, physical examination, and laboratory findings were consistent with acute appendicitis. The patient was incidentally found to have a well-demarcated 3.9x4.6 cm right adrenal mass measuring 10 HU. A prior CT scan of the abdomen performed four years earlier showed a 2.5x3.2 cm right adrenal mass. Hormonal evaluation had not been conducted at that time.Further evaluation during the hospitalization revealed normal electrolytes, dehydroepiandrosterone, overnight dexamethasone suppression test, aldosterone/renin ratio and plasma catecholamines. However, 24-hour urine catecholamines and metanephrines were elevated: epinephrine - 63 mcg/24hr (n<21), norepinephrine - 106 mcg/24hr (n 15-80) and dopamine - 540 mcg/24hr (n 65-400). Due to the size of the lesion (>4 cm), surgical resection was recommended. Due to concern that abnormal urinary values could indicate pheochromocytoma, the surgery was preceded by 14 days of alpha-adrenergic blockade. The patient underwent a successful laparoscopic right adrenalectomy with concomitant interval appendectomy. Final pathology results revealed a cystic lymphangioma of the right adrenal gland with positive D2-40 and CD-31 immunohistochemical stains supporting this diagnosis. During follow-up evaluation, the patient reported interval resolution of intermittent anxiety and urine catecholamines/metanephrines gradually normalized. While not confirmatory of a catecholamine secreting adrenal lymphangioma, interval resolution of the anxiety disorder could suggest this diagnosis as a possibility to consider. Conclusion:The rare nature of adrenal lymphangiomas has led to a paucity of information regarding their detection and management [2]. Although typically considered benign, there are no methods at our disposal to confirm this diagnosis without surgical removal. Adrenal lymphangiomas mimicking other adrenal masses, including pheochromocytoma, have been reported [2]. Increasing the awareness regarding these rare tumors may enable providers to be on the lookout for adrenal lymphangiomas when evaluating patients for large unilateral adrenal lesions. References:1. Hodish I, Schmidt L, Moraitis AG. Adrenal Lymphangioma Masquerading as a Catecholamine Producing Tumor. Case Rep Endocrinol. 2015;2015:380151.2. Michalopoulos N, Laskou S, Karayannopoulou G, et al. Adrenal Gland Lymphangiomas. Indian J Surg. 2015; 77:S1334-S1342.

Reduced sensitivity of multiparametric MRI for clinically significant prostate cancer in men under the age of 50

Introduction

Three percent of all new diagnosed prostate cancer (PC) patients are under the age of 50. Multiparametric MRI (mpMRI) is considered as increasingly powerful tool for decision-making in diagnosis of PC and in some active surveillance protocols. Since prostate architecture changes with age, we evaluated the sensitivity of mpMRI to detect clinically significant PC in patients under the age of 50 compared to pair-matched older patients.

Methods

Data from a prospective collected and ethics approved database were retrospectively analyzed. We reviewed 1,395 records of PC patients from the years 2012–2017, identifying those under the age of 50 who had radical prostatectomy as primary treatment, a pre-operative mpMRI, a full clinical data set and who had clinically significant cancer (N=51). Tumor size and International Society of Urological Pathology (ISUP) score pair-matching was performed for patients older than 55 years. Clinically significant cancer was defined as ISUP >2 or ISUP 2 with >5% Gleason 4. The sensitivity to detect clinically significant cancer with mpMRI was calculated using pre-operative Prostate Imaging Reporting and Data System (PI-RADS) score and whole-gland final pathology.

Results

The median patient age in the young and older groups was 47 and 62, respectively. Both cohorts matched significantly regarding tumor volume (P =0.91) and ISUP score (P =1.0). The median PI-RADS score for the young group was 3, and 4 for the older group. The sensitivity for mpMRI, for PI-RADS 3,4 and 5 was 80.3% (95% CI 66.8%–90.1%) in the young group and 84.3% in the older group (95% CI 71.4%–92.9%), demonstrating no statistically significant difference (P=0.603). Sensitivity of mpMRI for PI-RADS 4,5 was 49.0% (95% CI 34.7%–63.4%) for the young group and 72.5% (95% CI 58.2%–84.1%) for the older group, which differ significantly (P=0.014).

Conclusions

mpMRI may have a reduced sensitivity for detecting clinically significant PC in patients under the age of 50 for PI-RADS score 4,5 lesions. Many significant PC lesions were reported as PI-RADS 3 under the age of 50. We recommend that increased significance is placed on PI-RADS 3 lesions found in patients under the age of 50.

Wettability Alteration of Calcite by Nonionic Surfactants

The process of selecting an effective surfactant for wettability alteration is dependent on a number of factors, including mineral type, temperature, salinity, and nature of adsorbed oil and ultimately how the molecular structure of the surfactant interacts with all of these. Here, we present an experimental study of the effectiveness of nonionic surfactants with different hydrophobic groups and different lengths of hydrophilic ethylene oxide oligomers. The surfactants selected alter the wettability of the rock primarily by acting on the water-rock and oil-rock interfaces. The dynamics of wettability alteration is measured by the evolution of contact angles of oil drops on initially oil-wet surfaces at three different temperatures. Wettability alteration is found to be enhanced by surfactants with shorter hydrophilic units and increased temperatures. Experimental observations are efficiently summarized by a few thermodynamic and kinetic parameters. Qualitative experiments are performed to study surfactant-induced dewetting of oil films. Finally, a model involving "coating" and "sweeping" mechanisms is proposed to explain the mechanism of surfactant action.

Association of the Platelet Glycoprotein IIIa PIA1/A2 Gene Polymorphism to Coronary Artery Disease but not to Nonfatal Myocardial Infarction in Low Risk Patients

Background. The platelet membrane glycoprotein IIb/IIIa functions as a receptor for fibrinogen and von Willebrand factor during platelet aggregation. In a small case-control study, evidence has been presented that the PlA2 allele of the platelet glycoprotein GPIIIa PlA1/A2 gene polymorphism might be an independent risk factor for acute myocardial infarction (MI). Methods and Results. We explored the association of the PlA1A2 to the severity of coronary artery disease (CAD), as assessed angiographically in 2252 male individuals, and to myocardial infarction (MI). The severity of coronary heart disease (CHD) was also estimated by calculating a CHD score according to Gensini. The PlA genotype was determined by allele specific restriction digestion. Relation of the PlA2 allele to CAD: In the total population, the frequency of the PlA2 allele was not associated to the presence or to the extent of CAD. Also the CHD scores of PlA1/PlA2 genotypes were essentially the same. However, after exclusion of individuals with high BMI (≥26.9 kg/m2) and/or low apoAI (<1.43 g/l) PlA2PlA2 carriers had clearly higher CHD scores than PlA1PlA1 genotypes; PlA1PlA2 heterozygotes had intermediate values (p <0.05). After division of the study population into one group of individuals without any angiographic signs of CAD (CHD score = 0) and into another group of patients with severe CAD (CHD score (≥120), a strong association of the PlA2 allele with severe CAD was also found in the same low risk groups; e.g. exclusion of persons with high BMI and low apoAI resulted in an Odds ratio of 5.37 (1.46-19.7) (p <0.02). Relation of the PlA2 allele to MI: No association was found between PlA1/PlA2 genotypes and risk of MI neither in the total population nor in low risk subgroups.

Conclusions. Whereas no difference in the distribution of allele and genotype frequencies between controls and survivors of MI could be detected, the PlA2 allele is associated with CHD in low risk patients.

Patterns of failure on Ga PSMA (GaPSMA) and F18 FDG (FDG) PET CT in a prospective phase 2 trial of 177Lu DKFZ PSMA 617 (LuPSMA) in men with castrate resistant metastatic prostate cancer (mCRPC)

2562

Background: LuPSMA is emerging as an effective therapy in mCRPC, with retrospective series reporting high PSA response rates in men undergoing treatment (tx). However, not all men have prolonged tx responses. We report the prospective imaging (GaPSMA/FDG) and PSA response of men who progress biochemically during LuPSMA tx to gain information on characteristics of failure patterns, to determine optimal future tx strategies. Methods: Men with mCRPC, who had failed androgen blockade, failed/ ineligible/refused chemotherapy, with GaPSMA positive disease were enrolled in a prospective phase 2 trial. All men underwent LuPSMA therapy 6-8Gbq, 4 doses at 6 weekly intervals. Imaging with FDG, GaPSMA, bone scan and CT scans was at screening, at subsequent PSA rise, or 3 months post completion of 4 cycles of therapy. Results: 14 men met eligibility criteria and enrolled. 4/14 (28%) men had progressive disease (no PSA response). 10/14 (72%) PSA reduced by a mean 56% .Overall 9/14 (64%) men had >30% decline in PSA, and 5/15(36%) >50% reduction in PSA. 7/15 men were reimaged with GaPSMA, FDG at biochemical failure or 3/12 post tx completion. Imaging revealed 4 distinct patterns (P) of progression. Conclusions: PSMA acts as both target for radionuclide therapy and biomarker for effective tx response. PSMA and FDG imaging at PSA failure following or during LU PSMA therapy identifies phenotypic patterns of failure that have implications for determining next best tx options in men with mCRPC. [Table: see text]

Select men benefit from androgen deprivation therapy delivered with salvage radiation therapy after prostatectomy

BACKGROUND

Which men benefit most from adding androgen deprivation therapy (ADT) to salvage radiation therapy (SRT) after prostatectomy has not clearly been defined; therefore, we evaluated the impact of ADT to SRT on failure-free survival (FFS) in men with a rising or persistent PSA after prostatectomy.

METHODS

We identified 332 men who received SRT after prostatectomy from 1987 to 2010. Recursive partitioning analysis (RPA) identified favorable, intermediate and unfavorable groups based on the risk of failure after SRT alone. Kaplan-Meier and log-rank tests compared FFS with and without ADT.

RESULTS

Forty-three percent received SRT alone and 57% received SRT with ADT (median 6.6 months (interquartile range (IQR) 5.8-18.1) ADT). Median SRT dose was 70 Gy (IQR 70-70), and median follow-up after SRT was 6.7 years (IQR 4.5-10.8). On Cox's proportional hazard regression, ADT improved FFS (adjusted hazard ratio 0.60, 95% confidence interval: 0.42-0.86; P=0.006). RPA classified unfavorable disease as negative surgical margins (SMs) and preradiation PSA of ⩾0.5 ng ml^-1. Favorable disease had neither adverse factor, and intermediate disease had one adverse factor. The addition of ADT to SRT improved 5-year FFS for men with unfavorable disease (70.3% vs 23.4%; P<0.001) and intermediate disease (69.8% vs 48.0%; P=0.003), but not for men with favorable disease (81.2% vs 78.0%; P=0.971).

CONCLUSIONS

The addition of ADT to SRT appears to improve FFS for men with a preradiation PSA of ⩾0.5 ng ml^-1 or with negative SM at prostatectomy. Men with involved surgical margins and PSA <0.5 ng ml^-1 appear to be at a lower risk of failure after SRT alone and may not derive as much benefit from the administration of ADT with SRT. These results are hypothesis-generating only, and further prospective data are required to see if ADT can safely be omitted in this select group of men.