A gel-coated air-liquid-interface culture system with tunable substrate stiffness matching healthy and diseased lung tissues

Since its invention in the late 1980s, the air-liquid-interface (ALI) culture system has been the standard in vitro model for studying human airway biology and pulmonary diseases. However, in a conventional ALI system, cells are cultured on a porous plastic membrane that is much stiffer than human airway tissues. Here, we develop a gel-ALI culture system by simply coating the plastic membrane with a thin layer of hydrogel with tunable stiffness matching that of healthy and fibrotic airway tissues. We determine the optimum gel thickness that does not impair the transport of nutrients and biomolecules essential to cell growth. We show that the gel-ALI system allows human bronchial epithelial cells (HBECs) to proliferate and differentiate into pseudostratified epithelium. Furthermore, we discover that HBECs migrate significantly faster on hydrogel substrates with stiffness matching that of fibrotic lung tissues, highlighting the importance of mechanical cues in human airway remodeling. The developed gel-ALI system provides a facile approach to studying the effects of mechanical cues in human airway biology and in modeling pulmonary diseases.NEW & NOTEWORTHY In a conventional ALI system, cells are cultured on a plastic membrane that is much stiffer than human airway tissues. We develop a gel-ALI system by coating the plastic membrane with a thin layer of hydrogel with tunable stiffness matching that of healthy and fibrotic airway tissues. We discover that human bronchial epithelial cells migrate significantly faster on hydrogel substrates with pathological stiffness, highlighting the importance of mechanical cues in human airway remodeling.

Cardiovascular Risk Stratification of Patients Undergoing Hematopoietic Stem Cell Transplantation: The CARE-BMT Risk Score

BACKGROUND

Evidence guiding the pre-hematopoietic stem cell transplantation (HSCT) cardiovascular evaluation is limited. We sought to derive and validate a pre-HSCT score for the cardiovascular risk stratification of HSCT candidates.

METHODS AND RESULTS

We leveraged the CARE-BMT (Cardiovascular Registry in Bone Marrow Transplantation) study, a contemporary multicenter observational study of adult patients who underwent autologous or allogeneic HSCT between 2008 and 2019 (N=2435; mean age at transplant of 55 years; 4.9% Black). We identified the subset of variables most predictive of post-HSCT cardiovascular events, defined as a composite of cardiovascular death, myocardial infarction, heart failure, stroke, atrial fibrillation or flutter, and sustained ventricular tachycardia. We then developed a point-based risk score using the hazard ratios obtained from Cox proportional hazards modeling. The score was externally validated in a separate cohort of 919 HSCT recipients (mean age at transplant 54 years; 20.4% Black). The risk score included age, transplant type, race, coronary artery disease, heart failure, peripheral artery disease, creatinine, triglycerides, and prior anthracycline dose. Risk scores were grouped as low-, intermediate-, and high-risk, with the 5-year cumulative incidence of cardiovascular events being 4.0%, 10.3%, and 22.4%, respectively. The area under the receiver operating curves for predicting cardiovascular events at 100 days, 5 and 10 years post-HSCT were 0.65 (95% CI, 0.59-0.70), 0.73 (95% CI, 0.69-0.76), and 0.76 (95% CI, 0.69-0.81), respectively. The model performed equally well in autologous and allogeneic recipients, as well as in the validation cohort.

CONCLUSIONS

The CARE-BMT risk score is easy to calculate and could help guide referrals of high-risk HSCT recipients to cardiovascular specialists before transplant and guide long-term monitoring.

Cardiovascular Events After Hematopoietic Stem Cell Transplant: Incidence and Risk Factors

Background

Hematopoietic stem cell transplantation (HSCT) is associated with various cardiovascular (CV) complications.

Objectives

We sought to characterize the incidence and risk factors for short-term and long-term CV events in a contemporary cohort of adult HSCT recipients.

Methods

We conducted a multicenter observational study of adult patients who underwent autologous or allogeneic HSCT between 2008 and 2019. Data on demographics, clinical characteristics, conditioning regimen, and CV outcomes were collected through chart review. CV outcomes were a composite of CV death, myocardial infarction, heart failure, atrial fibrillation/flutter, stroke, and sustained ventricular tachycardia and were classified as short-term (≤100 days post-HSCT) or long-term (>100 days post-HSCT).

Results

In 3,354 patients (mean age 55 years; 40.9% female; 30.1% Black) followed for a median time of 2.3 years (Q1-Q3: 1.0-5.4 years), the 100-day and 5-year cumulative incidences of CV events were 4.1% and 13.9%, respectively. Atrial fibrillation/flutter was the most common short- and long-term CV event, with a 100-day incidence of 2.6% and a 5-year incidence of 6.8% followed by heart failure (1.1% at 100 days and 5.4% at 5 years). Allogeneic recipients had a higher incidence of long-term CV events compared to autologous recipients (5-year incidence 16.4% vs 12.1%; P = 0.002). Baseline CV comorbidities were associated with a higher risk of long-term CV events.

Conclusions

The incidence of short-term CV events in HSCT recipients is relatively low. Long-term events were more common among allogeneic recipients and those with pre-existing CV comorbidities.

A Pilot Trial of Consolidation Bevacizumab after Hypo-Fractionated Concurrent Chemoradiotherapy in Patients with Unresectable Locally Advanced Non-Squamous Non-Small-Cell Lung Cancer

PURPOSE/OBJECTIVE(S)

To assess the feasibility of adding bevacizumab consolidation into hypo-fractionated concurrent chemoradiotherapy (hypo-CCRT) in patients with unresectable locally advanced non-squamous non-small cell lung cancer (LA-NS-NSCLC).

MATERIALS/METHODS

Eligible patients were treated with hypo-RT (40 Gy in 10 fractions) followed by hypo-boost (24-28 Gy in 6-7 fractions) combined with concurrent weekly chemotherapy. Patients completed the hypo-CCRT without≥G2 toxicities then received consolidation bevacizumab every 3 weeks for up to 1 year, or disease progression or unacceptable treatment related toxicities. The primary endpoint was the risk of G4 or higher hemorrhage. The secondary endpoint was progression-free survival (PFS), overall survival (OS), locoregional failure-free survival (LRFS), distant metastasis-free survival (DMFS) and objective response rate (ORR). All time-to-event endpoints (OS, PFS, LRFS and DMFS) were measured from the start of radiotherapy.

RESULTS

From December 2017 to July 2020, a total of 27 patients were analyzed with a median follow-up duration of 28.0 months. One patient (3.7%) developed G5 hemorrhage during bevacizumab consolidation. Besides, there were 7 patients (25.9%) had G3 cough and 3 patients (11.1%) had G3 pneumonitis. The ORR was 92.6% of the whole cohort. The median OS was 37.0 months (95% confidence interval, 8.9-65.1 months), the median PFS was 16.0 months (95% confidence interval, 14.0-18.0 months), the median LRFS was not reached and the median DMFS was 18.0 months.

CONCLUSION

This pilot study met its goal of demonstrating the tolerability of consolidation bevacizumab after hypo-CCRT. Further investigation of antiangiogenic and immunotherapy combinations in LA-NSCLC is warranted while G3 respiratory toxicities is worth considering.

Prospective Clinical Trial of Premastectomy Radiotherapy Followed by Immediate Breast Reconstruction for Operable Breast Cancer

PURPOSE/OBJECTIVE(S)

Radiation delivered prior to mastectomy and autologous breast reconstruction may avoid the adverse effects of radiation on autologous donor tissue while providing the psychologic benefit of immediate reconstruction. We aimed to study the feasibility of premastectomy radiation therapy (PreMRT).

MATERIALS/METHODS

A total of 50 women enrolled in a prospective trial of preoperative radiation to the breast and regional nodes followed by mastectomy with axillary evaluation and immediate breast reconstruction. The trial was embedded in a randomized trial of hypofractionated versus conventionally fractionated regional nodal irradiation (NCT02912312). Eligible women enrolled from 2018-22, had cT0-T3 N0-3 breast cancer, and a pre-operative recommendation for radiation. The primary outcome was frequency of complete free flap loss. Mastectomy skin flap necrosis was assessed by validated SKIN grading score. The Satisfaction with Breast Cosmetic Outcomes Scales evaluated patient satisfaction with cosmetic result. Descriptive statistics and 95% exact confidence intervals were calculated.

RESULTS

One patient withdrew prior to any treatment and one elected not to have breast reconstruction. Median age of the 48 women completing PreMRT and reconstruction was 48 [range 31-72]. Most had ER-positive HER2-negative (77%), cT3 (54%) or cT2 (38%), cN1 (79%) disease and received 50 Gy in 25 fractions (n = 24) or 40.05 Gy in 15 fractions (n = 23). Four received 10-16 Gy internal mammary or infraclavicular boost. 35% VMAT, 48% matched photon-electron, and 17% partially-wide-tangent technique. Median time to surgery was 23 days [14-85]. Skin reaction delayed surgery for one patient. Most had skin-sparing mastectomy (92%) and axillary lymph node dissection (67%). 12 surgeons performed the reconstructions: 35 deep inferior epigastric perforators; 4 profunda artery perforator; 2 muscle-sparing transverse rectus abdominis myocutaneous; 1 latissimus dorsi (LD); 2 LD/implant; 2 LD/tissue expander (TE); and 2 subpectoral (SP) TE. There were no complete flap losses. Two patients (4.4%, 95% CI 0.5%-14.8%) with free flaps had partial flap loss with revision surgery. Both patients with SP TEs had infections and unplanned reoperation. The protocol was subsequently amended to not allow SP TE reconstruction. Eight patients had skin flap necrosis: 5 partial and 3 full thickness necrosis; only 1 required operative debridement. Seven had pathologic complete response. At six months 19/31 (61%) reported being "quite a bit" or "very much" satisfied with how they looked in the mirror clothed. There are no recurrences with a median follow up of 33 months [5-119].

CONCLUSION

Radiation treatment of the breast and lymph node basins prior to mastectomy with immediate autologous reconstruction is feasible. There were no autologous flap loses and complication rates are similar to reconstruction after radiation series. This promising strategy reduces time to autologous reconstruction and merits further prospective study.

Perspectives on long-acting formulations of pre-exposure prophylaxis (PrEP) among men who have sex with men who are non-adherent to daily oral PrEP in the United States

INTRODUCTION

Pre-exposure prophylaxis (PrEP) persistence among men who have sex with men (MSM) in real world clinical settings for HIV prevention is suboptimal. New longer-acting formulations of PrEP are becoming available, including injectables, subdermal implants, and other oral medications. These longer-acting formulations have the potential to improve retention among those who have challenges remaining adherent to daily oral PrEP.

METHODS

We interviewed 49 MSM who had initiated but discontinued oral PrEP at three diverse clinics across the United States. We examined participants' perspectives about long-acting PrEP formulations and how long-acting options could affect PrEP use using thematic analysis.

RESULTS

Participants were not very knowledgeable about long-acting formulations of PrEP but were open to learning about them and considering use. Participants were concerned about safety and efficacy of products given that they were still newer and/or in development. Finally, participants had clear preferences for oral pills, injectables, and then subdermal implants and were most interested in options that reduced the number of visits to the clinic.

CONCLUSION

Long-acting formulations of PrEP are acceptable to MSM with suboptimal PrEP persistence and have the potential to improve PrEP persistence. However, many felt they needed more information on safety, efficacy, and use to consider these options. As these long-acting formulations are implemented, public health campaigns and clinical interventions to encourage may maximize uptake particularly among those who are not currently adherent to daily oral PrEP.

Three-dimensional evaluation of the mandibular condyle in adults with various skeletal patterns

Objective

Morphometric and morphological evaluation of the mandibular condyle in adults and to identify its correlation with skeletal malocclusion patterns.

Methods

Cone-beam computed tomography scans of 135 adult patients were used in this study and classified into groups according to four criteria: (1) sex (male and female); (2) sagittal skeletal discrepancy (Class I, Class II, and Class III); (3) vertical skeletal discrepancy (hyperdivergent, normodivergent, and hypodivergent); and age (group 1 ≤ 20 years, 21 ≤ group 2 < 30, and group 3 ≥ 30 years). The morphometrical variables were mandibular condyle height and width, and the morphological variable was the mandibular condyle shape in coronal and sagittal sections. Three-dimensional standard tessellation language files were created using itk-snap (open-source software), and measurements were performed using Meshmixer (open-source software).

Results

The mandibular condyle height was significantly greater (p < 0.05) in patients with class III malocclusion than in those with class I or II malocclusion; the mandibular condyle width was not significantly different among different sexes, age groups, and sagittal and vertical malocclusions. There were no statistical associations between various mandibular condyle shapes and the sexes, age groups, and skeletal malocclusions.

Conclusions

The condylar height was greatest in patients with class III malocclusion. The condylar height and width were greater among males than in females. The mandibular condyle shapes observed in sagittal and coronal sections did not affect the skeletal malocclusion patterns.

New-Onset Cardiac Amyloidosis while in Remission from Systemic AL Amyloidosis

In light chain amyloidosis, a reduction in dFLC to below 40 mg/l is a prerequisite for organ recovery as nearly half of the patients who achieve very good partial haematological responses have improvement in the function of the involved organ. We describe a patient who developed new-onset cardiac amyloidosis despite a post-treatment reduction in dFLC to <10 mg/l.

Facilitators for retaining men who have sex with men in pre-exposure prophylaxis care in real world clinic settings within the United States

BACKGROUND

Pre-exposure prophylaxis (PrEP) can significantly reduce HIV acquisition especially among communities with high HIV prevalence, including men who have sex with men (MSM). Much research has been finding suboptimal PrEP persistence; however, few studies examine factors that enhance PrEP persistence in real-world settings.

METHODS

We interviewed 33 patients who identified as MSM at three different PrEP clinics in three regions of the U.S. (Northeast, South, Midwest). Participants were eligible if they took PrEP and had been retained in care for a minimum of 6 months. Interviews explored social, structural, clinic-level and behavioral factors that influencing PrEP persistence.

RESULTS

Through thematic analysis we identified the following factors as promoting PrEP persistence: (1) navigation to reduce out-of-pocket costs of PrEP (structural), (2) social norms that support PrEP use (social), (3) access to LGBTQ + affirming medical providers (clinical), (4) medication as part of a daily routine (behavioral), and (5) facilitation of sexual health agency (belief).

DISCUSSION

In this sample, persistence in PrEP care was associated with structural and social supports as well as a high level of perceived internal control over protecting their health by taking PrEP. Patients might benefit from increased access, LGBTQ + affirming medical providers, and communications that emphasize PrEP can promote sexual health.

Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia

Low levels of high density lipoprotein-cholesterol (HDL-C) are associated with an elevated risk of arteriosclerotic coronary heart disease. Heritability of HDL-C levels is high. In this research discovery study, we used whole-exome sequencing to identify damaging gene variants that may play significant roles in determining HDL-C levels. We studied 204 individuals with a mean HDL-C level of 27.8 ± 6.4 mg/dl (range: 4-36 mg/dl). Data were analyzed by statistical gene burden testing and by filtering against candidate gene lists. We found 120 occurrences of probably damaging variants (116 heterozygous; four homozygous) among 45 of 104 recognized HDL candidate genes. Those with the highest prevalence of damaging variants were ABCA1 (n = 20), STAB1 (n = 9), OSBPL1A (n = 8), CPS1 (n = 8), CD36 (n = 7), LRP1 (n = 6), ABCA8 (n = 6), GOT2 (n = 5), AMPD3 (n = 5), WWOX (n = 4), and IRS1 (n = 4). Binomial analysis for damaging missense or loss-of-function variants identified the ABCA1 and LDLR genes at genome-wide significance. In conclusion, whole-exome sequencing of individuals with low HDL-C showed the burden of damaging rare variants in the ABCA1 and LDLR genes is particularly high and revealed numerous occurrences in HDL candidate genes, including many genes identified in genome-wide association study reports. Many of these genes are involved in cancer biology, which accords with epidemiologic findings of the association of HDL deficiency with increased risk of cancer, thus presenting a new area of interest in HDL genomics.

Characteristics of Neonates with Cardiopulmonary Disease Who Experience Seizures: A Multicenter Study

OBJECTIVE

To compare key seizure and outcome characteristics between neonates with and without cardiopulmonary disease.

STUDY DESIGN

The Neonatal Seizure Registry is a multicenter, prospectively acquired cohort of neonates with clinical or electroencephalographic (EEG)-confirmed seizures. Cardiopulmonary disease was defined as congenital heart disease, congenital diaphragmatic hernia, and exposure to extracorporeal membrane oxygenation. We assessed continuous EEG monitoring strategy, seizure characteristics, seizure management, and outcomes for neonates with and without cardiopulmonary disease.

RESULTS

We evaluated 83 neonates with cardiopulmonary disease and 271 neonates without cardiopulmonary disease. Neonates with cardiopulmonary disease were more likely to have EEG-only seizures (40% vs 21%, P < .001) and experience their first seizure later than those without cardiopulmonary disease (174 vs 21 hours of age, P < .001), but they had similar seizure exposure (many-recurrent electrographic seizures 39% vs 43%, P = .27). Phenobarbital was the primary initial antiseizure medication for both groups (90%), and both groups had similarly high rates of incomplete response to initial antiseizure medication administration (66% vs 68%, P = .75). Neonates with cardiopulmonary disease were discharged from the hospital later (hazard ratio 0.34, 95% CI 0.25-0.45, P < .001), although rates of in-hospital mortality were similar between the groups (hazard ratio 1.13, 95% CI 0.66-1.94, P = .64).

CONCLUSION

Neonates with and without cardiopulmonary disease had a similarly high seizure exposure, but neonates with cardiopulmonary disease were more likely to experience EEG-only seizures and had seizure onset later in the clinical course. Phenobarbital was the most common seizure treatment, but seizures were often refractory to initial antiseizure medication. These data support guidelines recommending continuous EEG in neonates with cardiopulmonary disease and indicate a need for optimized therapeutic strategies.

[Retrospective analysis of infliximab in the treatment of Kawasaki disease]

Objective: To investigate the efficacy and safety of infliximab (IFX) therapy for children with Kawasaki disease. Methods: Sixty-eight children with Kawasaki disease who received IFX therapy in Children's Hospital of Fudan University from January 2014 to April 2021 were enrolled. The indications for IFX administration, changes in laboratory parameters before and after IFX administration, response rate, drug adverse events and complications and outcomes of coronary artery aneurysms (CAA) were retrospectively analyzed. Comparisons between groups were performed with unpaired Student t test or Mann-Whitney U test or chi-square test. Results: Among 68 children with Kawasaki disease, 52 (76%) were males and 16 (24%) were females. The age of onset was 2.1 (0.5, 3.8) years. IFX was administered to: (1) 35 children (51%) with persistent fever who did not respond to intravenous immunoglobulin (IVIG) or steroids, 28 of the 35 children (80%) developed CAA before IFX therapy; (2) 32 children (47%) with continuous progression of CAA; (3) 1 child with persistent arthritis. In all cases, IFX was administered as an additional treatment (the time from the onset of illness to IFX therapy was 21 (15, 30) days) which consisted of second line therapy in 20 (29%), third line therapy in 20 (29%), and fourth (or more) line therapy in 28 (41%). C-reactive protein (8 (4, 15) vs. 16 (8, 43) mg/L, Z=-3.38, P=0.001), serum amyloid protein A (17 (10, 42) vs. 88 (11, 327) mg/L, Z=-2.36, P=0.018) and the percentage of neutrophils (0.39±0.20 vs. 0.49±0.21, t=2.63, P=0.010) decreased significantly after IFX administration. Fourteen children (21%) did not respond to IFX and received additional therapies mainly including steroids and cyclophosphamide. There was no significant difference in gender, age at IFX administration, time from the onset of illness to IFX administration, the maximum coronary Z value before IFX administration, and the incidence of systemic aneurysms between IFX-sensitive group and IFX-resistant group (all P>0.05). Infections occurred in 11 cases (16%) after IFX administration, including respiratory tract, digestive tract, urinary tract, skin and oral infections. One case had Calmette-Guérin bacillus-related adverse reactions 2 months after IFX administration. All of these adverse events were cured successfully. One child died of CAA rupture, 6 children were lost to follow up, the remaining 61 children were followed up for 6 (4, 15) months. No CAA occurred in 7 children before and after IFX treatment, while CAA occurred in 54 children before IFX treatment. CAA regressed in 23 (43%) children at the last follow-up, and the diameter of coronary artery recovered to normal in 10 children. Conclusion: IFX is an effective and safe therapeutic choice for children with Kawasaki disease who are refractory to IVIG or steroids therapy or with continuous progression of CAA.

Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation

Segmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. Population-level characterization of SDs has generally been lacking because most techniques used for analyzing these complex regions are both labor and cost intensive. In this study, we have used a high-throughput technique to genotype complex structural variation with a single molecule, long-range optical mapping approach. We characterized SDs and identified novel structural variants (SVs) at 7q11.23, 15q13.3, and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising five super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we localized the microdeletion breakpoints to specific paralogous duplicons located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.

Exercise, cancer and cardiovascular disease: what should clinicians advise?

Cardiovascular disease is one of the leading causes of morbidity and mortality in persons with cancer. The elevated risk is thought to derive from the combination of cardiovascular risk factors and direct cardiotoxicity from cancer therapies. Exercise may be a potential strategy to counteract these toxicities and maintain cardiovascular reserve. In this article, we review the evidence for the potential cardioprotective effects of exercise training in cancer patients before, during, and following treatment. We also propose a patient-tailored approach for the development of targeted prescriptions based on individual exercise capacity and cardiovascular reserve.

Evaluation of Clinical Trials in Onco-haematology: A New Method Based on Risk Analysis and Multidisciplinarity

BACKGROUND

European member states are increasingly vying with one another to recruit patients for clinical trials (CTs). The French national agency for medicines (ANSM) now receives an ever-growing number of CTs, extending response times. The aim of the new methodology presented herein is to reduce assessment times below the national mandatory timeframe of 60 days and to improve patient safety.

MATERIALS AND METHODS

Based on an analysis of the criteria defining CTs, 4 key points were identified (safety, fragile population, loss of opportunity, design complexity) to build a criticality score which would determine evaluation type. This score also determines the resources needed (complete evaluation, multidisciplinary advice, ad hoc evaluation) and the timeframe required for appropriate analysis. All post-phase I CTs were analysed from the implementation of the new assessment method, on 01/02/2018 through to 31/12/2019.

RESULTS

447 CTs were analysed (63% industry and 37% academic sponsors). Based on a criticality scale, 27% of the CTs received a type A evaluation (complete), 37% a type B (multidisciplinary evaluation), 23% a type C evaluation (ad hoc evaluation) and 13% a type D evaluation (fast evaluation). From 2014 to 2017, 37% of the CTs were analysed within the mandatory timeframe, with a mean of 68 days, reaching a maximum of 102 days in 2017. Using this new assessment method, 92% of CTs respected the mandatory timeframe in 2019; the mean time in 2018-2019 was 34 days; Grounds for Non-Acceptance (GNA) were raised for 66% of the CTs (69% from academic sponsors and 65% from industrial firms). 3 CTs were refused.

CONCLUSION

Here, we demonstrate the feasibility of risk analysis and multidisciplinarity method, which resulted in a dramatic improvement of assessment times.

Development of Expert-Level Automated Detection of Epileptiform Discharges During Electroencephalogram Interpretation

Importance

Interictal epileptiform discharges (IEDs) in electroencephalograms (EEGs) are a biomarker of epilepsy, seizure risk, and clinical decline. However, there is a scarcity of experts qualified to interpret EEG results. Prior attempts to automate IED detection have been limited by small samples and have not demonstrated expert-level performance. There is a need for a validated automated method to detect IEDs with expert-level reliability.

Objective

To develop and validate a computer algorithm with the ability to identify IEDs as reliably as experts and classify an EEG recording as containing IEDs vs no IEDs.

Design, Setting, and Participants

A total of 9571 scalp EEG records with and without IEDs were used to train a deep neural network (SpikeNet) to perform IED detection. Independent training and testing data sets were generated from 13 262 IED candidates, independently annotated by 8 fellowship-trained clinical neurophysiologists, and 8520 EEG records containing no IEDs based on clinical EEG reports. Using the estimated spike probability, a classifier designating the whole EEG recording as positive or negative was also built.

Main Outcomes and Measures

SpikeNet accuracy, sensitivity, and specificity compared with fellowship-trained neurophysiology experts for identifying IEDs and classifying EEGs as positive or negative or negative for IEDs. Statistical performance was assessed via calibration error and area under the receiver operating characteristic curve (AUC). All performance statistics were estimated using 10-fold cross-validation.

Results

SpikeNet surpassed both expert interpretation and an industry standard commercial IED detector, based on calibration error (SpikeNet, 0.041; 95% CI, 0.033-0.049; vs industry standard, 0.066; 95% CI, 0.060-0.078; vs experts, mean, 0.183; range, 0.081-0.364) and binary classification performance based on AUC (SpikeNet, 0.980; 95% CI, 0.977-0.984; vs industry standard, 0.882; 95% CI, 0.872-0.893). Whole EEG classification had a mean calibration error of 0.126 (range, 0.109-0.1444) vs experts (mean, 0.197; range, 0.099-0.372) and AUC of 0.847 (95% CI, 0.830-0.865).

Conclusions and Relevance

In this study, SpikeNet automatically detected IEDs and classified whole EEGs as IED-positive or IED-negative. This may be the first time an algorithm has been shown to exceed expert performance for IED detection in a representative sample of EEGs and may thus be a valuable tool for expedited review of EEGs.

Interrater Reliability of Experts in Identifying Interictal Epileptiform Discharges in Electroencephalograms

Importance

The validity of using electroencephalograms (EEGs) to diagnose epilepsy requires reliable detection of interictal epileptiform discharges (IEDs). Prior interrater reliability (IRR) studies are limited by small samples and selection bias.

Objective

To assess the reliability of experts in detecting IEDs in routine EEGs.

Design, Setting, and Participants

This prospective analysis conducted in 2 phases included as participants physicians with at least 1 year of subspecialty training in clinical neurophysiology. In phase 1, 9 experts independently identified candidate IEDs in 991 EEGs (1 expert per EEG) reported in the medical record to contain at least 1 IED, yielding 87 636 candidate IEDs. In phase 2, the candidate IEDs were clustered into groups with distinct morphological features, yielding 12 602 clusters, and a representative candidate IED was selected from each cluster. We added 660 waveforms (11 random samples each from 60 randomly selected EEGs reported as being free of IEDs) as negative controls. Eight experts independently scored all 13 262 candidates as IEDs or non-IEDs. The 1051 EEGs in the study were recorded at the Massachusetts General Hospital between 2012 and 2016.

Main Outcomes and Measures

Primary outcome measures were percentage of agreement (PA) and beyond-chance agreement (Gwet κ) for individual IEDs (IED-wise IRR) and for whether an EEG contained any IEDs (EEG-wise IRR). Secondary outcomes were the correlations between numbers of IEDs marked by experts across cases, calibration of expert scoring to group consensus, and receiver operating characteristic analysis of how well multivariate logistic regression models may account for differences in the IED scoring behavior between experts.

Results

Among the 1051 EEGs assessed in the study, 540 (51.4%) were those of females and 511 (48.6%) were those of males. In phase 1, 9 experts each marked potential IEDs in a median of 65 (interquartile range [IQR], 28-332) EEGs. The total number of IED candidates marked was 87 636. Expert IRR for the 13 262 individually annotated IED candidates was fair, with the mean PA being 72.4% (95% CI, 67.0%-77.8%) and mean κ being 48.7% (95% CI, 37.3%-60.1%). The EEG-wise IRR was substantial, with the mean PA being 80.9% (95% CI, 76.2%-85.7%) and mean κ being 69.4% (95% CI, 60.3%-78.5%). A statistical model based on waveform morphological features, when provided with individualized thresholds, explained the median binary scores of all experts with a high degree of accuracy of 80% (range, 73%-88%).

Conclusions and Relevance

This study's findings suggest that experts can identify whether EEGs contain IEDs with substantial reliability. Lower reliability regarding individual IEDs may be largely explained by various experts applying different thresholds to a common underlying statistical model.

Towards a reference genome that captures global genetic diversity

The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity.

The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.

Association of arterial stiffness in non-hypertensive offspring with parental hypertension: the Hanzhong adolescent hypertension cohort study

OBJECTIVE

Arterial stiffness may be an early marker for vascular changes associated with hypertension in young adults. Individuals with a family history of hypertension are at high risk of developing hypertension. We investigated whether arterial stiffness measured, such as mean arterial pressure (MAP) and brachial to ankle pulse wave velocity (baPWV), were increased in normotensive offspring with a parental history of hypertension.

PATIENTS AND METHODS

We compared MAP and baPWV in a sample of 1953 non-hypertensive participants (974 men, mean age 42±3 years) recruited in the previous Hanzhong adolescent hypertension cohort study. Standardized questionnaires, physical examinations and laboratory tests were used to obtain information, with a particular focus on family hypertension history, anthropometric, hemodynamic, and biochemical factors.

RESULTS

A total of 1039, 759, 155 participants had 0, 1, and 2 parents with hypertension, respectively. Parental hypertension was associated with elevated offspring MAP (in multivariable-adjusted models, B=1.5 mm Hg, 95% CI 0.8-2.2 for 1 parent with hypertension; B=3.0 mm Hg, 95% CI 1.8-4.3, for 2 parents with hypertension; p<0.001 for each). A significant positive correlation was also observed between MAP and baPWV (r=0.543, p<0.001). BaPWV displayed a similar correlation with parental hypertension in age-adjusted, sex-adjusted and body mass index (BMI)-adjusted models (B=23.1 cm/s, 95% CI 8.0-38.1, for 1 parent with hypertension, p<0.01; B=53.0 cm/s, 95% CI 25.8-80.2, p<0.001 for 2 parents with hypertension), but associations were attenuated in multicovariate models after adjustment for MAP. In multivariable-adjusted models, logistic regression analysis showed that the risk of belonging to the upper quartile of MAP was significantly increased for offspring whose parents had hypertension (OR=1.5, 95% CI 1.2-1.9, for 1 parent with hypertension; OR=2.3, 95% CI 1.6-3.4, for 2 parents with hypertension; p<0.001 for each). Similarly, the odds ratios of belonging to the upper quartile of baPWV increased (OR=1.3, 95% CI 1.1-1.6, for 1 parent with hypertension, p<0.05; OR=2.1, 95% CI 1.5-3.0, for 2 parents with hypertension, p<0.001, in age-sex-BMI-adjusted models), and were then brought down in the fully adjusted models including MAP, but the increase remained significant for 2 parents with hypertension (OR=1.6, 95% CI 1.0-2.3, p<0.05).

CONCLUSIONS

These findings provide evidence that arterial stiffness is higher in young-to middle-aged normotensive subjects with a family history of hypertension, suggesting that increased arterial stiffness may occur in the early stages during the pathogenesis of hypertension.

Evaluation of cell transplant-mediated attenuation of diffuse injury in experimental autoimmune encephalomyelitis using onVDMP CEST MRI

The development and translation of cell therapies have been hindered by an inability to predict and evaluate their efficacy after transplantation. Using an experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis (MS), we studied attenuation of the diffuse injury characteristic of EAE and MS by transplanted glial-restricted precursor cells (GRPs). We assessed the potential of on-resonance variable delay multiple pulse (onVDMP) chemical exchange saturation transfer (CEST) MRI to visualize this attenuation. Allogeneic GRPs transplanted in the motor cortex or lateral ventricles attenuated paralysis in EAE mice and attenuated differences compared to naïve mice in onVDMP CEST signal 5 days after transplantation near the transplantation site. Histological analysis revealed that transplanted GRPs co-localized with attenuated astrogliosis. Hence, diffuse injury-sensitive onVDMP CEST MRI may complement conventional MRI to locate and monitor tissue regions responsive to GRP therapy.

[The correlation between blood pressure response to cold pressor test and long-term blood pressure changes]

Objective: The aim of the study was to investigate the correlation between blood pressure response to cold pressor test (CPT) and follow-up blood pressure after 8 years in subjects, and to evaluate the predictive value of CPT for long-term blood pressure levels. Methods: A total of 365 individuals from eight natural villages were enrolled by stratified cluster sampling from Mei County, Shaanxi Province in 2004. Baseline characteristics of subjects were collected and CPTs were conducted. Subjects were followed up in 2009 and 2012, respectively. According to the maximal change of systolic response (SR), the area under the curve (AUC) of systolic blood pressure change (AUC-SBP), the maximal change of diastolic response (DR) and the AUC of diastolic blood pressure change (AUC-DBP) in CPT, the individuals were divided into four quartile groups by above parameters, respectively: group Ⅰ (P(25)), group Ⅱ (P(50)), group Ⅲ (P(75)) and group Ⅳ (P(100)). The correlation between blood pressure response to CPT and the follow-up blood pressure was analyzed. Results: (1) There were no significant differences in baseline blood pressure levels and prevalence of hypertension among four quartile groups no matter it was grouped on SR, DR, AUC-SBP or AUC-DBP. (2) The prevalence of hypertension in each group from lowest (P(25)) to highest (P(100)) in 2012 was 25.64%, 30.67%, 38.03%, 55.74% on SR grouping (P<0.01), and 27.5%, 29.17%, 38.46%, 57.35% on AUC-SBP grouping (P<0.05), respectively. (3) There were no significant differences in the prevalence of hypertension among four groups in 2012 (P>0.05) either on DR or on AUC-DBP grouping. (4) The random effects model analysis showed that the correlation coefficient between SR, AUC-SBP and long-term systolic blood pressure increase were 1.91 (P<0.05) and 1.44 (P<0.05), respectively, and the correlation coefficient between DR, AUC-DBP and long-term diastolic blood pressure increase were 0.82 (P<0.05) and 0.78 (P>0.05), respectively. Age, male, body mass index, and fasting blood glucose were independent risk factors for long-term blood pressure elevation, and age, body mass index and fasting blood glucose positively correlated with changes in long-term blood pressure (all P<0.05). Conclusion: Individual systolic blood pressure response to CPT can be used as a predictor of long-term hypertension.

44 Wirral's Teletriage Service

Introduction

The Wirral Teletriage Service provides non-urgent clinical support to Wirral Care Homes in order to help avoid unnecessary hospital admissions for their residents. It also aims to provide quicker access to clinical assessment than via NHS 111 and to provide this care in the patient’s residence wherever possible.

Methods

Care homes call the Teletriage service when they have concerns about the health of one of their residents. The Teletriage nurse undertakes a clinical assessment of the resident remotely via Skype. Care Homes have been provided with a secure NHS email address to facilitate secure sharing of data. They have also been provided with iPads and training for their staff. After being assessed by Teletriage, residents are signposted to the most appropriate care pathway for their needs.

Results

76 Care Homes have signed up to the service. On average, the Teletriage Service receives 300-400 calls a month. In an 18 month period, the number of calls to NHS 111 have reduced by 76%. Out of all the calls to Teletriage, 22% of patients were managed by the Teletriage team with no onward referral, 57% were managed via community services e.g GPs, Community Geriatricians, and 10% were referred to the ambulance service. Emergency Health Care Plans (EHCPs), Preferred Priorities of Care and EOL (End of Life) wishes are taken into account.

Conclusions

The Teletriage project has reduced the number of phone calls to NHS 111 and the ambulance service, and subsequently has reduced the number of patients conveyed to hospital by 12%. The Teletriage nurses work very closely with various community services as well as GPs, NWAS and Community Geriatricians. The ongoing training and education provided to the Care Home Staff means that overall there has been good engagement with the project from the majority of the Wirral Care Homes.

Being Born Large for Gestational Age is Associated with Increased Global Placental DNA Methylation

Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p < 0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p < 0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p = 0.001).

Three patients with homozygous familial hypercholesterolemia: Genomic sequencing and kindred analysis

Background

Homozygous Familial Hypercholesterolemia (HoFH) is an inherited recessive condition associated with extremely high levels of low‐density lipoprotein (LDL) cholesterol in affected individuals. It is usually caused by homozygous or compound heterozygous functional mutations in the LDL receptor (LDLR). A number of mutations causing FH have been reported in literature and such genetic heterogeneity presents great challenges for disease diagnosis.

Objective

We aim to determine the likely genetic defects responsible for three cases of pediatric HoFH in two kindreds.

Methods

We applied whole exome sequencing (WES) on the two probands to determine the likely functional variants among candidate FH genes. We additionally applied 10x Genomics (10xG) Linked‐Reads whole genome sequencing (WGS) on one of the kindreds to identify potentially deleterious structural variants (SVs) underlying HoFH. A PCR‐based screening assay was also established to detect the LDLR structural variant in a cohort of 641 patients with elevated LDL.

Results

In the Caucasian kindred, the FH homozygosity can be attributed to two compound heterozygous LDLR damaging variants, an exon 12 p.G592E missense mutation and a novel 3kb exon 1 deletion. By analyzing the 10xG phased data, we ascertained that this deletion allele was most likely to have originated from a Russian ancestor. In the Mexican kindred, the strikingly elevated LDL cholesterol level can be attributed to a homozygous frameshift LDLR variant p.E113fs.

Conclusions

While the application of WES can provide a cost‐effective way of identifying the genetic causes of FH, it often lacks sensitivity for detecting structural variants. Our finding of the LDLR exon 1 deletion highlights the broader utility of Linked‐Read WGS in detecting SVs in the clinical setting, especially when HoFH patients remain undiagnosed after WES.

OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps

BACKGROUND

Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples.

FINDINGS

We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains.

CONCLUSIONS

With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.

Mitochondrial DNA mutation m.3243A>G is associated with altered mitochondrial function in peripheral blood mononuclear cells, with heteroplasmy levels and with clinical phenotypes

AIMS

To investigate the associations among heteroplasmy levels (i.e. the proportions of mutant and wild-type mitochondrial DNA in the same cell), mitochondrial function and clinical severity of the m.3243A>G mutation.

METHODS

A total of 17 participants carrying the m.3243A>G mutation and 17 sex- and age-matched healthy controls were included in this study. Heteroplasmy levels of the m.3243A>G mutation in leukocytes, saliva and urine sediment were determined by pyrosequencing. The clinical evaluation included endocrinological, audiological and ophthalmological examinations. Mitochondrial function was determined in peripheral blood mononuclear cells isolated from participants.

RESULTS

Heteroplasmy levels in urine sediment were higher than those in leukocytes and saliva. Reduced levels of adenosine triphosphate and mitochondrial membrane potential, and increased reactive oxygen species production were observed in mutant peripheral blood mononuclear cells (all P < 0.05). Linear regression analysis indicated that higher heteroplasmy levels in peripheral blood leukocytes were associated with increased levels of glycated albumin and HbA_1c , and decreased total hip bone mineral density T-score after adjustment for age and sex (all P < 0.05). Furthermore, mitochondrial membrane potential was independently associated with bone mineral density T-score at the femoral neck (P < 0.05).

CONCLUSIONS

Heteroplasmy levels in peripheral blood leukocytes and mitochondrial membrane potential in peripheral blood mononuclear cells were closely associated with clinical manifestations and were valuable for evaluation of the clinical severity of the m.3243A>G mutation.

Epididymal small non-coding RNA studies: progress over the past decade

BACKGROUND

Small non-coding RNAs (sncRNAs) accomplish a huge variety of biological functions. Over the past decade, we have witnessed the substantial progress in the epididymal sncRNA studies. In the Epididymis 7, we had the true privilege of having a whole session to share our findings and exchange ideas on the epididymal sncRNA studies.

OBJECTIVES

This mini-review attempts to provide an overview of what is known about the sncRNAs in the mammalian epididymis and discuss the future directions in this field.

METHODS

We surveyed literature regarding the sncRNA studies in the mammalian epididymis, and integrated some of our unpublished findings as well. We focus on the progress in methodology and the advances in our understanding of the expression and functions of epididymal sncRNAs.

RESULTS AND DISCUSSION

The applications of high-throughput approaches have made great contributions in the discovery of new sncRNA species and profiling their dynamics in the epithelial cells, the passing spermatozoa, and the luminal environment. The diverse classes of epididymal sncRNAs exert important biological functions from the in situ regulation of epididymal gene expression to the epigenetic inheritance in the offspring.

CONCLUSION

Although still in its infancy, we believe that the research on epididymal sncRNAs will not only lead to a better understanding of their physiological and pathological functions, but also contribute to the whole landscape of the RNA field.

Abstract P1-10-05: Analysis of genetic mutation in ethnically diverse population with Breast and ovarian cancer: Single institution experience

Only 5-10% of all breast and ovarian cancers have been attributed to inherited mutation. In unselected breast cancer patients, prevalence of germline BRCA 1 & 2 is about 2%. In Ashkenazi Jewish population the prevalence is estimated to be 11.7%. The rate of mutations in other populations has not been well characterized. The purpose of this study is to identify and characterize the risk of genetic mutations in an ethnically diverse population referred for genetic testing according to NCCN guidelines.

Method:

In this single institution retrospective study, we analyzed 782 patients referred for genetic testing between 2009-2018. Information regarding reason for referral, ethnicity, cancer history and results of genetic mutation using multigene panels were collected.

Results:

Reasons for referral were:

· Family History of cancer (142; 18.6%),

· Breast cancer diagnosed at early age (207; 26.4%),

· Triple negative breast cancer (12 ;53%

· Ovarian cancer (61; 7.8%)

· Multiple cancer (32; 4.09%)

· Known BRCA 1 or 2 mutation (51;6.5%)

· Known other mutation (9;1.15%)

· Family h/o cancer but not diagnosed with cancer (268)

Ethnic distribution:

· 328 Hispanic (41.94%)

· 177 Caucasian (22.6%),

· 27 Chinese, (3.4%)

· 52 Vietnamese (6.6%)

· 86 other- Asian (11%)

· 32 Middle eastern (4.1%),

· 14 South Asian (1.8%)

· 35 African American (4.5%)

· 8 Ashkenazi Jewish (1%)

· 19 Mixed Hispanic (2.1%)

Genetic testing was done in 545 /782 patients.

Deleterious Mutation detected: 88 patients (16.5% of tested)

· BRCA 1: 32(5.8%)

· BRCA 2:28 (5.14%)

· MSH2:5(0.9%)

· p53:39 (0.5%)

· PLB2:3 (0.38%)

· MUTYH:3 (0.38%)

· CDH1 :2 (0.26%)

· PMS2: 2 ( 0.26%)

· ATM: 1(0.13%)

· CCKn2A: 1(0.13%)

· CHEK 2: 1(0.13)

· MET:1(0.13%)

· MSH6:1 (0.13%)

· RAD50 :1(0.13%)

· RET1;1(0.13%)

BRCA1/BRCA2 mutation: 60

Mutation in BRCA 1/ 2 distribution by ethnicity:

· Hispanic (28; 8.54 %),

· Chinese (4;14.8%)

· Vietnamese (4; 7.7%)

· other Asian (12;13.9%)

· African American (3, 8.5, %)

· South Asian (0 %)

· Caucasian (8; 4.5 %)

· All Asian (20/165: 12.1%)

Mutation in other gene by Ethnicity: total 26

Hispanic (16, 4.5%), Caucasian: (3, 1.7%) Asian other than Chinese and Vietnamese (4, 4.65%)

Mutation in Breast cancer: 333 Breast cancer patients tested, 39 patients (11.17%) were found to have mutations.

10/32 triple negative (31%) 4/49 her2neu positive patients (8.1%) and 15/252 (5.9%) ER+ patients found to have mutations.

17/39 breast cancer patients with mutation had prophylactic BSO.

Mutation in BRCA 1& 2 by reason for referral:

Known family h/o of BRCA1 or 2 mutations (18; 39.5%)

Early age of cancer (10, 7.4%)

Cancer with positive family history (17, 8.2%)

Triple negative (2, 16%).

Variant of Unknown significance (VUS): 140 patients (25 %)

VUS in BRCA 2 were most common. VUS were found in 17% of Hispanic and African American patients.

No significant difference in PFS and OS was found in patient with mutation and without mutation

Conclusion:

We found much higher rates (16.5%) than previously reported mutation detection in this very highly diverse patient population.

Rate of BRCA 1&2 mutation was 8.55% in Hispanic and 12.1% in Asian patients compared with 4.5% in Caucasian patient when selected for high risk factors.

We Also noted very high rate of VUS especially in Hispanic and African American patients.

Citation Format: Aggarwal S, Chu C, Ngumi M. Analysis of genetic mutation in ethnically diverse population with Breast and ovarian cancer: Single institution experience [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-10-05.