Inference of tobacco and alcohol consumption habits from DNA methylation analysis of blood

DNA methylation has become a biomarker of great interest in the forensic and clinical fields. In criminal investigations, the study of this epigenetic marker has allowed the development of DNA intelligence tools providing information that can be useful for investigators, such as age prediction. Following a similar trend, when the origin of a sample in a criminal scenario is unknown, the inference of an individual's lifestyle such as tobacco use and alcohol consumption could provide relevant information to help in the identification of DNA donors at the crime scene. At the same time, in the clinical domain, prediction of these trends of consumption could allow the identification of people at risk or better identification of the causes of different pathologies. In the present study, DNA methylation data from the UK AIRWAVE study was used to build two binomial logistic models for the inference of smoking and drinking status. A total of 348 individuals (116 non-smokers, 116 former smokers and 116 smokers) plus a total of 237 individuals (79 non-drinkers, 79 moderate drinkers and 79 drinkers) were used for development of tobacco and alcohol consumption prediction models, respectively. The tobacco prediction model was composed of two CpGs (cg05575921 in AHRR and cg01940273) and the alcohol prediction model three CpGs (cg06690548 in SLC7A11, cg0886875 and cg21294714 in MIR4435-2HG), providing correct classifications of 86.49% and 74.26%, respectively. Validation of the models was performed using leave-one-out cross-validation. Additionally, two independent testing sets were also assessed for tobacco and alcohol consumption. Considering that the consumption of these substances could underlie accelerated epigenetic ageing patterns, the effect of these lifestyles on the prediction of age was evaluated. To do that, a quantile regression model based on previous studies was generated, and the potential effect of tobacco and alcohol consumption with the epigenetic age was assessed. The Wilcoxon test was used to evaluate the residuals generated by the model and no significant differences were observed between the categories analyzed.

Women at Altitude: Menstrual-Cycle Phase, Menopause, and Exogenous Progesterone Are Not Associated with Acute Mountain Sickness

Gardner, Laurel, Linda E. Keyes, Caleb Phillips, Elan Small, Tejaswi Adhikari, Nathan Barott, Ken Zafren, Rony Maharjan, and James Marvel. Women at altitude: Menstrual-cycle phase, menopause, and exogenous progesterone are not associated with acute mountain sickness. High Alt Med Biol. 00:000-000, 2024. Background: Elevated progesterone levels in women may protect against acute mountain sickness (AMS). The impact of hormonal contraception (HC) on AMS is unknown. We examined the effect of natural and exogenous progesterone on the occurrence of AMS. Methods: We conducted a prospective observational convenience study of female trekkers in Lobuche (4,940 m) and Manang (3,519 m). We collected data on last menstrual period, use of exogenous hormones, and development of AMS. Results: There were 1,161 trekkers who met inclusion criteria, of whom 307 (26%) had AMS. There was no significant difference in occurrence of AMS between women in the follicular (28%) and the luteal (25%) phases of menstruation (p = 0.48). The proportion of premenopausal (25%) versus postmenopausal women (30%) with AMS did not differ (p = 0.33). The use of HC did not influence the occurrence of AMS (HC 23% vs. no HC 26%, p = 0.47), nor did hormonal replacement therapy (HRT) (HRT 11% vs. no HRT 31%, p = 0.13). Conclusion: We found no relationship between menstrual-cycle phase, menopausal status, or use of exogenous progesterone and the occurrence of AMS in trekkers and conclude that hormonal status is not a risk factor for AMS. Furthermore, women should not be excluded from future AMS studies based on hormonal status.

Adapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCR

We have adapted an established Ampliseq microhaplotype panel for nanopore sequencing with the Oxford Nanopore Technologies (ONT) system, as a cost-effective and highly scalable solution for forensic genetics applications. For this purpose, we designed a protocol combining direct PCR amplification from unextracted DNA with ONT library construction and sequencing using the MinION device and workflow. The analysis of reference samples at input amounts of 5-10 ng of DNA demonstrates stable coverage patterns, allele balance, and strand bias, reaching profile completeness and concordance rates of ∼95%. Similar levels were achieved when using direct-PCR from blood, buccal and semen swabs. Dilution series results indicate sensitivity is maintained down to 250 pg of input DNA, and informative profiles are produced down to 62.5 pg. Finally, we demonstrated the forensic utility of the nanopore workflow by analyzing two third degree pedigrees that showed low likelihood ratio values after the analysis of an extended panel of 38 STRs, achieving likelihood ratios 2-3 orders of magnitude higher when testing with the MinION-based haplotype data.

Development of an epigenetic age predictor for costal cartilage with a simultaneous somatic tissue differentiation system

Age prediction from DNA has been a topic of interest in recent years due to the promising results obtained when using epigenetic markers. Since DNA methylation gradually changes across the individual's lifetime, prediction models have been developed accordingly for age estimation. The tissue-dependence for this biomarker usually necessitates the development of tissue-specific age prediction models, in this way, multiple models for age inference have been constructed for the most commonly encountered forensic tissues (blood, oral mucosa, semen). The analysis of skeletal remains has also been attempted and prediction models for bone have now been reported. Recently, the VISAGE Enhanced Tool was developed for the simultaneous DNA methylation analysis of 8 age-correlated loci using targeted high-throughput sequencing. It has been shown that this method is compatible with epigenetic age estimation models for blood, buccal cells, and bone. Since when dealing with decomposed cadavers or postmortem samples, cartilage samples are also an important biological source, an age prediction model for cartilage has been generated in the present study based on methylation data collected using the VISAGE Enhanced Tool. In this way, we have developed a forensic cartilage age prediction model using a training set composed of 109 samples (19-74 age range) based on DNA methylation levels from three CpGs in FHL2, TRIM59 and KLF14, using multivariate quantile regression which provides a mean absolute error (MAE) of ± 4.41 years. An independent testing set composed of 72 samples (19-75 age range) was also analyzed and provided an MAE of ± 4.26 years. In addition, we demonstrate that the 8 VISAGE markers, comprising EDARADD, TRIM59, ELOVL2, MIR29B2CHG, PDE4C, ASPA, FHL2 and KLF14, can be used as tissue prediction markers which provide reliable blood, buccal cells, bone, and cartilage differentiation using a developed multinomial logistic regression model. A training set composed of 392 samples (n = 87 blood, n = 86 buccal cells, n = 110 bone and n = 109 cartilage) was used for building the model (correct classifications: 98.72%, sensitivity: 0.988, specificity: 0.996) and validation was performed using a testing set composed of 192 samples (n = 38 blood, n = 36 buccal cells, n = 46 bone and n = 72 cartilage) showing similar predictive success to the training set (correct classifications: 97.4%, sensitivity: 0.968, specificity: 0.991). By developing both a new cartilage age model and a tissue differentiation model, our study significantly expands the use of the VISAGE Enhanced Tool while increasing the amount of DNA methylation-based information obtained from a single sample and a single forensic laboratory analysis. Both models have been placed in the open-access Snipper forensic classification website.

Prior Ambulatory Mild Coronavirus Disease 2019 Does Not Increase Risk of Acute Mountain Sickness

Small, Elan, Caleb Phillips, William Bunzel, Lakota Cleaver, Nishant Joshi, Laurel Gardner, Rony Maharjan, and James Marvel. Prior ambulatory mild coronavirus disease 2019 does not increase risk of acute mountain sickness. High Alt Med Biol. 24:201-208, 2023. Background: Given its long-term morbidity, understanding how prior coronavirus disease 2019 (COVID-19) may affect acute mountain sickness (AMS) susceptibility is important for preascent risk stratification. The objective of this study was to examine if prior COVID-19 impacts risk of AMS. Materials and Methods: This was a prospective observational study conducted in Lobuje (4,940 m) and Manang (3,519 m), Nepal, from April to May 2022. AMS was defined by the 2018 Lake Louise Questionnaire criteria. COVID-19 severity was defined using the World Health Organization-developed criteria. Results: In the Lobuje cohort of 2,027, 46.2% of surveyed individuals reported history of COVID-19, with 25.7% AMS point-prevalence. There was no significant relationship between prior ambulatory mild COVID-19 and AMS (p = 0.6) or moderate AMS (p = 1.0). In the Manang cohort of 908, 42.8% reported history of COVID-19, with 14.7% AMS point-prevalence. There was no significant relationship between prior ambulatory mild COVID-19 and AMS (p = 0.3) or moderate AMS (p = 0.4). Average months since COVID-19 was 7.4 (interquartile range [IQR] 3-10) for Lobuje, 6.2 (IQR 3-6) for Manang. Both cohorts rarely exhibited moderate COVID-19 history. Conclusions: Prior ambulatory mild COVID-19 was not associated with increased risk of AMS and should not preclude high-altitude travel.

Vaginal laser therapy for GSM/VVA: where we stand now - a review by the EUGA Working Group on Laser

Vulvovaginal atrophy (VVA) is a chronic progressive condition that involves the genital and lower urinary tracts, related to the decrease of serum estrogenic levels when menopause occurs. The definition of genitourinary syndrome of menopause (GSM) is a medically more accurate, all-encompassing and publicly acceptable term than VVA. Due to the chronic progressive trend of GSM, symptoms tend to reappear after the cessation of therapy, and frequently long-term treatment is required. First-line therapies include vulvar and vaginal lubricant or moisturizers, and, in the case of failure, low-dose vaginal estrogens are the preferred pharmacological therapy. Populations of patients, such as breast cancer (BC) survivors, are affected by iatrogenic GSM symptoms with concerns about the use of hormonal therapies. The non-ablative erbium:YAG laser and the fractional microablative CO2 vaginal laser are the two main lasers evaluated for GSM treatment. The aim of this comprehensive review is to report the efficacy and safety of Er:YAG and CO2 vaginal lasers for GSM treatment. Vaginal laser therapy has been demonstrated to be effective in restoring vaginal health, improving VVA symptoms and sexual function. The data suggest that both Er:YAG and CO2 vaginal lasers are safe energy-based therapeutic options for management of VVA and/or GSM symptoms in postmenopausal women and BC survivors.

Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry

The VISAGE Enhanced Tool for Appearance and Ancestry (ET) has been designed to combine markers for the prediction of bio-geographical ancestry plus a range of externally visible characteristics into a single massively parallel sequencing (MPS) assay. We describe the development of the ancestry panel markers used in ET, and the enhanced analyses they provide compared to previous MPS-based forensic ancestry assays. As well as established autosomal single nucleotide polymorphisms (SNPs) that differentiate sub-Saharan African, European, East Asian, South Asian, Native American, and Oceanian populations, ET includes autosomal SNPs able to efficiently differentiate populations from Middle East regions. The ability of the ET autosomal ancestry SNPs to distinguish Middle East populations from other continentally defined population groups is such that characteristic patterns for this region can be discerned in genetic cluster analysis using STRUCTURE. Joint cluster membership estimates showing individual co-ancestry that signals North African or East African origins were detected, or cluster patterns were seen that indicate origins from central and Eastern regions of the Middle East. In addition to an augmented panel of autosomal SNPs, ET includes panels of 85 Y-SNPs, 16 X-SNPs and 21 autosomal Microhaplotypes. The Y- and X-SNPs provide a distinct method for obtaining extra detail about co-ancestry patterns identified in males with admixed backgrounds. This study used the 1000 Genomes admixed African and admixed American sample sets to fully explore these enhancements to the analysis of individual co-ancestry. Samples from urban and rural Brazil with contrasting distributions of African, European, and Native American co-ancestry were also studied to gauge the efficiency of combining Y- and X-SNP data for this purpose. The small panel of Microhaplotypes incorporated in ET were selected because they showed the highest levels of haplotype diversity amongst the seven population groups we sought to differentiate. Microhaplotype data was not formally combined with single-site SNP genotypes to analyse ancestry. However, the haplotype sequence reads obtained with ET from these loci creates an effective system for de-convoluting two-contributor mixed DNA. We made simple mixture experiments to demonstrate that when the contributors have different ancestries and the mixture ratios are imbalanced (i.e., not 1:1 mixtures) the ET Microhaplotype panel is an informative system to infer ancestry when this differs between the contributors.

Neutron star mass estimates from gamma-ray eclipses in spider millisecond pulsar binaries

Reliable neutron star mass measurements are key to determining the equation of state of cold nuclear matter, but such measurements are rare. Black widows and redbacks are compact binaries consisting of millisecond pulsars and semi-degenerate companion stars. Spectroscopy of the optically bright companions can determine their radial velocities, providing inclination-dependent pulsar mass estimates. Although inclinations can be inferred from subtle features in optical light curves, such estimates may be systematically biased due to incomplete heating models and poorly understood variability. Using data from the Fermi Large Area Telescope, we have searched for gamma-ray eclipses from 49 spider systems, discovering significant eclipses in 7 systems, including the prototypical black widow PSR B1957+20. Gamma-ray eclipses require direct occultation of the pulsar by the companion, and so the detection, or significant exclusion, of a gamma-ray eclipse strictly limits the binary inclination angle, providing new robust, model-independent pulsar mass constraints. For PSR B1957+20, the eclipse implies a much lighter pulsar (1.81 ± 0.07 solar masses) than inferred from optical light curve modelling.

Development of a prototype modeling system to estimate the GHG mitigation potential of forest and wildfire management

Having recently experienced the three worst wildfire seasons in British Columbia's history in 2017, 2018 and 2021, and anticipating more severe impacts in the future, a key Carbon (C) research priority is to develop reliable models to explore options and identify a portfolio of regionally differentiated solutions for wildfire and forest management. We contribute to this effort by developing a prototype integrated C modeling framework which includes future wildfires that respond to forest stand characteristics and wildfire history. Model validation evaluated net GHG emissions relative to a 'do-nothing' baseline for several management scenarios and included emissions from forest ecosystems, harvested wood products and substitution benefits from avoided fossil fuel burning and avoided emissions-intensive materials. Data improvements are needed to accurately quantify the baseline and scenario GHG emissions, and to identify trade-offs and uncertainties. • A Fire Tolerant scenario included post-fire restoration with planting of climatically suitable fire-resistant species and salvage harvest in place of clearcut harvest.

Rare Presentation of Crescentic Glomerulonephritis in a 4-Week-Old Infant

Introduction/Objective

Rapidly progressive glomerulonephritis is characterized by sudden decline in renal function and glomerular crescents. Crescentic glomerulonephritis develops along three pathways: glomerular basement membrane antibody in situ deposition , circulating immune complex glomerular deposition, or pauci-immune (typically ANCA-associated). For the latter, histopathologic diagnosis is more frequently obtained in adults than in children. Therefore, tissue examination opportunities in infants and neonates is exceptionally rare.

Methods/Case Report

Here we report the autopsy findings from a 4-week-old infant who was part of dichorionic, diamniotic twin pregnancy and born prematurely at 34 weeks to a 30-year-old G6P4 mother. The infant initially presented with labored breathing and poor oral intake, but subsequently developed Enterobactor meningoencephalitis and sepsis, leading to extensive strokes andstatus epilepticus. An infectious source was not identified clinically, and evaluation for an underlying immunodeficiency was indeterminant. The mother had no known autoimmune diseases or antenatal infections. At autopsy, kidney histology showed focal fibrinoid necrosis and/or cellular and fibrocellular crescents (~5%), especially mid to deep cortex. Intracapillary hypercellularity was minimal to absent. Mesangial matrix was not expanded. The interstitium contained patchy inflammatory infiltrates (mononuclear > polymorphonuclear). Direct immunofluorescence (IF) on pronase-treated paraffin sections did not show glomerular deposition of IgG, IgA, or IgM. Electron microscopy (EM) did not show electron dense deposits despite autolysis.

Results (if a Case Study enter NA)

NA.

Conclusion

The absence of immune complex deposition by IF and dense deposits by EM favors the rare diagnosis of pauci-immune glomerulonephritis in this case of neonatal crescentic glomerulonephritis associated with Enterobactor meningoencephalitis and sepsis, with no associated maternal autoimmune disease or antenatal infections.

Eurasiaplex-2: Shifting the focus to SNPs with high population specificity increases the power of forensic ancestry marker sets

To compile a new South Asian-informative panel of forensic ancestry SNPs, we changed the strategy for selecting the most powerful markers for this purpose by targeting polymorphisms with near absolute specificity - when the South Asian-informative allele identified is absent from all other populations or present at frequencies below 0.001 (one in a thousand). More than 120 candidate SNPs were identified from 1000 Genomes datasets satisfying an allele frequency screen of ≥ 0.1 (10 % or more) allele frequency in South Asians, and ≤ 0.001 (0.1 % or less) in African, East Asian, and European populations. From the candidate pool of markers, a final panel of 36 SNPs, widely distributed across most autosomes, were selected that had allele frequencies in the five 1000 Genomes South Asian populations ranging from 0.4 to 0.15. Slightly lower average allele frequencies, but consistent patterns of informativeness were observed in gnomAD South Asian datasets used to validate the 1000 Genomes variant annotations. We named the panel of 36 South Asian-specific SNPs Eurasiaplex-2, and the informativeness of the panel was evaluated by compiling worldwide population data from 4097 samples in four genome variation databases that largely complement the global sampling of 1000 Genomes. Consistent patterns of allele frequency distribution, which were specific to South Asia, were observed in all populations in, or closely sited to, the Indian sub-continent. Pakistani populations from the HGDP-CEPH panel had markedly lower allele frequencies, highlighting the need to develop a statistical system to evaluate the ancestry inference value of counting the number of population-specific alleles present in an individual.

Effect of medical education on European psychiatrists’ knowledge in management of major depressive disorder and psychiatric emergencies

Introduction

The challenge for psychiatrists is keeping up to date with the latest clinical trial data in managing major depressive disorder (MDD) and psychiatric emergencies.

Objectives

We evaluated whether an online educational video lecture directed at psychiatrists, could improve knowledge and confidence regarding management of psychiatric emergencies associated with MDD.

Methods

Educational effect was assessed using a 3-question repeated pairs, pre/post assessment survey. A paired-samples t-test was conducted to assess overall number correct and confidence change. A McNemar’s test was conducted to assess question-level significance. P values < 0.05 are statistically significant. Cohen’s d test was used to estimate the magnitude of effect of education. The activity launched on 8 April 2021, and preliminary data analysed as of 24 June 2021.

Results

807 psychiatrists participated in the programme, of which 150 completed the pre- and post-assessment test. An average overall correct response rate of 44% pre- increased to 74% post- (67% relative increase, P<0.001; Cohen’s d = 0.91). Knowledge on the burden of suicide and MDD improved from 38% pre- to 85% post- (124% relative increase,P<0.001). Knowledge regarding clinical data for novel therapies for use in psychiatric emergencies improved from 47% pre- to 68% post- (45% relative increase, P<0.01). Knowledge regarding signs of suicidal intent in patients with MDD improved from 49% pre- to 71% (45% relative increase, P<0.001) following education.

Conclusions

This study demonstrates the positive effect of online medical education on psychiatrists’ knowledge in contemporary management of psychiatric emergencies associated with MDD in Europe.

Disclosure

The results of this study were from an educational programme that was developed through independent educational funding from Janssen Neuroscience.

Effect of medical education on European primary care physicians’ knowledge in management of major depressive disorder and psychiatric emergencies

Introduction

The challenge for primary care physicians (PCPs) is keeping up to date in managing major depressive disorder (MDD) and psychiatric emergencies.

Objectives

We evaluated whether an online educational video lecture directed at PCPs, could improve knowledge and confidence regarding management of psychiatric emergencies associated with MDD.

Methods

Educational effect was assessed using a 3-question repeated pairs, pre/post assessment survey. A paired-samples t-test was conducted to assess overall number correct and confidence change. A McNemar’s test was conducted to assess question-level significance. P values < 0.05 are statistically significant. Cohen’s d test was used to estimate the magnitude of effect of education. The activity launched on 8 April 2021, and preliminary data analysed as of 24 June 2021.

Results

511 PCPs participated in the programme, of which 86 PCPs completed the pre- and post-assessment test. An average overall correct response rate of 28% pre- increased to 64% post- (129% relative increase, P<0.001; Cohen’s d = 1.13). Knowledge on the burden of suicide and MDD improved from 23% pre- to 87% post- (278% relative increase,P<0.001). Knowledge regarding clinical data for novel therapies for use in psychiatric emergencies improved from 29% pre- to 50% post- (72% relative increase, P<0.01). Knowledge regarding signs of suicidal intent in patients with MDD improved from 31% pre- to 53% (71% relative increase, P<0.001) following education.

Conclusions

This study demonstrates the positive effect of online medical education on PCPs’ knowledge and confidence in contemporary management of psychiatric emergencies associated with MDD in Europe.

Disclosure

The results of this study were derived from an educational programme which was developed through independent educational funding from Janssen Neuroscience

Ethnic differences in success at application for consultant posts among United Kingdom physicians from 2011 to 2019: a retrospective cross-sectional observational study

OBJECTIVES

To identify associations between success following application for consultant physician posts and demographic factors.

DESIGN

Logistic regression analysis of nationwide survey data.

SETTING

United Kingdom (UK) physicians with a recent certificate of completion of training (CCT).

PARTICIPANTS

All UK trainee physicians who received a CCT between 2010 and 2019 were surveyed. Respondents were excluded if they had not applied for a consultant post or if application data were incomplete.

MAIN OUTCOME MEASURES

The primary outcome measure was success over the entire consultant application process, i.e. shortlisted and offered the post following the first application. Secondary outcomes were: shortlisted following first application and offered a consultant post at first interview.

RESULTS

From 7037 CCT holders surveyed, 50.7% responded. While 1198 (59.7%) respondents were white, 760 (37.9%) were from minority ethnic groups and 50 (3.5%) were of unknown ethnicity. Primary medical qualification (PMQ) country was the UK in 75.3% (n = 1512). On multivariable logistic regression analysis the independent negative associations with success were: minority ethnicity (odds ratio [OR] 0.55, 95% confidence interval [CI] 0.43-0.71); p < 0.001) vs. white; PMQ from Europe (OR 0.47, 95% CI 0.28-0.79; p = 0.004) or Asia (OR 0.68, 95% CI 0.49-0.96; p = 0.027) vs. UK PMQ; year of CCT 2012 (OR 0.40, 95% CI 0.24-0.68; p = 0.001), 2013 (OR 0.39, 95% CI 0.23-0.65; p < 0.001), and 2014 (OR 0.26, 95% CI 0.15-0.43; p < 0.001) vs. 2019. Specialties associated with lower success rates included Cardiology, Endocrinology, Genitourinary medicine, Palliative care, Renal and Respiratory, compared to Acute medicine.

CONCLUSIONS

Minority ethnic group candidates for consultant physician posts had lower success rates compared to white candidates after correction for important variables including specialty, time from and country of PMQ. This finding requires further evaluation to identify the causes for this variation.

Older Age as a Predictive Risk Factor for Acute Mountain Sickness

BACKGROUND

Older populations are increasing and comprise a substantial portion of high-altitude travelers. Aging physiology may influence susceptibility to acute mountain sickness, though prior research remains inconclusive. The goal of this study was to investigate the relationship between increasing age and acute mountain sickness.

METHODS

This study was a pooled analysis of 5 prospective randomized controlled trials conducted at White Mountain, California from 2010, 2016-2019 with identical 4-hour rapid ascent from 1242 m to overnight sojourn at 3810 m. Acute mountain sickness was defined by the 2018 Lake Louise Questionnaire criteria.

RESULTS

There were 491 participants analyzed, 234 (48%) diagnosed with acute mountain sickness and 71 (14%) with moderate acute mountain sickness. Mean age was 37 years (±13). There was no significant correlation between Lake Louise Questionnaire severity and age (r = -0.02; 95% confidence interval [CI], -0.11-0.07, P = .7), 40-year-old dichotomy (t = -0.6; 95% CI, -0.53-0.28, P = .6), or decade of life (P = .4). Logistic regression found no increased odds of acute mountain sickness for increasing age by decade of life (odds ratio [OR] 1.0; 95% CI, 0.97-1.0) or 40-year-old dichotomy (OR 1.4; 95% CI, 0.97-2.1). A history of acute mountain sickness increased odds of acute mountain sickness (OR 3.2; 95% CI, 1.5-7.7).

CONCLUSIONS

Older age was not associated with incidence nor severity of acute mountain sickness. A history of altitude illness increased odds of acute mountain sickness and should be used for pre-ascent risk stratification.

COVID-19: using chest CT of major trauma patients to monitor and evaluate the second wave in London and the development of routine monitoring in practice

AIM

To follow-up previous work evaluating incidental findings of COVID-19 signs on computed tomography (CT) images of major trauma patients to include the second wave prior to any major effects from vaccines.

MATERIALS AND METHODS

The study population included all patients admitted following major trauma between 1 January 2020 and 28 February 2021 with CT including the lungs (n=1776). Major trauma patients admitted pre-COVID-19 from alternate months from January 2019 to November 2019 comprised a control group (n=837). The assessing radiologists were blinded to the time period and used double reading in consensus to determine if the patient had signs of COVID-19. Lung appearances were classified as no evidence of COVID-19, minor signs, or major signs.

RESULTS

The method successfully tracked the second wave of the COVID-19 pandemic in London. The estimated population affected by the disease based on those with major signs was similar to estimates of the proportion of the population in London with antibodies (around 30% by end February 2021) and the total of major and minor signs produced a much higher figure of 68%, which may include all those with both antibody and just T-cell responses.

CONCLUSIONS

Incidental findings on CT from major trauma patients may provide a novel and sensitive way of tracking the virus. It is recommended that all major trauma units include a simple question on signs of COVID-19 to provide an early warning system for further waves.

Research data infrastructure for high-throughput experimental materials science

The High-Throughput Experimental Materials Database (HTEM-DB, htem.nrel.gov) is a repository of inorganic thin-film materials data collected during combinatorial experiments at the National Renewable Energy Laboratory (NREL). This data asset is enabled by NREL's Research Data Infrastructure (RDI), a set of custom data tools that collect, process, and store experimental data and metadata. Here, we describe the experimental data flow from the RDI to the HTEM-DB to illustrate the strategies and best practices currently used for materials data at NREL. Integration of the data tools with experimental instruments establishes a data communication pipeline between experimental researchers and data scientists. This work motivates the creation of similar workflows at other institutions to aggregate valuable data and increase their usefulness for future machine learning studies. In turn, such data-driven studies can greatly accelerate the pace of discovery and design in the materials science domain.

•

Automated curation of experimental materials data

•

Integration of data tools into the experimental laboratory

•

Simple, effective, and flexible data archival system

•

Collection of metadata for enhanced total data value

For machine learning to make significant contributions to a scientific domain, algorithms must ingest and learn from high-quality, large-volume datasets. The Research Data Infrastructure (RDI) that feeds the High-Throughput Experimental Materials Database (HTEM-DB, htem.nrel.gov) provides such a dataset from existing experimental data streams at the National Renewable Energy Laboratory (NREL). The described methods for curating experimental data can be applied to other materials research laboratory settings, paving the way for increased application of machine learning to materials science. In turn, the resulting new materials and new knowledge will benefit the society by advancing new technologies in energy, fuels, computing, security, and other important areas.

Effect of Sodium Supplements and Climate on Dysnatremia During Ultramarathon Running

OBJECTIVE

Analyze the effect of sodium supplementation, hydration, and climate on dysnatremia in ultramarathon runners.

DESIGN

Prospective observational study.

SETTING

The 2017 80 km (50 mile) stage of the 250 km (150 mile) 6-stage RacingThePlanet ultramarathon in 2017 Chilean, Patagonian, and 2018 Namibian, Mongolian, and Chilean deserts.

PARTICIPANTS

All race entrants who could understand English were invited to participate, with 266 runners enrolled, mean age of 43 years (± 9), 61 (36%) females, average weight 74 kg (± 12.5), and average race time 14.5 (± 4.1) hours. Post-race sodium collected on 174 (74%) and 164 (62%) participants with both the blood sample and post-race questionnaire.

INTERVENTION

Weight change and finish line serum sodium levels were gathered.

MAIN OUTCOME MEASURES

Incidence of exercise-associated hyponatremia (EAH; <135 mmol·L-1) and hypernatremia (>145 mmol·L-1) by sodium ingestion and climate.

RESULTS

Eleven (6.3%) runners developed EAH, and 30 (17.2%) developed hypernatremia. Those with EAH were 14 kg heavier at baseline, had significantly less training distances, and averaged 5 to 6 hours longer to cover 50 miles (80 km) than the other participants. Neither rate nor total ingested supplemental sodium was correlated with dysnatremia, without significant differences in drinking behaviors or type of supplement compared with normonatremic runners. Hypernatremic runners were more often dehydrated [8 (28%), -4.7 kg (± 9.8)] than EAH [4 (14%), -1.1 kg (± 3.8)] (P < 0.01), and EAH runners were more frequently overhydrated (6, 67%) than hypernatremia (1, 11%) (P < 0.01). In the 98 (56%) runners from hot races, there was EAH OR = 3.5 [95% confidence interval (CI), 0.9-25.9] and hypernatremia OR = 8.8 (95% CI, 2.9-39.5) compared with cold races.

CONCLUSIONS

This was the first study to show that hot race climates are an independent risk factor for EAH and hypernatremia. Sodium supplementation did not prevent EAH nor cause hypernatremia. Longer training distances, lower body mass, and avoidance of overhydration were shown to be the most important factors to prevent EAH and avoidance of dehydration to prevent hypernatremia.

Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq

Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.

Weight Bias 2.0: The Effect of Perceived Weight Change on Performance Evaluation and the Moderating Role of Anti-fat Bias

Overweight employees are viewed as lazy, slow, inactive, and even incapable. Even if such attributes are false, this perspective can seriously undermine others' evaluation of their work performance. The current study explores a broader phenomenon of weight bias that has an effect on weight change. In a longitudinal study with a time lag of 6 months, we surveyed 226 supervisor-employee dyads. We found supervisor perceptions of employee weight change notably altered their evaluation of the employee performance from Time 1, especially following low vs. high Time-1 performance evaluation. Meanwhile, the moderating effects among different levels of supervisor anti-fat bias functioned as boundary conditions for such performance evaluation alteration. In particular, the interaction between the Time-1 performance evaluation and the impact of supervisor perception of employee weight change on the Time-2 performance evaluation was significant only if supervisors held a stronger anti-fat bias.

The effect of local estrogen therapy on the urinary microbiome composition of postmenopausal women with and without recurrent urinary tract infections

INTRODUCTION AND HYPOTHESIS

Recurrent urinary tract infections (rUTIs) occur in 2-10% of postmenopausal women. Local estrogen therapy (LET) has been shown to reduce UTIs. This study aimed to compare the urinary microbiome between patients with and without a history of rUTIs and to examine whether treatment with LET influences the diversity and richness of microbiome species in two groups.

METHODS

Postmenopausal women with and without rUTIs attending the urogynecology clinic between April 2019 and December 2020 were recruited. Participant baseline characteristics and demographics were recorded. Aseptic transurethral urine samples were collected at recruitment and at 3-6 months following treatment with LET. The V1-V2 and ITS regions of the 16S rRNA gene were sequenced to identify bacteria.

RESULTS

A total of 37 women were recruited, 20 controls and 17 patients with rUTI. During follow-up, symptomatic UTIs occurred in 3/17 (17.6%) and 0/20 in the rUTI group and control group, respectively. Klebsiella aerogenes was present in 80% of rUTI samples and in 53.3% of control samples before LET. Abundance of Finegoldia magna was present in 33.3% of samples before LET, but only in 6.7% after LET. There was no change in relative abundance of lactobacillus species following LET in both groups.

CONCLUSIONS

Treatment with vaginal LET altered the local hormonal environment of the urinary bladder and likely protected women from development of rUTI by decreasing the presence of F. magna. To confirm the significance of this bacterial species in rUTI symptomatology, our finding needs to be validated on a larger patient cohort.

Predictive Capacity of Pulmonary Function Tests for Acute Mountain Sickness

Small, Elan, Nicholas Juul, David Pomeranz, Patrick Burns, Caleb Phillips, Mary Cheffers, and Grant S. Lipman. Predictive capacity of pulmonary function tests for acute mountain sickness. High Alt Med Biol. 22: 193-200, 2021. Background: Pulmonary function as measured by spirometry has been investigated at altitude with heterogenous results, though data focused on spirometry and acute mountain sickness (AMS) are limited. The objective of this study was to investigate the capacity of pulmonary function tests (PFTs) to predict the development of AMS. Materials and Methods: This study was a blinded prospective observational study run during a randomized controlled trial comparing acetazolamide, budesonide, and placebo for AMS prevention on White Mountain, CA. Spirometry measurements of forced expiratory volume in one second (FEV₁), forced vital capacity (FVC), and peak expiratory flow were taken at a baseline altitude of 1,250 m, and the evening of and morning after ascent to 3,810 m. Measurements were assessed for correlation with AMS. Results: One hundred three participants were analyzed with well-matched baseline demographics and AMS incidence of 75 (73%) and severe AMS of 48 (47%). There were no statistically significant associations between changes in mean spirometry values on ascent to high altitude with incidence of AMS or severe AMS. Lake Louise Questionnaire scores were negatively correlated with FVC (r = -0.31) and FEV₁ (r = -0.29) the night of ascent. Baseline PFT had a predictive accuracy of 65%-73% for AMS, with a receiver operating characteristic of 0.51-0.65. Conclusions: Spirometry did not demonstrate statistically significant changes on ascent to high altitude, nor were there significant associations with incidence of AMS or severe AMS. Low-altitude spirometry did not accurately predict development of AMS, and it should not be recommended for risk stratification.

Prospective Observational Study of Weight-based Assessment of Sodium Supplements on Ultramarathon Performance (WASSUP)

BACKGROUND

Sodium supplements are ubiquitous in endurance running, but their impact on performance has been subjected to much debate. The objective of the study was to assess the effect of sodium supplementation as a weight-based predictor of race performance in ultramarathon runners.

METHODS

Prospective observational study during an 80 km (50 mi) stage of a 6-stage 250 km (155 mi) ultramarathon in Chile, Patagonia, Namibia, and Mongolia. Finish line hydration status as measured by weight change, point-of-care serum sodium, and questionnaire provided sodium ingestion categories at 33rd percentile and 66th percentile both for weight-adjusted rate and total sodium consumption, then analyzed for significant relationships to race performance, dysnatremia, and hydration.

RESULTS

Two hundred sixty-six participants were enrolled, with 217 (82%) with complete sodium supplement rate data, 174 (80%) with finish line sodium, and 161 (74%) with both pre-race weights and total sodium ingestion allowing weight-based analysis. Sodium intake ranged from 131-533 mg/h/kg (2-7.2 gm), with no statistically significant impact on pace, race time, or quintile rank. These outcomes did not change when sodium intake was analyzed as a continuous variable or by sub-group analysis of the 109 (68%) normonatremic runners. When controlled for weight-adjusted sodium intake, performance was poorly correlated with hydration (r = - 0.152, 95% CI - 0.348-0.057). Dehydrated runners outperformed those overhydrated, with 11% of top 25th percentile finishers dehydrated (versus 2.8% overhydrated), with 3.6 min/km faster pace and time 4.6 h faster finishing time.

CONCLUSIONS

No association was found between sodium supplement intake and ultramarathon performance. Dehydrated runners were found to have the best performance. This reinforces the message to avoid overhydration.

Host population size is linked to orchid mycorrhizal fungal communities in roots and soil, which are shaped by microenvironment

Interaction with orchid mycorrhizal fungi (OMF) is essential to all members of the Orchidaceae, yet we know little about whether or how OMF abundances in substrates shape orchid populations. While root-associated OMF diversity is catalogued frequently, technological constraints have impeded the assessments of OMF communities in substrates until recently, thereby limiting the ability to link OMF communities in a habitat to population responses. Furthermore, there is some evidence that edaphic and microclimatic conditions impact OMF in soil, yet we lack an understanding of the coupled influences of abiotic environment and OMF structure on orchid population dynamics. To discover the linkages between abiotic environment, OMF community structure, and population size, we characterized the microclimatic conditions, soil physicochemistry, and OMF communities hosted by roots and soil across large and small populations of a terrestrial orchid endemic to California Floristic Province in North America. By using high-throughput sequencing of the ITS2 region of nrDNA amplified from root and soil DNAs, we determined that both roots and soil of larger populations, which were high in phosphorus but low in zinc, organic matter, and silt, were dominated by Tulasnellaceae OTUs. In comparison, roots and soil from smaller populations of the orchid hosted higher relative abundances of the Ceratobasidiaceae. In this multiyear, range-wide study that simultaneously measured habitat environmental conditions, and soil and root OMF communities, our results suggest that soil chemistry is clearly linked to soil and root OMF communities, which then likely alter and shape orchid populations.

Integrating Quantitative Assays with Biologically Based Mathematical Modeling for Predictive Oncology

We provide an overview on the use of biological assays to calibrate and initialize mechanism-based models of cancer phenomena. Although artificial intelligence methods currently dominate the landscape in computational oncology, mathematical models that seek to explicitly incorporate biological mechanisms into their formalism are of increasing interest. These models can guide experimental design and provide insights into the underlying mechanisms of cancer progression. Historically, these models have included a myriad of parameters that have been difficult to quantify in biologically relevant systems, limiting their practical insights. Recently, however, there has been much interest calibrating biologically based models with the quantitative measurements available from (for example) RNA sequencing, time-resolved microscopy, and in vivo imaging. In this contribution, we summarize how a variety of experimental methods quantify tumor characteristics from the molecular to tissue scales and describe how such data can be directly integrated with mechanism-based models to improve predictions of tumor growth and treatment response.

Long-term Survival with 18-Fluorodeoxyglucose Positron Emission Tomography-directed Therapy in Non-small Cell Lung Cancer with Synchronous Solitary Brain Metastasis

AIMS

At diagnosis, <1% of patients with non-small cell lung cancer (NSCLC) have synchronous solitary brain metastasis (SSBM). In prior cohorts without 18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) staging, definitive treatment to intracranial and intrathoracic disease showed a 5-year overall survival (OS) of 11-21%. We investigated the long-term survival outcomes for patients with SSBM NSCLC, diagnosed in the FDG-PET/CT era and treated definitively with local therapies to both intracranial and intrathoracic sites of disease.

MATERIALS AND METHODS

This retrospective study assessed patients staged with FDG-PET/CT who received definitive lung and SSBM treatment from February 1999 to December 2017. A lung-molecular graded prognostic assessment (lung-molGPA) score was assigned for each patient using age, performance status score, and, where carried out, molecular status. Overall survival and progression-free survival (PFS) were calculated using Kaplan-Meier methods. Cox proportional hazard models determined OS and PFS prognostic factors.

RESULTS

Forty-nine patients newly diagnosed with NSCLC and SSBM had a median age of 63 years (range 34-76). The median follow-up of all patients was 3.9 years. Thirty-three patients (67%) had ≥T2 disease, 23 (47%) had ≥N2. At 2 years, 45% of first failures were intracranial only (95% confidence interval 30-59). At 3 and 5 years, OS was 45% (95% confidence interval 32-63) and 30% (95% confidence interval 18-51), respectively. In ≥N1 disease, 5-year OS was 34% (95% confidence interval 18-63). The 3- and 5-year PFS was 8% (95% confidence interval 3-22) and 0%, respectively. Higher lung-molGPA was associated with longer OS (hazard ratio 0.26, 95% confidence interval 0.11-0.61, P = 0.002). Higher lung-molGPA (hazard ratio 0.33, 95% confidence interval 0.15-0.71, P = 0.005) and lower N-stage (hazard ratio 1.56, 95% confidence interval 1.13-2.15, P = 0.007) were associated with longer PFS.

CONCLUSIONS

Definitive treatment of patients with NSCLC and SSBM staged with FDG-PET/CT can result in 5-year survivors, including those with ≥N1 disease.

A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies

Individual age estimation can be applied to criminal, legal, and anthropological investigations. DNA methylation has been established as the biomarker of choice for age prediction, since it was observed that specific CpG positions in the genome show systematic changes during an individual’s lifetime, with progressive increases or decreases in methylation levels. Subsequently, several forensic age prediction models have been reported, providing average age prediction error ranges of ±3–4 years, using a broad spectrum of technologies and underlying statistical analyses. DNA methylation assessment is not categorical but quantitative. Therefore, the detection platform used plays a pivotal role, since quantitative and semi-quantitative technologies could potentially result in differences in detected DNA methylation levels. In the present study, we analyzed as a shared sample pool, 84 blood-based DNA controls ranging from 18 to 99 years old using four different technologies: EpiTYPER^®, pyrosequencing, MiSeq, and SNaPshot^TM. The DNA methylation levels detected for CpG sites from ELOVL2, FHL2, and MIR29B2 with each system were compared. A restricted three CpG-site age prediction model was rebuilt for each system, as well as for a combination of technologies, based on previous training datasets, and age predictions were calculated accordingly for all the samples detected with the previous technologies. While the DNA methylation patterns and subsequent age predictions from EpiTYPER^®, pyrosequencing, and MiSeq systems are largely comparable for the CpG sites studied, SNaPshot^TM gives bigger differences reflected in higher predictive errors. However, these differences can be reduced by applying a z-score data transformation.

In vitro vascularized tumor platform for modeling tumor-vasculature interactions of inflammatory breast cancer

Inflammatory breast cancer (IBC), a rare form of breast cancer associated with increased angiogenesis and metastasis, is largely driven by tumor-stromal interactions with the vasculature and the extracellular matrix (ECM). However, there is currently a lack of understanding of the role these interactions play in initiation and progression of the disease. In this study, we developed the first three-dimensional, in vitro, vascularized, microfluidic IBC platform to quantify the spatial and temporal dynamics of tumor-vasculature and tumor-ECM interactions specific to IBC. Platforms consisting of collagen type 1 ECM with an endothelialized blood vessel were cultured with IBC cells, MDA-IBC3 (HER2+) or SUM149 (triple negative), and for comparison to non-IBC cells, MDA-MB-231 (triple negative). Acellular collagen platforms with endothelialized blood vessels served as controls. SUM149 and MDA-MB-231 platforms exhibited a significantly (p < .05) higher vessel permeability and decreased endothelial coverage of the vessel lumen compared to the control. Both IBC platforms, MDA-IBC3 and SUM149, expressed higher levels of vascular endothelial growth factor (p < .05) and increased collagen ECM porosity compared to non-IBCMDA-MB-231 (p < .05) and control (p < .01) platforms. Additionally, unique to the MDA-IBC3 platform, we observed progressive sprouting of the endothelium over time resulting in viable vessels with lumen. The newly sprouted vessels encircled clusters of MDA-IBC3 cells replicating a key feature of in vivo IBC. The IBC in vitro vascularized platforms introduced in this study model well-described in vivo and clinical IBC phenotypes and provide an adaptable, high throughput tool for systematically and quantitatively investigating tumor-stromal mechanisms and dynamics of tumor progression.

Forensic evaluation of the Asia Pacific ancestry-informative MAPlex assay

DNA intelligence, and particularly the inference of biogeographical ancestry (BGA) is increasing in interest, and relevance within the forensic genetics community. The majority of current MPS-based forensic ancestry-informative assays focus on the differentiation of major global populations. The recently published MAPlex (Multiplex for the Asia Pacific) panel contains 144 SNPs and 20 microhaplotypes and aims to improve the differentiation of populations in the Asia Pacific region. This study reports the first forensic evaluation of the MAPlex panel using AmpliSeq technology and Ion S5 sequencing. This study reports on the overall performance of MAPlex including the assay's sequence coverage distribution and stability, baseline noise and description of problematic SNPs. Dilution series, artificially degraded and mixed DNA samples were also analysed to evaluate the sensitivity of the panel with challenging or compromised forensic samples. As the first panel to combine biallelic SNPs, multiple-allele SNPs and microhaplotypes, the MAPlex assay demonstrated an enhanced capacity for mixture detection, not easily performed with common binary SNPs. This performance evaluation indicates that MAPlex is a robust, stable and highly sensitive assay that is applicable to forensic casework for the prediction of BGA.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Quantifying Soft Tissue Artefacts and Imaging Variability in Motion Capture of the Fingers

This study assessed the accuracy of marker-based kinematic analysis of the fingers, considering soft tissue artefacts (STA) and marker imaging uncertainty. We collected CT images of the hand from healthy volunteers with fingers in full extension, mid- and full-flexion, including motion capture markers. Bones and markers were segmented and meshed. The bone meshes for each volunteer's scans were aligned using the proximal phalanx to study the proximal interphalangeal joint (PIP), and using the middle phalanx to study the distal interphalangeal joint (DIP). The angle changes between positions were extracted. The HAWK protocol was used to calculate PIP and DIP joint flexion angles in each position based on the marker centroids. Finally the marker locations were 'corrected' relative to the underlying bones, and the flexion angles recalculated. Static and dynamic marker imaging uncertainty was evaluated using a wand. A strong positive correlation was observed between marker- and CT-based joint angle changes with 0.980 and 0.892 regression slopes for PIP and DIP, respectively, and Root Mean Squared Errors below 4°. Notably for the PIP joint, correlation was worsened by STA correction. The 95% imaging uncertainty interval was < ± 1° for joints, and < ± 0.25 mm for segment lengths. In summary, the HAWK marker set's accuracy was characterised for finger joint flexion angle changes in a small group of healthy individuals and static poses, and was found to benefit from skin movements during flexion.

Abstract P6-06-02: An in vitro microfluidic tumor platform for modeling and investigating tumor stromal interactions in inflammatory breast cancer

Introduction: Inflammatory breast cancer (IBC) is an aggressive and rare disease with poor prognosis, accounting for 10% of breast cancer mortality [1]. A primary factor contributing to the bleak prognosis is the lack of IBC specific treatments. There are currently no IBC specific therapies due to a lack of IBC specific diagnostic and targeting markers. Efforts focused on identifying driver mutations and tumor targets have implicated tumor stroma including stromal cells such as macrophages in mediating IBC-like symptoms. This highlights the significance of understanding the interactions of tumor cells with the tumor stroma in greater detail and the knowledge would enable determination of targetable biology from these interactions which would facilitate development of IBC specific treatments and therapeutics. What is needed is a model to capture the complexity of IBC, identify critical spatial hetero-cellular interactions and target them successfully in a physiologically relevant and high-throughput manner.

Approach: To address this need, we developed a 3D IBC microfluidic platform, unique in its simultaneous integration of functional blood vessels, tumor cells, macrophages, and type I collagen whose density, stiffness, and porosity mimics cancerous breast stroma. The platform will be used to study the influence of macrophage-tumor-endothelial interactions on 2 key critical features of IBC: vascular sprouting and formation of IBC emboli surrounded by vascular sprouts.

Results: The 3D IBC microfluidic platform composed of MDA-IBC3 cells and a functional endothelial blood vessel demonstrated both vascular sprouting and emboli formation, key features of IBC tumors seen in IBC patient derived xenograft (PDX) models. Additionally, we observed vascular nesting of MDA-IBC3 emboli, recreating a characteristic IBC phenomenon observed in Mary-X PDX models. Incorporation of macrophages significantly increased the number of new vascular sprouts, sprouting rate and resulted in sprouts forming at earlier time points. Additionally, the presence of macrophages resulted in the formation of a significantly more porous collagen matrix (p&lt;0.05), increased endothelial vessel permeability (p&lt;0.05) and expression of proangiogenic factors, IL-8 and MMP9 (p&lt;0.05, p&lt;0.05) compared to platforms without macrophages. 3D platforms with macrophages also exhibited vascular nesting of MDA-IBC3 emboli but no significant differences in the number of nested emboli were detected. Finally, in 3D platforms with macrophages, we observed intravasation of MDA-IBC3 emboli which was absent in platforms without macrophages.

Conclusion: IBC is an aggressive and invasive breast cancer with a poor prognosis linked to tumor-stroma interactions. Current preclinical to study IBC consist primarily of PDX models where determining the influence of specific signaling pathways and microenvironmental stimuli on tumor progression is challenging. Here we present a novel 3D microfluidic IBC platform to study tumor stromal interactions in a controlled manner. The MDA-IBC3 breast tumor platform demonstrated both vascular sprouting and emboli formation, key features of IBC seen in PDX models and the presence of macrophages increased both angiogenic sprouting and remodeling of the collagen matrix. The stark differences in the tumor platform response associated with macrophage presence strengthens the hypothesis of tumor stroma as a key player driving the aggressive nature of IBC and reveals a potential target for IBC therapeutics.

[1] Fernandez, S.V., et al., Breast cancer research and treatment, 140(1): p. 23-33, 2013

Citation Format: Manasa Gadde, Caleb Phillips, Omar Rahal, Wendy Woodward, Marissa Rylander, Thomas Yankeelov. An in vitro microfluidic tumor platform for modeling and investigating tumor stromal interactions in inflammatory breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-06-02.

PIMA: A population informative multiplex for the Americas

We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment I_n values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.