Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types

Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types ¹ . Neural cell types have previously been defined by morphology ^{2, 3} , electrophysiology ^{4, 5} , transcriptomic expression ^6-8 , connectivity ^9-13 , or even a combination of such modalities ^14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells ^17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex ²¹ . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type ^{22, 23} known to be Somatostatin positive (Sst+) ^{24, 25} , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.

p27Kip1 V109G as a biomarker for CDK4/6 inhibitors indication in hormone receptor-positive breast cancer

CDK4/6 inhibitors benefit a minority of patients who receive them in the breast cancer adjuvant setting. p27Kip1 is a protein that inhibits CDK/Cyclin complexes. We hypothesized that single-nucleotide polymorphisms that impaired p27Kip1 function could render patients refractory to endocrine therapy but responsive to CDK4/6 inhibitors, narrowing the patient subpopulation that requires CDK4/6 inhibitors. We found that the p27Kip1 V109G single-nucleotide polymorphism is homozygous in approximately 15% of hormone-positive breast cancer patients. Polymorphic patients experience rapid failure in response to endocrine monotherapy compared with wild-type or heterozygous patients in the first-line metastatic setting (progression-free survival: 92 vs 485 days, P < .001); when CDK4/6 inhibitors are added, the differences disappear (progression-free survival: 658 vs 761 days, P = .92). As opposed to wild-type p27Kip1, p27Kip1 V109G is unable to suppress the kinase activity of CDK4 in the presence of endocrine inhibitors; however, palbociclib blocks CDK4 kinase activity regardless of the p27Kip1 status. p27Kip1 genotyping could constitute a tool for treatment selection.

Abstract P5-02-28: p27Kip1 V109G single-nucleotide polymorphism (SNP): pinpointing the hormone-receptor positive breast cancer subpopulation that requires CDK4/6 inhibitors in addition to endocrine therapy

Background: CDK4/6 inhibitors benefit a limited percentage of hormone receptor-positive breast cancer (HRPBC) patients in the adjuvant setting: according to the MonarchE study, from all patients treated with the endocrine plus CDK4/6 inhibitor combination, 84% were adequately treated with endocrine therapy alone, ~5% experienced benefit from the combination, and 11% were not rescued from relapse by abemaciclib. Given the side effects and the cost, biomarkers to guide treatment decisions in this setting are appealing. We found that the p27Kip1 V109G SNP was enriched in HRPBC patients experiencing relapse despite endocrine treatment. p27Kip1 binds to cyclins and CDKs, restraining cells from cycling by inhibiting the formation of CDK/cyclin complexes and their kinase activity, resulting in less phosphorylation of Rb. A functionally impaired p27Kip1 could render tumor cells insensitive to endocrine therapy, while being rescued by CDK4/6 inhibitors. Thus, this SNP could narrow down the patient population that requires adjuvant CDK4/6 inhibitors. Methods: Isogenic HRPBC cell lines, wild-type or polymorphic homozygous for the p27Kip1 V109G SNP were generated with CRISPR-Cas9. Cell cycle and cell viability were assessed with BRDU incorporation and colony assays. Immunoprecipitation coupled with western blot (WB) was used to measure the formation of CDK/Cyclin complexes; Rb phosphorylation was assessed by WB. An in vitro kinase assay was set up to measure the CDK4 activity of p27Kip1/CDK/Cyclin complexes. Patients (n=115) with metastatic, HRPBC receiving endocrine monotherapy or in combination with CDK4/6 inhibitors were genotyped for the p27Kip1 V109G SNP, and PFS by genotype and therapy compared with the Kaplan-Meier method. All statistical tests were two-sided. Results: three isogenic polymorphic clones were generated from the wild-type T47-D hormone-positive cell line. The three clones were resistant to hormonal deprivation compared to wild-type cells. The relative plating efficiency (RPE) in the colony assays of the polymorphic clones exposed to hormonal deprivation compared to that of deprived T47-D cells was 550% (clone C1), 165% (clone E1) and 100% (Clone F5); P&lt; 0.005. The three clones were also resistant to fulvestrant (Fulv) (300%, 170% and 180%, respectively); P&lt; 0.005. Cell cycle (positive BRDU cells) decreased ~3 fold in wild type cells (18% to 6.5%) when exposed to hormonal deprivation or Fulv, but remained unaltered in the polymorphic clones. However, when palbociclib was added to hormonal deprivation or Fulv, the effects in RPE increased and were similar in polymorphic clones and parental cells (&gt;5% RPE compared to vehicle, both in polymorphic and wild-type cells). The p27Kip1 V109G SNP was found in homozygosity in ~15% of metastatic HRPBC patients. When patients received endocrine monotherapy in the first-line setting, polymorphic patients experience rapid failure (N=51) compared to wild-type/heterozygous patients (4.3 vs. 21.1 months; P &lt; 0.0001). However, when patients received hormonal plus CDK4/6 inhibitors, the differences disappeared (18.3 vs. 24.3 months; P=0.85). Mechanistically, we observed that the formation of CDK2/CyclinA, CDK2/CyclinE and CDK4/Cyclin D1 complexes was &gt;200% higher in polymorphic than in wild-type cells (P&lt; 0.05). Regarding CDK4 kinase activity of p27Kip1/CDK/Cyclin complexes, as opposed to wild-type p27Kip1, p27Kip1 V109G was unable to suppress the kinase activity of CDK4 in presence of Fulv or hormonal deprivation. However, palbociclib was able to fully suppress CDK4 kinase activity regardless of the p27Kip1 genotype. Conclusion: Germline p27Kip1 genotyping can constitute a tool for treatment selection: whereas wild-type patients are adequately treated with endocrine monotherapy, polymorphic patients are inherently resistant, but are rescued with CDK4/6 inhibitors. Thus, hormonal+CDK4/6 inhibitor combos could be reserved for the polymorphic patients.

Citation Format: Miguel Quintela-Fandino, Silvana Mouron, Maria J. Bueno, Manuel Muñoz, Raul Torres, Sandra Rodriguez, Rodrigo Sánchez-Bayona, Luis Manso, Jorge Silva, Marcos Malumbres. p27Kip1 V109G single-nucleotide polymorphism (SNP): pinpointing the hormone-receptor positive breast cancer subpopulation that requires CDK4/6 inhibitors in addition to endocrine therapy. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-28.

Applying Deep Learning Cancer Subtyping Algorithms Trained on Physical Slides to Multiphoton Imaging of Unembedded Samples

Introduction/Objective

Deep learning algorithms on digital images of physical tissue slides have shown potential improvements in accuracy and precision of diagnostic interpretation of neoplastic histology. Clustering-constrained- attention multiple-instance learning (CLAM) is one such method that identifies diagnostic sub-regions to accurately classify whole slides. Often, algorithm performance degrades when deployed on datasets that differ from the original set and it is subject to physical slide preparation variability. New multiphoton imaging modalities have potential workflow and quality advantages over physical slides, producing images analogous to whole slide imaging (WSI) without cutting artifacts, but performance of existing algorithms trained on digitized physical slides and applied to multiphoton images remains completely unknown. Given this, we aimed to test the performance of CLAM algorithms for subtyping renal cell carcinoma (RCC) and lung cancer (LC) applied to pseudo-colored multiphoton WSI.

Methods/Case Report

Clinical RCC and LC surgical resection samples were processed and imaged by Clearing Histology with MulitPhoton microscopy (CHiMP, Applikate Technologies, Fairfield, CT), producing digital images of un- cut, un-embeded tissue to generate H&E-like optical slices. Multiphoton images were downscaled to 0.5 um/px to match algorithm target resolution. CLAM models for subtyping RCC (chromophobe, clear cell, papillary) and LC (squamous & adenocarcinoma) previously trained using TCGA and CPTAC whole slide images of physical slides were applied directly to CHiMP multiphoton images without adjustment. Reference cancer subtype classifications were provided from physical and digital slides.

Results (if a Case Study enter NA)

For the subtypes included during training, multiphoton WSIs of RCC and LC were accurately subtyped by the CLAM models without stain normalization nor network fine tuning producing high prediction levels. Subtypes not included during the training (namely oncocytoma for RCC) resulted in low scoring model predictions (below 0.85), indicating specificity of identification. Multiple slide levels improved interpretation of several difficult cases for CLAM predictions.

Conclusion

This preliminary data suggests that CLAM models trained on standard H&E WSIs for RCC and LC subtyping are applicable to pseudo-H&E multiphoton WSIs without domain adaptations. This implies that diagnostic histologic features have been learned by these CLAM models and are efficiently recognized in digital histology images produced via CHiMP.

Case report: Asymptomatic bronchopulmonary sequestration in an adult with dual celiac and aortic supply

A rare congenital malformation of the respiratory tract, bronchopulmonary sequestration generally presents in childhood and adolescence with recurrent pneumonia or in adulthood as an incidental finding on thoracic imaging. Manifesting as intrapulmonary or extrapulmonary types, bronchopulmonary sequestration characteristically receives blood supply from the systemic rather than pulmonary circulation. We present a 45-year-old male patient who received a provisional diagnosis of bronchopulmonary sequestration following an incidental finding on routine imaging. This case describes the way in which a provisional diagnosis may be made based upon imaging as well as underscoring the importance of alleviating the burden of additional imaging studies.

Perceived stress and physiological consistency during mental stress exercises and controlled breathing

Introduction

The measurement of the physiological coherence, the order and the quality of the connection of complex systems such as the cardiac and the respiratory system, varies in situations of stress and relaxation.

Objectives

We aim to assess changes in physiological coherence and perception of stress during mental stress and directed breathing exercises.

Methods

Repeated-measures study in healthy adults without prior training in breathing techniques, aged between 18 and 65 years of both sexes who were evaluated in three situations: baseline, mental stress (Stroop test and successive subtractions), and directed breathing, during which were captured heart rate and respiratory signals to estimate physiological coherence and the participants rated the perceived stress at each moment.

Results

34 participants were analyzed, 59% women, with a median age of 36 years (Rq = 13). During mental stress tasks, the median for physiological coherence was similar to baseline coherence but increased significantly with five minutes of directed breathing exercises (38% vs. 63% p <0.0001). The highest perception of stress was during successive subtractions (Me 7, Rq = 4) and the lowest during directed breathing exercises (Me 2 Rq = 3.0). The correlation was sought between physiological coherence and perception of stress during each of the four moments of the study. Basal (Rho Spearman -0.05, p 0.54); Stroop (Rho -0.17, p 0.03); successive subtractions (Rho 0.50, p 0.77); and directed breathing (Rho -0.28, p 0.09).

Conclusions

A correlation was found between physiological coherence and perception of stress during the Stroop test; however, no association was found.

Disclosure

No significant relationships.

A guidelines-consistent carrier screening panel that supports equity across diverse populations

PURPOSE

The American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics and Genomics (ACMG) suggest carrier screening panel design criteria intended to ensure meaningful results. This study used a data-driven approach to interpret the criteria to identify guidelines-consistent panels.

METHODS

Carrier frequencies in >460,000 individuals across 11 races/ethnicities were used to assess carrier frequency. Other criteria were interpreted on the basis of published data. A total of 176 conditions were then evaluated. Stringency thresholds were set as suggested by ACOG and/or ACMG or by evaluating conditions already recommended by ACOG and ACMG.

RESULTS

Forty and 75 conditions had carrier frequencies of ≥1 in 100 and ≥1 in 200, respectively; 175 had a well-defined phenotype; and 165 met at least 1 severity criterion and had an onset early in life. Thirty-seven conditions met conservative thresholds, including a carrier frequency of ≥1 in 100, and 74 conditions met permissive thresholds, including a carrier frequency of ≥1 in 200; thus, both were identified as guidelines-consistent panels.

CONCLUSION

Clear panel design criteria are needed to ensure quality and consistency among carrier screening panels. Evidence-based analyses of criteria resulted in the identification of guidelines-consistent panels of 37 and 74 conditions.

Asociación Mexicana de Hepatología A.C. Clinical guideline on hepatitis B

Hepatitis B virus (HBV) infection continues to be a worldwide public health problem. In Mexico, at least three million adults are estimated to have acquired hepatitis B (total hepatitis B core antibody [anti-HBc]-positive), and of those, 300,000 active carriers (hepatitis B surface antigen [HBsAg]-positive) could require treatment. Because HBV is preventable through vaccination, its universal application should be emphasized. HBV infection is a major risk factor for developing hepatocellular carcinoma. Semi-annual liver ultrasound and serum alpha-fetoprotein testing favor early detection of that cancer and should be carried out in all patients with chronic HBV infection, regardless of the presence of advanced fibrosis or cirrhosis. Currently, nucleoside/nucleotide analogues that have a high barrier to resistance are the first-line therapies.

Asociación Mexicana de Hepatología A.C. Clinical guideline on hepatitis B

Hepatitis B virus (HBV) infection continues to be a worldwide public health problem. In Mexico, at least three million adults are estimated to have acquired hepatitis B (total hepatitis B core antibody [anti-HBc]-positive), and of those, 300,000 active carriers (hepatitis B surface antigen [HBsAg]-positive) could require treatment. Because HBV is preventable through vaccination, its universal application should be emphasized. HBV infection is a major risk factor for developing hepatocellular carcinoma. Semi-annual liver ultrasound and serum alpha-fetoprotein testing favor early detection of that cancer and should be carried out in all patients with chronic HBV infection, regardless of the presence of advanced fibrosis or cirrhosis. Currently, nucleoside/nucleotide analogues that have a high barrier to resistance are the first-line therapies.

P–403 Sodium tungstate increases embryo adhesion through a direct effect on endometrial cells

Study question

Does sodium tungstate treatment induce a change in endometrial cells’ capacity to implant trophoblasts?

Summary answer

Administration of sodium tungstate to endometrial cells increases trophoblast adhesion.

What is known already

Sodium tungstate (ST) has shown its capacity to modulate the activity of cytokines, such as leptin, an activator of an obligatory signalling cascade in the embryo-implantation process. STAT3, a signal transducer molecule critical for the embryo implantation process, is also known to be activated by ST. Still, ST’s effect on implantation using biological systems has never been studied. Embryo implantation process and endometrium roles are complicated to study in vivo due to a lack of animal models and appropriate techniques. In vitro techniques using immortalised cell lines allows a first approach to study early implantation stages, such as embryo adhesion.

Study design, size, duration

An in vitro study was carried out using a human endometrial carcinoma cell line (HEC–1-A) treated with sodium tungstate for 24 and 48h, and choriocarcinoma cell spheroids (JAr). Different times of treatment and concentrations were studied. Each experiment was performed in triplicate.

Participants/materials, setting, methods

Confluent endometrial HEC–1-A cultures were treated with ST at concentrations (0–150mM) and withaferin A (1mM), negative control for embryo adhesion. After the treatment period, HEC–1-A cultures were washed with ST-free culture medium to eliminate ST. Immediately, 15 JAr trophoblast spheroids were added to cultures and coincubated with gentle agitation for 30, 60 and 90 minutes. An inverted light microscope was used to count adhered and floating spheroids, and determine the trophoblast adherence ratio.

Main results and the role of chance

HEC–1-A cells treated with ST showed normal morphology and growth at all doses except 150mM. At the highest dose tested, the cells’ culture was still viable (negative blue trypan staining) and maintained morphology, but the adhesion to the plate surface was affected. Doses from 0.15 to 15mM were used to perform adhesion assays.

HEC–1-A cells treated with ST for 24h showed an increased capacity to adhere JAr trophoblast spheroids. Adhesion rates reached significant differences at doses of 1.5 and 15mM after 60 and 90 minutes of coincubation. After 90 minutes, untreated cells reached 32.8% adhesion rate, while 1.5 and 15mM ST-treated cells reached 54.6% and 53.4% respectively (p &lt; 0.05 ST vs untreated). Thus, the increment of trophoblast adhesion rate induced by ST reached 66%. Lower adhesion rates were observed after 60 minutes of coincubation but were also significant with a relative increase of 49.1% at 1.5mM and 50.5% at 1.5mM when compared with untreated cells (p &lt; 0.05)

Longer treatments (48h) showed similar trends to 24h-treatments, but with a lower extent of ST effect on HEC–1-A receptivity. Maximum adhesion rates were also observed at 90 minutes of coincubation and 1.5 and 15mM doses. The Mean adhesion rate increase was &gt;40% with both doses. Limitations, reasons for caution: The current study is the first approach to evaluate sodium tungstate effect on endometrium using an in vitro model. Future research using in vivo models should be performed to assess sodium tungstate effect on endometrium receptivity and its potential as a fertility treatment.

Wider implications of the findings: We conclude that the direct effect of sodium tungstate on endometrial cells increases embryo adhesion rate. These results open a new research line to a potential treatment in human reproduction management with sodium tungstate to solve the unmet need of inducing embryo implantation.

Trial registration number

Not applicable

Effects of sub-optimal illumination in plants. Comprehensive chlorophyll fluorescence analysis

The fluorescence signals emitted by chlorophyll molecules of plants is a promising non-destructive indicator of plant physiology due to its close link to photosynthesis. In this work, a deep photophysical study of chlorophyll fluorescence was provided, to assess the sub-optimal illumination effects on three plant species: L. sativa, A. hybridus and S. dendroideum. In all the cases, low light (LL) treatment induced an increase in pigment content. Fluorescence ratios - corrected by light reabsorption processes - remained constant, which suggested that photosystems stoichiometry was conserved. For all species and treatments, quantum yields of photophysical decay remained around 0.2, which meant that the maximum possible photosynthesis efficiency was about 0.8. L. sativa (C3) acclimated to low light illumination, displayed a strong increase in the LHC size and a net decrease in the photosynthetic efficiency. A. hybridus (C4) was not appreciably stressed by the low light availability whereas S. dendroideum (CAM), decreased its antenna and augmented the quantum yield of primary photochemistry. A novel approach to describe NPQ relaxation kinetics was also presented here and used to calculate typical deactivation times and amplitudes for NPQ components. LL acclimated L. sativa presented a much larger deactivation time for its state-transition-related quenching than the other species. Comprehensive fluorescence analysis allowed a deep study of the changes in the light-dependent reactions of photosynthesis upon low light illumination treatment.

Evaluating the efficacy of three carrier screening workflows designed to identify at-risk carrier couples

OBJECTIVE

To evaluate the efficacy of three different carrier screening workflows designed to identify couples at risk for having offspring with autosomal recessive conditions.

METHODS

Partner testing compliance, unnecessary testing, turnaround time, and ability to identify at-risk couples (ARCs) were measured across all three screening strategies (sequential, tandem, or tandem reflex).

RESULTS

A total of 314,100 individuals who underwent carrier screening were analyzed. Sequential, tandem, and tandem reflex screening yielded compliance frequencies of 25.8%, 100%, and 95.9%, respectively. Among 14,595 couples tested in tandem, 42.2% of females were screen-negative, resulting in unnecessary testing of the male partner. In contrast, less than 1% of tandem reflex couples included unnecessary male testing. The median turnaround times were 29.2 days (sequential), 8 days (tandem), and 13.3 days (tandem reflex). The proportion of ARCs detected per total number of individual screens were 0.5% for sequential testing and 1.3% for both tandem and tandem reflex testing.

CONCLUSION

The tandem reflex strategy simplifies a potentially complex clinical scenario by providing a mechanism by which providers can maximize partner compliance and the detection of at-risk couples while minimizing workflow burden and unnecessary testing and is more efficacious than both sequential and tandem screening strategies.

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.

Evaluation and classification of severity for 176 genes on an expanded carrier screening panel

Background

Disease severity is important when considering genes for inclusion on reproductive expanded carrier screening (ECS) panels. We applied a validated and previously published algorithm that classifies diseases into four severity categories (mild, moderate, severe, and profound) to 176 genes screened by ECS. Disease traits defining severity categories in the algorithm were then mapped to four severity‐related ECS panel design criteria cited by the American College of Obstetricians and Gynecologists (ACOG).

Methods

Eight genetic counselors (GCs) and four medical geneticists (MDs) applied the severity algorithm to subsets of 176 genes. MDs and GCs then determined by group consensus how each of these disease traits mapped to ACOG severity criteria, enabling determination of the number of ACOG severity criteria met by each gene.

Results

Upon consensus GC and MD application of the severity algorithm, 68 (39%) genes were classified as profound, 71 (40%) as severe, 36 (20%) as moderate, and one (1%) as mild. After mapping of disease traits to ACOG severity criteria, 170 out of 176 genes (96.6%) were found to meet at least one of the four criteria, 129 genes (73.3%) met at least two, 73 genes (41.5%) met at least three, and 17 genes (9.7%) met all four.

Conclusion

This study classified the severity of a large set of Mendelian genes by collaborative clinical expert application of a trait‐based algorithm. Further, it operationalized difficult to interpret ACOG severity criteria via mapping of disease traits, thereby promoting consistency of ACOG criteria interpretation.

AB0688 GAIT PATTERN DIFFERENCES BETWEEN PATIENTS WITH RADIOGRAPHIC AND NON-RADIOGRAPHIC AXIAL SPONDYLOARTHRITIS, THE MyoSpA STUDY

Background:

Axial spondyloarthritis (axSpA) is a chronic inflammatory disease classified as radiographic (r-axSpA) or non-radiographic (nr-axSpA). Defining the gait patterns associated with these two groups can improve its detection and promote early intervention. In normal walking, body segments move around the joints as struts of an inverted pendulum. The resultant cyclic rotations contribute to the forward translation of the body, while minimizing muscle work and maintaining stability. Recent literature describes a decline in this pendulum-like mechanism associated with aging and some neurological diseases (Parkinson and multiple sclerosis).

Objectives:

The aim was to compare the 3D gait kinematics of patients with r-axSpA and nr-axSpA.

Methods:

A cross-sectional study was conducted on 54 participants (18-50 years old), 27 patients with axSpA (according to ASAS criteria, with less than 10 years since symptoms onset) and 27 healthy controls, matched by gender, age and level of physical activity. A sub-analysis was performed involving the whole group of patients classified as r-axSpA (n=14) and nr-axSpA (n=6). Subjects movement was reconstructed using a 3D full-body kinematic model (Kinetikos, Coimbra, Portugal) fed by 15 inertial sensors placed in the head, arms, trunk, pelvis, thighs, shanks and feet. 3D gait kinematics was characterised based on variables that analyse the body movement as a whole (e.g. center of mass displacement, speed), conventional spatiotemporal parameters (e.g. stance/swing time, step length) and joints kinematics time-normalized to 101 points, comprising the gait cycle from 0 to 100%. Nonparametric statistical tests were used.

Results:

In the r-axSpA group, 71,4% were male, with a mean age of 34.43±7.84 years and a BASDAI of 2.84±2.39, whereas in the nr-axSpA, 50% were male, with a mean age of 41.83±6.27 years and a BASDAI of 2.99±0.58. A statistically significant difference was observed in the displacement of the center of mass (with respect to the pelvis local coordinate system) along the anteroposterior axis between the two studied groups (H = 4.96, p = 0.03), with a mean rank displacement of 8.6 for r-axSpA and 15.00 for nr-axSpa, corresponding to a reduction in displacement of 38% (mean 0.00986 vs 0.01579m), in the r-axSpa group.

Conclusion:

Our preliminary results in r-axSpA subjects show a reduction of the pendulum mechanism. Although no significant segmental (kinematics) changes were observed, the sum of all studied variables result in a clear different gait pattern between the two groups. The observed decline can be an early sign of the inefficiency of the r-axSpA group to minimise the cost of transport of the center of mass during walking (i.e. increased instability). This study shows the potential of gait analysis to identify subjects who may benefit from early physiotherapy intervention.

Disclosure of Interests:

Nuno Gonçalves: None declared, Lúcia Domingues: None declared, Atlas Mashayekhi Sardoo: None declared, Lucian Radu: None declared, Santiago Rodrigues-Manica Speakers bureau: Jansse, MSD, Novartis, Agna Neto: None declared, Rita Torres: None declared, José Marona: None declared, Jaime Branco Speakers bureau: Vitoria, César Mendes: None declared, Ricardo Matias: None declared, Fernando Pimentel dos Santos Speakers bureau: Novartis, Pfizer, Biogen, Vitoria,

The value of lncRNA FENDRR and FOXF1 as a prognostic factor for survival of lung adenocarcinoma

It is increasingly evident that non-coding RNAs play a significant role in tumour development. However, we still have a limited knowledge of the clinical significance of long non-coding RNAs (lncRNAs) in lung cancer. The FENDRR is a long coding RNA (also named FOXF1-AS1) located in the vicinity of the protein-coding gene FOXF1 at 16q24.1 chromosomal region. The present study aimed to define the clinic pathological significance of the long-non-coding RNA FENDRR in lung adenocarcinomas. FENDRR expression measured by quantitative PCR was found significantly downregulated (p<0.001) in lung adenocarcinoma samples in comparison with their normal adjacent tissues (n=70). RNA in situ hybridization (RNA-FISH) corroborated independently the down-regulation of FENDRR. Interestingly, the expression of FENDRR correlated positively (p<0.001) with the expression of its protein-coding neighbor gene FOXF1. Additionally, FOXF1 expression was also found downregulated in adenocarcinomas compared to normal samples (p<0.001) and its expression was significantly correlated with overall survival alone (p=0.003) or in combination with FENDRR expression (p=0.01). In conclusion, our data support that FENDRR and FOXF1 expression is decreased in lung adenocarcinoma and should be considered as new potential diagnostic/prognosis biomarkers.

Gene editing of PKLR gene in human hematopoietic progenitors through 5' and 3' UTR modified TALEN mRNA

Pyruvate Kinase Deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene, which encodes the erythroid specific Pyruvate Kinase enzyme. Erythrocytes from PKD patients show an energetic imbalance and are susceptible to hemolysis. Gene editing of hematopoietic stem cells (HSCs) would provide a therapeutic benefit and improve safety of gene therapy approaches to treat PKD patients. In previous studies, we established a gene editing protocol that corrected the PKD phenotype of PKD-iPSC lines through a TALEN mediated homologous recombination strategy. With the goal of moving toward more clinically relevant stem cells, we aim at editing the PKLR gene in primary human hematopoietic progenitors and hematopoietic stem cells (HPSCs). After nucleofection of the gene editing tools and selection with puromycin, up to 96% colony forming units showed precise integration. However, a low yield of gene edited HPSCs was associated to the procedure. To reduce toxicity while increasing efficacy, we worked on i) optimizing gene editing tools and ii) defining optimal expansion and selection times. Different versions of specific nucleases (TALEN and CRISPR-Cas9) were compared. TALEN mRNAs with 5’ and 3’ added motifs to increase RNA stability were the most efficient nucleases to obtain high gene editing frequency and low toxicity. Shortening ex vivo manipulation did not reduce the efficiency of homologous recombination and preserved the hematopoietic progenitor potential of the nucleofected HPSCs. Lastly, a very low level of gene edited HPSCs were detected after engraftment in immunodeficient (NSG) mice. Overall, we showed that gene editing of the PKLR gene in HPSCs is feasible, although further improvements must to be done before the clinical use of the gene editing to correct PKD.

Epigenetic reprogramming of primary pancreatic cancer cells counteracts their in vivo tumourigenicity

Pancreatic ductal adenocarcinoma (PDAC) arises through accumulation of multiple genetic alterations. However, cancer cells also acquire and depend on cancer-specific epigenetic changes. To conclusively demonstrate the crucial relevance of the epigenetic programme for the tumourigenicity of the cancer cells, we used cellular reprogramming technology to reverse these epigenetic changes. We reprogrammed human PDAC cultures using three different techniques - (1) lentivirally via induction of Yamanaka Factors (OSKM), (2) the pluripotency-associated gene OCT4 and the microRNA mir-302, or (3) using episomal vectors as a safer alternative without genomic integration. We found that induction with episomal vectors was the most efficient method to reprogram primary human PDAC cultures as well as primary human fibroblasts that served as positive controls. Successful reprogramming was evidenced by immunostaining, alkaline phosphatase staining, and real-time PCR. Intriguingly, reprogramming of primary human PDAC cultures drastically reduced their in vivo tumourigenicity, which appeared to be driven by the cells' enhanced differentiation and loss of stemness upon transplantation. Our study demonstrates that reprogrammed primary PDAC cultures are functionally distinct from parental PDAC cells resulting in drastically reduced tumourigenicity in vitro and in vivo. Thus, epigenetic alterations account at least in part for the tumourigenicity and aggressiveness of pancreatic cancer, supporting the notion that epigenetic modulators could be a suitable approach to improve the dismal outcome of patients with pancreatic cancer.

Graphene and its derivatives: Opportunities and challenges in dentistry

The emerging science of graphene-based engineered nanomaterials as either nanomedicines or dental materials in dentistry is growing. Apart from its exceptional mechanical characteristics, electrical conductivity and thermal stability, graphene and its derivatives can be functionalized with several bioactive molecules, allowing them to be incorporated into and improve different scaffolds used in regenerative dentistry. This review presents state of the art graphene-based engineered nanomaterial applications to cells in the dental field, with a particular focus on the control of stem cells of dental origin. The interactions between graphene-based nanomaterials and cells of the immune system, along with the antibacterial activity of graphene nanomaterials are discussed. In the last section, we offer our perspectives on the various applications of graphene and its derivatives in association with titanium dental implants, membranes for bone regeneration, resins, cements and adhesives, as well as tooth-whitening procedures.

Abstract GS2-04: Efficacy results from CIBOMA/2004-01_GEICAM/2003-11 study: A randomized phase III trial assessing adjuvant capecitabine after standard chemotherapy for patients with early triple negative breast cancer

Background: Triple negative breast cancers (TNBC) have a greater risk of relapse than non-TNBC. New therapeutic approaches are needed for these patients (pts). CIBOMA/2004-01_GEICAM/2003-11 is a multinational, randomized phase III trial exploring adjuvant capecitabine (X) after completion of standard treatment in early TNBC pts.

Materials and Methods: Patients with operable, node-positive (or node-negative with tumor size ≥ 1 cm), centrally confirmed hormone receptor-negative, HER2-negative early BC, who had received 6–8 cycles (cy) of standard anthracycline and/or taxane-containing chemotherapy or 4 cy of doxorubicin-cyclophosphamide (for node-negative disease) in the (neo)adjuvant setting, were eligible. Patients were randomized to either 8 cy of X (1,000 mg/m2 bid, days 1–14, every 3 weeks) or observation. Stratification factors included center, prior taxane-based therapy, number of involved axillary lymph nodes and phenotype (basal vs non-basal, according to cytokeratins 5/6 and/or EGFR positivity). The primary objective was to compare the disease-free survival (DFS) between both treatment arms, and secondary objectives included the comparison in terms of 5-year DFS, overall survival (OS) and safety. Assuming a 30% risk reduction in DFS rate at 5 years (from 64.7% to 73.7%, hazard ratio 0.70) with 80% power and a two-tailed log-rank test at 0.05, 834 evaluable pts were needed. 876 pts had to be finally enrolled considering a drop-out rate of 5%.

Results: Recruitment of 876 pts from 8 countries was completed in September 2011. Median age was 49 years; 68.5% of pts were postmenopausal, 55.5% were lymph node negative, 71.7% had a basal phenotype, 67.5% received chemotherapy based on anthracyclines and taxanes. Median follow-up was 7.3 years (range 0.0 to 11.1). DFS was not significantly prolonged with X vs observation (hazard ratio (HR) 0.82; 95% confidence interval (CI), 0.63 to 1.06; P=0.1353). Five-year DFS was 79.6% (95% CI, 75.8% to 83.4%) with X and 76.8% (95% CI, 72.7% to 80.9%) with observation. OS was not statistically different between treatment arms (HR 0.92; 95% CI, 0.66 to 1.28; P=0.6228). In subgroup analysis for DFS, we found no statistically significant interaction between X treatment and different subgroups, with the exception of basal vs non-basal phenotypes (basal HR 0.97, 95% CI 0.72 to 1.32, P=0.8620; non-basal HR 0.51, 95% CI, 0.31 to 0.86, P=0.0101; interaction P=0.0357). Similar results were found for OS (basal HR 1.20, 95% CI 0.81 to 1.77, P=0.3684; non-basal HR 0.48, 95% CI, 0.26 to 0.91, P=0.0205; interaction P=0.0155). 75.2% of pts completed 8 cy of X, with a median relative dose intensity of 86.3%. Grade (G) 3 or higher adverse events (AEs) were observed in 40.4% of pts in X arm. In 9.6% of pts the AEs were related with X. Hand-foot syndrome was the most common AE in X arm (G3 on 18.8% of pts).

Conclusions: In our study, the addition of adjuvant X after standard (neo) adjuvant anthracycline and/or taxane-containing chemotherapy was not associated with a statistically significant improvement of DFS or OS compared to observation in pts with early TNBC. However, in a subgroup analysis a significant DFS and OS improvement was observed with X in pts with non-basal phenotype.

Sponsor: CIBOMA.

Citation Format: Martín M, Barrios CH, Torrecillas L, Ruiz-Borrego M, Bines J, Segalla J, Ruiz A, García-Sáenz JA, Torres R, de la Haba J, García E, Gómez HL, Llombart A, Rodríguez de la Borbolla M, Baena JM, Barnadas A, Calvo L, Pérez-Michel L, Ramos M, Castellanos J, Rodríguez-Lescure A, Cárdenas J, Vinholes J, Martínez de Dueñas E, Godes MJ, Seguí MA, Antón A, López-Álvarez P, Moncayo J, Amorim G, Villar E, Reyes S, Sampaio C, Cardemil B, Escudero MJ, Bezares S, Carrasco E, Lluch A. Efficacy results from CIBOMA/2004-01_GEICAM/2003-11 study: A randomized phase III trial assessing adjuvant capecitabine after standard chemotherapy for patients with early triple negative breast cancer [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 GS2-04.

Abstract A202: Lysophosphatidic acid impedes the effector function of CD8+ T-cells through LPA5R

Immunotherapies have demonstrated the utility of targeting the immune system for the eradication of tumors, yet a majority of patients remain refractory to such treatments. Therefore, further advances in our understanding of T-cell activation and inhibitory signals are required to find alternative combinational strategies to treat cancers. Lysophosphatidic acid (LPA) is a bioactive lipid that has been characterized to promote tumor growth via distinct mechanisms and thus displays multiple “hallmarks” of tumorgenesis, including enhancing tumor-promoting inflammation, metastasis, and angiogenesis. Despite LPA receptors (LPARs) being expressed on all immune cells, the impact of LPA on immune cells remains unclear. Work from our lab has previously shown that LPA signals via LPAR5 expressed by CD8+ T-cells to suppress TCR-mediated intracellular calcium mobilization. Thus, we propose that aberrant expression of LPA by diverse tumors serves also to dampen adaptive immune responses, thereby creating an immune suppressive tumor microenvironment. Here, we demonstrate that CD8+ T-cells express three of the six known LPA receptors, and that LPA signaling through LPA5R on CD8+ T-cells has not only a profound inhibition of Ca2+ release after TCR stimulation, but also impedes ERK and Nur77 TCR induced signaling pathway. Importantly we now demonstrate that LPA signaling also decreases the cytolytic function of CD8+ T-cells by inhibiting granule exocytosis. Both adoptive transfer of Lpar5-/- CD8+ T-cells and implantation of tumors into Lpar5-/- hosts leads to greater control of tumor growth, underscoring an immunosuppressive signal mediated by LPA through LPA5R on CD8+ T-cells. Finally, human CD8+ T-cells also express the same LPARs as in the mouse and similarly fail to efficiently release Ca2+ upon TCR stimulation in the presence of LPA. Pharmaceutical inhibition of the human LPA5 receptor restores Ca2+ flux, suggesting a similar mechanism seen in mice. Thus, our data illuminate a novel lipid-receptor interaction that suppresses CD8+ T-cell function in both human and murine cells.

Citation Format: Divij Mathew, Pamela Strauch, Roberta Pelanda, Raul Torres. Lysophosphatidic acid impedes the effector function of CD8+ T-cells through LPA5R [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A202.

Genetic parameters for medullated fiber and its relationship with other productive traits in alpacas

The alpaca fiber diameter (FD) varies from 18 to 36 μm, being the finer fiber categories highly appreciated. However, the alpaca fiber presents some limitations in the textile industry due to the high incidence of fiber medullation and diameter variability, both reduces the comfort feeling of the garments. Decreasing or even removing medullation could be a possible selection objective in alpaca breeding programs for increasing economic value of the alpaca fiber. Therefore, the present work aimed to estimate genetic parameters regarding medullation traits, as well as the genetic correlations with other economical important traits, to be able to select the appropriate criteria to reduce or remove medullation on alpaca fiber and help to reduce the prickle factor in the garments. The data was collected from 2000 to 2017 and belonged to the Pacomarca experimental farm. There were 3698 medullation records corresponding to 1869 Huacaya and 414 Suri genetic types. The fiber samples were taken from the mid side, and were analyzed in an OFDA 100® device. The traits analyzed were percentage of medullation (PM), medullated fiber diameter (MFD), FD, standard deviation of FD, greasy fleece weight as fiber traits; density, crimp in Huacaya and lock structure in Suri, head conformation, leg coverage as morphological traits; weaning weight and age at first calving as secondary and functional traits. Genetic parameters were estimated via a multitrait restricted maximum likelihood. The heritabilities for PM and MFD were 0.225 and 0.237 in Huacaya genetic type and 0.664 and 0.237 in Suri genetic type, respectively; heritabilities for other traits were moderate for productive and morphological traits, and low to moderate for secondary and functional traits. The genetic correlations PM-FD and MFD-FD were high and favorable in both genetic types, between 0.531 and 0.975; the genetic correlation PM-MFD was 0.121 in Huacaya and 0.427 in Suri. The rest of genetic correlations with other traits were in general moderate and favorable. The repeatabilities were 0.556 and 0.668 for PM, and 0.322 and 0.293 for MFD in Huacaya and Suri genetic types, respectively. As a conclusion, PM was identified to be a good selection criterion, probably combined in an index with FD to reduce prickling factor.

The energetic physiology of juvenile mussels, Mytilus chilensis (Hupe): The prevalent role of salinity under current and predicted pCO2 scenarios

As a result of human activities, climate forecasts predict changes in the oceans pCO₂ and salinity levels with unknown impacts on marine organisms. As a consequence, an increasing number of studies have begun to address the individual influence of pCO₂ and salinity but much remains to be done to understand their combined effects on the physiology and ecology of marine species. Our study addressed this knowledge gap by measuring the influence of current and predicted levels of pCO₂ (380 and 1200 ppm, respectively) and salinity (20, 25 and 30 psμ) on the energetic physiology of juvenile mussels (Mytilus chilensis) from the south-eastern Pacific region. Our results indicate that a reduced salinity caused a significant reduction in clearance rate, absorption efficiency and scope for growth of this species. Meanwhile, an increase in pCO₂ levels caused a reduction in excretion rates and interacted significantly with salinity in the rate of oxygen uptake measured in the mussel. These results suggest that potential changes in salinity might have a direct role on the physiology of M. chilensis. The effect of pCO₂, although less prevalent among the variables measured here, did interact with salinity and is also likely to alter the physiology of this species. Given the ecological and economic importance of M. chilensis, we call for further studies exploring the influence of pCO₂ across a wider range of salinities.

Enhanced shelf-life of the formulated biocontrol agent Bacillus amyloliquefaciens CPA-8 combining diverse packaging strategies and storage conditions

Two effective biocontrol products (named as BA3 and BA4) based on Bacillus amyloliquefaciens CPA-8 have been reported as a potential alternative to chemical applications against brown rot caused by Monilinia spp. on stone fruit. To have practical use, this study aimed to describe the best packaging strategies (bags or flasks, atmosphere, and temperature of storage) to not only guarantee efficacy but also stability and ease of application of the products to be handled through the normal channels of distribution and storage. In terms of the viability neither the BA3 nor the BA4 product has been compromised after twelve months of storage. However, storage at 4 °C affected the stability and visual aspect of both CPA-8 formulations, mainly associated not only to the increase of RH but also a_w. Moreover, it should be pointed out that flasks did not conserve refrigerated BA3 samples in a suitable way, since RH and a_w increased noticeably making their visual properties unsightly after 10 months of cold storage. At that time, the BA4 products were better preserved at 4 °C when packaged in flasks. Finally, this study also demonstrated that the most suitable packaging conditions for long-term storability (stored at 22 °C) did not show any negative effect in the biocontrol efficacy of CPA-8 in nectarines artificially infected with M. fructicola and provide suitable product delivery and field application. In conclusion, these results contribute to the final stage of development of these two CPA-8 products, practically ready for registration, thus contributing to the environmental-friendly management of postharvest diseases in stone fruit.

The My Child Matters Programme: The Effect of the Implementation of a Childhood Cancer Care Network (ReNaCI) in the Treatment Abandonment of Acute Lymphoblastic Leukemia in Paraguay

Background: In Paraguay, a low-middle income country (GDP per capita of USD 4,728.7), pediatric cancer is the second cause of mortality in children and adolescents 5-19 years of age. There are approximately 300 new cases of pediatric cancer per year. The Pediatric Cancer Center (PCC) of the School of Medicine (SoM) receives 120 new cases per year, of which 40% correspond to acute lymphoblastic leukemia (ALL). Treatment abandonment is the interruption of patient contact with the health personnel and the treatment of more than 30 days after treatment initiation. At our cancer center, ALL treatment abandonment has been a serious problem. The rates were as high as 20% in 2006, lowering to 17.5% in 2008. To prevent abandonment at our center, we assessed the risk for abandonment, then, we concentrated in three basic interventions: review of compliance with appointment, training of parents and teachers, and access for care at satellites clinics closer to home. For missed appointment, parents are contacted via telephone, or through home visits; and in occasions assistance of child protection services was solicited. We systematically trained parents in the importance of the adherence to cancer treatment. Since 2009, we implemented a comprehensive system for referrals of new cases and follow-up by establishing the ReNaCI, (Red Nacional de Atencion al Cancer Infantil) network. Essential funds for building and sustaining the network has been provided by My Child Matters program under the auspices of Sanofi Espoir Fundation, Paris, France. Currently, as part of this network, there is 4 regional pediatric clinics for early cancer detection, referral, treatment, social assistance and follow up of pediatrics patients with cancer. Aim: Assess the effect of the network in the percentage of abandonment of treatment in patients with ALL treated at the PCC of the SoM in Asunción. Methods: We conducted a longitudinal descriptive study of children diagnosed with ALL at the PCC of the SoM between January 2009 and December 2017. We analyzed the percentage of abandonment since the implementation of the ReNACI network and compared with historical data. Results: From January 2009 to December 2017, 396 new patients with ALL diagnose at the PCC of the SoM. More than 70% of the families were evaluated as having an elevated social risk for abandonment. Abandonment rate decreased from 17.5% in 2008, in 2010%-1.96%, and since 2011 there were no abandonment. However, we still observed in the study period 12% of missed appointments to continue the treatment protocol. Conclusion: The ReNaCI network allowed a successful implementation of interventions to address abandonment by establishing a systems of satellite clinics for a medical and social support for the child and his family closer to home during the entire treatment period. But, despite the achievements, a continuous monitoring is still required to sustain the success of our intervention. Funding: Sanofi Espoir Foundation

Efficacy of environmental friendly disinfectants against the major postharvest pathogens of stone fruits on plastic and wood surfaces

Disinfection of surface facilities during postharvest handling operation is an important practice to avoid secondary fruit infections at stone fruit packinghouses. The aim of this work was to evaluate the effect of six environmental friendly disinfectants against Monilinia fructicola, Penicillium expansum, Rhizopus spp., and Alternaria spp. on plastic and wood surfaces. Hydrogen peroxide, peracetic acid, sodium hypochlorite, Mico-E-pro®, Proallium FRD-N®, and DMC Clean-CNS® were used as the disinfectants. Untreated and surfaces treated with water were used as controls. Plastic and wood surfaces were sampled with Rodac plates at 2 and 24 h after treatments and the number of colonies were counted. In general, all disinfectants reduce the number of viable conidia from all studied surfaces. Hydrogen peroxide used in a concentration of 150 mg L^-1 was the less effective disinfectant in all studied pathogens. The commercial product Mico-E-pro® composed of oregano, onion, and orange extract at a dose of 10 mg L^-1 was the most effective disinfectant. Rhizopus spp. was the pathogen more resistant to the disinfectants followed by P. expansum, M. fructicola, and Alternaria spp. Water decreased the number of conidia adhered to the surface. In addition, the untreated control showed substantial conidia reduction after 24 h of artificial inoculation.

Concentrations of Mercury and Other Inorganic Ions in Wet Precipitation Collected from a Mountain Mining Zone and an Urban Area in Central Mexico

We measured and compared mercury (Hg) and other ions in rainwater collected in San Joaquin (mining zone) and Juriquilla (urban area), central Mexico, from 2009 to 2012. A total of 274 rainwater samples were collected and analyzed for pH, electrical conductivity, [Formula: see text] Cl^-, [Formula: see text] Na⁺, K⁺, Ca²⁺, Mg²⁺ and Hg. Mercury concentrations in rainwater varied from 24.21 to 248.89 (x-bar = 86.97 ± 10.77) µg L^- 1 in San Joaquin (mining zone) and 11.26 to 176.91 (x-bar = 81.51 ± 10.24) µg L^- 1 in Juriquilla (urban area). Rainwater sample were collected over periods 1-3 days, depending upon precipitation frequency. Significant correlations (p < 0.05) were found between [Formula: see text] Cl^-, [Formula: see text] Na⁺, K⁺, Ca²⁺, Mg²⁺ and Hg at the San Joaquin site. Significant correlations were obtained between [Formula: see text] Na⁺, K⁺, Ca²⁺, Mg²⁺ and Hg at the Juriquilla site. In order to determine if there were significant differences among each measured parameter in rainwater collected in San Joaquin and Juriquilla, Kruskal-Wallis test was applied to data. We emphasized that the distribution and concentrations of Hg and the studied ions in rainwater samples were affected by atmospheric dust and local meteorological conditions of wind-speed and direction.

Human demographic history has amplified the effects of background selection across the genome

Natural populations often grow, shrink, and migrate over time. Such demographic processes can affect genome-wide levels of genetic diversity. Additionally, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes affect not only the sites directly under selection but also nearby neutral variation through genetic linkage via processes referred to as genetic hitchhiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the consequences of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes influence the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in strong BGS regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been affected more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and the inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences of selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data

Motivation

Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X).

Results

We have applied our classifier to compare call sets generated with different calling methods, including both single-sample and multi-sample callers. At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illuminas single-sample caller CASAVA, Real Time Genomics multisample variant caller, and the GATK UnifiedGenotyper, respectively. Since NGS sequencing data may be accompanied by genotype data for the same samples, either collected concurrent to sequencing or from a previous study, our method can be trained on each dataset to provide a more accurate computational validation of site calls compared to generic methods. Moreover, our method allows for adjustment based on allele frequency (e.g. a different set of criteria to determine quality for rare versus common variants) and thereby provides insight into sequencing characteristics that indicate call quality for variants of different frequencies.

Availability and Implementation

Code is available on Github at: https://github.com/suyashss/variant_validation.

Contacts

suyashs@stanford.edu or mtaub@jhsph.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

3D curved multiplanar cone beam CT reconstruction for intracochlear position assessment of straight electrodes array. A temporal bone and clinical study

A retrospective review of post-op cone beam CT (CBCT) of 8 adult patients and 14 fresh temporal bones that underwent cochlear implantation with straight flexible electrodes array was performed to determine if the position of a long and flexible electrodes array within the cochlear scalae could be reliably assessed with CBCT. An oto-radiologist and two otologists examined the images and assessed the electrodes position. The temporal bone specimens underwent histological analysis for confirm the exact position. The position of the electrodes was rated as scala tympani, scala vestibule, or intermediate position for the electrodes at 180°, 360° and for the apical electrode. In the patient group, for the electrodes at 180° all observers agreed for scala tympani position except for 1 evaluation, while a discrepancy in 3 patients both for the 360° and for the apical electrode assessment were found. In five temporal bones the evaluations were in discrepancy for the 180° electrode, while at 360° a disagreement between raters on the scalar positioning was seen in six temporal bones. A higher discrepancy between was found in assessment of the scalar position of the apical electrode (average pairwise agreement 45.4%, Fleiss k = 0.13). A good concordance was found between the histological results and the consensus between raters for the electrodes in the basal turn, while low agreement (Cohen's k 0.31, pairwise agreement 50%) was found in the identification of the apical electrode position confirming the difficulty to correct identify the electrode position in the second cochlear turn in temporal bones. In conclusion, CBCT is a reliable radiologic exam to correctly evaluate the position of a lateral wall flexible array in implanted patients using the proposed imaging reconstruction method, while some artefacts impede exact evaluation of the position of the apical electrode in temporal bone and other radiological techniques should be preferred in ex vivo studies.

Intraoperative Conebeam CT for Assessment of Intracochlear Positioning of Electrode Arrays in Adult Recipients of Cochlear Implants

BACKGROUND AND PURPOSE

Intraoperative conebeam CT has been introduced into the operating room and provides quick radiologic feedback. This study aimed to investigate its utility in the assessment of the positioning of the electrode array after cochlear implantation.

MATERIALS AND METHODS

This was a retrospective study of 51 patients (65 ears) with intraoperative imaging by conebeam CT (O-arm) after cochlear implantation between 2013 and 2017. Correct placement into the cochlea was immediately identified. Positioning assessments were later analyzed with OsiriX software.

RESULTS

Intraoperative imaging was quickly performed in all cases. No misplacement into the vestibule or semicircular canals was found. A foldover of the implanted array was identified in 1 patient. Secondary analysis by 2 raters showed excellent agreement on insertion depth angle (intraclass correlation = 0.96, P < .001) and length of insertion of the electrode array (intraclass correlation coefficient = 0.93, P = .04) measurements. The evaluation of the number of extracochlear electrodes was identical between the 2 raters in 78% of cases (Cohen κ = 0.55, P < .001). The scalar position was inconsistent between raters. When we compared O-arm and high-resolution CT images in 14 cases, the agreement was excellent for insertion depth angle (intraclass correlation coefficient = 0.97, P < .001) and insertion length (intraclass correlation coefficient = 0.98, P < .001), good for the number of extracochlear electrodes (Cohen κ = 0.63, P = .01), but moderate for the scalar position (Cohen κ = 0.59, P = .02).

CONCLUSIONS

Intraoperative conebeam CT using the O-arm is a safe, rapid, easy, and reliable procedure to immediately identify a misplacement or foldover of an electrode array. The insertion depth angle, insertion length, and number of electrodes inserted can be accurately assessed.

Comparative Study of Vitrectomy with and without Vein Decompression for Branch Retinal Vein Occlusion: A Pilot Study

Purpose

To report the clinical outcomes in patients undergoing pars plana vitrectomy with and without vein decompression for treatment of branch retinal vein occlusion (BRVO).

METHODS

Thirty-five eyes with macular edema and visual acuity worse than 20/100 secondary to BRVO were prospectively evaluated. Vitrectomy with posterior hyaloid removal and vein decompression at the arteriovenous crossing was performed on 15 eyes (Group 1); consecutively, the same technique without vein decompression was performed on 20 eyes (Group 2). Primary outcome was visual acuity and secondary outcomes were resolution of macular edema and development of neovascularization.

Results

No differences were found between groups in either patient age (p=0.566) or preoperative visual acuity (p=0.505). No differences were found in visual acuity at 3 (p=0.651), 6 (p =0.697), 9 (p =0.763), 12 (p=0.881), or 18 (p=0.748) months. Mean time for macular edema resolution and visual acuity improvement was 9 months in both groups, with a mean improvement of 3.5 ± 2.35 lines in Group 1 and 3.2 ± 2.97 lines in Group 2. No eyes in either group developed new vessels.

CONCLUSIONS

Results suggest that vitrectomy with posterior hyaloid removal without vein decompression can resolve macular edema, improve vision, and prevent development of new vessels in BRVO.

Assessing Genetic Diversity in Four Stink Bug Species, Chinavia hilaris, Chlorochroa uhleri, Chlorochroa sayi, and Thyanta pallidovirens (Hemiptera: Pentatomidae), Using DNA Barcodes

Stink bugs (Hemiptera: Pentatomidae) are an economically important group of insects that attack numerous crops in the central valley of California. Management of these pests using pheromones or biological control can be species specific, and proper identification of insect species is essential for effective management. The objective was to examine genetic variability in four species of stink bugs, which included Chinavia hilaris (Say) (= Acrosternum hilare) (Hemiptera: Pentatomidae) , Chlorochroa uhleri (Stål) (Hemiptera: Pentatomidae) , Chlorochroa sayi (Stål) (Hemiptera: Pentatomidae), and Thyanta pallidovirens (Stål) (Hemiptera: Pentatomidae) and to determine whether there may be cryptic species present. Stink bugs were collected in pistachios or on adjacent vegetation when abundant in the central valley of California. The mitochondrial DNA cytochrome oxidase I (COI) gene region (i.e., the barcode) was sequenced for each individual. Data were combined with available GenBank accessions for each species and used to construct a phylogenetic tree. Divergence between genera ranged from 11.2 to 15.7%, whereas divergence between the two Chlorochroa spp. was 4.6%. Genetic variation within Chinavia hilaris collections was up to 4.7%, which suggests the presence of a cryptic species. Genetic divergence was highest between individuals of Chinavia hilaris from the west coast and the east coast of the United States. In contrast, genetic variation within individuals of C. uhleri and Ch. sayi was less than 1%. Nine haplotypes were found for Chinavia hilaris, five for C. uhleri, three for Ch. sayi, and five for T. pallidovirens. The relevance of correct species identification and genetic diversity to stink bug management practices was discussed.