Comprehensive analyses of brain cell communications based on multiple scRNA-seq and snRNA-seq datasets for revealing novel mechanism in neurodegenerative diseases

AIMS

Complex cellular communications between glial cells and neurons are critical for brain normal function and disorders, and single-cell level RNA-sequencing datasets display more advantages for analyzing cell communications. Therefore, it is necessary to systematically explore brain cell communications when considering factors such as sex and brain region.

METHODS

We extracted a total of 1,039,459 cells derived from 28 brain single-cell RNA-sequencing (scRNA-seq) or single-nucleus RNA-sequencing (snRNA-seq) datasets from the GEO database, including 12 human and 16 mouse datasets. These datasets were further divided into 71 new sub-datasets when considering disease, sex, and region conditions. In the meanwhile, we integrated four methods to evaluate ligand-receptor interaction score among six major brain cell types (microglia, neuron, astrocyte, oligodendrocyte, OPC, and endothelial cell).

RESULTS

For Alzheimer's disease (AD), disease-specific ligand-receptor pairs when compared with normal sub-datasets, such as SEMA4A-NRP1, were identified. Furthermore, we explored the sex- and region-specific cell communications and identified that WNT5A-ROR1 among microglia cells displayed close communications in male, and SPP1-ITGAV displayed close communications in the meninges region from microglia to neurons. Furthermore, based on the AD-specific cell communications, we constructed a model for AD early prediction and confirmed the predictive performance using multiple independent datasets. Finally, we developed an online platform for researchers to explore brain condition-specific cell communications.

CONCLUSION

This research provided a comprehensive study to explore brain cell communications, which could reveal novel biological mechanisms involved in normal brain function and neurodegenerative diseases such as AD.

Pathogenic SCN2A variants cause early-stage dysfunction in patient-derived neurons

Pathogenic heterozygous variants in SCN2A, which encodes the neuronal sodium channel NaV1.2, cause different types of epilepsy or intellectual disability (ID)/autism without seizures. Previous studies using mouse models or heterologous systems suggest that NaV1.2 channel gain-of-function typically causes epilepsy, whereas loss-of-function leads to ID/autism. How altered channel biophysics translate into patient neurons remains unknown. Here, we investigated iPSC-derived early-stage cortical neurons from ID patients harboring diverse pathogenic SCN2A variants [p.(Leu611Valfs*35); p.(Arg937Cys); p.(Trp1716*)] and compared them with neurons from an epileptic encephalopathy (EE) patient [p.(Glu1803Gly)] and controls. ID neurons consistently expressed lower NaV1.2 protein levels. In neurons with the frameshift variant, NaV1.2 mRNA and protein levels were reduced by ~ 50%, suggesting nonsense-mediated decay and haploinsufficiency. In other ID neurons, only protein levels were reduced implying NaV1.2 instability. Electrophysiological analysis revealed decreased sodium current density and impaired action potential (AP) firing in ID neurons, consistent with reduced NaV1.2 levels. In contrast, epilepsy neurons displayed no change in NaV1.2 levels or sodium current density, but impaired sodium channel inactivation. Single-cell transcriptomics identified dysregulation of distinct molecular pathways including inhibition of oxidative phosphorylation in neurons with SCN2A haploinsufficiency and activation of calcium signaling and neurotransmission in epilepsy neurons. Together, our patient iPSC-derived neurons reveal characteristic sodium channel dysfunction consistent with biophysical changes previously observed in heterologous systems. Additionally, our model links the channel dysfunction in ID to reduced NaV1.2 levels and uncovers impaired AP firing in early-stage neurons. The altered molecular pathways may reflect a homeostatic response to NaV1.2 dysfunction and can guide further investigations.

1182 THE PREVALENCE OF ORAL FRAILTY AND ITS ASSOCIATION WITH DYSPHAGIA, FRAILTY AND FORMAL CARE NEEDS

Introduction

Oral frailty (OF), gradual loss of oral function combined associated with presbyphagia often in conjunction with cognitive and physical decline, has been recommended to be considered as a geriatric giant. DENTAL has been suggested as a possible screening tool for OF. We have looked at the prevalence of OF and its association with dysphagia, frailty and formal care, amongst people admitted acutely to the acute medical/frailty wards in our hospital.

Methods

OF, dysphagia and frailty were screened for as part of the routine clinical assessment of patients during the usual clinical ward round. Screening tools used were DENTAL for OF, Rockwood Score for frailty and 4QT for dysphagia. Age, sex comorbidities and the need for formal care was documented.

Results

101 people were assessed over a 4-week period. Mean age was 84 years (65-99), 58 (57.4%) were female, 31(30.7%) were independent, 33 (32.6%) dementia, 57 (56.4%) frail, 54 (53.4%) had swallowing problems, and 34 (33.6%) OF. Of those with OF 97% had dysphagia, 88% were frail and 85% required formal care support (85%). OF was associated with dysphagia (p<0.0001), frailty (p< 0.0001), formal care support (p<0.05) and dementia (p<0.05). There was an association between needing care and frailty (p<0.01).

Conclusions

OF is associated with dysphagia, frailty and the need for formal care. OF may result in poor oral health and contribute to dysphagia and frailty, conversely frailty and dysphagia may result in poor oral health due to dependency and poor nutrition and dehydration. The associations are most likely be bidirectional. Further work is required to elucidate this. Clinical staff need to be aware of OF and oral health and include oral screening in their clinical assessment of an older adult.

Exploring the Associations between Alzheimer's Disease and GBM Mediated by Microglia Based on Network Analysis

Previous studies have revealed that there existed epidemic associations between Alzheimer's disease (AD) and many types of tumors, however, the inner biological mechanism connecting these diseases was not clear currently. In this study, we explored the transcriptome associations between AD and glioblastoma multiforme (GBM) that both originate in the brain, using microglia as a bridge, from gene and network levels. Firstly, we extracted human scRNA sequencing datasets from Gene Expression Omnibus (GEO) database, and identified differentially expressed genes within microglia after cell annotation. It was observed that there were 11 common genes shared by AD and GBM dys-regulated genes. Next, we utilized DIAMOnD and Flow Centrality algorithms to identify microglia modules and mediating pathways connecting these two diseases based on global network topology. Among these candidate pathways, the mediating genes FURIN and BACE1 (from SPIKN5 to CSNK1A1) were not only related to the formation of amyloid beta plaques that accumulate in the brain of AD patients, but also involved in cancer biology. Furthermore, the biological explorations of mediating pathways connecting AD and GBM modules reveal inflammatory response, lipid metabolism disorder, and cell proliferation terms. Finally, novel signatures for early AD detection as well as risk models for glioma prognosis were identified based on mediating genes involved in these pathways. In conclusion, this study provided a novel network-based strategy for exploring microglia mediation between AD and GBM and identified candidate signatures for disease detection and prognosis.

Vitamin D supplementation for patients with alopecia areata: A protocol for systematic review and meta-analysis

BACKGROUND

Several studies have reported an association between low Vitamin D (VD) levels and Alopecia areata (AA), and suggested VD preparations as a potential therapy. VD has immunomodulatory function closely associated with a variety of skin diseases, but there is no conclusive evidence to support VD supplementation for patients with AA. Therefore, we will conduct a meta-analysis to collect and evaluate the efficacy and safety of VD supplementation in the treatment of AA.

METHODS

We will search the following databases according to the developed strategy: Cochrane Library, PubMed, Web of Science, EMBASE, Scopus, Google scholar for Randomized controlled trials related to VD supplementation for AA. The retrieval time is from the establishment of each database to July 2022. Two reviewers will independently complete the literature search and screening, risk of bias assessment and data extraction. Severity of Alopecia Tool, Alopecia Density and Extent, Lesional area and senstivity (score) will be the primary results. RevMan V.5.3 will be used for data analysis and synthesis. For dichotomous outcomes and the continuous outcomes, we will calculate risk ratio with 95% Confidence intervals and mean differences or standardized mean differences with 95% Confidence intervals respectively. The reporting bias will be investigated using funnel plots, and the asymmetry of the funnel plots will be explained using the Harbord modified test or the Egger's regression test.

RESULTS

The results of the study expect to provide a high-quality, evidence-based recommendation on VD supplementation in the treatment of AA for clinicians.

CONCLUSIONS

The study will provide scientific and useful evidence for better use of VD supplementation in treating AA.

Identifying proteomic profiles as indicators of disease severity in arrhythmogenic cardiomyopathy

Introduction

Arrhythmogenic cardiomyopathy (ACM) is an inherited heart muscle disease characterized by progressive fibrofatty replacement of the myocardium and ventricular arrhythmias. Biventricular (BiV) involvement may lead to heart failure. This study aimed to investigate characteristic proteomic patterns in plasma of ACM patients, and correlated them with clinical outcome as well as physical exercise, to assess if key soluble molecules may serve as specific biomarkers for ACM, and whether mechanical stress induced by physical exercise may alter proteomic patterns in ACM patients.

Methods

In 38 ACM patients clinical parameters and major adverse cardiovascular events (MACE defined as presence of sustained ventricular tachycardia, ventricular fibrillation, appropriate therapy from implantable cardioverter defibrillator, sudden cardiac death, death related to end-stage heart failure or cardiac transplant) were obtained prospectively during a mean follow-up period of 36 months. All patients received genetic testing using next generation DNA sequencing. Plasma protein expression was analysed using the Proximity Extension Assay (PEA) technology, where a pair of oligonucleotide-labelled antibody probe binds to each targeted protein. In a subgroup of 11 patients blood was drawn immediately before and 3 hours after standardised bicycle exercise testing, and plasma protein expression was compared.

Results

12 patients had ACM with BiV involvement, and 26 patients had isolated right ventricular (RV) involvement. During the follow-up period, 34 patients had a MACE (30% with RV and 14% with BiV). Over 360 proteins were assessed in all ACM patients and compared to 24 healthy controls. The proteomic signature of ACM patients differed significantly compared to controls, and 32 proteins were upregulated in ACM (Figure 1). The proteomic profiles of patients with RV involvement also differed from those with BiV involvement. Most importantly, after exercise, over 40 proteins were upregulated specifically in ACM patients compared to controls, including key pro-inflammatory, adipogenic molecules and also markers of cardiac fibrosis.

Conclusion

Our study shows that ACM patients with RV and BiV involvement have different plasma proteomic profiles compared to healthy controls. Furthermore we were able to demonstrate that, specifically in ACM patients, several pro-inflammatory pathways are upregulated after exercise compared to healthy controls, further elucidating the molecular pathways associated with arrhythmogenicity and disease progression and highlighting the key role of physical stress. Our results may enable the identification of potential future biomarkers for diagnosis and risk stratification and may pave the way for personalized patient specific treatments.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Baugarten Foundation ZurichSwiss National Foundation

Comprehensive analysis of microglia gene and subpathway signatures for glioma prognosis and drug screening: linking microglia to glioma

Glioma is the most common malignant tumors in the brain. Previous studies have revealed that, as the innate immune cells in nervous system, microglia cells were involved in glioma pathology. And, the resident microglia displayed its specific biological roles which distinguished with peripheral macrophages. In this study, an integrated analysis was performed based on public resource database to explore specific biological of microglia within glioma. Through comprehensive analysis, the biological characterization underlying two conditions, glioma microglia compared to glioma macrophage (MicT/MacT) as well as glioma microglia compared to normal microglia (MicT/MicN), were revealed. Notably, nine core MicT/MicN genes displayed closely associations with glioma recurrence and prognosis, such as P2RY2, which was analyzed in more than 2800 glioma samples from 25 studies. Furthermore, we applied a random walk based strategy to identify microglia specific subpathways and developed SubP28 signature for glioma prognostic analysis. Multiple validation data sets confirmed the predictive performance of SubP28 and involvement in molecular subtypes. The associations between SuP28 score and microglia M1/M2 polarization were also explored for both GBM and LGG types. Finally, a comprehensive drug-subpathway network was established for screening candidate medicable molecules (drugs) and identifying therapeutic subpathway targets. In conclusions, the comprehensive analysis of microglia related gene and functional signatures in glioma pathobiologic events by large-scale data sets displayed a framework to dissect inner connection between microglia and glioma, and identify robust signature for glioma clinical implications.

Prognostic Features of the Tumor Immune Microenvironment in Glioma and Their Clinical Applications: Analysis of Multiple Cohorts

Glioma is the most common malignant tumor of the central nervous system. Tumor purity is a source of important prognostic factor for glioma patients, showing the key roles of the microenvironment in glioma prognosis. In this study, we systematically screened functional characterization related to the tumor immune microenvironment and constructed a risk model named Glioma MicroEnvironment Functional Signature (GMEFS) based on eight cohorts. The prognostic value of the GMEFS model was also verified in another two glioma cohorts, glioblastoma (GBM) and low-grade glioma (LGG) cohorts, from The Cancer Genome Atlas (TCGA). Nomograms were established in the training and testing cohorts to validate the clinical use of this model. Furthermore, the relationships between the risk score, intrinsic molecular subtypes, tumor purity, and tumor-infiltrating immune cell abundance were also evaluated. Meanwhile, the performance of the GMEFS model in glioma formation and glioma recurrence was systematically analyzed based on 16 glioma cohorts from the Gene Expression Omnibus (GEO) database. Based on multiple-cohort integrated analysis, risk subpathway signatures were identified, and a drug–subpathway association network was further constructed to explore candidate therapy target regions. Three subpathways derived from Focal adhesion (path: 04510) were identified and contained known targets including platelet derived growth factor receptor alpha (PDGFRA), epidermal growth factor receptor (EGFR), and erb-b2 receptor tyrosine kinase 2 (ERBB2). In conclusion, the novel functional signatures identified in this study could serve as a robust prognostic biomarker, and this study provided a framework to identify candidate therapeutic target regions, which further guide glioma patients’ clinical decision.

10 Tip-Apex Distance in DHS & IM Nail Fixations for Hip Fractures

Aim

Dynamic hip screws (DHS) and intramedullary nail (IMN) fixations have been successful in treating extracapsular hip fractures. Tip to apex distance (TAD) is defined as the total sum of distance from tip of the lag screw to the femoral head tip on both AP and lateral radiographs. Baumgartner et al. defined TAD<25 mm to be predictive of a successful result, with reduced rates of metalwork failure. Therefore, this study aims to assess if TAD principles are practiced during DHS and IMN fixations.

Method

102 patients were identified between December 2019 and February 2020. The distance was measured on AP and lateral radiographs to calculate the TAD. Patients were followed up for 1 year where the fractures either united or failed.

Results

Patients recruited had age ranges between 19–103 years old, of which 36% are male and 64% are female. 68% had underwent DHS while 32% underwent IM nail. In the DHS group, 13 patients had TAD of >25 mm, 28 with TAD of 20–25 mm, 18 with TAD of 15–20mm and 6 with TAD of <15 mm. For the IM nail group, there are 7 with TAD of 20–25 mm, 13 with TAD of 15–20mm and 10 with TAD of <15 mm.

Conclusions

There were no IM nails that exceeded TAD of 25mm, but 13 DHS fixations were >25mm. 12/13 DHS fixations >25mm TAD were performed by trainees. We advocate emphasis on the TAD principle and re-enforcing to orthopaedic trainees to improve the outcome of DHS in patients with neck of femur fractures.

11 Robotic Left Lower Sleeve Lobectomy with Bronchoplasty for the Removal of a Carcinoid Tumour

Lung carcinoid tumours constitute approximately 1–2% of all pulmonary tumours. They are derived from enterochromaffin cells, which are also known as ‘Kulchitsky cells' and generally have indolent growth and development patterns. Carcinoid tumours are categorized as typical or atypical, depending on the number of mitoses per high power field and the presence of necrosis. In terms of management, surgical resection has been recognized to be the standard treatment for pulmonary carcinoid tumours. To our knowledge, the da Vinci system and robotic surgery have not been applied in sleeve lobectomies and bronchoplasty for the removal of carcinoid tumours in the United Kingdom. Therefore, we present a case of a sleeve lobectomy with bronchoplasty procedure for the removal of a carcinoid tumour located in the left lower lobe of the patient. The bronchus was repaired using a V-lock suture & Prolene sutures with the surgery performed using the da Vinci robotic surgical system.

Increased retention of tau PET ligand [18F]-AV1451 in Alzheimer's Disease Psychosis

Psychosis in Alzheimer's disease (AD) represents a distinct disease subtype with a more rapid progression of illness evidenced by an increased velocity of cognitive decline and a hastened mortality. Previous biomarker and post-mortem studies have implicated tau neuropathology as a possible mediator of the accelerated decline in AD psychosis. Tau positron emission tomography (PET) neuroimaging provides the opportunity to evaluate tau pathology in-vivo, so that clinical symptomatology can be correlated with disease pathology. [¹⁸F]-AV1451 (Flortaucipir) is a PET ligand with high affinity for insoluble paired-helical filaments (PHFs) of hyperphosphorylated tau. In order to determine whether the development of psychosis and worsened prognosis in AD is associated with an increased burden of tau pathology that can be identified with tau imaging, we identified subjects within the Alzheimer's disease neuroimaging initiative (ADNI) who had [¹⁸F]-AV1451 imaging at baseline and became psychotic over the course of the study (N = 17) and matched them 1:3 for gender, age, and education to subjects who had [¹⁸F]-AV1451 imaging at baseline and did not become psychotic (N = 50). We compared baseline [¹⁸F]-AV1451 retention, in addition to cognitive and functional baseline and longitudinal change, in those who became psychotic over the course of participation in ADNI with those who did not. Results suggest that increases in tau pathology in frontal, medial temporal, and occipital cortices, visualized with [¹⁸F]-AV1451 binding, are associated with psychosis and a more rapid cognitive and functional decline.

Identification of a Novel Prognostic Signature for Gastric Cancer Based on Multiple Level Integration and Global Network Optimization

Gastric Cancer (GC) is a common cancer worldwide with a high morbidity and mortality rate in Asia. Many prognostic signatures from genes and non-coding RNA (ncRNA) levels have been identified by high-throughput expression profiling for GC. To date, there have been no reports on integrated optimization analysis based on the GC global lncRNA-miRNA-mRNA network and the prognostic mechanism has not been studied. In the present work, a Gastric Cancer specific lncRNA-miRNA-mRNA regulatory network (GCsLMM) was constructed based on the ceRNA hypothesis by combining miRNA-target interactions and data on the expression of GC. To mine for novel prognostic signatures associated with GC, we performed topological analysis, a random walk with restart algorithm, in the GCsLMM from three levels, miRNA-, mRNA-, and lncRNA-levels. We further obtained candidate prognostic signatures by calculating the integrated score and analyzed the robustness of these signatures by combination strategy. The biological roles of key candidate signatures were also explored. Finally, we targeted the PHF10 gene and analyzed the expression patterns of PHF10 in independent datasets. The findings of this study will improve our understanding of the competing endogenous RNA (ceRNA) regulatory mechanisms and further facilitate the discovery of novel prognostic biomarkers for GC clinical guidelines.

CHANGES OF WNT/B-CATENIN SIGNALING AND DIFFERENTIATION POTENTIAL OF BONE MARROW MESENCHYMAL STEM CELLS IN PROCESS OF BONE LOSS IN OVARIECTOMIZED RATS

Background

In vitro studies of the changes about osteoblastogenesis and adipogenesis potential of BMSCs were not clear. As it is the critical pathway for osteogenic differentiation and bone formation, whether or not Wnt/β-catenin signalling is involved in the changes of osteogenic and adipogenic potential of BMSCs and participates in bone content decrease of ovariectomized (OVX)osteoporosis rats has been rarely reported.

Material/Methods

BMSCs from femurs of ovariectomzed rats were isolated and cultured in vitro. The proliferation potential of BMSCs was analysed by CCK-8 assays . Osteoblastic and adipogenic differentiation potential of the BMSCs was assessed by ALP activity assay, Alizarin red S staining, Oil red O staining and RT-PCR analysis.

Results

The results demonstrated that BMSCs from bilateral ovariectomization rats were endowed with lower proliferation and osteoblastic differentiation potential but higher adipogenic potential than the control group in vitro. In addition, β-catenin was found to have been decreased in OVX BMSCs, indicating that Wnt/β-catenin signalling pathways were suppressed in OVX BMSCs .

Conclusions

Results suggested that changes in the Wnt canonical signalling pathway may be related to imbalances of osteogenic and adipogenic potential of BMSCs, and this may be an important factor related to bone content decrease in ovariectomized osteoporosis rats.

[Cancer metabolism: a novel perspective on precision diagnosis and treatment for liver cancer]

Metabolic reprogramming has been identified as a hallmark of cancer. Liver is an essential hub in the body for the metabolism of three major nutrients including glucose, lipids and amino acids. Hepatocellular carcinoma(HCC) usually presents a variety of changes in characteristic metabolism, such as increased aerobic glycolysis, enhanced de novo lipid synthesis, glutamine depletion, and oxidative metabolism imbalance, which can provide energy and bio-macromolecular raw materials for rapidly growing and proliferating tumor cells. The process of tumor metabolic reprogramming is regulated by multiple factors, such as alterations in metabolic enzyme activity, abnormal gene expression, and signaling pathway disturbance. Advances in high-throughout metabolomics technology have provided a powerful platform for discovering the novel biomarkers and metabolic targets of HCC. Therefore, in-depth study of the metabolic characteristics and regulatory mechanisms of HCC is critical for the development of novel antimetabolites.

Evaluation of self-collected vaginal specimens for the detection of high-risk human papillomavirus infection and the prediction of high-grade cervical intraepithelial lesions in a high-burden, low-resource setting

OBJECTIVES

To compare the performance of self-collected vaginal (V) specimens with clinician-collected cervical (C) specimens for detection of high-risk human papillomavirus (hrHPV) and cervical disease using the Cepheid Xpert HPV, Roche Cobas 4800 HPV and Hologic Aptima HPV assays.

METHODS

Women aged 30-59 years (n = 1005) were recruited at two clinics in Papua New Guinea, and they provided specimens for testing at point-of-care using the Xpert HPV Test, and for subsequent testing using the Cobas HPV (n = 981) and Aptima HPV (n = 983) assays. Liquid-based cytology was performed on C specimens to predict underlying high-grade squamous intraepithelial lesions (HSIL). V specimen results of each assay were evaluated against a constructed reference standard and for detection of HSIL or worse.

RESULTS

There was substantial (κ >0.6) agreement in hrHPV detection between V and C specimens across all three assays. The sensitivity, specificity, and positive and negative predictive values of Xpert HPV using self-collected V specimens for the detection of HPV type 16 according to the constructed reference standard were 92.1%, 93.1%, 63.6% and 98.9%, respectively; compared with 90.4%, 94.3%, 67.8% and 98.7% for Cobas 4800 HPV; and 63.2%, 97.2%, 75.0% and 95.3% for Aptima HPV. Similar results were observed for all hrHPV types (combined) and for HPV types 18/45, on all three assays. The detection of any hrHPV using self-collected specimens had high sensitivity (86%-92%), specificity (87%-94%) and negative predictive value (>98%) on all assays for HSIL positivity.

CONCLUSIONS

Xpert HPV, using self-collected vaginal specimens, has sufficient accuracy for use in point-of-care 'test-and-treat' cervical screening strategies in high-burden, low-resource settings.

Antitumor activity of chitosan from mayfly with comparison to commercially available low, medium and high molecular weight chitosans

Insects' cuticles have a potential to be evaluated as a chitin source. Especially adults of aquatic insects like mayflies (order Ephemeroptera) swarm in enormous numbers in artificially lit areas while mating in spring and then die by leaving huge amounts of dead insects' bodies. Here in this study, mayfly corpses were harvested and used for production of low MW chitosan. Dried mayfly bodies had 10.21% chitin content; mayfly chitin was converted into chitosan with efficiency rate of 78.43% (deacetylation degree, 84.3%; MW, 3.69 kDa). Cytotoxicity and anti-proliferative activity of mayfly and commercially available shrimp chitosans (low, medium, and high MW) were determined on L929 fibroblast and three different cancer types including HeLa, A549, and WiDr. Apoptosis and necrosis stimulating potential of mayfly and commercial chitosans were also evaluated on A549 and WiDr cells using acridine orange and propidium iodide dual staining to observe morphological changes in nuclei and thus to reveal the predominant cell death mechanism. The effects of chitosans have varied depending on cell types, concentration, and chitosan derivatives. Mayfly and low MW chitosans had a cytotoxic effect at a concentration of 500 μg mL^-1 on non-cancer cells. At concentrations below this value (250 μg mL^-1), mayfly and commercial chitosans except high MW one exhibited strong inhibitory activity on cancer cells especially A549 and WiDr cells. Mayfly chitosan induced early and late apoptosis in A549 cells, but late apoptosis and necrosis in WiDr cells. This study suggests that dead bodies of mayflies can be used for production of low MW chitosan with anti-proliferative activity.

Abstract P1-08-12: p53 status and 17q21.3 amplicon formation in HER2-positive breast cancer

Breast cancers that overexpress HER2/neu are associated with poor clinical outcome. Treatment of HER2-positive breast cancers with trastuzumab, a monoclonal antibody that antagonizes HER2 receptor signaling, increases patient overall and disease-free survival. While targeted therapy is reasonably effective, resistance to trastuzumab remains a problem, particularly in the case of metastatic disease. Tumor suppressor p53 is the most commonly mutated gene in human cancer and mutations that lead to the stabilization and accumulation of p53 in HER2-positive breast cancers are associated with worse clinical outcome. Another feature of HER2-enriched breast cancers are amplifications of the HER2 locus on chromosome 17q21.3.

Table 1 Wildtype p53Mutated p53No amplification12.8%63.9%17q21.3 amplification13.1%8.7%Table 1: Among 58 cases, Her2-positive tumors with mutated p53 (n=37, 63.9%) occurred at a 4.9-fold higher frequency than amplification of the 17q21.3 gene set (n=8, 13.1%), with significant mutual exclusivity (p=0.005), The patient genomic data set was obtained from the Breast Invasive Carcinoma Study conducted by the TCGA Network (Nature, 2012) and visualized using cBioPortal (MSKCC), Copy alterations of genes were assessed using GISTIC2.0 (Broad Institute) via cBioPortal.

We studied the genomic profiles of 58 HER2-positive breast tumor samples using cBioPortal to determine p53 mutation status. 74.1% of samples expressed mutant p53 and a large fraction of mutations occurred in the key DNA binding domain. We assessed the amplification status of 24 genes within the chromosome 17q21.3 locus as an indicator of amplicon formation, and found that 21.8% of breast tumors demonstrated copy number amplification (Table 2). Mutant p53 tumors with no amplicon formation occurred 5 times more frequently than tumors with only 17q21.3 amplicon formation. These alterations tended to occur exclusive of one another (p=0.005, Table 1). Separately, using gene expression data from Kaplan-Meier Plotter, we observed that alterations in gene expression within the 17q21.3 amplicon can have differential effects on the survival of HER2-positive breast cancer patients (Table 2).

Table 217q21.3 Gene SetHazard RatioP-valueCOL1A11.760.01MBTD10.530.01SPATA200.650.04UBE2Z0.680.07EME10.650.08Table 2: List of relevant genes within the chromosome 17q21.3 amplicon. Genes in this amplicon can influence both beneficial and hazardous survival outcomes in HER2-positive breast cancer patients (n=208). Hazard ratios (HR) were determined from gene expression data available through Kaplan-Meier Plotter (Gyorffy, 2010).

Our data shows that HER2-positive breast cancers can be divided into p53 mutant and non-mutant subsets with p53 mutations relatively exclusive to 17q21.3 gene amplification. However, p53 mutation status and 17q21.3 copy number have a variety of effects on patient outcome. We are interested in understanding the interaction between these two genetic alterations and whether subdividing HER2-positive breast cancer into these subtypes will improve our ability to provide effective therapy to patients.

Citation Format: Tan G, Seeliger M, Cohen J. p53 status and 17q21.3 amplicon formation in HER2-positive breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-08-12.

Clinical motivation and the surgical safety checklist

Background

Although the surgical safety checklist (SSC) has been adopted worldwide, its efficacy can be diminished by poor clinical motivation. Systematic methods for improving implementation are lacking.

Methods

A multicentre prospective study was conducted in 2015 in four academic/teaching hospitals to investigate changes during revision of the SSC for content, staffing and workflow. All modifications were based on feedback from medical staff. Questionnaires were used to monitor dynamic changes in surgeons', nurses' and anaesthetists' perceptions.

Results

Complete information was obtained from 30 654 operations in which the newly developed SSC system was used. Implementation quality was evaluated in 1852 operations before, and 1822 after the changes. The revised SSC content was simplified from 34 to 22 items. Anaesthetists achieved widespread recommendation as SSC coordinators. Completion rates of all stages reached over 80·0 per cent at all sites (compared with 10·2–59·5 per cent at the sign-out stage in the baseline survey). There was a significant change in doctors who participated (for example, surgeon: from 24·6 to 64·5 per cent at one site). The rates of hasty (15·1–33·7 per cent) or casual (0·4–4·4 per cent) checking decreased to less than 6·0 per cent overall. Perceptions about the SSC were studied from 2211 forms. They improved, with a converging trend among the three different professions, to a uniform 80·0 per cent agreeing on the need for its regular use.

Conclusion

Medical staff members are both the users and owners of the SSC. High-quality SSC implementation can be achieved by clinically motivated adaptation.

A full-body transcriptome and proteome resource for the European common carp

Background

The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.

Results

Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.

Conclusions

The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.

Atomic step-and-terrace surface of polyimide sheet for advanced polymer substrate engineering

Typical thermostable and flexible polyimide polymers exhibit many excellent properties such as strong mechanical and chemical resistance. However, in contrast to single-crystal substrates like silicon or sapphire, polymers mostly display disordered and rough surfaces, which may result in instability and degradation of the interfaces between thin films and polymer substrates. As a step toward the development of next-generation polymer substrates, we here report single-atom-layer imprinting onto the polyimide sheets, resulting in an ultrasmooth 0.3 nm high atomic step-and-terrace surface on the polyimides. The ultrasmooth polymer substrates are expected to be applied to the fabrication of nanostructures such as superlattices, nanowires, or quantum dots in nanoscale-controlled electronic devices. We fabricate smooth and atomically stepped indium tin oxide transparent conducting oxide thin films on the imprinted polyimide sheets for future use in organic-based optoelectronic devices processed with nanoscale precision. Furthermore, toward 2D polymer substrate nanoengineering, we demonstrate nanoscale letter writing on the atomic step-and-terrace polyimide surface via atomic force microscopy probe scratching.

The utility of 18F-FDG PET/CT in solitary fibrous tumors of the pleura

OBJECTIVE

To demonstrate the utility of (18)F-FDG PET/CT in the differentiation of benign and malignant solitary fibrous tumors of the pleura (SFTP).

MATERIALS AND METHODS

A retrospective review was performed on the (18)F-FDG PET/CT data from 17 patients with histopathologically diagnosed benign or malignant SFTP. The size, side of SFTP, presence of necrosis, calcification, pleural effusion, hilar lymphadenopathy (LAP), density on CT images (Hounsfield unit-HU), and (18)F-FDG uptake (SUVmax) were recorded and compared in order to detect malignant SFTP. Statistical significance was set as p<0.05.

RESULTS

The difference in size, presence of necrosis, and hilar LAP on CT images were statistically significant (p=0.004, p<0.001, p=0.015, respectively) in a comparison of benign and malignant SFTPs. The mean HU of benign SFTP was 46.16±5.52HU, and for malignant SFTP it was 35.03±4.61HU (p=0.003). The mean SUVmax was 3.02±1.02 for benign SFTP and 4.89±2.12 for malignant SFTP (p=0.021). A cut-off value of ≥7cm for size, ≤39.81HU for density, and ≥3.47 for SUVmax was obtained by ROC analysis for detecting malignant SFTP.

CONCLUSIONS

(18)F-FDG PET/CT may have a limited role in diagnosing malignant SFTP in suspected patients.

A randomized controlled trial of hypnosis compared with biofeedback for adults with chronic low back pain

BACKGROUND

Chronic low back pain (CLBP) is common and results in significant costs to individuals, families and society. Although some research supports the efficacy of hypnosis for CLBP, we know little about the minimum dose needed to produce meaningful benefits, the roles of home practice and hypnotizability on outcome, or the maintenance of treatment benefits beyond 3 months.

METHODS

One hundred veterans with CLBP participated in a randomized, four-group design study. The groups were (1) an eight-session self-hypnosis training intervention without audio recordings for home practice; (2) an eight-session self-hypnosis training intervention with recordings; (3) a two-session self-hypnosis training intervention with recordings and brief weekly reminder telephone calls; and (4) an eight-session active (biofeedback) control intervention.

RESULTS

Participants in all four groups reported significant pre- to post-treatment improvements in pain intensity, pain interference and sleep quality. The hypnosis groups combined reported significantly more pain intensity reduction than the control group. There was no significant difference among the three hypnosis conditions. Over half of the participants who received hypnosis reported clinically meaningful (≥ 30%) reductions in pain intensity, and they maintained these benefits for at least 6 months after treatment. Neither hypnotizability nor amount of home practice was associated significantly with treatment outcome.

CONCLUSIONS

The findings indicate that two sessions of self-hypnosis training with audio recordings for home practice may be as effective as eight sessions of hypnosis treatment. If replicated in other patient samples, the findings have important implications for the application of hypnosis treatment for chronic pain management.