AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data

(1) Background: A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome. Post-transcriptional alternative splicing contributes to the complexity of the proteome and is critical in understanding gene expression. mRNA-sequencing (RNA-seq) has been widely used to study the transcriptome and provides opportunity to detect alternative splicing events among different biological conditions. Despite the popularity of studying transcriptome variants with RNA-seq, few efficient and user-friendly bioinformatics tools have been developed for the genome-wide detection and visualization of alternative splicing events. (2) Results: We propose AS-Quant, (Alternative Splicing Quantitation), a robust program to identify alternative splicing events from RNA-seq data. We then extended AS-Quant to visualize the splicing events with short-read coverage plots along with complete gene annotation. The tool works in three major steps: (i) calculate the read coverage of the potential spliced exons and the corresponding gene; (ii) categorize the events into five different categories according to the annotation, and assess the significance of the events between two biological conditions; (iii) generate the short reads coverage plot for user specified splicing events. Our extensive experiments on simulated and real datasets demonstrate that AS-Quant outperforms the other three widely used baselines, SUPPA2, rMATS, and diffSplice for detecting alternative splicing events. Moreover, the significant alternative splicing events identified by AS-Quant between two biological contexts were validated by RT-PCR experiment. (3) Availability: AS-Quant is implemented in Python 3.0. Source code and a comprehensive user's manual are freely available online.

Analysis of local invasion and regional spread in malignant sublingual gland tumour: Implications for surgical planning

Malignant tumours arising from the sublingual glands are very rare, and the extent and frequency of local invasion or regional spread in malignant sublingual gland tumour (MSLT) has not been fully studied due to the disease rarity. To provide comprehensive features of local and regional spread of MSLT, we reviewed 20 surgical cases for detailed pathological analyses among 26 cases diagnosed as having primary MSLT. Adenoid cystic carcinoma (ACC) was the most common pathological subtype, followed by mucoepidermoid carcinoma. Disease-free and overall survivals at 5 years were 76.1 % and 77.7 %, respectively. High-grade malignant tumours and grade 2-3 ACC accounted for 41.7 % and 85.7 %. Clinical and pathological extraparenchymal extensions were found in 34.6 % and 80.0 %, respectively. Tumour invasion to the lingual nerve and submandibular gland/ductal system were also detected in 40.0 % and 28.6 %. The incidences of lingual nerve invasion in ACC and ACC ≥4 cm were 30.8 % and 42.9 %. Regional nodal involvement occurred in seven of 26 cases, and all metastatic lymph nodes were found in neck levels Ib and IIa. In summary, a significant portion of MSLT cases consisted of high-grade tumours and grade 2-3 ACC; therefore local invasion into adjacent structures should be cautiously evaluated in cases of MSLT.

Abstract SP112: Spatial variance signatures/Intra-tumor zonation in TNBC

It is increasingly clear that triple negative breast cancer (TNBC) is a heterogeneous disease with variable clinical presentation, histological features and response to therapy. While these differences have been partially explained by inter- and intra-tumoral heterogeneity, spatial heterogeneity represented by the tumor architecture plays a critical role in clonal evolution and displays a landscape for different compartment-specific processes and cell-to-cell specific interactions. To better understand the impact of spatial heterogeneity on gene-expression-defined cell populations, we have coupled single-cell RNA sequencing with multiplex immunofluorescence (IF). Multiplex immunofluorescence using specific markers for each cell cluster, integrated with computational image analyses and neighborhood maps, has revealed spatial zonation of single cell subpopulations. Zonation of single cell populations was coupled to hypoxia and overlayed distinct metabolic tumor zones and defined areas of differential stress and cell plasticity that give rise to tumor cells with enhanced fitness and aggressivity.

Citation Format: M Park, C Martínez Ramirez, Y Yang, A Blanchet-Cohen, H Kuasne, A Fortier, J Ragoussis, P Savage, A Omeroglou, S Meterissian, S Costantino, C Kleinman. Spatial variance signatures/Intra-tumor zonation in TNBC [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP112.

Biodegradable-polymer versus durable-polymer drug eluting stents for coronary artery disease: systematic review and a meta-analysis

Background

Biodegradable polymer drug-eluting stents (BP-DES) has been developed to overcome the potential drawbacks of the first-generation durable polymer drug-eluting stents (DP-DES). However, it is still under debate whether BP-DES is associated with superior efficacy and safety over DP-DES.

Purpose

We sought to compare the effects of BP-DES and DP-DES in patients with coronary artery disease.

Methods

We performed systematic review and a meta-analysis of randomized controlled trials comparing BP-DES and DP-DES on clinical outcomes in patients with coronary artery disease using CE-mark approved drug-eluting stents (DES) with at least 1-year follow-up. We included 32 studies involving 39,686 patients (BP-DES: 21,439 patients, and DP-DES: 18,247 patients). Primary outcome measure was target vessel failure (TVF; equivalent to the composite of cardiac death, target-vessel myocardial infarction, or ischemia-driven target vessel revascularization). We performed subgroup analysis according to the DP-DES generations (newer-generation DP-DES: 15,179patients, and first-generation DP-DES: 3,068 patients), and the effects of newer-generation DP-DES was compared with the BP-DES according to the BP-DES strut thickness (Ultra-thin strut [<80μm]: 7,572 patients, Thin-strut [80–100μm]: 5,465 patients, and Thick-strut [≥80μm]: 5,876 patients).

Results

The odds for TVF was not significantly different between the BP-DES group and the DP-DES group in the entire study population (odds ratio [OR] 0.96, 95% confidence interval [CI] [0.90–1.02], P=0.20). The odds for TVF was significantly low in the BP-DES group relative to the first-generation DP-DES group, however the odds were comparable between the BP-DES group and the newer-generation DP-DES group (BP-DES versus first-generation DP-DES: OR 0.82, 95% CI [0.73–0.92], P<0.001, and BP-DES versus newer-generation DP-DES: OR 1.00, 95% CI [0.93–1.08], P=0.99). We also found no significant differences between the BP-DES and newer-generation DP-DES, in all subgroups stratified by the BP-DES strut thickness (Ultra-thin strut BP-DES versus newer-generation DP-DES: OR 0.88, 95% CI [0.76–1.02], P=0.10, Thin-strut BP-DES versus newer-generation DP-DES: OR 1.01, 95% CI [0.90–1.13], P=0.89, and Thick strut BP-DES versus newer-generation DP-DES: OR 1.11, 95% CI [0.99–1.25], P=0.08).

Conclusions

In this meta-analysis of randomized controlled trials evaluating clinical outcomes, there was no significant differences between BP-DES and DP-DES. We found beneficial effects of BP-DES relative to the first-generation DP-DES, however, there was no statistical differences between BP-DES and newer-generation DP-DES, irrespective of the BP-DES strut thickness.

Pooled odds ratios for clinical outcomes

Funding Acknowledgement

Type of funding source: None

0558 Sleep Disordered Breathing and Right Ventricular Electrocardiographic and Functional Characteristics in Group 1 Pulmonary Arterial Hypertension

Introduction

Right ventricular (RV) electrophysiologic and functional alterations related to sleep disordered breathing (SDB) in pulmonary arterial hypertension (PAH) are not well understood. We hypothesize an association between SDB and RV electrophysiological/functional measures in World Symposium of Pulmonary Hypertension (WSPH) Group 1 PAH.

Methods

The NHLBI multicenter PVDOMICS study (NCT02980887) enrolls patients with PAH undergoing a battery of assessments including home sleep apnea testing(NOX-T3, Carefusion®) or with historical sleep study data. Logistic(OR,95%CI) and linear(beta coefficients,95%CI) regression models adjusted for age, sex, race, body mass index (BMI, kg/m2), PAH medications, supplemental oxygen(O2), positive airway pressure(PAP) were used to assess associations of SDB(apnea hypopnea index,(AHI), ≥3% desaturations(hypopnea), percentage recording time with SaO2<90% (TRT<90%) with electrocardiographic measures: RV hypertrophy(RVH), right bundle branch block(RBBB), and right axis deviation(RAD), echocardiographically-derived RV systolic pressure(RVSP) and RV ejection fraction(RVEF) from cardiac MRI. Analyses were performed based on an overall significance level of 0.05, using SAS software (version 9.4, Cary, NC).

Results

The analysis consisted of 182 PAH participants with age: 52.5±13.9 years, 71.4% female, 88.9% Caucasian, BMI:30.3±7.8 kg/m2, RVEF: 37.3±11.6, and RVSP: 67.0±23.4. None of the electrocardiographic measures were associated with AHI and only RVH was significantly associated with TRT<90% (1.25:1.09,1.43),p=0.001. Although AHI was not associated with RVSP, a 10% increase in TRT<90% was associated with a 2.60mmHg increase in RVSP (2.60:1.44,3.76),p<0.001. Each 10-unit increase in AHI was associated with a 2.72% reduction of RVEF (-2.72:-4.89,-0.56),p=0.014, and each 10-unit increase in TRT<90% was associated with a 0.72% reduction of RVEF (-0.72:-1.38,-0.06),p=0.033.

Conclusion

We identify nocturnal hypoxia as a predictor of RV electrophysiological and functional alterations even after consideration of confounding factors. SDB as determined by AHI was also more so associated with reduced RVEF than hypoxia. Future mechanistic studies should focus on further elucidation of SDB and nocturnal hypoxia on pathogenesis of RV dysfunction in PAH.

Support

U01HL125218/U01HL125205/U01HL125212/U01HL125208/U01HL125175/U01HL125215, U01HL125177/Pulmonary Hypertension Association

1151 Is Timing Of Light Exposure Different In Women With Chronic Migraine?

Introduction

Light avoidance is a common coping behavior of individuals with migraine headaches. It is not known whether timing of light exposure is different in individuals with chronic migraine (CM) compared to those without migraine and how this may relate to headache frequency and severity. We tested this by examining timing of the brightest and darkest light and headaches in women with chronic migraines and healthy controls.

Methods

Sixteen women with CM (mean age = 33.07) and 18 female healthy controls (HC; mean age = 32.22) completed daily ratings of headache severity (0-10, severity > 2 classified as headache) concurrent with light exposure measured by wrist actigraphy for approximately one month (M=28.00 days, range=21-36). Start time of each day’s 10-hour periods of maximum light (M10) and 5-hour periods of lowest light (L5) were calculated and averaged for each participant. T-tests and Cohen’s d effect sizes were used to compare groups. Pearson correlation coefficients were calculated to examine associations between M10/L5 timing and headache frequency and severity.

Results

M10 was earlier in the CM group compared to the HC group (07:42±00:47 vs. 08:50±00:58, t(32)=3.69, p=0.0008, d=1.08). The CM group exhibited non-significant trend towards earlier L5 compared to the HC group (12:26±00:48 vs. 01:07±01:03, t(32)=1.89, p=0.0723, d=0.62). Among individuals with CM, later M10 timing was associated with more severe average daily headache (r=0.60, p=0.0136) and more frequent headaches (r=0.55, p=0.0257). Later L5 timing was significantly associated with more severe average daily headache (r=0.66, p=0.0052) and showed a non-significant trend toward association with more frequent headaches (r=0.47, p=0.0686).

Conclusion

Timing of the greatest light exposure period was earlier in CM compared to HC. Within the CM group, those who had earlier light and dark periods reported lower headache severity and fewer days with headaches. These findings suggest the possibility of a role for the circadian system in chronic migraine.

Support

This study was supported by grant R21NS081088 from the National Institutes of Health.

Modification of the RANKL-RANK-binding site for the immunotherapeutic treatment of osteoporosis

Here, we proposed the use of mutated RANKL as an immunogen for active immunization and to induce anti-cytokine antibodies for osteoporosis treatment.

INTRODUCTION

Osteoclasts are responsible for bone resorption in bone-related disorders. Anti-cytokine therapeutic antibodies such as denosumab are effective for the treatment of osteoporosis. However, problems with antibody manufacturing and the immunogenicity caused by multiple antibody doses have led to the use of auto-cytokines as immunogens to induce anti-cytokine antibodies.

METHODS

RANKL was point-mutated based on the crystal structure of the complex of RANKL and its receptor RANK.

RESULTS

As a proof of concept, immunization with RANKL produced high levels of specific antibodies and blocked osteoclast development in vitro and inhibited osteoporosis in RANKL-treated or ovariectomized mouse models.

CONCLUSIONS

The results demonstrate the successful use of mutated RANKL as an immunogen for the induction of anti-RANKL immune response. This strategy is useful in general anti-cytokine immunotherapy to avoid toxic side effects of osteoporosis treatment.

Factors influencing the release of potentially toxic elements (PTEs) during thermal processing of electronic waste

The release of potentially toxic elements as airborne fine particulates is a significant environmental risk associated with recycling e-waste. Some of these may redeposit near emission sites or be transported over long distances causing wide-spread pollution. With an aim to identify key factors affecting particulate emissions, we report novel investigations on the adsorptive capture of particulate matter (PM) released during low temperature pyrolysis (600 °C; 15 min) of waste printed circuit boards (PCBs). A significant proportion of the released particulates (5.3 to 37%) were captured by adsorbents located downstream and in close proximity to the emitting source. Data was collected for four different PCBs and three adsorbents: alumina, silica-gel and activated carbon. With sizes ranging from nanoparticles to over 10 µm, adsorbed particulates were present as fines, spheres, oblongs, clusters and larger particles with no specific shape. Of the 24 elements identified initially in waste PCBs, only 14 were detected in released particulates: major PTEs- Zn, Sn, Pb and Cu (up to 400 ppm); minor PTEs- Ni, Mn, Cd, Cr and Ba (up to 10 ppm); trace PTEs- Co, In, Bi, Be and Sb (up to 1 ppm). Key factors influencing the release of PTEs during thermal processing were identified as basic elemental characteristics, densities, melting points, vapor pressures, initial concentrations, local bonding and mechanical strength. These results show that the presence of low melting point/high vapour pressure elements (Zn, Pb, Sn) should be minimised for a significant reduction in PTE emissions during e-waste processing.

P361 Assessment of accuracy and reproducibility of coronary flow reserve measured by SPECT in patients with known or suspected coronary artery disease

Funding Acknowledgements

Spectrum Dynamics

Background

Traditional relative assessment of regional myocardial perfusion by single photon emission computed tomography (SPECT) has limited ability to identify multivessel coronary artery disease, as well as diffuse atherosclerosis and coronary microvascular dysfunction. Current gamma cameras with cadmium-zinc-telluride (CZT) detectors have higher temporal resolution and sensitivity and allow the acquisition of multi-frame images and quantification of absolute myocardial blood flow (MBF) and coronary flow reserve (CFR

Purpose

The aim of this study was to assess the accuracy and reproducibility of quantitative measurements of MBF and CFR obtained with a CZT SPECT system compared to PET in a cohort of patients with known or suspected coronary artery disease.

Methods

Accuracy was assessed in 22 patients who underwent dynamic rest/stress 99mTc-sestamibi-SPECT and 13N-ammonia PET myocardial perfusion imaging within two weeks of each other. Fourteen patients comprised the reproducibility cohort and underwent two dynamic 99mTc-sestamibi SPECT scans within two weeks. A rest/pharmacological stress single-day SPECT protocol was performed, using a 1:3 dose ratio. SPECT image reconstruction was performed using a spline-fitting method and SPECT MBF was quantified using a net retention kinetic model in commercially available software. Rest MBF and CFR were adjusted for heart-rate pressure product.

Results

Global MBF at rest and stress showed a good correlation between SPECT and PET (r = 0.814, p < 0.001). For global rest MBF the mean difference between the two techniques was -0.25 ± 0.24 ml/min/g, while for stress MBF mean difference was -0.21 ± 0.40 ml/min/g. We also observed a significant correlation between global SPECT and PET CFR measurements (r = 0.745, p < 0.001), with no significant difference between the two (mean difference: 0.16 ± 0.50). Regarding the reproducibility cohort, the correlation between global CFR measured by two SPECT scans was also significant (r = 0.616, p = 0.019), with a mean difference of 0.14 ±0.51. The mean difference between scans for rest MBF (-0.05 ± 0.19) and stress MBF (0.01 ± 0.42) were also not significant.

Conclusion

MBF and CFR quantification is feasible using a CZT gamma camera and provides accurate and reproducible results that correlate with 13N-ammonia PET. This may be of special relevance in sites where PET is not available, enabling MBF and CFR quantification with CZT SPECT cameras.

Abstract P361 Figure.

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

U2 auxiliary factor 1 (U2AF1) functions in 3′-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms’ inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3′-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5′-untranslated region (5′-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5′-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.

A survey of health care professionals and oncology patients at the McGill University Health Centre reveals enthusiasm for establishing a postmortem rapid tissue donation program

Background

In the early developmental phase of a postmortem rapid tissue donation (rtd) program for patients with metastatic cancer, we surveyed health care professionals (hcps) and oncology patients at the McGill University Health Centre (muhc) to assess their knowledge and attitudes pertaining to rtd from metastatic cancer patients for research purposes.

Methods

A 23-item survey was developed and distributed to hcps at tumour board meetings, and a related 26-item survey was developed and distributed to oncology patients at the muhc Cedars Cancer Centre.

Results

The survey attracted participation from 73 hcps, including 37 attending physicians, and 102 oncology patients. Despite the fact that 88% of hcps rated their knowledge of rtd as none or limited, 42% indicated that they would feel comfortable discussing rtd with their cancer patients. Of the responding hcps, 67% indicated that their current knowledge of rtd would affect their decision to discuss such a program with patients, which implies the importance of education for hcps to facilitate enrolment of patients into a rtd program. Of responding patients, 78% indicated that they would not be uncomfortable if their doctor discussed rtd with them, and 61% indicated that they would like it if their doctor were to discuss rtd with them. The hcps and patients felt that the best time for patients to be approached about consenting to a rtd program would be at the transition to palliative care when no treatment options remain.

Conclusions

At the muhc, hcps and patients are generally enthusiastic about adopting a rtd program for patients with metastatic cancer. Education of hcps and patients will be an important determinant of the program's success.

A Novel Collateral Imaging Method Derived from Time-Resolved Dynamic Contrast-Enhanced MR Angiography in Acute Ischemic Stroke: A Pilot Study

BACKGROUND AND PURPOSE

Assessment of the collateral status has been emphasized for appropriate treatment decisions in patients with acute ischemic stroke. The purpose of this study was to introduce a multiphase MRA collateral imaging method (collateral map) derived from time-resolved dynamic contrast-enhanced MRA and to verify the value of the multiphase MRA collateral map in acute ischemic stroke by comparing it with the multiphase collateral imaging method (MRP collateral map) derived from dynamic susceptibility contrast-enhanced MR perfusion.

MATERIALS AND METHODS

From a prospectively maintained registry of acute ischemic stroke, MR imaging data of patients with acute ischemic stroke caused by steno-occlusive lesions of the unilateral ICA and/or the M1 segment of the MCA were analyzed. We generated collateral maps using dynamic signals from dynamic contrast-enhanced MRA and DSC-MRP using a Matlab-based in-house program and graded the collateral scores of the multiphase MRA collateral map and the MRP collateral map independently. Interobserver reliabilities and intermethod agreement between both collateral maps for collateral grading were tested.

RESULTS

Seventy-one paired multiphase MRA and MRP collateral maps from 67 patients were analyzed. The interobserver reliabilities for collateral grading using multiphase MRA or MRP collateral maps were excellent (weighted κ = 0.964 and 0.956, respectively). The agreement between both collateral maps was also excellent (weighted κ = 0.884; 95% confidence interval, 0.819-0.949).

CONCLUSIONS

We demonstrated that the dynamic signals of dynamic contrast-enhanced MRA could be used to generate multiphase collateral images and showed the possibility of the multiphase MRA collateral map as a useful collateral imaging method in acute ischemic stroke.