Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

The analysis of extracellular vesicles (EV) in blood samples is under intense investigation and holds the potential to deliver clinically meaningful biomarkers for health and disease. Technical variation must be minimized to confidently assess EV-associated biomarkers, but the impact of pre-analytics on EV characteristics in blood samples remains minimally explored. We present the results from the first large-scale EV Blood Benchmarking (EVBB) study in which we systematically compared 11 blood collection tubes (BCT; six preservation and five non-preservation) and three blood processing intervals (BPI; 1, 8 and 72 h) on defined performance metrics (n = 9). The EVBB study identifies a significant impact of multiple BCT and BPI on a diverse set of metrics reflecting blood sample quality, ex-vivo generation of blood-cell derived EV, EV recovery and EV-associated molecular signatures. The results assist the informed selection of the optimal BCT and BPI for EV analysis. The proposed metrics serve as a framework to guide future research on pre-analytics and further support methodological standardization of EV studies.

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

BACKGROUND

Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.

RESULTS

To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×.

CONCLUSIONS

Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.

Abstract B49: Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study—important considerations for liquid biopsies

Cancer biomarker studies require procedures that provide accurate and precise test results with high analytical sensitivity. Consequently, the growing use of extracellular RNA from human biofluids as clinically relevant biomarker requires the implementation of benchmarked methods for sample collection, processing, and profiling. While several small-scale studies have pointed at the impact of individual preanalytical factors, no comprehensive study has addressed the many preanalytical variables affecting downstream sequencing of blood-derived exRNAs. In the Extracellular RNA Quality Control study, we have systematically evaluated the type of blood collection tube (n=10, including 5 so-called preservation tubes), the time between blood draw and plasma preparation (n=3), different plasma types (n=3, i.e., platelet-free, -poor, and -rich plasma), and RNA purification methods using the supplier-specified minimum and maximum plasma input volumes (n=15). The impact of these preanalytical factors is assessed by deep transcriptome profiling of all small and messenger RNAs from healthy donors’ plasma, using TruSeq Small RNA sequencing and TruSeq RNA Exome sequencing, respectively. All experiments are conducted in triplicate (for a total of 270 transcriptomes) using 191 synthetic RNA spike-in molecules as processing controls over a relevant dynamic range. When comparing blood collection tubes, serum mRNA seems very similar to EDTA plasma mRNA, but serum-derived small RNAs are markedly different in biotype composition compared to their plasma counterparts. Furthermore, several plasma tubes with preservation reagents do not stabilize RNA very well, as is reflected by increasing RNA concentrations and number of detected genes over time. Also, their reproducibility is generally compromised. In addition, we demonstrate large differences in RNA purification kit performance in terms of reproducibility, sensitivity, and observed transcriptome complexity. Among others, we note a 50-fold difference in mRNA yield and a 5-fold difference in the number of detected mRNAs. We summarized the results in 12 performance parameters that enable an informed selection of the most optimal sample processing workflow. In conclusion, using a systematic approach, we put forward robust quality control metrics for exRNA quantification methods with validated SOPs for sample collection, processing, and profiling. Our results are crucially important for all future RNA-based liquid biopsy-guided precision oncology applications. Authors in random order; abstract submitted on behalf of the exRNAQC Consortium.

Citation Format: Anneleen Decock, Jasper Anckaert, Celine Everaert, Justine Nuytens, Scott Kuersten, An Hendrix, Jo Vandesompele, Pieter Mestdagh, Bert Dhondt, Ruben Van Paemel, Kimberly Verniers, Gary Schroth, Carolina Fierro, Nurten Yigit, Kathleen Schoofs, Annelien Morlion, Jill Deleu, Eva Hulstaert, Francisco Avila Cobos, Nele Nijs, Eveline Vanden Eynde, Hetty Hilde Helsmoortel, Olivier De Wever, Annouck Philippron. Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study—important considerations for liquid biopsies [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B49.

Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

Background

Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing.

Results

This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage.

Conclusions

Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users.

Impact of Anesthesia on the Outcome of Acute Ischemic Stroke after Endovascular Treatment with the Solitaire Stent Retriever

BACKGROUND AND PURPOSE

General anesthesia during endovascular treatment of acute ischemic stroke may have an adverse effect on outcome compared with conscious sedation. The aim of this study was to examine the impact of the type of anesthesia on the outcome of patients with acute ischemic stroke treated with the Solitaire stent retriever, accounting for confounding factors.

MATERIALS AND METHODS

Four-hundred one patients with consecutive acute anterior circulation stroke treated with a Solitaire stent retriever were included in this prospective analysis. Outcome was assessed after 3 months by the modified Rankin Scale.

RESULTS

One-hundred thirty-five patients (31%) underwent endovascular treatment with conscious sedation, and 266 patients (69%), with general anesthesia. Patients under general anesthesia had higher NIHSS scores on admission (17 versus 13, P < .001) and more internal carotid artery occlusions (44.6% versus 14.8%, P < .001) than patients under conscious sedation. Other baseline characteristics such as time from symptom onset to the start of endovascular treatment did not differ. Favorable outcome (mRS 0-2) was more frequent with conscious sedation (47.4% versus 32%; OR, 0.773; 95% CI, 0.646-0.925; P = .002) in univariable but not multivariable logistic regression analysis (P = .629). Mortality did not differ (P = .077). Independent predictors of outcome were age (OR, 0.95; 95% CI, 0.933-0.969; P < .001), NIHSS score (OR, 0.894; 95% CI, 0.855-0.933; P < .001), time from symptom onset to the start of endovascular treatment (OR, 0.998; 95% CI, 0.996-0.999; P = .011), diabetes mellitus (OR, 0.544; 95% CI, 0.305-0.927; P = .04), and symptomatic intracerebral hemorrhage (OR, 0.109; 95% CI, 0.028-0.428; P = .002).

CONCLUSIONS

In this single-center study, the anesthetic management during stent retriever thrombectomy with general anesthesia or conscious sedation had no impact on the outcome of patients with large-vessel occlusion in the anterior circulation.

Feasibility and Safety of Repeat Instant Endovascular Interventions in Patients with Refractory Cerebral Vasospasms

BACKGROUND AND PURPOSE

For patients with cerebral vasospasm refractory to medical and hemodynamic therapies, endovascular therapies often remain the last resort. Data from studies in large cohorts on the efficacy and safety of multiple immediate endovascular interventions are sparse. Our aim was to assess the feasibility and safety of multiple repeat instant endovascular interventions in patients with cerebral vasospasm refractory to medical, hemodynamic, and initial endovascular interventions.

MATERIALS AND METHODS

This was a single-center retrospective study of prospectively collected data on patients with cerebral vasospasm refractory to therapies requiring ≥3 endovascular interventions during the course of treatment following aneurysmal subarachnoid hemorrhage. The primary end point was functional outcome at last follow-up (mRS ≤2). The secondary end point was angiographic response to endovascular therapies and the appearance of cerebral infarctions.

RESULTS

During a 4-year period, 365 patients with aneurysmal subarachnoid hemorrhage were treated at our institution. Thirty-one (8.5%) met the inclusion criteria. In 52 (14%) patients, ≤2 endovascular interventions were performed as rescue therapy for refractory cerebral vasospasm. At last follow-up, a good outcome was noted in 18 (58%) patients with ≥3 interventions compared with 31 (61%) of those with ≤2 interventions (P = .82). The initial Hunt and Hess score of ≤2 was a significant independent predictor of good outcome (OR, 4.7; 95% CI, 1.2-18.5; P = .03), whereas infarcts in eloquent brain areas were significantly associated with a poor outcome (mRS 3-6; OR, 13.5; 95% CI, 2.3-81.2; P = .004).

CONCLUSIONS

Repeat instant endovascular intervention is an aggressive but feasible last resort treatment strategy with a favorable outcome in two-thirds of patients with refractory cerebral vasospasm and in whom endovascular treatment has already been initiated.

Magnetic Resonance Imaging in Small Lesions of the Central Nervous System

T1 values and T2 values (CPGM-sequence) of neurinomas and meningiomas were determined, and showed values close to those of white and grey matter or, in regressive cystic neurinomas, near the cerebrospinal fluid (CSF). By this overlapping in relaxation times, as well as by crossover and boundary effects, small tumors may be obscured. The application of gadolinium-DTPA allows easier identification even of small lesions, by the high contrast achieved on the T1 weighted imaging sequences, which also avoids crossover and boundary effects with the adjacent parenchyma and CSF. This is demonstrated in intrameatal acoustic neurinomas, vascular tumors, small and en plaque growing meningiomas, and tumors of the spinal canal.

Reduced evolutionary rate in reemerged Ebola virus transmission chains

On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.

Exome-level comparison of primary well-differentiated neuroendocrine tumors and their cell lines

Neuroendocrine cancer cell lines are used to investigate therapeutic targets in neuroendocrine tumors (NET) and have been instrumental in the design of clinical trials targeting the PI3K/AKT/mTOR pathways, VEGF inhibitors, and somatostatin analogues. It remains unknown, however, whether the genomic makeup of NET cell lines reflect that of primary NET since comprehensive unbiased genome sequencing has not been performed on the cell lines. Four bronchopulmonary NET (BP-NET)-NCI-H720, NCI-H727, NCI-H835, and UMC11-and two pancreatic neuroendocrine tumors (panNET)-BON-1 and QGP1-were cultured. DNA was isolated, and exome sequencing was done. GATK and EXCAVATOR were used for bioinformatic analysis. We detected a total of 1,764 nonsynonymous single nucleotide variants at a rate of 8 per Mb in BP-NET and 4.3 per Mb in panNET cell lines, including 52 mutated COSMIC cancer genes in these cell lines, such as TP53, BRCA1, RB1, TSC2, NOTCH1, EP300, GNAS, KDR, STK11, and APC but not ATRX, DAXX, nor MEN1. Our data suggest that mutation rate, the pattern of copy number variations, and the mutational spectra in the BP-NET cell lines are more similar to the changes observed in small cell lung cancer than those found in primary BP-NET. Likewise, mutation rate and pattern including the absence of mutations in ATRX/DAXX, MEN1, and YY1 in the panNET cell lines BON1 and QGP1 suggest that these cell lines do not have the genetic signatures of a primary panNET. These results suggest that results from experiments with BP-NET and panNET cell lines need to be interpreted with caution.

Whole-Brain Susceptibility-Weighted Thrombus Imaging in Stroke: Fragmented Thrombi Predict Worse Outcome

BACKGROUND AND PURPOSE

The prevalence and clinical importance of primarily fragmented thrombi in patients with acute ischemic stroke remains elusive. Whole-brain SWI was used to detect multiple thrombus fragments, and their clinical significance was analyzed.

MATERIALS AND METHODS

Pretreatment SWI was analyzed for the presence of a single intracranial thrombus or multiple intracranial thrombi. Associations with baseline clinical characteristics, complications, and clinical outcome were studied.

RESULTS

Single intracranial thrombi were detected in 300 (92.6%), and multiple thrombi, in 24 of 324 patients (7.4%). In 23 patients with multiple thrombi, all thrombus fragments were located in the vascular territory distal to the primary occluding thrombus; in 1 patient, thrombi were found both in the anterior and posterior circulation. Only a minority of thrombus fragments were detected on TOF-MRA, first-pass gadolinium-enhanced MRA, or DSA. Patients with multiple intracranial thrombi presented with more severe symptoms (median NIHSS scores, 15 versus 11; P = .014) and larger ischemic areas (median DWI ASPECTS, 5 versus 7; P = .006); good collaterals, rated on DSA, were fewer than those in patients with a single thrombus (21.1% versus 44.2%, P = .051). The presence of multiple thrombi was a predictor of unfavorable outcome at 3 months (P = .040; OR, 0.251; 95% CI, 0.067-0.939).

CONCLUSIONS

Patients with multiple intracranial thrombus fragments constitute a small subgroup of patients with stroke with a worse outcome than patients with single thrombi.

Abstract 3563: New tools for RNA-sequencing of FFPE tumor samples

Next generation RNA sequencing is an ideal platform to leverage archival formalin-fixed paraffin-embedded (FFPE) tissue samples for cancer research, as it offers extensive functional genomic information including transcriptome expression profiling, differential expression analysis and fusion detection. However, both RNA degradation from the formalin fixation process as well as limited sample material, pose major challenges for RNA sequencing of FFPE samples. Here we describe a novel method for generating whole-transcriptome RNA sequencing libraries from moderate to poor quality FFPE samples starting with as low as 20ng total RNA. This approach provides increased transcriptome coverage and robust measurement of gene expression levels compared to currently available FFPE RNA sequencing methods. Furthermore, we demonstrate that we can detect both known and novel gene fusions in clinical tumor samples that are potential drivers of disease. We anticipate this new technology will enable functional genomic studies on numerous FFPE tumor samples that would not previously be possible, providing invaluable information for developing cancer diagnostics and therapeutics.

Citation Format: Lisa Watson, Smita Pathak, Stephen Gross, Irina Khrebtukova, Gary Schroth. New tools for RNA-sequencing of FFPE tumor samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3563. doi:10.1158/1538-7445.AM2014-3563

Dose reduction in standard head CT: first results from a new scanner using iterative reconstruction and a new detector type in comparison with two previous generations of multi-slice CT

Purpose

Computed tomography (CT) accounts for more than half of the total radiation exposure from medical procedures, which makes dose reduction in CT an effective means of reducing radiation exposure. We analysed the dose reduction that can be achieved with a new CT scanner [Somatom Edge (E)] that incorporates new developments in hardware (detector) and software (iterative reconstruction).

Methods

We compared weighted volume CT dose index (CTDI_vol) and dose length product (DLP) values of 25 consecutive patients studied with non-enhanced standard brain CT with the new scanner and with two previous models each, a 64-slice 64-row multi-detector CT (MDCT) scanner with 64 rows (S64) and a 16-slice 16-row MDCT scanner with 16 rows (S16). We analysed signal-to-noise and contrast-to-noise ratios in images from the three scanners and performed a quality rating by three neuroradiologists to analyse whether dose reduction techniques still yield sufficient diagnostic quality.

Results

CTDI_Vol of scanner E was 41.5 and 36.4 % less than the values of scanners S16 and S64, respectively; the DLP values were 40 and 38.3 % less. All differences were statistically significant (p < 0.0001).

Signal-to-noise and contrast-to-noise ratios were best in S64; these differences also reached statistical significance. Image analysis, however, showed “non-inferiority” of scanner E regarding image quality.

Conclusions

The first experience with the new scanner shows that new dose reduction techniques allow for up to 40 % dose reduction while still maintaining image quality at a diagnostically usable level.

A mutation in TGFB3 associated with a syndrome of low muscle mass, growth retardation, distal arthrogryposis and clinical features overlapping with Marfan and Loeys-Dietz syndrome

The transforming growth factor β (TGF-β) family of growth factors are key regulators of mammalian development and their dysregulation is implicated in human disease, notably, heritable vasculopathies including Marfan (MFS, OMIM #154700) and Loeys-Dietz syndromes (LDS, OMIM #609192). We described a syndrome presenting at birth with distal arthrogryposis, hypotonia, bifid uvula, a failure of normal post-natal muscle development but no evidence of vascular disease; some of these features overlap with MFS and LDS. A de novo mutation in TGFB3 was identified by exome sequencing. Several lines of evidence indicate the mutation is hypomorphic suggesting that decreased TGF-β signaling from a loss of TGFB3 activity is likely responsible for the clinical phenotype. This is the first example of a mutation in the coding portion of TGFB3 implicated in a clinical syndrome suggesting TGFB3 is essential for both human palatogenesis and normal muscle growth.

mRNA-Seq of single prostate cancer circulating tumor cells reveals recapitulation of gene expression and pathways found in prostate cancer

Circulating tumor cells (CTC) mediate metastatic spread of many solid tumors and enumeration of CTCs is currently used as a prognostic indicator of survival in metastatic prostate cancer patients. Some evidence suggests that it is possible to derive additional information about tumors from expression analysis of CTCs, but the technical difficulty of isolating and analyzing individual CTCs has limited progress in this area. To assess the ability of a new generation of MagSweeper to isolate intact CTCs for downstream analysis, we performed mRNA-Seq on single CTCs isolated from the blood of patients with metastatic prostate cancer and on single prostate cancer cell line LNCaP cells spiked into the blood of healthy donors. We found that the MagSweeper effectively isolated CTCs with a capture efficiency that matched the CellSearch platform. However, unlike CellSearch, the MagSweeper facilitates isolation of individual live CTCs without contaminating leukocytes. Importantly, mRNA-Seq analysis showed that the MagSweeper isolation process did not have a discernible impact on the transcriptional profile of single LNCaPs isolated from spiked human blood, suggesting that any perturbations caused by the MagSweeper process on the transcriptional signature of isolated cells are modest. Although the RNA from patient CTCs showed signs of significant degradation, consistent with reports of short half-lives and apoptosis amongst CTCs, transcriptional signatures of prostate tissue and of cancer were readily detectable with single CTC mRNA-Seq. These results demonstrate that the MagSweeper provides access to intact CTCs and that these CTCs can potentially supply clinically relevant information.

Classification of mild cognitive impairment and Alzheimer disease using model-based MR and magnetization transfer imaging

BACKGROUND AND PURPOSE

Early stratification of degenerative processes is a prerequisite to warrant therapeutic options in prodromal Alzheimer disease. Our aim was to investigate differences in cerebral macromolecular tissue composition between patients with AD, mild cognitive impairment, and age- and sex-matched healthy controls by using model-based magnetization transfer with a binary spin-bath magnetization transfer model and magnetization transfer ratio at 1.5 T.

MATERIALS AND METHODS

We investigated patients with de novo AD (n=18), MCI (n=18), and CTRLs (n=18). A region-of-interest analysis of the entorhinal cortex, hippocampal head and body, insula, and temporal neocortex was performed with fuzzy clustering to associate every subregion to a cluster representative for each group.

RESULTS

Cluster analysis achieved a concordance of 0.92 (50 of 54 subjects) between a combination of the calculated mMT parameters (kf,kr,T2r,F,T2f) in the entorhinal cortex and the neuropsychological diagnosis. The sensitivity and specificity for the discrimination of AD from MCI reached 1 and 0.94, with a positive predictive value of 0.95 and a negative predictive value of 1. Compared with mMT, the concordance for MTR was 0.83 (45 of 54 subjects) with a lower specificity of 0.5 and positive predictive value of 0.67 to discriminate patients with AD and MCI.

CONCLUSIONS

mMT imaging detects macromolecule-related alterations and allows an improved classification of patients with early AD and MCI compared with MTR.

Relapse and subarachnoid dissemination of a pineal germinoma 14 years after radiation therapy

Intracranial germinomas are rare tumours which are highly curable with radiotherapy. In recent years treatment with chemotherapy has gained importance. Recurrence and dissemination is seen in about 10-20% of cases within the first 2 years after diagnosis; late recurrence and dissemination is very rare. We describe a patient with a recurrent germinoma 14 years after radiotherapy of a pineal tumour. We further report the management with chemotherapy, the late side effects of radiotherapy and the course of the disease with its fatal dissemination. We conclude that the use of radiotherapy, despite being highly effective, is clearly limited by its late side-effects. New regimens with chemotherapy seem promising but proved to be less effective in our case with tumour seeding throughout the subarachnoid space.

Experimental evaluation of immediate recanalization effect and recanalization efficacy of a new thrombus retriever for acute stroke treatment in vivo

BACKGROUND AND PURPOSE

Currently, several new stent retriever devices for acute stroke treatment are under development and early clinical evaluation. Preclinical testing under standardized conditions is an important first step to evaluate the technical performance and potential of these devices. The aim of this study was to evaluate the immediate recanalization effect, recanalization efficacy, thrombus-device interaction, and safety of a new stent retriever intended for thrombectomy in patients with acute stroke.

MATERIAL AND METHODS

The pREset thrombectomy device (4 × 20 mm) was evaluated in 16 vessel occlusions in an established swine model. Radiopaque thrombi (10-mm length) were used for visualization of thrombus-device interaction during application and retrieval. Flow-restoration effect immediately after deployment and after 5-minute embedding time before retrieval, recanalization rate after retrieval, thromboembolic events, and complications were assessed. High-resolution FPCT was performed to illustrate thrombus-device interaction during the embedding time.

RESULTS

Immediate flow restoration was achieved in 75% of occlusions. An increase or stable percentage of recanalizations during embedding time before retrieval was seen in 56.3%; a decrease, in 12.5%; reocclusion of a previously recanalized vessel, in 18.8%; and no recanalization effect at all, in 12.5%. Complete recanalization (TICI 3) after retrieval was achieved in 93.8%; partial recanalization (TICI 2b), in 6.2%. No distal thromboembolic events were observed. High-resolution FPCT illustrated entrapment of the thrombus between the stent struts and compression against the contralateral vessel wall, leading to partial flow restoration. During retrieval, the thrombus was retained in a straight position within the stent struts.

CONCLUSIONS

In this experimental study, the pREset thrombus retriever showed a high recanalization rate in vivo. High-resolution FPCT allows detailed illustration of the thrombus-device interaction during embedding time and is advocated as an add-on tool to the animal model used in this study.

Technical feasibility and application of mechanical thrombectomy with the Solitaire FR Revascularization Device in acute basilar artery occlusion

BACKGROUND AND PURPOSE

Acute BAO is a devastating neurological condition associated with a poor clinical outcome and a high mortality rate. Recanalization has been identified as a major prognostic factor for good outcome in BAO. Mechanical thrombectomy using retrievable stents is an emerging treatment option for acute stroke. First clinical trials using stent retrievers have shown promising high recanalization rates. However, these studies mainly included large artery occlusions in the anterior circulation with only a few or single cases of BAO. Therefore, the purpose of this study was to evaluate technical feasibility, safety, and efficacy of mechanical thrombectomy using retrievable stent in the treatment of acute BAO.

MATERIALS AND METHODS

Fourteen consecutive patients with BAO undergoing endovascular therapy using retrievable stents (Solitaire FR Revascularization Device) were included. Additional multimodal treatment approaches included thromboaspiration, intravenous and/or intra-arterial thrombolysis, and PTA/ permanent stent placement. Recanalization rates after multimodal therapy and stent retrieval were determined. Clinical outcome and mortality were assessed 3 months after treatment.

RESULTS

Median patient age was 64.5 years (range 55-85). Median NIHSS score at presentation was 21 (range 5-36). Overall, successful recanalization (TICI 3 or 2b) was achieved in all patients (TICI 3 in 78.6%, 11/14). In 4 patients (28.6%), insufficient recanalization after stent retrieval was due to an underlying atherosclerotic stenosis. Additional deployment of a permanent intracranial stent was performed in 3 patients (21.4%) and PTA alone in 1 patient (7.1%), resulting in final TICI 3 in 1 patient and TICI 2b in 3 patients. Stent retrieval alone was performed in 4 patients (28.6%). Average number of device passes was 1.3 (range 1-3). Median procedure time to maximal recanalization was 47 minutes (range 10-252). No device-related complications or thromboembolic occlusion of a previously unaffected artery occurred. There was no symptomatic intracranial hemorrhage. At 3 months, good functional outcome (mRS 0-2) was observed in 28.6% (4/14); overall mortality was 35.7% (5/14).

CONCLUSIONS

A multimodal endovascular approach using retrievable stents in BAO has high recanalization rates, with very low complication rates. Underlying atherothrombotic stenotic lesions of the basilar artery may still necessitate additional permanent stent placement to achieve complete recanalization.

Passing the thrombus in endovascular treatment of acute ischemic stroke: do we penetrate the thrombus?

Mechanical thrombectomy is increasingly applied during the treatment of acute stroke. Various devices have been advocated with different sites of force effect at the thrombus. The purpose of this study was to evaluate the angiographic route of passing systematically and therefore to assess the site of deployment of mechanical devices in correlation to the thrombus in interventional stroke treatment. Twenty-one consecutive patients with endovascular treatment for acute ischemic stroke with 26 passing procedures were evaluated prospectively. Occlusion site was the M1-segment in 17 cases (65.4%), ICA termination in five cases (19.2%), M2-segment in two cases (7.7%), the A2-segment in one case (3.8%) and basilar artery in one case (3.8%). On angiographic images the microwire and microcatheter passage was evaluated by illustrating the entry point and course across the occlusion site in relation to the thrombus in different projections and in correlation to the recanalisation result. Results were correlated to the origin of the thrombi according to the TOAST criteria. In all cases the point of entry to the occlusion site was delineated laterally to the thrombus in at least one projection. The course of the wire across the occluded segment in relation to the thrombus was found to be laterally in 22 procedures (84.6%). In the majority of M1-occlusions (12/17, 70.6%) the passage was found in the cranial aspect of the thrombus. In four procedures (15.4%) angiograms in different projections did not unequivocally confirm a passage laterally to the thrombus. The route of passing the thrombus was independent of thrombus origin according to the TOAST criteria. In the majority of cases the complete route of passing the occlusion site was visualized angiographically. Entrance of the microwire and microcatheter at proximal surface of the thrombus takes place laterally to the thrombus and accordingly the passage takes place between the thrombus and the vessel wall independent of thrombus origin. A penetration of the thrombus was not observed. This route of passing has implications on deployment and transmission of force in relation to the thrombus in mechanical approaches and consequently on the development of retrieval devices.

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.

PaperClip

Applicability of tableside flat panel detector CT parenchymal cerebral blood volume measurement in neurovascular interventions: preliminary clinical experience

BACKGROUND AND PURPOSE

CBV is a vital perfusion parameter in estimating the viability of brain parenchyma (eg, in cases of ischemic stroke or after interventional vessel occlusion). Recent technologic advances allow parenchymal CBV imaging tableside in the angiography suite just before, during, or after an interventional procedure. The aim of this work was to analyze our preliminary clinical experience with this new imaging tool in different neurovascular interventions.

MATERIALS AND METHODS

FPD-CBV measurement was performed on a biplane FPD angiographic system. Eighteen patients (11 women, 7 men) were examined (age range, 18-86 years; median, 58.7 years). In the 10 patients with stroke, the extent of intracranial hypoperfusion was evaluated. The remaining 8 patients had an intracranial hemorrhage; periprocedural CBV was evaluated during the course of interventional treatment.

RESULTS

In the 18 cases studied, 23 CBV measurements were performed. Twenty acquisitions were of sufficient diagnostic quality. The remaining 3 acquisitions failed technically, 1 due to motion artifacts and 2 due to injection technique and/or hardware failure.

CONCLUSIONS

FPD-CBV measurement in the angiography suite provides a feasible and helpful tool for peri-interventional neuroimaging. It extends the intraprocedural imaging modalities to the level of tissue perfusion. However, the technique has technical limitations and shows room for improvement in the future.

Susceptibility-weighted MR imaging for diagnosis of capillary telangiectasia of the brain

BACKGROUND AND PURPOSE

BCT is a benign entity, whose appearance on conventional MR imaging makes its differentiation from neoplastic, inflammatory, or subacute ischemic disease challenging. SWI is sensitive to susceptibility effects from deoxyhemoglobin with excellent spatial resolution. Only scarce case reports have described the utility of SWI in cases of BCT. Our aim was to show the diagnostic value of SWI applied to a larger series of cases.

MATERIALS AND METHODS

This was an observational retrospective study of 33 BCTs in 27 consecutive patients examined from August 2009 to January 2011 with MR imaging, including SWI. Morphology, signal intensity characteristics, and additional vascular malformations were analyzed. Preceding or follow-up examinations were available in 18 patients with a median time interval of 14.5 months (range, 2-115 months).

RESULTS

Twenty-five pontine and 8 supratentorial BCTs demonstrated distinct signal-intensity loss on SWI in combination with postcontrast enhancement. Mean lesion diameter was 4.9 mm (range, 1.5-17 mm). Thirty-nine percent showed slight signal-intensity changes on T1 and/or T2; the remainder were isointense to normal brain. In 30%, a prominent draining vessel was observed. Additional cerebral vascular malformations were found in 5 patients.

CONCLUSIONS

SWI represents a valuable tool for confirmation of presumed BCT. Demonstration of signal-intensity loss on SWI in an enhancing focal brain lesion, otherwise unremarkable on conventional MR images, is highly specific for BCT, thus excluding serious pathology and reassuring the patient and referring physician. This is particularly helpful for BCT in less typical locations.

Computed tomography angiography (CTA) to prove circulatory arrest for the diagnosis of brain death in the context of organ transplantation

QUESTION UNDER STUDY

For the determination of brain death (BD) in potential organ donors, confirmatory tests that show cessation of cerebral circulation are used in many countries. Conventional angiography is considered the golden standard among these ancillary examinations. In recent years other angiographic techniques such as CT angiography (CTA) have been increasingly employed to establish the diagnosis of BD. We report our experience with CTA in this setting.

MATERIAL AND METHODS

From 2007 to 2010, 29 patients were examined in order to determine BD using CTA. The studies consisted of an unenhanced head scan, a CT angiogram of the brain supplying vessels in the head and neck and a second head scan 80 seconds after contrast injection (venous phase). The studies were retrospectively re-evaluated by two experienced neuroradiologists according to the criteria accepted by the Swiss Academy of Medical Sciences.

RESULTS

In 22 patients, cessation of cerebral circulation was confirmed in the venous phase CT. In seven patients, cessation of brain circulation was not confirmed due to residual contrast enhancement in the relevant cerebral vessels, i.e. the M4-segments of the middle cerebral artery and/or the internal cerebral veins. In these patients, clinical re-evaluation after a minimum of six hours confirmed the diagnosis of BD. Using the clinical examination as the "golden standard," CTA achieved a sensitivity of 75.9%.

CONCLUSION

CTA is a useful additional tool for the confirmation of the diagnosis of brain death. Pooling of contrast in the relevant cerebral vessels, however, can be detected in up to 25% of CTAs in clinically brain dead patients.

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

Sequencing of small RNA cDNA libraries is an important tool for the discovery of new RNAs and the analysis of their mutational status as well as expression changes across samples. It requires multiple enzyme-catalyzed steps, including sequential oligonucleotide adapter ligations to the 3' and 5' ends of the small RNAs, reverse transcription (RT), and PCR. We assessed biases in representation of miRNAs relative to their input concentration, using a pool of 770 synthetic miRNAs and 45 calibrator oligoribonucleotides, and tested the influence of Rnl1 and two variants of Rnl2, Rnl2(1-249) and Rnl2(1-249)K227Q, for 3'-adapter ligation. The use of the Rnl2 variants for adapter ligations yielded substantially fewer side products compared with Rnl1; however, the benefits of using Rnl2 remained largely obscured by additional biases in the 5'-adapter ligation step; RT and PCR steps did not have a significant impact on read frequencies. Intramolecular secondary structures of miRNA and/or miRNA/3'-adapter products contributed to these biases, which were highly reproducible under defined experimental conditions. We used the synthetic miRNA cocktail to derive correction factors for approximation of the absolute levels of individual miRNAs in biological samples. Finally, we evaluated the influence of 5'-terminal 5-nt barcode extensions for a set of 20 barcoded 3' adapters and observed similar biases in miRNA read distribution, thereby enabling cost-saving multiplex analysis for large-scale miRNA profiling.

Percutaneous and open retrograde endovascular stenting of symptomatic high-grade innominate artery stenosis: technique and follow-up

BACKGROUND AND PURPOSE

Angioplasty and stenting of the IA have been reported with high technical and clinical success rates, low complication rates and good mid-term patency rates. Different antegrade or retrograde endovascular catheter-based approaches and combinations with surgical exposure of the CCA are used. The purpose of this study was to determine safety, efficacy and mid-term clinical and radiological outcome of the stent-assisted treatment of atherosclerotic stenotic disease of the IA with special focus on the different technical approaches.

MATERIALS AND METHODS

Between 1996 and 2008, 18 patients (12 men, 6 women) with symptomatic high-grade stenosis (>80%) of the IA were treated with endovascular stent placement. Their mean age was 60.4 years (range, 48-78 years). Mean angiographic and clinical follow-up was 2.7 years (range, 0.3-9.1 years). Clinical follow-up was performed by using the mRS at hospital discharge, routine follow-up controls, and a questionnaire. In 11 patients, a percutaneous approach was used. In 7 patients, the lesions were accessed retrogradely through a cervical cut-down with common carotid arteriotomy. In 2 patients, a simultaneous ipsilateral carotid endarterectomy was performed.

RESULTS

In all patients, primary stent placement was performed. There were 2 procedure-related transient complications (11.1%) due to cerebral embolism without permanent morbidity or mortality. During the follow-up, all patients showed improvement of the preprocedural symptoms. At the latest clinical follow-up (mean, 2.7 years), all patients showed an excellent or good outcome (mRS, 0 or 1). In 2 patients (11.1%), a secondary stent placement was needed due to a significant symptomatic in-stent stenosis.

CONCLUSIONS

Percutaneous and open retrograde stenting of high-grade stenosis of the IA is a viable less invasive alternatives to open bypass surgery with good midterm clinical results and patency rates.

Evaluation of the Contribution of CAS in Combination with the Subcranial/Subfrontal Approach in Anterior Skull Base Surgery

In this study, 31 cases with different anterior skull base lesions mandating broad exposure, including the sphenoidal, parasellar, and clival region, were surgically treated using the frameless computer assisted surgery (CAS) system. The contribution of navigated surgery in relation to the broad exposure and direct visualization of this region rendered by the subcranial-subfrontal approach was evaluated. In group I, consisting of extensive tumors, the contribution of CAS was only given in five cases for the exposure of the tumor extensions located to the parasellar sphenoclival complex with concomitant distortion of the anatomic landmarks. No advantages were experienced in the more anterior locations along the ethmoidal compartment and frontal sinus. In the cases in group II, consisting of congenital anomaly implying fronto-orbital advancement and a meningoencephalocele as well as extensive mucoceles, the CAS was only helpful in those cases with an extremely aberrative anatomy in these regions.

Impact of retrievable stents on acute ischemic stroke treatment

BACKGROUND AND PURPOSE

Retrievable stents combine the high recanalization rate of stents and the capability of removing the thrombus offered by mechanical thrombectomy devices. We hypothesized that retrievable stents shorten time to recanalization in the multimodal approach for endovascular stroke treatment.

MATERIALS AND METHODS

Forty consecutive patients with acute ischemic stroke and undergoing endovascular therapy were included. Treatment included thromboaspiration, thrombus disruption, thrombolysis, PTA, and stent placement. In 17 patients, a retrievable stent was used (group A) in addition to multimodal therapy. The remaining 23 patients constituted group B. Baseline characteristics, occlusion sites, urokinase dose, recanalization rate, and time to recanalization were compared between the groups.

RESULTS

Median NIHSS scores were higher in group A compared with group B on admission (19 versus 12.5; P = .018) but were not significantly different at day 1 (14 versus 10; P = .6). Intra-arterial thrombolysis was used in significantly fewer patients of group A than group B (53% versus 87%, respectively; P = .017), and median urokinase dose was lower in group A than in group B (250,000 IU versus 700,000 IU; P = .006). Time to recanalization was significantly shorter in group A compared with group B (median time to recanalization 52.5 minutes versus 90 minutes, respectively; P = .001). Recanalization rate was higher in group A than group B (94% versus 78%; P = .17).

CONCLUSIONS

Addition of retrievable stents to the multimodal endovascular approach for acute ischemic stroke treatment significantly reduces time to recanalization and further increases the recanalization rate.

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.

In vivo evaluation of the first dedicated combined flow-restoration and mechanical thrombectomy device in a swine model of acute vessel occlusion

BACKGROUND AND PURPOSE

The use of self-expanding retrievable stents is an emerging and promising treatment strategy for acute stroke treatment. The concept combines the advantages of stent deployment with immediate flow-restoration and of mechanical thrombectomy with definitive thrombus removal. The present study was performed to gain more knowledge about the principle of combined flow restoration and thrombectomy in an established animal model using radiopaque thrombi evaluating efficiency, thrombus-device interaction and possible complications of the first dedicated flow-restoration and mechanical thrombectomy device.

MATERIALS AND METHODS

The Solitaire FR (4 × 20 mm) was evaluated in 15 vessel occlusions in an established animal model in swine. Flow-restoration effect at T0, T5, and T10; recanalization rate after retrieval; thromboembolic events; and complications were assessed. Radiopaque thrombi (10-mm length) were used for visualization of thrombus-device interaction during application and retrieval.

RESULTS

Immediate flow restoration was achieved in 80% of occlusions. Mean percentage of recanalization compared with the initial vessel diameter at T0 was 30.8%; at T5, 30.7%; and at T10, 25.4%. Re-occlusion occurred in 20.0% between T0 and T5 and in 13.3% between T5 and T10. Complete recanalization (TICI 3) after retrieval was achieved in 86.7%. In 2 cases (13.3%), partial recanalization was achieved, with the remaining thrombus in a side branch (TICI 2b). No thromboembolic event was observed. The assessment of thrombus-device interaction illustrated the compression of the thrombus against the vessel wall during deployment leading to partial flow restoration. During retrieval, the thrombus was retained by the stent struts even during the passage of vessel curvatures.

CONCLUSIONS

The Solitaire FR is a safe and effective combined flow-restoration and thrombectomy device in vivo. Partial flow restoration is achieved by thrombus compression immediately after deployment, but flow restoration decreases afterward until final retrieval results in maximal recanalization.