Highly Sensitive and Specific Detection of Bladder Cancer via Targeted Ultra-deep Sequencing of Urinary DNA

BACKGROUND

There is an unmet need for an accurate, validated, noninvasive test for diagnosing and monitoring bladder cancer (BC). Detection of BC-associated mutations in urinary DNA via targeted deep sequencing could meet this need.

OBJECTIVE

To test the ability of mutational analysis of urinary DNA to noninvasively detect BC within the context of haematuria investigations and non-muscle-invasive BC (NMIBC) surveillance.

DESIGN, SETTING, AND PARTICIPANTS

Capture-based ultra-deep sequencing was performed for 443 somatic mutations in 23 genes in 591 urine cell-pellet DNAs from haematuria clinic patients and 293 from NMIBC surveillance patients. Variant calling was optimised to minimise false positives using urine samples from 162 haematuria clinic patients without BC.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The sensitivity and specificity for BC diagnosis were determined.

RESULTS AND LIMITATIONS

Mutational analysis of urinary DNA detected 144 of the 165 haematuria patients diagnosed with incident BC from two independent cohorts, yielding overall sensitivity of 87.3% (95% confidence interval [CI] 81.2-92.0%) at specificity of 84.8% (95% CI 79.9-89.0%). The sensitivity was 97.4% for grade 3, 86.5% for grade 2, and 70.8% for grade 1 BC. Among NMIBC surveillance patients, 25 out of 29 recurrent BCs were detected, yielding sensitivity of 86.2% (95% CI 70.8-97.7%) at specificity of 62.5% (95% CI 56.1-68.0%); a positive urine mutation test in the absence of clinically detectable disease was associated with a 2.6-fold increase in the risk of future recurrence. The low number of recurrences in the NMIBC surveillance cohort and the lower sensitivity for detecting grade 1 pTa BC are limitations.

CONCLUSIONS

Detection of mutations in a small panel of BC-associated genes could facilitate noninvasive BC testing and expedite haematuria investigations. Following further validation, the test could also play a role in NMIBC surveillance.

PATIENT SUMMARY

Identification of alterations in genes that are frequently mutated in bladder cancer appears to be a promising strategy for detecting disease from urine samples and reducing reliance on examination of the bladder via a telescopic camera inserted through the urethra.

Weight reduction after bariatric surgery improves myocardial work indices and global longitudinal strain

Funding Acknowledgements

Type of funding sources: None.

Background

Obesity is known to affect cardiovascular morphology, function and outcomes. Most parameters used to evaluate cardiac function, especially ejection fraction, but also strain are load dependent and the research focused on the effects of the weight loss on cardiac systolic function are inconsistent.  Myocardial work is a novel cardiovascular parameter that characterizes cardiac systolic function and is less load dependent. However, there is lack of data how bariatric surgery affects parameters of the non-invasively calculated myocardial work indices obtained from pressure-strain loops obtained in patients referred with severe obesity.

Purpose

The purpose of the study was to analyze whether myocardial work indices change after bariatric surgery.

Methods

Out of 171 consecutive subjects that were referred to bariatric surgery and characterized elsewhere (1) 15 subjects, that had both, adequate visualization, and post- surgery transthoracic echo (TTE) performed, were taken into analysis. Echocardiographic examination was performed using GE Vivid 9 and analyzed with EchoPac 204 software.

Results

Global myocardial work (GWI), global constructive work (GCW) and global work efficiency (GWE) indexes increased, while global wasted work index (GWW) decreased significantly after bariatric surgery (Figure). GLS increased significantly after bariatric surgery (Figure). LV ejection fraction did not change significantly after surgery (60.2 ± 6.5% vs. 60.9 ± 7 %, p = 0.68). LV end-diastolic diameter (LVEDD) did not change (4.86 cm ± 0.35 vs. 4.89 cm ± 0.38, p = 0.55), while posterior wall thickness (PW) and relative wall thickness (RWT) decreased significantly (1.08 ± 0.13 vs. 0.99 ± 0.13, p = 0.001 and 0.45 ± 0.05 vs. 0.41 ± 0.06, p= 0.0003, respectively). Left atrial diameter (Figure) and left atrial area were lower after bariatric surgery (18.6 cm2 ± 2.5 vs. 16.7 cm2 ± 2.5, p = 0.027). Both systolic blood pressure and heart rate decreased after bariatric surgery (Figure). Mean time to post – surgery TTE was 400 days ± 151 and mean weight reduction was 38 kg ± 8.

Conclusion

Left ventricular systolic function evaluated using myocardial work indexes increased after bariatric surgery. After bariatric surgery, the myocardial work parameters returned to normal range, when based on the values recorded in the reference STAAB cohort study (2). Abstract Figure

Genome-wide association study identifies susceptibility loci for acute myeloid leukemia

Acute myeloid leukemia (AML) is a hematological malignancy with an undefined heritable risk. Here we perform a meta-analysis of three genome-wide association studies, with replication in a fourth study, incorporating a total of 4018 AML cases and 10488 controls. We identify a genome-wide significant risk locus for AML at 11q13.2 (rs4930561; P = 2.15 × 10-8; KMT5B). We also identify a genome-wide significant risk locus for the cytogenetically normal AML sub-group (N = 1287) at 6p21.32 (rs3916765; P = 1.51 × 10-10; HLA). Our results inform on AML etiology and identify putative functional genes operating in histone methylation (KMT5B) and immune function (HLA).

RT-qPCR and RT-Digital PCR: A Comparison of Different Platforms for the Evaluation of Residual Disease in Chronic Myeloid Leukemia

BACKGROUND

Tyrosine kinase inhibitors (TKIs) are the cornerstone of successful clinical management of patients with chronic myeloid leukemia (CML). Quantitative monitoring of the percentage of the fusion transcript BCR-ABL1 (breakpoint cluster region–c-abl oncogene 1, non-receptor tyrosine kinase) BCR-ABL1IS (%BCR-ABL1IS) by reverse transcription–quantitative PCR (RT-qPCR) is the gold standard strategy for evaluating patient response to TKIs and classification into prognostic subgroups. However, this approach can be challenging to perform in a reproducible manner. Reverse-transcription digital PCR (RT-dPCR) is an adaptation of this method that could provide the robust and standardized workflow needed for truly standardized patient stratification.

METHODS

BCR-ABL1 and ABL1 transcript copy numbers were quantified in a total of 102 samples; 70 CML patients undergoing TKI therapy and 32 non-CML individuals. 3 commercially available digital PCR platforms (QS3D, QX200 and Raindrop) were compared with the platform routinely used in the clinic for RT-qPCR using the EAC (Europe Against Cancer) assay.

RESULTS

Measurements on all instruments correlated well when the %BCR-ABL1IS was ≥0.1%. In patients with residual disease below this level, greater variations were measured both within and between instruments limiting comparable performance to a 4 log dynamic range.

CONCLUSIONS

RT-dPCR was able to quantify low-level BCR-ABL1 transcript copies but was unable to improve sensitivity below the level of detection achieved by RT-qPCR. However, RT-dPCR was able to perform these sensitive measurements without use of a calibration curve. Adaptions to the protocol to increase the amount of RNA measured are likely to be necessary to improve the analytical sensitivity of BCR-ABL testing on a dPCR platform.

Visualization of the joining of ribosomal subunits reveals the presence of 80S ribosomes in the nucleus

In eukaryotes the 40S and 60S ribosomal subunits are assembled in the nucleolus, but there appear to be mechanisms preventing mRNA binding, 80S formation, and initiation of translation in the nucleus. To visualize association between ribosomal subunits, we tagged pairs of Drosophila ribosomal proteins (RPs) located in different subunits with mutually complementing halves of fluorescent proteins. Pairs of tagged RPs expected to interact, or be adjacent in the 80S structure, showed strong fluorescence, while pairs that were not in close proximity did not. Moreover, the complementation signal is found in ribosomal fractions and it was enhanced by translation elongation inhibitors and reduced by initiation inhibitors. Our technique achieved 80S visualization both in cultured cells and in fly tissues in vivo. Notably, while the main 80S signal was in the cytoplasm, clear signals were also seen in the nucleolus and at other nuclear sites. Furthermore, we detected rapid puromycin incorporation in the nucleolus and at transcription sites, providing an independent indication of functional 80S in the nucleolus and 80S association with nascent transcripts.