Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS

BACKGROUND

Gene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions.

METHODS

We developed Fusion-sq to overcome existing disadvantages of detecting gene fusions. Fusion-sq integrates and "fuses" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure to identify tumor-specific protein coding gene fusions. Fusion-sq was then applied to the data generated from a pediatric pan-cancer cohort of 128 patients by WGS and RNA sequencing.

RESULTS

In a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterized by underlying SVs, in some cases leading to expression changes indicative of activating or disruptive effects.

CONCLUSIONS

Our results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate gene fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific gene fusions for future clinical decision making.

Molecular Characterization Reveals Subclasses of 1q Gain in Intermediate Risk Wilms Tumors

Simple Summary

Chromosomal alterations and other structural variants have been recurrently identified in Wilms tumors (WT) and are promising biomarkers for risk stratification. Chromosome 1q gain occurs in one in three WTs and is associated with poor prognosis, but its impact on tumor biology remains unknown. Here, we investigated the mutational mechanisms and functional effects of chromosomal alterations in WTs, and in particular 1q gain. We identified subgroups of tumors with typical activated biological processes: muscle differentiation, immune system, kidney development and proliferation. Combining these subgroups with genomic data showed that tumors with 1q gain occur in all subgroups and can be associated with different functional effects. Also, 1q gain tumors differ in mutational mechanisms and co-occurring tumor-specific mutations. In conclusion, we identified subgroups of tumors with 1q gain and therefore propose that incorporating expression data in risk stratification could improve the clinical utility of 1q gain.

Abstract

Chromosomal alterations have recurrently been identified in Wilms tumors (WTs) and some are associated with poor prognosis. Gain of 1q (1q+) is of special interest given its high prevalence and is currently actively studied for its prognostic value. However, the underlying mutational mechanisms and functional effects remain unknown. In a national unbiased cohort of 30 primary WTs, we integrated somatic SNVs, CNs and SVs with expression data and distinguished four clusters characterized by affected biological processes: muscle differentiation, immune system, kidney development and proliferation. Combined genome-wide CN and SV profiles showed that tumors profoundly differ in both their types of 1q+ and genomic stability and can be grouped into WTs with co-occurring 1p−/1q+, multiple chromosomal gains or CN neutral tumors. We identified 1q+ in eight tumors that differ in mutational mechanisms, subsequent rearrangements and genomic contexts. Moreover, 1q+ tumors were present in all four expression clusters reflecting activation of various biological processes, and individual tumors overexpress different genes on 1q. In conclusion, by integrating CNs, SVs and gene expression, we identified subgroups of 1q+ tumors reflecting differences in the functional effect of 1q gain, indicating that expression data is likely needed for further risk stratification of 1q+ WTs.

Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here, we describe the generation of a collection of 19 pediatric RMS tumor organoid (tumoroid) models (success rate of 41%) comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within 4-8 weeks, indicating the feasibility of personalized drug screening. Molecular, genetic, and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to 6 months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 with TP53 knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions.

Drug use is associated with lower plasma magnesium levels in geriatric outpatients; possible clinical relevance

BACKGROUND

Hypomagnesemia has been associated with diabetes, cardiovascular disease, and other disorders. Drug use has been suggested as one of the risk factors for low magnesium (Mg) levels. In the elderly population, prone to polypharmacy and inadequate Mg intake, hypomagnesemia might be relevant. Therefore, we aimed to investigate associations between drug use and plasma Mg.

METHODS

Cross-sectional data of 343 Dutch geriatric outpatients were analysed by Cox and linear regression, while adjusting for covariates. Drug groups were coded according to the Anatomical Therapeutic Chemical classification system; use was compared to non-use. Hypomagnesemia was defined as plasma Mg < 0.75 mmol/l and <0.70 mmol/l.

RESULTS

Prevalence of hypomagnesemia was 22.2% (Mg < 0.75 mmol/l) or 12.2% (Mg < 0.70 mmol/l); 67.6% of the patients used ≥5 medications (polypharmacy). The number of different drugs used was inversely linearly associated with Mg level (beta -0.01; p < 0.01). Fully adjusted Cox regression showed significant associations of polypharmacy with hypomagnesemia (Mg < 0.75 mmol/l) (prevalence ratio (PR) 1.81; 95%CI 1.08-3.14), proton pump inhibitors (PR 1.80; 95%CI 1.20-2.72), and metformin (PR 2.34; 95%CI 1.56-3.50). Moreover, stratified analyses pointed towards associations with calcium supplements (PR 2.26; 95%CI 1.20-4.26), insulins (PR 3.88; 95%CI 2.19-6.86), vitamin K antagonists (PR 2.01; 95%CI 1.05-3.85), statins (PR 2.44; 95%CI 1.31-4.56), and bisphosphonates (PR 2.97; 95%CI 1.65-5.36) in patients <80 years; selective beta blockers (PR 2.01; 95%CI 1.19-3.40) if BMI <27.0 kg/m²; and adrenergic inhalants in male users (PR 3.62; 95%CI 1.73-7.56). Linear regression supported these associations.

CONCLUSION

As polypharmacy and several medications are associated with hypomagnesemia, Mg merits more attention, particularly in diabetes, cardiovascular disease, and in side-effects of proton pump inhibitors and calcium supplements.

Efficacy of web-based cognitive-behavioural therapy for chronic fatigue syndrome: randomised controlled trial

BACKGROUND

Face-to-face cognitive-behavioural therapy (CBT) leads to a reduction of fatigue in chronic fatigue syndrome (CFS). Aims To test the efficacy of internet-based CBT (iCBT) for adults with CFS.

METHOD

A total of 240 patients with CFS were randomised to either iCBT with protocol-driven therapist feedback or with therapist feedback on demand, or a waiting list. Primary outcome was fatigue severity assessed with the Checklist Individual Strength (Netherlands Trial Register: NTR4013).

RESULTS

Compared with a waiting list, intention-to-treat (ITT) analysis showed a significant reduction of fatigue for both iCBT conditions (protocol-driven feedback: B = -8.3, 97.5% CI -12.7 to -3.9, P < 0.0001; feedback on demand: B = -7.2, 97.5% CI -11.3 to -3.1, P < 0.0001). No significant differences were found between both iCBT conditions on all outcome measures (P = 0.3-0.9). An exploratory analysis revealed that feedback-on-demand iCBT required less therapist time (mean 4 h 37 min) than iCBT with protocol-driven feedback (mean 6 h 9 min, P < 0.001) and also less than face-to-face CBT as reported in the literature.

CONCLUSIONS

Both iCBT conditions are efficacious and time efficient. Declaration of interest None.

Vitamin D deficiency as adverse drug reaction? A cross-sectional study in Dutch geriatric outpatients

PURPOSE

Adverse drug reactions as well as vitamin D deficiency are issues of public health concern in older people. However, relatively little is known about the impact of drug use on vitamin D status. Our primary aim is to explore associations between drug use and vitamin D status in older people. Furthermore, prevalences of drug use and vitamin D deficiency are estimated.

METHODS

In a population of 873 community-dwelling Dutch geriatric outpatients, we explored the cross-sectional relationships of polypharmacy (≥5 medications concomitantly used), severe polypharmacy (≥10 medications), and use of twenty-one specific drug groups, with serum 25-hydroxyvitamin D (25(OH)D) by analysis of covariance.

RESULTS

Overall prevalence of polypharmacy was 65 %, of severe polypharmacy 22 %. Depending on the cut-off value, prevalence of vitamin D deficiency was 49 % (<50 nmol/l) or 77 % (<75 nmol/l). Of the patients using a vitamin D supplement, 17 % (<50 nmol/l) or 49 % (<75 nmol/l) were still deficient. In non-users of supplemental vitamin D, after adjustment for age and gender, negative associations were found for severe polypharmacy, metformin, sulphonamides and urea derivatives (SUDs), vitamin K antagonists, cardiac glycosides, loop diuretics, potassium-sparing diuretics, ACE inhibitors, and serotonin reuptake inhibitors; for non-selective monoamine reuptake inhibitors (NSMRIs) the association was positive. The most extreme impacts of drug use on adjusted mean 25(OH)D were -19 nmol/l for SUDs and +18 nmol/l for NSMRIs.

CONCLUSION

Drug use should be considered a risk factor for vitamin D deficiency amongst geriatric outpatients.

[IC triage in patients with an acutely worsening condition; challenges, considerations and decisions]

Acute intensive care (IC) triage involves a challenging decision-making process. Physicians are required to make life or death decisions about an unfamiliar patient within a short time frame. An 84-year-old female was admitted to the stroke unit following an extensive cerebral infarction. The intensive care unit (ICU) physician was consulted because of a suspected severe abdominal sepsis even though ICU treatment had never previously been discussed. A 77-year-old female with a previous history of myocardial infarction and severe COPD developed acute respiratory failure on the ward, and was admitted to the ICU for support by a mechanical ventilator. The family felt this was an inappropriate course of treatment, considering her former poor quality of life. When physicians are confronted with sudden deterioration of the patient's clinical condition without advanced care planning a limited-time IC treatment trial is often initiated, possibly leading to inappropriate ICU admissions. ICU treatment options should preferably be discussed beforehand; preliminary background information regarding the patient's wishes is essential for adequate decision-making.

The old lady who liked liquorice: hypertension due to chronic intoxication in a memory-impaired patient

The authors report an 85-year-old patient admitted because of cognitive impairment. During examination hypertension and hypokalaemia were found. After some time it was discovered that the patient was eating too much liquorice. The case demonstrates that liquorice intoxication should be considered as a cause of hypertension in old age. Furthermore the case demonstrates that missing an intoxication is a pitfall for medical history taking of patients with cognitive impairment.

Determination of stroke volume by means of electrical impedance tomography

ECG-gated electrical impedance tomography (EIT) is a non-invasive imaging technique, developed to monitor blood volume changes. This study is the first in comparing this non-invasive technique in measuring stroke volume with established techniques. The objective of this study was to validate EIT variables derived from the EIT images with paired obtained stroke volume measurements by thermodilution and MRI. After right cardiac catheterization, EIT measurements were performed in 25 patients. Regression analysis was used to analyse the relation between the EIT results and stroke volume determined by thermodilution. From the regression line an equation was derived to estimate stroke volume (in ml) by EIT. A strong correlation was found between EIT and stroke volume measured by the thermodilution method (r = 0.86). In a group of 11 healthy subjects this equation was validated to MRI. The mean and standard deviation of the difference between EIT and MRI was 0.7 ml and 5.4 ml respectively. These data indicate that EIT is a valid and reproducible method for the assessment of stroke volume.

Pulmonary perfusion measured by means of electrical impedance tomography

Electrical impedance tomography (EIT) is a recent imaging technique based on electrical impedance, offering the possibility of measuring pulmonary perfusion. In the present study the influence of several pulmonary haemodynamical parameters on the EIT signal were investigated. First, the influence on the systolic wave of the EIT signal (delta Zsys) of stroke volume, large pulmonary artery distensibility (both assessed by means of MRI) and the extent of the pulmonary peripheral vascular bed in 11 emphysematous patients (reduced peripheral vascular bed) and 9 controls (normal peripheral vascular bed) was investigated. Second, the influence of hypoxic pulmonary vasoconstriction on delta Zsys was examined in 14 healthy subjects. Finally, the origin of the diastolic wave was examined in three patients with atrioventricular dissociation. Multiple regression analysis showed that delta Zsys was only dependent on the variable emphysema (p < 0.02), but not dependent on stroke volume (p < 0.3) or pulmonary artery distensibility (p > 0.9). The mean value of delta Zsys for emphysematous patients (131 +/- 32 arbitrary units (AU)) was significantly lower (p < 0.001) than in the control group (200 +/- 39). In the group of healthy subjects delta Zsys decreased significantly (p < 0.001) during hypoxia (193 +/- 38 AU) compared with rest measurements (260 +/- 62 AU). The absence of the diastolic wave in the cardiological patients suggests the influence of reverse venous blood flow on the EIT signal. It is concluded that volume changes in the small pulmonary vessels contribute significantly to the EIT signal. Moreover, the hypoxia induced decrease in delta Zsys indicates the potential of EIT for measuring pulmonary vascular responses to external stimuli.

Sagittal position of the left and right maxillary segment in children with cleft lip and palate

OBJECTIVE

The purpose of the present study was to investigate left-right differences in the sagittal position of the maxillary segments in children with cleft lip and palate.

METHOD

The sample consisted of children with operated cleft lip or cleft lip and alveolus [CL/CLA (n = 16) mean age, 9.3 yr], operated unilateral cleft lip and palate [UCLP (n = 27) mean age, 9.1 yr], and operated bilateral cleft lip and palate [BCLP (n = 17) mean age, 9.5 yr]. Computed tomography (CT) horizontal slices of the maxilla were obtained and used to determine the sagittal position of the left and right segment of the maxilla in relation to the mandibular rami and the cranial base. Significant effects were analyzed with multivariate analyses of variance (MANOVA).

RESULTS AND CONCLUSIONS

It was concluded that, in contrast to children having CL/CLA or UCLP, children with BCLP showed left-right differences in the sagittal position of the maxillary segments. The segment on the left side was more posteriorly positioned compared to the right side. Because the same results were obtained in relation to the mandibular rami as well as in relation to the cranial base, it can be assumed that the position of these rami are not affected by the different types of oral clefts.

Noninvasive assessment of right ventricular diastolic function by electrical impedance tomography

STUDY OBJECTIVES

Electrical impedance tomography (EIT) offers the possibility to study blood volume changes within the right atrium during the cardiac cycle. The aim of this study was to determine the applicability of EIT in the assessment of right ventricular diastolic function in COPD.

DESIGN

By means of region of interest analysis, impedance changes within the right atrium during the cardiac cycle were plotted as a function of time. As a diastolic index of the right ventricle, the right atrium emptying volume (RAEV), defined as the ratio between the volume change during the rapid filling phase relative to the total ventricular filling volume, was calculated. In a first study, the validity of the EIT method was assessed by comparison of the RAEV measured by EIT and MRI in a group of eight patients with severe COPD and seven control subjects. A second study was undertaken to assess the relation between RAEV and pulmonary artery pressure in a group of 27 patients measured by right-sided heart catheterization.

RESULTS

The correlation coefficient between RAEV measured with MRI and EIT was 0.78. The difference between RAEV measured by MRI and EIT was 8.3 +/- 15.7% (mean +/- SD) for the control subjects and 3.5 +/- 10.9% for the COPD patients. RAEV values measured by EIT and MRI were larger in the control group (47.1 +/- 7.6%) compared with the patient group (38.1 +/- 10.4%). There was a clear nonlinear relationship between RAEV and the pulmonary artery pressure (y = 315 x-0.64, r = 0.83, p < 0.001).

CONCLUSION

Our results indicate that RAEV measured by EIT is a useful noninvasive and inexpensive method for assessing right ventricular diastolic function in COPD patients.

Validity and reproducibility of electrical impedance tomography for measurement of calf blood flow in healthy subjects

The Sheffield electrical impedance tomography; (EIT) system produces images of changes in the distribution of resistivity within tissue. The paper reports on the application of electrical impedance tomography in monitoring volume changes in the limb during venous occlusion. The aim of the study is to assess the feasibility, reproducibility and validity of calf blood flow measurements by EIT. In 14 healthy volunteers calf blood flow is compared, as determined in a calf segment by strain-gauge plethysmography (SGP), with the impedance changes measured by EIT during rest and post-ischaemic hyperaemia. The measurements are repeated to assess reproducibility. The reproducibility for the EIT, assessed from the repeated measurements and expressed as a reproducibility coefficient, is 0.88 during rest and 0.89 during hyperaemia. The reproducibility coefficient for SGP data is 0.83 at rest and 0.67 during hyperaemia. Flow measurements, assessed by means of two methods, correlate well at rest (r = 0.89), but only moderately during hyperaemia (r = 0.51). The correlation coefficient for the pooled flow measurements is 0.98. It is concluded that EIT is a valid and reliable method for assessing blood flow in the limb. Possible applications of EIT in localising fluid changes are discussed.

Improvement of cardiac imaging in electrical impedance tomography by means of a new electrode configuration

Until now, electrical impedance tomography (EIT) has been used for cardiac imaging with the electrodes attached transversally at the level of the fourth intercostal space at the anterior side. However, the results obtained with this electrode configuration have been disappointing. The aim of the present study was to improve the measurement design of EIT for cardiac imaging. Therefore, magnetic resonance imaging (MRI) scans were analysed in two healthy subjects to determine the optimum anatomical plane in which atria and ventricles are clearly visually separated. From these findings, we proposed a new oblique plane at the level of the ictus cordis anteriorly and 10 cm higher posteriorly. EIT pictures obtained in the oblique plane revealed a better visual separation between the ventricles and atria than with the electrodes attached in the transverse plane. Comparison between volume changes measured by means of MRI and impedance changes in different regions of interest measured with EIT were performed with the electrodes in the proposed oblique plane. Ventricular and atrial volume changes measured by MRI show the same pattern as do impedance changes measured by EIT. Furthermore, we assessed the reproducibility and validity of the oblique electrode configuration in ten healthy mate volunteers during rest and during exercise compared with the currently used transverse electrode configuration. The reproducibility coefficient assessed from repeated measurements with the electrodes attached in the oblique plane was 0.98 at rest and 0.85 during exercise. For the transverse plane the reproducibility coefficient was 0.96 at rest and 0.66 during exercise. The well-known increase in stroke volume during exercise is 40% in healthy subjects. The increase in impedance change during exercise compared with rest was 34 +/- 13% (20-59%) for the oblique plane and 68 +/- 57% (13-140%) for the transverse plane. From these results we infer that the stroke volume is assessed more accurately by using the oblique plane. From these findings, we conclude that the oblique plane improved the cardiac measurements, because (i) a better spatial separation of the heart compartments is obtained, (ii) the results are more reliable and (iii) measurements during exercise are more accurate with the electrodes attached in an oblique plane.