How we approach paediatric renal tumour core needle biopsy in the setting of preoperative chemotherapy: A Review from the SIOP Renal Tumour Study Group.

The International Society of Paediatric Oncology Renal Tumour Study Group (SIOP-RTSG) advocate treating children with Wilms tumour (WT) with preoperative chemotherapy, whereas the Renal Tumor Committee of the Children's Oncology Group (COG) advocates primary nephrectomy (without biopsy) when feasible. Successive SIOP-RTSG trial protocols recommended pretreatment biopsy of children with unilateral tumours only where there were features to suggest an increased probability of a non-WT requiring a change in management. The UK experience in the SIOP WT 2001 trial showed that an alternate approach of performing biopsies on all children with renal tumour masses to determine histology at diagnosis rarely changes management, and can result in misdiagnosis (particularly patients in the age range typical for WT). Although a more selective approach to biopsy has been routine practice in all other countries participating in SIOP-RTSG trials, there was variation between national groups. To address this variation and provide evidence-based recommendations for the indications and recommended approach to renal tumour biopsy within the SIOP paradigm, an international, multidisciplinary working group of SIOP-RTSG members was convened. We describe the resulting recommendations of this group, which are to be incorporated in the ongoing SIOP-RTSG UMBRELLA study.

mTORC1-mediated translational elongation limits intestinal tumour initiation and growth.

Inactivation of APC is a strongly predisposing event in the development of colorectal cancer, prompting the search for vulnerabilities specific to cells that have lost APC function. Signalling through the mTOR pathway is known to be required for epithelial cell proliferation and tumour growth, and the current paradigm suggests that a critical function of mTOR activity is to upregulate translational initiation through phosphorylation of 4EBP1 (refs 6, 7). This model predicts that the mTOR inhibitor rapamycin, which does not efficiently inhibit 4EBP1 (ref. 8), would be ineffective in limiting cancer progression in APC-deficient lesions. Here we show in mice that mTOR complex 1 (mTORC1) activity is absolutely required for the proliferation of Apc-deficient (but not wild-type) enterocytes, revealing an unexpected opportunity for therapeutic intervention. Although APC-deficient cells show the expected increases in protein synthesis, our study reveals that it is translation elongation, and not initiation, which is the rate-limiting component. Mechanistically, mTORC1-mediated inhibition of eEF2 kinase is required for the proliferation of APC-deficient cells. Importantly, treatment of established APC-deficient adenomas with rapamycin (which can target eEF2 through the mTORC1-S6K-eEF2K axis) causes tumour cells to undergo growth arrest and differentiation. Taken together, our data suggest that inhibition of translation elongation using existing, clinically approved drugs, such as the rapalogs, would provide clear therapeutic benefit for patients at high risk of developing colorectal cancer.

The diagnostic accuracy and clinical utility of pediatric renal tumor biopsy: Report of the UK experience in the SIOP UK WT 2001 trial.

INTRODUCTION: The International Society of Paediatric Oncology (SIOP) protocols recommend preoperative chemotherapy appropriate for Wilms tumors (WTs) in children with renal tumors aged ≥6 months, reserving biopsy for "atypical" cases. The Children's Cancer and Leukaemia Group (CCLG) joined the SIOP-WT-2001 study but continued the national practice of biopsy at presentation. METHOD: Retrospective study of concordance between locally reported renal tumor biopsies and central pathology review nephrectomy diagnoses of children enrolled by CCLG centers in the SIOP-WT-2001 study. RESULTS: Biopsy reports were available for 552/787 children with unilateral tumors. 36 of 552 (6.5%) were nondiagnostic: 2 normal tissue, 12 necrotic, 9 insufficient sample, and 13 indeterminate results (disproportionately non-WTs). The sensitivity and specificity of biopsy to identify tumors that did not require SIOP empirical preoperative chemotherapy were 86.0% and 99.6%, respectively. 13 of 548 (2.4%) biopsy results were discordant with nephrectomy; non-WTs other than renal cell carcinoma and clear cell sarcoma of the kidney (CCSK) were poorly recognized. In children aged 6-119 months, 480 of 518 (91.6%) had WT or nephroblastomatosis. 5 of 518 (1%) had benign tumors, and only one diagnosed on biopsy. Biopsy results correctly changed clinical management in 25 of 518 (4.8%), including identifying 19 of 20 CCSKs, but would have led to overtreatment in 5 of 518 (1%) or undertreatment in 4 of 518 (0.8%). In children aged ≥10 years, biopsy correctly changed management in 5 of 19 (26%) cases with no discordance. CONCLUSION: Biopsy is less effective at identifying non-WTs than WTs and rarely changes management in younger children. Biopsy should be reserved in SIOP protocols for children ≥10 years and in younger children with clinical or radiological features inconsistent with WT.

PASSIVE/ACTIVE MICROWAVE SOIL MOISTURE CHANGE DISAGGREGATION USING SMAPVEX12 DATA.

The SMAPVEX12 (Soil Moisture Active Passive (SMAP) Validation Experiment 2012) experiment was conducted during June-July 2012 in Manitoba, Canada with the goal of collecting remote sensing data and ground measurements for the development and testing of soil moisture retrieval algorithms under varying vegetation and soil conditions for the SMAP satellite. The aircraft based soil moisture data provided by the passive/active microwave sensor PALS (Passive and Active L-band System) has a nominal spatial resolution of 1600 m. However, this resolution is not compatible with agricultural, meteorological and hydrological studies that require high spatial resolutions and this issue can be solved by soil moisture disaggregation. The soil moisture disaggregation algorithm integrates radiometer soil moisture retrievals and high-resolution radar observations and it can provide soil moisture estimates at a finer scale than the radiometer data alone. In this study, a change detection algorithm was used for disaggregation of coarse resolution passive microwave soil moisture retrievals with radar backscatter coefficients obtained from the higher spatial resolution UAVSAR (Unmanned Air Vehicle Synthetic Aperture Radar) at crop field scale. The accuracy of the disaggregated change in soil moisture was evaluated using ground based soil moisture measurements collected during SMAPVEX12 campaign. The results showed that soil moisture spatial variabilities were better characterized by the disaggregated change in soil moisture estimates at 5 m / 800 m resolution as well as good agreement with in situ measurements. It also showed that VWC (Vegetation Water Content) did not have a big impact on disaggregation algorithm performance, with R2 of the disaggregated results ranging 0.628-0.794. The 5 m and 800m resolution disaggregated soil moisture did no show significant difference in statistical performance variables.

A Comparative Study of the SMAP Passive Soil Moisture Product With Existing Satellite-Based Soil Moisture Products.

The NASA Soil Moisture Active Passive (SMAP) satellite mission was launched on January 31, 2015 to provide global mapping of high-resolution soil moisture and freeze-thaw state every 2-3 days using an L-band (active) radar and an L-band (passive) radiometer. The Level 2 radiometer-only soil moisture product (L2_SM_P) provides soil moisture estimates posted on a 36-km Earth-fixed grid using brightness temperature observations from descending passes. This paper provides the first comparison of the validated-release L2_SM_P product with soil moisture products provided by the Soil Moisture and Ocean Salinity (SMOS), Aquarius, Advanced Scatterometer (ASCAT), and Advanced Microwave Scanning Radiometer 2 (AMSR2) missions. This comparison was conducted as part of the SMAP calibration and validation efforts. SMAP and SMOS appear most similar among the five soil moisture products considered in this paper, overall exhibiting the smallest unbiased root-mean-square difference and highest correlation. Overall, SMOS tends to be slightly wetter than SMAP, excluding forests where some differences are observed. SMAP and Aquarius can only be compared for a little more than two months; they compare well, especially over low to moderately vegetated areas. SMAP and ASCAT show similar overall trends and spatial patterns with ASCAT providing wetter soil moistures than SMAP over moderate to dense vegetation. SMAP and AMSR2 largely disagree in their soil moisture trends and spatial patterns; AMSR2 exhibits an overall dry bias, while desert areas are observed to be wetter than SMAP.

Surface Soil Moisture Retrieval Using the L-Band Synthetic Aperture Radar Onboard the Soil Moisture Active-Passive Satellite and Evaluation at Core Validation Sites.

This paper evaluates the retrieval of soil moisture in the top 5-cm layer at 3-km spatial resolution using L-band dual-copolarized Soil Moisture Active-Passive (SMAP) synthetic aperture radar (SAR) data that mapped the globe every three days from mid-April to early July, 2015. Surface soil moisture retrievals using radar observations have been challenging in the past due to complicating factors of surface roughness and vegetation scattering. Here, physically based forward models of radar scattering for individual vegetation types are inverted using a time-series approach to retrieve soil moisture while correcting for the effects of static roughness and dynamic vegetation. Compared with the past studies in homogeneous field scales, this paper performs a stringent test with the satellite data in the presence of terrain slope, subpixel heterogeneity, and vegetation growth. The retrieval process also addresses any deficiencies in the forward model by removing any time-averaged bias between model and observations and by adjusting the strength of vegetation contributions. The retrievals are assessed at 14 core validation sites representing a wide range of global soil and vegetation conditions over grass, pasture, shrub, woody savanna, corn, wheat, and soybean fields. The predictions of the forward models used agree with SMAP measurements to within 0.5 dB unbiased-root-mean-square error (ubRMSE) and -0.05 dB (bias) for both copolarizations. Soil moisture retrievals have an accuracy of 0.052 m3/m3 ubRMSE, -0.015 m3/m3 bias, and a correlation of 0.50, compared to in situ measurements, thus meeting the accuracy target of 0.06 m3/m3 ubRMSE. The successful retrieval demonstrates the feasibility of a physically based time series retrieval with L-band SAR data for characterizing soil moisture over diverse conditions of soil moisture, surface roughness, and vegetation.

Longitudinal analysis of the neurological features of ataxia-telangiectasia.

AIM: To assess the relationship between genotype and neurological progression in ataxia-telangiectasia (A-T). METHODS: Clinical and laboratory data were extracted retrospectively from the records of patients attending the UK National Ataxia-Telangiectasia Clinic. Neurological assessments were performed using the A-T Index (Crawford Score) and the A-T Neurological Examination Scale Toolkit (A-T NEST). Variables influencing phenotype were identified by using an information-theoretic approach starting from a maximal model to generate estimates of coefficients for each variable. Per-individual progression was assessed for patients with three or more clinic attendances. RESULTS: The genotype could be determined for 125/135 patients. Crawford and A-T NEST scores were well correlated. For both scoring systems the estimated coefficients were significantly positive for Age x kinase activity but not Age x protein expression. Unlike the per-genotype analysis, the individual progression of neurological scores in the 34 patients that attended on three or more occasions was not smooth and linear (and in some cases improved over time). INTERPRETATION: Residual kinase activity confers a milder phenotype but there is no difference between kinase-dead and protein-null genotypes. The non-linear progression of individual patients' neurological scores may reflect biological complexity, day-to-day variability, limitations of the assessment methods or a combination of all three.

Eukaryotic elongation factor 2 kinase regulates the cold stress response by slowing translation elongation.

Cells respond to external stress conditions by controlling gene expression, a process which occurs rapidly via post-transcriptional regulation at the level of protein synthesis. Global control of translation is mediated by modification of translation factors to allow reprogramming of the translatome and synthesis of specific proteins that are required for stress protection or initiation of apoptosis. In the present study, we have investigated how global protein synthesis rates are regulated upon mild cooling. We demonstrate that although there are changes to the factors that control initiation, including phosphorylation of eukaryotic translation initiation factor 2 (eIF2) on the α-subunit, the reduction in the global translation rate is mediated by regulation of elongation via phosphorylation of eukaryotic elongation factor 2 (eEF2) by its specific kinase, eEF2K (eukaryotic elongation factor 2 kinase). The AMP/ATP ratio increases following cooling, consistent with a reduction in metabolic rates, giving rise to activation of AMPK (5'-AMP-activated protein kinase), which is upstream of eEF2K. However, our data show that the major trigger for activation of eEF2K upon mild cooling is the release of Ca2+ ions from the endoplasmic reticulum (ER) and, importantly, that it is possible to restore protein synthesis rates in cooled cells by inhibition of this pathway at multiple points. As cooling has both therapeutic and industrial applications, our data provide important new insights into how the cellular responses to this stress are regulated, opening up new possibilities to modulate these responses for medical or industrial use at physiological or cooler temperatures.

Evaluating bias-reducing protocols for RNA sequencing library preparation.

BACKGROUND: Next-generation sequencing does not yield fully unbiased estimates for read abundance, which may impact on the conclusions that can be drawn from sequencing data. The ligation step in RNA sequencing library generation is a known source of bias, motivating developments in enzyme technology and library construction protocols. We present the first comparison of the standard duplex adaptor protocol supplied by Life Technologies for use on the Ion Torrent PGM with an alternate single adaptor approach involving CircLigase (CircLig protocol).A correlation between over-representation in sequenced libraries and degree of secondary structure has been reported previously, therefore we also investigated whether bias could be reduced by ligation with an enzyme that functions at a temperature not permissive for such structure. RESULTS: A pool of small RNA fragments of known composition was converted into a sequencing library using one of three protocols and sequenced on an Ion Torrent PGM. The CircLig protocol resulted in less over-representation of specific sequences than the standard protocol. Over-represented sequences are more likely to be predicted to have secondary structure and to co-fold with adaptor sequences. However, use of the thermostable ligase Methanobacterium thermoautotrophicum RNA ligase K97A (Mth K97A) was not sufficient to reduce bias. CONCLUSIONS: The single adaptor CircLigase-based approach significantly reduces, but does not eliminate, bias in Ion Torrent data. Ligases that function at temperatures to remove the possible influence of secondary structure on library generation may be of value, although Mth K97A is not effective in this case.

microRNAs in cancer management.

Since the identification of microRNAs (miRNAs) in 1993, and the subsequent discovery of their highly conserved nature in 2000, the amount of research into their function--particularly how they contribute to malignancy--has greatly increased. This class of small RNA molecules control gene expression and provide a previously unknown control mechanism for protein synthesis. As such, it is unsurprising that miRNAs are now known to play an essential part in malignancy, functioning as tumour suppressors and oncogenes. This Review summarises the present understanding of how miRNAs operate at the molecular level; how their dysregulation is a crucial part of tumour formation, maintenance, and metastasis; how they can be used as biomarkers for disease type and grade; and how miRNA-based treatments could be used for diverse types of malignancies.

Dexmedetomidine improves success of paediatric MRI sedation.

OBJECTIVE: To improve success rates of children requiring sedation for MRI. METHODS: Audits of sedation success for children attending planned MRI using three different approaches: (1) National Institute for Health and Care Excellence (NICE) guidance (chloral hydrate if <15 kg and oral midazolam if ≥15 kg), (2) Chloral hydrate for all patients, (3) Chloral hydrate±intranasal dexmedetomidine if <15 kg and intranasal dexmedetomidine alone if ≥15 kg. RESULTS: 74 patients had 85 MRI scan attempts. Overall success rates were significantly higher when using intranasal dexmedetomidine compared with following NICE guidance (81% vs 52% p=0.017). Dexmedetomidine performed better than oral midazolam for the same indication (76% vs 33% p=0.026). The side effect profile for dexmedetomidine was as reported in larger studies. CONCLUSIONS: Intranasal dexmedetomidine is an effective alternative to oral midazolam for sedation for MRI and as a rescue medication where chloral hydrate has been ineffective.

Data Assimilation to extract Soil Moisture Information from SMAP Observations.

This study compares different methods to extract soil moisture information through the assimilation of Soil Moisture Active Passive (SMAP) observations. Neural Network (NN) and physically-based SMAP soil moisture retrievals were assimilated into the NASA Catchment model over the contiguous United States for April 2015 to March 2017. By construction, the NN retrievals are consistent with the global climatology of the Catchment model soil moisture. Assimilating the NN retrievals without further bias correction improved the surface and root zone correlations against in situ measurements from 14 SMAP core validation sites (CVS) by 0.12 and 0.16, respectively, over the model-only skill and reduced the surface and root zone ubRMSE by 0.005 m3 m-3 and 0.001 m3 m-3, respectively. The assimilation reduced the average absolute surface bias against the CVS measurements by 0.009 m3 m-3, but increased the root zone bias by 0.014 m3 m-3. Assimilating the NN retrievals after a localized bias correction yielded slightly lower surface correlation and ubRMSE improvements, but generally the skill differences were small. The assimilation of the physically-based SMAP Level-2 passive soil moisture retrievals using a global bias correction yielded similar skill improvements, as did the direct assimilation of locally bias-corrected SMAP brightness temperatures within the SMAP Level-4 soil moisture algorithm. The results show that global bias correction methods may be able to extract more independent information from SMAP observations compared to local bias correction methods, but without accurate quality control and observation error characterization they are also more vulnerable to adverse effects from retrieval errors related to uncertainties in the retrieval inputs and algorithm. Furthermore, the results show that using global bias correction approaches without a simultaneous re-calibration of the land model processes can lead to a skill degradation in other land surface variables.

Temporal Regulation of Distinct Internal Ribosome Entry Sites of the Dicistroviridae Cricket Paralysis Virus.

Internal ribosome entry is a key mechanism for viral protein synthesis in a subset of RNA viruses. Cricket paralysis virus (CrPV), a member of Dicistroviridae, has a positive-sense single strand RNA genome that contains two internal ribosome entry sites (IRES), a 5'untranslated region (5'UTR) and intergenic region (IGR) IRES, that direct translation of open reading frames (ORF) encoding the viral non-structural and structural proteins, respectively. The regulation of and the significance of the CrPV IRESs during infection are not fully understood. In this study, using a series of biochemical assays including radioactive-pulse labelling, reporter RNA assays and ribosome profiling, we demonstrate that while 5'UTR IRES translational activity is constant throughout infection, IGR IRES translation is delayed and then stimulated two to three hours post infection. The delay in IGR IRES translation is not affected by inhibiting global translation prematurely via treatment with Pateamine A. Using a CrPV replicon that uncouples viral translation and replication, we show that the increase in IGR IRES translation is dependent on expression of non-structural proteins and is greatly stimulated when replication is active. Temporal regulation by distinct IRESs within the CrPV genome is an effective viral strategy to ensure optimal timing and expression of viral proteins to facilitate infection.

Experimental therapy of disseminated B-Cell lymphoma xenografts with 213Bi-labeled anti-CD74.

A (213)Bi-labeled antibody to CD74 was evaluated as a therapeutic agent for B-cell lymphoma. The alpha-particle emission, with a half-life of 46 min, is appropriate for therapy of micrometastases. The labeled Ab retained full immunoreactivity, and was potent at single-cell kill of the Raji B-lymphoma cell line. Approximately 30 decays of cell-bound (213)Bi was required for a cell kill of 99%, and dosimetry calculations suggested that the cGy dose delivered was sufficient to produce the level of toxicity observed. A non-reactive control Ab, labeled similarly, also produced toxicity, due to decays occurring in the medium, but was approximately 3-fold less potent than the reactive Ab. In a SCID mouse xenograft micrometastatic model, Ab injection at day 2 or day 5 after tumor inoculation resulted in strong, specific suppression of tumor growth, with some apparent cures.