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1.
Nat Rev Urol ; 21(3): 158-180, 2024 03.
Article in English | MEDLINE | ID: mdl-37848532

ABSTRACT

The modern study of Wilms tumour was prompted nearly 50 years ago, when Alfred Knudson proposed the 'two-hit' model of tumour development. Since then, the efforts of researchers worldwide have substantially expanded our knowledge of Wilms tumour biology, including major advances in genetics - from cloning the first Wilms tumour gene to high-throughput studies that have revealed the genetic landscape of this tumour. These discoveries improve understanding of the embryonal origin of Wilms tumour, familial occurrences and associated syndromic conditions. Many efforts have been made to find and clinically apply prognostic biomarkers to Wilms tumour, for which outcomes are generally favourable, but treatment of some affected individuals remains challenging. Challenges are also posed by the intratumoural heterogeneity of biomarkers. Furthermore, preclinical models of Wilms tumour, from cell lines to organoid cultures, have evolved. Despite these many achievements, much still remains to be discovered: further molecular understanding of relapse in Wilms tumour and of the multiple origins of bilateral Wilms tumour are two examples of areas under active investigation. International collaboration, especially when large tumour series are required to obtain robust data, will help to answer some of the remaining unresolved questions.


Subject(s)
Kidney Neoplasms , Wilms Tumor , Humans , Kidney Neoplasms/therapy , Neoplasm Recurrence, Local , Wilms Tumor/therapy , Biomarkers , Biology
2.
PLoS One ; 18(3): e0281933, 2023.
Article in English | MEDLINE | ID: mdl-36888610

ABSTRACT

Quantitative descriptions of stream network and river catchment characteristics provide valuable context for enabling geomorphologically-informed sustainable river management. For countries where high-quality topographic data are available, there are opportunities to enable open access availability of baseline products from systematic assessment of morphometric and topographic characteristics. In this study, we present a national-scale assessment of fundamental topographic characteristics of Philippine river systems. We applied a consistent workflow using TopoToolbox V2 to delineate stream networks and river catchments using a nationwide digital elevation model (DEM) acquired in 2013 and generated through airborne Interferometric Synthetic Aperture Radar (IfSAR). We assessed morphometric and topographic characteristics for 128 medium- to large-sized catchments (catchment area > 250 km2) and organised the results in a national-scale geodatabase. The dataset realises the potential of topographic data as part of river management applications, by enabling variations in hydromorphology to be characterised and contextualised. The dataset is used to reveal the diversity of stream networks and river catchments in the Philippines. Catchments have a continuum of shapes (Gravelius compactness coefficient ranges from 1.05 to 3.29) with drainage densities that range from 0.65 to 1.23 km/km2. Average catchment slope ranges from 3.1 to 28.1° and average stream slope varies by more than an order of magnitude from 0.004 to 0.107 m/m. Inter-catchment analyses show the distinctive topographic signatures of adjacent river catchments; examples from NW Luzon highlight topographic similarity between catchments whereas examples from Panay Island shown marked topographic differences. These contrasts underline the importance of using place-based analyses for sustainable river management applications. By designing an interactive ArcGIS web-application to display the national-scale geodatabase, we improve data accessibility and enable users to freely access, explore and download the data (https://glasgow-uni.maps.arcgis.com/apps/webappviewer/index.html?id=a88b9ca0919f4400881eab4a26370cee). The national-scale geodatabase provides a baseline understanding of fundamental topographic characteristics in support of varied geomorphological, hydrological and geohazard susceptibility applications.


Subject(s)
Hydrology , Rivers , Philippines
3.
Pediatr Nephrol ; 37(4): 821-832, 2022 04.
Article in English | MEDLINE | ID: mdl-34608521

ABSTRACT

BACKGROUND: Wilms tumour (WT) survivors, especially patients with associated syndromes or genitourinary anomalies due to constitutional WT1 pathogenic variant, have increased risk of kidney failure. We describe the long-term kidney function in children with WT and WT1 pathogenic variant to inform the surgical strategy and oncological management of such complex children. METHODS: Retrospective analysis of patients with WT and constitutional WT1 pathogenic variant treated at a single centre between 1993 and 2016, reviewing genotype, phenotype, tumour histology, laterality, treatment, patient survival, and kidney outcome. RESULTS: We identified 25 patients (60% male, median age at diagnosis 14 months, range 4-74 months) with WT1 deletion (4), missense (2), nonsense (8), frameshift (7), or splice site (4) pathogenic variant. Thirteen (52%) had bilateral disease, 3 (12%) had WT-aniridia, 1 had incomplete Denys-Drash syndrome, 11 (44%) had genitourinary malformation, and 10 (40%) had no phenotypic anomalies. Patient survival was 100% and 3 patients were in remission after relapse at median follow-up of 9 years. Seven patients (28%) commenced chronic dialysis of which 3 were after bilateral nephrectomies. The overall kidney survival for this cohort as mean time to start of dialysis was 13.38 years (95% CI: 10.3-16.4), where 7 patients experienced kidney failure at a median of 5.6 years. All of these 7 patients were subsequently transplanted. In addition, 2 patients have stage III and stage IV chronic kidney disease and 12 patients have albuminuria and/or treatment with ACE inhibitors. Four patients (3 frameshift; 1 WT1 deletion) had normal blood pressure and kidney function without proteinuria at follow-up from 1.5 to 12 years. CONCLUSIONS: Despite the known high risk of kidney disease in patients with WT and constitutional WT1 pathogenic variant, nearly two-thirds of patients had sustained native kidney function, suggesting that nephron-sparing surgery (NSS) should be attempted when possible without compromising oncological risk. Larger international studies are needed for accurate assessment of WT1genotype-kidney function phenotype correlation.


Subject(s)
Kidney Neoplasms , Renal Insufficiency , WT1 Proteins , Wilms Tumor , Child , Child, Preschool , Female , Genes, Wilms Tumor , Humans , Infant , Kidney/pathology , Kidney/surgery , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Kidney Neoplasms/surgery , Male , Mutation , Neoplasm Recurrence, Local/genetics , Renal Dialysis , Renal Insufficiency/genetics , Retrospective Studies , WT1 Proteins/genetics , Wilms Tumor/genetics , Wilms Tumor/pathology , Wilms Tumor/surgery
4.
Sci Total Environ ; 768: 144460, 2021 May 10.
Article in English | MEDLINE | ID: mdl-33450685

ABSTRACT

River migration represents a geomorphic hazard at sites of critical bridge infrastructure, particularly in rivers where migration rates are high, as in the tropics. In the Philippines, where exposure to flooding and geomorphic risk are considerable, the recent expansion of infrastructural developments warrants quantification of river migration in the vicinity of bridge assets. We analysed publicly available bridge inventory data from the Philippines Department of Public Works and Highways (DPWH) to complete multi-temporal geospatial analysis using three decades worth of Landsat satellite imagery in Google Earth Engine (GEE). For 74 large bridges, we calculated similarity coefficients and quantified changes in width for the active river channel (defined as the wetted channel and unvegetated alluvial deposits) over decadal and engineering (30-year) timescales. Monitoring revealed the diversity of river planform adjustment at bridges in the Philippines (including channel migration, contraction, expansion and avulsion). The mean Jaccard index over decadal (0.65) and engineering (0.50) timescales indicated considerable planform adjustment throughout the national-scale inventory. However, planform adjustment and morphological behaviour varied between bridges. For bridges with substantial planform adjustment, maximum active channel contraction and expansion was equal to 25% of the active channel width over decadal timescales. This magnitude of lateral adjustment is sufficient to imply the need for bridge design to accommodate channel dynamism. For other bridges, the planform remained stable and changes in channel width were limited. Fundamental differences in channel characteristics and morphological behaviours emerged between different valley confinement settings, and between rivers with different channel patterns, indicating the importance of the local geomorphic setting. We recommend satellite remote sensing as a low-cost approach to monitor river planform adjustment with large-scale planimetric changes detectable in Landsat products; these approaches can be applied to other critical infrastructure adjacent to rivers (e.g. road, rail, pipelines) and extended elsewhere to other dynamic riverine settings.

5.
JBJS Case Connect ; 10(2): e0519, 2020.
Article in English | MEDLINE | ID: mdl-32649117

ABSTRACT

CASE: An otherwise healthy 13-year-old girl presented with a firm nodule on the plantar right forefoot that was tender after cheerleading. Initial workup was unremarkable, but magnetic resonance imaging revealed a multilobulated mass surrounding the flexor hallucis longus tendon. Surgical resection revealed a tenosynovial mass without tendon infiltration. Pathologic examination was consistent with tenosynovial giant cell tumor. The patient resumed cheerleading and remained asymptomatic after 1 year. CONCLUSION: As far as we know, this is the first report of a tenosynovial giant cell tumor of the flexor hallucis longus in a pediatric patient; it illustrates the importance of considering this lesion when diagnosing a pediatric plantar mass.


Subject(s)
Foot/pathology , Giant Cell Tumor of Tendon Sheath/pathology , Adolescent , Female , Foot/diagnostic imaging , Foot/surgery , Giant Cell Tumor of Tendon Sheath/diagnostic imaging , Giant Cell Tumor of Tendon Sheath/surgery , Humans , Magnetic Resonance Imaging
6.
Environ Sci Technol ; 53(8): 4088-4098, 2019 04 16.
Article in English | MEDLINE | ID: mdl-30829475

ABSTRACT

Results from the analysis of aqueous and solid-phase V speciation within samples collected from the Hazeltine Creek catchment affected by the August 2014 Mount Polley mine tailings dam failure in British Columbia, Canada, are presented. Electron microprobe and X-ray absorption near-edge structure (XANES) analysis found that V is present as V3+ substituted into magnetite and V3+ and V4+ substituted into titanite, both of which occur in the spilled Mount Polley tailings. Secondary Fe oxyhydroxides forming in inflow waters and on creek beds have V K-edge XANES spectra exhibiting E1/2 positions and pre-edge features consistent with the presence of V5+ species, suggesting sorption of this species on these secondary phases. PHREEQC modeling suggests that the stream waters mostly contain V5+ and the inflow and pore waters contain a mixture of V3+ and V5+. These data, and stream, inflow, and pore water chemical data, suggest that dissolution of V(III)-bearing magnetite, V(III)- and V(IV)-bearing titanite, V(V)-bearing Fe(-Al-Si-Mn) oxhydroxides, and V-bearing Al(OH)3 and/or clay minerals may have occurred. In the circumneutral pH environment of Hazeltine Creek, elevated V concentrations are likely naturally attenuated by formation of V(V)-bearing secondary Fe oxyhydroxide, Al(OH)3, or clay mineral colloids, suggesting that the V is not bioavailable. A conceptual model describing the origin and fate of V in Hazeltine Creek that is applicable to other river systems is presented.


Subject(s)
Vanadium , Water Pollutants, Chemical , British Columbia , Minerals , Rivers
7.
Pediatr Blood Cancer ; 66(6): e27627, 2019 06.
Article in English | MEDLINE | ID: mdl-30761727

ABSTRACT

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.


Subject(s)
Carcinoma, Renal Cell/diagnosis , Kidney Neoplasms/diagnosis , Wilms Tumor/diagnosis , Adolescent , Biopsy , Carcinoma, Renal Cell/surgery , Child , Child, Preschool , Diagnosis, Differential , Female , Follow-Up Studies , Humans , Infant , Kidney Neoplasms/surgery , Male , Neoplasm Staging , ROC Curve , Retrospective Studies , United Kingdom , Wilms Tumor/surgery
8.
Transl Oncol ; 11(6): 1301-1306, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30172241

ABSTRACT

BACKGROUND: Diffuse anaplastic Wilms tumor (DAWT) is a rare, high-risk subtype that is often missed on diagnostic needle biopsy. Somatic mutations in TP53 are associated with the development of anaplasia and with poorer survival, particularly in advanced-stage disease. Early identification of DAWT harboring TP53 abnormalities could improve risk stratification of initial therapy and monitoring for recurrence. METHODS: Droplet digital polymerase chain reaction (ddPCR) was used to evaluate 21 samples from 4 patients with DAWT. For each patient, we assessed TP53 status in frozen tumor, matched germline DNA, and circulating tumor DNA (ctDNA) from plasma, serum, and urine collected throughout treatment. RESULTS: Mutant TP53 was detectable in ctDNA from plasma and serum in all patients. We did not detect variant TP53 in the same volume (200 µl) of urine. One patient displayed heterogeneity of TP53 in the tumor despite both histological sections displaying anaplasia. Concentration of ctDNA from plasma/serum taken prenephrectomy varied significantly between patients, ranging from 0.44 (0.05-0.90) to 125.25 (109.75-140.25) copies/µl. We observed variation in ctDNA throughout treatment, and in all but one patient, ctDNA levels fell significantly following nephrectomy. CONCLUSION: We demonstrate for the first time that ddPCR is an effective method for detection of mutant TP53 in ctDNA from children with DAWT even when there is intratumoral somatic heterogeneity. This should be further explored in a larger cohort of patients, as early detection of circulating variant TP53 may have significant clinical impact on future risk stratification and surveillance.

9.
Pediatr Blood Cancer ; 64(11)2017 Nov.
Article in English | MEDLINE | ID: mdl-28383760

ABSTRACT

BACKGROUND: Nephrogenic rests (NRs) are abnormally persistent foci of embryonal cells, thought to be the precursor lesion of Wilms tumors (WTs). To date, their presence has not been systematically examined in WTs treated with preoperative chemotherapy. METHODS: A systematic analysis of the data on NRs in WTs treated with preoperative chemotherapy obtained from the UK cohort of the International Society of Pediatric Oncology (SIOP) WT 2001 Trial. The study was based on central pathology review of full sets of slides from pathological specimens, with a median of 28 slides reviewed per case. RESULTS: NRs were identified in 40% of unilateral WTs, including 25% perilobar nephrogenic rest (PLNR), 9% intralobar nephrogenic rest (ILNR), 5% both PLNR and ILNR, and 1% nephroblastomatosis, and in 93% of cases with bilateral lesions. ILNRs were associated with stromal histology and a younger age at diagnosis and found frequently in patients with congenital anomalies associated with WT1 mutation. PLNRs were found frequently in patients with overgrowth syndromes. CONCLUSIONS: The prevalence of NRs in WTs after preoperative chemotherapy observed in SIOP UK WT 2001 Trial is similar to the previously published data on NRs not treated with preoperative chemotherapy. Their epidemiology supports at least two pathways to Wilms tumorigenesis.


Subject(s)
Antineoplastic Agents/therapeutic use , Kidney Neoplasms/pathology , Wilms Tumor/pathology , Follow-Up Studies , Humans , International Agencies , Kidney Neoplasms/drug therapy , Kidney Neoplasms/epidemiology , Neoplasm Staging , Preoperative Care , Prevalence , Prognosis , United Kingdom/epidemiology , Wilms Tumor/drug therapy , Wilms Tumor/epidemiology
11.
EBioMedicine ; 9: 120-129, 2016 Jul.
Article in English | MEDLINE | ID: mdl-27333041

ABSTRACT

The evolution of pediatric solid tumors is poorly understood. There is conflicting evidence of intra-tumor genetic homogeneity vs. heterogeneity (ITGH) in a small number of studies in pediatric solid tumors. A number of copy number aberrations (CNA) are proposed as prognostic biomarkers to stratify patients, for example 1q+ in Wilms tumor (WT); current clinical trials use only one sample per tumor to profile this genetic biomarker. We multisampled 20 WT cases and assessed genome-wide allele-specific CNA and loss of heterozygosity, and inferred tumor evolution, using Illumina CytoSNP12v2.1 arrays, a custom analysis pipeline, and the MEDICC algorithm. We found remarkable diversity of ITGH and evolutionary trajectories in WT. 1q+ is heterogeneous in the majority of tumors with this change, with variable evolutionary timing. We estimate that at least three samples per tumor are needed to detect >95% of cases with 1q+. In contrast, somatic 11p15 LOH is uniformly an early event in WT development. We find evidence of two separate tumor origins in unilateral disease with divergent histology, and in bilateral WT. We also show subclonal changes related to differential response to chemotherapy. Rational trial design to include biomarkers in risk stratification requires tumor multisampling and reliable delineation of ITGH and tumor evolution.


Subject(s)
Kidney Neoplasms/pathology , Loss of Heterozygosity/physiology , Wilms Tumor/pathology , Alleles , Biomarkers, Tumor/genetics , Child, Preschool , Chromosomes, Human, Pair 11 , Clonal Evolution , Female , Gene Dosage , Genome , Humans , Infant , Kidney Neoplasms/diagnostic imaging , Kidney Neoplasms/genetics , Magnetic Resonance Imaging , Male , Oligonucleotide Array Sequence Analysis , Wilms Tumor/diagnostic imaging , Wilms Tumor/genetics
12.
J Thorac Cardiovasc Surg ; 151(4): 1191-200.e3, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26769537

ABSTRACT

OBJECTIVE: Heart failure is accompanied by up-regulation of transforming growth factor beta signaling, accumulation of collagen and dysregulation of sarcoplasmic reticulum calcium adenosine triphosphatase cardiac isoform 2a (SERCA2a). We examined the fibrotic response in small and large myocardial infarct, and the effect of overexpression of the SERCA2a gene. METHODS: Ischemic cardiomyopathy was induced via creation of large or small infarct in 26 sheep. Animals were divided into 4 groups: small infarct; large infarct with heart failure; gene-treated (large infarct with heart failure followed by adeno-associated viral vector, serotype 1.SERCA2a gene construct transfer by molecular cardiac surgery with recirculating delivery); and control. RESULTS: Heart failure was significantly less pronounced in the gene-treated and small-infarct groups than in the large-infarct group. Expression of transforming growth factor beta signaling components was significantly higher in the large-infarct group, compared with the small-infarct and gene-treated groups. Both the angiotensin II type 1 receptor and angiotensin II were significantly elevated in the small- and large-infarct groups, whereas gene treatment diminished this effect. Active fibrosis with de novo collagen synthesis was evident in the large-infarct group; the small-infarct and gene-treated groups showed less fibrosis, with a lower ratio of de novo to mature collagen. CONCLUSIONS: The data presented provide evidence that progression of fibrosis is mediated through increased transforming growth factor beta and angiotensin II signaling, which is mitigated by increased SERCA2a gene expression.


Subject(s)
Cardiomyopathies/therapy , Genetic Therapy/methods , Heart Failure/prevention & control , Myocardial Infarction/therapy , Myocardium/enzymology , Sarcoplasmic Reticulum Calcium-Transporting ATPases/biosynthesis , Angiotensin II/metabolism , Animals , Calcium/metabolism , Cardiomyopathies/enzymology , Cardiomyopathies/genetics , Cardiomyopathies/pathology , Cardiomyopathies/physiopathology , Collagen/metabolism , Disease Models, Animal , Enzyme Induction , Fibronectins/metabolism , Fibrosis , Heart Failure/enzymology , Heart Failure/genetics , Heart Failure/pathology , Heart Failure/physiopathology , Hemodynamics , Male , Myocardial Infarction/enzymology , Myocardial Infarction/genetics , Myocardial Infarction/pathology , Myocardial Infarction/physiopathology , Myocardium/pathology , Myofibroblasts/enzymology , Myofibroblasts/pathology , Receptor, Angiotensin, Type 1/metabolism , Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics , Sheep , Time Factors , Transforming Growth Factor beta/metabolism
13.
Genome Med ; 7(1): 11, 2015.
Article in English | MEDLINE | ID: mdl-25763109

ABSTRACT

BACKGROUND: Wilms tumours (WTs) are characterised by several hallmarks that suggest epimutations such as aberrant DNA methylation are involved in tumour progression: loss of imprinting at 11p15, lack of recurrent mutations and formation of nephrogenic rests (NRs), which are lesions of retained undifferentiated embryonic tissue that can give rise to WTs. METHODS: To identify such epimutations, we performed a comprehensive methylome analysis on 20 matched trios of micro-dissected WTs, NRs and surrounding normal kidneys (NKs) using Illumina Infinium HumanMethylation450 Bead Chips and functionally validated findings using RNA sequencing. RESULTS: Comparison of NRs with NK revealed prominent tissue biomarkers: 629 differentially methylated regions, of which 55% were hypermethylated and enriched for domains that are bivalent in embryonic stem cells and for genes expressed during development (P = 2.49 × 10(-5)). Comparison of WTs with NRs revealed two WT subgroups; group-2 WTs and NRs were epigenetically indistinguishable whereas group-1 WTs showed an increase in methylation variability, hypomethylation of renal development genes, hypermethylation and relative loss of expression of cell adhesion genes and known and potential new WT tumour suppressor genes (CASP8, H19, MIR195, RB1 and TSPAN32) and was strongly associated with bilateral disease (P = 0.032). Comparison of WTs and NRs to embryonic kidney highlighted the significance of polycomb target methylation in Wilms tumourigenesis. CONCLUSIONS: Methylation levels vary during cancer evolution. We have described biomarkers related to WT evolution from its precursor NRs which may be useful to differentiate between these tissues for patients with bilateral disease.

14.
Oncotarget ; 6(9): 7232-43, 2015 Mar 30.
Article in English | MEDLINE | ID: mdl-25749049

ABSTRACT

Genomic gain of the proto-oncogene transcription factor gene MYCN is associated with poor prognosis in several childhood cancers. Here we present a comprehensive copy number analysis of MYCN in Wilms tumour (WT), demonstrating that gain of this gene is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. Using whole exome and gene-specific sequencing, together with methylation and expression profiling, we show that MYCN is targeted by other mechanisms, including a recurrent somatic mutation, P44L, and specific DNA hypomethylation events associated with MYCN overexpression in tumours with high risk histologies. We describe parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumours of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolve over time. We report a second bilateral case in which MYCN gain is a germline aberration. Our results suggest a significant role for MYCN dysregulation in the molecular biology of Wilms tumour. We conclude that MYCN gain is prognostically significant, and suggest that the novel P44L somatic variant is likely to be an activating mutation.


Subject(s)
Gene Expression Regulation, Neoplastic , Genes, myc , Kidney Neoplasms/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Wilms Tumor/metabolism , DNA Methylation , DNA Mutational Analysis , Disease-Free Survival , Exome , Gene Dosage , Gene Expression Profiling , Genes, p53 , Humans , Kaplan-Meier Estimate , Kidney Neoplasms/genetics , Mutation , Neoplasm Recurrence, Local/genetics , Oligonucleotide Array Sequence Analysis , Point Mutation , Polymorphism, Single Nucleotide , Prognosis , Proto-Oncogene Mas , Tumor Suppressor Protein p53/metabolism , Wilms Tumor/genetics
15.
Cancer Cell ; 27(2): 298-311, 2015 Feb 09.
Article in English | MEDLINE | ID: mdl-25670083

ABSTRACT

Blastemal histology in chemotherapy-treated pediatric Wilms tumors (nephroblastoma) is associated with adverse prognosis. To uncover the underlying tumor biology and find therapeutic leads for this subgroup, we analyzed 58 blastemal type Wilms tumors by exome and transcriptome sequencing and validated our findings in a large replication cohort. Recurrent mutations included a hotspot mutation (Q177R) in the homeo-domain of SIX1 and SIX2 in tumors with high proliferative potential (18.1% of blastemal cases); mutations in the DROSHA/DGCR8 microprocessor genes (18.2% of blastemal cases); mutations in DICER1 and DIS3L2; and alterations in IGF2, MYCN, and TP53, the latter being strongly associated with dismal outcome. DROSHA and DGCR8 mutations strongly altered miRNA expression patterns in tumors, which was functionally validated in cell lines expressing mutant DROSHA.


Subject(s)
Homeodomain Proteins/genetics , Nerve Tissue Proteins/genetics , RNA-Binding Proteins/genetics , Ribonuclease III/genetics , Wilms Tumor/genetics , Gene Expression Regulation, Neoplastic , Humans , MicroRNAs/biosynthesis , Mutation , Neoplasm Proteins/biosynthesis , Transcriptome , Wilms Tumor/pathology
16.
Future Cardiol ; 10(6): 789-800, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25495820

ABSTRACT

Pathogenesis of heart diseases is associated with an altered expression profile of hundreds of genes. miRNAs are a newly identified layer of gene regulation operating at the post-transcriptional level by pairing to complementary base sequences in target mRNAs. Genetic data have identified the roles of miRNAs in basic pathological processes associated with heart failure: apoptosis, fibrosis, myocardial hypertrophy and cardiac remodeling. Many reports demonstrated that aberrantly expressed miRNAs and their modulation have effects on cardiac insufficiency. Here, we overview the advances in miRNAs as potential targets in the modulation of the heart failure phenotype. miRNA-based therapy holds great promise as a future strategy for treating heart diseases and identifying emerging signaling pathways responsible for the progression of heart failure.


Subject(s)
Heart Failure/etiology , Heart Failure/pathology , MicroRNAs/physiology , Humans , Ventricular Remodeling/physiology
17.
PLoS One ; 9(10): e109924, 2014.
Article in English | MEDLINE | ID: mdl-25313908

ABSTRACT

PURPOSE: The presence of diffuse anaplasia in Wilms tumours (DAWT) is associated with TP53 mutations and poor outcome. As patients receive intensified treatment, we sought to identify whether TP53 mutational status confers additional prognostic information. PATIENTS AND METHODS: We studied 40 patients with DAWT with anaplasia in the tissue from which DNA was extracted and analysed for TP53 mutations and 17p loss. The majority of cases were profiled by copy number (n = 32) and gene expression (n = 36) arrays. TP53 mutational status was correlated with patient event-free and overall survival, genomic copy number instability and gene expression profiling. RESULTS: From the 40 cases, 22 (55%) had TP53 mutations (2 detected only after deep-sequencing), 20 of which also had 17p loss (91%); 18 (45%) cases had no detectable mutation but three had 17p loss. Tumours with TP53 mutations and/or 17p loss (n = 25) had an increased risk of recurrence as a first event (p = 0.03, hazard ratio (HR), 3.89; 95% confidence interval (CI), 1.26-16.0) and death (p = 0.04, HR, 4.95; 95% CI, 1.36-31.7) compared to tumours lacking TP53 abnormalities. DAWT carrying TP53 mutations showed increased copy number alterations compared to those with wild-type, suggesting a more unstable genome (p = 0.03). These tumours showed deregulation of genes associated with cell cycle and DNA repair biological processes. CONCLUSION: This study provides evidence that TP53 mutational analysis improves risk stratification in DAWT. This requires validation in an independent cohort before clinical use as a biomarker.


Subject(s)
Biomarkers, Tumor/genetics , Kidney Neoplasms/genetics , Kidney/pathology , Neoplasm Recurrence, Local/genetics , Tumor Suppressor Protein p53/genetics , Wilms Tumor/genetics , Anaplasia/genetics , Anaplasia/metabolism , Anaplasia/mortality , Child , Child, Preschool , DNA Copy Number Variations , DNA Mutational Analysis , Frameshift Mutation , Genetic Association Studies , Genomic Instability , Humans , Infant , Kidney Neoplasms/metabolism , Kidney Neoplasms/mortality , Polymorphism, Single Nucleotide , Prognosis , Proportional Hazards Models , Risk Assessment , Transcriptome , Wilms Tumor/metabolism , Wilms Tumor/mortality
18.
Genome Biol ; 15(8): 434, 2014 Aug 19.
Article in English | MEDLINE | ID: mdl-25134821

ABSTRACT

BACKGROUND: Wilms tumor is the most common pediatric renal malignancy and there is a clinical need for a molecular biomarker to assess treatment response and predict relapse. The known mutated genes in this tumor type show low mutation frequencies, whereas aberrant methylation at 11p15 is by far the most common aberration. We therefore analyzed the epigenome, rather than the genome, to identify ubiquitous tumor-specific biomarkers. RESULTS: Methylome analysis of matched normal kidney and Wilms tumor identifies 309 preliminary methylation variable positions which we translate into three differentially methylated regions (DMR) for use as tumor-specific biomarkers. Using two novel algorithms we show that these three DMRs are not confounded by cell type composition. We further show that these DMRs are not methylated in embryonic blastema but are intermediately methylated in Wilms tumor precursor lesions. We validate the biomarker DMRs using two independent sample sets of normal kidney and Wilms tumor and seven Wilms tumor histological subtypes, achieving 100% and 98% correct classification, respectively. As proof-of-principle for clinical utility, we successfully use biomarker DMR-2 in a pilot analysis of cell-free circulating DNA to monitor tumor response during treatment in ten patients. CONCLUSIONS: These findings define the most common methylated regions in Wilms tumor known to date which are not associated with their embryonic origin or precursor stage. We show that this tumor-specific methylated DNA is released into the blood circulation where it can be detected non-invasively showing potential for clinical utility.


Subject(s)
Biomarkers, Tumor/blood , Biomarkers, Tumor/genetics , DNA Methylation , Kidney Neoplasms/genetics , Wilms Tumor/genetics , Algorithms , Cell-Free System , Epigenesis, Genetic , Genome, Human , Humans , Kidney Neoplasms/blood , Kidney Neoplasms/pathology , Pilot Projects , Wilms Tumor/blood , Wilms Tumor/pathology
19.
J Thorac Cardiovasc Surg ; 148(3): 1065-72, 1073e1-2; discussion1072-3, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25037619

ABSTRACT

OBJECTIVE: Therapeutic safety and efficacy are the basic prerequisites for clinical gene therapy. We investigated the effect of high-dose molecular cardiac surgery with recirculating delivery (MCARD)-mediated adeno-associated virus 9 (AAV9)/sarcoplasmic reticulum Ca(2+) adenosine triphosphatase (SERCA2a) gene delivery on clinical parameters, oxidative stress, humoral and cellular immune responses, and cardiac remodeling. METHODS: Ischemic cardiomyopathy was generated in a sheep model. The sheep were assigned to 1 of 2 groups: control (n = 10) and study (MCARD, n = 6). The control group underwent no intervention and the study group received 10(14) genome copies of AAV9/SERCA2a 4 weeks after infarction. RESULTS: Our ischemic model produced reliable infarcts leading to heart failure. The baseline ejection fraction in the MCARD group was 57.6% ± 1.6% versus 61.2% ± 1.9% in the control group (P > .05). At 12 weeks after infarction, the MCARD group had superior left ventricular function compared with the control group: stroke volume index, 46.6 ± 1.8 versus 35.8 ± 2.5 mL/m(2) (P < .05); ejection fraction, 46.2% ± 1.9% versus 38.7% ± 2.5% (P < .05); and left ventricular end-systolic and end-diastolic dimensions, 41.3 ± 1.7 versus 48.2 ± 1.4 mm and 51.2 ± 1.5 versus 57.6 ± 1.7 mm, respectively (P < .05). The markers of oxidative stress were significantly reduced in the infarct zone in the MCARD group. No positive T-cell-mediated immune response was seen in the MCARD group at any point. Myocyte hypertrophy was also significantly attenuated in the MCARD group compared with the control group. CONCLUSIONS: Cardiac overexpression of the SERCA2a gene by way of MCARD is a safe therapeutic intervention. It significantly improves left ventricular function, decreases markers of oxidative stress, abrogates myocyte hypertrophy, arrests remodeling, and does not induce a T-cell-mediated immune response.


Subject(s)
Cardiac Surgical Procedures , Dependovirus/enzymology , Gene Transfer Techniques , Genetic Vectors , Myocardial Infarction/therapy , Myocardium/enzymology , Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism , Animals , Biomarkers/metabolism , Cardiac Surgical Procedures/adverse effects , Cardiomegaly/enzymology , Cardiomegaly/genetics , Cardiomegaly/prevention & control , Dependovirus/genetics , Disease Models, Animal , Gene Transfer Techniques/adverse effects , Humans , Immunity, Cellular , Immunity, Humoral , Male , Myocardial Infarction/enzymology , Myocardial Infarction/genetics , Myocardial Infarction/immunology , Myocardial Infarction/pathology , Myocardial Infarction/physiopathology , Myocardium/immunology , Myocardium/pathology , Oxidative Stress , Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics , Sheep , Stroke Volume , T-Lymphocytes/immunology , Time Factors , Ventricular Function, Left , Ventricular Remodeling
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