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1.
Br Ir Orthopt J ; 19(1): 44-51, 2023.
Article in English | MEDLINE | ID: mdl-37332843

ABSTRACT

Introduction: Cerebral visual impairment (CVI) is the most common cause of visual impairment in children in the UK. Diagnosis is based on identification of visual behaviours (ViBes) relating to visual dysfunction. Examination techniques and inventories have been developed to elicit these in children with a developmental age of two years or more. The absence of a structured approach to recording visual behaviours in children with complex needs is a barrier to diagnosis. The aim of the study was to develop a matrix of visual behaviours seen in pre-verbal and pre-motor children with visual impairment and establish its content validity and inter-rater reliability. Methods: ViBe content validation:: Visual behaviour descriptors relating to visual function were collated and categorised by expert consensus of vision professionals into a matrix composed of three functions (attention, field/fixation, motor response) and five levels (0 = no awareness; 1 = visual awareness; 2 = visual attention; 3 = visual detection; 4 = visual understanding).ViBe inter-rater reliability:: The participants (two orthoptists, an optometrist, an ophthalmologist and two qualified teachers of the visually impaired) used the ViBe matrix to independently score each of 17 short video clips of children demonstrating visual behaviours seen in CVI. Results: The ViBe matrix will be presented. Cohen's kappa for the matrix was 0.67, demonstrating moderate-to-strong inter-rater reliability. Conclusion: The development of standardised descriptors can support clinicians and teachers in identifying areas of concern for children with complex needs. In addition, the ViBe matrix could be utilised in research, clinical and diagnostic reports to clearly communicate the areas of visual dysfunction and track progress resulting from interventions. Key Points: The absence of a structured approach to recording visual behaviours in children with complex needs is a barrier to diagnosis.The ViBe matrix offers descriptors relating to visual behaviours and has demonstrated acceptable inter-rater reliability.The tool may support the identification and diagnosis of cerebral visual impairment in a population of children who cannot access standard testing.

2.
Bioengineering (Basel) ; 9(10)2022 Oct 17.
Article in English | MEDLINE | ID: mdl-36290529

ABSTRACT

Optimisation of tissue engineering (TE) processes requires models that can identify relationships between the parameters to be optimised and predict structural and performance outcomes from both physical and chemical processes. Currently, Design of Experiments (DoE) methods are commonly used for optimisation purposes in addition to playing an important role in statistical quality control and systematic randomisation for experiment planning. DoE is only used for the analysis and optimisation of quantitative data (i.e., number-based, countable or measurable), while it lacks the suitability for imaging and high dimensional data analysis. Machine learning (ML) offers considerable potential for data analysis, providing a greater flexibility in terms of data that can be used for optimisation and predictions. Its application within the fields of biomaterials and TE has recently been explored. This review presents the different types of DoE methodologies and the appropriate methods that have been used in TE applications. Next, ML algorithms that are widely used for optimisation and predictions are introduced and their advantages and disadvantages are presented. The use of different ML algorithms for TE applications is reviewed, with a particular focus on their use in optimising 3D bioprinting processes for tissue-engineered construct fabrication. Finally, the review discusses the future perspectives and presents the possibility of integrating DoE and ML in one system that would provide opportunities for researchers to achieve greater improvements in the TE field.

3.
Bioengineering (Basel) ; 8(10)2021 Oct 18.
Article in English | MEDLINE | ID: mdl-34677217

ABSTRACT

Cartilage is an avascular tissue with extremely limited self-regeneration capabilities. At present, there are no existing treatments that effectively stop the deterioration of cartilage or reverse its effects; current treatments merely relieve its symptoms and surgical intervention is required when the condition aggravates. Thus, cartilage damage remains an ongoing challenge in orthopaedics with an urgent need for improved treatment options. In recent years, major advances have been made in the development of three-dimensional (3D) bioprinted constructs for cartilage repair applications. 3D bioprinting is an evolutionary additive manufacturing technique that enables the precisely controlled deposition of a combination of biomaterials, cells, and bioactive molecules, collectively known as bioink, layer-by-layer to produce constructs that simulate the structure and function of native cartilage tissue. This review provides an insight into the current developments in 3D bioprinting for cartilage tissue engineering. The bioink and construct properties required for successful application in cartilage repair applications are highlighted. Furthermore, the potential for translation of 3D bioprinted constructs to the clinic is discussed. Overall, 3D bioprinting demonstrates great potential as a novel technique for the fabrication of tissue engineered constructs for cartilage regeneration, with distinct advantages over conventional techniques.

4.
Sensors (Basel) ; 19(10)2019 May 17.
Article in English | MEDLINE | ID: mdl-31108837

ABSTRACT

Understanding hydrological processes in large, open areas, such as catchments, and further modelling these processes are still open research questions. The system proposed in this work provides an automatic end-to-end pipeline from data collection to information extraction that can potentially assist hydrologists to better understand the hydrological processes using a data-driven approach. In this work, the performance of a low-cost off-the-shelf self contained sensor unit, which was originally designed and used to monitor liquid levels, such as AdBlue, fuel, lubricants etc., in a sealed tank environment, is first examined. This process validates that the sensor does provide accurate water level information for open water level monitoring tasks. Utilising the dataset collected from eight sensor units, an end-to-end pipeline of automating the data collection, data processing and information extraction processes is proposed. Within the pipeline, a data-driven anomaly detection method that automatically extracts rapid changes in measurement trends at a catchment scale. The lag-time of the test site (Dodder catchment Dublin, Ireland) is also analyzed. Subsequently, the water level response in the catchment due to storm events during the 27 month deployment period is illustrated. To support reproducible and collaborative research, the collected dataset and the source code of this work will be publicly available for research purposes.

5.
PLoS One ; 8(8): e71777, 2013.
Article in English | MEDLINE | ID: mdl-23990986

ABSTRACT

Gene amplification at chromosome 4q12 is a common alteration in human high grade gliomas including glioblastoma, a CNS tumour with consistently poor prognosis. This locus harbours the known oncogenes encoding the receptor tyrosine kinases PDGFRA, KIT, and VEGFR2. These receptors are potential targets for novel therapeutic intervention in these diseases, with expression noted in tumour cells and/or associated vasculature. Despite this, a detailed assessment of their relative contributions to different high grade glioma histologies and the underlying heterogeneity within glioblastoma has been lacking. We studied 342 primary high grade gliomas for individual gene amplification using specific FISH probes, as well as receptor expression in the tumour and endothelial cells by immunohistochemistry, and correlated our findings with specific tumour cell morphological types and patterns of vasculature. We identified amplicons which encompassed PDGFRA only, PDGFRA/KIT, and PDGFRA/KIT/VEGFR2, with distinct phenotypic correlates. Within glioblastoma specimens, PDGFRA amplification alone was linked to oligodendroglial, small cell and sarcomatous tumour cell morphologies, and rare MGMT promoter methylation. A younger age at diagnosis and better clinical outcome in glioblastoma patients is only seen when PDGFRA and KIT are co-amplified. IDH1 mutation was only found when all three genes are amplified; this is a subgroup which also harbours extensive MGMT promoter methylation. Whilst PDGFRA amplification was tightly linked to tumour expression of the receptor, this was not the case for KIT or VEGFR2. Thus we have identified differential patterns of gene amplification and expression of RTKs at the 4q12 locus to be associated with specific phenotypes which may reflect their distinct underlying mechanisms.


Subject(s)
Chromosomes, Human, Pair 4/genetics , Gene Amplification , Glioblastoma/genetics , Proto-Oncogene Proteins c-kit/genetics , Receptor, Platelet-Derived Growth Factor alpha/genetics , Vascular Endothelial Growth Factor Receptor-2/genetics , Adult , Aged , Aged, 80 and over , Chromosomes, Human, Pair 4/metabolism , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Glioblastoma/metabolism , Glioblastoma/parasitology , Humans , Immunohistochemistry , In Situ Hybridization, Fluorescence , Kaplan-Meier Estimate , Male , Middle Aged , Phenotype , Prognosis , Proto-Oncogene Proteins c-kit/metabolism , Receptor, Platelet-Derived Growth Factor alpha/metabolism , Vascular Endothelial Growth Factor Receptor-2/metabolism
6.
Cancer Res ; 72(7): 1614-20, 2012 Apr 01.
Article in English | MEDLINE | ID: mdl-22311673

ABSTRACT

Intratumoral heterogeneity in human solid tumors represents a major barrier for the development of effective molecular treatment strategies, as treatment efficacies will reflect the molecular variegation in individual tumors. In glioblastoma, the generation of composite genomic profiles from bulk tumor samples has allowed one to map the genomic amplifications of putative genetic drivers and to prioritize therapeutic targeting strategies aimed at eradicating the tumor burden. Notably, amplification of multiple receptor tyrosine kinases (RTK) within a single tumor specimen obtained from patients is frequently observed. In this study, use of a detailed multicolor FISH mapping procedure in pathologic specimens revealed a mutual exclusivity of gene amplification in the majority of glioblastoma tumors examined. In particular, the two most commonly amplified RTK genes, EGFR and PDGFRA, were found to be present in variable proportions across the tumors, with one or the other gene predominating in certain areas of the same specimen. Our findings have profound implications for designing efficacious therapeutic regimens, as it remains unclear that how the cells with different gene amplification events contribute to disease propagation or the response to molecular targeted therapies.


Subject(s)
Brain Neoplasms/genetics , ErbB Receptors/genetics , Gene Amplification , Glioblastoma/genetics , Receptor, Platelet-Derived Growth Factor alpha/genetics , Adult , Aged , Aged, 80 and over , Female , Gene Dosage , Humans , Male , Middle Aged
7.
Genes Chromosomes Cancer ; 50(12): 982-95, 2011 Dec.
Article in English | MEDLINE | ID: mdl-21882282

ABSTRACT

Anaplasia in Wilms tumor, a distinctive histology characterized by abnormal mitoses, is associated with poor patient outcome. While anaplastic tumors frequently harbour TP53 mutations, little is otherwise known about their molecular biology. We have used array comparative genomic hybridization (aCGH) and cDNA microarray expression profiling to compare anaplastic and favorable histology Wilms tumors to determine their common and differentiating features. In addition to changes on 17p, consistent with TP53 deletion, recurrent anaplasia-specific genomic loss and under-expression were noted in several other regions, most strikingly 4q and 14q. Further aberrations, including gain of 1q and loss of 16q were common to both histologies. Focal gain of MYCN, initially detected by high resolution aCGH profiling in 6/61 anaplastic samples, was confirmed in a significant proportion of both tumor types by a genomic quantitative PCR survey of over 400 tumors. Overall, these results are consistent with a model where anaplasia, rather than forming an entirely distinct molecular entity, arises from the general continuum of Wilms tumor by the acquisition of additional genomic changes at multiple loci.


Subject(s)
Anaplasia/genetics , Chromosome Aberrations , Chromosomes, Human, Pair 14 , Chromosomes, Human, Pair 4 , Kidney Neoplasms/genetics , Nuclear Proteins/genetics , Oncogene Proteins/genetics , Wilms Tumor/genetics , Adolescent , Child , Child, Preschool , Comparative Genomic Hybridization/methods , DNA Copy Number Variations , Female , Genetic Predisposition to Disease , Humans , Infant , Male , Microarray Analysis/methods , N-Myc Proto-Oncogene Protein , Neoplasm Recurrence, Local/genetics , Oligonucleotide Array Sequence Analysis/methods , Survival Analysis
8.
Cancer Res ; 70(22): 9243-52, 2010 Nov 15.
Article in English | MEDLINE | ID: mdl-20935218

ABSTRACT

Sensitivity to temozolomide is restricted to a subset of glioblastoma patients, with the major determinant of resistance being a lack of promoter methylation of the gene encoding the repair protein DNA methyltransferase MGMT, although other mechanisms are thought to be active. There are, however, limited preclinical data in model systems derived from pediatric glioma patients. We screened a series of cell lines for temozolomide efficacy in vitro, and investigated the differential mechanisms of resistance involved. In the majority of cell lines, a lack of MGMT promoter methylation and subsequent protein overexpression were linked to temozolomide resistance. An exception was the pediatric glioblastoma line KNS42. Expression profiling data revealed a coordinated upregulation of HOX gene expression in resistant lines, especially KNS42, which was reversed by phosphoinositide 3-kinase pathway inhibition. High levels of HOXA9/HOXA10 gene expression were associated with a shorter survival in pediatric high-grade glioma patient samples. Combination treatment in vitro of pathway inhibition and temozolomide resulted in a highly synergistic interaction in KNS42 cells. The resistance gene signature further included contiguous genes within the 12q13-q14 amplicon, including the Akt enhancer PIKE, significantly overexpressed in the KNS42 line. These cells were also highly enriched for CD133 and other stem cell markers. We have thus shown an in vitro link between phosphoinositide 3-kinase-mediated HOXA9/HOXA10 expression, and a drug-resistant, progenitor cell phenotype in MGMT-independent pediatric glioblastoma.


Subject(s)
Dacarbazine/analogs & derivatives , Homeodomain Proteins/genetics , O(6)-Methylguanine-DNA Methyltransferase/genetics , Phosphatidylinositol 3-Kinases/genetics , Antineoplastic Agents, Alkylating/pharmacology , Blotting, Western , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Survival/drug effects , Child , Cluster Analysis , DNA Methylation/drug effects , Dacarbazine/pharmacology , Drug Resistance, Neoplasm/genetics , Flow Cytometry , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Glioblastoma/genetics , Glioblastoma/metabolism , Glioblastoma/pathology , Homeobox A10 Proteins , Homeodomain Proteins/metabolism , Humans , Inhibitory Concentration 50 , Neoplastic Stem Cells/metabolism , O(6)-Methylguanine-DNA Methyltransferase/metabolism , Oligonucleotide Array Sequence Analysis , Phosphatidylinositol 3-Kinases/metabolism , Promoter Regions, Genetic/genetics , Temozolomide
9.
Clin Cancer Res ; 16(13): 3368-77, 2010 Jul 01.
Article in English | MEDLINE | ID: mdl-20570930

ABSTRACT

PURPOSE: As genome-scale technologies begin to unravel the complexity of the equivalent tumors in adults, we can attempt detailed characterization of high-grade gliomas in children, that have until recently been lacking. Toward this end, we sought to validate and extend investigations of the differences between pediatric and adult tumors. EXPERIMENTAL DESIGN: We carried out copy number profiling by array comparative genomic hybridization using a 32K bacterial artificial chromosome platform on 63 formalin-fixed paraffin-embedded cases of high-grade glioma arising in children and young people (<23 years). RESULTS: The genomic profiles of these tumors could be subclassified into four categories: those with stable genomes, which were associated with a better prognosis; those with aneuploid and those with highly rearranged genomes; and those with an amplifier genotype, which had a significantly worse clinical outcome. Independent of this was a clear segregation of cases with 1q gain (more common in children) from those with concurrent 7 gain/10q loss (a defining feature of adults). Detailed mapping of all the amplification and deletion events revealed numerous low-frequency amplifications, including IGF1R, PDGFRB, PIK3CA, CDK6, CCND1, and CCNE1, and novel homozygous deletions encompassing unknown genes, including those at 5q35, 10q25, and 22q13. Despite this, aberrations targeting the "core signaling pathways" in adult glioblastomas are significantly underrepresented in the pediatric setting. CONCLUSIONS: These data highlight that although there are overlaps in the genomic events driving gliomagenesis of all ages, the pediatric disease harbors a distinct spectrum of copy number aberrations compared with adults.


Subject(s)
Brain Neoplasms/genetics , DNA Copy Number Variations , Glioma/genetics , Adolescent , Adult , Child , Child, Preschool , Comparative Genomic Hybridization , Gene Amplification , Gene Deletion , Glioblastoma/genetics , Humans
10.
Explore (NY) ; 5(6): 330-7, 2009.
Article in English | MEDLINE | ID: mdl-19913759

ABSTRACT

Chronic depression is a highly debilitating psychobiological disorder that affects mind, body, and spirit. The need for effective integrative treatments for depression is fueled by high recurrence and relapse rates, as well as growing consumer demand for natural and holistic approaches that recognize depression is a systemic problem. A 24-week multimodal group treatment program was piloted to assess whether psychoeducation, lifestyle modification, meditation, and mind/body skills training would reduce symptomatology and improve overall balance and well-being in nonmedicated patients with moderate depression. The group treatment was conducted in a healing space associated with an academic integrative medicine center. Fourteen adult patients (mean age = 51.7 years) participated in two treatment groups (seven patients per group). Treatment efficacy was evaluated by changes on the Beck Depression Inventory (BDI-II), the primary outcome measure, completed at pretreatment (week zero), posttreatment (week 12), and two follow-up points (weeks 16 and 24). Positive affect and overall well-being were assessed using the Symptom Checklist-90 Revised, the Life Orientation Test, the Short Form Health Survey-12, and the Psychological Well-Being Index. Comparisons of pretreatment and posttreatment scores on the BDI-II showed a clinically significant decline in depressed mood and negative affect (P < .001), as well as significant improvement across the positive affect and well-being measures. This outcome, which was statistically sustained for six months, suggests that a multimodal holistic mind/body group approach can benefit a segment of the chronically depressed population.


Subject(s)
Depressive Disorder/therapy , Mind-Body Therapies , Adult , Affect , Chronic Disease , Combined Modality Therapy , Female , Health Education , Humans , Life Style , Male , Meditation , Middle Aged , Pilot Projects , Psychotherapy, Group , Treatment Outcome
11.
Clin Cancer Res ; 15(18): 5753-61, 2009 Sep 15.
Article in English | MEDLINE | ID: mdl-19737945

ABSTRACT

PURPOSE: The epidermal growth factor receptor (EGFR) is amplified and overexpressed in adult glioblastoma, with response to targeted inhibition dependent on the underlying biology of the disease. EGFR has thus far been considered to play a less important role in pediatric glioma, although extensive data are lacking. We have sought to clarify the role of EGFR in pediatric high-grade glioma (HGG). EXPERIMENTAL DESIGN: We retrospectively studied a total of 90 archival pediatric HGG specimens for EGFR protein overexpression, gene amplification, and mutation and assessed the in vitro sensitivity of pediatric glioma cell line models to the small-molecule EGFR inhibitor erlotinib. RESULTS: Amplification was detected in 11% of cases, with corresponding overexpression of the receptor. No kinase or extracellular domain mutations were observed; however, 6 of 35 (17%) cases harbored the EGFRvIII deletion, including two anaplastic oligodendrogliomas and a gliosarcoma overexpressing EGFRvIII in the absence of gene amplification and coexpressing platelet-derived growth factor receptor alpha. Pediatric glioblastoma cells transduced with wild-type or deletion mutant EGFRvIII were not rendered more sensitive to erlotinib despite expressing wild-type PTEN. Phosphorylated receptor tyrosine kinase profiling showed a specific activation of platelet-derived growth factor receptor alpha/beta in EGFRvIII-transduced pediatric glioblastoma cells, and targeted coinhibition with erlotinib and imatinib leads to enhanced efficacy in this model. CONCLUSIONS: These data identify an elevated frequency of EGFR gene amplification and EGFRvIII mutation in pediatric HGG than previously recognized and show the likely necessity of targeting multiple genetic alterations in the tumors of these children.


Subject(s)
ErbB Receptors/genetics , ErbB Receptors/metabolism , Glioma/drug therapy , Glioma/genetics , Sequence Deletion , Adolescent , Blotting, Western , Cell Proliferation/drug effects , Child , ErbB Receptors/antagonists & inhibitors , Erlotinib Hydrochloride , Glioma/diagnosis , Humans , Prognosis , Quinazolines/pharmacology , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Tumor Cells, Cultured
12.
PLoS One ; 4(4): e5209, 2009.
Article in English | MEDLINE | ID: mdl-19365568

ABSTRACT

BACKGROUND: Although paediatric high grade gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular and phenotypic characterisation of a series of paediatric high grade glioma cell lines in comparison to routinely used adult lines. PRINCIPAL FINDINGS: All lines proliferate as adherent monolayers and express glial markers. Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways. Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response. SIGNIFICANCE: These data demonstrate that glioma cell lines derived from paediatric patients show key molecular differences to those from adults, some of which are well known, whilst others may provide novel targets for evaluation in primary tumours. We thus provide the rationale and demonstrate the practicability of using paediatric glioma cell lines for preclinical and mechanistic studies.


Subject(s)
Cell Line, Tumor , Drug Design , Glioma , Phenotype , Adult , Astrocytes/metabolism , Biomarkers/metabolism , Cell Line, Tumor/metabolism , Cell Line, Tumor/pathology , Child , Chromosome Aberrations , Enzyme Activation , Epigenesis, Genetic , Gene Expression Profiling , Glioma/genetics , Glioma/metabolism , Glioma/pathology , Humans , Immunophenotyping , Loss of Heterozygosity , Mitogen-Activated Protein Kinases/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Signal Transduction/physiology , Stem Cells/metabolism
13.
Clin Cancer Res ; 13(15 Pt 1): 4360-4, 2007 Aug 01.
Article in English | MEDLINE | ID: mdl-17646270

ABSTRACT

PURPOSE: Epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase overexpressed in a variety of human malignancies, against which targeted therapies have shown efficacy in lung and brain tumors. Clinical responses to EGFR inhibitors have been found to be highly dependent on the presence of activating mutations, whereas gene amplification, downstream activation of Akt, and abnormalities in PTEN are also reported predictive factors. We sought to evaluate these variables in pediatric renal tumors. EXPERIMENTAL DESIGN: We screened a series of 307 pediatric renal tumors for EGFR expression by immunohistochemistry and gene amplification by chromogenic in situ hybridization. In identifying a striking predilection for certain tumor types, we further analyzed the clear cell sarcomas of the kidney (CCSK) for mutations in EGFR and PTEN. RESULTS: Although only 23 of 177 (13.0%) nonanaplastic Wilms' tumors were EGFR positive, 4 of 11 (36.4%) anaplastic tumors showed receptor overexpression. In addition, 5 of 9 (55.6%) mesoblastic nephromas and 12 of 12 (100%) CCSKs were strongly immunoreactive for EGFR. In studying the CCSKs in more detail, we identified gene amplification in 1 of 12 (8.3%) cases and a somatic T790M EGFR mutation in a further case. These two samples additionally harbored mutations in PTEN. Downstream pathway activation, as assayed by phosphorylated Akt expression, was observed in 8 of 12 (66.7%) cases. CONCLUSIONS: Together, these data show dysregulation of the EGFR pathway at multiple levels in CCSKs. Identification of factors predictive of poor response to targeted therapy, including the drug resistance T790M mutation, may provide a rationale for upfront trials with irreversible inhibitors of EGFR in children with these tumors.


Subject(s)
ErbB Receptors/metabolism , Kidney Neoplasms/metabolism , PTEN Phosphohydrolase/metabolism , Sarcoma, Clear Cell/metabolism , Signal Transduction , Child, Preschool , Gene Amplification , Humans , Immunoenzyme Techniques , In Situ Hybridization , Infant , Kidney Neoplasms/pathology , Mutation , Nephroma, Mesoblastic/metabolism , Nephroma, Mesoblastic/pathology , Phosphorylation , Proto-Oncogene Proteins c-akt/metabolism , Rhabdoid Tumor/metabolism , Rhabdoid Tumor/pathology , Sarcoma, Clear Cell/pathology , Tissue Array Analysis , Wilms Tumor/metabolism , Wilms Tumor/pathology
14.
Clin Cancer Res ; 12(24): 7284-93, 2006 Dec 15.
Article in English | MEDLINE | ID: mdl-17189400

ABSTRACT

PURPOSE: The most well established molecular markers of poor outcome in Wilms' tumor are loss of heterozygosity at chromosomes 1p and/or 16q, although to date no specific genes at these loci have been identified. We have previously shown a link between genomic gain of chromosome 1q and tumor relapse and sought to further elucidate the role of genes on 1q in treatment failure. EXPERIMENTAL DESIGN: Microarray-based comparative genomic hybridization identified a microamplification harboring a single gene (CACNA1E) at 1q25.3 in 6 of 76 (7.9%) Wilms' tumors, correlating with a shorter relapse-free survival (P = 0.0044, log-rank test). Further characterization of this gene was carried out by measuring mRNA and protein expression as well as stable transfection of HEK293 cells. RESULTS: Overexpression of the CACNA1E transcript was associated with DNA copy number (P = 0.0204, ANOVA) and tumor relapse (P = 0.0851, log-rank test). Immunohistochemistry against the protein product Ca(V)2.3 revealed expression localized to the apical membrane in the distal tubules of normal kidney but not to the metanephric blastemal cells of fetal kidney from which Wilms' tumors arise. Nuclear localization in 99 of 160 (61.9%) Wilms' tumor cases correlated with a reduced relapse-free survival, particularly in cases treated with preoperative chemotherapy (P = 0.009, log-rank test). Expression profiling of stably transfected HEK293 cells revealed specific up-regulation of the immediate early response genes EGR1/EGR2/EGR3 and FOS/FOSB, mediated by activation of the MEK/ERK5/Nur77 pathway. CONCLUSIONS: These data identify a unique genetic aberration with direct clinical relevance in Wilms' tumor relapse and provide evidence for a potential novel mechanism of treatment resistance in these tumors.


Subject(s)
Calcium Channels, R-Type/genetics , Calcium Channels, R-Type/metabolism , Cation Transport Proteins/genetics , Cation Transport Proteins/metabolism , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Wilms Tumor/metabolism , Wilms Tumor/pathology , Cells, Cultured , Chromosomes, Human, Pair 1 , Disease-Free Survival , Early Growth Response Protein 1/metabolism , Early Growth Response Protein 2/metabolism , Early Growth Response Protein 3/metabolism , Gene Amplification , Gene Expression Regulation, Neoplastic , Genes, Wilms Tumor , Humans , Kidney/cytology , Kidney/embryology , Kidney/metabolism , Kidney Neoplasms/genetics , Kidney Neoplasms/therapy , MAP Kinase Kinase 5/metabolism , Neoplasm Staging , Oligonucleotide Array Sequence Analysis , Proto-Oncogene Proteins c-fos/metabolism , Recurrence , Wilms Tumor/genetics , Wilms Tumor/therapy
15.
Cancer Res ; 66(23): 11148-55, 2006 Dec 01.
Article in English | MEDLINE | ID: mdl-17145858

ABSTRACT

Most Wilms' tumors are of low stage, favorable histology, and have a high likelihood of cure with current multimodal therapy. Despite this, there remains a group of patients whose tumors recur for whom intensive salvage regimens result in survival of only 50%. Fitting a Cox proportional hazards model to microarray-based comparative genomic hybridization (aCGH) data on 68 Wilms' tumor samples, we identified a significant correlation between increased copy number at chromosome 15q26.3 insulin-like growth factor I receptor (IGFIR) and tumor relapse (adjusted P = 0.014). Wilms' tumors (13%) exhibited a low-level gain corresponding to three to four copies of the gene by aCGH analysis, 9 of 10 of which exhibited high IGFIR mRNA levels. Although IGFIR protein expression was restricted to the epithelial cells of fetal kidney and Wilms' tumors in most cases, 12% of tumors were also found to express IGFIR in the blastemal compartment. Blastemal IGFIR protein expression was associated with an increased copy number and a shorter relapse-free survival time (P = 0.027, log-rank test). In addition to the membrane localization, IGFIR was localized to the perinuclear region of the blastemal cells in 6% of Wilms' tumors. These data provide evidence that an increase in IGFIR gene copy number results in aberrant expression in the blastemal compartment of some Wilms' tumors and is associated with an adverse outcome in these patients. These findings suggest the possibility of use of targeted agents in the therapy of these children.


Subject(s)
Gene Expression Regulation, Neoplastic , Receptor, IGF Type 1/genetics , Wilms Tumor/pathology , Cell Nucleus/metabolism , Chromosomes, Human, Pair 15/genetics , Epithelial Cells/metabolism , Gene Dosage , Genome, Human/genetics , Humans , Immunohistochemistry/statistics & numerical data , In Situ Hybridization, Fluorescence/methods , In Situ Hybridization, Fluorescence/statistics & numerical data , Kaplan-Meier Estimate , Kidney/cytology , Kidney/metabolism , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Neoplasm Recurrence, Local , Nucleic Acid Hybridization/methods , Prognosis , Proportional Hazards Models , Receptor, IGF Type 1/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Wilms Tumor/genetics , Wilms Tumor/metabolism
16.
Genomics ; 87(2): 298-306, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16271290

ABSTRACT

The ability to utilize formalin-fixed, paraffin-embedded (FFPE) archival specimens reliably for high-resolution molecular genetic analysis would be of immense practical application in the study of human disease. We have evaluated the ability of the GenomePlex whole genome amplification (WGA) kit to amplify frozen and FFPE tissue for use in array CGH (aCGH). GenomePlex gave highly representative data compared with unamplified controls both from frozen material (Pearson's R(2) = 0.898) and from FFPE (R(2) = 0.883). Artifactual amplification observed using DOP-PCR at chromosomes 1p, 3, 13q, and 16p was not seen with GenomePlex. Highly reproducible aCGH profiles were obtained using as little as 5 ng starting material from FFPE (R(2) = 0.918). This WGA method should readily lend itself to the determination of DNA copy number alterations from small fresh-frozen and FFPE clinical tumor specimens, although some care must be taken to optimize the DNA extraction procedure.


Subject(s)
DNA, Neoplasm/genetics , Formaldehyde/chemistry , Genome , Nucleic Acid Hybridization , Paraffin Embedding , Tissue Fixation , Humans , Polymerase Chain Reaction
17.
Leuk Res ; 29(7): 803-12, 2005 Jul.
Article in English | MEDLINE | ID: mdl-15927676

ABSTRACT

WT1 has been implicated in human leukemia and hematopoiesis, but its role in stem cell differentiation is not yet fully defined. We show that Wt1-null murine fetal liver cells are capable of reconstituting functional hematopoiesis following transplantation into irradiated recipients. There was also no significant difference between the in vitro colony-forming ability of wild-type and Wt1-null cells. Using a reporter gene assay in a transgenic mouse system, expression from the WT1 promoter was detectable in adult bone marrow, but undetectable in subsets of different hematopoietic cells. We conclude that Wt1 is not essential for murine hematopoiesis and that there may be significant differences in its role between mouse and man.


Subject(s)
Hematopoiesis/physiology , WT1 Proteins/genetics , Animals , Cell Differentiation/physiology , Colony-Forming Units Assay , Humans , Mice , Mice, Knockout , Mice, Transgenic , Promoter Regions, Genetic , Stem Cells/cytology , Stem Cells/physiology , WT1 Proteins/deficiency
19.
Pediatr Nephrol ; 20(1): 81-5, 2005 Jan.
Article in English | MEDLINE | ID: mdl-15503171

ABSTRACT

Denys-Drash syndrome (DDS) is characterized by nephropathy, genital abnormalities, and predisposition to Wilms tumor. DDS is associated with constitutional WT1 mutations, the majority being missense mutations in the zinc-finger region. A dominant-negative mode of action of the mutant DDS proteins is thought to explain the more severe genitourinary phenotype seen in DDS compared with children with complete deletion of one WT1 allele. We present a phenotypically female child who presented with bilateral Wilms tumor at 8 months of age. She was found to have an XY karyotype and diagnosed with DDS. In the constitutional DNA of this child we found a previously unreported mutation in exon 1 of WT1. This de novo mutation, delT in codon 40, is predicted to produce a termination signal in codon 90 (F40fsX90). This frameshift mutation results in a severely truncated protein, which would remove both the zinc-finger DNA-binding domain and the majority of the N-terminal regulatory domain, including regions previously shown in vitro to be necessary for inhibition of WT1 transcriptional activity. Our results provide important physiological evidence that the first 40 amino acids of WT1 are capable of functionally important interactions, presumably through their ability to self-associate with full-length WT1.


Subject(s)
Denys-Drash Syndrome/genetics , Genes, Wilms Tumor , Female , Humans , Infant , Mutation
20.
J Clin Oncol ; 22(20): 4140-6, 2004 Oct 15.
Article in English | MEDLINE | ID: mdl-15483024

ABSTRACT

PURPOSE: Constitutional WT1 mutations in patients with Wilms' tumor (WT) have specifically been associated with genitourinary abnormalities, such as cryptorchidism and hypospadias. We sought to ascertain the frequency and heritability of constitutional WT1 mutations in nonsyndromic WT patients. PATIENTS AND METHODS: Constitutional DNA from 282 patients treated at seven United Kingdom Children's Cancer Study Group centers was screened for WT1 mutations using heteroduplex analysis. Bidirectional sequencing was used to confirm the mutation and to analyze the corresponding parental DNA samples. RESULTS: Five different constitutional WT1 mutations were identified in six children. Mutations in four patients were confirmed to be de novo, and all five mutations are predicted to produce truncated protein. The WT1 mutation group had a young median age at diagnosis of 13.8 months, compared with 34.9 months in the group in whom no WT1 mutations were found; four were female and two were male; and all tumors were of favorable histology. The three tumors with known histologic subtype were stromal-predominant. Contrary to expectation, four of six mutations occurred in children with unilateral tumors without any associated genitourinary abnormality. CONCLUSION: Constitutional WT1 mutations occur with a low frequency (2.1%; 95% CI, 0.8% to 4.6%) in nonsyndromic WT patients. Most mutations occurred in children with unilateral WT without associated genitourinary abnormalities, creating difficulties in identifying individuals with germline mutations on phenotype alone. Two factors that may indicate that an individual is carrying a germline WT1 mutation are an early age of onset and stromal-predominant histology of the WT.


Subject(s)
Genes, Wilms Tumor , Kidney Neoplasms/genetics , WT1 Proteins/genetics , Wilms Tumor/genetics , Child, Preschool , Cohort Studies , Congenital Abnormalities/genetics , Female , Gene Frequency , Germ-Line Mutation , Humans , Infant , Male , Mutation
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