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Open AccessUHRF1/UBE2L6/UBR4-mediated ubiquitination regulates EZH2 abundance and thereby melanocytic differentiation phenotypes in melanoma
Cellular heterogeneity in cancer is linked to disease progression and therapy response, although mechanisms regulating distinct cellular states within tumors are not well understood. We identified melanin pigm...
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Article
T-ALL can evolve to oncogene independence
The majority of cases of T-cell acute lymphoblastic leukemia (T-ALL) contain chromosomal abnormalities that drive overexpression of oncogenic transcription factors. However, whether these initiating oncogenes ...
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Open AccessAuthor Correction: Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer
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Open AccessLow-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer
Low-coverage whole-genome sequencing (LC-WGS) can provide insight into oncogenic molecular changes. Serum extracellular vesicles (EV) represent a novel liquid biopsy source of tumoral DNA. This study compared ...
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Article
A 9-gene score for risk stratification in B-cell acute lymphoblastic leukemia
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Open AccessFrom reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the m...
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Article
Open AccessRestricted cell cycle is essential for clonal evolution and therapeutic resistance of pre-leukemic stem cells
Pre-leukemic stem cells (pre-LSCs) give rise to leukemic stem cells through acquisition of additional gene mutations and are an important source of relapse following chemotherapy. We postulated that cell-cycle...
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Open AccessGenome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas
DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be f...
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Article
Open AccessMethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing
DNA methylation at a gene promoter region has the potential to regulate gene transcription. Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region...
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Open AccessExemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat
DNA methylation is a complex epigenetic marker that can be analyzed using a wide variety of methods. Interpretation and visualization of DNA methylation data can mask complexity in terms of methylation status ...
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Open AccessStability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigating molecular mechanisms of drug resistance
Patient-derived tumour xenografts are an attractive model for preclinical testing of anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to chemotherapeutic drugs can also be...
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Open AccessHypermethylation and down-regulation of DLEU2 in paediatric acute myeloid leukaemia independent of embedded tumour suppressor miR-15a/16-1
Acute Myeloid Leukaemia (AML) is a highly heterogeneous disease. Studies in adult AML have identified epigenetic changes, specifically DNA methylation, associated with leukaemia subtype, age of onset and patie...
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Open AccessA critical re-assessment of DNA repair gene promoter methylation in non-small cell lung carcinoma
DNA repair genes that have been inactivated by promoter methylation offer potential therapeutic targets either by targeting the specific repair deficiency, or by synthetic lethal approaches. This study evaluat...
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Open AccessReducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array
The Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, ...
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Article
Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes
The condensin complex is essential for correct packaging and segregation of chromosomes during mitosis and meiosis in all eukaryotes. To date, the genome-wide location and the nature of condensin-binding sites...
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Open AccessThe use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array
Dried blood (Guthrie card) spots provide an efficient way to collect and store blood specimens. DNA from this source has been utilised for a number of molecular analyses including genome-wide association studi...
