A5031212174- Epigenetics and DNA Methylation
- Acute Myeloid Leukemia Research
- CAR-T cell therapy research
- Renal and related cancers
- Renal cell carcinoma treatment
- Telomeres, Telomerase, and Senescence
- Gene expression and cancer classification
- Acute Lymphoblastic Leukemia research
- RNA modifications and cancer
- Ferroptosis and cancer prognosis
- Prostate Cancer Treatment and Research
- Bioinformatics and Genomic Networks
- Intergenerational Family Dynamics and Caregiving
- Cancer-related gene regulation
- Bone health and treatments
- Genetics and Neurodevelopmental Disorders
- Corneal surgery and disorders
- Cancer Diagnosis and Treatment
- Retinal Diseases and Treatments
- Molecular Biology Techniques and Applications
- Genetics, Aging, and Longevity in Model Organisms
- Genomic variations and chromosomal abnormalities
- Bacterial Genetics and Biotechnology
- Dementia and Cognitive Impairment Research
- Genomics and Chromatin Dynamics
Umeå University
2016-2025
Statistics Sweden
2009
Epigenetic alterations during aging have been proposed to contribute decline in physical and cognitive functions, accelerated epigenetic has associated with disease all-cause mortality later life. In this study, we estimated age dynamics groups different memory trajectories (maintained high performance, average decline, decline) over a 15-year period. (DNA-methylation [DNAm]) was assessed, delta (DNAm - chronological age) calculated blood samples at baseline (age: 55-65 years) 15 years 52...
Abstract Background Leukocyte telomere length (LTL) has been shown to predict Alzheimer’s disease (AD), albeit inconsistently. Failing account for the competing risks between AD, other dementia types, and mortality, can be an explanation inconsistent findings in previous time-to-event analyses. Furthermore, studies indicate that association LTL AD is non-linear may differ depending on apolipoprotein E ( APOE ) ε4 allele carriage, strongest genetic predictor. Methods We analyzed whether...
Abstract Background Large B-cell lymphoma (LBCL) is the most common and known to be a biologically heterogeneous disease regarding genetic, phenotypic, clinical features. Although prognosis good, one-third has primary refractory or relapsing which underscores importance of developing predictive biological markers capable identifying high- low-risk patients. DNA methylation (DNAm) telomere maintenance alterations are hallmarks cancer aging. Both these may contribute heterogeneity disease,...
Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim discover new classes, or sub-classes, of either individuals genes. Performing a cluster analysis commonly involve decisions on how to; handle missing values, standardize the data select In addition, pre-processing, involving various types filtration normalization procedures, can have an effect ability biologically relevant classes. Here we consider broad sense...
Background Despite increased knowledge about genetic aberrations in pediatric T‐cell acute lymphoblastic leukemia (T‐ALL), no clinically feasible treatment‐stratifying marker exists at diagnosis. Instead patients are enrolled intensive induction therapies with substantial side effects. In modern protocols, therapy response is monitored by minimal residual disease (MRD) analysis and used for postinduction risk group stratification. DNA methylation profiling a candidate subtype discrimination...
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called island methylator phenotype (CIMP) remains poorly understood. Here, we show methylation human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs promoters of Polycomb Repressor Complex 2 (PRC2) target genes are not expressed or malignant T-cells and which a reciprocal association with H3K27me3 binding. In addition, revealed...
Telomere length (TL) is regarded as a marker of cellular aging due to the gradual shortening by each cell division, but influenced number factors including oxidative stress and inflammation. Parkinson's disease atypical forms parkinsonism occur mainly in elderly, with inflammation afflicted cells. In this study relationship between blood TL prognosis 168 patients idiopathic (136 [PD], 17 Progressive Supranuclear Palsy [PSP], 15 Multiple System Atrophy [MSA]) 30 controls was investigated....
Patients with metastatic prostate cancer (PC) are treated androgen deprivation therapy (ADT) that initially reduces metastasis growth, but after some time lethal castration-resistant PC (CRPC) develops. A better understanding of the tumor biology in bone metastases is needed to guide further treatment developments. Subgroups based on transcriptome profiling have been previously identified by our research team, and specifically, heterogeneities related receptor (AR) activity described....
Abstract Background Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine methods, these often do not account fact that (e.g. error rate) result series analysis steps which most important are data normalization, gene selection learning. Results In this study, we used seven previously published cancer-related sets to compare effects on classification...
Few biological markers are associated with survival after relapse of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In pediatric T-cell ALL, we have identified promoter-associated methylation alterations that correlate prognosis. Here, the prognostic relevance CpG island phenotype (CIMP) classification was investigated in BCP-ALL patients. Six hundred and one samples from Nordic patients (age 1–18) were CIMP classified at initial diagnosis analyzed relation to clinical data. Among...
Abstract Classification of pediatric T‐cell acute lymphoblastic leukemia (T‐ALL) patients into CIMP (CpG Island Methylator Phenotype) subgroups has the potential to improve current risk stratification. To investigate biology behind these subgroups, diagnostic samples from Nordic T‐ALL were characterized by genome‐wide methylation arrays, followed targeted exome sequencing, telomere length measurement, and RNA sequencing. The did not correlate significantly with variations in epigenetic...
Clear cell renal carcinoma (ccRCC) is the most common subtype among cancer and associated with poor prognosis if metastasized. Up to one third of patients local disease at diagnosis will develop metastasis after nephrectomy, there a need for new molecular markers identify high risk tumor progression. In present study, we performed genome-wide promoter DNA methylation analysis profiles progress. Diagnostic tissue samples from 115 ccRCC were analysed by Illumina HumanMethylation450K arrays...
Despite having common overlapping immunophenotypic and morphological features, T-cell lymphoblastic leukemia (T-ALL) lymphoma (T-LBL) have distinct clinical manifestations, which may represent separate diseases. We investigated compared the epigenetic genetic landscape of adult pediatric T-ALL (n = 77) T-LBL 15) patient samples by high-resolution genome-wide DNA methylation Copy Number Variation (CNV) BeadChip arrays. profiling identified presence CpG island methylator phenotype (CIMP)...
Abstract Leukocyte telomere length (LTL) is a proposed biomarker for aging-related disorders, including cognitive decline and dementia. Long-term longitudinal studies measuring intra-individual changes in both LTL outcomes are scarce, precluding strong conclusions about potential relationship between shortening decline. This study investigated associations baseline levels memory performance across an up to 20-year follow-up 880 dementia-free participants from population-based (mean age: 56.8...
<h3>Background</h3> Cartilage-hair hypoplasia (CHH) is an autosomal recessive chondrodysplasia caused by <i>RMRP</i> (RNA component of mitochondrial RNA processing endoribonuclease) gene mutations. Manifestations include short stature, variable immunodeficiency, anaemia and increased risk malignancies, all which have been described also in telomere biology disorders. interacts with the telomerase RT (TERT) subunit, but influence mutations on length unknown. We measured relative (RTL)...
Abstract Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length disease severity. Epigenetic alterations also markers of we aimed evaluate whether DNA methylation (DNAm) could be part the pathogenesis TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed cases grouped based on relative (RTL): (S), RTL close normal controls, extremely (ES). had...
Late-onset Fuchs endothelial corneal dystrophy (FECD) is a disease affecting the endothelium (CE), associated with cytosine-thymine-guanine repeat expansion at CTG18.1 locus in transcription factor 4 (TCF4) gene. It unknown whether expansions affect global methylation including TCF4 gene CE or changes advanced age. Using genome-wide DNA array, we investigated from FECD patients and studied healthy different ages. The most revealing findings were analyzed by expression protein analysis. 3488...
We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate role genome-wide methylation in process at different time points pre-crisis post-crisis using high-resolution arrays. show that over culture there is an overall accumulation alterations, with preferential increased close transcription start...
Epigenetic alterations in the methylome have been associated with tumor development and progression renal cell carcinoma (RCC). In this study, 45 samples, 12 tumor-free kidney cortex tissues, 24 peripheral blood samples from patients clear RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays related to clinicopathological parameters. Unsupervised hierarchical clustering separated tumors into two distinct groups (clusters A B), where cluster B had higher average...
Recently, a large number of methods for the analysis microarray data have been proposed but there are few comparisons their relative performances. By using so-called spike-in experiments, it is possible to characterize analyzed and thereby enable different methods.A experiment eight in-house produced arrays was used evaluate established novel filtration, background adjustment, scanning, channel censoring. The S-plus package EDMA, stand-alone tool providing characterization cDNA-microarray...
Background: DNA methylation (DNAm), an epigenetic mark reflecting both inherited and environmental influences, has shown promise for Alzheimer’s disease (AD) prediction. Objective: Testing long-term predictive ability (>15 years) of existing DNAm-based age acceleration (EAA) measures identifying novel early blood-based DNAm AD-prediction biomarkers. Methods: EAA calculated from Illumina EPIC data blood were tested with linear mixed-effects models (LMMs) in a longitudinal case-control...
Genome-wide analysis of gene expression or protein binding patterns using different array sequencing based technologies is now routinely performed to compare populations, such as treatment and reference groups. It often necessary normalize the data obtained remove technical variation introduced in course conducting experimental work, but standard normalization techniques are not capable eliminating bias cases where distribution truly altered variables skewed, i.e. when a large fraction...
T-cell lymphoblastic lymphoma (T-LBL) is a rare and aggressive lymphatic cancer, often diagnosed at young age. Patients are treated with intensive chemotherapy, potentially followed by hematopoietic stem cell transplantation. Although prognosis of T-LBL has improved intensified treatment protocols, they associated side effects 10-20% patients still die from relapsed or refractory disease. Given this, the search toward less toxic anti-lymphoma therapies ongoing. Here, we targeted recently...