Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer

Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state–specific “regulatory transposable elements.” Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements.</p

Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer

Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state–specific “regulatory transposable elements.” Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements.</p

The spectrum and clinical impact of epigenetic modifier mutations in myeloma

Epigenetic dysregulation is known to be an important contributor to myeloma pathogenesis but, unlike in other B cell malignancies, the full spectrum of somatic mutations in epigenetic modifiers has not been previously reported. We sought to address this using results from whole-exome sequencing in the context of a large prospective clinical trial of newly diagnosed patients and targeted sequencing in a cohort of previously treated patients for comparison.Whole-exome sequencing analysis of 463 presenting myeloma cases entered in the UK NCRI Myeloma XI study and targeted sequencing analysis of 156 previously treated cases from the University of Arkansas for Medical Sciences. We correlated the presence of mutations with clinical outcome from diagnosis and compared the mutations found at diagnosis with later stages of disease.In diagnostic myeloma patient samples we identify significant mutations in genes encoding the histone 1 linker protein, previously identified in other B-cell malignancies. Our data suggest an adverse prognostic impact from the presence of lesions in genes encoding DNA methylation modifiers and the histone demethylase KDM6A/UTX. The frequency of mutations in epigenetic modifiers appears to increase following treatment most notably in genes encoding histone methyltransferases and DNA methylation modifiers.Numerous mutations identified raise the possibility of targeted treatment strategies for patients either at diagnosis or relapse supporting the use of sequencing-based diagnostics in myeloma to help guide therapy as more epigenetic targeted agents become available

The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population

IntroductionThe imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. MethodsHere, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. ResultsWe show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. DiscussionAltogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients

Statistical methods to interpret genotypic data

Recent developments in genetic techniques have provided high throughput tools such as single nucleotide polymorphism (SNP) chips and cDNA microarrays to assist in genetic selection. Such high throughput devices necessitate new statistical approaches so that the massive amounts of data gathered can be exploited in an effective manner. This thesis describes some statistical methods that can be applied to SNP data and microarray data. Firstly, the use of SNP data to predict molecular breeding value (MBV) is studied. Principal component analysis (PCA) is used to summarize the variation of the high dimensional SNP space within a smaller dimensional projection space of principal components (PCs). It is demonstrated how the PCs can be used in principal component regression (PCR) to predict the MBV of dairy cattle from their SNP values alone with both simulated and real data. Highly reliable estimated breeding values (EBVs) are available for the real animals. A cross-validation method is used to predict MBVs for dairy sires, with a correlation of 0.69 between the EBVs and estimated MBVs obtained for these real data. The impact of erroneous SNP values, missing SNP values and the number of animals with known EBVs genotyped is also examined. Through simulation, it is found that erroneous SNP values of greater than 2% reduce the accuracy of prediction, whereas the number of missing SNP values has little impact on the accuracy of prediction. As expected, an increase in the number of animals with already known EBVs increases the accuracy of prediction. Kernel regression is used to predict MBV from the intrinsically discrete SNP data. Binomial kernels, which treat the SNP values as a discrete variable, and a Gaussian kernel, which imposes a continuous structure on the marker data, are employed and compared. It is empirically demonstrated that the Gaussian kernel outperforms the binomial kernel when used in Nadaraya-Watson kernel regression. Secondly, statistical methods to account for the nuisance spatial trends found in microarray slides are assessed. Wavelets are proposed as a method of modeling spatial effects in two colour cDNA microarrays where the spatial error component may be represented as a fractal surface. This method is compared with smoothing splines plus first order autoregressive detrending using data collected from mice in a time-course experiment. Two schemes for selecting control genes are also assessed for these data,(i) pre-determined and (ii) the genes that do not over- or under-express throughout the experiment. It is shown that the spatial adjustment and the set of control genes can influence the interpretation of test genes. Results from this microarray study are also used to generate simulated data to assess the models to remove spatial trends. The wavelets threshold approach is the most successful when the nuisance spatial trends in the images are rough and fractal, but there is little difference between the models for images with smoother spatial bias

Climate Change Impacts on Water Temperatures in Urban Lakes: Implications for the Growth of Blue Green Algae in Fairy Lake

Cyanobacteria, also known as blue-green algae, are photosynthetic bacteria that play a crucial role in aquatic ecosystems and are susceptible to changes in temperature. Hence, as global temperatures rise due to climate change, some Cyanobacterial species will thrive in warmer temperatures, which will result in increased blooms during the growing season. The MIKE-3 model is calibrated to existing (2022) conditions and is used to assess the impact of the RCP 4.5 scenario for the year 2050 in Fairy Lake (a shallow urban lake in Ontario). The simulations projected indicate that in 2050, in the central parts of Fairy Lake’s central basin, water temperatures will be above 20 °C for 2281 h compared to 2060 h in 2022. This situation indicates there will be a 10.7% increase in the duration of Cyanobacteria blooms in the central area of Fairy Lake. Similarly, in the northern area of Fairy Lake, the MIKE-3 model results indicate that surface temperature durations above 20 °C will increase from 1628 h to 2275 h for the year 2050, resulting in an additional 647 h of increased temperatures at the surface under RCP 4.5 scenario conditions. This situation indicates there will be a 39.7% increase in the duration of Cyanobacteria blooms in the northern portion of Fairy Lake. These modeling conditions indicate there will be significantly more habitat amenable to Cyanobacteria growth when surface water temperatures are above 20 °C, indicating substantial increases in the available growth time of Cyanobacteria due to climate change, all of which translate to major concerns caused by climate change

Early-life antibiotic treatment enhances the pathogenicity of CD4⁺ T cells during intestinal inflammation

The incidence of inflammatory bowel diseases (IBDs) has steadily increased in recent decades—a phenomenon that cannot be explained by genetic mutations alone. Other factors, including the composition of the intestinal microbiome, are potentially important contributors to the increased occurrence of this group of diseases. Previous reports have shown a correlation between early-life antibiotic (Abx) treatment and an increased incidence of IBD. In this report, we investigated the effects of early-life Abx treatments on the pathogenicity of CD4+ T cells using an experimental T cell transfer model of IBD. Our results show that CD4+ T cells isolated from adult mice that had been treated with Abx during gestation and in early life induced a faster onset of IBD in Rag1-deficient mice compared with CD4+ T cells of untreated mice. Ex vivo functional analyses of IBD-inducing CD4+ T cells did not show significant differences in their immunologic potential ex vivo, despite their in vivo phenotype. However, genome-wide gene-expression analysis revealed that these cells displayed dysregulated expression of genes associated with cell-cycle regulation, metabolism, and cellular stress. Analysis of Abx-treated CD4+ T cell donors showed systemically elevated levels of the stress hormone corticosterone throughout life compared with untreated donors. The cohousing of Abx-treated mice with untreated mice decreased serum corticosterone, and a consequent transfer of the cells from cohoused mice into Rag1-deficient mice restored the onset and severity of disease to that of untreated animals. Thus, our results suggest that early-life Abx treatment results in a stress response with high levels of corticosterone that influences CD4+ T cell function

Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance

Abstract Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy