The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progression.

Just like the androgen receptor (AR), the estrogen receptor α (ERα) is expressed in the prostate and is thought to influence prostate cancer (PCa) biology. Yet the incomplete understanding of ERα functions in PCa hinders our ability to fully comprehend its clinical relevance and restricts the repurposing of estrogen-targeted therapies for the treatment of this disease. Using 2 human PCa tissue microarray cohorts, we first demonstrate that nuclear ERα expression was heterogeneous among patients, being detected in only half of the tumors. Positive nuclear ERα levels were correlated with disease recurrence, progression to metastatic PCa, and patient survival. Using in vitro and in vivo models of the normal prostate and PCa, bulk and single-cell RNA-Seq analyses revealed that estrogens partially mimicked the androgen transcriptional response and activated specific biological pathways linked to proliferation and metabolism. Bioenergetic flux assays and metabolomics confirmed the regulation of cancer metabolism by estrogens, supporting proliferation. Using cancer cell lines and patient-derived organoids, selective estrogen receptor modulators, a pure anti-estrogen, and genetic approaches impaired cancer cell proliferation and growth in an ERα-dependent manner. Overall, our study revealed that, when expressed, ERα functionally reprogrammed PCa metabolism, was associated with disease progression, and could be targeted for therapeutic purposes.

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.

Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.

Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants.

The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole-genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for the locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild-type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.

Toll-like receptors in normal and malignant human bladders.

PURPOSE: Toll-like receptors have a major role in the innate immune response. They are expressed by immune cells and some epithelial cells. To study the role of urothelial cells in the intrabladder innate immune response we analyzed toll-like receptor expression and functionality in normal and malignant urothelial cells. MATERIALS AND METHODS: Toll-like receptor 1 to 10 mRNA expression was analyzed using reverse transcriptase-polymerase chain reaction in 4 primary cultures of normal urothelium and 15 bladder cancer cell lines. Immunohistochemistry was used to detect toll-like receptor expression in 11 normal urothelial samples and 26 bladder tumors. Proinflammatory cytokine secretion by toll-like receptor agonist or bacillus Calmette-Guérin treated cultured cells was assessed by enzyme-linked immunosorbent assay. Mitogen-activated protein kinase phosphorylation was analyzed by Western blot and nuclear factor-κB localization was assessed by confocal microscopy. RESULTS: Expression of most toll-like receptor mRNA was detected in cultured normal or tumor urothelial cells. Expression of toll-like receptors 2 to 4, 5, 7 and 9 protein was detected in all normal urothelial samples and most nonmuscle invasive tumors, although its intensity was decreased in the latter. Expression was markedly decreased in muscle invasive tumors. Treatment with toll-like receptor 2 and 3 agonists showed the strongest inflammatory response in 2 primary cultures of normal urothelial cells and 3 bladder cancer cell lines. Toll-like receptor 2 and 3 functionality was confirmed by the nuclear translocation of nuclear factor-κB and the induction of phosphorylated c-Jun N-terminal kinase mitogen-activated protein-kinase. CONCLUSIONS: Toll-like receptors are expressed in normal urothelium and nonmuscle invasive bladder tumors. In cultured urothelial cells agonist inducible toll-like receptor 2 or constitutively expressed toll-like receptor 3 is functional. These data suggest the potential use of toll-like receptor agonists for antitumor immunotherapy of nonmuscle invasive tumors.