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Colon Cancer Prevention Using Selenium

ABSTRACT: Selenium’s ability to prevent colorectal cancer (CRC) has been suspected for nearly 30 years, but has never been directly studied in humans. The investigators will directly assess selenium’s ability to prevent CRC by measuring alterations in aberrant crypt foci (ACF), an accepted surrogate marker for CRC. ACF’s are very small (i.e., microscopic) collections of abnormally shaped cells that are a commonly used marker of CRC risk. Screening colonoscopy at UIC routinely uses methods that allow ACF counting to be done as a part of standard practice. ACF’s are not fixed, like polyps or cancers, but can disappear as a person’s risk for developing CRC decreases. The investigators propose giving patient’s with 6 or more ACF’s 200 mcg selenized yeast or placebo, and determining if there is a drug-dependant decrease in ACF number. The primary objective is to determine whether selenized yeast supplementation, compared to placebo, causes significant reduction of ACF number from baseline levels. The primary endpoint will be change in ACF number

DISEASE(S): Colorectal Neoplasms,Prevention Of Colorectal Cancer

PROVIDER: 2095836 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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Efficacy of Vitamin D in Colorectal Cancer Chemoprevention

Project description:Vitamin D’s ability to prevent colorectal cancer (CRC) has been suspected for nearly 30 years, but has never been directly studied in humans. The biologically active version of vitamin D, 1,25(OH)2D3, cannot be readily used in humans because of its tendency to cause serum calcium levels to rise. In contrast, 25(OH)D3 (ie calcifediol) does not have this side effect. The investigators previous research suggests that the enzyme necessary to convert 25(OH)D3 (calcifediol) into active 1,25(OH)D3 is present in cells lining the large intestine (colon). Aberrant crypt foci (ACF) are very small (ie microscopic) collections of abnormally shaped cells that are a commonly used marker of CRC risk. Screening colonoscopy at UIC routinely uses methods that allow ACF counting to be done as a part of standard practice. ACF’s are not fixed, like polyps or cancers, but can disappear as a person’s risk for developing CRC decreases. The investigators propose giving patient’s with 10 or more ACF’s 25(OH)D3 (calcifediol) or placebo, and determining if there is a drug-dependant decrease in ACF number. The primary objective is to determine whether 25(OH)D3 (calcifediol) supplementation, compared to placebo, causes significant reduction of ACF number from baseline levels. The primary endpoint will be change in ACF number.

| 2123484 | ecrin-mdr-crc

DNA methylation analysisof KRAS mutated colorectal tumors and adjacent tissues from cancer patinets and KRAS mutated Aberrant Crypt Foci and matching normal crypts from healthy individuals by using RRBS

Project description:Colorectal cancer (CRC) is characterized by genome-wide alterations to DNA methylation that influence gene expression and genomic stability. Less is known about the extent to which methylation is disrupted in the earliest stages of CRC development. In this study we have combined laser-capture microdissection (LCM) with reduced representation bisulfite sequencing (RRBS) to identify cancer associated DNA methylation changes in human aberrant crypt foci (ACF), the earliest putative precursor to CRC. Using this approach, methylation profiles have been generated for 10 KRAS-mutant ACF and 10 CRCs harboring a KRAS mutation, as well as matched samples of normal mucosa. Of 811 differentially methylated regions (DMRs) identified in ACF, 537 (66%) were hypermethylated and 274 (34%) were hypomethylated. DMRs located within intergenic regions were heavily enriched for AP-1 transcription factor binding sites and were frequently hypomethylated. Furthermore, gene ontology (GO) analysis demonstrated that DMRs associated with promoters were enriched for genes involved in intestinal development, including homeobox genes and targets of the Polycomb repressive complex 2 (PRC2).Consistent with their role in the earliest stages of colonic neoplasia, 75% of the methylation changes identified in ACF were also present in the CRC samples. Together, these data demonstrate that DNA methylation changes, including significant hypomethylation, occur more frequently in early colonic neoplasia than previously believed, and identify epigenomic features of ACF that may provide new targets for cancer chemoprevention or lead to the development of new biomarkers for CRC risk.

2018-01-23 | GSE95654 | GEO

Coding and noncoding transcriptome sequencing of KRAS mutated colorectal tumors and adjacent tissues from cancer patients and KRAS mutated Aberrant Crypt Foci and matching normal crypts from healthy individuals [RNA-Seq]

2018-01-23 | GSE95132 | GEO

Genome wide binding of Top2 (in WT and uls1 delta cells) and Uls1 (in WT cells) both in the presence and absence of the Top2 poison acriflavine (ACF)

Project description:Topoisomerase II (Top2) is an essential enzyme that decatenates DNA via a transient Top2-DNA covalent intermediate. This intermediate can be stabilised by a class of drugs termed Top2 poisons, resulting in massive DNA damage. Thus, Top2 activity is a double-edged sword that needs to be carefully controlled to maintain genome stability. We show that Uls1, an ATP-dependent chromatin remodelling (Snf2) enzyme, can alter Top2 chromatin binding and prevent Top2 poisoning in yeast. Deletion mutants of ULS1 are hypersensitive to the Top2 poison acriflavine (ACF), activating the DNA damage checkpoint. We map Uls1’s Top2 interaction domain and show that this, together with its ATPase activity, is essential for Uls1 function. By performing ChIP-seq, we show that ACF leads to a general increase in Top2 binding across the genome. We map Uls1 binding sites and identify tRNA genes as key regions where Uls1 associates after ACF treatment. Importantly, the presence of Uls1 at these sites prevents ACF-dependent Top2 accumulation. Our data reveal the effect of Top2 poisons on the global Top2 binding landscape and highlights the role of Uls1 in antagonising Top2 function. Remodelling Top2 binding is thus an important new means by which Snf2 enzymes promote genome stability.

2019-04-17 | GSE123707 | GEO

Profiling of epithelial and stromal cells in early proximal colon preneoplasia with matched normals.

Project description:Progression of nonmalignant colonic cells harboring somatic mutations depends upon interactions with surrounding stroma; however, details of this interaction are poorly understood. We performed targeted transcriptional profiling of laser-captured epithelial and stromal cells from ACF, the earliest detectable human colonic pre-neoplastic lesion. Within ACF epithelium carrying non-overlapping mutations in KRAS, BRAF, or APC, we observed broad NF-kB-related inflammatory changes and specific differences associated with each mutation, including BRAFV600E-mediated senescence. Additionally, we identified ACF-associated stromal changes indicative of immune cell infiltration and fibroblast activation. Our results provide new insight into intercellular signaling changes that control the earliest stages of CRC development.

2016-11-23 | GSE77312 | GEO

Strain abundance assay of barcoded DAmP loss of function S. cerevisiae strains exposed to various compounds

Project description:The ability to perform complex bioassays in parallel enables experiments otherwise impossible due to throughput and cost constraints. By way of example, highly parallel chemical-genetic screens using pooled collections of thousands of defined Saccharomyces cerevisiae gene deletion strains are feasible because each strain is barcoded with unique DNA sequences. It is, however, time consuming and expensive to individually barcode individual strains. To provide a simple and general method of barcoding yeast collections, we built a set of donor strains, called Barcoders, with unique barcodes that can be systematically transferred to any S. cerevisiae collection. We applied this technology by generating a collection of barcoded DAmP (Decreased Abundance by mRNA Perturbation) loss-of-function strains comprising 87.1% of all essential yeast genes. This test collection validates both the Barcoders and the DAmP collection as useful tools for genome-wide chemical genetic assays.

2008-07-03 | E-MEXP-1671 | biostudies-arrayexpress

Cbf11 Regulates Periodic Expression of Genes Required to Prevent Catastrophic Mitosis in the Fission Yeast Cell Cycle

Project description:The expression of a large proportion of the fission yeast genome changes periodically with the cell cycle. Several key transcription factors have been identified that regulate these oscillating and interdependent waves of gene expression. However, for a significant number of cell cycle-regulated genes the regulator(s) driving these oscillations remain unknown. Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell cycle progression, yet the details of their functioning are poorly understood. Using a combination of transcriptome profiling and genome-wide mapping of CSL-DNA interactions we have identified a comprehensive set of CSL-regulated genes. Our data indicate that Cbf11 and Cbf12 contribute directly and indirectly to the regulation of periodically expressed genes in fission yeast. We show that during S phase/cytokinesis Cbf11 directly activates the transcription of several periodic genes required in the cell to prevent catastrophic mitosis. In agreement with these findings, multiple aspects of cell cycle progression are perturbed when CSL cellular levels are genetically manipulated. We have identified Cbf11 as a novel cell cycle phase-specific activator of genes required for proper coordination of cell and nuclear division, and prevention of catastrophic mitosis in fission yeast.

2015-09-18 | E-MTAB-2724 | biostudies-arrayexpress

CSL ChIP-seq

2015-09-18 | E-MTAB-2725 | biostudies-arrayexpress

Saccharomyces cerevisiae deletion and DAmP collections chemogenomic screen with Selenomethionine

Project description:Growth assay in the presence of Selenomethionine that uses the barcoded collections of yeast gene modification (deletion or DamP) to identify strains that are hypersensitive to the presence of the aminoacid.

2017-03-17 | GSE84340 | GEO

Saccharomyces cerevisiae deletion collections chemogenomic screen with Triclosan, Methylparaben and Ethylzingerone

Project description:Growth assay in the presence of a toxic chemical that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.

2019-12-31 | GSE125353 | GEO

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