Complexes of N, N- and N, N, N- Sulfonamide Ligands as Therapeutic and Diagnostic Agents

Ethylenediamine, diethylenetriamine and dipicolylamine have been used as the carrier ligands to synthesize bidentate (N,N) or tridentate (N,N,N) chelate systems that coordinate with metal centers. The terminal amine groups of ethylenediamine and diethylenetriamine and the central amine group of dipicolylamine can be easily substituted to give sulfonamide ligands having bulky aromatic fragments. In the formation of metal sulfonamides, the sulfonamide nitrogens of primary or secondary sulfonamidesdeprotonate and coordinate with metal centers forming M-N bonds while the free amines coordinate to metal centers through lone pairs. The reported synthetic approaches and the properties of these complexes and ligands are discussed in this review. The bulky sulfonamide moieties bring about unique biological features to the ligand system while enhancing the fluorescent properties of the ligand. The metal center itself incorporates interesting biological features to the complex. These properties of the metal center andthe ligand show a synergistic effect in the complexes that may come in handy when designing therapeutic or diagnostic agents. The increased lipophilicity of the ligands and thereby the complexes will ensure better uptake by target cells making them ideal candidates for biological applications. Keywords: Sulfonamide, ethylenediamine, diethylenetriamine, dipicolylamin

BloodChIP: A database of comparative genome-wide transcription factor binding profiles in human blood cells

The BloodChIP database (http://www.med.unsw.edu.au/CRCWeb.nsf/page/ BloodChIP) supports exploration and visualization of combinatorial transcription factor (TF) binding at a particular locus in human CD34-positive and other normal and leukaemic cells or retrieval of target gene sets for user-defined combinations of TFs across one or more cell types. Increasing numbers of genome-wide TF binding profiles are being added to public repositories, and this trend is likely to continue. For the power of these data sets to be fully harnessed by experimental scientists, there is a need for these data to be placed in context and easily accessible for downstream applications. To this end, we have built a user-friendly database that has at its core the genome-wide binding profiles of seven key haematopoietic TFs in human stem/progenitor cells. These binding profiles are compared with binding profiles in normal differentiated and leukaemic cells. We have integrated these TF binding profiles with chromatin marks and expression data in normal and leukaemic cell fractions. All queries can be exported into external sites to construct TF-gene and protein-protein networks and to evaluate the association of genes with cellular processes and tissue expression. © 2013 The Author(s). Published by Oxford University Press.Link_to_subscribed_fulltex

Cancer-Associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression

© 2017 The Author(s). Cancer is a multifactorial disease driven by a combination of genetic and environmental factors. Many cancer driver mutations have been characterised in protein-coding regions of the genome. However, mutations in noncoding regions associated with cancer have been less investigated. G-quadruplex (G4) nucleic acids are four-stranded secondary structures formed in guanine-rich sequences and prevalent in the regulatory regions. In this study, we used published whole cancer genome sequence data to find mutations in cancer patients that overlap potential RNA G4-forming sequences in 5ⲠUTRs. Using RNAfold, we assessed the effect of these mutations on the thermodynamic stability of predicted RNA G4s in the context of full-length 5ⲠUTRs. Of the 217 identified mutations, we found that 33 are predicted to destabilise and 21 predicted to stabilise potential RNA G4s. We experimentally validated the effect of destabilising mutations in the 5ⲠUTRs of BCL2 and CXCL14 and one stabilising mutation in the 5ⲠUTR of TAOK2. These mutations resulted in an increase or a decrease in translation of these mRNAs, respectively. These findings suggest that mutations that modulate the G4 stability in the noncoding regions could act as cancer driver mutations, which present an opportunity for early cancer diagnosis using individual sequencing information.Link_to_subscribed_fulltex

Investigating the role of non-coding mutations in cancer.

Whole genomes are being sequenced at an accelerated pace but research into cancer causing mutations has focused primarily on protein-coding mutations owing to difficulties associated with identifying and interpreting causality of noncoding mutations. Nevertheless, projects such as ENCODE and the Epigenome Atlas have led to the generation of genome-wide datasets that have contributed to our understanding of the noncoding parts of the human genome. The integration of these datasets has the potential to shed light on the functions of noncoding sequences, gene regulatory modules and epistatic interactions underlying disease associations. Moreover, through technological advances it is now feasible to routinely sequence whole genomes of cancer samples which has enable large international consortiums such as TCGA and ICGC to create public datasets consisting of mutations from whole genome sequencing of 1000s of tumour samples. The integrative analyses of datasets from these resources have provided new opportunities to interrogate non-coding cancer mutations. In order to elucidate the role of cis-regulatory mutations in cancer, I developed an annotation method and web tool to study the effect of cis-regulatory mutations in cancer and to identify potential causal mutations for further investigations. Applying this tool to whole breast cancer genome sequencing data, I discovered a point mutation in the enhancer of CDK6 that results in the overexpression of the gene. I then conducted a pan-cancer analysis of cis-regulatory mutations using somatic mutations from 1161 whole tumour genomes across 14 cancer types from publicly available data sources which revealed a previously unknown mechanism linking transcription initiation and NER as a major contributor of somatic point mutation hotspots at active gene promoters in cancer genomes. In the final chapter of the thesis, I examined cancer mutations in non-coding RNA and their effect on structure and function. Through this thesis, I have been able to significantly contribute to our understanding of non-coding or regulatory regions of the genome and the role of mutations in these regions in cancer and to develop computational methods and tools to assist experimentalists to further explore this field of science

SONDEO ARQUEOLÓGICO HUERTO NUEVO [Material gráfico]

Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte, 201

Scarcity of Recurrent Regulatory Driver Mutations in Colorectal Cancer Revealed by Targeted Deep Sequencing

Background: Genetic testing of cancer samples primarily focuses on protein-coding regions, despite most mutations arising in noncoding DNA. Noncoding mutations can be pathogenic if they disrupt gene regulation, but the benefits of assessing promoter mutations in driver genes by panel testing has not yet been established. This is especially the case in colorectal cancer, for which few putative driver variants at regulatory elements have been reported.Methods: We designed a unique target capture sequencing panel of 39 colorectal cancer driver genes and their promoters, together with more than 35 megabases of regulatory elements focusing on gene promoters. Using this panel, we sequenced 95 colorectal cancer and matched normal samples at high depth, averaging 170x and 82x coverage, respectively.Results: Our target capture sequencing design enabled improved coverage and variant detection across captured regions. We found cases with hereditary defects inmismatch and base excision repair due to deleterious germline coding variants, and we identified mutational spectra consistent with these repair deficiencies. Focusing on gene promoters and other regulatory regions, we found little evidence for base or region-specific recurrence of functional somatic mutations. Promoter elements, including TERT, harbored few mutations, with none showing strong functional evidence. Recurrent regulatory mutations were rare in our sequenced regions in colorectal cancer, though we highlight some candidate mutations for future functional studies.Conclusions: Our study supports recent findings that regulatory driver mutations are rare in many cancer types and suggests that the inclusion of promoter regions into cancer panel testing is currently likely to have limited clinical utility in colorectal cancer

Epigenetic inactivation of the candidate tumor suppressor USP44 is a frequent and early event in colorectal neoplasia

In mouse models, loss of the candidate tumor suppressor gene Ubiquitin Specific protease 44 (USP44) is associated with aneuploidy and cancer. USP44 is also transcriptionally silenced in human cancers. here we investigated the molecular mechanism of USP44 silencing and whether this correlated with aneuploidy in colorectal adenomas. DNA methylation at the USP44 cpG island (CGI) promoter was measured using combined bisulfite restriction analysis (COBRA) in colorectal cancer (CRC) cell lines (n = 18), and with COBRA and bisulfite sequencing in colorectal adenomas (n = 89) and matched normal colonic mucosa (n = 51). the USP44 CGI was hypermethylated in all CRC cell lines, in most colorectal adenomas (79 of 89, 89%) but rarely in normal mucosa samples (3 of 51, 6%). USP44 expression was also compared between normal mucosa and paired hypermethylated adenomas in six patients using qRT-pCR. hypermethylation of the USP44 CGI in adenomas was associated with a 1.8 to 5.5-fold reduction in expression compared with paired normal mucosa. treatment of CRC cell lines with the DNA hypomethylating agent decitabine resulted in a 14 to 270-fold increase in USP44 expression. Whole genome SNP array data showed that gain or loss of individual chromosomes occurred in adenomas, but hypermethylation did not correlate with more aneuploidy. in summary, our data shows that USP44 is epigenetically inactivated in colorectal adenomas, but this alone is not sufficient to cause aneuploidy in colorectal neoplasia. © 2014 Landes Bioscience.Link_to_subscribed_fulltex

Genome-wide analysis of transcriptional regulators in human HSPCs reveals a densely interconnected network of coding and noncoding genes

© 2013 by The American Society of Hematology. Genome-wide combinatorial binding patterns for key transcription factors (TFs) have not been reported for primary human hematopoietic stem and progenitor cells (HSPCs), and have constrained analysis of the global architecture of molecular circuits controlling these cells. Here we provide high-resolution genome-wide binding maps for a heptad of key TFs (FLI1, ERG, GATA2, RUNX1, SCL, LYL1, and LMO2) in human CD341 HSPCs, together with quantitative RNA and microRNA expression profiles. We catalog binding of TFs at coding genes and microRNA promoters, and report that combinatorial binding of all 7 TFs is favored and associated with differential expression of genes and microRNA in HSPCs. We also uncover a previously unrecognized association between FLI1 and RUNX1 pairing in HSPCs, we establish a correlation between the density of histone modifications that mark active enhancers and the number of overlapping TFs at a peak, we demonstrate bivalent histone marks at promoters of heptad target genes in CD341 cells that are poised for later expression, and we identify complex relationships between specific microRNAs and coding genes regulated by the heptad. Taken together, these data reveal the power of integrating multifactor sequencing of chromatin immunoprecipitates with coding and noncoding gene expression to identify regulatory circuits controlling cell identity.Link_to_subscribed_fulltex