Paired Tumor and Normal Whole Genome Sequencing of Metastatic Olfactory Neuroblastoma

Olfactory neuroblastoma (ONB) is a rare cancer of the sinonasal tract with little molecular characterization. We performed whole genome sequencing (WGS) on paired normal and tumor DNA from a patient with metastatic-ONB to identify the somatic alterations that might be drivers of tumorigenesis and/or metastatic progression.Genomic DNA was isolated from fresh frozen tissue from a metastatic lesion and whole blood, followed by WGS at >30X depth, alignment and mapping, and mutation analyses. Sanger sequencing was used to confirm selected mutations. Sixty-two somatic short nucleotide variants (SNVs) and five deletions were identified inside coding regions, each causing a non-synonymous DNA sequence change. We selected seven SNVs and validated them by Sanger sequencing. In the metastatic ONB samples collected several months prior to WGS, all seven mutations were present. However, in the original surgical resection specimen (prior to evidence of metastatic disease), mutations in KDR, MYC, SIN3B, and NLRC4 genes were not present, suggesting that these were acquired with disease progression and/or as a result of post-treatment effects.This work provides insight into the evolution of ONB cancer cells and provides a window into the more complex factors, including tumor clonality and multiple driver mutations

FOXM1 binds directly to non-consensus sequences in the human genome.

BACKGROUND: The Forkhead (FKH) transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in most types of cancer. FOXM1, similar to other FKH factors, binds to a canonical FKH motif in vitro. However, genome-wide mapping studies in different cell lines have shown a lack of enrichment of the FKH motif, suggesting an alternative mode of chromatin recruitment. We have investigated the role of direct versus indirect DNA binding in FOXM1 recruitment by performing ChIP-seq with wild-type and DNA binding deficient FOXM1. RESULTS: An in vitro fluorescence polarization assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell lines expressing either wild-type or DNA binding deficient GFP-tagged FOXM1 were used for genome-wide mapping studies comparing the distribution of the DNA binding deficient protein to the wild-type. This shows that interaction of the FOXM1 DNA binding domain with target DNA is essential for recruitment. Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions. CONCLUSIONS: A functional DNA binding domain is essential for FOXM1 chromatin recruitment. Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected. These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.We would like to acknowledge the Genomics and bioinformatics core at the CRUK Research Institute for the Illumina sequencing and the Proteomics core for the LC/MS-MS protein analysis for the RIME experiments. We acknowledge the support from The University of Cambridge and Cancer Research UK. The Balasubramanian Laboratory is supported by core funding from Cancer Research UK (C14303/A17197). SB is a Wellcome Trust Principle Investigator.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13059-015-0696-

Voluntary Feed Intake in Rainbow Trout Is Regulated by Diet-Induced Differences in Oxygen Use

This study investigated the hypothesis that the voluntary feed intake in fish is regulated by diet-induced differences in oxygen use. Four diets were prepared with a similar digestible protein:digestible energy ratio (18 mg/kJ), but which differed in the composition of nonprotein energy source. This replacement of fat (F) by starch (S) was intended to create a diet-induced difference in oxygen use (per unit of feed): diets F30-S70, F50-S50, F65-S35, and F80-S20 with digestible fat providing 28, 49, 65, and 81% of the nonprotein digestible energy (NPDE), respectively. Each diet was fed to satiation to triplicate groups of 20 rainbow trout for 6 wk. As expected, diet-induced oxygen use decreased linearly (R(2) = 0.89; P <0.001) with increasing NPDE as fat. The digestible and metabolizable energy intakes of trout slightly increased with increasing NPDE as fat (i.e., decreasing starch content) (R(2) = 0.30, P = 0.08; and R(2) = 0.34, P = 0.05, respectively). Oxygen consumption of trout fed to satiation declined with increasing dietary NPDE as fat (R(2) = 0.48; P = 0.01). The inverse relation between digestible energy intake of trout and the diet-induced oxygen use (R(2) = 0.33; P = 0.05) suggests a possible role of diet-induced oxygen use in feed intake regulation as shown by the replacement of dietary fat by starch