Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach:A multi-institutional research study

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RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample

Identification and characterization of noncalcemic, tissue-selective, nonsecosteroidal vitamin D receptor modulators

Vitamin D receptor (VDR) ligands are therapeutic agents for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism. VDR ligands also show immense potential as therapeutic agents for autoimmune diseases and cancers of skin, prostate, colon, and breast as well as leukemia. However, the major side effect of VDR ligands that limits their expanded use and clinical development is hypercalcemia that develops as a result of the action of these compounds mainly on intestine. In order to discover VDR ligands with less hypercalcemia liability, we sought to identify tissue-selective VDR modulators (VDRMs) that act as agonists in some cell types and lack activity in others. Here, we describe LY2108491 and LY2109866 as nonsecosteroidal VDRMs that function as potent agonists in keratinocytes, osteoblasts, and peripheral blood mononuclear cells but show poor activity in intestinal cells. Finally, these nonsecosteroidal VDRMs were less calcemic in vivo, and LY2108491 exhibited more than 270-fold improved therapeutic index over the naturally occurring VDR ligand 1,25-dihydroxyvitamin D(3) [1,25-(OH)(2)D(3)] in an in vivo preclinical surrogate model of psoriasis

Validated MCF-7 gene fusions and TaqMan expression ratios.

<p><b>Notes:</b> Each exon name (gene name-dash-exon-order) was obtained from RefSeq database. Inverted fusions are on same chromosome but different strands. Last four columns show the Cycle Threshold (CT) value in TaqMan assays. Lower CT values indicate higher expression.</p

Fusion breakpoints are biased to 5′ end of the genes.

<p>Histogram of order of 5′ (yellow) and 3′ (green) intron breakpoints for <b>A.</b> MCF-7, <b>B.</b> UHR and HBR combined gene fusions. Breakpoint is inferred to happen at the intron (X axis) following the exon that is fused. Y axis shows the count of breakpoints that are inferred to happen at numbered intron. <b>C.</b> Boxplot of the distribution of simulated gene fusion locations for each of the 23 genes in which a fusion was observed. Magenta star marks the location of the observed fusion, relative to the 5′ exon. 23 fusions correspond to the gene fusions from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002464#pcbi-1002464-t002" target="_blank">Table 2</a> (except for <i>ESR1- C6orf97</i>, and <i>ADAMTS19- SLC27A6</i> alternatively spliced fusions merged into single data points).</p