ChIP-seq and Functional Analysis of the SOX2 Gene in Colorectal Cancers

SOX2 is anHMGbox containing transcription factor that has been implicated in various types of cancer, but its role in colorectal cancers (CRC) has not been studied. Here we show that SOX2 is overexpressed in CRC tissues compared with normal adjacent tissues using immunohistochemical staining and RT-PCR. We also observed an increased SOX2 expression in nucleus of colorectal cancer tissues (46%, 14/30 cases vs. 7%, 2/30 adjacent tissues). Furthermore, knockdown of SOX2 in SW620 colorectal cancer cells decreased their growth rates in vitro cell line, and in vivo in xenograft models. ChIP-Seq analysis of SOX2 revealed a consensus sequence of wwTGywTT. An integrated expression profiling and ChIP-seq analysis show that SOX2 is involved in the BMP signaling pathway, steroid metabolic process, histone modifications, and many receptor-mediated signaling pathways such as IGF1R and ITPR2 (Inositol 1,4,5-triphosphate receptor, type 2).MOST, Chin

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis

<p>Abstract</p> <p>Background</p> <p><it>SOX2 </it>is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. <it>SOX2 </it>appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of <it>SOX2 </it>in GBM has not yet been defined.</p> <p>Results</p> <p>We show that knockdown of the <it>SOX2 </it>gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the <it>SOX2 </it>response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 <it>SOX2 </it>binding regions in the GBM cancer genome. <it>SOX2 </it>binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 <it>SOX2 </it>binding regions. Microarray analysis identified 489 genes whose expression altered in response to <it>SOX2 </it>knockdown. Interesting findings include that <it>SOX2 </it>regulates the expression of SOX family proteins <it>SOX1 </it>and <it>SOX18</it>, and that <it>SOX2 </it>down regulates <it>BEX1 </it>(brain expressed X-linked 1) and <it>BEX2 </it>(brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by <it>SOX2</it>, including down regulation of miR-143, -145, -253-5p and miR-452. We also show that miR-145 and <it>SOX2 </it>form a double negative feedback loop in GBM cells, potentially creating a bistable system in GBM cells.</p> <p>Conclusions</p> <p>We present an integrated dataset of ChIP-seq, expression microarrays and microRNA sequencing representing the <it>SOX2 </it>response program in LN229 GBM cells. The insights gained from our integrated analysis further our understanding of the potential actions of <it>SOX2 </it>in carcinogenesis and serves as a useful resource for the research community.</p

Identification of Novel SNPs by Next-Generation Sequencing of the Genomic Region Containing the APC Gene in Colorectal Cancer Patients in China

We described an approach of identifying single nucleotide polymorphisms (SNPs) in complete genomic regions of key genes including promoters, exons, introns, and downstream sequences by combining long-range polymerase chain reaction (PCR) or NimbleGen sequence capture with next-generation sequencing. Using the adenomatous polyposis coli (APC) gene as an example, we identified 210 highly reliable SNPs by next-generation sequencing analysis program MAQ and Samtools, of which 69 were novel ones, in the 123-kb APC genomic region in 27 pair of colorectal cancers and normal adjacent tissues. We confirmed all of the eight randomly selected high-quality SNPs by allele-specific PCR, suggesting that our false discovery rate is negligible. We identified 11 SNPs in the exonic region, including one novel SNP that was not previously reported. Although 10 of them are synonymous, they were predicted to affect splicing by creating or removing exonic splicing enhancers or exonic splicing silencers. We also identified seven SNPs in the upstream region of the APC gene, three of which were only identified in the cancer tissues. Six of these upstream SNPs were predicted to affect transcription factor binding. We also observed that long-range PCR was better in capturing GC-rich regions than the NimbleGen sequence capture technique.MOST, Chin

A Genome-wide hybrid incompatibility landscape between Caenorhabditis briggsae and C. nigoni.

Systematic characterization of ẖybrid incompatibility (HI) between related species remains the key to understanding speciation. The genetic basis of HI has been intensively studied in Drosophila species, but remains largely unknown in other species, including nematodes, which is mainly due to the lack of a sister species with which C. elegans can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However, the paucity of dominant and visible marker prevents the efficient mapping of HI loci between the two species. To elucidate the genetic basis of speciation in nematode species, we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome and mapped them into the defined locations by PCR and Next-Generation Sequencing (NGS). Aided by the marker, we backcrossed the GFP-associated C. briggsae genomic fragments into C. nigoni for at least 15 generations and produced 111 independent introgressions. The introgression fragments cover most of the C. briggsae genome. We finally dissected the patterns of HI by scoring the embryonic lethality, larval arrest, sex ratio and male sterility for each introgression line, through which we identified pervasive HI loci and produced a genome-wide landscape of HI between the two nematode species, the first of its type for any non-Drosophila species. The HI data not only provided insights into the genetic basis of speciation, but also established a framework for the possible cloning of HI loci between the two nematode species. Furthermore, the data on hybrids confirmed Haldane's rule and suggested the presence of a large X effect in terms of fertility between the two species. Importantly, this work opens a new avenue for studying speciation genetics between nematode species and allows parallel comparison of the HI with that in Drosophila and other species

Exo-miR-1290-induced by COX-2 overexpression promotes cancer-associated fibroblasts activation and tumor progression by CUL3-Nrf2 pathway in lung adenocarcinoma

Abstract Background Cancer-associated fibroblasts (CAFs) are critically involved in tumor progression by maintaining extracellular mesenchyma (ECM) production and improving tumor development. Cyclooxygenase-2 (COX-2) has been proved to promote ECM formation and tumor progression. However, the mechanisms of COX-2 mediated CAFs activation have not yet been elucidated. Therefore, we conducted this study to identify the effects and mechanisms of COX-2 underlying CAFs activation by tumor-derived exosomal miRNAs in lung adenocarcinoma (LUAD) progression. Methods As measures of CAFs activation, the expressions of fibroblasts activated protein-1 (FAP-1) and α-smooth muscle actin (α-SMA), the main CAFs markers, were detected by Western blotting and Immunohistochemistry. And the expression of Fibronectin (FN1) was used to analyze ECM production by CAFs. The exosomes were extracted by ultracentrifugation and exo-miRNAs were detected by qRT-PCR. Herein, we further elucidated the implicated mechanisms using online prediction software, luciferase reporter assays, co-immunoprecipitation, and experimental animal models. Results In vivo, a positive correlation was observed between the COX-2 expression levels in parenchyma and α-SMA/FN1 expression levels in mesenchyma in LUAD. However, PGE2, one of major product of COX-2, did not affect CAFs activation directly. COX-2 overexpression increased exo-miR-1290 expression, which promoted CAFs activation. Furthermore, Cullin3 (CUL3), a potential target of miR-1290, was found to suppress COX-2/exo-miR-1290-mediated CAFs activation and ECM production, consequently impeding tumor progression. CUL3 is identified to induce the Nuclear Factor Erythroid 2–Related Factor 2 (NFE2L2, Nrf2) ubiquitination and degradation, while exo-miR-1290 can prevent Nrf2 ubiquitination and increase its protein stability by targeting CUL3. Additionally, we identified that Nrf2 is direcctly bound with promoters of FAP-1 and FN1, which enhanced CAFs activation by promoting FAP-1 and FN1 transcription. Conclusions Our data identify a new CAFs activation mechanism by exosomes derived from cancer cells that overexpress COX-2. Specifically, COX-2/exo-miR-1290/CUL3 is suggested as a novel signaling pathway for mediating CAFs activation and tumor progression in LUAD. Consequently, this finding suggests a novel strategy for cancer treatment that may tackle tumor progression in the future. Video Abstrac

A genome-wide hybrid incompatible landscape between <i>C. briggsae</i> and <i>C. nigoni</i>.

<p>Individual introgressions (indicated by its strain name) are drawn in scale as horizontal bars above their source <i>C. briggsae</i> chromosomes (blue horizontal lines with the identity indicated on the left). The introgressions are differentially color coded according to their observed HI phenotypes as indicated when present as a homozygote or hemizygote in the <i>C. nigoni</i> background. Positions of the PCR primers used for genotyping are indicated in scale as small vertical blue bars. Only the introgressions that were selected for rendering homozygous are shown. *All HI phenotypes including sterility, viability, Emb, Lva and brood size were scored; # only viability and sterility were scored.</p

Refined mapping of HI loci on X chromosome by contrasting the HI phenotypes between independent introgressions.

<p>Male fertile (green), male sterile (blue) and male inviable introgressions (red) are depicted along the X chromosome, which is drawn as a horizontal black line with positions of the genotyping primers indicated by black vertical bars. The corresponding chromosomal coordinates in Mb are indicated below the bars. Small intervals mapped for male viability and male sterility are shaded in blue and pink respectively. The region containing a potential suppressor of male viability is shaded in brown. The strain names for a subset of introgressions are indicated.</p

A <i>C. briggsae</i> physical map consisting of a subset of 48 chromosomally integrated transgenic GFP markers.

<p>Chromosome and mapped position for transgenic marker are depicted in scale as solid and dashed horizontal lines respectively based on the <i>C. briggsae</i> “cb4” genome assembly. Mid-point of the mapped transgene is indicated with an inverted triangle. Name of the transgene is indicated above. All the mapped boundaries are derived from a single transgene except for the transgene <i>zzyIs20137</i> (highlighted in blue) for which the boundaries were calculated from the overlapping regions of the two independent introgressions. Chromosome numbers are indicated on the left. Chromosomal coordinates are labeled at 1 Mb interval with vertical bars.</p

Hybrid incompatible phenotypes for the homozygous introgressions between <i>C. briggsae</i> and <i>C. nigoni</i>.

<p>(A) Shown are the mean percentages of Emb, Lva and male out of the total progeny for the homozygous introgressions. (B) Shown are the mean brood sizes for the homozygous introgressions. Names of the strains used for phenotypic scoring are indicated at the bottom. The names of the strains carrying an X-linked introgression are shaded. Emb, embryonic lethality; Lva: larval arrest; percentage of male progeny is calculated as the ratio of males out of total hybrid progeny (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004993#sec013" target="_blank">Materials and Methods</a>). Standard deviations (SD) are indicated as error bars. Statistical significances from comparing mean of Emb, Lva and brood size are indicated with “*” or “**” which denotes p<0.05 and p<0.01 respectively (One-way ANOVA followed by post-hoc test); “#” and “##” indicate p<0.05 and p<0.01 respectively in X² test with an expected percentage of 50%. Sample size tested was listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004993#pgen.1004993.s012" target="_blank">S4 Table</a>.</p