Light-dependent induction of Edn2 expression and attenuation of retinal pathology by endothelin receptor antagonists in Prominin-1- deficient mice

Retinitis pigmentosa (RP) and macular dystrophy (MD) are prevalent retinal degenerative diseases associated with gradual photoreceptor death. These diseases are often caused by genetic mutations that result in degeneration of the retina postnatally after it has fully developed. The Prominin-1 gene (Prom1) is a causative gene for RP and MD, and Prom1- knockout (KO) mice recapitulate key features of these diseases including light-dependent retinal degeneration and stenosis of retinal blood vessels. The mechanisms underlying progression of such degeneration have remained unknown, however. We here analysed early events associated with retinal degeneration in Prom1-KO mice. We found that photoreceptor cell death and glial cell activation occur between 2 and 3 weeks after birth. High-throughput analysis revealed that expression of the endothelin-2 gene (Edn2) was markedly up-regulated in the Prom1-deficient retina during this period. Expression of Edn2 was also induced by light stimulation in Prom1-KO mice that had been reared in the dark. Finally, treatment with endothelin receptor antagonists attenuated photoreceptor cell death, gliosis, and retinal vessel stenosis in Prom1-KO mice. Our findings suggest that inhibitors of endothelin signalling may delay the progression of RP and MD and therefore warrant further study as potential therapeutic agents for these diseases

Somatic mutation

<p>Supplemental data</p

test.data

<p>Supplmental data</p

Germline Variants of Prostate Cancer in Japanese Families

<div><p>Prostate cancer (PC) is the second most common cancer in men. Family history is the major risk factor for PC. Only two susceptibility genes were identified in PC, <i>BRCA2</i> and <i>HOXB13</i>. A comprehensive search of germline variants for patients with PC has not been reported in Japanese families. In this study, we conducted exome sequencing followed by Sanger sequencing to explore responsible germline variants in 140 Japanese patients with PC from 66 families. In addition to known susceptibility genes, <i>BRCA2</i> and <i>HOXB13</i>, we identified <i>TRRAP</i> variants in a mutually exclusive manner in seven large PC families (three or four patients per family). We also found shared variants of <i>BRCA2</i>, <i>HOXB13</i>, and <i>TRRAP</i> from 59 additional small PC families (two patients per family). We identified two deleterious <i>HOXB13</i> variants (F127C and G132E). Further exploration of the shared variants in rest of the families revealed deleterious variants of the so-called cancer genes (<i>ATP1A1</i>, <i>BRIP1</i>, <i>FANCA</i>, <i>FGFR3</i>, <i>FLT3</i>, <i>HOXD11</i>, <i>MUTYH</i>, <i>PDGFRA</i>, <i>SMARCA4</i>, and <i>TCF3</i>). The germline variant profile provides a new insight to clarify the genetic etiology and heterogeneity of PC among Japanese men.</p></div

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses

<div><p>Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified “HERV/LTR-shared regulatory element (HSRE),” defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (<a href="http://herv-tfbs.com/" target="_blank">http://herv-tfbs.com/</a>). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.</p></div

Pedigrees of the seven large PC families.

<p>Solid black rectangles represent affected patients with PC. Patients with PC analyzed by exome-seq were numbered (from 01 to 22). PC, prostate cancer.</p

Long-range interactions between HERV-TFBSs/HSREs and promoters of host genes.

<p>The interactions were extracted using pcHi-C dataset in GM12878 cells [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006883#pgen.1006883.ref054" target="_blank">54</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006883#pgen.1006883.ref055" target="_blank">55</a>]. Results from unique-read TFBSs are shown. A) Proportion of HERV/LTR copies overlapped with promoter-interacting regions. Proportions of total HERV/LTRs, HERV/LTRs with HERV-TFBSs, and HERV/LTRs with HSREs are separately shown. B) Transcription levels (log₁₀ (RPKM+1)) of protein-coding genes and number of HERV-TFBSs interacting with the genes. Genes were divided into five categories based on the number of HERV-TFBSs interacting with the genes (0, 1, 2–5, 6–10, and 10<). Categories of the 0, 1, 2–5, 6–10, and 10< respectively contained 13,265, 1,179, 1,946, 822, and 1,639 of genes. P values were calculated using the Mann-Whitney U test with adjustment for multiple tests using the BH method. C) The word cloud indicating HERV/LTR types enriched in the interacting regions. Word sizes are proportional to the −log₁₀ (p value) calculated using the Fisher’s exact test. The word colors indicate HERV/LTR families. D) Hi-C-based GO enrichment analysis. A set of all HERV-TFBSs in GM12878 cells was used. HERV-TFBSs identified in cells treated with special conditions (e.g., supplement of interferon) were excluded. GO terms were summarized by REVIGO [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006883#pgen.1006883.ref073" target="_blank">73</a>]. GO terms with hold enrichment scores of >2 are shown.</p

Shared genes with variants.

<p>(A) Heat map of the shared genes with variants. Each column shows the family identification of large PC families or PC pairs of the small PC families. Each row shows the gene names and shared variants are filled with red (deleterious) or orange (nondeleterious) color. (B) Deleterious variants of the Cancer Gene Census genes. The variant status is shown. ExAC_all, MAF of all subjects in the ExAC; iJGVD, MAF in the iJGVD; HGVD, MAF in the HGVD; NA, Not applicable; PC, prostate cancer.</p