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Several models have been described as potential mechanisms for the progression of ductal carcinoma in situ (DCIS) to invasive breast cancer (IBC). The aim of our study was to increase our understanding of DCIS progression by using massive parallel sequencing of synchronous DCIS and IBC. We included patients with synchronous DCIS and IBC (n = 4). Initially, IBC and normal tissue were subjected to whole exome sequencing. Subsequently, targeted sequencing was performed to validate those tumor-specific variants identified by whole exome sequencing. Finally, we analyzed whether those specific variants of the invasive component were also present in the DCIS component. There was a high genomic concordance between synchronous DCIS and IBC (52 out of 92 mutations were present in both components). However, the remaining mutations (40 out of 92) were restricted to the invasive component. The proportion of tumor cells with these mutations was higher in the invasive component compared to the DCIS component in a subset of patients. Our findings support the theory that the progression from DCIS to IBC could be driven by the selection of subclones with specific genetic aberrations. This knowledge improves our understanding of DCIS progression, which may lead to the identification of potential markers of progression and novel therapeutic targets in order to develop a more personalized treatment of patients with DCIS. [ABSTRACT FROM AUTHOR]

The vast majority of esophageal adenocarcinoma cases are sporadic and caused by somatic mutations. However, over the last decades several families have been identified with clustering of Barrett’s esophagus and esophageal adenocarcinoma. This observation suggests that one or more hereditary factors may play a role in the initiation of Barrett’s esophagus and esophageal adenocarcinoma in these families. A Dutch family with clustering of Barrett’s esophagus and esophageal adenocarcinoma was identified. Normal DNA obtained from the proband diagnosed with Barrett’s esophagus was analyzed with SNP array and exome sequencing. A custom-made panel consisting of potential germline variants was verified in the normal DNA of the affected family members. In addition, the respective tumors were analyzed for somatic loss of the wild type allele or the presence of an inactivating somatic mutation in the wild type allele. Exome sequencing revealed 244 candidate variants in the normal DNA of the proband, of which 212 variants were verified successfully. After the normal DNA of the affected family members was analyzed for the presence of the 212 potential germline variants and subsequently the respective tumors, only one potential germline variant in MSX1 (chr4: 4861985 T > G, c.359T > G, p.V120G, NM_002448) showed loss of the wild type allele in the tumor DNAs of the affected family members. A germline variant in MSX1 was identified in a Dutch family with clustering of Barrett’s esophagus and esophageal adenocarcinoma. This finding indicates that the germline defect in MSX1 may be associated with Barrett’s esophagus and cancer in this particular family. [ABSTRACT FROM AUTHOR]

Background:Gastrointestinal stromal tumours (GIST) are characterised by high expression of KIT and ETV1, which cooperate in GIST oncogenesis. Our aim was to identify microRNAs that are deregulated in GIST, have a role in GIST pathogenesis, and could potentially be used as therapeutic tool.Methods:Differentially expressed microRNAs between primary GIST (n=50) and gastrointestinal leiomyosarcomas (GI-LMS, n=10) were determined using microarrays. Selected microRNA mimics were transfected into GIST-882 and GIST-T1 cell lines to study the effects of microRNA overexpression on GIST cells. Luciferase reporter assays were used to establish regulation of target genes by selected microRNAs.Results:MiR-17-92 and miR-221/222 cluster members were significantly (P<0.01) lower expressed in GIST vs GI-LMS and normal gastrointestinal control tissues. MiR-17/20a/222 overexpression in GIST cell lines severely inhibited cell proliferation, affected cell cycle progression, induced apoptosis and strongly downregulated protein and - to a lesser extent - mRNA levels of their predicted target genes KIT and ETV1. Luciferase reporter assays confirmed direct regulation of KIT and ETV1 by miR-222 and miR-17/20a, respectively.Conclusion:MicroRNAs that may have an essential role in GIST pathogenesis were identified, in particular miR-17/20a/222 that target KIT and ETV1. Delivering these microRNAs therapeutically could hold great potential for GIST management, especially in imatinib-resistant disease. [ABSTRACT FROM AUTHOR]

Background: Gastrointestinal stromal tumours (GIST) are characterised by high expression of KIT and ETV1, which cooperate in GIST oncogenesis. Our aim was to identify microRNAs that are deregulated in GIST, have a role in GIST pathogenesis, and could potentially be used as therapeutic tool.Methods: Differentially expressed microRNAs between primary GIST (n=50) and gastrointestinal leiomyosarcomas (GI-LMS, n=10) were determined using microarrays. Selected microRNA mimics were transfected into GIST-882 and GIST-T1 cell lines to study the effects of microRNA overexpression on GIST cells. Luciferase reporter assays were used to establish regulation of target genes by selected microRNAs.Results: MiR-17-92 and miR-221/222 cluster members were significantly (P<0.01) lower expressed in GIST vs GI-LMS and normal gastrointestinal control tissues. MiR-17/20a/222 overexpression in GIST cell lines severely inhibited cell proliferation, affected cell cycle progression, induced apoptosis and strongly downregulated protein and--to a lesser extent--mRNA levels of their predicted target genes KIT and ETV1. Luciferase reporter assays confirmed direct regulation of KIT and ETV1 by miR-222 and miR-17/20a, respectively.Conclusion: MicroRNAs that may have an essential role in GIST pathogenesis were identified, in particular miR-17/20a/222 that target KIT and ETV1. Delivering these microRNAs therapeutically could hold great potential for GIST management, especially in imatinib-resistant disease. [ABSTRACT FROM AUTHOR]

Epithelial ovarian cancer is the most lethal gynecological malignancy in the Western world. A major impediment for the successful treatment is the development of drug resistance. The molecular processes that contribute to resistance have been extensively studied; however, there is not much known about regulation by microRNAs (miRNAs). We compared miRNA expression profiles of an isogenic cisplatin-sensitive and -resistant ovarian cancer cell line pair (A2780/A2780 DDP) and found 27 miRNAs to be differentially expressed (2-fold). Five of these, including the family members miR-141/200c, showed a correlation with cisplatin sensitivity in the NCI-60 panel. Overexpression of miR-141 resulted in enhanced resistance to cisplatin in ovarian cancer cell lines. We next correlated the expression level of miR-141 in 132 primary ovarian tumors (108 serous and 24 non-serous) with response to platinum-based chemotherapy. Although no differences were observed in the serous tumors, miR-141 levels were higher in non-serous ovarian tumors that did not respond well to therapy (platinum-free interval <6 months). We demonstrate that miR-141 directly targets KEAP1, and that downregulation of KEAP1 induces cisplatin resistance. Conversely, overexpression of KEAP1 significantly enhanced cisplatin sensitivity. Expression of KEAP1 with its 3′-UTR, and a 3′-UTR in which the miR-141 target site has been mutated, revealed that miR-141 regulates KEAP1 upon exposure to cisplatin. Finally, we show that the NF-κB pathway, which can be regulated by KEAP1, is activated upon miR-141 overexpression, and that inhibition of this pathway partially reverses miR-141-mediated cisplatin resistance. These findings demonstrate that the miR-141-mediated regulation of KEAP1 has a crucial role in the cellular response to cisplatin. [ABSTRACT FROM AUTHOR]

Abstract: RNA-binding proteins play a crucial role in the post-transcriptional regulation of gene expression. Polypyrimidine tract binding protein (PTB in humans) has been extensively characterized as an important splicing factor, and has additional functions in 3′ end processing and translation. ROD1 is a PTB paralog containing four RRM (RNA recognition motif) domains. Here, we discover a function of ROD1 in nonsense-mediated mRNA decay (NMD). We show that ROD1 and the core NMD factor UPF1 interact and co-regulate an extensive number of target genes. Using a reporter system, we demonstrate that ROD1, similarly to UPF1 and UPF2, is required for the destabilization of a known NMD substrate. Finally, we show through RIP-seq that ROD1 and UPF1 associate with a significant number of common transcripts. Structured summary of protein interactions: ROD1 physically interacts with TMED10 , RNP1 , PCD6 , LOC493753 , RBM39 , BCL7C , GST-PI , AP-3 , RAE1 , ASH2L2 , SF3B10 , SDP3 , CDC23 , ARL10C , CAF1B , CEP55 , EXPORTIN 1 , NCOR1 , LENG1 , SNAP29 , RCBTB1 , RPS10 , NUP155 , DYNLL2 , LSF , HSPC137 , TNRC6C , XPO5 , TMPO , SRP19 , SRI , UPF2 , TRF2 , SSRP1 , HOXB9 , C11ORF73 , TAF15 , WDR48 , SMARCA5 , CUL-2 , THOC2 , SEC16A , CAD , LSM2 , U11/U12 snRNP , TUBA , NEZHA , TRANSPORTIN 2 , CGI-135 , RER1 , snRP E , PRPF19 , TRANSPORTIN , IER3ip1 , DGCR14 , RPS19BP1 , TOPBP1 , YIP1 , CPSF6 , ASF1 , RBM9 , ARCN1 , U4/U6 snRNP , CUGbp2 , WDR41 , p53 , DNAJC9 , DAZap1 , TDP43 , MYL6 , HEY1 , RAB8B , BET1 , COFILIN1 , MYO12A , VAT1 , PRA1 , MAP7D2 , MAZ , PCD7 , DNAJ , GNL3L , BCAS2 , NUP50 , RGSip1 , TRIM33B , HMG-1 , RAB10 , ANNEXIN A2 , YKT6 , TRANSFERRIN , TIM44 , CTP synthase , CDC42 , PPIL1 , HOXA9B , GCN1 , hnRNP A1 , LDH-B , TRAP25 , mtSSB , MED8 , TIA1 , HMMR , B99 , H1d , IMPORTIN 5 , HOX7 , ZMAT5 , RPR1A , MARCKS , NACA , PRMT1 , HOXC9 , KIAA1741 , HSP90AA1 , LSM14 , COL1A1 , PRC1 , CDK2 , TRX-1 , CSE1 , COX5B , ARL1 , SEPT9 , BCR/ABL , CLIP-ap1 , ALY , BACH1 , TRIP230 , DES , GFAP , APC10 , MARK2 , FIP1l1 , RPL38 , HOXC8 , GATAd2A , HSPC128 , TUBB , RPL11 , FAM83D , UPF1 , ZFP768 , RPL35A , RPL30 , RAB1A , BTEbp4 , RNA Pol II , SEC24B , RAN , RAC3 , RPS28 , RPS27 , snRP A , SNF5/INI1 , C1ORF35 , RPS7 , RPS4X , RAMA1 , RPS14 , TUBA6 , FAM128B , T-PLASTIN , FLYWCH , MYH10 , ARP1 , U2AF , SERPINE1 , NEFM , KIAA1826 , Ki-67 and RPS11 by anti bait coimmunoprecipitation (View interaction) ROD1 physically interacts with LOC100288473, PTBP1 , LOC100291593, RRP36 , PCMT1 , BBS9 , FAM83H , ARHGEF17 , VIPAR , LOC100132738, PTBP2 , SACS , KBTBD5 , GPR98 , hnRNP F , OTUD4 , CAMSAP1L1 , C16ORF48 , FAM64A , SCN3A , IQGAP3 , ZMAT5 , TEX15 , NOL8 , RBM4 , snRNP48 , TMEM33 , UNC45A , OGT , DIAPH3 , CDK17 , LARS , FAM83D , TMTC2 , HSPA1A , PCM1 , CSNK1A1 , PHF5A , CCDC77 , PLECTIN , SETX , HSPB1 , HuR , NARF , MYH2 , HSP90AA1 , HLTF , GSK3b , CDC42 , MAGOH , TRIM21 , UPF1 , RBMS1 , ERI1 , CROCC , CSNK1D , CTNNA1 , AIMP2 , VPS33B , FLII , CTNNB1 , eIF4G2 , APC , TCF20 , CYCLIN T1 , HIRA , BACH1 , XRCC6 , HMMR , RPL9 , HSD17B4 , MAP2 , hnRNP H1 , GRIA4 , FRG1 , HistH1e , MSH6 , CELF2 , CELF1 , MYBbp1A , CLASP2 , STIP1 , GIPC1 , SF3a1 , CSNK1E , CDC14A , PPIH , RBM14 , DYNLL2 , RALY , PUF60 , TRIM33 , SF3b1 , TARDBP , PAPD7 , SF3b2 , LRRFIP2 , SUPT16H , FAM110B , hnRNP Ul1 , KIAA1543 , AXIN1 , RNP1 , HERC1 , BANF1 , XRCC5 , XPC , FYTTD1 , PDCD7 , TAF15 , YWHAH , RB1CC1 , MATR3 , SRRM1 , SFRS14 , LAGE3 , XIRP1 , ARHGEF2 , PRPF3 , PUM1 and IQCB1 by anti bait coimmunoprecipitation (View interaction) [Copyright &y& Elsevier]

MicroRNAs (miRNAs) relevant to acute lymphoblastic leukemia (ALL) in children are hypothesized to be largely unknown as most miRNAs have been identified in non-leukemic tissues. In order to discover these miRNAs, we applied high-throughput sequencing to pooled fractions of leukemic cells obtained from 89 pediatric cases covering seven well-defined genetic types of ALL and normal hematopoietic cells. This resulted into 78 million small RNA reads representing 554 known, 28 novel and 431 candidate novel miR genes. In all, 153 known, 16 novel and 170 candidate novel mature miRNAs and miRNA-star strands were only expressed in ALL, whereas 140 known, 2 novel and 82 candidate novel mature miRNAs and miRNA-star strands were unique to normal hematopoietic cells. Stem-loop reverse transcriptase (RT)-quantitative PCR analyses confirmed the differential expression of selected mature miRNAs in ALL types and normal cells. Expression of 14 new miRNAs inversely correlated with expression of predicted target genes (−0.49Spearman's correlation coefficients (Rs)−0.27, P0.05); among others, low levels of novel sol-miR-23 associated with high levels of its predicted (antiapoptotic) target BCL2 (B-cell lymphoma 2) in precursor B-ALL (Rs −0.36, P=0.007). The identification of >1000 miR genes expressed in different types of ALL forms a comprehensive repository for further functional studies that address the role of miRNAs in the biology of ALL. [ABSTRACT FROM AUTHOR]

There is emerging interest in the application of mesenchymal stem cells (MSC) for the prevention and treatment of autoimmune diseases, graft- versus-host disease and allograft rejection. It is, however, unknown how inflammatory conditions affect phenotype and function of MSC. Adipose tissue-derived mesenchymal stem cells (ASC) were cultured with alloactivated peripheral blood mononuclear cells (PBMC) (mixed lymphocyte reaction: MLR), with proinflammatory cytokines [interferon (IFN)-γ, tumour necrosis factor (TNF)-α and interleukin (IL)-6] or under control conditions, and their full genome expression and function examined. Proinflammatory cytokines mainly increased indoleamine-2,3-dioxygenase expression, whereas ASC cultured with MLR showed increased expression of COX-2, involved in prostaglandin E production. Both conditions had a stimulatory, but differential, effect on the expression of proinflammatory cytokines and chemokines, while the expression of fibrotic factors was decreased only in response to proinflammatory cytokines. Functional analysis demonstrated that inflammatory conditions affected morphology and proliferation of ASC, while their differentiation capacity and production of trophic factors was unaffected. The immunosuppressive capacity of ASC was enhanced strongly under inflammatory conditions. In conclusion, ASC showed enhanced immunosuppressive capacity under inflammatory conditions, while their differentiation capacity was preserved. Therefore, in vitro preconditioning provides ASC with improved properties for immediate clinical immune therapy. [ABSTRACT FROM AUTHOR]

The article discusses a study which examined the introduction of either the H1N1v virus or a seasonal human H1N1 influenza virus into cynomolgus macaques for the establishment of a nonhuman primate model of influenza pneumonia. It explains the methodology used for the study, such as virological, pathological, and microarray analyses. The result of the study showed that H1N1v virus affects the alveolar epithelial cells which ten causes diffuse alveolar damage in a nonhuman primate model.

Background: Endocrine therapies of breast cancer are effective but ultimately fail because of the development of treatment resistance. We have previously revealed several genes leading to tamoxifen resistance in vitro by retroviral insertion mutagenesis. To understand the manner in which these genes yield tamoxifen resistance, their effects on global gene expression were studied and those genes resulting in a distinct gene expression profile were further investigated for their clinical relevance.Methods: Gene expression profiles of 69 human breast cancer cell lines that were made tamoxifen resistant through retroviral insertion mutagenesis were obtained using oligonucleotide arrays and analysed with bioinformatic tools. mRNA levels of NCOR2 and CITED2 in oestrogen receptor-positive breast tumours were determined by quantitative RT-PCR. mRNA levels were evaluated for association with metastasis-free survival (MFS) in 620 patients with lymph node-negative primary breast cancer who did not receive systemic adjuvant therapy, and with clinical benefit in 296 patients receiving tamoxifen therapy for recurrent breast cancer.Results: mRNA expression profiles of most tamoxifen-resistant cell lines were strikingly similar, except for the subgroups of cell lines in which NCOR2 or CITED2 were targeted by the retrovirus. Both NCOR2 and CITED2 mRNA levels were associated with MFS, that is, tumour aggressiveness, independently of traditional prognostic factors. In addition, high CITED2 mRNA levels were predictive for a clinical benefit from first-line tamoxifen treatment in patients with advanced disease.Conclusions: Most retrovirally targeted genes yielding tamoxifen resistance in our cell lines do not impose a distinctive expression profile, suggesting that their causative role in cell growth may be accomplished by post-transcriptional processes. The associations of NCOR2 and CITED2 with outcome in oestrogen receptor-positive breast cancer patients underscore the clinical relevance of functional genetic screens to better understand disease progression, which may ultimately lead to the development of improved treatment options. [ABSTRACT FROM AUTHOR]

Summary: The NARWHAL software pipeline has been developed to automate the primary analysis of Illumina sequencing data. This pipeline combines a new and flexible de-multiplexing tool with open-source aligners and automated quality assessment. The entire pipeline can be run using only one simple sample-sheet for diverse sequencing applications. NARWHAL creates a sample-oriented data structure and outperforms existing tools in speed.Availability: https://trac.nbic.nl/narwhal/Contact: w.vanijcken@erasmusmc.nlSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]