Project description:Fetal health is dependent upon the epigenetic-based regulation of gene expression in placenta. Genomic imprinting is an epigenetic phenomenon common to placenta and refers to the monoallelic expression of a gene in a parental-specific manner. We aimed to detect novel imprinted genes in human placenta by applying whole transcriptome RNA-sequencing and genotyping of coding variants. Ten family trios with healthy spontaneous single term pregnancy were recruited. Parental and child DNA genotypes were analysed using exome SNP genotyping microarrays, revealing the inheritance of parental alleles. Total RNA was extracted from placental tissue for whole transcriptome analysis. The imprinted genes showed consistent expression from either parental allele as demonstrated by the SNP content of sequenced transcripts. We found seven novel imprinted genes (ABP1, BCLAF1, IFI30, LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed five known imprinted genes (AIM1, PEG10, RHOBTB3, ZFAT and ZFAT-AS1). The main functions of the proteins encoded by the imprinted genes can be grouped as being involved in: i) cellular apoptosis and tissue development; ii) regulating inflammation and modulating the immune system; iii) facilitating metabolic processes and iv) regulating the cell cycle. Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.
Project description:Illumina 1M Omni Quad arrays were used to test mutation calling accuracy of qSNP tool (a mutation caller) Ilumina array genotypes with GenCal (GC score)>0.70 were used in the comparison of genotype calls using next generation sequencing data and qSNP (mutation caller) 2 samples (control cell line and Melanoma cell line). This is the data for a validation step. contributor: Australian Pancreatic Cancer Genome Initiative
Project description:PEO1 is part of the PEO/PEA series of ovarian cancer cell lines established in 1988 from progressive samples from three separate cases of ovarian cancer (Langdon et al., 1988). Copy number profiling of PEO1 ovarian cancer cell line on Illumina HumanOmni1-Quad BeadChip
Project description:Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle. Placentas from ten family trios were analysed using RNA-Seq.
Project description:Recently genome-wide association studies have identified significant association between Alzheimer’s disease and variations in CLU, PICALM, BIN1, CR1, MS4A4/MS4A6E, CD2AP, CD33, EPHA1 and ABCA7. However, the pathogenic variants in these loci have not yet been found. We conducted a genome-wide scan for large copy number variations (CNVs) in a dataset of Caribbean Hispanic origin (554 controls and 559 cases with late-onset Alzheimer’s disease) that was previously investigated in a SNP-based genome-wide association study using Illumina HumanHap 650Y platform. We ran four CNV calling algorithms and analyzed rare large CNVs (>100 Kb) to obtain high-confidence calls that were detected by at least two algorithms. In total, 734 such CNVs were observed in our dataset. Global burden analyses did not reveal significant differences between cases and controls in CNV rate, distribution of deletions or duplications, total or average CNV size; and number of genes affected by CNVs. However, we observed a nominal association between Alzheimer’s disease and a ~470 Kb duplication on chromosome15q11.2 (P=0.037). This duplication, encompassing up to five genes (TUBGCP5, CYFIP1, NIPA2, NIPA1 and WHAMML1) was present in 10 cases (2.6%) and 3 controls (0.8%). The dosage increase of CYFIP1 and NIPA1 genes was further confirmed by quantitative PCR. The current study did not detect CNVs (including common CNVs) that affect novel Alzheimer’s disease loci reported by large genome-wide association studies. However, since the array technology used in our study has limitations in detecting small CNVs, future studies must carefully assess novel AD associated genes for the presence of disease related CNVs. Case-control analysis, screening of large copy number variation in 559 Alzheimer cases and 554 control subjects of Caribbean Hispanic ancestry
Project description:Background: In present study we performed whole transcriptome analysis in plaque psoriasis patients and compared lesional skin with non-lesional skin and with the skin from healthy controls. We sequenced total RNA from 12 lesional (LP), 12 non-lesional (NLP) and from 12 normal (C) skin biopsies. Results: Compared with previous gene expression profiling studies we had three groups under analysis - LP, NLP and C. Using NLP samples allows to see the transcriptome of visually normal skin from psoriasis patient. In LP skin S100A12, S100A7A, LCE3E, DEFB4A, IL19 were found up regulated. In addition to already well-described genes, we also found several other, not so widely recognized transcripts, related to psoriasis. Namely, KLK9, OAS2, OAS3, PLA2G, IL36G, IL36RN were found to be significantly and consistently related to the psoriatic lesions. Ingenuity pathway analysis was used to define functional networks significantly enriched in the studied samples. The genes up-regulated in the LP samples were related to the innate immunity, IL17 and IL10 networks. In NLP samples innate immunity and IL17 network were activated, but activation of IL10 network was not evident. The transcriptional changes characteristic in the NLP samples can be considered as a molecular signature of “dormant psoriasis”. Conclusions: Taken together, our study described the transcriptome profile characteristic for LP and NLP psoriatic skin. RNA profile of the NLP skin is in between the lesional and healthy skin, with its own specific pattern. We found that both LP and NLP have up-regulated IL17 network, whereas LP skin has up regulated IL10 related cytokines (IL19, IL20, IL24). Moreover, IL36G and IL36RN were identified as strong regulators of skin pathology in both LP and NLP skin samples, with stronger influence in LP samples. 36 samples, 24 from psoriasis and 12 from controls
Project description:Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability. Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability. 24 samples, 14 controls and 10 with intervention
Project description:Using a mouse model of human MLL-AF9 leukemia, we identified the lysine-specific demethylase KDM1A (LSD1 or AOF2) as an essential regulator of leukemia stem cell (LSC) potential. KDM1A acts at genomic loci bound by MLL-AF9 to sustain expression of the associated oncogenic program, thus preventing differentiation and apoptosis. In vitro and in vivo pharmacologic targeting of KDM1A using tranylcypromine analogues active in the nanomolar range phenocopied Kdm1a knockdown in both murine and primary human AML cells exhibiting MLL translocations. By contrast, the clonogenic and repopulating potential of normal hematopoietic stem and progenitor cells was spared. Our data establish KDM1A as a key effector of the differentiation block in MLL leukemia which may be selectively targeted to therapeutic effect. To investigate the effects of Kdm1a KD on histone modifications, we performed chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) in control and Kdm1a KD MLL-AF9 AML cells for dimethyl-H3K4 and dimethyl-H3K9, as well as for trimethyl-H3K4 and trimethyl-H3K9. Dimethyl-H3K4 and dimethyl-H3K9 are targeted for demethylation by KDM1A. For each of these histone modifications, we compared the mean ChIP-Seq signal across and around protein coding genes bound by the MLL-AF9 oncoprotein (Bernt et al., 2011) with the mean signal from genes not bound by MLL-AF9 expressed at high, middle or low levels.
Project description:Oct4 stemness gene encoding a transcription factor has been shown to overexpress in cancers. However, precise mechanisms of Oct4 relevant to transcriptional reprogramming leading to somatic cancer progression remain unclear. To address the Oct4-mediated transcriptional program in lung cancer, we integrated genome-wide Oct4 binding profiles from chromatin-immunoprecipitation sequencing and ENCODE datasets. We identified that Oct4 occupied at functional promoter and enhancer regions of genes which play key roles in several signaling pathways involving tumorigenesis. Genome-wide Oct4 binding sites were identified via chromatin immunoprecipitation-sequencing analysis of vecoter control and stably Oct4-overexpressing A549 lung cancer cells. ChIP-seq analyses were performed in duplicated samples using Applied Biosystems SOLiD system.