Mutational signatures in colon cancer.

ObjectiveRecently, many tumor sequencing studies have inferred and reported on mutational signatures, short nucleotide patterns at which particular somatic base substitutions appear more often. A number of signatures reflect biological processes in the patient and factors associated with cancer risk. Our goal is to infer mutational signatures appearing in colon cancer, a cancer for which environmental risk factors vary by cancer subtype, and compare the signatures to those in adult stem cells from normal colon. We also compare the mutational signatures to others in the literature.ResultsWe apply a probabilistic mutation signature model to somatic mutations previously reported for six adult normal colon stem cells and 431 colon adenocarcinomas. We infer six mutational signatures in colon cancer, four being specific to tumors with hypermutation. Just two signatures explained the majority of mutations in the small number of normal aging colon samples. All six signatures are independently identified in a series of 295 Chinese colorectal cancers

miR-22 regulates expression of oncogenic neuro-epithelial transforming gene 1, NET1

MicroRNAs control cellular processes by regulating expression of their target genes. Here we report that neuro-epithelial transforming gene 1 (NET1) is a target of tumor suppressor microRNA 22 (miR-22). miR-22 is downregulated in peripheral blood mononuclear cells derived from chronic myeloid leukemia (CML) patients and in CML cell line K562. NET1 was identified as one of the targets of miR-22 using both in vitro and in vivo experiments. Either mutations or naturally occurring single-nucleotide polymorphisms in NET1 3′-UTR that map at the miR-22 binding site were found to affect binding of miR-22 to NET1 mRNA. Over expression of NET1 in K562 cells resulted in increased proliferation. However decreased proliferation and alteration in cell cycle were observed on either overexpression of miR-22 or knockdown of NET1 expression respectively. We also found that overexpression of miR-22 or NET1 knockdown inhibits actin fiber formation, probably by downregulation of NET1 as NET1 knockdown also resulted in depletion of actin fiber formation. We suggest that the oncogenic properties of CML cells are probably due to deregulated expression of NET1 as a result of altered expression of miR-22

De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski.

Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30,677 unigenes that led to the annotation of 12,380 genes. Annotation of the assembled transcripts enabled insight into processes and pathways in the intestinal fluke, such as RNAi pathway and energy metabolism. The expressed kinome of the organism was characterized by identifying all protein kinases. A rough draft genome assembly for Fasciolopsis buski is also reported herewith with SRA accessions for crosschecking the findings in the analyzed transcriptome data. Transcriptome data also helped us to identify some of the expressed transposable elements. Though many Long Interspersed elements (LINEs) were identified, only two Short Interspersed Elements (SINEs) were visible. Overall transcriptome and draft genome analysis of F. buski helped us to characterize some of its important biological characteristics and provided enormous resources for development of a suitable diagnostic system and anti-parasitic therapeutic molecules

Mutational signatures in colon cancer.

ObjectiveRecently, many tumor sequencing studies have inferred and reported on mutational signatures, short nucleotide patterns at which particular somatic base substitutions appear more often. A number of signatures reflect biological processes in the patient and factors associated with cancer risk. Our goal is to infer mutational signatures appearing in colon cancer, a cancer for which environmental risk factors vary by cancer subtype, and compare the signatures to those in adult stem cells from normal colon. We also compare the mutational signatures to others in the literature.ResultsWe apply a probabilistic mutation signature model to somatic mutations previously reported for six adult normal colon stem cells and 431 colon adenocarcinomas. We infer six mutational signatures in colon cancer, four being specific to tumors with hypermutation. Just two signatures explained the majority of mutations in the small number of normal aging colon samples. All six signatures are independently identified in a series of 295 Chinese colorectal cancers

HiLDA: a statistical approach to investigate differences in mutational signatures

We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs and to compare the estimated frequencies between tumor sets. We apply our method to two datasets, one containing somatic mutations in colon cancer by the time of occurrence, before or after tumor initiation, and the second containing somatic mutations in esophageal cancer by sex, age, smoking status, and tumor site. In colon cancer, the relative frequencies of mutational patterns were found significantly associated with the time of occurrence of mutations. In esophageal cancer, the relative frequencies were significantly associated with the tumor site. Our novel method provides higher statistical power for detecting differences in mutational signatures

Analysis of the microRNA transcriptome and expression of different isomiRs in human peripheral blood mononuclear cells

Background: MicroRNAs (miRNAs) have been recognized as one of the key regulatory non-coding RNAs that are involved in a number of basic cellular processes. miRNA expression profiling helps to identify miRNAs that could serve as biomarkers. Next generation sequencing (NGS) platforms provide the most effective way of miRNA profiling, particularly as expression of different isoforms of miRNA (IsomiRs) can be estimated by NGS. Therefore, it is now possible to discern the overall complexity of miRNA populations that participate in gene regulatory networks. It is thus important to consider different isoforms of miRNA as part of total profiling in order to understand all aspects of the biology of miRNAs. Results: Here next generation sequencing data of small RNAs derived from normal peripheral blood mononuclear cells (PBMC) and Chronic myeloid leukemia (CML) patients has been used to generate miRNA profiles using a computation pipeline which can identify isomiRs that are natural variants of mature miRNAs. IsomiR profiles have been generated for all the 5p and 3p miRNAs (previously known as major mature miRNA and minor or miRNA*) and the data has been presented as a composite total miRNA transcriptome. The results indicated that the most abundant isomiR sequence of about 68% miRNAs, did not match the reference miRNA sequence as entered in the miRBase and that there is a definite pattern in relative concentration of different isomiRs derived from same precursors. Finally, a total of 17 potential novel miRNA sequences were identified suggesting that there are still some new miRNAs yet to be discovered. Conclusions: Inclusion of different isoforms provides a detailed miRnome of a cell type or tissues. Availability of miRnome will be useful for finding biomarkers of different cell types and disease states. Our results also indicate that the relative expression levels of different isoforms of a miRNA are likely to be dynamic and may change with respect to changes in the cell or differentiation status

Development of a Droplet Digital™ PCR DNA methylation detection and quantification assay of prenatal tobacco exposure.

DNA methylation is a labile modification associated with gene expression control and environmental adaptations. High throughput, scalable and quantitative assessments of specific DNA methylation modifications in complex genomic regions for use in large population studies are needed. The performance of Droplet Digital™ PCR (ddPCR™) was investigated for DNA methylation detection against next-generation bisulfite sequencing (NGS) to demonstrate the ability of ddPCR to detect and validate DNA methylation levels and complex patterns among neighboring CpGs in regions associated with prenatal tobacco exposure. While both techniques are reproducible, ddPCR demonstrates a unique advantage for high-throughput DNA methylation analysis in large-scale population studies and provides the specificity to accurately measure DNA methylation of target CpGs in complex regions

Application of Additive Method of Fused Deposition Modeling to Production of Sprinkler Head

The thesis is focused on the design, modeling and manufacturing of a prototype sprinkler using modern additive technology Rapid Prototyping. The model was created using parametrical software SolidWorks, made ready to print by Cura software and printed in A602 3D printer working on Fused Deposition Modeling method. The theoretical basis of the work is involved in Rapid Prototyping, CAD systems technology, description of additive materials and their applications. Conclusion of this work compares this method with other options of production and evaluates which method is more efficient and more economical