Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events

AbstractHere we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method. Previous studies indicated that tumor-specific alternative splicing is important in the regulation of gene expression and corresponding protein functions during cancer development. Multiple alternative splicing transcripts have been identified as progression markers, including generalized splicing abnormalities and tumor- and stage-specific events. We used a set of computer tools which were recently applied to analysis of gene expression in laboratory animals to study differential splicing events. We found 69 transcripts that are differentially alternatively spliced. Three cancer-associated genes were considered in detail, in particular: APP (amyloid beta precursor protein), CASC4 (cancer susceptibility candidate 4) and TP53. Such alternative splicing opens new perspectives for cancer research.

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Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals

Journal of Integrative Bioinformatics ◽

10.1515/jib-2016-292 ◽

2016 ◽

Vol 13 (4) ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Vladimir N. Babenko ◽

Anatoly O. Bragin ◽

Anastasia M. Spitsina ◽

Irina V. Chadaeva ◽

Elvira R. Galieva ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Protein Transport ◽

Laboratory Animals ◽

Neuron Development ◽

Brain Areas ◽

Computer Tools ◽

Genetic Mechanisms ◽

Differential Gene ◽

Alternative Splicing Events

Summary Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.

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A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model

Neurochemical Research ◽

10.1007/s11064-021-03241-0 ◽

2021 ◽

Vol 46 (5) ◽

pp. 1101-1111

Author(s):

Jun Li ◽

Hongyu Zhao ◽

Yongqiang Xing ◽

Tongling Zhao ◽

Lu Cai ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Mouse Model ◽

Hypoxic Preconditioning ◽

Whole Body ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome ◽

Alternative Splicing Events

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Comparative gene expression profiling of mouse ovaries upon stimulation with natural equine chorionic gonadotropin (N-eCG) and tethered recombinant-eCG (R-eCG)

10.21203/rs.3.rs-18763/v5 ◽

2020 ◽

Author(s):

Kwan-Sik Min ◽

Jong-Ju Park ◽

So-Yun Lee ◽

Munkhzaya Byambaragchaa ◽

Myung-Hwa Kang

Keyword(s):

Gene Expression ◽

Chorionic Gonadotropin ◽

Expression Profiles ◽

Expression System ◽

Laboratory Animals ◽

Metabolic Clearance ◽

Qrt Pcr ◽

Significant Difference ◽

Equine Chorionic Gonadotropin

Abstract Background: Equine chorionic gonadotropin (eCG) induces super-ovulation in laboratory animals. Notwithstanding its extensive usage, limited information is available regarding the differences between the in vivo effects of natural eCG (N-eCG) and recombinant eCG (R-eCG). This study aimed to investigate the gene expression profiles of mouse ovaries upon stimulation with N-eCG and R-eCG produced from CHO-suspension (CHO-S) cells. R-eCG gene was constructed and transfected into CHO-S cells and quantified. Subsequently, we determined the metabolic clearance rate (MCR) of N-eCG and R-eCG up to 24 h after intravenous administration through the mice tail vein and identified differentially expressed genes in both ovarian tissues, via quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC).Results: R-eCG was markedly expressed initially after transfection and maintained until recovery on day 9. Glycan chains were substantially modified in R-eCG protein produced from CHO-S cells and eliminated through PNGase F treatment. The MCR was higher for R-eCG than for N-eCG, and no significant difference was observed after 60 min. Notwithstanding their low concentrations, R-eCG and N-eCG were detected in the blood at 24h post-injection. Microarray analysis of ovarian tissue revealed that 20 of 12,816 genes assessed therein were significantly up-regulated and 43 genes were down-regulated by >2-fold in the group that received R-eCG (63 [0.49%] differentially regulated genes in total). The microarray results were concurrent with and hence validated by those of RT-PCR, qRT-PCR, and IHC analyses.Conclusions: The present results indicate that R-eCG can be adequately produced through a cell-based expression system through post-translational modification of eCG and can induce ovulation in vivo. These results provide novel insights into the molecular mechanisms underlying the up- or down-regulation of specific ovarian genes and the production of R-eCG with enhanced biological activity in vivo.

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Three Years Follow-Up Study Showed Prenatal Methamphetamine Exposure May Cause Chronic Abnormalities In Transcriptomic Pattern

10.21203/rs.3.rs-668566/v1 ◽

2021 ◽

Author(s):

Arvin Haghighatfard ◽

Soha Seifollahi ◽

Pegah Rajabi ◽

Niloofar Rahmani ◽

Rojin Ghannadzadeh

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Expression Profiles ◽

Expression Patterns ◽

Rna Extraction ◽

Childbearing Age ◽

Methamphetamine Use ◽

Methamphetamine Use Disorder

Abstract Background: The high rate of methamphetamine use disorder among young adults and women of childbearing age makes it imperative to clarify the long-term effects of Methamphetamine exposure on the offspring. Behavioral and cognitive problems had been reported in children with parental Methamphetamine exposure (PME). The present study aimed to assess the acute and chronic effects of PME in molecular regulations and gene expression profiles of children during their first years of life.Methods: All subjects were recruited before birth, and sampling was conducted from the first ten days of birth, twelve months, twenty months, and thirty-six months of age. Finally, 2658 children with PME and 3573 normal children had been finished the follow-up. RNA extraction was operated from blood samples and gene expression profiling was conducted by using the Affymetrix GeneChip Human Genome U133 plus 2.0 Array Platform. Gene expression data were confirmed by Real-time PCR. Results: Gene expression profiling during thirty-six months showed several constant mRNA level alterations in children with PME compared with normal. These genes are involved in several gene ontologies and pathways involved with the immune system, neuronal functions, and bioenergetic metabolism. It seems that Methamphetamine use disorder before and during the pregnancy period may affect the expression profile of children, and these changes could remain years after birth. Affected genes have some similarities with the gene expression patterns of addiction, psychiatric disorders, neurodevelopmental disabilities, and immune deficiencies. Conclusion: Findings may shed light on the molecular effects of prenatal methamphetamine exposure and may lead to new psychological and somatic caring protocols for these children based on their potential abnormalities.

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High resolution spatial transcriptome analysis by photo-isolation chemistry

10.1101/2020.03.20.000984 ◽

2020 ◽

Author(s):

Mizuki Honda ◽

Shinya Oki ◽

Akihito Harada ◽

Kazumitsu Maehara ◽

Kaori Tanaka ◽

...

Keyword(s):

Gene Expression ◽

Transcriptome Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Transcriptome Profiling ◽

Tissue Sections ◽

Complex Functions ◽

Multicellular Organisms

ABSTRACTIn multicellular organisms, individual cells are characterized by their gene expression profiles and the spatial interactions among cells enable the elaboration of complex functions. Expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of whole tissues. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. After photo-irradiation of limited areas, gene expression was detected from at least 10 cells in the tissue sections. PIC transcriptome analysis detected genes specifically expressed in small distinct areas of the mouse embryo. Thus, PIC enables transcriptome profiles to be determined from limited regions at a spatial resolution up to the diffraction limit.

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Biological Insights into Chemotherapy Resistance in Ovarian Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms20092131 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2131 ◽

Cited By ~ 2

Author(s):

Michelle A. Glasgow ◽

Peter Argenta ◽

Juan E. Abrahante ◽

Mihir Shetty ◽

Shobhana Talukdar ◽

...

Keyword(s):

Gene Expression ◽

Ovarian Cancer ◽

Expression Profiles ◽

Rna Extraction ◽

Chemotherapy Resistance ◽

Gene Expression Profiles ◽

Gene Set Enrichment Analysis ◽

Before And After ◽

Tumor Gene Expression ◽

Tumor Gene

The majority of patients with high-grade serous ovarian cancer (HGSOC) initially respond to chemotherapy; however, most will develop chemotherapy resistance. Gene signatures may change with the development of chemotherapy resistance in this population, which is important as it may lead to tailored therapies. The objective of this study was to compare tumor gene expression profiles in patients before and after treatment with neoadjuvant chemotherapy (NACT). Tumor samples were collected from six patients diagnosed with HGSOC before and after administration of NACT. RNA extraction and whole transcriptome sequencing was performed. Differential gene expression, hierarchical clustering, gene set enrichment analysis, and pathway analysis were examined in all of the samples. Tumor samples clustered based on exposure to chemotherapy as opposed to patient source. Pre-NACT samples were enriched for multiple pathways involving cell cycle growth. Post-NACT samples were enriched for drug transport and peroxisome pathways. Molecular subtypes based on the pre-NACT sample (differentiated, mesenchymal, proliferative and immunoreactive) changed in four patients after administration of NACT. Multiple changes in tumor gene expression profiles after exposure to NACT were identified from this pilot study and warrant further attention as they may indicate early changes in the development of chemotherapy resistance.

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Evaluation of TGF-Beta 2 and VEGFα Gene Expression Levels in Epiretinal Membranes and Internal Limiting Membranes in the Course of Retinal Detachments, Proliferative Diabetic Retinopathy, Macular Holes, and Idiopathic Epiretinal Membranes

Journal of Ophthalmology ◽

10.1155/2018/8293452 ◽

2018 ◽

Vol 2018 ◽

pp. 1-6

Author(s):

Joanna Stafiej ◽

Karolina Kaźmierczak ◽

Katarzyna Linkowska ◽

Paweł Żuchowski ◽

Tomasz Grzybowski ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Rna Extraction ◽

Retinal Diseases ◽

Epiretinal Membranes ◽

Expression Levels ◽

Macular Holes ◽

Retinal Disorders ◽

Pars Plana ◽

Gene Expression Levels

Purpose. To evaluate the expression profiles of the VEGFα and TGFβ in the ERMs and ILMs in retinal disorders. Methods. In this nonrandomized prospective study, 75 patients (34 females and 41 males) referred to pars plana vitrectomy (PPV) due to different retinal diseases were enrolled to the study. The samples of ERMs and ILMs collected during PPV were immediately put in TRIzol® Reagent (Life Technologies, USA) and stored at −70°C until RNA extraction. Gene expression analysis was done with TaqMan® Gene Expression Assays (Applied Biosystems, USA) following the manufacturer’s instructions. Results. The gene expression levels of VEGFα as well as of TGFβ2 were significantly higher in ERMs than in ILMs in all studied groups. The level of TGFβ2 expression exhibits a significantly lower values in iERMs as compared with the RRD group (p=0.043). There were differences in TGFβ2 expression in ILM in groups studied: DR versus RRD, p=0.003; DR versus iERM, p=0,047; and iERM versus RRD, p=0.004. Conclusions. Our results revealed that factors associated with angiogenesis and wound healing processes in eyes with RRD, PDR, iERM, and MH were more upregulated in ERMs than in ILMs. This may indicate that ILM is not responsible for reproliferation and its peeling should be avoided in routine PPV.

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