cDNA Microarrays - Providing Insight into Organism/Chemotherapeutic Interactions

2010 ◽  
Vol 63 (8) ◽  
pp. 1308
Author(s):  
Elise P. Wright

cDNA microarrays are a technique for interrogating gene expression responses to novel compounds, including chemotherapeutics. This holistic approach to gene expression measurement provides a genome wide appraisal of which molecular mechanisms are targeted by or associated with a drug.

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ying Mao ◽  
Peng Huang ◽  
Yan Wang ◽  
Maiqiu Wang ◽  
Ming D. Li ◽  
...  

Abstract Background Smoking is a major causal risk factor for lung cancer, chronic obstructive pulmonary disease (COPD), cardiovascular disease (CVD), and is the main preventable cause of deaths in the world. The components of cigarette smoke are involved in immune and inflammatory processes, which may increase the prevalence of cigarette smoke-related diseases. However, the underlying molecular mechanisms linking smoking and diseases have not been well explored. This study was aimed to depict a global map of DNA methylation and gene expression changes induced by tobacco smoking and to explore the molecular mechanisms between smoking and human diseases through whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). Results We performed WGBS on 72 samples (36 smokers and 36 nonsmokers) and RNA-seq on 75 samples (38 smokers and 37 nonsmokers), and cytokine immunoassay on plasma from 22 males (9 smokers and 13 nonsmokers) who were recruited from the city of Jincheng in China. By comparing the data of the two groups, we discovered a genome-wide methylation landscape of differentially methylated regions (DMRs) associated with smoking. Functional enrichment analyses revealed that both smoking-related hyper-DMR genes (DMGs) and hypo-DMGs were related to synapse-related pathways, whereas the hypo-DMGs were specifically related to cancer and addiction. The differentially expressed genes (DEGs) revealed by RNA-seq analysis were significantly enriched in the “immunosuppression” pathway. Correlation analysis of DMRs with their corresponding gene expression showed that genes affected by tobacco smoking were mostly related to immune system diseases. Finally, by comparing cytokine concentrations between smokers and nonsmokers, we found that vascular endothelial growth factor (VEGF) was significantly upregulated in smokers. Conclusions In sum, we found that smoking-induced DMRs have different distribution patterns in hypermethylated and hypomethylated areas between smokers and nonsmokers. We further identified and verified smoking-related DMGs and DEGs through multi-omics integration analysis of DNA methylome and transcriptome data. These findings provide us a comprehensive genomic map of the molecular changes induced by smoking which would enhance our understanding of the harms of smoking and its relationship with diseases.


2019 ◽  
Author(s):  
Hiroshi Ochiai ◽  
Tetsutaro Hayashi ◽  
Mana Umeda ◽  
Mika Yoshimura ◽  
Akihito Harada ◽  
...  

AbstractTranscriptional bursting is stochastic activation and inactivation of promoters, leading to discontinuous production of mRNA, and is considered to be a contributing factor to cell-to-cell heterogeneity in gene expression. However, it remains elusive how the kinetic properties of transcriptional bursting (e.g., burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing. We found that the kinetics of transcriptional bursting was determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. Furthermore, large-scale CRISPR-Cas9-based screening and functional analysis revealed that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncover key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 245-245
Author(s):  
Jung-Mi Lee ◽  
Bryan Goddard ◽  
Ashwini S. Hinge ◽  
Bruce J. Aronow ◽  
Nathan Salomonis ◽  
...  

Abstract Obesity is a complex pathological state defined by the excessive accumulation of adipose tissue and an array of hormonal, immunological and metabolic dysregulations. As such, obesity is a systemic stress that directly affects numerous organs and tissues. Notably, obesity and its sequelae modulate the immune system and the hematopoietic activity in the bone marrow (BM). Not surprisingly, obesity is also a well-established risk factor for leukemia associated with increased incidence and poor prognosis. However, despite their clinical relevance, mechanisms by which obesity affects the hematopoietic system remain elusive. Particularly, the impact of obesity on the hematopoietic stem cell (HSC) compartment has not been described. Using genetic and dietary mouse models of obesity, we conducted a "HSC-centered study" to determine how obesity affects HSCs and how these cells develop specific compensatory mechanisms to respond to this environment. Although HSCs in an obese environment displayed limited phenotypic and functional perturbations at steady state, they showed an aberrant response to hematopoietic stresses. In serial competitive transplantation assays, obesity-primed HSCs (defined as Lin- Sca-1+ c-Kit+ CD48- CD150+) showed a higher level of engraftment than controls in primary recipient mice (control, 20.8% +/-6.2 vs obese, 45.5% +/-14.6, p=0.022) but a dramatically reduced level of engraftment in secondary recipient mice (control: 25.8% +/-14.0 vs obese: 5.4% +/-3.9, p=0.033). Interestingly, BM analysis of secondary recipients showed reduced chimerism in all hematopoietic compartments but not in the HSC compartment. Altogether these results uncovered a biphasic behavior of the obesity-primed HSCs, characterized by an excessive differentiation response followed by a functional decline in which HSCs self-renew but fail to produce downstream progenitors. To unveil the molecular mechanisms involved in this aberrant activity, we performed a genome-wide gene expression analysis on HSCs isolated from normal and obese mice. Although the phenotype observed upon serial transplantation partially mimics HSC aging, obesity-primed HSCs did not share the molecular signature of old HSCs. Furthermore, down-regulation of interferon response-related genes (e.g Irak4, Irf7, Ifi27) and stress response-related genes (e.g. Stip1, Cgrrf1) showed that, unlike what has been described for committed progenitors, HSCs do not elicit a dramatic response to the inflammatory environment associated with obesity. In contrast obesity leads to the activation of specific molecular programs in HSCs. Firstly, obesity-primed HSCs showed up-regulation of multiples genes involved in the phosphatidylinositol signaling pathway (e.g. Pi4ka, Pi4k2b, Pi3kap1, Pi3kip1). Phosphoflow cytometry analysis indicated that this gene expression pattern was associated with the constitutive activation of the protein kinase AKT. While AKT activation is linked to functional HSC exhaustion, obesity-primed HSCs appeared refractory to this signal, suggesting the existence of compensatory mechanisms that protect the integrity of the HSCs in an obese environment. In parallel, we found that the aberrant activity of the obesity-primed HSCs was correlated with an elevated expression of Gfi1, a transcription factor critical for HSC quiescence and differentiation. Interestingly, the 2-fold increase in Gfi1 expression (p<10-5) observed in obesity-primed HSCs was maintained after serial transplantations in normal recipient mice indicating that the obese environment was able to promote the selection of a stable molecular program in the HSC compartment. Consistent with this idea, single-cell genome-wide analyses suggested a significant clonal shift within the obesity-primed HSC compartment. Finally, consistent with epidemiological data, we found that disruption of HSC homeostasis by obesity promotes the development of spontaneous hematopoietic pathologies resembling to myeloproliferative diseases. Altogether, our results establish the long lasting impact of obesity on the HSC compartment and uncover potential molecular mechanisms linking obesity to hematological diseases. Notably our results support the intriguing possibility that obesity, by directly acting on the HSC compartment, contributes to the development of a clonal hematopoiesis and favors the emergence of aberrant HSC clones. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Divya Mehta ◽  
Karen Grewen ◽  
Brenda Pearson ◽  
Shivangi Wani ◽  
Leanne Wallace ◽  
...  

AbstractMaternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29–53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4–2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura Bernhardt ◽  
Marcus Dittrich ◽  
Rabih El-Merahbi ◽  
Antoine-Emmanuel Saliba ◽  
Tobias Müller ◽  
...  

AbstractPaternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.


2020 ◽  
Vol 14 ◽  
Author(s):  
Mette Soerensen ◽  
Dominika Marzena Hozakowska-Roszkowska ◽  
Marianne Nygaard ◽  
Martin J. Larsen ◽  
Veit Schwämmle ◽  
...  

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Benjamin I. Laufer ◽  
J. Antonio Gomez ◽  
Julia M. Jianu ◽  
Janine M. LaSalle

Abstract Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS.


2003 ◽  
Vol 24 (3) ◽  
pp. 458-465 ◽  
Author(s):  
Hiroko Matsunaga ◽  
Takashi Anazawa ◽  
Edward S. Yeung

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