The DNA methylation profile of oocytes in mice with hyperinsulinaemia and hyperandrogenism as detected by single-cell level whole genome bisulphite sequencing (SC-WGBS) technology

Polycystic ovary syndrome (PCOS), a familial aggregation disease that causes anovulation in women, has well-recognised characteristics, two of which are hyperinsulinaemia and hyperandrogenaemia. To determine whether the DNA methylation status is altered in oocytes by high insulin and androgen levels, we generated a mouse model with hyperinsulinaemia and hyperandrogenaemia by injection of insulin and human chorionic gonadotrophin and investigated DNA methylation changes through single-cell level whole genome bisulphite sequencing. Our results showed that hyperinsulinaemia and hyperandrogenaemia had no significant effects on the global DNA methylation profile and different functional regions of genes, but did alter methylation status of some genes, which were significantly enriched in 17 gene ontology (GO) terms (P < 0.05) by GO analysis. Among differently methylated genes, some were related to the occurrence of PCOS. Based on our results, we suggest that hyperinsulinaemia and hyperandrogenaemia may cause changes in some DNA methylation loci in oocytes.

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Analysis at the single-cell level indicates an important role of heterogeneous global DNA methylation status on the progression of lung adenocarcinoma

Scientific Reports ◽

10.1038/s41598-021-02786-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Quan-Fang Chen ◽

Han Gao ◽

Qing-Yun Pan ◽

Ying-Ju Wang ◽

Xiao-Ning Zhong

Keyword(s):

Dna Methylation ◽

Lung Adenocarcinoma ◽

Single Cell ◽

Tumor Cells ◽

Methylation Status ◽

Cell Junctions ◽

Global Dna Methylation ◽

Single Cell Level ◽

Cell Level ◽

Global Methylation

AbstractAberrant DNA modifications affect the tumorigenesis and progression of lung cancer. However, the global methylation status of tumor cells and the heterogeneous methylation status of cells within the same tumor need further study. We used publicly available single-cell RNAseq data to investigate the impact and diversity of global methylation status on lung adenocarcinoma. Clustering cells into subgroups and cell differentiation pseudotime analysis, based on expression profile, demonstrated that the global methylation status was crucial to lung adenocarcinoma function and progression. Hypermethylated tumor cells had increased activity related to the hypoxia response. Hyper- and hypomethylated cells indicated upregulation in pathways involving focal adhesion and cell junctions. Pseudotime analysis showed that cell clusters with unique methylation activities were located at the ends of the putative trajectories, suggesting that DNA methylation and demethylation activities were essential to tumor cell progression. Expression of SPP1 was associated with the global methylation status of tumor cells and with patient prognosis. Our study identified the importance and diversity of global DNA methylation status by analysis at the single-cell level. Our findings provide new information about the global DNA methylation status of tumor cells and suggest new approaches for precision medical treatments for lung adenocarcinoma.

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Abstract 1072: DNA methylation profile analysis of gliomas revealed a change in methylation status during malignant progression

10.1158/1538-7445.am2015-1072 ◽

2015 ◽

Author(s):

Mukasa Akitake ◽

Kuniaki Saito ◽

Koki Aihara ◽

Genta Nagae ◽

Mayu Omata ◽

...

Keyword(s):

Dna Methylation ◽

Profile Analysis ◽

Methylation Status ◽

Methylation Profile ◽

Malignant Progression ◽

Dna Methylation Profile

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Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification

Clinical Chemistry ◽

10.1373/clinchem.2011.162131 ◽

2011 ◽

Vol 57 (7) ◽

pp. 1032-1041 ◽

Cited By ~ 28

Author(s):

Thomas Kroneis ◽

Jochen B Geigl ◽

Amin El-Heliebi ◽

Martina Auer ◽

Peter Ulz ◽

...

Keyword(s):

Single Cell ◽

Tumor Cells ◽

Whole Genome Amplification ◽

Single Cells ◽

Molecular Genetic ◽

Target Cells ◽

Whole Genome ◽

Single Cell Level ◽

Cell Level ◽

Genome Amplification

BACKGROUND Analysis of chromosomal aberrations or single-gene disorders from rare fetal cells circulating in the blood of pregnant women requires verification of the cells' genomic identity. We have developed a method enabling multiple analyses at the single-cell level that combines verification of the genomic identity of microchimeric cells with molecular genetic and cytogenetic diagnosis. METHODS We used a model system of peripheral blood mononuclear cells spiked with a colon adenocarcinoma cell line and immunofluorescence staining for cytokeratin in combination with DNA staining with the nuclear dye TO-PRO-3 in a preliminary study to define candidate microchimeric (tumor) cells in Cytospin preparations. After laser microdissection, we performed low-volume on-chip isothermal whole-genome amplification (iWGA) of single and pooled cells. RESULTS DNA fingerprint analysis of iWGA aliquots permitted successful identification of all analyzed candidate microchimeric cell preparations (6 samples of pooled cells, 7 samples of single cells). Sequencing of 3 single-nucleotide polymorphisms was successful at the single-cell level for 20 of 32 allelic loci. Metaphase comparative genomic hybridization (mCGH) with iWGA products of single cells showed the gains and losses known to be present in the genomic DNA of the target cells. CONCLUSIONS This method may be instrumental in cell-based noninvasive prenatal diagnosis. Furthermore, the possibility to perform mCGH with amplified DNA from single cells offers a perspective for the analysis of nonmicrochimeric rare cells exhibiting genomic alterations, such as circulating tumor cells.

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Association Between miR-148a and DNA Methylation Profile in Individuals Exposed to Lead (Pb)

Frontiers in Genetics ◽

10.3389/fgene.2021.620744 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marília Ladeira de Araújo ◽

Bruno Costa Gomes ◽

Paula Pícoli Devóz ◽

Nathália de Assis Aguilar Duarte ◽

Diego Luis Ribeiro ◽

...

Keyword(s):

Dna Methylation ◽

Methylation Status ◽

Epidemiologic Studies ◽

Methylation Profile ◽

Taqman Assay ◽

Inverse Association ◽

Dna Methylation Profile ◽

Lead Levels ◽

Mirnas Expression ◽

The Impact

Experimental and epidemiologic studies have shown that lead (Pb) is able to induce epigenetic modifications, such as changes in DNA methylation profiles, in chromatin remodeling, as well as the expression of non-coding RNAs (ncRNAs). However, very little is known about the interactions between microRNAs (miRNAs) expression and DNA methylation status in individuals exposed to the metal. The aim of the present study was to investigate the impact of hsa-miR-148a expression on DNA methylation status, in 85 workers exposed to Pb. Blood and plasma lead levels (BLL and PLL, respectively) were determined by ICP-MS; expression of the miRNA-148a was quantified by RT-qPCR (TaqMan assay) and assessment of the global DNA methylation profile (by measurement of 5-methylcytosine; % 5-mC) was performed by ELISA. An inverse association was seen between miR-148a and % 5-mC DNA, as a function of BLL and PLL (β = −3.7; p = 0.071 and β = −4.1; p = 0.049, respectively) adjusted for age, BMI, smoking, and alcohol consumption. Taken together, our study provides further evidence concerning the interactions between DNA methylation profile and miR-148a, in individuals exposed to Pb.

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