Differential expression patterns of AIP, UCKL1, and PKN1 genes in breast cancer of different molecular subtypes

Kovalevska, Larysa; Kashuba, Elena; Zadvornyj, T; Astrid, K; Lukianova, N Yu; Чехун, В Ф

doi:10.32471/exp-oncology.2312-8852.vol-43-no-4.17067

Cited by 3 publications

(1 citation statement)

References 29 publications

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“…RGS19 promotes cell proliferation and differentiation, and plays a role in immune processes by regulating the survival of macrophages through the Notch signaling pathway (Sangphech et al, 2014). UCKL1 is a uridine-cytidine kinase that plays a role in cell proliferation and survival and is highly expressed in breast cancer (Ambrose and Kornbluth, 2009;Kovalevska et al, 2021).…”

Section: Candidate Genes Associated With the Strongest Selection Signalmentioning

confidence: 99%

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Xiong

Bao

et al. 2023

Front. Genet.

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The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.

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Section: Candidate Genes Associated With the Strongest Selection Signalmentioning

confidence: 99%

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Xiong

Bao

et al. 2023

Front. Genet.

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Comprehensive analysis of DNA methylation gene expression profiles in GEO dataset reveals biomarkers related to malignant transformation of sinonasal inverted papilloma

Mu,

Hu,

et al. 2024

Discov Onc

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Background DNA methylation may be involved in the regulation of malignant transformation from sinonasal inverted papilloma (SNIP) to squamous cell carcinoma (SCC). The study of gene methylation changes and screening of differentially methylated loci (DMLs) are helpful to predict the possible key genes in the malignant transformation of SNIP-SCC. Materials and methods Microarray dataset GSE125399 was downloaded from the Gene Expression Omnibus (GEO) database and differentially methylated loci (DMLs) were analyzed using R language (Limma package). ClusterProfiler R package was used to perform Gene Ontology (GO) analysis on up-methylated genes and draw bubble maps. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and its visualization analysis were analyzed to speculate the possible key Genes in SNIP-SCC malignant transformation. Subsequently, SNIP cases archived in our department were collected, tissue microarray was made, and immunohistochemical staining was performed to analyze the expression levels of UCKL1, GSTT1, HLA-G, MAML2 and NRGN in different grades of sinonasal papilloma tissues. Results Analysis of dataset GSE125399 identified 56 DMLs, including 49 upregulated DMLs and 7 downregulated DMLs. Thirty-one genes containing upregulated DNA methylation loci and three genes containing downregulated DNA methylation loci were obtained by methylation microarray annotation analysis. In addition, KEGG pathway visualization analysis of 31 up-methylated genes showed that there were four significantly up-methylated genes including UCKL1, GSTT1, HLA-G and MAML2, and one significantly down-methylated gene NRGN. Subsequently, compared with non-neoplasia nasal epithelial tissues, the expression of HLA-G and NRGN was upregulated in grade I, II, III and IV tissues, while the expression of MAML2 was lost. The protein expression changes of MAML2 and NRGN were significantly negatively correlated with their gene methylation levels. Conclusions By analyzing the methylation dataset, we obtained four up-regulated methylation genes UCKL1, GSTT1, HLA-G and MAML2 and one down-regulated gene NRGN. MAML2, a tumor suppressor gene with high methylation modification but loss of protein expression, and NRGN, a tumor gene with low methylation modification but upregulated protein expression, can be used as biological indicators to judge the malignant transformation of SNIP-SCC.

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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis

Stephenson-Gussinye,

Rendón-Bautista,

Ruiz-Medina

et al. 2024

Front. Mol. Biosci.

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Molecular and cellular characterization of tumors is essential due to the complex and heterogeneous nature of cancer. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a hurdle for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows the recovery of highly viable cell suspensions from breast cancer primary tumor biopsies. Using these cell suspensions we have successfully characterized genome architecture through Hi-C. Also, we have evaluated single-cell gene expression and the tumor cellular microenvironment through single-cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here is a cost-effective alternative to obtain viable cell suspensions from biopsies simply and efficiently.

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Differential expression patterns of AIP, UCKL1, and PKN1 genes in breast cancer of different molecular subtypes

Cited by 3 publications

References 29 publications

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Comprehensive analysis of DNA methylation gene expression profiles in GEO dataset reveals biomarkers related to malignant transformation of sinonasal inverted papilloma

Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis

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