miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

Glogovitis, Ilias; Yahubyan, Galina; Würdinger, Thomas; Koppers-Lalić, Danijela; Baev, Vesselin

doi:10.3390/cancers13225663

Cited by 6 publications

(2 citation statements)

References 36 publications

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“…The miRNA datasets were pre-processed and analyzed to identify the differentially expressed genes between healthy and infected MECs using Galaxy and R software [42]. The data was quality controlled using FastQC tool [43,44], and reads with average Phred quality less than 20 were removed.…”

Section: Data Collectionmentioning

confidence: 99%

A meta-analysis of differentially expressed microRNA during mastitis disease in dairy cattle

Panahi,

hasanpour,

ghahramani

et al. 2023

Preprint

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Background: Bovine mastitis is an important inflammation disease that affects the mammary gland and causing adverse effects on the quality and quantity of the produced milk, leads to a major economic lost in dairy industry. Streptococcus uberisis one of the bacteria commonly responsible for inducing mastitis in dairy cattle. Susceptibility to develop mastitis is a complex multifactorial phenotype and the improvement of the miRNAs and their target genes has not been comprehensively illustrated. Methods and Results:The purpose of this investigation was to perform a meta-analysis of the miRNAs expression profiling datasets to detect the key miRNAs, targets, and regulatory networks associated with mastitis. To this, publicly available miRNA datasets belong to three experiments on dairy cattle which challenged with S. uberiswere included in our meta-analyzed. The identified differentially expressed miRNAs were used in TargetScan to identify their target genes. The functional impacts of the meta-miRNAs were further analyzed using Gene ontology and Protein-Protein Interaction network analysis. Three meta-miRNAs, namely bta-miR-98, bta-miR-138 and bta-miR-193a-3p, were obtained to be associated with the progress of the immune system and cell differentiation of the mammary gland during the mastitis. A total of 2061 target genes were identified that which bta-miR-98, bta-miR-138 and bta-miR-193a-3p were regulated 1121, 268 and 672 target genes respectively. Gene ontology analysis results were represented 237 biological process, 41 molecular function, 54 cellular component roles and nine KEGG pathways in mastitis disease. A total of 319, 113 and 124 target genes for bta-miR-98, bta-miR-193a-3p and bta-miR-138, respectively were inputted to cytoscape. The resulted network analysis showed that bta-miR-98 and bta-miR-138 have nine, bta-miR-138 and bta-miR-193a-3p have six, and bta-miR-193a-3p and bta-miR-98 have four common target genes. Twenty-one common genes were revealed by combing 360 common meta-genes in our previous research and 2061 meta-miRNA target genes. The procedure reported in this research offers a comprehensive scheme for the identification of the key miRNAs and target genes in mastitis disease by using global transcriptome data, meta-analysis, gene ontology, enrichment analysis and protein protein interaction. Conclusion: The findings of the current work suggest miRNAs are crucial amplifiers of inflammatory response by controlling metabolic pathway and inhibitors of several biological processes during S. uberis infection.

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Section: Data Collectionmentioning

confidence: 99%

A meta-analysis of differentially expressed microRNA during mastitis disease in dairy cattle

Panahi,

hasanpour,

ghahramani

et al. 2023

Preprint

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“…In a different study, Diest and colleagues examined the value of nipple aspirate fluid as a source of valuable cancer biomolecules (such as microRNAs) for use in breast cancer liquid biopsy [ 8 ]. Additionally, Glogovitis et al demonstrated the application of a framework that is based on Galaxy [ 9 ]. miRGalaxy is an open-source platform for analyzing NGS data, focusing on microRNAs and their sequence variants—isomiRs (template and non-template)—across samples.…”

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confidence: 99%

Liquid Biopsy: Current Status and Future Perspectives

Baev

Koppers-Lalić

Costa-Silva

2023

Cancers

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Aging promotes accumulation of senescent and multiciliated cells in human endometrial epithelium

Loid,

Obukhova,

Kask

et al. 2024

Human Reproduction Open

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STUDY QUESTION What changes occur in endometrium during aging, and do they impact fertility? SUMMARY ANSWER Both the transcriptome and cellular composition of endometrial samples from women of advanced maternal age are significantly different to that of samples from the young women, suggesting that specific changes in epithelial cells which may affect endometrial receptivity. WHAT IS KNOWN ALREADY Aging is associated with the accumulation of senescent cells in aging tissues. Reproductive aging is mostly attributed to the decline in ovarian reserve and oocyte quality, whereas the endometrium is a unique complex tissue which is monthly renewed under hormonal regulation. Several clinical studies have reported lower implantation and pregnancy rates in oocyte recipients of advanced maternal age (AMA) during in vitro fertilisation (IVF). Molecular studies have indicated the presence of specific mutations within the epithelial cells of AMA endometrium, along with altered gene expression of bulk endometrial tissue. STUDY DESIGN, SIZE, DURATION Endometrial transcriptome profiling was done for 44 women undergoing endometrial receptivity evaluation at hormonal replacement therapy (HRT) before IVF. Patients younger than 28 years were considered as the young maternal age group (YMA, age 23-27) and women older than 45 years were considered as the advanced maternal age group (AMA, age 47-50). Endometrial biopsies were obtained on day 5 of progesterone treatment, and RNA was extracted. All endometrial samples were evaluated as being receptive based on the expression of 68 common endometrial receptivity markers. Endometrial samples from another 24 women classified into four age groups (YMA, intermediate age group 1 (IMA1, age 29-35), intermediate age group 2 (IMA2, age 36-44) and AMA) were obtained in the mid-secretory stage of a natural cycle (NC) and used for validation studies across the reproductive lifespan. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 24 HRT samples (12 YMA and 12 AMA) were subject to RNA sequencing (RNA-seq) and differential gene expression analysis, 20 samples (10 YMA and 10 AMA) were used for qPCR validation, and 24 NC samples (6 YMA, 6 IMA1, 6 IMA2 and 6AMA) were used for RNA-seq validation of AMA genes across the woman’s reproductive lifespan. Immunohistochemistry (IHC) was used to confirm some expression changes at the protein level. Computational deconvolution using six endometrial cell type-specific transcriptomic profiles was conducted to compare the cellular composition between the groups. MAIN RESULTS AND THE ROLE OF CHANCE Comparisons between YMA and AMA samples identified a lower proportion of receptive endometria in AMA group (p = 0.007). Gene expression profiling identified 491 differentially expressed age-sensitive genes (p adj < 0.05) that revealed the effects of age on endometrial epithelial growth and receptivity, likely contributing to decreased reproductive performance. Our results indicate that changes in the expression of cellular senescence marker p16INK4a and genes associated with metabolism, inflammation and hormone response are involved in endometrial aging. Importantly, we demonstrate that the proportion of multi-ciliated cells, as discovered based on RNA-seq data deconvolution and tissue IHC results, is affected by endometrial aging, and propose a putative onset of age-related changes. Furthermore, we propose that aging has an impact on the transcriptomic profile of endometrial tissue in the context of endometrial receptivity. LARGE SCALE DATA The raw sequencing data reported in this article is deposited at the Gene Expression Omnibus under accession code GSE236128. LIMITATIONS, REASONS FOR CAUTION This retrospective study identified changes in the endometrium of patients undergoing hormonal replacement and validated these changes using samples obtained during a natural cycle. However, future studies must clarify the importance of these findings on the clinical outcomes of assisted reproduction. WIDER IMPLICATIONS OF THE FINDINGS The findings reported in this study have important implications for devising future strategies aimed at improving fertility management in women of advanced reproductive age. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Estonian Research Council (grant no. PRG1076), Horizon 2020 innovation grant (ERIN, grant no. EU952516), Enterprise Estonia (grant no. EU48695), MSCA-RISE-2020 project TRENDO (grant no. 101008193), EU 874867 project HUTER, the Horizon Europe NESTOR grant (grant no. 101120075) of the European Commission, the EVA specialty program (grant no. KP111513) of Maastricht University Medical Center (MUMC+), MICIU/AEI/10.13039/501100011033 and FEDER, EU projects Endo-Map (grant no. PID2021-12728OB-100), ROSY (grant no. CNS2022-135999), and the National Science Fund of Bulgaria (grant no. KII-06 H31/2). The authors declare no competing interests.

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miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

Cited by 6 publications

References 36 publications

A meta-analysis of differentially expressed microRNA during mastitis disease in dairy cattle

A meta-analysis of differentially expressed microRNA during mastitis disease in dairy cattle

Liquid Biopsy: Current Status and Future Perspectives

Aging promotes accumulation of senescent and multiciliated cells in human endometrial epithelium

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