Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

Rosati, Diletta; Palmieri, Maria; Brunelli, Giulia; Morrione, Andrea; Iannelli, Francesco; Frullanti, Elisa; Giordano, Antonio

doi:10.1016/j.csbj.2024.02.018

Cited by 5 publications

(1 citation statement)

References 189 publications

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“…In our case, these are the hub genes whose interactome was most strongly up-or downregulated with the change of ploidy. It is important to note that the identification of hub regulators increases the sensitivity and robustness of the method and therefore is particularly appropriate for the identification of subtle effects with high robustness [128].…”

Section: Obtaining the Sets Of Ploidy-induced Or Ploidy-suppressed Ma...mentioning

confidence: 99%

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

Anatskaya,

Vinogradov

2024

IJMS

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Mesenchymal stem cells (MSC) attract an increasing amount of attention due to their unique therapeutic properties. Yet, MSC can undergo undesirable genetic and epigenetic changes during their propagation in vitro. In this study, we investigated whether polyploidy can compromise MSC oncological safety and therapeutic properties. For this purpose, we compared the impact of polyploidy on the transcriptome of cancer cells and MSC of various origins (bone marrow, placenta, and heart). First, we identified genes that are consistently ploidy-induced or ploidy-repressed through all comparisons. Then, we selected the master regulators using the protein interaction enrichment analysis (PIEA). The obtained ploidy-related gene signatures were verified using the data gained from polyploid and diploid populations of early cardiomyocytes (CARD) originating from iPSC. The multistep bioinformatic analysis applied to the cancer cells, MSC, and CARD indicated that polyploidy plays a pivotal role in driving the cell into hypertranscription. It was evident from the upregulation of gene modules implicated in housekeeping functions, stemness, unicellularity, DNA repair, and chromatin opening by means of histone acetylation operating via DNA damage associated with the NUA4/TIP60 complex. These features were complemented by the activation of the pathways implicated in centrosome maintenance and ciliogenesis and by the impairment of the pathways related to apoptosis, the circadian clock, and immunity. Overall, our findings suggest that, although polyploidy does not induce oncologic transformation of MSC, it might compromise their therapeutic properties because of global epigenetic changes and alterations in fundamental biological processes. The obtained results can contribute to the development and implementation of approaches enhancing the therapeutic properties of MSC by removing polyploid cells from the cell population.

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Section: Obtaining the Sets Of Ploidy-induced Or Ploidy-suppressed Ma...mentioning

confidence: 99%

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

Anatskaya,

Vinogradov

2024

IJMS

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Tools and Databases in Transcriptomics Analysis: Recent Knowledge and Advancements

Mishra,

Roy,

Chhetri

et al. 2024

Reference Module in Life Sciences

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Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells

Liu,

Petinrin,

Chen

et al. 2024

BMC Infect Dis

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Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

Cited by 5 publications

References 189 publications

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

Tools and Databases in Transcriptomics Analysis: Recent Knowledge and Advancements

Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells

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