Biology subjects

Vlachavas, E.-I.

Publications and source records attributed to Vlachavas, E.-I..

3 recordsLinked to original sources

bioRxiv2026

mRNA deep sequencing profiling and integrative miRNA-mRNA network analysis in pediatric Burkitt leukemia and lymphoma

Background: Although the genomic alterations in Burkitt leukemia and lymphoma (BL) have been extensively studied, data on genome-wide dysregulation of messenger RNA (mRNA) and microRNA (miRNA) in Burkitt leukemia (BuAL) and Burkitt lymphoma (BuLY) are scarce. The aim of this study was to analyze mRNA and miRNA expression profiles in pediatric BuAL/BuLY to identify dysregulated mRNA-miRNA networks. Methods: Total RNA from fresh tumor samples of 13 pediatric BL patients (BuAL n=7, BuLY n=6) and 4 pediatric normal control lymphoid tissue (NCLT) samples was included for mRNA-deep sequencing and miRNA-microarrays studies. Differential expression (DE) analysis of mRNAs and miRNAs as well as gene set and functional enrichment analysis were performed. The multiMiR R package was used to identify the validated target genes for the dysregulated miRNAs. miRNA-mRNA target interaction analysis was performed combining DE, validated targets observed among the inverse-significant miRNA-mRNA correlations, with evidence statistics retained (p[≤]-0.5 and Benjamini-Hochberg (BH) -adjusted correlation p-value< 0.05). Results: BL showed 1965 DE genes (DEG) compared to NCLT (1214 upregulated, 751 downregulated) (p-adj<0.05, log2FC>0.5) and 11 DE miRNAs (three upregulated and eight downregulated) (FC>1.5, p-adj<0.05). The transcriptional differences observed between BL and normal lymphoid tissue inferred by functional enrichment analysis identified along a MYC-driven proliferative backbone with strong E2F4 and MYB pathway activity, activation of the MAPK, PI3K and the G2/M checkpoint signaling pathways and repression of the JAK-STAT, NFkB, TP53, TRAIL and hypoxia pathways (p-adj<0.05). Functional enrichment analysis highlighted an upregulation of proliferative and metabolic pathways accompanied by an attenuated inflammatory and immunosurveillance signaling in BL compared to NCLT. Correlated miRNA-mRNA expression analysis identified DE dysregulated miRNAs and their validated target genes. DE downregulated miRNAs (hsa-miR-150-5p, hsa-miR-342-3p and hsa-miR-450-5p, among others) inversely correlated with upregulated mRNA targets showing pathway enrichment related to transcriptional activity and nuclear organization modules. mRNA targets of DE upregulated miRNAs (hsa-miR-106a-5p, hsa-miR-17-5p and hsa-miR-7-5p) were enriched in downregulated pathways related to immune response processes. Conclusions: Overall, this pilot study provides new insights on key proliferative, metabolic and cytokine-mediated immune signaling pathways in BL and highlights miRNA-mRNA networks influencing transcriptional activity and immune surveillance, paving the way for experimental validation models.

cancer biology↗

bioRxiv2025

PAK1 activation drives divergent resistance mechanisms to aromatase inhibition and Tamoxifen in a luminal A breast cancer model

Breast cancer is the most frequent malignancy and the second leading cause of cancer-related mortality in women worldwide, and is a heterogeneous disease regarding driver mechanisms, therapies, and outcome. Estrogen receptor-positive (ER+) tumors are treated with endocrine therapies such as Tamoxifen or aromatase inhibitors (AI), aimed at disrupting tumor-promoting estrogen signaling. While these therapies are initially effective, resident tumor cells can develop resistance, leading to relapse. The p21-activated kinase 1 (PAK1) is a key regulator of multiple oncogenic signaling pathways and has been implicated in resistance to Tamoxifen. However, it remains unclear, whether PAK1 also affects the response to other endocrine therapies. Using global phosphoproteomic profiling of endocrine resistant cell line models, we observed elevated PAK1 activity in cells resistant to Tamoxifen and to estrogen deprivation, respectively, with further increases following EGF stimulation. Pharmacological inhibition of PAK1 effectively reduced cell proliferation in both resistance models, however, with distinct effects on PAK1 downstream substrates and pathways. In the Tamoxifen resistance context, PAK1 reduces apoptosis via inhibition of the pro-apoptotic protein BAD, whereas in the AI resistance model PAK1 rather triggers proliferation via RAF1. Our findings position PAK1 as a common mediator of resistance to different endocrine therapies and offer insights into the distinct signaling networks that are involved. In summary, our results suggest that targeting PAK1 may present a novel therapeutic strategy to overcome endocrine therapy resistance in ER+ breast cancer, potentially enhancing the efficacy of both Tamoxifen and AI treatments.

cancer biology↗

bioRxiv2022

Genomic characteristics and clinical significance of CD56+ Circulating Tumor Cells in Small Cell Lung Carcinoma

IntroductionCirculating Tumor Cells (CTC) have been studied in various solid tumors but clinical utility of CTC in Small Cell Lung Cancer (SCLC) remains unclear. The aim of the CTC-CPC study was to develop an EpCAM-independent CTC isolation method allowing isolation of a broader range of living CTC from SCLC and decipher their genomic and biological characteristics. Patients and methodsCTC-CPC is a monocentric prospective non-interventional study including treatment-naive newly diagnosed SCLC. CD56+CTC were isolated from whole blood samples, at diagnosis and relapse after first-line treatment and submitted to Whole-exome-sequencing (WES). ResultsPhenotypic study confirms tumor lineage and tumorigenic properties of isolated cells for the 4 patients analyzed with WES. WES of CD56+CTC and matched tumor biopsy reveal genomic alteration frequently impaired in SCLC. At diagnosis CD56+CTC were characterized by a high mutation load, a distinct mutational profile and a unique genomic, compared to match tumors biopsies. In addition to classical pathways altered in SCLC, we found new biological processes specifically affected in CD56+CTC at diagnosis. High numeration of CD56+CTC (>7/ml) at diagnosis was associated with ES-SCLC. Comparing CD56+CTC isolated at diagnosis and relapse, we identify differentially altered oncogenic pathways (e.g. DLL3 or MAPK pathway). ConclusionsWe report a versatile method of CD56+CTC detection in SCLC. Numeration of CD56+CTC at diagnosis is correlated with disease extension. Isolated CD56+CTC are tumorigenic and a distinct mutational profile. We report a minimal gene set as a unique signature of CD56+CTC and identify new affected biological pathways enriched in EpCAM-independent isolated CTC in SCLC.

cancer biology↗