Biology subjects

Turiello, R.

Publications and source records attributed to Turiello, R..

6 recordsLinked to original sources

bioRxiv2026

Integrated transcriptomic analysis identifies Paternally Expressed Gene 10 as a novel candidate biomarker associated with aggressive features in liposarcoma

Abstract Background Liposarcoma is a rare cancer, comprising four major histological subtypes: well-differentiated, dedifferentiated, myxoid and pleomorphic liposarcoma. Therapeutic options remain limited for advanced disease, and additional biomarkers that may support biological characterization, diagnosis, or risk stratification are needed. Methods Bulk RNA sequencing (RNA-seq) was performed on paired tumour and adjacent non-tumour tissues from an analysable subset of 16 patients (22 tumour specimens) within a clinicopathological cohort of 21 patients. Differential gene expression analysis, principal component analysis, gene set enrichment (GSEA) analysis and single-sample GSEA (ssGSEA) were used to define subtype-specific transcriptional programs and imprinted-gene dysregulation. PEG10 expression was validated by RT-qPCR and RNA fluorescence in situ hybridization (FISH), and its cellular localization was explored by combined FISH and immunofluorescence for P53, vimentin, Ki67, and CD34. PEG10 expression in liposarcoma was further investigated in an external single-cell RNA-sequencing dataset of dedifferentiated liposarcoma. An exploratory survival analysis was performed in the pan-sarcoma TCGA-SARC cohort. Results Transcriptomic profiling identified distinct subtype-specific gene expression patterns and broad dysregulation of imprinted genes in liposarcoma compared with adjacent non-tumour tissue. Among all the imprinted genes, PEG10 showed a marked tumour-to-normal expression difference and good discriminatory performance between tumour and normal tissues in the discovery cohort (AUC=0.867). In the TCGA sarcoma cohort high PEG10 expression was associated with shorter overall survival. Immuno-FISH and single-cell analyses revealed that PEG10 was predominantly detected in tumour and proliferating cell populations. Importantly, PEG10 expression was higher in high-grade tumours. In bulk RNA-seq data, PEG10 expression correlated with hypoxia, extracellular matrix remodelling and invasion ssGSEA signatures. In the external single-cell RNA-seq dataset PEG10high tumours showed a reduced immune cell infiltration. Conclusions This study provides an integrated transcriptomic characterisation of liposarcoma and identifies PEG10 as a candidate tumour-associated biomarker linked to aggressive disease features. The diagnostic and prognostic value of PEG10 requires validation in larger, independent, subtype-balanced liposarcoma cohorts, and its potential therapeutic relevance requires direct functional investigation.

genomics↗

bioRxiv2026

SPARQ-MI leverages end-to-end spatial single-cell analysis of the tumor microenvironment

Detailed spatial analysis of the tumor micro-environment (TME) through multiplexed fluorescence imaging requires quantitative image-processing and data-analysis methods. While data-preprocessing down to segmentation of individual cells is captured by available methods, statistical analysis of single-cell features is compromised by the uneven noise distribution especially in complex tissues such as the TME, as well as by labor-intensive manual cell-type annotation and region segmentation. Here, we present SPARQ-MI (Spatial Phenotyping, Architecture Reconstruction and Quantification from Multiplexed Imaging) for streamlined spatial single-cell analysis, along with a tissue microarray PhenoCycler data-set with 37 fluorescent channels from melanoma patients under immunotherapy. We demonstrate that SPARQ-MI enables robust reconstruction of the cellular and spatial composition in this and other tissue types. Our analysis reveals associations of the cell-state and spatial location of CD8 T cells with response to immunotherapy. Overall, SPARQ-MI allows for quantitative analysis of complex fluorescence histology samples under minimal user input, and accounting for spatially uneven coverage of antibody signals, setting the stage for quantitative analysis of clinical samples.

bioinformatics↗

bioRxiv2026

Longitudinal spatial profiling of neutrophils during adoptive T cell therapy in murine melanoma reveals distinct lymph node infiltration patterns across anatomical sites

Reactive neutrophil infiltration can restrain CD8+ T cell expansion in lymph nodes during adoptive T cell therapy (ACT), yet its spatiotemporal regulation remains incompletely understood. Levaraging flow cytometry and multiplex immunofluorescence data, we performed a time-resolved quantitative assessment of immune cell dynamics in tumor-draining lymph node (tdLN) and non-tumor-draining lymph node (non-tdLN) in a melanoma mouse model receiving ACT. Transferred tumor-reactive CD8+ T cells accumulated and expanded early after treatment initiation, showing the highest frequency of a favorable central memory CD8+ T cell phenotype in the tdLN. Enhancing innate immune signaling in melanomas increased neutrophil influx into lymph nodes, particularly the non-tdLN; however, within the tdLN, neutrophils were enriched in the T cell zone, which also contained the largest absolute reservoir of transferred CD8+ T cells. Together, these findings indicate that tdLN and non-tdLN differ in early neutrophil dynamics and compartmentalization during ACT, influenced by the strength of innate immune signaling in the tumor.

immunology↗

bioRxiv2026

A novel pharmacogenetic testing panel for CYP2C19 genetic polymorphisms

Specific drug metabolism rates are defined by the constituency of the cytochrome P450 (CYP) genome, including polymorphic changes in any of 200+ CYP genes. An example is CYP2C19, where associations of gene polymorphisms with variability in certain drug metabolism rates have been linked to inter-individual and inter-ethnic differences in therapeutic outcomes. While pharmacogenomic screening for these variants prior to drug and dosage prescription has well-defined links to better treatment outcomes, current implementation is limited to complex and costly variant-probing and DNA sequencing protocols, which have limited availability in clinical laboratories, leading to slow turnaround times, impacting effective clinical intervention. Here we describe a novel, cost-effective, multiplex genotyping approach to screening CYP2C19 variants. Fluorescence nested allele-specific (FAS) PCR was used with primers to detect CYP2C19 variants of interest in specific hot spots, including the Tier 1 haplotypes identified by the Association for Molecular Pathology (AMP): CYP2C19*2, *3, and *17. The presence/absence of wild-type and mutant alleles were identified independently as haplotypes, and in a multiplex reaction as diplotypes representing the 10 possible genotype combinations/profiles. FAS-PCR achieved the same genotype calls as a pyrosequencing protocol optimized for validating genotypes, but with a simpler and more sensitive interface. The FAS-PCR method correctly identified the genotypes of both synthesized DNA and a human genomic DNA standard. Uniquely, the FAS-PCR protocol generates patterns using one fluorescently-labeled primer irrespective of the number of variants targeted, establishing it as considerably more cost-effective than other allele-specific PCR-based techniques that involve labeling both the forward and reverse primers.

pharmacology and toxicology↗

bioRxiv2025

NKG7 is a stable marker of cytotoxicity across immune contexts and within the tumor microenvironment

Cytotoxicity is a cornerstone of immune defense, critical for combating tumors and infections. This process relies on the coordinated action of granzymes and pore-forming proteins, with Granzyme B (GZMB) and Perforin (PRF1) being key markers and the most widely studied molecules pertaining to cytotoxicity. However, other human granzymes and cytotoxic components remain underexplored, despite growing evidence of their distinct, context-dependent roles. Natural Killer Cell Granule Protein 7 (NKG7) has recently emerged as a crucial cytotoxicity regulator, yet its expression patterns and function are poorly understood. Using large publicly available single-cell RNA sequencing atlases, we performed a comprehensive profiling of cytotoxicity across immune subsets and tissues. Our analysis highlights NKG7 expression as a strong marker of cytotoxicity, exhibiting a strong correlation with overall cytotoxic activity (r = 0.97) and surpassing traditional markers such as Granzyme B and Perforin in reliability. Furthermore, NKG7 expression is notably consistent across diverse immune subsets and tissues, reinforcing its versatility and robustness as a cytotoxicity marker. These findings position NKG7 as an invaluable tool for evaluating immune responses and a reliable indicator of cytotoxic functionality across biological and clinical contexts.

immunology↗

bioRxiv2022

A2A Receptor contributes to tumor progression in P2X7 null mice

ATP and adenosine are key constituents of the tumor niche where they exert opposite and complementary roles. ATP promotes tumor growth but also immune eradicating responses mainly via the P2X7 receptor (P2X7R), while adenosine acts as a potent immune suppressor and facilitates neovascularization thanks to A2A receptor (A2AR) activity. However, studies exploring the interplay between P2X7R and A2AR in the tumor microenvironment are as yet missing. Here we investigated tumor growth in C57/bl6 P2X7 null mice inoculated with B16-F10 melanoma cells, showing that several pro-inflammatory cytokines (IL1-{beta}, TNF-, IL-6, IL-12, IL-17, IFN-{gamma}) were significantly decreased while the immune suppressant TGF-{beta} was almost three-fold increased. Interestingly, tumors growing in P2X7-null mice also upregulated tumor-associated and splenic A2AR, suggesting that immunosuppression associated to lack of the P2X7R might depend upon A2AR overexpression. Immunohistochemical analysis showed that tumor cells A2AR expression was increased, especially around necrotic areas, and that VEGF and the endothelial marker CD31 were also upregulated. The A2AR antagonist SCH-58261 reduced tumor growth similarly in the P2X7 WT, or null mice strain. However, SCH-58261only reduced VEGF in the P2X7-KO mice, thus supporting the hypothesis of an A2AR mediated increase in vascularisation in P2X7-null host. SCH-58261 administration also significantly reduced intratumor TGF-{beta}, thus supporting a key immune suppressive role of A2AR in our model. This study shows a novel direct correlation between P2X7R and A2AR in oncogenesis and paves the way for new combined therapies promoting anti-cancer immune responses and reducing tumor vascularization.

cancer biology↗