Development of a microRNA-based prognostic model for accurate prediction of distant metastasis in breast cancer patients Andrea Fontana, Raffaela Barbano, Barbara Pasculli, Tommaso Mazza, Orazio Palumbo, Elena Binda, Nadia Trivieri, Gandino Mencarelli, Ilaria Laurenzana, Daniela Lamorte, Luciana De Luca, Antonella Caivano, Tommaso Biagini, Michelina Rendina, Antonio lo Mele, Giuseppina Prencipe, Sara Bravaccini, Roberto Murgo, Luigi Ciuffreda, Maria Morritti, Vanna Maria Valori, Francesca Sofia Di Lisa, Patrizia Vici, Marina Castelvetere, Massimo Carella, Paolo Graziano, Evaristo Maiello, Massimiliano Copetti, Manel Esteller, Paola Parrella Breast Cancer Research, 2025 BACKGROUND: The attempt to exploit molecular subtyping for risk stratification in breast cancer patients has been only partially successful with a limited application in the clinical practice. In the BREMIR study, we aimed to identify a panel of miRNAs as prognostic biomarkers for breast cancer. We first confirmed the association of previously linked miRNAs with critical clinical parameters, then adopted a discovery-driven approach to identify novel biomarkers. METHODS: miRNA expression was analyzed using the Affymetrix Gene Chip 4.0 array in a discovery cohort of 34 patients (3 with synchronous metastases, 14 who developed metastases after 10 years, and 17 who remained metastasis-free) and 6 controls. RT-qPCR validated selected miRNAs in an extended cohort (n = 223) with a median follow up of 6.6 years. A stepwise logistic regression model incorporating miRNA levels and clinicopathological features was developed to predict metastasis risk. Additionally, miRNA expression was assessed in plasma extracellular vesicles (EVs) using digital PCR in an independent cohort (n = 39). In silico enrichment analyses explored the functional role of relevant miRNAs in metastasis development. RESULTS: Eight differentially expressed miRNAs were identified in the discovery cohort. In the extended cohort, miR-3916 and miR-3613-5p were the most effective in distinguishing patients who developed metastases. Higher miR-3916 expression was associated with reduced metastasis risk (OR = 0.42, 95%CI 0.23-0.70, p = 0.002), while higher miR-3613-5p expression was linked to increased risk (OR = 2.06, 95%CI 1.27-3.50, p = 0.005). Adding these miRNAs to a model with clinicopathological features improved discrimination (AUC = 0.85 vs. AUC = 0.76, p = 0.001). The model was effective across all breast cancer subtypes. In extracellular vesicles, miR-3613-5p was more abundant in tumors than benign lesions (p = 0.039), while miR-3916 was lower in metastatic samples than in non-metastatic tumors (p = 0.020). In-silico pathway enrichment analyses indicates their involvement in critical steps of the metastatic process including EMT plasticity, DNA damage response and metastatic niche formation. CONCLUSIONS: This is the first study integrating miRNA expression with clinicopathological features in a logistic model for breast cancer prognosis. While further validation is needed, our model shows promise as a prognostic tool across all breast cancer subtypes. In silico pathway enrichment analysis highlights miR-3613-5p and miR-3916 as critical regulators of metastasis development, underscoring the need for further investigation. TRIAL REGISTRATION: ClinicalTrials.gov ID NCT06555354 retrospectively registered on August 14th, 2024.
Generation and characterization of the CSSi021-A (15665) human induced pluripotent stem cell line from a Smith-Magenis syndrome patient with a heterozygous RAI1 mutation Angela Maria Giada Giovenale, Elisa Maria Turco, Ilaria Ferrone, Chiara Giacometti, Silvia Tomaselli, Edvige Vulcano, Daniela Ferrari, Ornella Candido, Laura Bernardini, Alessandro De Luca, Nadia Trivieri, Elena Binda, Roberta Onesimo, Stefano D’Arrigo, Giuseppe Zampino, Maria Pennuto, Angelo Luigi Vescovi, Jessica Diana Rosati Stem Cell Research, 2025 Smith-Magenis syndrome (SMS) is a rare neurodevelopmental disorder caused by haploinsufficiency of the Retinoic Acid Induced 1 (RAI1) gene located at 17p11.2. It is estimated that approximately 90% of patients have a 17p11.2 deletion, including the RAI1 gene, while the remaining 10% exhibit a heterozygous mutation in the RAI1 gene. In this study, we report the generation of a human induced pluripotent stem cell (hiPSC) line derived from a 14-year-old female with an RAI1 mutation, which led to the onset of the SMS phenotype, starting from primary fibroblasts.
Integrated periodontal pathogens and circulating miRNAs: a novel non-invasive panel of biomarkers for pancreatic cancer Zeinab Hesami, Valerio Pazienza, Meysam Olfatifar, Amir Sadeghi, Samira Mohammadi-Yeganeh, Nadia Trivieri, Hesameddin Eghlimi, Mojdeh Hakemi-Vala, Elena Binda, Hamidreza Houri Frontiers in Cellular and Infection Microbiology, 2025 Introduction The associations between oral bacterial pathogens and the risk of pancreatic cancer (PC) have been reported in several epidemiological studies. In this study, we evaluated the diagnostic potential of periodontal pathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans in combination with circulating oncomiRNAs, including miR-21 and miR-155. Methods A total of 41 PC patients and 40 age- and sex-matched controls were recruited for the study. The salivary bacterial load of P. gingivalis and A. actinomycetemcomitans , along with the copy number of miR-21 and miR-155 in blood, were measured using quantitative real-time PCR. Subsequently, logistic regression and receiver operating characteristic (ROC) analysis were used to determine the association of biomarkers with PC risk and their diagnostic performance, respectively. Results Elevated load of the periodontal pathogens P. gingivalis in females (OR = 2.31; 95% CI 0.98-5.47) and A. actinomycetemcomitans in diabetic individuals (OR = 3.66; 95% CI 0.47-6.68) was associated with a higher risk of PC. Moreover, the diagnostic model incorporating two salivary species and two circulating miRNAs demonstrated an area under the curve (AUC) of 0.878 (95% CI 0.802-0.955). Discussion This study offers compelling new evidence supporting the idea that the combined analysis of salivary microbiota and circulating miRNAs serves as an informative avenue for the discovery of non-invasive biomarkers for PC, potentially applicable to early detection and clinical screening.
A functional role of Ephrin type-B receptor 6 (EPHB6) in T-cell acute lymphoblastic leukemia Mattia Colucci, Nadia Trivieri, Gandino Mencarelli, Elisabetta De Santis, Francesca Sansico, Francesco Tamiro, Alberto Visioli, Chiara Barile, Riccardo Pracella, Giovanni Rossi, Elena Binda, Vincenzo Giambra Biomarker Research, 2023 T-cell lymphoblastic acute leukemia (T-ALL) is an aggressive blood cancer, characterized by restricted cellular subsets with enriched leukemia initiating cells (LICs). Recently, Ephrin receptors (Eph) were described to be highly expressed in cancer stem cells. Here, using public RNA-Seq datasets of human T-ALL, we reported that EphB6 was the only member within the Eph family overexpressed in over 260 samples. We also found the highest level of EphB6 in a minor cell subpopulation within bulk tumors of patient-derived xenografts, obtained through the injection of primary patient biopsy material into immunocompromised NOD-Scid/IL2Rγc−/− (NSG) mice. Interestingly, this EphB6 positive (EphB6+) subset showed an enriched LIC activity after in vivo transplantation into NSG mice. Additionally, gene expression data at the single-cell level of primary patients’ leukemic cells revealed that EphB6 + cells were significantly selected in minimal residual disease up to 30 days from the standard treatments and characterized by high levels of markers related to cell proliferation and poor clinical outcome, such as CCNB1 and KIF20A. Taken together, our data suggest that EphB6 supports LICs’ maintenance and progression in T-ALL and, thus, targeting EphB6 + cells could be therapeutically relevant for the treatment of T-ALL patients.
Different states of stemness of glioblastoma stem cells sustain glioblastoma subtypes indicating novel clinical biomarkers and high-efficacy customized therapies Alberto Visioli, Nadia Trivieri, Gandino Mencarelli, Fabrizio Giani, Massimiliano Copetti, Orazio Palumbo, Riccardo Pracella, Maria Grazia Cariglia, Chiara Barile, Luigi Mischitelli, Amata Amy Soriano, Pietro Palumbo, Federico Legnani, Francesco DiMeco, Leonardo Gorgoglione, Graziano Pesole, Angelo L. Vescovi, Elena Binda Journal of Experimental and Clinical Cancer Research, 2023 Background Glioblastoma (GBM) is the most malignant among gliomas with an inevitable lethal outcome. The elucidation of the physiology and regulation of this tumor is mandatory to unravel novel target and effective therapeutics. Emerging concepts show that the minor subset of glioblastoma stem cells (GSCs) accounts for tumorigenicity, representing the true target for innovative therapies in GBM. Methods Here, we isolated and established functionally stable and steadily expanding GSCs lines from a large cohort of GBM patients. The molecular, functional and antigenic landscape of GBM tissues and their derivative GSCs was highlited in a side-by-side comprehensive genomic and transcriptomic characterization by ANOVA and Fisher’s exact tests. GSCs’ physio-pathological hallmarks were delineated by comparing over time in vitro and in vivo their expansion, self-renewal and tumorigenic ability with hierarchical linear models for repeated measurements and Kaplan–Meier method. Candidate biomarkers performance in discriminating GBM patients’ classification emerged by classification tree and patients’ survival analysis. Results Here, distinct biomarker signatures together with aberrant functional programs were shown to stratify GBM patients as well as their sibling GSCs population into TCGA clusters. Of importance, GSCs cells were demonstrated to fully resemble over time the molecular features of their patient of origin. Furthermore, we pointed out the existence of distinct GSCs subsets within GBM classification, inherently endowed with different self-renewal and tumorigenic potential. Particularly, classical GSCs were identified by more undifferentiated biological hallmarks, enhanced expansion and clonal capacity as compared to the more mature, relatively slow-propagating mesenchymal and proneural cells, likely endowed with a higher potential for infiltration either ex vivo or in vivo. Importantly, the combination of DCX and EGFR markers, selectively enriched among GSCs pools, almost exactly predicted GBM patients’ clusters together with their survival and drug response. Conclusions In this study we report that an inherent enrichment of distinct GSCs pools underpin the functional inter-cluster variances displayed by GBM patients. We uncover two selectively represented novel functional biomarkers capable of discriminating GBM patients’ stratification, survival and drug response, setting the stage for the determination of patient-tailored diagnostic and prognostic strategies and, mostly, for the design of appropriate, patient-selective treatment protocols.
Local delivery of hrBMP4 as an anticancer therapy in patients with recurrent glioblastoma: a first-in-human phase 1 dose escalation trial Eelke M. Bos, Elena Binda, Iris S.C. Verploegh, Eva Wembacher, Daphna Hoefnagel, Rutger K. Balvers, Anne L. Korporaal, Andrea Conidi, Esther A. H. Warnert, Nadia Trivieri, Alberto Visioli, Paola Zaccarini, Laura Caiola, Rogier van Wijck, Peter van der Spek, Danny Huylebroeck, Sieger Leenstra, Martine L.M. Lamfers, Zvi Ram, Manfred Westphal, David Noske, Federico Legnani, Francesco DiMeco, Angelo Luigi Vescovi, Clemens M.F. Dirven Molecular Cancer, 2023 Background This Phase 1 study evaluates the intra- and peritumoral administration by convection enhanced delivery (CED) of human recombinant Bone Morphogenetic Protein 4 (hrBMP4) – an inhibitory regulator of cancer stem cells (CSCs) – in recurrent glioblastoma. Methods In a 3 + 3 dose escalation design, over four to six days, fifteen recurrent glioblastoma patients received, by CED, one of five doses of hrBMP4 ranging from 0·5 to 18 mg. Patients were followed by periodic physical, neurological, blood testing, magnetic resonance imaging (MRI) and quality of life evaluations. The primary objective of this first-in-human study was to determine the safety, dose-limiting toxicities (DLT) and maximum tolerated dose (MTD) of hrBMP4. Secondary objectives were to assess potential efficacy and systemic exposure to hrBMP4 upon intracerebral infusion. Results Intra- and peritumoral infusion of hrBMP4 was safe and well-tolerated. We observed no serious adverse events related to this drug. Neither MTD nor DLT were reached. Three patients had increased hrBMP4 serum levels at the end of infusion, which normalized within 4 weeks, without sign of toxicity. One patient showed partial response and two patients a complete (local) tumor response, which was maintained until the most recent follow-up, 57 and 30 months post-hrBMP4. Tumor growth was inhibited in areas permeated by hrBMP4. Conclusion Local delivery of hrBMP4 in and around recurring glioblastoma is safe and well-tolerated. Three patients responded to the treatment. A complete response and long-term survival occurred in two of them. This warrants further clinical studies on this novel treatment targeting glioblastoma CSCs. Trial registration : ClinicaTrials.gov identifier: NCT02869243.
Gut microbiota composition in COVID-19 hospitalized patients with mild or severe symptoms Antonio Mazzarelli, Maria Letizia Giancola, Andrea Fontana, Pierluca Piselli, Elena Binda, Nadia Trivieri, Gandino Mencarelli, Luisa Marchioni, Antonella Vulcano, Chiara De Giuli, Concetta Panebianco, Annacandida Villani, Massimiliano Copetti, Francesco Perri, Carla Fontana, Emanuele Nicastri, Valerio Pazienza Frontiers in Microbiology, 2022 Background and aimCOVID-19, the infectious disease caused by SARS-CoV-2 virus that has been causing a severe pandemic worldwide for more than 2 years, is characterized by a high heterogeneity of clinical presentations and evolution and, particularly, by a varying severity of respiratory involvement. This study aimed to analyze the diversity and taxonomic composition of the gut microbiota at hospital admission, in order to evaluate its association with COVID-19 outcome. In particular, the association between gut microbiota and a combination of several clinical covariates was analyzed in order to characterize the bacterial signature associate to mild or severe symptoms during the SARS-CoV-2 infection.Materials and methodsV3–V4 hypervariable region of 16S rRNA gene sequencing of 97 rectal swabs from a retrospective cohort of COVID-19 hospitalized patients was employed to study the gut microbiota composition. Patients were divided in two groups according to their outcome considering the respiratory supports they needed during hospital stay: (i) group “mild,” including 47 patients with a good prognosis and (ii) group “severe,” including 50 patients who experienced a more severe disease due to severe respiratory distress that required non-invasive or invasive ventilation. Identification of the clusters of bacterial population between patients with mild or severe outcome was assessed by PEnalized LOgistic Regression Analysis (PELORA).ResultsAlthough no changes for Chao1 and Shannon index were observed between the two groups a significant greater proportion of Campylobacterota and Actinobacteriota at phylum level was found in patients affected by SARS-CoV-2 infection who developed a more severe disease characterized by respiratory distress requiring invasive or non-invasive ventilation. Clusters have been identified with a useful early potential prognostic marker of the disease evolution.DiscussionMicroorganisms residing within the gut of the patients at hospital admission, were able to significantly discriminate the clinical evolution of COVID-19 patients, in particular who will develop mild or severe respiratory involvement. Our data show that patients affected by SARS-CoV-2 with mild or severe symptoms display different gut microbiota profiles which can be exploited as potential prognostic biomarkers paving also the way to new integrative therapeutic approaches.
Growth factor independence underpins a paroxysmal, aggressive Wnt5aHigh/EphA2Low phenotype in glioblastoma stem cells, conducive to experimental combinatorial therapy Nadia Trivieri, Alberto Visioli, Gandino Mencarelli, Maria Grazia Cariglia, Laura Marongiu, Riccardo Pracella, Fabrizio Giani, Amata Amy Soriano, Chiara Barile, Laura Cajola, Massimiliano Copetti, Orazio Palumbo, Federico Legnani, Francesco DiMeco, Leonardo Gorgoglione, Angelo L. Vescovi, Elena Binda Journal of Experimental and Clinical Cancer Research, 2022 Background Glioblastoma multiforme (GBM) is an incurable tumor, with a median survival rate of only 14–15 months. Along with heterogeneity and unregulated growth, a central matter in dealing with GBMs is cell invasiveness. Thus, improving prognosis requires finding new agents to inhibit key multiple pathways, even simultaneously. A subset of GBM stem-like cells (GSCs) may account for tumorigenicity, representing, through their pathways, the proper cellular target in the therapeutics of glioblastomas. GSCs cells are routinely enriched and expanded due to continuous exposure to specific growth factors, which might alter some of their intrinsic characteristic and hide therapeutically relevant traits. Methods By removing exogenous growth factors stimulation, here we isolated and characterized a subset of GSCs with a “mitogen-independent” phenotype (I-GSCs) from patient’s tumor specimens. Differential side-by-side comparative functional and molecular analyses were performed either in vitro or in vivo on these cells versus their classical growth factor (GF)-dependent counterpart (D-GSCs) as well as their tissue of origin. This was performed to pinpoint the inherent GSCs’ critical regulators, with particular emphasis on those involved in spreading and tumorigenic potential. Transcriptomic fingerprints were pointed out by ANOVA with Benjamini-Hochberg False Discovery Rate (FDR) and association of copy number alterations or somatic mutations was determined by comparing each subgroup with a two-tailed Fisher’s exact test. The combined effects of interacting in vitro and in vivo with two emerging GSCs’ key regulators, such as Wnt5a and EphA2, were then predicted under in vivo experimental settings that are conducive to clinical applications. In vivo comparisons were carried out in mouse-human xenografts GBM model by a hierarchical linear model for repeated measurements and Dunnett’s multiple comparison test with the distribution of survival compared by Kaplan–Meier method. Results Here, we assessed that a subset of GSCs from high-grade gliomas is self-sufficient in the activation of regulatory growth signaling. Furthermore, while constitutively present within the same GBM tissue, these GF-independent GSCs cells were endowed with a distinctive functional and molecular repertoire, defined by highly aggressive Wnt5aHigh/EphA2Low profile, as opposed to Wnt5aLow/EphA2High expression in sibling D-GSCs. Regardless of their GBM subtype of origin, I-GSCs, are endowed with a raised in vivo tumorigenic potential than matched D-GSCs, which were fast-growing ex-vivo but less lethal and invasive in vivo. Also, the malignant I-GSCs’ transcriptomic fingerprint faithfully mirrored the original tumor, bringing into evidence key regulators of invasiveness, angiogenesis and immuno-modulators, which became candidates for glioma diagnostic/prognostic markers and therapeutic targets. Particularly, simultaneously counteracting the activity of the tissue invasive mediator Wnt5a and EphA2 tyrosine kinase receptor addictively hindered GSCs’ tumorigenic and invasive ability, thus increasing survival. Conclusion We show how the preservation of a mitogen-independent phenotype in GSCs plays a central role in determining the exacerbated tumorigenic and high mobility features distinctive of GBM. The exploitation of the I-GSCs' peculiar features shown here offers new ways to identify novel, GSCs-specific effectors, whose modulation can be used in order to identify novel, potential molecular therapeutic targets. Furthermore, we show how the combined use of PepA, the anti-Wnt5a drug, and of ephrinA1-Fc to can hinder GSCs’ lethality in a clinically relevant xenogeneic in vivo model thus being conducive to perspective, novel combinatorial clinical application.
High levels of prebiotic resistant starch in diet modulate a specific pattern of mirnas expression profile associated to a better overall survival in pancreatic cancer Nadia Trivieri, Concetta Panebianco, Annacandida Villani, Riccardo Pracella, Tiziana Pia Latiano, Francesco Perri, Elena Binda, Valerio Pazienza Biomolecules, 2021 Dietary patterns are well known risk factors involved in cancer initiation, progression, and in cancer protection. Previous in vitro and in vivo studies underline the link between a diet rich in resistant starch (RS) and slowing of tumor growth and gene expression in pancreatic cancer xenograft mice. The aim of this study was to investigate the impact of a diet rich in resistant starch on miRNAs and miRNAs-target genes expression profile and on biological processes and pathways, that play a critical role in pancreatic tumors of xenografted mice. miRNA expression profiles on tumor tissues displayed 19 miRNAs as dysregulated in mice fed with RS diet as compared to those fed with control diet and differentially expressed miRNA-target genes were predicted by integrating (our data) with a public human pancreatic cancer gene expression dataset (GSE16515). Functional and pathway enrichment analyses unveiled that miRNAs involved in RS diet are critical regulators of genes that control tumor growth and cell migration and metastasis, inflammatory response, and, as expected, synthesis of carbohydrate and glucose metabolism disorder. Mostly, overall survival analysis with clinical data from TCGA (n = 175) displayed that almost four miRNAs (miRNA-375, miRNA-148a-3p, miRNA-125a-5p, and miRNA-200a-3p) upregulated in tumors from mice fed with RS were a predictor of good prognosis for pancreatic cancer patients. These findings contribute to the understanding of the potential mechanisms through which resistant starch may affect cancer progression, suggesting also a possible integrative approach for enhancing the efficacy of existing cancer treatments.
Improving gemcitabine sensitivity in pancreatic cancer cells by restoring mirna‐217 levels Concetta Panebianco, Nadia Trivieri, Annacandida Villani, Fulvia Terracciano, Tiziana Pia Latiano, Adele Potenza, Francesco Perri, Elena Binda, Valerio Pazienza Biomolecules, 2021 Chemoresistance is a major problem in the therapeutic management of pancreatic cancer, concurring to poor clinical outcome. A number of mechanisms have been proposed to explain resistance to gemcitabine, a standard of care for this malignancy, among which is included aberrant miRNA expression. In the current study, we investigated the role of miR-217, which is strongly down-regulated in cancerous, compared to normal, pancreatic tissues or cells, in sensitizing human pancreatic cancer cell lines to this drug. The low expression of miR-217 in pancreatic cancer patients was confirmed in two gene expression datasets (GSE41372 and GSE60980), and the prognostic value of two target genes (ANLN and TRPS1), was estimated on clinical data from the Tumor Cancer Genome Atlas (TCGA). Transfecting miR-217 mimic in pancreatic cancer cells reduced viability, enhanced apoptosis, and affected cell cycle by promoting a S phase arrest in gemcitabine-treated cells. Moreover, in drug-exposed cells subjected to miR-217 forced expression, a down-regulation for several genes involved in cancer drug resistance was observed, many of which are cell cycle regulators, such as CCND1, CCNE1, CDK2, CDKN1A, CDKN1B, while others, such as ARNT, BRCA1, BRCA2, ELK1, EGFR, ERBB4, and RARA are involved in proliferation and cell cycle progression. Our results support the notion that miR-217 enhances pancreatic cancer sensitivity to gemcitabine, mainly impairing cell cycle progression.
Stemness underpinning all steps of human colorectal cancer defines the core of effective therapeutic strategies Alberto Visioli, Fabrizio Giani, Nadia Trivieri, Riccardo Pracella, Elide Miccinilli, Maria Grazia Cariglia, Orazio Palumbo, Andrea Arleo, Fabio Dezi, Massimiliano Copetti, Laura Cajola, Silvia Restelli, Valerio Papa, Antonio Sciuto, Tiziana Pia Latiano, Massimo Carella, Dino Amadori, Giulia Gallerani, Riccardo Ricci, Sergio Alfieri, Graziano Pesole, Angelo L. Vescovi, Elena Binda Ebiomedicine, 2019
Wnt5a drives an invasive phenotype in human glioblastoma stem-like cells Elena Binda, Alberto Visioli, Fabrizio Giani, Nadia Trivieri, Orazio Palumbo, Silvia Restelli, Fabio Dezi, Tommaso Mazza, Caterina Fusilli, Federico Legnani, Massimo Carella, Francesco Di Meco, Rohit Duggal, Angelo L. Vescovi Cancer Research, 2017
