Deep learning for predicting stem cell efficiency for use in beta cell differentiation Franziska J. Schöb, Alexander Binder, Valentina Zamarian, Valeria Sordi, Hanne Scholz, Anders Malthe-Sørenssen, Dag Kristian Dysthe Scientific Reports, 2026 Recent clinical trial data show curative potential of cell therapy for diabetes, however the cells required are a bottleneck. Cell differentiation exhibits substantial variability, even among clones of stem cells generated from the same patient. Human experts struggle to see the difference between highly- and lowly-efficient cell clones early. We therefore propose an image-based deep learning model to guide the selection of the most efficient clones. We apply different deep learning models to learn the morphological differences between good and bad stem cell clones and classify them based on phase-contrast imaging. To gain insight into the learned features, we use layer-wise relevance propagation, and Fourier-based frequency analysis. Using an EfficientNet-V2-S model, we obtain a novel early prediction for the outcome of the differentiation process from patient-derived stem cells to [Formula: see text] -cells using imaging. Clone level accuracy is 96.7 % at 53 hours after start of differentiation. The analysis of learned features shows that the structure of the cell population is an important predictive feature. This study is a proof-of-concept that deep learning combined with label-free imaging can be highly predictive and guide selection of stem cell clones, thereby reducing cost of [Formula: see text] -cell production.
Gene Expression at the Pluripotency Stage Predicts Pancreatic Endocrine Differentiation in iPSC Clones Valentina Zamarian, Laura Monaco, Manuela Marras, Chiara Ceriani, Silvia Pellegrini, Lorenzo Piemonti, Valeria Sordi Stem Cell Reviews and Reports, 2026 Induced pluripotent stem cell (iPSC)-derived β-like cells hold great promise for cell replacement therapy in type 1 diabetes. However, the reprogramming process generates iPSC clones with variable differentiation capacity, hindering the selection of optimal cell lines. This study aimed to identify an early-stage transcriptional signature capable of predicting the β cell differentiation potential of donor-matched iPSC clones. Eleven iPSC clones derived from a single donor were differentiated to the definitive endoderm (DE) stage; six were further driven toward pancreatic progenitors (PP) and insulin-producing cells. Differentiation efficiency was evaluated by flow cytometry and qPCR at iPSC, DE, PP, and β cell stages. At the pluripotent stage, expression profiling of 770 genes related to pluripotency and trilineage specification was performed to identify predictive molecular markers. Transcriptomic analysis segregated the clones into two groups (Gr1 and Gr2) with significantly different differentiation outcomes. Gr2 clones exhibited superior DE efficiency (Cxcr4⁺: 90.1 ± 5.6% vs. 79.8 ± 3.6%; P = 0.027) and higher expression of PP markers (Pdx1⁺, Nkx6.1⁺, and double-positive cells; P ≤ 0.05). At the β cell stage, Gr2 clones showed increased frequencies of Pdx1⁺/Ins⁺ and Nkx6.1⁺/Ins⁺ cells (P ≤ 0.05), along with enhanced glucose-stimulated insulin secretion. A set of 73 differentially expressed genes, enriched in pathways related to naïve/primed pluripotency, endoderm commitment, and metabolism, was identified. From this, a ten-gene signature validated by qPCR strongly correlated with pancreatic marker expression at all stages. An early gene expression signature at the pluripotent stage predicts the pancreatic endocrine differentiation potential of iPSC clones. This molecular screening approach may enable rapid preselection of high-performing clones, thereby accelerating the development of personalized stem cell–based therapies for diabetes. Cellular reprogramming is a fundamental tool in regenerative medicine but often produces iPSC clones with heterogeneous differentiation potential. Identifying the most suitable clones typically requires time-consuming assays and prolonged in vitro testing. This study presents a streamlined transcriptomic approach to predict, at the pluripotent stage, the differentiation efficiency of iPSC clones into pancreatic endoderm and insulin-producing cells, enabling early selection of high-performing lines for the development of diabetes cell therapy.
Vav1 Sustains the Expression of Insulin, PDX1 and miR-375 During Differentiation of hiPSCs to β Cells: A Potential Target to Improve the In Vitro Generation of Insulin-Producing Cells Marina Pierantoni, Valentina Zamarian, Federica Brugnoli, Silvia Grassilli, Laura Monaco, Marcello Dell’Aira, Valeria Sordi, Valeria Bertagnolo Tissue Engineering and Regenerative Medicine, 2026 Backround: Human-induced pluripotent stem cells (hiPSCs) have emerged as a promising source of transplantable insulinproducing cells (IPCs) to restore insulin levels in Type 1 Diabetes (T1D) patients. Despite progress, obtaining fully functional β cells from hiPSCs remains challenging, underscoring the need to better understand the intracellular mechanisms involved. We investigated here the potential role of Vav1, a multidomain protein that we identified as crucial for the maturation of human biliary stem cells (hBTSCs) into β-like cells and in the trans-differentiation of pancreatic adenocarcinoma (PDAC) cells into IPCs; Methods: Levels and subcellular localization of Vav1 were investigated throughout a seven-step differentiation process of hiPSCs to β cells. Vav1expression was forcedly modulated in pancreatic progenitors, and the potential effects were evaluated on insulin production and on PDX1, miR-375, and Akt, key regulators of β cells generation; RESULTS. Vav1 showed dynamic modulation, with pancreatic precursor cells requiring adequate levels of the protein to generate IPCs. Results: Vav1 sustains the expression of PDX1, a primary regulator of insulin expression, and of its target miR-375, essential for determining β cell mass. Furthermore, Vav1 reduction correlated with increased activation of Akt, which regulates cell survival and insulin secretion in β cells and is down-regulated by miR- 375. Conclusion: Our findings suggest the existence of a Vav1/PDX1/miR-375/Akt axis as part of the complex network orchestrating the generation of functional β cells. These insights indicate that strategies aimed at specifically modulating Vav1 levels may positively impact the generation of IPCs in vitro and, ultimately, β cell replacement therapy for T1D.
Liraglutide Treatment Reverses Unconventional Cellular Defects in Induced Pluripotent Stem Cell–Derived β-Cells Harboring a Partially Functional WFS1 Variant Silvia Torchio, Gabriel Siracusano, Federica Cuozzo, Valentina Zamarian, Silvia Pellegrini, Fabio Manenti, Riccardo Bonfanti, Giulio Frontino, Valeria Sordi, Raniero Chimienti, Lorenzo Piemonti Diabetes, 2025 Wolfram syndrome 1 (WS1) is a rare genetic disorder caused by WFS1 variants that disrupt wolframin, an endoplasmic reticulum-associated protein essential for cellular stress responses, Ca2+ homeostasis, and autophagy. Here, we investigated how the c.316-1G>A and c.757A>T WFS1 mutations, which yield partially functional wolframin, affect the molecular functions of β-cells and explored the therapeutic potential of the glucagon-like peptide 1 receptor (GLP-1R) agonist liraglutide. Pancreatic β-cells obtained from patient-derived induced pluripotent stem cells (iPSCs) carrying this WFS1 variant exhibited reduced insulin processing and impaired secretory granule maturation, as evidenced by proinsulin accumulation and decreased prohormone convertase PC1/3. Moreover, they exhibited dysregulated Ca2+ fluxes due to altered transcription of Ca2+-related genes, including CACNA1D, and significantly reduced SNAP25 levels, leading to uncoordinated oscillations and poor glucose responsiveness. Affected cells also showed increased autophagic flux and heightened susceptibility to inflammatory cytokine-induced apoptosis. Notably, liraglutide treatment rescued these defects by normalizing Ca2+ handling, enhancing insulin processing and secretion, and reducing apoptosis, likely through modulation of the unfolded protein response. These findings underscore the importance of defining mutation-specific dysfunctions in WS1 and support targeting the GLP-1/GLP-1R axis as a therapeutic strategy. Article Highlights The molecular basis of WFS1-related mutations remains poorly investigated, and no definitive therapies exist for Wolfram syndrome 1. We dissected the molecular defects associated with c.316-1G>A and c.757A>T WFS1 mutations in patient-derived induced pluripotent stem cell islets and analyzed whether they are potential therapeutic targets of the glucagon-like peptide 1 receptor agonist liraglutide. We found impaired insulin granule maturation, altered Ca2+ fluxes, increased autophagic activity, and heightened susceptibility to inflammatory apoptosis in mutated cells. Liraglutide restored critical β-cell functions suggesting a route for personalized therapy based on WFS1 mutations.
A WFS1 variant disrupting acceptor splice site uncovers the impact of alternative splicing on beta cell apoptosis in a patient with Wolfram syndrome Raniero Chimienti, Silvia Torchio, Gabriel Siracusano, Valentina Zamarian, Laura Monaco, Marta Tiffany Lombardo, Silvia Pellegrini, Fabio Manenti, Federica Cuozzo, Greta Rossi, Paola Carrera, Valeria Sordi, Vania Broccoli, Riccardo Bonfanti, Giorgio Casari, Giulio Frontino, Lorenzo Piemonti Diabetologia, 2025 AIMS/HYPOTHESIS: Wolfram syndrome 1 (WS1) is an inherited condition mainly manifesting in childhood-onset diabetes mellitus and progressive optic nerve atrophy. The causative gene, WFS1, encodes wolframin, a master regulator of several cellular responses, and the gene's mutations associate with clinical variability. Indeed, nonsense/frameshift variants correlate with more severe symptoms than missense/in-frame variants. As achieving a genotype-phenotype correlation is crucial for dealing with disease outcome, works investigating the impact of transcriptional and translational landscapes stemming from such mutations are needed. Therefore, we sought to elucidate the molecular determinants behind the pathophysiological alterations in a WS1 patient carrying compound heterozygous mutations in WFS1: c.316-1G>A, affecting the acceptor splice site (ASS) upstream of exon 4; and c.757A>T, introducing a premature termination codon (PTC) in exon 7. METHODS: Bioinformatic analysis was carried out to infer the alternative splicing events occurring after disruption of ASS, followed by RNA-seq and PCR to validate the transcriptional landscape. Patient-derived induced pluripotent stem cells (iPSCs) were used as an in vitro model of WS1 and to investigate the WFS1 alternative splicing isoforms in pancreatic beta cells. CRISPR/Cas9 technology was employed to correct ASS mutation and generate a syngeneic control for the endoplasmic reticulum stress induction and immunotoxicity assays. RESULTS: We showed that patient-derived iPSCs retained the ability to differentiate into pancreatic beta cells. We demonstrated that the allele carrying the ASS mutation c.316-1G>A originates two PTC-containing alternative splicing transcripts (c.316del and c.316-460del), and two open reading frame-conserving mRNAs (c.271-513del and c.316-456del) leading to N-terminally truncated polypeptides. By retaining the C-terminal domain, these isoforms sustained the endoplasmic reticulum stress response in beta cells. Otherwise, PTC-carrying transcripts were regulated by the nonsense-mediated decay (NMD) in basal conditions. Exposure to cell stress inducers and proinflammatory cytokines affected expression levels of the NMD-related gene SMG7 (>twofold decrease; p<0.001) without eliciting a robust unfolded protein response in WFS1 beta cells. This resulted in a dramatic accumulation of the PTC-containing isoforms c.316del (>100-fold increase over basal; p<0.001) and c.316-460del (>20-fold increase over basal; p<0.001), predisposing affected beta cells to undergo apoptosis. Cas9-mediated recovery of ASS retrieved the canonical transcriptional landscape, rescuing the normal phenotype in patient-derived beta cells. CONCLUSIONS/INTERPRETATION: This study represents a new model to study wolframin, highlighting how each single mutation of the WFS1 gene can determine dramatically different functional outcomes. Our data point to increased vulnerability of WFS1 beta cells to stress and inflammation and we postulate that this is triggered by escaping NMD and accumulation of mutated transcripts and truncated proteins. These findings pave the way for further studies on the molecular basis of genotype-phenotype relationship in WS1, to uncover the key determinants that might be targeted to ameliorate the clinical outcome of patients affected by this rare disease. DATA AVAILABILITY: The in silico predicted N-terminal domain structure file of WT wolframin was deposited in the ModelArchive, together with procedures, ramachandran plots, inter-residue distance deviation and IDDT scores, and Gromacs configuration files (doi/10.5452/ma-cg3qd). The deep-sequencing data as fastq files used to generate consensus sequences of AS isoforms of WFS1 are available in the SRA database (BioProject PRJNA1109747).
Plasma small extracellular vesicles from dogs affected by cutaneous mast cell tumors deliver high levels of miR-21-5p Clarissa Zamboni, Valentina Zamarian, Damiano Stefanello, Roberta Ferrari, Luigi Auletta, Samantha Milanesi, Samuele Mauri, Valeria Grieco, Fabrizio Ceciliani, Cristina Lecchi Frontiers in Veterinary Science, 2023 Small extracellular vesicles (sEV) are a class of extracellular vesicles (30–150 nm), delivering molecules including proteins, metabolites, and microRNAs (miRNAs), involved in physiological intercellular crosstalk and disease pathogenesis. The present pilot study aims are (I) to develop an easy and fast protocol for the isolation of sEV from plasma of mast cell tumor (MCT)-affected dogs; (II) to evaluate if miR-21-5p (sEV-miR-21-5p), a miRNA overexpressed by MCT, is associated with sEV. Seventeen dogs have been enrolled in the study: 4 healthy and 13 (6 with and 7 without nodal metastasis) MCT-affected dogs. sEV were isolated using size exclusion chromatography (SEC) (IZON column 35nm) and were characterized by Western blot, Nanoparticle tracking analysis, and transmission electron microscopy. sEV-miR-21-5p was quantified using digital PCR. sEV expressed the specific markers CD9 and TSG101, and a marker of mast cell tryptase. The sEV mean concentration and size were 2.68E + 10 particles/ml, and 99.6 nm, 2.89E + 10 particles/ml and 101.7 nm, and 3.21E + 10 particles/ml and 124 nm in non-metastatic, nodal metastatic, and healthy samples, respectively. The comparative analysis demonstrated that the level of sEV-miR-21-5p was significantly higher in dogs with nodal metastasis compared to healthy (P = 0.038) and without nodal metastasis samples (P = 0.007). In conclusion, the present work demonstrated that a pure population of sEV can be isolated from the plasma of MCT-affected dogs using the SEC approach and that the level of sEV-miR-21-5p is higher in nodal metastatic MCT-affected dogs compared with healthy and MCT-affected dogs without nodal involvement.
Salivary miR-21 is a potential biomarker for canine mast cell tumors Valentina Zamarian, Damiano Stefanello, Roberta Ferrari, Lavinia E. Chiti, Valeria Grieco, Emanuela DallaCosta, Fabrizio Ceciliani, Cristina Lecchi Veterinary Pathology, 2023 MicroRNAs (miRNAs) are a class of noncoding RNA molecules playing a crucial role in tumor modulation targeting mRNA. This study aimed to validate the diagnostic potential of a panel of 3 miRNAs previously identified in canine mast cell tumors (MCTs), miR-21, miR-379, and miR-885, as markers of lymph node involvement in terms of histological absence (nonmetastatic: HN0; premetastatic: HN1) and presence (early-metastatic: HN2; overt-metastatic: HN3) of metastasis, in the saliva of mast cell tumor (MCT)-affected dogs by quantitative polymerase chain reaction (PCR). Forty-seven saliva samples were analyzed: 36 from MCT-affected dogs (12 subcutaneous [3 HN0-1 and 9 HN2-3] and 24 cutaneous [9 HN0-1 and 15 HN2-3—MCT]) and 11 from healthy dogs. MCT-group effects were investigated using analysis of variance (ANOVA). The origin of the tumor affected the expression of salivary miR-21 ( P = .011) with an increase in cases with subcutaneous MCTs compared with the healthy group ( P = .0005) and those with cutaneous MCTs ( P = .004). Salivary miR-21 was higher in the HN2-3 class compared with the healthy group ( P = .004). Salivary miR-885 was not affected by the presence of MCT, while miR-379 was not detected in saliva. The diagnostic potential of salivary miR-21 in discriminating MCT-affected dogs from the healthy group (AUC = 0.8917), cutaneous from subcutaneous (AUC = 0.8111), and subcutaneous HN0-1 (AUC = 0.7250) and HN2-3 (AUC = 0.9750) classes from healthy samples was demonstrated by receiver operating characteristic curve analysis. Overall, salivary miR-21 was identified as a promising tool, representing a novel approach to detecting MCT-associated epigenetic alterations in a minimally invasive manner.
Treating iPSC-Derived β Cells with an Anti-CD30 Antibody–Drug Conjugate Eliminates the Risk of Teratoma Development upon Transplantation Silvia Pellegrini, Valentina Zamarian, Elisa Landi, Alessandro Cospito, Marta Tiffany Lombardo, Fabio Manenti, Antonio Citro, Marco Schiavo Lena, Lorenzo Piemonti, Valeria Sordi International Journal of Molecular Sciences, 2022 Insulin-producing cells derived from induced pluripotent stem cells (iPSCs) are promising candidates for β cell replacement in type 1 diabetes. However, the risk of teratoma formation due to residual undifferentiated iPSCs contaminating the differentiated cells is still a critical concern for clinical application. Here, we hypothesized that pretreatment of iPSC-derived insulin-producing cells with an anti-CD30 antibody–drug conjugate could prevent in vivo teratoma formation by selectively killing residual undifferentiated cells. CD30 is expressed in all human iPSCs clones tested by flow cytometry (n = 7) but not in iPSC-derived β cells (iβs). Concordantly, anti-CD30 treatment in vitro for 24 h induced a dose-dependent cell death (up to 90%) in human iPSCs while it did not kill iβs nor had an impact on iβ identity and function, including capacity to secrete insulin in response to stimuli. In a model of teratoma assay associated with iβ transplantation, the pretreatment of cells with anti-CD30 for 24 h before the implantation into NOD-SCID mice completely eliminated teratoma development (0/10 vs. 8/8, p < 0.01). These findings suggest that short-term in vitro treatment with clinical-grade anti-CD30, targeting residual undifferentiated cells, eliminates the tumorigenicity of iPSC-derived β cells, potentially providing enhanced safety for iPSC-based β cell replacement therapy in clinical scenarios.
Strategies to Improve the Safety of iPSC-Derived β Cells for β Cell Replacement in Diabetes Silvia Pellegrini, Valentina Zamarian, Valeria Sordi Transplant International, 2022 Allogeneic islet transplantation allows for the re-establishment of glycemic control with the possibility of insulin independence, but is severely limited by the scarcity of organ donors. However, a new source of insulin-producing cells could enable the widespread use of cell therapy for diabetes treatment. Recent breakthroughs in stem cell biology, particularly pluripotent stem cell (PSC) techniques, have highlighted the therapeutic potential of stem cells in regenerative medicine. An understanding of the stages that regulate β cell development has led to the establishment of protocols for PSC differentiation into β cells, and PSC-derived β cells are appearing in the first pioneering clinical trials. However, the safety of the final product prior to implantation remains crucial. Although PSC differentiate into functional β cells in vitro, not all cells complete differentiation, and a fraction remain undifferentiated and at risk of teratoma formation upon transplantation. A single case of stem cell-derived tumors may set the field back years. Thus, this review discusses four approaches to increase the safety of PSC-derived β cells: reprogramming of somatic cells into induced PSC, selection of pure differentiated pancreatic cells, depletion of contaminant PSC in the final cell product, and control or destruction of tumorigenic cells with engineered suicide genes.
Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa Cristina Lecchi, Valentina Zamarian, Giorgia Borriello, Giorgio Galiero, Guido Grilli, Mario Caniatti, Elisa Silvia D'Urso, Paola Roccabianca, Roberta Perego, Michela Minero, Sara Legnani, Raffaele Calogero, Maddalena Arigoni, Fabrizio Ceciliani Frontiers in Immunology, 2020
