DANEELpath open source digital analysis tools for histopathological research in neuroblastoma models Isaac Vieco-Martí, Amparo López-Carrasco, Samuel Navarro, Sofia Granados-Aparici, Rosa Noguera Scientific Reports, 2026 Despite the considerable expansion of bioimage analysis as a subfield of biomedical sciences, there is an ongoing need for comprehensive image analysis pipelines to address specific biological inquiries. In the tumor microenvironment, the extracellular matrix (ECM) plays a pivotal role in cancer progression, promoting tumor cell adaptability, intratumor heterogeneity, and therapeutic resistance. In neuroblastoma (NB), the ECM glycoprotein vitronectin (VN) has been associated with more aggressive tumors. Three-dimensional (3D) hydrogels are an emerging biomimetic tool with significant potential for studying the role of ECM elements and testing new mechano-drugs such as cilengitide, a potential therapeutic agent to treat high-risk NB due to its ability to inhibit VN activity in cells. To gain a more detailed understanding of 3D-grown NB cell dynamics, we developed DANEELpath, an open-source image analysis toolkit. DANEELpath integrates deep learning techniques, specific segmentation of individual and cluster cells through mathematical morphology pipelines, and extraction of spatial features within whole-slide images. Thanks to its versatility, DANEELpath is adaptable to address different biological questions and has significant potential for use in a variety of research fields and model systems, which could help advance biomedical discovery.
GSPT1-specific protein degradation is effective in preclinical models of chemoresistant MYCN-amplified neuroblastoma Aleksandra Adamska, Hanna Chahin, Erick Andrés Muciño-Olmos, Javanshir Esfandyari, Kristina Aaltonen, Sofia Granados-Aparici, Joachim Tetteh Siaw, Katarzyna Radke, Chiara Lago, Paweł Pasikowski, Roman Pluta, Anna Sawicka, Przemysław Glaza, David Gisselsson, Samuel Navarro, Rosa Noguera, Joanna Majkut, Paweł Dobrzański, Sylvain Cottens, Michał J. Walczak, Daniel Bexell Journal of Experimental and Clinical Cancer Research, 2026 High-risk neuroblastoma (HR-NB) is associated with therapy-resistant relapse, and novel therapeutic strategies are needed. GSPT1 is a GTPase involved in protein translation whose disruption may offer therapeutic potential in translation-dependent cancers. GSPT1 expression was assessed in publicly available clinical data and tissue microarrays. GSPT1-degrading molecular glues were tested in MYCN-amplified NB organoids. Cell viability, cell death assays, western blotting, and proteomics were used to evaluate GSPT1 degraders. Effects on tumor growth and mouse survival were benchmarked against standard-of-care chemotherapy in a chemoresistant NB patient-derived xenograft (PDX) model. RNA sequencing and histopathological analysis were used to assess mechanisms of action in vivo. GSPT1 expression is associated with unfavorable outcomes in NB patients. Single-cell analysis revealed elevated GSPT1 expression in MYCN-amplified NB, whereas the E3 ligase CRBN (essential for protein degradation) was predominantly expressed in NB cells relative to non-malignant cells. GSPT1-specific degradation decreased cell viability and induced apoptosis in MYCN-amplified NB organoids and PDX models. GSPT1 degradation in vivo resulted in NB differentiation and suppression of MYCN and its related core regulatory gene networks. In vivo treatment further outperformed standard-of-care chemotherapy and increased survival in a highly chemoresistant NB PDX model. Inhibition of the translational machinery by GSPT1-degrading molecular glues shows therapeutic potential in chemoresistant MYCN-amplified NB.
Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial Xavier Santamaria, María Pardo-Figuerez, Javier González-Fernández, Sergi Querol, Luciano Rodríguez, David Valcárcel, Carla González, Estefanía Fernandez, Diego Amorós, Michael Robles, Sofia Granados-Aparici, Sheila Zuñiga, Francisco Martinez, Diana Valbuena, Carlos Gómez, Julio Herrero, Ramon Aurell, Juan José Torrent, Felipe Vilella, Petr Volkov, Francisco Raga, Rosa Noguera, Hugh S. Taylor, Carlos Simon Nature Communications, 2026 Autologous CD133+ bone marrow-derived stem cell (BMDSC) therapy has been designated as an Orphan Drug by the EMA and FDA for the treatment of Asherman Syndrome (AS). This phase 1/2, non-randomized, open-label, single-arm trial assessed the safety and efficacy of this novel therapy in 20 infertile women with moderate to severe AS, unresponsive to prior hysteroscopic treatments. Primary endpoints were safety and tolerability over 15 months follow-up, including during pregnancy and after live birth. The therapy was well tolerated with a mean dosage of 125.41 × 106 cells, with no treatment-related serious adverse events and only reversible events such as arm pain, headache, and nausea. In pregnant patients, minor obstetric complications were reflux-related cough (n = 1), gestational diabetes (n = 2), cervical shortening requiring pessary placement (n = 2), and postpartum placenta accreta (n = 1). No preterm labor occurred, and all six newborns remained free of significant adverse events. Our findings suggest that autologous CD133 + BMDSC therapy is a safe and effective treatment for AS. Clinical trial registration (Eudra CT): 2016-003975-23 The authors present the results of a phase I/II clinical trial using autologous CD133+ bone marrow stem cell therapy to restore fertility in patients with Asherman Syndrome. The intervention was safe and showed promising results for the restoration of menstruation and reproductive function.
Evaluation of TRPA1 as a Therapeutic Target in MYCN-Amplified Neuroblastoma Alexandra Seger, Dora Adamič, Erick Muciño Olmos, Johannes Nilsson, Sofia Granados‐Aparici, Isaac Vieco‐Marti, Javanshir Esfandyari, Matilda Engström, Julia Martinez, Adriana Mañas, Samuel Navarro, Rosa Noguera, Kristina Aaltonen, Daniel Bexell Pediatric Blood and Cancer, 2025 BackgroundNeuroblastoma (NB) is a childhood cancer with a high relapse rate despite intensive treatment. TRPA1 is a pain‐sensing ion channel with downstream impacts on proliferative and pro‐apoptotic pathways. Here, we evaluated TRPA1 expression in NB and performed pharmacological inhibition in preclinical models to assess its potential as a therapeutic target in NB.MethodsTRPA1 protein levels were assessed in NB patient tumors on tissue microarrays. Bulk and single‐cell gene expression data were retrieved from publicly available databases. The effects of three TRPA1 inhibitors (AP‐18, A967079, and Bay 390) on NB cell viability and cell death were evaluated using NB patient‐derived xenograft (PDX)‐derived organoids. In vivo testing was performed in a MYCN‐amplified NB PDX model. Drug combination testing was performed using combination or sequential treatments and evaluated using drug synergy scores.ResultsTRPA1 is widely expressed in NB patient tumors and preclinical patient‐derived NB models. Pharmacological TRPA1 inhibition decreased NB cell viability and increased cell death. In vivo TRPA1 inhibition alone did not significantly affect NB tumor growth. Pretreatment with TRPA1 inhibition prior to chemotherapy resulted in synergistic effects in vitro.ConclusionsTRPA1 is expressed in NB tumors, and pharmacological TRPA1 inhibition can be effective in vitro and synergistic when used as pretreatment to chemotherapy. However, the tested inhibitors did not show in vivo efficacy, at least as monotherapy.
Multi-omics-based mapping of decidualization resistance in patients with a history of severe preeclampsia Irene Muñoz-Blat, Raúl Pérez-Moraga, Nerea Castillo-Marco, Teresa Cordero, Ana Ochando, et al. Nature Medicine, 2025 Endometrial decidualization resistance (DR) is implicated in various gynecological and obstetric conditions. Here, using a multi-omic strategy, we unraveled the cellular and molecular characteristics of DR in patients who have suffered severe preeclampsia (sPE). Morphological analysis unveiled significant glandular anatomical abnormalities, confirmed histologically and quantified by the digitization of hematoxylin and eosin-stained tissue sections. Single-cell RNA sequencing (scRNA-seq) of endometrial samples from patients with sPE (n = 11) and controls (n = 12) revealed sPE-associated shifts in cell composition, manifesting as a stromal mosaic state characterized by proliferative stromal cells (MMP11 and SFRP4) alongside IGFBP1+ decidualized cells, with concurrent epithelial mosaicism and a dearth of epithelial–stromal transition associated with decidualization. Cell–cell communication network mapping underscored aberrant crosstalk among specific cell types, implicating crucial pathways such as endoglin, WNT and SPP1. Spatial transcriptomics in a replication cohort validated DR-associated features. Laser capture microdissection/mass spectrometry in a second replication cohort corroborated several scRNA-seq findings, notably the absence of stromal to epithelial transition at a pathway level, indicating a disrupted response to steroid hormones, particularly estrogens. These insights shed light on potential molecular mechanisms underpinning DR pathogenesis in the context of sPE. A multi-omics analysis of decidualization resistance, which is implicated in various gynecological and obstetric conditions, in patients with a history of severe preeclampsia revealed defects in the stroma, epithelium and epithelial-to-stromal transition, with findings validated in a separate replication cohort.
Nicotine exposure is associated with targeted impairments in primordial follicle phenotype in cultured neonatal mouse ovaries Sara M. Idrees, Sarah L. Waite, Sofia Granados Aparici, Mark A. Fenwick Ecotoxicology and Environmental Safety, 2024 The ovarian reserve consists of a limited supply of primordial follicles (PFs), each containing an oocyte surrounded by a layer of granulosa cells (GCs). PFs are relatively quiescent and must remain viable for a long period, thereby making them susceptible to environmental and lifestyle influences. Given the widespread prevalence of e-cigarette use, this study aimed to investigate the effects of nicotine and its metabolite cotinine in a mouse model and to elucidate the mechanisms by which nicotine influences the ovarian reserve. Neonatal ovaries were cultured for 7-days in nicotine or cotinine reflective of concentrations in plasma of e-cigarette users. From histological evaluation, nicotine or cotinine had no impact on the number of PFs or early growing follicles; however, the medium (15 ng/ml) and high (45 ng/ml) concentrations of nicotine (but not cotinine) caused a small reduction in oocyte and GC size within PFs relative to controls (0 ng/ml; both P<0.01). These morphological effects were not associated with changes in immunofluorescent markers of apoptosis (active caspase-3) or proliferation (Pcna), but were associated with increased gH2AX in PF oocytes, indicative of DNA damage and repair. RNA-sequencing of cultured ovaries exposed to nicotine (45 ng/ml) relative to control (0 ng/ml), revealed a suite of differentially expressed candidates, as well as numerous gene ontology biological processes associated with increased DNA damage, metabolism, respiration and immune function, alongside suppression of meiosis, cell adhesion, differentiation and morphogenesis. Findings from this study indicate that direct nicotine exposure has a limited effect on the quantity of PFs, but importantly highlights a range of processes that could impinge on the quality of the ovarian reserve.
Concordance in the estimation of tumor percentage in non-small cell lung cancer using digital pathology Irene Carretero-Barrio, Lara Pijuan, Adrián Illarramendi, Daniel Curto, Fernando López-Ríos, Ángel Estébanez-Gallo, Josep Castellvi, Sofía Granados-Aparici, Desamparados Compañ-Quilis, Rosa Noguera, Isabel Esteban-Rodríguez, Ignacio Sánchez-Güerri, Ana Delia Ramos-Guerra, Juan Enrique Ortuño, Pilar Garrido, María Jesús Ledesma-Carbayo, Amparo Benito, José Palacios Scientific Reports, 2024 The incorporation of digital pathology in clinical practice will require the training of pathologists in digital skills. Our study aimed to assess the reliability among pathologists in determining tumor percentage in whole slide images (WSI) of non-small cell lung cancer (NSCLC) using digital image analysis, and study how the results correlate with the molecular findings. Pathologists from nine centers were trained to quantify epithelial tumor cells, tumor-associated stromal cells, and non-neoplastic cells from NSCLC WSI using QuPath. Then, we conducted two consecutive ring trials. In the first trial, analyzing four WSI, reliability between pathologists in the assessment of tumor cell percentage was poor (intraclass correlation coefficient (ICC) 0.09). After performing the first ring trial pathologists received feedback. The second trial, comprising 10 WSI with paired next-generation sequencing results, also showed poor reliability (ICC 0.24). Cases near the recommended 20% visual threshold for molecular techniques exhibited higher values with digital analysis. In the second ring trial reliability slightly improved and human errors were reduced from 5.6% to 1.25%. Most discrepancies arose from subjective tasks, such as the annotation process, suggesting potential improvement with future artificial intelligence solutions.
Real-time morphometric analysis of targeted therapy for neuroblastoma cells in monolayer and 3D hydrogels using digital holographic microscopy Sofia Granados-Aparici, Isaac Vieco-Martí, Amparo López-Carrasco, Samuel Navarro, Rosa Noguera Iscience, 2024 -mutated SH-SY5Y human neuroblastoma cell lines. Cell detachment and aggregation were maintained in hydrogel-free monolayer cells whereas cells embedded in hydrogels presented different responses to treatment, suggesting differential anoikis resistance between the two cell lines. This underscores the advantages of testing therapeutic approaches using real-time imaging of tumor cells in 3D biomimetic models and its contribution to precision medicine.
Stromal Tissue Segmentation in Multi-Stained Serial Histopathological Sections of Pancreatic Tumors Proceedings of Machine Learning Research, 2024
Integrating digital pathology with transcriptomic and epigenomic tools for predicting metastatic uterine tumor aggressiveness Giorgia Sonzini, Sofia Granados-Aparici, Sabina Sanegre, Angel Diaz-Lagares, Juan Diaz-Martin, Carlos de Andrea, Núria Eritja, Aida Bao-Caamano, Nicolás Costa-Fraga, David García-Ros, Carmen Salguero-Aranda, Ben Davidson, Rafael López-López, Ignacio Melero, Samuel Navarro, Santiago Ramon y Cajal, Enrique de Alava, Xavier Matias-Guiu, Rosa Noguera Frontiers in Cell and Developmental Biology, 2022
