John De Vos

Infertility affects approximately one in six individuals worldwide and is a highly heterogeneous disorder resulting from the complex interplay of genetic, epigenetic, endocrine, environmental and lifestyle factors. Although numerous genes and molecular pathways involved in female and male infertility have been identified, elucidating the functional consequences of disease-associated variants remains challenging due to the lack of relevant human experimental models. In recent years, reproductive organoids have emerged as powerful three-dimensional systems that recapitulate key structural, cellular and functional characteristics of the ovary, fallopian tube, endometrium, testis and early embryo. Here, we review the current landscape of reproductive organoid models based on a focused analysis of the literature, with particular emphasis on original studies describing their generation, characterization and applications. Beyond modeling tissue development and reproductive physiology, these models provide unique opportunities to investigate infertility-associated mechanisms, gene regulatory networks, cell–cell communication and tissue-specific responses to environmental and pharmacological stimuli. Single-cell and spatial transcriptomics, multi-omics, CRISPR/Cas9 genome editing, artificial intelligence and bioengineering technologies, including organ-on-chip systems, are expanding their potential as next-generation platforms for functional genomics, disease modeling, biomarker discovery and therapeutic screening. However, current reproductive organoids remain simplified representations of native tissues, with limitations in physiological maturity, reproducibility and standardization, while their clinical predictive value remains to be established. Overall, by linking genomic variation with molecular regulation, cellular phenotypes and tissue organization, reproductive organoids represent promising preclinical platforms for understanding human infertility and may ultimately contribute to the development of precision reproductive medicine.

Respiratory infectious diseases are among the leading causes of global morbidity and mortality and remain a major public health concern. Progress in understanding early host-pathogen interactions has been hampered by the limited physiological relevance of existing experimental systems. Different models mimicking the human respiratory epithelium have been developed to study viral infections in vitro , such as tridimensional (3D) tissue models and organoids. However, many lack key features of human tissue architecture, particularly the lamina propria or immune cells. To address these limitations, we established an immunocompetent 3D model of the human respiratory mucosa by combining nasal epithelial cells isolated from nasal brushings, fibroblasts from mid-turbinate nasal biopsies, and macrophages derived from blood monocytes. These cells were sequentially seeded into collagen-chitosan scaffolds, resulting in a reconstructed respiratory mucosa closely resembling the in vivo nasal tissues. To further confirm the physiological relevance of the model, we infected it with influenza A virus. The mucosa model supported viral replication in the epithelium and consequently showed increased secretion of inflammatory cytokines and upregulation of type I interferon related genes, enabling the monitoring of early antiviral innate immune responses in a physiologically relevant context.

Background: Lung transplantation remains the ultimate treatment option for patients with end-stage lung disease, but has many limitations. This underlines the urgent need of developing alternative approaches to treat lung disorders. Among the emergent strategies, gene therapy holds great potential for the treatment of monogenic lung diseases. However, so far, aerosolized viral vector-based delivery for gene therapy has failed likely because of difficulties in accessing the target cells. Combined gene and cell therapy approaches could be a promising alternative. Trials using basal cell transplantation already showed encouraging results. Moreover, the induced pluripotent stem cell (iPSC) technology broadens the scope of personalized therapies by paving the way for autologous approaches. Our group previously derived iPSC lines from patients with Primary Ciliary Dyskinesia (PCD) and found that their correction by gene conversion allows functional recovery. This study aimed to identify the best progenitors and airway conditioning technique to develop an autologous cell replacement strategy for PCD. Methods: Airway epithelial cells were differentiated from induced pluripotent stem cell (iPSC) lines from a healthy donor (parental Hy03) and Hy03 in which MCIDAS was knocked out (PCD model) and maintained in air-liquid interface (iALI). The engraftment of GFP+ ventral Anterior Foregut Endoderm (vAFE) cells, differentiated from GFP-expressing Hy03 iPSCs, was assessed after conditioning of the recipient iALI. The efficacy (epithelial cell shedding) and toxicity (cell death) of different conditioning strategies were compared. Cilia functional repair was assessed using microbead motion tracking. Results: GFP+ vAFE cells can successfully integrate and repair trypsin- or EDTA-conditioned airway epithelia derived from the parental and MCIDAS ^-/- Hy03 iPSC lines. EDTA showed optimal efficacy/safety balance. Progenitor integration and differentiation were confirmed by E-cadherin, tubulin-IV, KRT5 and MUC5AC co-expression in GFP+ engrafted cells at day 35 post-graft (immunofluorescence analysis). The engrafted GFP+ population reached 35-45% of the total epithelial population, as indicated by flow cytometry quantification of EpCAM+/GFP+ cells. Functional analysis demonstrated cilia motion restoration after GFP+ cell engraftment onto MCIDAS ^-/- iALI. Conclusions: Our study shows that vAFE cells can integrate and differentiate to repair epithelial models of PCD. EDTA conditioning is promising for the clinical application of this therapeutic strategy.

Academic autologous cell manufacturing offers key advantages, including cost-effectiveness, accessibility, and flexibility. However, the management of Raw Materials, Reagents, and Consumables (RMRCs) is essential for ensuring product purity, safety, and effectiveness. Variations in RMRC quality can increase production costs and result in batch failures. This work from the GMP-Bioproduction group of the French Consortium in Advancing Cancer Cell and Gene Therapy (UNITC) outlines a multicenter study conducted from 2022 to 2024 across all 11 French academic cell and gene therapy facilities producing Advanced Therapy Medicinal Products, evaluating current RMRC management practices. The study highlights significant challenges, including supply shortages, reference changes, and inconsistent quality controls. While RMRC-related non-conformities accounted for only 6.8% of total issues, they frequently required complex procedural adjustments, resulting in added financial and operational burdens. Despite differences in production scale and ATMP types, all centers consistently evaluated the criticality of RMRC, reflecting strong alignment in risk assessment practices. To address these issues, the study proposes recommendations, including a unified RMRC risk classification system, harmonized quality assurance processes. These actions aim to strengthen regulatory compliance, enhance collaboration across academic centers, and improve the overall resilience of academic decentralized CAR-T cells manufacturing in France.

Background: Male infertility is evaluated using standard semen parameters. However, these criteria offer limited insight into sperm functionality and poorly predict natural fertility or assisted reproductive technology (ART) outcomes. Methods: In this study, the expression levels of three genes (AURKA, HDAC4, and CARHSP1) involved in mitosis regulation, epigenetic modulation and early embryonic development, were measured by RT-qPCR in sperm samples (training dataset). For each gene, thresholds of normal and reduced expression were established by biostatistical modeling and combined with the number of motile spermatozoa to develop the Spermatozoa Function Index (SFI). Results: The ROC analysis was used to interpret the SFI values: SFI > 320 (normal), 290–320 (intermediate), and <290 (low). Then, this index was validated using 627 fresh semen samples from 25- to 60-year-old men at our ART center. Based on the World Health Organization criteria, 54.5% of the 627 sperm samples were normospermic, 8.8% showed oligo-astheno-teratospermia, and 36.6% had one or two abnormal parameters. According to the SFI values, 41% of sperm samples displayed normal expression, 55.9% low expression, and 4.1% intermediate expression. Only 57% of the 342 normospermic samples had normal SFI values and 37% had low SFI values. Among the 81 samples with stringent normal criteria (≥50 million/mL, ≥50% total motility, ≥14% normal morphology), 67.9% displayed normal SFI and 22.2% low SFI values. These findings suggest that even sperm with normal parameters may harbor dysfunctions. Conclusions: Our data highlight a gene signature with strong discriminatory power and promising diagnostic value for detecting subclinical sperm defects and improving male infertility assessment.

Human-induced pluripotent stem cells (hiPSCs) have broad applications in basic research and cell-based regenerative medicine. Maintaining a stable genome in culture is crucial for the clinical use of hiPSCs. Indeed, their continuous propagation drives genetic instability, particularly copy number variants (CNV). Among the different methods available to identify gene alterations, digital PCR (dPCR) is a precise, rapid, and cost-effective tool for the sensitive and absolute quantification of CNV. Unlike conventional methods limited to two targets, multiplex dPCR assays allow the simultaneous detection of four targets. In this method paper, we describe strategies for multiplex dPCR assays to detect major CNVs using only small amounts of DNA extracted from hiPSCs. We confirmed this approach applicability for hiPSCs through validation following the International Council for Harmonization (ICH) guidelines that cover different aspects, such as specificity, precision, robustness, and limit of detection. The simultaneous measurement of four targets was possible through the generation of distinct fluorescence endpoints for each target by adjusting the concentrations of primers and/or probes. Compared to the classical dPCR (the “gold standard”), these multiplexed dPCR assays displayed 100% specificity and sensitivity for the simultaneous detection of CNVs. This study highlights the key role of multiplexing for monitoring genetic alterations in hiPSCs and for setting the standards required for the process safety evaluation of hiPSC-based stem cell therapies.

Respiratory infections are a major global health concern, as underscored by the COVID-19 pandemic. To better understand bronchial tissue responses to viral infection, we have developed a preclinical in vitro model mimicking the multiciliated airway epithelium, from induced pluripotent stem cell (iPSC) and cultured in an air-liquid interface (iALI). By using iPSCs reprogrammed from patients with chronic obstructive pulmonary disease (COPD), we successfully generated a fully differentiated and functional bronchial epithelium exhibiting key COPD features with goblet and basal cell hyperplasia and tissue inflammation. SARS-CoV-2 could infected and replicated for several weeks in both healthy and COPD models, with a recurrent peak at 3 days after infection. Infected iALI exhibited cilia destruction and increased mucus secretion. Innate immune response of different infected iALI reveals a differential expression of interferon-stimulated genes (ISGs) and pro-inflammatory cytokine secretion. Notably, COPD iALI displayed an earlier innate immune response to SARS-CoV-2 infection as compared to healthy iALI, suggesting a genetic susceptibility of COPD iALI towards inflammation induced by SARS-CoV-2 infection, and a less efficient response to antivirals. In conclusion, our study demonstrates that the iALI bronchial organoid model is a powerful tool for investigating bronchial tissue responses to long term respiratory viral infections, antivirals, and patients with COPD or other airway pathology. Grapical HighLights: hiPSC-derived COPD airway organoids SARS-CoV-2 productively infects induced pluripotent stem-cell derived bronchial organoids iALI and persisted over the long term SARS-CoV-2 iALI infection results in cilia destruction, increased mucus secretion and a strong innate immune response SARS-CoV-2 infection elicited a higher and earlier innate immune response in iCOPD SARS-CoV-2 infection in iCOPD respond less to antivirals Short SARS-CoV-2 causes severe lower respiratory tract infection in COVID-19 patients, which can persist over time. Here, we used an in-house developed in vitro airway organoid derived from induced human pluripotent stem cells (iALI) to study SARS-CoV-2 infection over long term in healthy or COPD patients whom respiratory failure is at risk during infection. Our results show that SARS-CoV-2 infection results in high and lethal infection of bronchial epithelial cells, that persist over time, inducing mucus secretion, destruction of ciliated cells and specific cytokine release. A late innate immune response is observed in the healthy iALI, while in iCOPD, it appears earlier and stronger, suggesting a different sensing of SARS-CoV-2 in COPD patients, accompanied by a reduce sensitivity to antivirals. In conclusion, our study demonstrates that the iALI organoid model is a powerful tool for investigating bronchial tissue responses to long term respiratory viral infections, from healthy to pathologic patients.

This position paper from the Bioproduction Working Group of the UNITC Consortium seeks to harmonize quality control (QC) procedures for academic production of autologous CAR-T cells. The primary objective is to standardize QC testing for batch release in academic cell therapy units. Academic CAR-T manufacturing under the hospital exemption pathway enables faster, more cost-effective production and the use of fresh cells, eliminating the need for cryopreservation. Standardized QC processes are critical to ensure consistent product quality and safety. This paper focuses on key QC measures, including mycoplasma detection using validated commercial kits or in-house methods with on-site validation, endotoxin testing via Limulus Amebocyte Lysate (LAL) or Recombinant Factor C (rFC) assays with validated protocols to prevent matrix interference, vector copy number (VCN) quantification through validated qPCR or ddPCR techniques, and potency assessment through IFN-γ ELISA following antigenic stimulation. Emphasizing method validation and standardized testing, this work underscores the importance of robust QC strategies to ensure the safety and efficacy of CAR-T cell therapies, with ongoing efforts dedicated to optimizing these processes. This workshop focuses on addressing the harmonization of some quality control (QC) measures required for the validation of academic CAR-T cell production :mycoplasma detection; endotoxin testing; vector copy number (VCN) quantification; potency testing and the use of surrogate markers, if applicable. Sterility testing and characterization/identity/purity assessments are not covered in this work.