Organoids

The development of brain organoids from human-induced pluripotent stem cells (iPSCs) has expanded research into neurodevelopment, disease modeling, and drug testing. More recently, the concept of organoid intelligence (OI) has emerged, proposing that these constructs could evolve to support learning, memory, or even sentience. While this perspective has driven enthusiasm in the field of organoid research and suggested new applications in fields such as neuromorphic computing, it also introduces significant scientific and conceptual concerns. Current brain organoids lack the anatomical complexity, network organization, and sensorimotor integration necessary for intelligence or sentience. Despite this, claims surrounding OI often rely on oversimplified interpretations of neural activity, fueled by neurorealist and reification biases that misattribute neurophysiological properties to biologically limited systems. Beyond scientific limitations, the framing of OI risks imposing ethical and regulatory challenges based on speculative concerns rather than empirical evidence. The assumption that organoids might possess sentience, or could develop it over time, could lead to unnecessary restrictions on legitimate research while misrepresenting their actual capabilities. Additionally, comparing biological systems to silicon-based computing overlooks fundamental differences in scalability, efficiency, and predictability, raising questions about whether organoids can meaningfully contribute to computational advancements. The field must recognize the limitations of these models rather than prematurely defining OI as a distinct research domain. A more cautious, evidence-driven approach is necessary to ensure that brain organoids remain valuable tools for neuroscience without overstating their potential. To maintain scientific credibility and public trust, it is essential to separate speculative narratives from grounded research, thus allowing for continued progress in organoid studies without reinforcing misconceptions about intelligence or sentience. Full article

Recent research works have shown the effect of nutrient concentration on cell activity, such as proliferation and differentiation. In 3D cell culture, the impact of scaffold geometry, including pore size, strut diameter, and pore shape, on the concentration gradient within scaffolds under two different loading conditions—constant fluid perfusion and non-fluid perfusion—in a perfusion bioreactor is investigated by developing an in silico model of scaffolds. In this study, both triply periodic minimal surface (TPMS) (with gyroid struts) and non-TPMS (with cubic and spherical pores) scaffolds were investigated. Two types of criteria are applied to the scaffolds: static and perfusion culture conditions. In a static environment, the scaffold in a perfusion bioreactor is loaded with a fluid velocity of $0 \mathrm{m}\mathrm{m}/\mathrm{s}$, whereas in a dynamic environment, perfusion flow with a velocity of 1 mm/s is applied. The results of in silico simulation indicate that the concentration gradient within the scaffold is significantly influenced by pore size, strut diameter, pore shape, and fluid flow, which in turn affects the diffusion rate during drug delivery. Full article

Lymphoid organs are critical for organizing the development of the immune system, generating immune tolerance, and orchestrating the adaptive immune response to foreign antigens. Defects in their structure and function can lead to immunodeficiency, hypersensitivity, cancer, or autoimmune diseases. To better understand these diseases and assess potential therapies, complex models that recapitulate the anatomy and physiology of these tissues are required. Organoid models possess a number of advantages, including complex 3D microarchitecture, scalability, and personalization, which make them ideal for modelling lymphoid organs and related pathologies. Organoids have been developed for both primary and secondary lymphoid tissues; however, these models possess several limitations, including immature phenotypes and incomplete stromal cell populations. Furthermore, these organoids are often heterogeneous in both structure and function. Several lymphoid organs, such as the spleen, do not yet have robust organoid models, offering opportunities for breakthroughs in the field. Overall, development of lymphoid organoids will pave the way for the rapid development and testing of novel therapies, organ modelling, and personalized medicine. This review summarizes current advances in models for the primary lymphoid organ—bone marrow and thymus—as well as the secondary lymphoid organs of the lymph node and spleen. Full article

In cell biology, the stem cell niche is the dynamic microenvironment in which stem cells reside and receive signals that determine their behavior and fate. The stem cell niche has largely been a theoretical construct due to the difficulty in identifying and manipulating individual stem cells and their surroundings. Recent technical advances have made it possible to characterize the niches that maintain and control stem cell activity in several organs, including the small intestine. Although the small intestine has a relatively simple architecture, it has an extraordinary capacity for fast self-renewal. Thus, the organ is a unique model for studying intestinal stem cells (ISCs) and their niche. The intestinal epithelium maintains the intestine, enabling it to perform its absorption, secretion, and barrier functions. ISCs reside at the base of crypts adjacent to Paneth cells. In vivo, ISCs are surrounded by the microenvironment that makes up the niche, which provides a variety of stimuli that determine the fate of the cells. Research on stem cell niches is beginning to deepen our understanding of ISC regulation at the cellular and molecular levels and is expected to provide insights that can be applied to ISC therapy. Intestinal organoids originate from a group of crypt base ISCs. These organoids possess a three-dimensional (3D) cell structure made up of the lumen facing inward. Therefore, 3D intestinal organoids are often digested and seeded in a two-dimensional (2D) manner to form confluent organoid monolayers. Here, we not only review our current understanding of ISC niches with a focus on systems that are well-characterized at the cellular and mechanistic levels, but we also summarize the current applications of intestinal organoids. Full article

In 2023, at the Center for Biological Resources (CRB) at the Institute of Genetics and Biophysics (IGB, Naples, Italy) of the National Research Council (CNR), the Breast Cancer Tissues and Organoids Biobank (BCTO BioBank) was founded. This is a new generation Biobank, dedicated to the collection, characterization, storage, and distribution of tissues and their 3D ‘organoid’ patients-derived. Tumor and healthy tissues from breast cancer patients have been collected from surgeons at Monaldi Hospital (Naples, Italy) and used to generate the corresponding tumor and healthy organoids from the same patient. After their establishment in culture, both organoids were characterized for their receptor status on a microfluidic 2-lane OrganoPlate, by immunofluorescence. The resulting data were compared with the expression profile obtained by immunohistochemistry on respective parental tissues. These data allowed us to phenotypically validate the generated organoids and classify them in a dedicated database, where also the clinical data of the corresponding patients were collected. During the six months of activities, we collected and characterized 27 samples. The continuous BCTO BioBank activity is fundamental to generating a high number of samples, for a broader and efficiently elaborated patient stratification at molecular level, biomarker discovery investigations, and for tailored treatment protocols design. Full article

The healthy gut masks a dynamic balance between pro- and anti-inflammatory activities, largely due to microbial factors in the lumen. IL-10 is vital among the anti-inflammatory mediators, yet confirming constitutive versus stimulated secretion in any cell type is difficult due to the cellular complexity in the gut. Seeking to determine whether intestinal epithelial cells are programmed to constitutively make IL-10, we confirmed that IL-10 mRNA was present in enteroids from C57BL/6 mice and IL-10 protein was co-localized with a Paneth cell marker but not with markers for goblet or tuft cells. Paneth cells positive for IL-10 also possessed apical and basal IL-10RA, while cells negative for IL-10 had only basal IL-10RA, suggesting a possible autocrine role for IL-10. Indeed, Paneth cells in IL-10 gene knockout (IL-10KO) enteroids possessed lower levels of anti-microbial protein mRNAs, which could not be restored by adding IL-10. Enteroids passaged onto Transwell^® filters to form monolayers were treated with IL-10 and STAT3 phosphorylation was measured. Apically applied IL-10 resulted in a stronger STAT3 signal than basally applied cytokine. Our results indicate that a subpopulation of Paneth cells constitutively secrete IL-10 apically, which binds apical IL-10RA, impacting the expression of anti-microbial proteins unique to Paneth cells. Full article

Intestinal organoids are useful for the in vitro investigation of the properties of intestinal epithelial cells and their interaction with the gut microbiome. In this study, we cultured cecal and colonic organoids from common marmosets, which are highlighted as model nonhuman primates but are susceptible to gastrointestinal diseases. The organoids established were capable of passaging and long-term culture. The results of quantitative reverse transcription PCR and immunostaining showed that the organoids differentiated into major cell types (colonocytes, goblet cells, and enteroendocrine cells) in the intestinal epithelium, enabling the in vitro analysis of these cells in marmosets. The organoids could therefore represent a useful model for the investigation of gut physiology in relation to gastrointestinal diseases and host-microbiome interactions, further expanding medical, biological, and veterinary research in the future. Full article

Peritoneal carcinomatosis from gastrointestinal tumours is considered a poor prognostic factor, with a median overall survival of six to nine months in the absence of intervention. The advent of patient-derived organoid cultures (PDOs) has provided a breakthrough in personalised medicine, allowing researchers and clinicians to model the complexity and heterogeneity of individual tumours in vitro. PDOs hold great promise in this field, as variations in the management of peritoneal carcinomatosis due to differences in the method of delivery of chemotherapeutics, drug selection, exposure duration, and tumour pathology make it impractical to use a single, standardised treatment regimen. We aim to summarise the methodologies and limitations of studies encapsulating organoids derived from peritoneal metastases to encourage design considerations that may improve future clinical relevance, standardise protocols, and address translational challenges in personalising treatment strategies. Full article

Summary Statement: A tailored image analysis workflow was applied to quantify cortical organoid health, development, morphology and cellular composition over time. The assessment of cellular composition and viability of stem cell-derived organoid models is a complex but essential approach to understanding the mechanisms of human development and disease. Aim: Our study was motivated by the need for an image-analysis workflow, including high-cell content, high-throughput methods, to measure the architectural features of developing organoids. We assessed stem cell-derived cortical organoids at 4 and 6 months post-induction using immunohistochemistry-labelled sections as the analysis testbed. The workflow leveraged fluorescence imaging tailored to classify cells as viable and dying or non-viable and assign neuronal and astrocytic perinuclear markers to count cells. Results/Outcomes: Image acquisition was accelerated by capturing the organoid slice in 3D using widefield-fluorescence microscopy. This method used computational clearing to resolve nuclear and perinuclear markers and retain their spatial information within the organoid’s heterogeneous structure. The customised workflow analysed over 1.5 million cells using DAPI-stained nuclei, filtering and quantifying viable and non-viable cells and the necrotic-core regions. Temporal analyses of neuronal cell number derived from perinuclear labelling were consistent with organoid maturation from 4 to 6 months of in vitro differentiation. Overall: We have provided a comprehensive and enhanced image analysis workflow for organoid structural evaluation, creating the ability to gather cellular-level statistics in control and disease models. Full article

Adipogenesis is a complex process influenced by various cellular interactions within adipose tissue, which plays a critical role in metabolic homeostasis. This study aimed to develop a novel in vitro three-dimensional (3D) co-culture model using murine 3T3-L1 pre-adipocytes, J774 macrophages, and NIH-3T3 fibroblasts to investigate adipogenic differentiation and inflammatory pathways. We first validated an adipogenic differentiation protocol in a two-dimensional (2D) model, where 3T3-L1 pre-adipocytes were subjected to a hormonal medium containing 3-isobutyl-1-methylxanthine, dexamethasone and insulin. After 7 days, differentiated cells were analyzed using Oil Red O and Nile Red staining, confirming lipid accumulation. Subsequently, spheroids were formed in 3D cultures, with monospheroids and heterospheroids maintained in either control medium or MDI for 11 days. Size measurements indicated significant growth in heterospheroids, particularly in the 3T3-L1:J774 combination, underscoring the importance of cellular interactions. Confocal microscopy and flow cytometry analyses demonstrated that even in the absence of hormonal stimuli, control spheroids exhibited adipogenic differentiation, evidenced by a notable proportion of Nile Red-positive cells (75.7 ± 1.7%). Inflammatory profiling revealed that the heterospheroid 3:J produced the highest levels of nitric oxide (NO), with no significant differences observed between control and MDI conditions. This study highlights the potential of 3D co-culture systems for elucidating the intricate interactions among adipocytes, macrophages, and fibroblasts. The findings may provide valuable insights into novel therapeutic targets for metabolic disorders. Full article

Background: Recent advances in the personalized treatment of non-small cell lung cancer (NSCLC) require representative in vitro model systems that reflect tumor heterogeneity and maintain the characteristic genetic aberrations. We therefore aimed to establish patient-derived NSCLC organoids that offer a reliable platform for further investigations. Methods: NSCLC organoids were cultured between May 2020 and February 2022 from surgically resected NSCLC tissue specimens. After histological and immunohistochemical validation, genetic validation was performed by targeted next-generation sequencing of tissue and organoid specimens using the Oncomine Focus Assay (ThermoFisher Scientific). Results: From 37 resected NSCLC samples, 18 primary organoid cultures were successfully established and expanded during early passages. Upon histomorphological validation, organoids showed complementary characteristics when compared to the resected parental tumor, including adenocarcinoma, squamous cell carcinoma, mucoepidermoid carcinoma, and lung carcinoid differentiation. Among nine parental tumors, traceable genetic alterations were detected, and three corresponding organoids lines retained this mutational profile, including a KRAS p.Gly12Val mutation, KRAS p.Gly12Cys mutation, and RET-fusion. Conclusions: The establishment of primary NSCLC organoids from surgically resected tissue is feasible. Histological, immunohistochemical, and genetic validation is essential to identify representative NSCLC organoids that maintain the characteristics of the parental tumor. Overall, low establishment rates remain a challenge for broad clinical applications. Full article

Gastric cancer (GC) presents a significant health challenge and ranks as the fifth most common cancer in the world. Unfortunately, most patients with GC exhaust standard care treatment options due to late diagnosis and tumour heterogeneity that leads to drug resistance, resulting in poor survival outcomes. Potentially, this situation can be improved by personalising treatment choice. Organoids are an emerging cell model system that recapitulates tumour heterogeneity and drug responses. Coupled with genomic analysis, organoid culture can be used to guide personalised medicine. The GC organoid field, however, lacks standardised methodologies for assessing organoid drug sensitivities. Comparing results across different GC organoid studies and correlating organoid drug responses with patient outcomes is challenging. Hence, we aim to summarise the methodologies used in GC organoid drug testing and correlation with clinical outcomes and discuss design considerations and limitations to enhance the robustness of such studies in the future. Full article

Tooth and periodontal organoids from stem and progenitor cells represent a significant advancement in regenerative dentistry, offering solutions for tooth loss and periodontal diseases. These organoids, which mimic the architecture and function of real organs, provide a cutting-edge platform for studying dental biology and developing therapies. Recent methodologies have been developed to optimize conditions for organoid production, advancing dental regenerative medicine, disease modeling, and developmental studies. The integration of bioengineering strategies with culture techniques enhances both our understanding and the therapeutic potential of these organoids. Additionally, factors such as the extracellular matrix, growth factors, and culture systems profoundly influence organoid formation and maturation. This review explores various bioengineering approaches for generating organoids, emphasizing the pivotal role of stem and progenitor cells. Full article

Recent advancements in vascular organoid (VO) and vessel-on-chip (VoC) technologies have revolutionized our approach to studying human diseases, offering unprecedented insights through more physiologically relevant models. VOs generated from human pluripotent stem cells exhibit remarkable self-organization capabilities, forming complex three-dimensional structures that closely mimic human blood vessel architecture and function, while VoCs are engineered with microfluidic systems that meticulously recreate the physical and functional attributes of blood vessels. These innovative constructs serve as powerful tools for investigating vascular development, disease progression, and therapeutic efficacy. By enabling the creation of patient-specific VOs and VoCs, they pave the way for personalized medicine approaches, allowing researchers to delve into genetic variations, intricate cellular interactions, and dynamic processes with exceptional resolution. The synergy between VOs and VoCs with newly developed cutting-edge technologies has further amplified their potential, unveiling novel mechanisms underlying human pathologies and identifying promising therapeutic targets. Herein, we summarize different types of VOs and VoCs and present an extensive overview on the generation and applications of VOs and VoCs. We will also highlight clinical and translational challenges and future perspectives around VOs and VoCs. Full article

Colorectal cancer (CRC) is the third most common cancer worldwide and it is the second leading cause of cancer death. In CRC, as in most cancers, the formation of metastasis through the migration and invasion of cancer cells to distant organs is associated with a dismal prognosis. The study of the mechanisms associated with cancer, and, in particular, CRC, changed in the last decade due to the introduction of organoids. These represent a step forward in terms of complexity from cell lines and allowed the use of mouse models in cancer research to be limited. Although organoids faithfully model the cellular complexity of CRC, current protocols do not allow for the use of organoids in some crucial processes of metastasis, such as migration and invasion. In this study, a method to study migration and invasion using mouse intestinal organoids in vitro is presented. This protocol provides researchers with the opportunity to investigate the migratory behavior of organoid lines and study the impact of distinct mutations on the migratory and invasive capacity of cancer cells. Full article

First trimester placental development comprises some of the most critical yet understudied events that impact fetal development. Improper placentation leads to a host of health issues that not only impact the fetal period but also influence offspring throughout their lives. Thus, a paradigm to study early placental development is necessary, and this has spurred on the pursuit of new in vitro model systems that recapitulate specific aspects of placentation. One of the most complex and translationally valid models to arise are organoids, three-dimensional structures comprising multiple differentiated cell types that originate from a common progenitor population. Trophoblasts are the progenitor cells of the placenta, serving as the proliferative base for placental development. Recent advances have enabled the derivation of organoids from primary tissue, yet access to first trimester human samples is ethically constrained; derivation from established trophoblast stem cell lines is an alternative source. Organoids have already proven useful in generating insights into molecular events that underlie trophoblast differentiation, with the identification of new cell subtypes that are primed to differentiate down different paths. In this review, (1) we recap early pregnancy development events, (2) provide an overview of the cellular complexity of the placenta, (3) discuss the generation of organoids from tissue versus cellular sources, (4) highlight the value of translational animal models, and (5) focus on the complexities of the molecular regulation of trophoblast organoid development, differentiation, and function. Full article

Globally, a number of diseases impact us and while treatment options exist, it is often found that similar treatments have variable effects on different patients with the same disease. Particularly in the case of conditions that are closely associated with genetics (like cancer), the intensity and results of a treatment vary between patients. Even for diseases like arthritis it is not uncommon for only a fraction of patients to achieve remission with the same therapeutic approach. With millions suffering from diseases like cancer and arthritis, precision medicine (PM) has been at the forefront of biomedical and pharmaceutical research since 2015. PM focusses on understanding the genetic and environmental factors affecting the patients and has several platforms. One of the platforms is the use of three-dimensional (3D) in vitro models, especially those derived from the patient themselves. These models, like organ-on-chip (OOC), organoid and spheroid models, 3D biomaterial scaffolds and others, have several advantages over traditional two-dimensional (2D) cell culture approaches. In this opinion paper, the author briefly discusses the different platforms used for PM. Then, the advantages that 3D in vitro models have over traditional 2D models and in vivo models are considered and an overview of their applications is provided. Finally, the author outlines the challenges and future directions and shares their opinion about using 3D in vitro models as a tool for PM towards enhanced patient outcomes. Full article

In zebrafish and various mammalian species, HB-EGF has been shown to promote Müller glia proliferation and activation of repair mechanisms that have not been fully investigated in human retina. In the current study, 70- to 90-day-old human retinal organoids were treated with 20 μM 4-hydroxytamoxifen (4-OHT), and CRX, REC, NRL, PAX6, VIM, GFAP, and VSX2 gene and protein expression were assessed at various times points after treatment. Organoids with or without 4-OHT-induced damage were then cultured with HB-EGF for 7 days. We showed that 20 μM 4-OHT caused a reduction in the number of recoverin-positive cells; an increase in the number of TUNEL-positive cells; and downregulation of the photoreceptor gene markers CRX, NRL, and REC. Culture of organoids with HB-EGF for 7 days after 4-OHT-induced damage caused a marked reduction in the number of TUNEL-positive cells and small increases in the number of Ki67-positive cells and PAX6 and NOTCH1 gene expression. The current results suggest that treatment of human ESC-derived retinal organoids with 4-OHT may be used as a model of retinal degeneration in vitro. Furthermore, HB-EGF treatment of human retinal organoids increases proliferating Müller cells, but only after 4-OHT induced damage, and may be an indication of Muller reactivity in response to photoreceptor damage. Further studies will aim to identify factors that may induce Müller cell-mediated regeneration of the human retina, aiding in the development of therapies for retinal degeneration. Full article

The mesolimbic pathway connects ventral tegmental area dopaminergic neurons and striatal medium spiny neurons, playing a critical role in reward and stress behaviors. Exposure to substances of abuse during development and adulthood has been linked to adverse outcomes and molecular changes. The rise of human cell repositories and whole-genome sequences enables human functional genomics ‘in a dish’, offering insights into human-specific responses to substances of abuse. Continued development of new models is needed, and the characterization of in vitro models is also necessary to ensure appropriate experimental designs and the accurate interpretation of results. This study introduces new culture conditions for generating medium spiny neurons and dopaminergic neurons with an early common media, allowing for coculture and assembloid generation. It then provides a comprehensive characterization of these and prior models and their responses to substances of abuse. Single-cell analysis reveals cell-type-specific transcriptomic responses to dopamine, cocaine, and morphine, including compound and cell-type-specific transcriptomic signatures related to neuroinflammation and alterations in signaling pathways. These findings offer a resource for future genomics studies leveraging human stem cell-derived models. Full article