Organogenesis in a dish: modeling development and disease using organoid technologies

Generation, interrogation, and future applications of microglia-containing brain organoids

Brain organoids encompass a large collection of in vitro stem cell-derived 3D culture systems that aim to recapitulate multiple aspects of in vivo brain development and function. First, this review provides a brief introduction to the current state-of-the-art for neuro-ectoderm brain organoid development, emphasizing their biggest advantages in comparison with classical two-dimensional cell cultures and animal models. However, despite their usefulness for developmental studies, a major limitation for most brain organoid models is the absence of contributing cell types from endodermal and mesodermal origin. As such, current research is highly investing towards the incorporation of a functional vasculature and the microglial immune component. In this review, we will specifically focus on the development of immune-competent brain organoids. By summarizing the different approaches applied to incorporate microglia, it is highlighted that immune-competent brain organoids are not only important for studying neuronal network formation, but also offer a clear future as a new tool to study inflammatory responses in vitro in 3D in a brain-like environment. Therefore, our main focus here is to provide a comprehensive overview of assays to measure microglial phenotype and function within brain organoids, with an outlook on how these findings could better understand neuronal network development or restoration, as well as the influence of physical stress on microglia-containing brain organoids. Finally, we would like to stress that even though the development of immune-competent brain organoids has largely evolved over the past decade, their full potential as a pre-clinical tool to study novel therapeutic approaches to halt or reduce inflammation-mediated neurodegeneration still needs to be explored and validated.

Rotenone-driven DNA hypermethylation of the miR-6991-3p promoter induces death of mouse brain organoids

Rotenone has potential chemical toxicity in the nervous system of both insects and mammals, but its deep molecular biological mechanisms have not been clarified. Here, the epigenetic regulatory mechanism underlying the toxicity of rotenone was studied using murine brain organoids (mBOs). Transmission electron microscopy indicated that rotenone destroyed mBOs'mitochondrial structure. RRBS-Seq showed that some promoter regions from the DLK1-DIO3 imprinted microRNA clusters were hypomethylated. But, rotenone stimulated hypermethylation significantly on the promoter DNA of miR-6991-3p. MiR-6991-3p in the rotenone-treated mBOs had the greatest decreased miRNA expression compared with the control. Meanwhile, luciferase report assay indicated that miR-6991-3p induced a decrease in luciferase activity via binding to specific sites on the 3'UTR of DEDD2 gene. To overexpression of miR-6991-3p attenuated mBO proliferated inhibition and cell death, accumulation for lipid peroxidation products significantly by rotenone inducing. Subsequently, results of cell staining and molecular biology experiment revealed that overexpression for miR-6991-3p significantly weakened expression levels of death-related genes (DEDD2, caspase-8, caspase-3, and caspase-1), but significantly elevated expression levels of cell proliferation-related genes (Ki67 and BCL2) in rotenone treated mBOs group. Here, we reveal a novel epigenetic mechanism of rotenone-induced neuronal death, in which rotenone induced promoter DNA hypermethylation of miR-6991-3p in the DLK1-DIO3 imprinted cluster. This caused miR-6991-3p transcriptional activity to be downregulated, which subsequently significantly increased the expression of its target gene, DEDD2, ultimately leading to neural organoid cell death.

Bavachinin causes cholestasis by down-regulating BAAT expression and disrupting glycocholic acid synthesis in human liver organoids

Psoraleae Fructus (Bu Gu Zhi, BGZ) is extensively utilized for dermatological and osseous disorders in China. BGZ-induced liver injury has become one of the major concerns, which predominantly cause cholestasis, with the pathogenesis not being fully elucidated. Currently, studies on hepatotoxic mechanisms of BGZ have mainly been conducted on 2D cell culture systems or rodent models, which may not fully encapsulate human pathophysiology. Therefore, we generated human liver organoids (HLOs) from healthy donor(s) for living-related liver transplantation to explore the hepatotoxic mechanism. We identified bavachinin (BVC) as the most hepatotoxic component for cholestasis. After validating by CLF tests, we identified BVC caused cholestasis by down-regulating BAAT, which catalyzes the amidation of bile acids. We also found that up-regulating BAAT with harmaline could mitigate cholestasis and enhance cell viabilities in HLOs. We further demonstrated that glycocholic acid (GCA) levels decreased in BVC-treated HLOs. Supplementation of GCA to BVC-treated HLOs significantly improved cell viabilities. Collectively, our data suggested that BVC impaired the GCA synthesis by down-regulating the expression of BAAT, thereby inducing cholestasis.

Psychiatric Genomics 2025: State of the Art and the Path Forward

Psychiatric genetics has evolved from candidate-gene studies to whole-genome sequencing efforts. With hundreds of disease-associated loci now identified, functional interpretation of the associated loci becomes the critical next step toward translational applications. The article discusses achievements, challenges, and opportunities in psychiatric genomics associated with complexity and heterogeneity. Brain expression quantitative trait loci, single-cell ribonucleic acid-sequence, and functional genomics technologies are highlighted. It also covers newly developed techniques with improved spatiotemporal resolution, quality and sensitivity, coupled with advanced analytical methods and artificial intelligence. The power of collaborative research and inclusion of diverse populations will ensure a bright future for precision psychiatry.

In vitro senescence and senolytic functional assays

A detailed understanding of aging biology and the development of anti-aging therapeutic strategies remain imperative yet inherently challenging due to the protracted nature of aging. Cellular senescence arises naturally through replicative exhaustion and is accelerated by clinical treatments or environmental stressors. The accumulation of senescent cells-defined by a loss of mitogenic potential, resistance to apoptosis, and acquisition of a pro-inflammatory secretory phenotype-has been implicated as a key driver of chronic disease, tissue degeneration, and organismal aging. Recent studies have highlighted the therapeutic promise of senolytic drugs, which selectively eliminate senescent cells. Compelling results from preclinical animal studies and ongoing clinical trials underscore this potential. However, the clinical translation of senolytics requires further pharmacological validation to refine selectivity, minimize toxicity, and determine optimal dosing. Equally important is the evaluation of senolytics' potential to restore tissue structure and function by reducing the senescent cell burden. In vitro tissue culture models offer a powerful platform to advance these efforts. This review summarizes the current landscape of in vitro systems used for inducing cellular senescence-referred to as "senescence assays"-and for screening senolytic drugs-referred to as "senolytic assays". We conclude by discussing key challenges to improving mechanistic insight, predictive accuracy, and clinical relevance in senolytic drug development, as well as emerging applications of senolytic therapies.

A high-throughput microfluidic platform for functional hiPSC-derived liver organoids with bile duct- and lobule-like structures

HiPSC-derived organoids have attracted significant attention in stem cell research and regenerative medicine. However, obtaining functional organoids in sufficient quantities, consistent sizes, and reproducible formats remains a significant challenge. Here, we present an innovative microfluidic platform for the high-throughput production of HAMA core-shell microspheres (HCSM) for the encapsulation and differentiation of hiPSCs. Fish gelatin and HAMA were employed as the core and shell materials, respectively. Using this platform, we successfully fabricated HCSM with uniform and controllable sizes in a high-throughput manner. Single-cell hiPSC suspensions self-organized into spheroids within HCSM, leading to the formation of EBs exhibiting cavitation. These EBs effectively differentiated into brain organoids, beating cardiac organoids, and liver organoids. Detailed structural and functional analyses of the liver organoids revealed a heterogeneous cellular composition including hepatocyte-, bile duct epithelial-, epithelial-, and stellate-like cells. Structurally, they exhibited bile duct- and hepatic lobule-like formations. Functionally, liver organoids displayed lipid and glycogen accumulation, ICG uptake and release, albumin and urea secretion, as well as metabolic responses to APAP and rifampin. Consequently, our study introduces a high-throughput manufacturing platform for hiPSC-derived organoids, with the potential to generate functional organoids for therapeutic applications and drug screening.

Recent Advances in Three-Dimensional In Vitro Models for Studies of Liver Fibrosis

BACKGROUND

Liver fibrosis is a reversible but complex pathological condition associated with chronic liver diseases, affecting over 1.5 billion people worldwide. It is characterized by excessive extracellular matrix deposition resulting from sustained liver injury, often advancing to cirrhosis and cancer. As its progression involves various cell types and pathogenic factors, understanding the intricate mechanisms is essential for the development of effective therapies. In this context, extensive efforts have been made to establish three-dimensional (3D) in vitro platforms that mimic the progression of liver fibrosis.

METHODS

This review outlines the pathophysiology of liver fibrosis and highlights recent advancements in 3D in vitro liver models, including spheroids, organoids, assembloids, bioprinted constructs, and microfluidic systems. It further assesses their biological relevance, with particular focus on their capacity to reproduce fibrosis-related characteristics.

RESULTS

3D in vitro liver models offer significant advantages over conventional two-dimensional cultures. Although each model exhibits unique strengths, they collectively recapitulate key fibrotic features, such as extracellular matrix remodeling, hepatic stellate cell activation, and collagen deposition, in a physiologically relevant 3D setting. In particular, multilineage liver organoids and assembloids integrate architectural complexity with scalability, enabling deeper mechanistic insights and supporting therapeutic evaluation with improved translational relevance.

CONCLUSION

3D in vitro liver models represent a promising strategy to bridge the gap between in vitro studies and in vivo realities by faithfully replicating liver-specific architecture and microenvironments. With enhanced reproducibility through standardized protocols, these models hold great potential for advancing drug discovery and facilitating the development of personalized therapies for liver fibrosis.

The 3C (Cell Culture, Computer Simulation, Clinical Trial) Solution for Optimizing the 3R (Replace, Reduction, Refine) Framework during Preclinical Research Involving Laboratory Animals

Preclinical research has traditionally utilized laboratory animals to elucidate the safety, tolerability, pharmacokinetics, and pharmacodynamics of new chemical entities prior to human trials. The use of animal models has been pivotal in advancing scientific knowledge and medical breakthroughs, contributing significantly to our understanding of the complex biological processes and human diseases. However, many promising treatments that have demonstrated efficacy in animal studies have failed to translate to human subjects during clinical trials. Consequently, animal testing faces ethical concerns and criticism regarding its predictive reliability for human responses. This has led to the development of 3R principles (Replacement, Reduction, Refinement), introduced in 1959, advocating for alternative methods and improved animal welfare in research. Furthermore, regulatory frameworks and recent legislation, such as the 2022 FDA Modernisation Act, emphasize modern scientific alternatives to traditional animal testing. Emerging approaches, known as the 3Cs-cell culture, computer simulation, and phase 0 clinical trials-offer promising nonanimal solutions that could accelerate drug development and address ethical concerns, potentially rendering preclinical research more humane and efficient.

State of the Art of Bioengineering Approaches in Beta-Cell Replacement

Purpose of the Review

Despite recent advancements in technology for the treatment of type 1 diabetes (T1D), exogenous insulin delivery through automated devices remains the gold standard for treatment. This review will explore progress made in pancreatic islet bioengineering within the field of beta-cell replacement for T1D treatment.

Recent Findings

First, we will focus on the use of decellularized extracellular matrices (dECM) as a platform for pancreatic organoid development. These matrices preserve microarchitecture and essential biochemical signals for cell differentiation, offering a promising alternative to synthetic matrices. Second, advancements in 3D bioprinting for creating complex organ structures like pancreatic islets will be discussed. This technology allows for increased precision and customization of cellular models, crucial for replicating native pancreatic islet functionality. Finally, this review will explore the use of stem cell-derived organoids to generate insulin-producing islet-like cells. While these organoids face challenges such as functional immaturity and poor vascularization, they represent a significant advancement for disease modeling, drug screening, and autologous islet transplantation.

Summary

These innovative approaches promise to revolutionize T1D treatment by overcoming the limitations of traditional therapies based on human pancreatic islets.

CRISPR-based genetically modified scaffold-free biomaterials for tissue engineering and regenerative medicine

CRISPR-based genetically modified scaffold-free biomaterials, including extracellular vehicles, cell sheets, cell aggregates, organoids and organs, have attracted significant attention in the fields of regenerative medicine and tissue engineering in recent years. With a wide range of applications in gene therapy, modeling disease, tissue regeneration, organ xenotransplantation, modeling organogenesis as well as gene and drug screening, they are at a critical juncture from clinical trials to therapeutic applications. Xenografts have already been tested on non-human primates and humans. However, we have to admit that a series of obstacles still need to be addressed, such as immune response, viral infection, off-target effects, difficulty in mass production, and ethical issues. Therefore, future research should pay more attention to improving their safety, accuracy of gene editing, flexibility of production, and ethical rationality. This review summarizes various types of CRISPR-based genetically modified scaffold-free biomaterials, including their preparation procedures, applications, and possible improvements.

Progress of personalized medicine of cystic fibrosis in the times of efficient CFTR modulators

BACKGROUND

Cystic fibrosis (CF) is a systemic disorder of exocrine glands that is caused by mutations in the CFTR gene.

MAIN BODY

The basic defect in people with CF (pwCF) leads to impaired epithelial transport of chloride and bicarbonate that can be assessed by CFTR biomarkers, i.e. the β-adrenergic sweat rate and sweat chloride concentration (SCC), chloride conductance of the nasal respiratory epithelium (NPD), urine secretion of bicarbonate, intestinal current measurements (ICM) of chloride secretory responses in rectal biopsies and in bioassays of chloride transport in organoids or cell cultures. CFTR modulators are a novel class of drugs that improve defective posttranslational processing, trafficking and function of mutant CFTR. By April 2025, triple combination therapy with the CFTR potentiator ivacaftor (IVA) and the CFTR correctors elexacaftor (ELX) and tezacaftor (TEZ) has been approved in Europe for the treatment of all pwCF who do not carry two minimal function CFTR mutations. Previous phase 3 and post-approval phase 4 studies in pwCF who harbour one or two alleles of the major mutation F508del consistently reported significant improvements of lung function and anthropometry upon initiation of ELX/TEZ/IVA compared to baseline. Normalization of SCC, NPD and ICM correlated with clinical outcomes on the population level, but the restoration of CFTR function was diverse and not predictive for clinical outcome in the individual patient. Theratyping of non-F508del CF genotypes in patient-derived organoids and cell cultures revealed for most cases clinically meaningful increases of CFTR activity upon exposure to ELX/TEZ/IVA. Likewise, every second CF patient with non-F508del genotypes improved in SCC and clinical outcome upon exposure to ELX/TEZ/IVA indicating that triple CFTR modulator therapy is potentially beneficial for all pwCF who do not carry two minimal function CFTR mutations. This group who is not eligible for CFTR modulators may opt for gene addition therapy in the future, as the first-in-human trial with a recombinant lentiviral vector is underway.

FUTURE DIRECTIONS

The upcoming generation of pwCF will probably experience a rather normal life in childhood and adolescence. To classify the upcoming personal signatures of CF disease in the times of efficient modulators, we need more sensitive CFTR biomarkers that address the long-term course of airway and gut microbiome, host defense, epithelial homeostasis and multiorgan metabolism.

iPSC-Derived Liver Organoids as a Tool to Study Medium Chain Acyl-CoA Dehydrogenase Deficiency

Medium chain acyl-CoA dehydrogenase deficiency (MCADD) is an inherited metabolic disease, characterized by biallelic variants in the ACADM gene. Interestingly, even with the same genotype, patients often present with very heterogeneous symptoms, ranging from fully asymptomatic to life-threatening hypoketotic hypoglycemia. The mechanisms underlying this heterogeneity remain unclear. Therefore, there is a need for in vitro models of MCADD that recapitulate the clinical phenotype as a tool to study the pathophysiology of the disease. Fibroblasts of control and symptomatic MCADD patients with the c.985A>G (p.K329E) were reprogrammed into induced pluripotent stem cells (iPSCs). iPSCs were then differentiated into hepatic expandable organoids (EHOs), further matured to Mat-EHOs, and functionally characterized. EHOs and Mat-EHOs performed typical hepatic metabolic functions, such as albumin and urea production. The organoids metabolized fatty acids, as confirmed by acyl-carnitine profiling and high-resolution respirometry. MCAD protein was fully ablated in MCADD organoids, in agreement with the instability of the mutated MCAD protein. MCADD organoids accumulated medium-chain acyl-carnitines, with a strongly elevated C8/C10 ratio, characteristic of the biochemical phenotype of the disease. Notably, C2 and C14 acyl-carnitines were found decreased in MCADD Mat-EHOs. Finally, MCADD organoids exhibited differential expression of genes involved in ω-oxidation, mitochondrial β-oxidation, TCA cycle, and peroxisomal coenzyme A metabolism, particularly upregulation of NUDT7. iPSC-derived organoids of MCADD patients recapitulated the major biochemical phenotype of the disease. Mat-EHOs expressed relevant pathways involved in putative compensatory mechanisms, notably CoA metabolism and the TCA cycle. The upregulation of NUDT7 expression may play a role in preventing excessive accumulation of dicarboxylic acids in MCADD. This patient-specific hepatic organoid system is a promising platform to study the phenotypic heterogeneity between MCADD patients.

Emerging brain organoids: 3D models to decipher, identify and revolutionize brain

Brain organoids are an emerging in vitro 3D brain model that is integrated from pluripotent stem cells. This model mimics the human brain's developmental process and disease-related phenotypes to a certain extent while advancing the development of human brain-based biological intelligence. However, many limitations of brain organoid culture (e.g., lacking a functional vascular system, etc.) prevent in vitro-cultured organoids from truly replicating the human brain in terms of cell type and structure. To improve brain organoids' scalability, efficiency, and stability, this paper discusses important contributions of material biology and microprocessing technology in solving the related limitations of brain organoids and applying the latest imaging technology to make real-time imaging of brain organoids possible. In addition, the related applications of brain organoids, especially the development of organoid intelligence combined with artificial intelligence, are analyzed, which will help accelerate the rational design and guidance of brain organoids.

m6A deficiency impairs hypothalamic neurogenesis of feeding-related neurons in mice and human organoids and leads to adult obesity in mice

N6-methyladenosine (m6A), the most prevalent internal modification on mRNAs, plays important roles in the nervous system. Whether neurogenesis in the hypothalamus, a region critical for controlling appetite, is regulated by m6A signaling, especially in humans, remains unclear. Here, we showed that deletion of m6A writer Mettl14 in the mouse embryonic hypothalamus led to adult obesity, with impaired glucose-insulin homeostasis and increased energy intake. Mechanistically, deletion of Mettl14 leads to hypothalamic arcuate nucleus neurogenesis deficits with reduced generation of feeding-related neurons and dysregulation of neurogenesis-related m6A-tagged transcripts. Deletion of m6A writer Mettl3 or m6A reader Ythdc1 shared similar phenotypes. METTL14 or YTHDC1 knockdown also led to reduced generation of feeding-related neurons in human brain subregion-specific arcuate nucleus organoids. Our studies reveal a conserved role of m6A signaling in arcuate nucleus neurogenesis in mice and human organoids and shed light on the developmental basis of epitranscriptomic regulation of food intake and energy homeostasis.

Vascular network-inspired diffusible scaffolds for engineering functional midbrain organoids

Organoids, 3D organ-like tissue cultures derived from stem cells, show promising potential for developmental biology, drug discovery, and regenerative medicine. However, the function and phenotype of current organoids, especially neural organoids, are still limited by insufficient diffusion of oxygen, nutrients, metabolites, signaling molecules, and drugs. Herein, we present vascular network-inspired diffusible (VID) scaffolds to mimic physiological diffusion physics for generating functional organoids and phenotyping their drug response. Specifically, the VID scaffolds, 3D-printed meshed tubular channel networks, successfully engineer human midbrain organoids almost without necrosis and hypoxia in commonly used well plates. Compared with conventional organoids, these engineered organoids develop more physiologically relevant features and functions, including midbrain-specific identity, oxygen metabolism, neuronal maturation, and network activity. Moreover, these engineered organoids also better recapitulate pharmacological responses, such as neural activity changes to fentanyl exposure, compared with conventional organoids with significant diffusion limits. This platform may provide insights for organoid development and therapeutic innovation.

Establishment and molecular characterisation of patient-derived organoids for primary central nervous system lymphoma

Primary central nervous system lymphoma (PCNSL) exhibits substantial intratumoural and intertumoural heterogeneity, complicating the development of effective treatment methods. Existing in vitro models fail to simulate the cellular and mutational diversity of native tumours and require prolonged generation times. Therefore, we developed a culture method for patient-derived PCNSL organoids (CLOs) and evaluated the organoids through extensive molecular characterisation, histopathological analysis, single-nucleus RNA sequencing, bulk RNA sequencing and whole-exome sequencing. These CLOs accurately mimicked the histological attributes, gene expression landscapes and mutational profiles of their original tumours. Single-nucleus RNA sequencing also revealed that CLOs maintained cell-type heterogeneity and the molecular signatures of their original tumours. CLOs were generated within 2 weeks, demonstrating rapid development and reliability. Therapeutic profiling was performed on three selected CLOs treated with four standard drugs. The CLOs exhibited specific sensitivity to methotrexate, and resistance to dexamethasone, ibrutinib and rituximab, suggesting that CLOs may be valuable tools for reflecting drug sensitivities. Taken together, these results emphasise that CLOs effectively emulate the key characteristics of PCNSL, increasing the understanding of the genetic landscape of this complex disease. CLOs provide a rapid and reliable platform for exploring individualised treatment strategies, potentially accelerating the transition of research findings to clinical practice.

Towards advanced regenerative therapeutics to tackle cardio-cerebrovascular diseases

The development of vascularized organoids as novel modelling tools of the human cardio-cerebrovascular system for preclinical research has become an essential platform for studying human vascularized tissues/organs for development of personalized therapeutics during recent decades. Organ-on-chip technology is promising for investigating physiological in vitro responses in drug screening development and advanced disease models. Vascularized tissue/organ-on-a-chip benefits every step of drug discovery pipeline as a screening tool with close human genome relevance to investigate human systems biology. Simultaneously, cardio-cerebrovascular-on-chip-integrated microfluidic system serves as an alternative to preclinical animal research for studying (patho-)physiological processes of human blood vessels during embryonic development and cardio-cerebrovascular disease. Integrated with next-generation techniques, such as three-dimensional bioprinting of both cells and matrix, may enable vascularized organoid-on-chip-based novel drug development as personalized therapeutics.

Establishment of a patient-derived 3D in vitro meningioma model in xeno-free hydrogel for clinical applications

BACKGROUND

Meningiomas exhibit a complex biology that, despite notable successes in preclinical studies, contributes to the failures of pharmaceutical clinical trials. Animal models using patient tumor cells closely mimic in vivo conditions but are labor-intensive, costly, and unsuitable for high-throughput pharmaceutical testing. In comparison, monolayer cell models (two-dimensional, 2D) are cost-efficient but lack primary tumor cell-cell interactions, potentially overestimating treatment effects. Three-dimensional (3D) models offer an alternative through more precise mimicking of tumor morphology and physiology than 2D models and are less costly than in vivo methods. Here, we aimed to establish a 3D cell model in a solid xeno-free medium using patient-derived tumors, thus creating a bench-to-clinic pathway for personalized pharmaceutical testing.

METHODS

Four WHO grade 1 and one WHO grade 2 (third-passage, fresh) and 12 WHO grade 1 patient-derived meningioma cells (sixth-passage, frozen) and the malignant IOMM-Lee cell line were used to establish 2D and 3D models. The 3D model was developed using a solid xeno-free medium. After 3 months for the primary tumor and 13 days for the IOMM-Lee cell line, the 3D models were extracted and assessed using histology, immunohistochemistry, and epigenetic analyses (EPICv2 array) on five pairs to evaluate their structural fidelity, cellular composition, and epigenetic landscape compared to the original tumor.

RESULTS

None of the frozen samples successfully generated 3D models. Models from fresh meningioma samples were more immunohistochemically similar to the primary tumors compared to 2D models, particularly regarding proliferation. 3D models displayed loss of fibrous tissue. All 3D models had similar copy number variation profiles, visually. Genome-wide DNA methylation level patterns were similar between pairs of 3D models and primary tumors. Correlation plots between CpG methylation levels showed high congruency between primary meningiomas and their corresponding 3D models for all samples (R > 0.95).

CONCLUSIONS

Our patient-derived 3D meningioma models closely mimicked primary tumors in terms of cell morphology, immunohistochemical markers and genome-wide DNA methylation patterns, providing a cost-effective and accessible alternative to in vivo models. This approach has the potential to facilitate personalized treatment strategies for patients requiring additional therapy beyond surgery.

Advanced organoid models for targeting Kras-driven lung adenocarcinoma in drug discovery and combination therapy

BACKGROUND

Lung cancer remains one of the most challenging diseases to treat due to its heterogeneity. Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) mutations are genetic drivers in numerous cancer types including lung adenocarcinoma (LUAD). Despite recent advances in KRAS-targeted therapies, treatment resistance and limited therapeutic options necessitate advanced preclinical models, such as organoids, to identify personalized cancer therapies by screening novel therapeutic strategies and synergistic drug combinations.

RESULTS

We established LUAD in genetically engineered mouse (GEM) models of KrasG12V & Trp53 Δex2-10 (KP) and KP with Ctnnb1Δex3 mutation (KPC). Tumor-derived organoids from these models recapitulated the genomic landscape and histopathological characteristics of their parental tumors. The organoids displayed tumorigenic potential when implanted in immunocompromised mice, forming tumors in contrast to unlike healthy lung-derived organoids. Drug screening identified effective kinase inhibitors and DNA methyltransferase (DNMT) inhibitors against the organoids. Notably, the combination of these drugs exhibited the highest synergy in KPC organoids.

CONCLUSION

We successfully developed LUAD organoids harboring Kras mutations and identified multiple potential therapeutic agents targeting these cells. Furthermore, we demonstrated the effectiveness of a DNMT inhibitor-based combination therapy, presenting a promising strategy for this challenging lung cancer subtype.

Chimeric brain models: Unlocking insights into human neural development, aging, diseases, and cell therapies

Human-rodent chimeric brain models serve as a unique platform for investigating the pathophysiology of human cells within a living brain environment. These models are established by transplanting human tissue- or human pluripotent stem cell (hPSC)-derived macroglial, microglial, or neuronal lineage cells, as well as cerebral organoids, into the brains of host animals. This approach has opened new avenues for exploring human brain development, disease mechanisms, and regenerative processes. Here, we highlight recent advancements in using chimeric models to study human neural development, aging, and disease. Additionally, we explore the potential applications of these models for studying human glial cell-replacement therapies, studying in vivo human glial-to-neuron reprogramming, and harnessing single-cell omics and advanced functional assays to uncover detailed insights into human neurobiology. Finally, we discuss strategies to enhance the precision and translational relevance of these models, expanding their impact in stem cell and neuroscience research.

Developments in gastrointestinal organoid cultures to recapitulate tissue environments

Culture platforms that closely mimic the spatial architecture, cellular diversity, and extracellular matrix composition of native tissues can serve as invaluable tools for a range of scientific discovery and biomedical applications. Organoids have emerged as a promising alternative to both traditional 2D cell culture and animal models, offering a physiologically relevant 3D culture system for studying human cell biology. Organoids provide a manipulable platform to investigate organ development and function as well as to model patient-specific phenotypes. This mini review examines various methods used for culturing organoids to model normal and disease conditions in gastrointestinal tissues. We focus on how the matrix composition and media formulations can impact cell signaling, altering the baseline cellular phenotypes as well as response to perturbations. We discuss future directions for optimizing organoid culture conditions to improve basic and translational potential.

Current Development of iPSC-Based Modeling in Neurodegenerative Diseases

Over the past two decades, significant advancements have been made in the induced pluripotent stem cell (iPSC) technology. These developments have enabled the broader application of iPSCs in neuroscience, improved our understanding of disease pathogenesis, and advanced the investigation of therapeutic targets and methods. Specifically, optimizations in reprogramming protocols, coupled with improved neuronal differentiation and maturation techniques, have greatly facilitated the generation of iPSC-derived neural cells. The integration of the cerebral organoid technology and CRISPR/Cas9 genome editing has further propelled the application of iPSCs in neurodegenerative diseases to a new stage. Patient-derived or CRISPR-edited cerebral neurons and organoids now serve as ideal disease models, contributing to our understanding of disease pathophysiology and identifying novel therapeutic targets and candidates. In this review, we examine the development of iPSC-based models in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease.

Developing a feasible fast-track testing method for developmental neurotoxicity studies: alternative model for risk assessment of micro- and nanoplastics

Micro- and nanoplastics (MNPs) are widespread environmental pollutants that pose significant health risks. They originate from industrial processes, consumer products, and environmental degradation, inducing oxidative stress through cellular dysfunctions such as membrane interaction, internalization, mitochondrial damage, inflammation, metal ion leaching, and impaired antioxidant defense. Despite increasing evidence of their toxicity-particularly developmental neurotoxicity (DNT) and mitochondrial impairment-our understanding remains limited due to the high costs of animal studies, which reduce the overall size of experimental data. This underscores the urgent need for alternative test methods that are cost-effective, rapid, and translational. This review examines new approach methodologies (NAMs) for DNT assessment, addressing the ethical, financial, and translational limitations of animal models. NAMs integrate three complementary non-animal models that enhance conventional testing. First, zebrafish models provide organismal insights into behavioral and neurodevelopmental outcomes at minimal cost. Second, neuronal organoids replicate human-specific neurodevelopmental processes in a 3D system, offering mechanistic insights. Lastly, human cell lines enable high-throughput screening, integrating findings from zebrafish and organoid studies. Establishing a new paradigm for DNT testing is crucial for faster and more efficient toxicity and risk assessments, ultimately protecting public health. Standardizing and gaining regulatory acceptance for NAMs will improve predictive accuracy and broaden their application in environmental toxicology. Advancing these methodologies is essential to addressing the risks of MNP exposure while promoting ethical and sustainable research practices.

AI-Assisted Label-Free Monitoring Bone Mineral Metabolism on Demineralized Bone Paper

Effective drug development for bone-related diseases, such as osteoporosis and metastasis, is hindered by the lack of physiologically relevant in vitro models. Traditional platforms, including standard tissue culture plastic, fail to replicate the structural and functional complexity of the natural bone extracellular matrix. Recently, osteoid-mimicking demineralized bone paper (DBP), which preserves the intrinsic collagen structure of mature bone and exhibits semitransparency, has demonstrated the ability to reproduce in-vivo-relevant osteogenic processes and mineral metabolism. Here, we present a label-free, longitudinal, and quantitative monitoring of mineralized collagen formation by osteoblasts and subsequent osteoclast-driven mineral resorption on DBP using brightfield microscopy. A Segment.ai machine learning algorithm is applied for time-lapse bright-field image analysis, enabling identification of osteoclast resorption areas and automated quantification of large image datasets over a three-week culture period. This work highlights the potential of DBP as a transformative platform for bone-targeting drug screening and osteoporosis research.

Improved Differentiation Towards Insulin Producing Beta-Cells Derived from Healthy Canine Pancreatic Ductal Organoids

BACKGROUND

Diabetes mellitus (DM) is a common potentially life-threatening endocrine disorder in pets and humans. Since only symptomatic treatment is available, a more sustainable treatment is urgently needed.

OBJECTIVE

The aim of this study is to establish functional differentiated canine pancreatic β-cells that release insulin upon glucose stimulus.

METHODS

Pancreatic tissue was obtained from surplus material of healthy dogs (n = 4), euthanized for non-pancreatic related research. Ductal cells were isolated and expanded in dog pancreas expansion media (dpEM) and differentiated and maturated in five sequentially added pancreas differentiation media (PDMs). Gene expression was analyzed by reversed transcriptase qPCR (RT-qPCR), and insulin release was analyzed with a canine-specific ELISA.

RESULTS

Canine pancreatic ductal cells (LGR5 and SOX9 expression) were differentiated into β-cells expressing key β-cell-related genes: Pancreatic and duodenal homeobox 1 (PDX1), NK6 Homeobox 1 (NKX6.1), Glucose Transporter Type 2 (GLUT2), Proprotein convertase subtilisin/kexin type 1 (PCSK1), and low levels of insulin. Neither Glucagon (α-cells) nor LGR5 and SOX9 were expressed, and somatostatin was expressed at low levels. The differentiated cells released insulin upon glucose stimulation.

CONCLUSION AND IMPLICATIONS

The step-by-step differentiation protocol, mimicking pancreatic organogenesis, resulted in β-cells secreting insulin levels suitable for β-cell disease modelling. It remains to be seen if stem cells from diseased animals behave similarly.

Three-Dimensional-Bioprinted Embedded-Based Cerebral Organoids: An Alternative Approach for Mini-Brain In Vitro Modeling Beyond Conventional Generation Methods

Cerebral organoids (cORGs) obtained from induced pluripotent stem cells (iPSCs) have become significant instruments for investigating human neurophysiology, with the possibility of simulating diseases and enhancing drug discovery. The current approaches require a strict process of manual inclusion in animal-derived matrix Matrigel® and are challenged by unpredictability, operators' skill and expertise, elevated costs, and restricted scalability, impeding their extensive applicability and translational potential. In this study, we present a novel method to generate brain organoids that address these limitations. Our approach does not require a manual, operator-dependent embedding. Instead, it employs a chemically defined hydrogel in which the Matrigel® is diluted in a solution enriched with sodium alginate (SA) and sodium carboxymethylcellulose (CMC) and used as a bioink to print neural embryoid bodies (nEBs). Immunohistochemical, immunofluorescence, and gene expression analyses confirmed that SA-CMC-Matrigel® hydrogel can sustain the generation of iPSC-derived cortical cORGs as the conventional Matrigel®-based approach does. By day 40 of differentiation, hydrogel-based 3D-bioprinted cORGs showed heterogeneous and consistent masses, with a cytoarchitecture resembling an early-stage developmental fetal brain composed of neural progenitor cells PAX6+/Ki67+ organized into tubular structures, and densely packed cell somas with extensive neurites SYP+, suggestive of cortical tissue-like neuronal layer formation.

Development of Sheep Duodenum Intestinal Organoids and Implementation of High-Throughput Screening Platform for Veterinary Applications

New therapeutic molecules for farm animals are needed to address worldwide problems in the food industry, like the rise of resistance among ruminant parasites and pathogenic microbes. Since in vivo testing would involve an excessive number of animals, with consequent ethical and economic issues, the generation of sheep intestinal organoids represents a promising close-to-reality in vitro model for veterinary drug development; however, the characterization and application of such organoids remain limited. In this study, ovine intestinal organoids were generated from adult LGR5+ stem cells from the intestinal crypts of freshly slaughtered lambs, and developed in an in vitro culture system. Morphological analysis via brightfield microscopy and immunocytochemical staining revealed a pseudostratified epithelium with multiple cell types, and distinct apical-basal polarity, while RNA sequencing validated the preservation of the physiological characteristics of the original organ. The development and characterization of a robust and reproducible protocol for culturing sheep duodenum intestinal organoids in a high-throughput screening (HTS) compatible format demonstrated reliability in HTS applications, with Z'-factor tests indicating robust assay performance. Dose-response studies using pre-identified compounds showed comparable pharmacodynamic profiles between mouse and sheep organoids. These findings establish sheep intestinal organoids as an innovative tool for veterinary pharmacology and toxicology, offering a cost-effective and sustainable platform to address challenges such as drug resistance and improve livestock health.

Cell therapies and liver organogenesis technologies: Promising strategies for end-stage liver disease

End-stage liver disease represents a critical hepatic condition with high mortality, for which liver transplantation remains the only effective treatment. However, the scarcity of suitable donors results in numerous patients dying while awaiting transplantation. Novel strategies, including cell therapies and technologies mimicking liver organogenesis, offer promising alternatives for treating end-stage liver disease by potentially providing new sources of liver grafts. Recently, significant progress has been made in this field, including stem cell transplantation, hepatocyte transplantation, in vitro liver tissue generation, and liver replacement technologies. Several clinical studies have demonstrated that stem cell transplantation and hepatocyte transplantation can prolong patient survival and serve as a bridge to liver transplantation. Furthermore, in vitro liver tissue generation technologies, such as liver organoids and three-dimensional bioprinting, can generate hepatic tissues with sophisticated structures and functions, making them promising transplantation materials. Notably, liver replacement technologies hold considerable potential for producing biologically functional and transplantable liver grafts. In this review, we discuss the fundamental principles and recent advancements in cell therapies and liver organogenesis technologies while also addressing the challenges and future prospects in this rapidly evolving field.

Cerebral organoid research for pediatric patients with neurological disorders

Cerebral organoids derived from human induced pluripotent stem cells offer a groundbreaking foundation for the analysis of pediatric neurological diseases. Unlike organoids from other somatic systems, cerebral organoids present unique challenges, such as the high sensitivity of neuronal cells to environmental conditions and the complexity of replicating brain-specific architectures. Cerebral organoids replicate the human brain development and pathology, enabling research on conditions such as microcephaly, Rett syndrome, autism spectrum disorders, and brain tumors. This review explores the utility of cerebral organoids for modeling diseases and testing therapeutic interventions. Despite current limitations such as variability and lack of vascularization, recent technological advancements have improved the reliability and application of such interventions. Cerebral organoids provide valuable insight into the mechanisms underlying complex neural disorders and hold promise as novel treatment strategies for pediatric neurological diseases.

Harnessing the potential of tissue engineering to target male infertility: Insights into testicular regeneration

Male infertility is among one of the most challenging health concerns in the world. Traditional therapeutic interventions such as semen and testicular tissue cryopreservation aim to restore or preserve male fertility. However, these methods are subject to limitations that impact their efficacy and are infeasible in cases such as patients who cannot produce mature sperm due to genetic or pathological disorders. Moreover, with the number of cases of prepubertal boys who must undergo gonadotoxic treatments rising, alternatives have been sought for fertility preservation to enhance reproductive rates in vitro and in vivo. Tissue engineering is a promising area that can address aspects that current therapies may not fully encompass through the creation of bioartificial testicular structures or 3D culture systems that allow the establishment of the essential conditions for sperm production. This study aims to first give a brief overview of stem cell therapy in treating male infertility and then go more in-depth regarding the novel methods and procedures based on tissue engineering that have the potential to offer new treatments for infertility caused by testicular disorders and defects.

Organoids of Musculoskeletal System for Disease Modeling, Drug Screening, and Regeneration

Musculoskeletal diseases have emerged as the leading cause of disability worldwide, with their prevalence increasing annually. In light of this escalating health challenge, organoids, an emerging technology in tissue engineering, offer promising solutions for disease modeling, drug screening, regeneration, and repair processes. The successful development of musculoskeletal organoids represents a significant breakthrough, providing a novel platform for studying musculoskeletal diseases and facilitating the discovery of new treatments. Moreover, organoids serve as valuable complements to traditional 2D culture methods and animal models, offering rich insights into musculoskeletal biology. This review provides an overview of organoid technology, outlining the construction processes of various musculoskeletal organoids and highlighting their similarities and differences. Furthermore, the challenges associated with organoid technology in musculoskeletal systems are discussed and insights into future perspectives are offered.

Development and Applications of Organoids in Gynecological Diseases

Organoids are rapidly self-organizing 3D in vitro cultures derived from pluripotent stem cells (PSCs) or adult stem cells (ASCs) that possess disease-like characteristics with high success rates. Due to their ability to retain tissue structure, biological phenotypes, and genetic information, they have been utilized as a novel in vitro model for disease research. In recent years, scientists have established self-organizing 3D organoids for human endometrium, fallopian tubes, ovaries, and cervix by culturing stem cells with cytokines in 3D scaffolds. The integration of organoids with animal models, organ-on-a-chip systems, and 3D printing technologies offers a novel preclinical model for exploring disease mechanisms and developing treatments. This review elaborate on the recent research progress of stem cells-formed organoids in the field of gynecology from the aspects of constructing gynecological disease organoids, drug screening and new drug development, simulation modeling, allogeneic transplantation, regenerative medicine and personalized treatment."

Asparagine prevents intestinal stem cell aging via the autophagy-lysosomal pathway

The age-associated decline in intestinal stem cell (ISC) function is a key factor in intestinal aging in organisms, resulting in impaired intestinal function and increased susceptibility to age-related diseases. Consequently, it is imperative to develop effective therapeutic strategies to prevent ISC aging and functional decline. In this study, we utilized an aging Drosophila model screening of amino acids and found that asparagine (Asn), a nonessential amino acid in vivo, exhibits its profound anti-aging properties on ISCs. Asn inhibits the hyperproliferation of aging ISCs in Drosophila, maintains intestinal homeostasis, and extends the lifespan of aging flies. Complementarily, Asn promotes the growth and branching of elderly murine intestinal organoids, indicating its anti-aging capacity to enhance ISC function. Mechanistic analyses have revealed that Asn exerts its effects via the activation of the autophagic signaling pathway. In summary, this study has preliminarily explored the potential supportive role of Asn in ameliorating intestinal aging, providing a foundation for further research into therapeutic interventions targeting age-related intestinal dysfunction.

Integration of Organoids With CRISPR Screens: A Narrative Review

Organoids represent a significant advancement in disease modeling, demonstrated by their capacity to mimic the physiological/pathological structure and functional characteristics of the native tissue. Recently CRISPR/Cas9 technology has emerged as a powerful tool in combination with organoids for the development of novel therapies in preclinical settings. This review explores the current literature on applications of pooled CRISPR screening in organoids and the emerging role of these models in understanding cancer. We highlight the evolution of genome-wide CRISPR gRNA library screens in organoids, noting their increasing adoption in the field over the past decade. Noteworthy studies utilizing these screens to investigate oncogenic vulnerabilities and developmental pathways in various organoid systems are discussed. Despite the promise organoids hold, challenges such as standardization, reproducibility, and the complexity of data interpretation remain. The review also addresses the ideas of assessing tumor organoids (tumoroids) against established cancer hallmarks and the potential of studying intercellular cooperation within these models. Ultimately, we propose that organoids, particularly when personalized for patient-specific applications, could revolutionize drug screening and therapeutic approaches, minimizing the reliance on traditional animal models and enhancing the precision of clinical interventions.

Innovative Therapeutic Approach Targeting Colon Cancer Stem Cells: Transitional Cold Atmospheric Plasma

Transitional cold atmospheric plasma (TCAP) represents a novel technique for generating plasma remotely from a primary source. It consists of a partially nonthermal ionized gas mixture containing charged and neutral particles, photons, and free radicals. In recent years, TCAP has attracted considerable attention in biomedical applications. In order to evaluate colon cancer stem cells' (CCSCs) proliferation, apoptotic induction, inflammatory response, and survival, TCAP was utilized both directly and indirectly in this study. Using argon and helium gases, TCAP was continuously delivered in two stages during the experiment. For direct state, TCAP was irradiated onto CCSCs for 3 and 5 min. In the indirect technique, Matrigel was treated with TCAP for 5 min before the introduction of cells. In vitro assays demonstrated that TCAP exposure significantly reduced the viability of CCSCs; helium gas and direct application had greater impacts than argon. Numerous investigations confirmed the induction of apoptosis, showing that the treated groups had more apoptotic cells and altered cellular structures than controls (****p < 0.0001). A substantial increase in the Bax/Bcl-2 ratio was found by analyzing the expression of the Bax and Bcl-2 genes, indicating increased susceptibility to apoptosis (*p = 0.0177 and ***p = 0.0004). The higher efficacy of the direct helium mode was further highlighted by inflammatory marker analysis, which showed a significant reduction in interleukin-6 and interleukin-8 expression in cells directly treated with TCAP-helium compared to TCAP-argon (**p = 0.0015 and ***p = 0.0007). Lastly, the proliferation test, which relies on K i-67 expression, demonstrated a noteworthy decline in all TCAP-treated groups, with the direct helium group exhibiting the most robust impact (**p = 0.0014). Overall, the findings highlight the potential of TCAP, particularly with helium, as a promising approach for selectively targeting CCSCs and providing insights into its therapeutic mechanisms for cancer treatment. TCAP, therefore, emerges as a unique therapeutic strategy with potential applications in cancer stem cell-targeted therapies.

Physiological Modeling of the Vascularized Human Lung Organoid

Human lung organoids (hLOs) derived from induced pluripotent stem cells (iPSCs) are of great interest, as they inform lung development, such as differentiation of lung epithelial subtypes in the distal alveolar unit. An unaddressed question is whether introducing endothelial cells (ECs) and vascularization provides a better representation of hLOs. Here we describe a method in which vessels become integrated with hLOs. hLOs were generated by combining human iPSC-derived lung progenitor cells (LPs) with ECs at varying LP:EC ratios. At the optimal combination of both cells, we observed vessel infiltration of hLOs compared to without ECs. Red blood cells were seen in hLOs implanted into kidney capsules of NOD/SCID mice. Both human and mouse ECs conjoined to form chimeric vessels in hLOs. The vascularized hLOs showed alveolar type II epithelial (ATII) cells and ATI cells, although there was no difference in 1:1 ATII/ATI ratio. We observed primitive airway sacs with alveolar epithelial cells lining the lumen of vascularized hLOs. Electron microscopy revealed surfactant production in ATII cells of vascularized hLOs in contrast to absence of vessels. The vascularized hLOs also mounted a robust inflammatory response characterized by influx of mouse neutrophils after challenging mice with LPS. Thus, interactions of ECs with LPs generated vascularized hLOs that induced ATII and ATI differentiation, although not reaching to the ratio of 1:9 seen in mature human lungs. hLOs also showed the LPS induced inflammatory response upon transplantation into recipient mice. Our results show the potential of vascularized hLOs for studying human lung development and inflammatory lung injury.

Models to evaluate the pulmonary toxicity of desert dust and what we have learned from them so far: a mini-review

Millions of people worldwide are exposed to aerosolised desert dust and are at risk of the adverse respiratory health effects it causes. This mini-review gives an overview of the study types that can be used to assess the respiratory toxicity of desert dust and the insights gained from these studies. We highlight the main advantages and disadvantages of epidemiological, in vivo, and in vitro studies. Regarding in vitro studies, we discuss models of increasing complexity, i.e., traditional submerged cell cultures, air-liquid interface cultures, organ-on-a-chip models, organoids, and precision-cut lung slices. Epidemiological studies have shown increased short-term mortality and exacerbated acute and chronic respiratory diseases after desert dust events. In contrast, a connection to the onset of chronic diseases is more difficult to prove. In vivo and in vitro studies have particularly addressed the cellular and molecular effects of desert dust. It was found that desert dust activates immune cells and induces the expression of inflammatory cytokines and oxidative stress markers. The specific effects and their extent vary between dust samples from different sources. The investigation of the role of the composition is still immature and needs further effort including more extensive screenings. The advancement of easy-to-handle and realistic pulmonary in vitro models is required to automate screenings, support mechanistic insights, and enable the assessment of long-term exposure scenarios. In agreement with striving to develop new approach methodologies, such advancements can reduce and replace animal experiments and strongly benefit the translatability of research outcomes to human health protection.

eIF3f promotes tumour malignancy by remodelling fatty acid biosynthesis in hepatocellular carcinoma

BACKGROUND & AIMS

Fatty acid metabolism is closely associated with hepatocellular carcinoma (HCC). Elucidating the molecules that influence fatty acid metabolism in HCC is important for developing precision therapies. However, uncovering the precise molecular mechanisms underlying changes in fatty acid metabolism in tumour cells is challenging. In this study, we aimed to determine the characteristics of fatty acid metabolism in HCC.

METHODS

We employed organoid models, single-cell RNA sequencing, and spatial transcriptomics to identify key genes involved in tumour fatty acid metabolism. Metabolomics, proteomics, metabolic flux analysis, and transmission electron microscopy were utilized to evaluate this metabolic process. Tumour malignancy was characterized using multi-species models. Changes in the immune microenvironment were analysed by time-of-flight mass cytometry and multiplexed immunohistochemistry. Gene knockdown targeting the liver was achieved using lipid nanoparticles.

RESULTS

Eukaryotic translation initiation factor 3 subunit f (eIF3f) is upregulated in HCC tissues and is associated with poor prognosis. eIF3f directly interacted with and stabilised long chain acyl CoA synthetase 4 (ACSL4) through K48-linked deubiquitination, promoting fatty acid biosynthesis and malignancy. The increased fatty acid levels in the tumour microenvironment indirectly reduced CD8+ T-cell infiltration. In addition, phosphorylated eIF3f enhanced the interaction between eIF3f and ACSL4.

CONCLUSIONS

Targeting the eIF3f-ACSL4-fatty acid biosynthesis axis could decelerate the progression of HCC and enhance anti-programmed cell death-1 efficacy, implicating eIF3f as a potential target for precision therapy in HCC.

IMPACT AND IMPLICATIONS

Fatty acid metabolism is closely associated with hepatocellular carcinoma (HCC), yet the underlying mechanisms involved remain unclear. Here, we found that eIF3f is upregulated in HCC and is associated with poor prognosis. eIF3f interacts with and stabilizes ACSL4, thereby promoting fatty acid biosynthesis. Additionally, increased fatty acid levels reduce CD8+ T-cell infiltration and activation. These findings are of significant importance for clinicians and researchers in the field of HCC treatment, as eIF3f inhibition combined with anti-PD-1 therapy significantly improved anti-tumour efficacy in a mouse model and could offer therapeutic benefits for patients. These findings have practical implications, as eIF3f could serve as a novel therapeutic target in HCC. However, further clinical studies are needed to confirm the efficacy of eIF3f targeting in human patients.

A New Perspective on Precision Medicine: The Power of Digital Organoids

Precision medicine is a personalized medical model based on the individual's genome, phenotype, and lifestyle that provides tailored treatment plans for patients. In this context, tumor organoids, a 3-dimensional preclinical model based on patient-derived tumor cell self-organization, combined with digital analysis methods, such as high-throughput sequencing and image processing technology, can be used to analyze the genome, transcriptome, and cellular heterogeneity of tumors, so as to accurately track and assess the growth process, genetic characteristics, and drug responsiveness of tumor organoids, thereby facilitating the implementation of precision medicine. This interdisciplinary approach is expected to promote the innovation of cancer diagnosis and enhance personalized treatment. In this review, the characteristics and culture methods of tumor organoids are summarized, and the application of multi-omics, such as bioinformatics and artificial intelligence, and the digital methods of organoids in precision medicine research are discussed. Finally, this review explores the main causes and potential solutions for the bottleneck in the clinical translation of digital tumor organoids, proposes the prospects of multidisciplinary cooperation and clinical transformation to narrow the gap between laboratory and clinical settings, and provides references for research and development in this field.

Bioengineering tools for next-generation neural organoids

Human stem cell-derived neural organoids were recently introduced as powerful in vitro 3D experimental model systems that innately undergo critical steps of organogenesis in culture and exhibit molecular, cellular, and structural features similar to the fetal human nervous system. These organoids have yielded new insights into human neurodevelopment and associated disorders. However, neural organoids have some crucial limitations that arise from the loosely controlled conditions for their development, an inability to maintain their spatial orientation in culture and a lack of technologies for taking long-term measurements on their morphology and electrical activity. Here, we review recent progress in using bioengineering methods to improve neural organoid formation and analysis by leveraging microfabrication, biomaterials, 3D printing, and flexible electrodes. We discuss how the applications of each technique can help to address critical limitations with standard neural organoid models. We conclude with a perspective on future applications of bioengineered next-generation neural organoids.

A microfluidic platform for anterior-posterior human endoderm patterning via countervailing morphogen gradients in vitro

Understanding how morphogen gradients spatially pattern tissues is a fundamental question in developmental biology but can be difficult to directly address using conventional approaches. Here, we expose hPSC-derived endoderm cells to countervailing gradients of anteriorizing and posteriorizing signals using a widely available microfluidic device. This approach yielded spatially patterned cultures comprising anterior foregut (precursor to the thyroid, esophagus, and lungs) and mid/hindgut (precursor to the intestines) cells, whose identities were confirmed using single-cell RNA sequencing (scRNA-seq). By exposing stem cells to externally applied signaling gradients, this widely accessible microfluidic platform should accelerate the production of spatially patterned tissues, complementing internally self-organizing organoids. Applying artificial morphogen gradients in vitro may also illuminate how developing tissues interpret signaling gradients in systems that are not readily accessible for in vivo studies.

Decoding Liver Fibrosis: How Omics Technologies and Innovative Modeling Can Guide Precision Medicine

The burden of chronic liver disease (CLD) is dramatically increasing. It is estimated that 20-30% of the population worldwide is affected by CLD. Hepatic fibrosis is a symptom common to all CLDs. Although it affects liver functional activities, it is a reversible stage if diagnosed at an early stage, but no resolutive therapy to contrast liver fibrosis is currently available. Therefore, efforts are needed to study the molecular insights of the disease. Emerging cutting-edge fields in cellular and molecular biology are introducing innovative strategies. Spatial and single-cell resolution approaches are paving the way for a more detailed understanding of the mechanisms underlying liver fibrosis. Cellular models have been generated to recapitulate the in-a-dish pathophysiology of liver fibrosis, yielding remarkable results that not only uncover the underlying molecular mechanisms but also serve as patient-specific avatars for precision medicine. Induced pluripotent stem cells (iPSC) and organoids are incredible tools to reshape the modeling of liver diseases, describe their architecture, and study the residents of hepatic tissue and their heterogeneous population. The present work aims to give an overview of innovative omics technologies revolutionizing liver fibrosis research and the current tools to model this disease.

Hydrogen Peroxide-Releasing Hydrogel-Mediated Cellular Senescence Model for Aging Research

Cellular senescence, a process that induces irreversible cell cycle arrest in response to diverse stressors, is a primary contributor to aging and age-related diseases. Currently, exposure to hydrogen peroxide is a widely used technique for establishing in vitro cellular senescence models; however, this traditional method is inconsistent, laborious, and ineffective in vivo. To overcome these limitations, we have developed a hydrogen peroxide-releasing hydrogel that can readily and controllably induce senescence in conventional 2-dimensional cell cultures as well as advanced 3-dimensional microphysiological systems. Notably, we have established 2 platforms using our hydrogen peroxide-releasing hydrogel for investigating senolytics, which is a promising innovation in anti-geronic therapy. Conclusively, our advanced model presents a highly promising tool that offers a simple, versatile, convenient, effective, and highly adaptable technique for inducing cellular senescence. This innovation not only lays a crucial foundation for future research on aging but also markedly accelerates the development of novel therapeutic strategies targeting age-related diseases.

Human Retinal Organoid Model of Ocular Toxoplasmosis

The health burden of ocular toxoplasmosis is substantial, and there is an unmet need for safe and curative anti-microbial drugs. One major barrier to research on new therapeutics is the lack of in vitro human-based models beyond two-dimensional cultured cells and tissue explants. We aimed to address this research gap by establishing a human retinal organoid model of ocular toxoplasmosis. Retinal organoids, generated from human induced pluripotent stem cells and grown to two stages of organization, were incubated with a suspension of live or heat-killed GT-1 strain T. gondii tachyzoites, or medium without tachyzoites. Both developing (1 month post-isolation) and matured (6 months post-isolation) organoids were susceptible to infection. Spread of live parasites from the margin to the entire organoid over 1 week was indicated by immunolabelling for T. gondii surface antigen 1. This progression was accompanied by changes in the levels of selected tachyzoite transcripts-SAG1, GRA6, and ROP16-and human cytokine transcripts-CCL2, CXCL8, CXCL10, and IL6-in infected versus control conditions. Our human retinal organoid model of ocular toxoplasmosis offers the opportunity for many future lines of study, including tachyzoite interactions with retinal cell populations and leukocyte subsets, parasite stage progression, and disease processes of different T. gondii strains, as well as drug testing.

A skin organoid-based infection platform identifies an inhibitor specific for HFMD

The EV-A71 poses a serious threat to the health and lives of children. The EV-A71 can be transmitted by direct and indirect skin contact. Therefore, there is an urgent need to create novel skin models using human-derived cells to study the biology and pathogenesis of the virus and facilitate drug screening. Here, we use human induced pluripotent stem cells-derived skin organoids (hiPSC-SOs) as a model for EV-A71 infection and find that multiple cell types within the skin organoids, including epidermal cells, hair follicle cells, fibroblasts, and nerve cells, express EV-A71 receptors and are susceptible to EV-A71 infection. We elucidate the specific response of different cell types to EV-A71 and reveal that EV-A71 infection can degrade extracellular collagen and affect fibroblasts. We find that EV-A71 can mediate epidermal cell damage through autophagy and Integrin/Hippo-YAP/TAZ signaling pathways, thereby promoting hyperproliferation of progenitor cells. Based on this finding, we identify an autophagy-associated protein as a drug target of EV-A71 and discover an EV-A71 replication inhibitor. Altogether, these data suggest that hiPSC-SOs can be used as an infectious disease model to study skin infectious diseases, providing a valuable resource for drug screening to identify candidate virus therapeutics.

Organoids-on-a-chip: microfluidic technology enables culture of organoids with enhanced tissue function and potential for disease modeling

Organoids are stem-cell derived tissue structures mimicking specific structural and functional characteristics of human organs. Despite significant advancements in the field over the last decade, challenges like limited long-term functional culture and lack of maturation are hampering the implementation of organoids in biomedical research. Culture of organoids in microfluidic chips is being used to tackle these challenges through dynamic and precise control over the organoid microenvironment. This review highlights the significant breakthroughs that have been made in the innovative field of "organoids-on-chip," demonstrating how these have contributed to advancing organoid models. We focus on the incorporation of organoids representative for various tissues into chips and discuss the latest findings in multi-organoids-on-chip approaches. Additionally, we examine current limitations and challenges of the field towards the development of reproducible organoids-on-chip systems. Finally, we discuss the potential of organoids-on-chip technology for both in vitro and in vivo applications.

Origin and cell type specificity of mitochondrial DNA mutations in C9ORF72 ALS-FTLD human brain organoids

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are primarily genetic in ~20% of patients. Mutations in C9ORF72 are the most frequent cause, but it is not understood why there is notable regional pathology. An increased burden of mitochondrial DNA (mtDNA) mutations in ALS-FTLD brains implicates mitochondrial mechanisms; however, it remains unclear how and when these mutations arise. To address this, we generated cerebral organoids derived from human-induced pluripotent stem cells (hiPSCs) of patients with ALS-FTLD harboring the C9ORF72 hexanucleotide repeat expansion alongside CRISPR-corrected isogenic and healthy controls. Here, we show a higher mtDNA single-nucleotide variant (mtSNV) burden in astroglia derived from C9ORF72-mutant organoids, with some de novo mtSNVs likely due to the C9ORF72 repeat and others evading selection to reach higher heteroplasmy levels. Thus, the functional consequences of the regional accumulation of mtSNVs in C9ORF72 ALS-FTLD brains are likely to manifest through astroglial mitochondrial dysfunction.

Novel CRISPR-Cas9 iPSC knockouts for PCCA and PCCB genes: advancing propionic acidemia research

Propionic acidemia (PA) is a rare autosomal recessive metabolic disorder caused by mutations in the PCCA and PCCB genes, which encode subunits of the mitochondrial enzyme propionyl-CoA carboxylase (PCC). This enzyme deficiency leads to the accumulation of toxic metabolites, resulting in severe metabolic dysfunction. To create ideal in vitro disease models of PA with isogenic controls and provide a robust platform for therapeutic research, we generated two induced pluripotent stem cell (iPSC) lines with knockout (KO) mutations in the PCCA and PCCB genes using CRISPR-Cas9 gene editing in a healthy control iPSC line. The KO iPS cells were successfully established and characterized, confirming the presence of frameshift insertions and deletions in each target gene, as well as the loss of the corresponding transcript, protein expression, and activity. Additionally, the generated iPSC lines exhibit hallmark characteristics of pluripotency, including the potential to differentiate into all three germ layers. Our PCCA and PCCB KO iPSC models provide a valuable tool for studying the molecular mechanisms underlying PA and hold potential for advancing new therapeutic approaches.

Effects of hydrogel stiffness and viscoelasticity on organoid culture: a comprehensive review

As an emerging technology, organoids are promising new tools for basic and translational research in disease. Currently, the culture of organoids relies mainly on a type of unknown composition scaffold, namely Matrigel, which may pose problems in studying the effect of mechanical properties on organoids. Hydrogels, a new material with adjustable mechanical properties, can adapt to current studies. In this review, we summarized the synthesis of recent advance in developing definite hydrogel scaffolds for organoid culture and identified the critical parameters for regulating mechanical properties. In addition, classified by different mechanical properties like stiffness and viscoelasticity, we concluded the effect of mechanical properties on the development of organoids and tumor organoids. We hope this review enhances the understanding of the development of organoids by hydrogels and provides more practical approaches to investigating them.