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Enhancing organoid technology with carbon-based nanomaterial biosensors: Advancements, challenges, and future directions.
Various carbon-based nanomaterials (CBNs) have been utilized to develop nano- and microscale biosensors that enable real-time and continuous monitoring of biochemical and biophysical changes in living biological systems. The integration of CBN-based biosensors into organoids has recently provided valuable insights into organoid development, disease modeling, and drug responses, enhancing their functionality and expanding their applications in diverse biomedical fields. These biosensors have been particularly transformative in studying neurological disorders, cardiovascular diseases, cancer progression, and liver toxicity, where precise, non-invasive monitoring is crucial for understanding pathophysiological mechanisms and assessing therapeutic efficacy. This review introduces intra- and extracellular biosensors incorporating CBNs such as graphene, carbon nanotubes (CNTs), graphene oxide (GO), reduced graphene oxide (rGO), carbon dots (CDs), and fullerenes. Additionally, it discusses strategies for improving the biocompatibility of CBN-based biosensors and minimizing their potential toxicity to ensure long-term organoid viability. Key challenges such as biosensor integration, data accuracy, and functional compatibility with specific organoid models are also addressed. Furthermore, this review highlights how CBN-based biosensors enhance the precision and relevance of organoid models in biomedical research, particularly in organ-specific applications such as brain-on-a-chip systems for neurodegenerative disease studies, liver-on-a-chip platforms for hepatotoxicity screening, and cardiac organoids for assessing cardiotoxicity in drug development. Finally, it explores how biosensing technologies could revolutionize personalized medicine by enabling high throughput drug screening, patient-specific disease modeling, and integrated sensing platforms for early diagnostics. By capturing current advancements and future directions, this review underscores the transformative potential of carbon-based nanotechnology in organoid research and its broader impact on medical science.
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Standardizing designed and emergent quantitative features in microphysiological systems.
Microphysiological systems (MPSs) are cellular models that replicate aspects of organ and tissue functions in vitro. In contrast with conventional cell cultures, MPSs often provide physiological mechanical cues to cells, include fluid flow and can be interlinked (hence, they are often referred to as microfluidic tissue chips or organs-on-chips). Here, by means of examples of MPSs of the vascular system, intestine, brain and heart, we advocate for the development of standards that allow for comparisons of quantitative physiological features in MPSs and humans. Such standards should ensure that the in vivo relevance and predictive value of MPSs can be properly assessed as fit-for-purpose in specific applications, such as the assessment of drug toxicity, the identification of therapeutics or the understanding of human physiology or disease. Specifically, we distinguish designed features, which can be controlled via the design of the MPS, from emergent features, which describe cellular function, and propose methods for improving MPSs with readouts and sensors for the quantitative monitoring of complex physiology towards enabling wider end-user adoption and regulatory acceptance.
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Generation of Functional Endodermal Hepatic Organoids.
Organoid technology has allowed us to generate a variety of human organ-like mini structures, such as for the liver, brain, and intestine, in vitro. The remarkable advances in organoid models have recently opened a new experimental era for various applications in disease modeling, developmental biology, and drug discovery. Adult stem cells or induced pluripotent stem cell (iPSC)-derived liver organoids govern the generation of hepatocytes to use for diverse applications. Here, we present a robust and reproducible protocol for generating hepatic organoids from pluripotent stem cells. This protocol is applicable to healthy and patient-derived cells. To achieve 3D endoderm-derived hepatic organoids (eHEPOs), iPSCs were directly first differentiated into endodermal cells, and then FACS-enriched EpCAM-positive (EpCAM+) cells were used to establish hepatic organoids using the expansion medium. We provide a fast and efficient method to generate hepatic organoids within 2 weeks. The generated organoids mimic the essential properties and functions of hepatocytes, such as albumin secretion, glycogen storage, and cytochrome P450 enzyme activity. Besides the liver-specific gene expression similarities, eHEPOs comprise polarized epithelial cells with bile canaliculi in between. In addition, eHEPOs can be expanded and serial passages long term (1 year) without losing their capacity to differentiate into mature hepatocytes. Thus, eHEPOs provide an alternative source to produce functional hepatocytes.
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Probing prodrug metabolism and reciprocal toxicity with an integrated and humanized multi-tissue organ-on-a-chip platform.
Current drug development techniques are expensive and inefficient, partially due to the use of preclinical models that do not accurately recapitulate in vivo drug efficacy and cytotoxicity. To address this challenge, we report on an integrated, in vitro multi-organoid system that enables parallel assessment of drug efficiency and toxicity on multiple 3D tissue organoids. Built in a low-cost, adhesive film-based microfluidic device, these miniaturized structures require less than 200 µL fluid volume and are amenable to both matrix-based 3D cell culture and spheroid aggregate integration, each supported with an in situ photocrosslinkable hyaluronic acid hydrogel. Here, we demonstrate this technology first with a three-organoid device consisting of liver, cardiac, and lung constructs. We show that these multiple tissue types can be kept in common circulation with high viability for 21 days and validate the platform by investigating liver metabolism of the prodrug capecitabine into 5-fluorouracil (5-FU) and observing downstream toxicity in lung and cardiac organoids. Then we expand the integrated system to accommodate six humanized constructs, including liver, cardiac, lung, endothelium, brain, and testes organoids. Following a 14-day incubation in common media, we demonstrate multi-tissue interactions by metabolizing the alkylating prodrug ifosfamide in the liver organoid to produce chloroacetaldehyde and induce downstream neurotoxicity. Our results establish an expandable, multi-organoid body-on-a-chip system that can be fabricated easily and used for the accurate characterization of drug interactions in vitro. STATEMENT OF SIGNIFICANCE: The use of 3-dimensional (3D) in vitro models in drug development has advanced over the past decade. However, with several exceptions, the majority of research studies using 3D in vitro models, such as organoids, employ single tissue types, in isolated environments with no "communication" between different tissues. This is a significant limiting factor because in the human body there is significant signaling between different cells, tissues, and organs. Here we employ a low-cost, adhesive film-based microfluidic device approach, paired with a versatile extracellular matrix-derived hyaluronic acid hydrogel to support integrated systems of 3 and 6 3D organoid and cell constructs. Moreover, we demonstrate an integrated response to drugs, in which downstream toxicity is dependent on the presence of liver organoids.
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Bioengineering innovations for neural organoids with enhanced fidelity and function.
Neural organoids have been utilized to recapitulate different aspects of the developing nervous system. While hailed as promising experimental tools for studying human neural development and neuropathology, current neural organoids do not fully recapitulate the anatomy or microcircuitry-level functionality of the developing brain, spinal cord, or peripheral nervous system. In this review, we discuss emerging bioengineering approaches that control morphogen signals and biophysical microenvironments, which have improved the efficiency, fidelity, and utility of neural organoids. Furthermore, advancements in bioengineered tools have facilitated more sophisticated analyses of neural organoid functions and applications, including improved neural-bioelectronic interfaces and organoid-based information processing. Emerging bioethical issues associated with advanced neural organoids are also discussed. Future opportunities of neural organoid research lie in enhancing their fidelity, maturity, and complexity and expanding their applications in a scalable manner.
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Evaluation of Mutation Risk Using Patient-Derived Organoids in Patients With Lynch Syndrome.
Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline mutation of DNA mismatch repair (MMR) genes, most notably associated with colorectal cancer. Although LS patients face high risk of CRC, risk can vary even among those with the same pathogenic MMR germline mutations. We suggest a functional assay platform for assessing mutation risk using patient-derived organoid (PDOs). We measured organoid response to the cytotoxic effects of a methylating agent, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) based on DNA damage-induced apoptosis. When normal (non-LS) colon organoids were used, treatment with MNNG and four passages of organoid culture led to decreased total growth (organoid area), but there was no significant change in number. To increase the effect of MNNG and induce apoptosis in normal colon organoids, we added O6BG (an MGMT inhibitor) and an ATR inhibitor. The cytotoxic effects of combined treatment with MNNG, O6BG and ATR inhibitor on non-LS-PDOs were significantly higher than in PDOs of LS patients. To detect the difference at an earlier phase, we examined DNA damage response by analyzing γH2AX expression after treatment with MNNG and O6BG for 24 h. Then, we found higher expression of γH2AX in non-LS-PDOs than in PDOs of LS patients, suggesting continued cell survival with mutation accumulation in LS-PDOs. In conclusion, treatment with MNNG and O6BG using PDOs and measurement of resulting DNA damage response could be used as a preclinical platform for risk stratification in LS patients.
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A human tumor-immune organoid model of glioblastoma.
A major obstacle to identifying effective therapies for the aggressive brain tumor glioblastoma is the lack of human-specific, immunocompetent models that reflect the human tumor microenvironment. To address this, we developed the immune-human organoid tumor transplantation (iHOTT) model, an autologous co-culture platform that integrates patient-derived tumor cells and matched peripheral blood mononuclear cells within human cortical organoids to enable the study of patient-specific immune responses and tumor-immune interactions. This platform preserves tumor and immune populations, immune signaling, and cell-cell interactions observed in patient tumors. Treatment of iHOTT with pembrolizumab, a checkpoint inhibitor, mirrors cell-type shifts and cell-cell interactions observed in patients. T cell receptor (TCR) sequencing further reveals pembrolizumab-driven expansion of stem-like CD4 T cell clonotypes exhibiting patient-specific repertoires. These findings establish iHOTT as a physiologically relevant platform for exploring autologous tumor-immune interactions and underscore the need for antigen-targeted strategies to enhance immunotherapy in glioblastoma.
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Genetically engineered cerebral organoids model brain tumor formation.
Brain tumors are among the most lethal and devastating cancers. Their study is limited by genetic heterogeneity and the incompleteness of available laboratory models. Three-dimensional organoid culture models offer innovative possibilities for the modeling of human disease. Here we establish a 3D in vitro model called a neoplastic cerebral organoid (neoCOR), in which we recapitulate brain tumorigenesis by introducing oncogenic mutations in cerebral organoids via transposon- and CRISPR-Cas9-mediated mutagenesis. By screening clinically relevant mutations identified in cancer genome projects, we defined mutation combinations that result in glioblastoma-like and central nervous system primitive neuroectodermal tumor (CNS-PNET)-like neoplasms. We demonstrate that neoCORs are suitable for use in investigations of aspects of tumor biology such as invasiveness, and for evaluation of drug effects in the context of specific DNA aberrations. NeoCORs will provide a valuable complement to the current basic and preclinical models used to study brain tumor biology.
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Cerebral organoids containing an AUTS2 missense variant model microcephaly.
Variants in the AUTS2 gene are associated with a broad spectrum of neurological conditions characterized by intellectual disability, microcephaly, and congenital brain malformations. Here, we use a human cerebral organoid model to investigate the pathophysiology of a heterozygous de novo missense AUTS2 variant identified in a patient with multiple neurological impairments including primary microcephaly and profound intellectual disability. Proband cerebral organoids exhibit reduced growth, deficits in neural progenitor cell (NPC) proliferation and disrupted NPC polarity within ventricular zone-like regions compared to control cerebral organoids. We used CRISPR-Cas9-mediated gene editing to correct this variant and demonstrate rescue of impaired organoid growth and NPC proliferative deficits. Single-cell RNA sequencing revealed a marked reduction of G1/S transition gene expression and alterations in WNT-β-catenin signalling within proband NPCs, uncovering a novel role for AUTS2 in NPCs during human cortical development. Collectively, these results underscore the value of cerebral organoids to investigate molecular mechanisms underlying AUTS2 syndrome.
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Guiding Principles: Reporting Elements for Gastrointestinal Organoid Research.
Gastrointestinal (GI) organoids are now widely used for disease modeling, drug discovery, regenerative-, and precision medicine. As publications using GI organoids have increased exponentially, methodological reporting across GI organoid studies remains inconsistent, making results difficult to interpret, compare, and reproduce. To address this, we present community-informed guidance for reporting key experimental details in GI organoid research. Our recommendations were developed by integrating established biomedical reporting frameworks, organoid-focused resources from international organizations, and structured input from the GI organoid community through an expert panel survey. These inputs informed a core set of reporting items, including stem cell source and donor context, media and supplement composition, extracellular matrix type, culture configuration, and other parameters essential for replication. We provide an "Organoid Reporting Toolkit" containing practical checklists and templates intended to help authors, reviewers, editors, and journals. Together, these resources aim to improve transparency and reproducibility, facilitate cross-study comparison, and streamline communication in the GI organoid field while preserving flexibility for methodological innovation.