Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

Intestinal organoids: The path towards clinical application

Organoids have revolutionized the whole field of biology with their ability to model complex three-dimensional human organs in vitro. Intestinal organoids were especially consequential as the first successful long-term culture of intestinal stem cells, which raised hopes for translational medical applications. Despite significant contributions to basic research, challenges remain to develop intestinal organoids into clinical tools for diagnosis, prognosis, and therapy. In this review, we outline the current state of translational research involving adult stem cell and pluripotent stem cell derived intestinal organoids, highlighting the advances and limitations in disease modeling, drug-screening, personalized medicine, and stem cell therapy. Preclinical studies have demonstrated a remarkable functional recapitulation of infectious and genetic diseases, and there is mounting evidence for the reliability of intestinal organoids as a patient-specific avatar. Breakthroughs now allow the generation of structurally and cellularly complex intestinal models to better capture a wider range of intestinal pathophysiology. As the field develops and evolves, there is a need for standardized frameworks for generation, culture, storage, and analysis of intestinal organoids to ensure reproducibility, comparability, and interpretability of these preclinical and clinical studies to ultimately enable clinical translation.

The biological macromolecules constructed Matrigel for cultured organoids in biomedical and tissue engineering

Matrigel is the most commonly used matrix for 3D organoid cultures. Research on the biomaterial basis of Matrigel for organoid cultures is a highly challenging field. Currently, many studies focus on Matrigel-based biological macromolecules or combinations to construct natural Matrigel and synthetic hydrogel scaffolds based on collagen, peptides, polysaccharides, microbial transglutaminase, DNA supramolecules, and polymers for organoid culture. In this review, we discuss the limitations of both natural and synthetic Matrigel, and describe alternative scaffolds that have been employed for organoid cultures. The patient-derived organoids were constructed in different cancer types and limitations of animal-derived organoids based on the hydrogel or Matrigel. The constructed techniques utilizing 3D bioprinting platforms, air-liquid interface (ALI) culture, microfluidic culture, and organ-on-a-chip platform are summarized. Given the potential of organoids for a wide range of therapeutic, tissue engineering and pharmaceutical applications, it is indeed imperative to develop defined and customized hydrogels in addition to Matrigel.

Prediction of Patient Drug Response via 3D Bioprinted Gastric Cancer Model Utilized Patient-Derived Tissue Laden Tissue-Specific Bioink

Despite significant research progress, tumor heterogeneity remains elusive, and its complexity poses a barrier to anticancer drug discovery and cancer treatment. Response to the same drug varies across patients, and the timing of treatment is an important factor in determining prognosis. Therefore, development of patient-specific preclinical models that can predict a patient's drug response within a short period is imperative. In this study, a printed gastric cancer (pGC) model is developed for preclinical chemotherapy using extrusion-based 3D bioprinting technology and tissue-specific bioinks containing patient-derived tumor chunks. The pGC model retained the original tumor characteristics and enabled rapid drug evaluation within 2 weeks of its isolation from the patient. In fact, it is confirmed that the drug response-related gene profile of pGC tissues co-cultured with human gastric fibroblasts (hGaFibro) is similar to that of patient tissues. This suggested that the application of the pGC model can potentially overcome the challenges associated with accurate drug evaluation in preclinical models (e.g., patient-derived xenografts) owing to the deficiency of stromal cells derived from the patient. Consequently, the pGC model manifested a remarkable similarity with patients in terms of response to chemotherapy and prognostic predictability. Hence, it is considered a promising preclinical tool for personalized and precise treatments.

Precision models in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) represents a global health challenge, and ranks among one of the most prevalent and deadliest cancers worldwide. Therapeutic advances have expanded the treatment armamentarium for patients with advanced HCC, but obstacles remain. Precision oncology, which aims to match specific therapies to patients who have tumours with particular features, holds great promise. However, its implementation has been hindered by the existence of numerous 'HCC influencers' that contribute to the high inter-patient heterogeneity. HCC influencers include tumour-related characteristics, such as genetic alterations, immune infiltration, stromal composition and aetiology, and patient-specific factors, such as sex, age, germline variants and the microbiome. This Review delves into the intricate world of HCC, describing the most innovative model systems that can be harnessed to identify precision and/or personalized therapies. We provide examples of how different models have been used to nominate candidate biomarkers, their limitations and strategies to optimize such models. We also highlight the importance of reproducing distinct HCC influencers in a flexible and modular way, with the aim of dissecting their relative contribution to therapy response. Next-generation HCC models will pave the way for faster discovery of precision therapies for patients with advanced HCC.

Evolution of organoid genetics

Organoids have revolutionized in vitro research by offering three-dimensional, multicellular systems that recapitulate the structure, function, and genetics of human tissues. Initially developed from both pluripotent stem cells (PSCs) and adult stem cells (AdSCs), organoids have expanded to model nearly every major human organ, significantly advancing developmental biology, disease modeling, and therapeutic screening. This review highlights the progression of organoid technologies, emphasizing the integration of genetic tools, including CRISPR-Cas9, prime editing, and lineage tracing. These advancements have facilitated precise modeling of human-specific pathologies and drug responses, often surpassing traditional 2D cultures and animal models in accuracy. Emerging technologies, such as organoid fusion, xenografting, and optogenetics, are expected to further enhance our understanding of cellular interactions and microenvironmental dynamics. As organoid complexity and genetic engineering methods continue to evolve, they will become increasingly indispensable for personalized medicine and translational research, bridging gaps between in vitro and in vivo systems.

Organoid drug profiling identifies methotrexate as a therapy for SCCOHT, a rare pediatric cancer

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and lethal tumor in adolescent and young adult patients. Now, there is no standard-of-care treatment for these patients. Reliable models that represent this disease and can be used for translational research are scarce. To model SCCOHTs, we have established eight patient-derived tumoroid lines from tumor lesions of three patients with SCCOHT. The tumoroids recapitulate genomic and transcriptomic characteristics of the corresponding patient tumors and capture intrapatient tumor heterogeneity. Organoid drug profiling using a library of 153 clinical compounds identified methotrexate as an effective and selective drug against SCCOHTs with a clinically relevant IC50 of 35 nanomolars. RNA sequencing demonstrated that methotrexate induced TP53 pathway activation and apoptosis. These data underscore that organoid technology can support the design of therapeutic strategies for rare cancers.

Rational Design of a Potent, Selective, and Metabolically Stable CDK9 Inhibitor to Counteract Osimertinib Resistance through Mcl-1 Suppression and Enhanced BRD4 Co-Targeting

Overcoming osimertinib resistance in NSCLC treatment remains a significant clinical challenge. CDK9 has emerged as a promising target due to its critical role in sustaining oncogenic transcriptional programs, particularly via Mcl-1 regulation. Herein, we report the structure-guided optimization of a previously identified CDK9 inhibitor (Z11), resulting in the discovery of T7, a potent, selective, and metabolically stable candidate (IC50 = 1.2 nM). T7 effectively suppressed cell proliferation, reduced colony formation, and induced apoptosis in Osimertinib-resistant NSCLC cells by downregulating Mcl-1. Furthermore, T7 significantly inhibited the growth of resistant organoids and demonstrated marked antitumor efficacy in a xenograft model. Notably, combining T7 with the BRD4 inhibitor JQ1 further enhanced antitumor activity both in vitro and in vivo, revealing a complementary therapeutic strategy. These findings identify T7 as a promising next-generation CDK9 inhibitor for addressing Osimertinib resistance in NSCLC and underscore the potential of transcriptional cotargeting approaches to improve clinical outcomes.

Significance of mouse xenograft tumor model using patient-derived cancer organoids for clinical drug development

Background

In vitro and in vivo preclinical examinations of cancer cell lines are performed to determine the effectiveness of new drugs before initiating clinical trials. However, there is often a significant disparity between the promising results observed in preclinical evaluations and actual outcomes in clinical trials. Therefore, we hypothesized that this inconsistency might be due to the differences between the characteristics of cell lines and actual cancers in patients. Therefore, we screened drugs for bile duct cancer to test our hypotheses.

Methods

We established patient-derived cancer organoids (PDCOs) from the surgical samples of patients with bile duct cancer and conducted multiple in vitro drug screening tests.

Results

We identified proteasome inhibitors (Bortezomib and Carfilzomib) as promising drugs in the screening. Bortezomib has demonstrated a significant antitumor effect on bile duct cancer cell-derived xenografts, as previously reported in preclinical trials. However, although Bortezomib showed significant proliferation inhibition in PDCOs in three-dimensional culture in vitro, it did not exhibit significant anti-tumor effects in mouse xenograft tumor models using our PDCOs. Bile duct cancer cell-line-derived xenografts are characterized by structurally uniform, irregular glandular structures surrounded by simple and sparse stromal components. However, organoid-derived xenografts exhibit a spectrum of differentiation levels within irregular glandular structures and consist of a complex and rich stromal microenvironment similar to those observed in surgical specimens.

Conclusion

These findings suggest that in vivo studies using PDCO xenograft tumor models may be more suitable than conventional mouse tumor models for determining the clinical development of drugs.

Organoids from pluripotent stem cells and human tissues: When two cultures meet each other

Human organoids are a widely used tool in cell biology to study homeostatic processes, disease, and development. The term organoids covers a plethora of model systems from different cellular origins that each have unique features and applications but bring their own challenges. This review discusses the basic principles underlying organoids generated from pluripotent stem cells (PSCs) as well as those derived from tissue stem cells (TSCs). We consider how well PSC- and TSC-organoids mimic the different intended organs in terms of cellular complexity, maturity, functionality, and the ongoing efforts to constitute predictive complex models of in vivo situations. We discuss the advantages and limitations associated with each system to answer different biological questions including in the field of cancer and developmental biology, and with respect to implementing emerging advanced technologies, such as (spatial) -omics analyses, CRISPR screens, and high-content imaging screens. We postulate how the two fields may move forward together, integrating advantages of one to the other.

Paired primary-metastasis patient-derived organoids and mouse models identify phenotypic evolution and druggable dependencies of peritoneal metastasis from appendiceal cancer

Peritoneal carcinomatosis is a common yet deadly manifestation of gastrointestinal cancers, with few effective treatments. To identify targetable determinants of peritoneal metastasis, we focused on appendiceal adenocarcinoma (AC), a gastrointestinal cancer that metastasizes almost exclusively to the peritoneum. Current treatments are extrapolated from colorectal cancer (CRC), yet AC has distinct genomic alterations, mucinous morphology and peritoneum restricted metastatic pattern. Further, no stable preclinical models of AC exist, limiting drug discovery and representing an unmet clinical need. We establish a first-in-class stable biobank of 16 long-term cultured AC patient-derived organoids (PDOs), including 3 matched, simultaneously resected primary AC-peritoneal carcinomatosis (AC-PC) pairs. By enriching for cancer cells, AC PDOs enable accurate genomic characterization relative to paucicellular AC tissue. We establish an organoid orthotopic intraperitoneal xenograft model that recapitulates diffuse peritoneal carcinomatosis and show that PC-organoids retain increased metastatic capacity, decreased growth factor dependency and sensitivity to standard of care chemotherapy relative to matched primary AC organoids. Single cell profiling of AC-PC pairs reveals dedifferentiation from mucinous differentiated states in primary AC into intestinal stem cell and fetal progenitor states in AC-PC, with upregulation of oncogenic signaling pathways. Through hypothesis-driven drug testing, we identify KRASMULTI-ON inhibitor RMC-7977 and Wnt-targeting tyrosine kinase inhibitor WNTinib as novel, clinically actionable strategies to target AC-PC more effectively.

Molecular probes for in vivo optical imaging of immune cells

Advancing the understanding of the various roles and components of the immune system requires sophisticated methods and technology for the detection of immune cells in their natural states. Recent advancements in the development of molecular probes for optical imaging have paved the way for non-invasive visualization and real-time monitoring of immune responses and functions. Here we discuss recent progress in the development of molecular probes for the selective imaging of specific immune cells. We emphasize the design principles of the probes and their comparative performance when using various optical modalities across disease contexts. We highlight molecular probes for imaging tumour-infiltrating immune cells, and their applications in drug screening and in the prediction of therapeutic outcomes of cancer immunotherapies. We also discuss the use of these probes in visualizing immune cells in atherosclerosis, lung inflammation, allograft rejection and other immune-related conditions, and the translational opportunities and challenges of using optical molecular probes for further understanding of the immune system and disease diagnosis and prognosis.

Opportunities of patient-derived organoids in drug development

Various model systems are utilised during drug development starting from basic research, moving to preclinical research and development for clinical applications in order to identify new drugs to improve human health. However, there are characteristics of humans that are not captured by established models. Such models include homogeneous two-dimensional (2D) cell lines, which lack cellular heterogeneity and physiological relevance, and species differences of animal models. Organoids can mitigate these differences by providing more physiologically relevant three-dimensional (3D) cell models that resemble the molecular state in healthy and pathological tissue. This review presents exemplary approaches using patient-derived organoids (PDOs) that have been developed and the new opportunities that are evolving in drug development with a focus on patient adult stem cell (ASC)-derived organoids. These demonstrate the potential of PDOs used alongside established cell and animal models to improve drug development from basic research to clinical applications such as personalised medicine.

3D bioprinting for the construction of drug testing models-development strategies and regulatory concerns

A drug to be successfully launched in the market requires a significant amount of capital, resources and time, where the unsuccessful results in the last stages lead to catastrophic failure for discovering drugs. This is the very reason which calls for the invention of innovative models that can closely mimic the human in vivo model for producing reliable results. Throughout the innovation line, there has been improvement in the rationale in silico designing but yet there is requirement for in vitro-in vivo correlations. During the evolving of the drug testing models, the 3D models produced by different methods have been proven to produce better results than the traditional 2D models. However, the in vitro fabrications of live tissues are still bottleneck in realizing their complete potential. There is an urgent need for the development of single, standard and simplified in vitro 3D tissue models that can be reliable for investigating the biological and pathological aspects of drug discovery, which is yet to be achieved. The existing pre-clinical models have considerable drawbacks despite being the gold standard in pre-clinical research. The major drawback being the interspecies differences and low reliability on the generated results. This gap could be overcome by the fabrication of bioengineered human disease models for drug screening. The advancement in the fabrication of 3D models will provide a valuable tool in screening drugs at different stages as they are one step closer to bio-mimic human tissues. In this review, we have discussed on the evolution of preclinical studies, and different models, including mini tissues, spheroids, organoids, bioengineered three dimensional models and organs on chips. Furthermore, we provide details of different disease models fabricated across various organs and their applications. In addition to this, the review also focuses on the limitations and the current prospects of the role of three dimensionally bioprinted models in drug screening and development.

Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images

Autofluorescence microscopy uses intrinsic sources of molecular contrast to provide cellular-level information without extrinsic labels. However, traditional cell segmentation tools are often optimized for high signal-to-noise ratio (SNR) images, such as fluorescently labeled cells, and unsurprisingly perform poorly on low SNR autofluorescence images. Therefore, new cell segmentation tools are needed for autofluorescence microscopy. Cellpose is a deep learning network that is generalizable across diverse cell microscopy images and automatically segments single cells to improve throughput and reduce inter-human biases. This study aims to validate Cellpose for autofluorescence imaging, specifically using multiphoton intensity images of NAD(P)H. Manually segmented nuclear masks of NAD(P)H images were used to train a new autofluorescence-trained model (ATM) in Cellpose for nuclear segmentation of NAD(P)H intensity images. These models were applied to PANC-1 cells treated with metabolic inhibitors and patient-derived cancer organoids (9 patients) treated with chemotherapies. These datasets include co-registered fluorescence lifetime imaging microscopy (FLIM) of NAD(P)H and FAD, so fluorescence decay parameters and the optical redox ratio (ORR) were compared between masks generated by the new ATM and manual segmentation. The Dice score between repeated manually segmented masks was significantly lower than that of repeated ATM masks (p < 0.0001) indicating greater reproducibility between ATM masks. There was also a high correlation (R2 > 0.9) between ATM and manually segmented masks for the ORR, mean NAD(P)H lifetime, and mean FAD lifetime across 2D and 3D cell culture treatment conditions. Masks generated from ATM and manual segmentation also maintain similar means, variances, and effect sizes between treatments for the ORR and FLIM parameters. Overall, the Cellpose ATM provides a fast, reliable, reproducible, and accurate method to segment single cells in autofluorescence microscopy images such that functional changes in cells are accurately captured in both 2D and 3D culture.

Design of ROS-Triggered Sesquiterpene Lactone SC Prodrugs as TrxR1 Covalent Inhibitors for the Treatment of Non-Small Cell Lung Cancer

Thioredoxin reductase 1 (TrxR1) is an important therapeutic target for nonsmall cell lung cancer (NSCLC) treatment due to its overexpression in NSCLC cells. In this work, to address the deficiency that sesquiterpene lactone containing α-methylene-γ-lactone moiety was rapidly metabolized by endogenous nucleophiles, series of novel thioether derivatives were designed and synthesized based on a reactive oxygen species (ROS)-triggered prodrug strategy. Among them, prodrug 5u exhibited potent cytotoxicity against NSCLC cells and better release rates in response to ROS. The active compound 6a released from 5u covalently binds to Cys475 and Sec498 sites on TrxR1, resulting in inhibition on TrxR1 activity, which led to redox homeostasis disorder, and caused apoptosis and ferroptosis. Moreover, prodrug 5u exhibited significant antitumor efficiency in nude mice and NSCLC organoids. Our results deliver ROS-triggered prodrug 5u as a novel TrxR1 inhibitor for the treatment of NSCLC and provide a promising strategy of ROS-activated prodrug for covalent compounds in cancer therapy.

Towards the Prediction of Responses to Cancer Immunotherapy: A Multi-Omics Review

Tumor treatment has undergone revolutionary changes with the development of immunotherapy, especially immune checkpoint inhibitors. Because not all patients respond positively to immune therapeutic agents, and severe immune-related adverse events (irAEs) are frequently observed, the development of the biomarkers evaluating the response of a patient is key for the application of immunotherapy in a wider range. Recently, various multi-omics features measured by high-throughput technologies, such as tumor mutation burden (TMB), gene expression profiles, and DNA methylation profiles, have been proved to be sensitive and accurate predictors of the response to immunotherapy. A large number of predictive models based on these features, utilizing traditional machine learning or deep learning frameworks, have also been proposed. In this review, we aim to cover recent advances in predicting tumor immunotherapy response using multi-omics features. These include new measurements, research cohorts, data sources, and predictive models. Key findings emphasize the importance of TMB, neoantigens, MSI, and mutational signatures in predicting ICI responses. The integration of bulk and single-cell RNA sequencing has enhanced our understanding of the tumor immune microenvironment and enabled the identification of predictive biomarkers like PD-L1 and IFN-γ signatures. Public datasets and machine learning models have also improved predictive tools. However, challenges remain, such as the need for large and diverse clinical datasets, standardization of multi-omics data, and model interpretability. Future research will require collaboration among researchers, clinicians, and data scientists to address these issues and enhance cancer immunotherapy precision.

Organoid models: applications and research advances in colorectal cancer

This review summarizes the applications and research progress of organoid models in colorectal cancer research. First, the high incidence and mortality rates of colorectal cancer are introduced, emphasizing the importance of organoids as a research model. Second, this review provides a detailed introduction to the concept, biological properties, and applications of organoids, including their strengths in mimicking the structural and functional aspects of organs. This article further analyzes the applications of adult stem cell-derived and pluripotent stem cell-derived organoids in colorectal cancer research and discusses advancements in organoids for basic research, drug research and development, personalized treatment evaluation and prediction, and regenerative medicine. Finally, this review summarizes the prospects for applying organoid technology in colorectal cancer research, emphasizing its significant value in improving patient survival rates. In conclusion, this review systematically explains the applications of organoids in colorectal cancer research, highlighting their tremendous potential and promising prospects in basic research, drug research and development, personalized treatment evaluation and prediction, and regenerative medicine.

Patient-derived glioblastoma organoids as real-time avatars for assessing responses to clinical CAR-T cell therapy

Patient-derived tumor organoids have been leveraged for disease modeling and preclinical studies but rarely applied in real time to aid with interpretation of patient treatment responses in clinics. We recently demonstrated early efficacy signals in a first-in-human, phase 1 study of dual-targeting chimeric antigen receptor (CAR)-T cells (EGFR-IL13Rα2 CAR-T cells) in patients with recurrent glioblastoma. Here, we analyzed six sets of patient-derived glioblastoma organoids (GBOs) treated concurrently with the same autologous CAR-T cell products as patients in our phase 1 study. We found that CAR-T cell treatment led to target antigen reduction and cytolysis of tumor cells in GBOs, the degree of which correlated with CAR-T cell engraftment detected in patients' cerebrospinal fluid (CSF). Furthermore, cytokine release patterns in GBOs mirrored those in patient CSF samples over time. Our findings highlight a unique trial design and GBOs as a valuable platform for real-time assessment of CAR-T cell bioactivity and insights into immunotherapy efficacy.

Organoids in lung cancer brain metastasis: Foundational research, clinical translation, and prospective outlooks

Brain metastasis stands as a leading contributor to mortality in lung cancer patients, yet the intricate mechanism underlying this phenomenon remains elusive. This underscores the need for robust preclinical models and effective treatment strategies. Emerging as viable in vitro models that closely replicate actual tumors, three-dimensional culture systems, particularly organoids derived from non-malignant cells or cancer organoids, have emerged as promising avenues. This review delves into the forefronts of fundamental research and clinical applications focused on lung cancer brain metastasis-derived organoids, highlighting current challenges and delineating prospects. These studies offer tremendous potential for clinical application despite being in nascent status.

A novel nanocarrier based on natural polyphenols enhancing gemcitabine sensitization ability for improved pancreatic cancer therapy efficiency

Pancreatic cancer (PC) is a highly lethal malignancy with rapid progression and poor prognosis. Despite the widespread use of gemcitabine (Gem)-based chemotherapy as the first-line treatment for PC, its efficacy is often compromised by significant drug resistance. 1,2,3,4,6-Pentagaloyl glucose (PGG), a natural polyphenol, has demonstrated potential in sensitizing PC cells to Gem. However, its clinical application is limited by poor water solubility and bioavailability. In this study, we developed a novel PGG-based nanocarrier (FP) using a straightforward, one-step self-assembly method with Pluronic F127 and PGG. Our results showed that FP induced DNA damage and immunogenic cell death (ICD) in both in vitro cell experiments and patient-derived organoid models, exhibiting potent anti-tumor effects. Furthermore, in mouse KPC and PDX models, FP, when combined with Gem, showed enhanced Gem sensitization compared to pure PGG, largely due to increased DNA damage and ICD induction. These findings demonstrate the potential of FP to improve the stability and utilization of PGG as effective Gem sensitizers in the treatment of pancreatic cancer, providing a promising pathway for clinical application and translational research.

A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine

Cancer is a highly heterogeneous disease, and thus treatment responses vary greatly between patients. To improve therapy efficacy and outcome for cancer patients, more representative and patient-specific preclinical models are needed. Organoids and tumoroids are 3D cell culture models that typically retain the genetic and epigenetic characteristics, as well as the morphology, of their tissue of origin. Thus, they can be used to understand the underlying mechanisms of cancer initiation, progression, and metastasis in a more physiological setting. Additionally, co-culture methods of tumoroids and cancer-associated cells can help to understand the interplay between a tumor and its tumor microenvironment. In recent years, tumoroids have already helped to refine treatments and to identify new targets for cancer therapy. Advanced culturing systems such as chip-based fluidic devices and bioprinting methods in combination with tumoroids have been used for high-throughput applications for personalized medicine. Even though organoid and tumoroid models are complex in vitro systems, validation of results in vivo is still the common practice. Here, we describe how both animal- and human-derived tumoroids have helped to identify novel vulnerabilities for cancer treatment in recent years, and how they are currently used for precision medicine.

Susceptibility of Mitophagy-Deficient Tumors to Ferroptosis Induction by Relieving the Suppression of Lipid Peroxidation

The identification of ferroptosis-sensitive cancers is critical for the application of ferroptosis-inducing therapies in cancer therapy. Here, patient-derived organoid screening models of colorectal cancer are established to identify tumors that are sensitive to ferroptosis-inducing therapy. This study discovers that patient-derived tumors characterized by mitophagy deficiency are hypersensitive to ferroptosis-inducing therapies. Mechanistically, a novel negative feedback regulatory pathway of lipid peroxidation is identified, which is one of the important intrinsic anti-ferroptosis mechanisms of cancer cells. Lipid peroxidation-mediated endoplasmic reticulum stress transcriptionally upregulates Parkin to promote mitophagy through ATF4. Mitophagy limits the generation of lipid peroxidation products and subsequently inhibits ferroptosis by inhibiting the accumulation of mitochondrial ROS. Mitophagy-deficient tumors lack this anti-ferroptotic mechanism, unleashing the generation of lipid peroxidation and potent ferroptotic cell death induced by erastin, RSL3, cysteine deprivation, radiotherapy, and immunotherapy. More importantly, ferroptosis-inducing therapy selectively inhibits the growth and distant metastasis of mitophagy-deficient tumors in vivo. In summary, patient-derived organoids of colorectal cancer patients for screening ferroptosis-sensitive tumors are established, providing a paradigm for identifying that patient-derived tumors are sensitive to ferroptosis-inducing therapies. This study concludes that mitophagy-deficient tumors are vulnerable to ferroptosis induction, which may lead to the development of new therapeutic strategies for tumors deficient in mitophagy.

Technological advances in clinical individualized medication for cancer therapy: from genes to whole organism

Efforts have been made to leverage technology to accurately identify tumor characteristics and predict how each cancer patient may respond to medications. This involves collecting data from various sources such as genomic data, histological information, functional drug profiling, and drug metabolism using techniques like polymerase chain reaction, sanger sequencing, next-generation sequencing, fluorescence in situ hybridization, immunohistochemistry staining, patient-derived tumor xenograft models, patient-derived organoid models, and therapeutic drug monitoring. The utilization of diverse detection technologies in clinical practice has made "individualized treatment" possible, but the desired level of accuracy has not been fully attained yet. Here, we briefly summarize the conventional and state-of-the-art technologies contributing to individualized medication in clinical settings, aiming to explore therapy options enhancing clinical outcomes.

Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection

BACKGROUND

Colorectal cancer (CRC) presents significant challenges in chemotherapy response prediction due to its molecular heterogeneity. Current methods often fail to account for the complexity and variability inherent in individual tumors.

METHODS

We developed a novel approach using matched CRC tumor and organoid gene expression data. We applied Consensus Weighted Gene Co-expression Network Analysis (WGCNA) across three datasets: CRC tumors, matched organoids, and an independent organoid dataset with IC50 drug response values, to identify key gene modules and hub genes linked to chemotherapy response, particularly 5-fluorouracil (5-FU).

FINDINGS

Our integrative analysis identified significant gene modules and hub genes associated with CRC chemotherapy response. The predictive model built from these findings demonstrated superior accuracy over traditional methods when tested on independent datasets. The matched tumor-organoid data approach proved effective in capturing relevant biomarkers, enhancing prediction reliability.

INTERPRETATION

This study provides a robust framework for improving CRC chemotherapy response predictions by leveraging matched tumor and organoid gene expression data. Our approach addresses the limitations of previous methods, offering a promising strategy for personalized treatment planning in CRC. Future research should aim to validate these findings and explore the integration of more comprehensive drug response data.

FUNDING

This research was supported by US National Cancer Institute grant R37CA248289, and Sylvester Comprehensive Cancer Center. which receives funding from the National Cancer Institute award P30CA240139. This work was supported by National Institutes of Health (NIH) under the following grants: T32CA009501-31A1 and R37CA248289. This work was also supported by the MSK P30CA008748 grant.

Organoids, tissue slices and organotypic cultures: Advancing our understanding of pancreatic ductal adenocarcinoma through in vitro and ex vivo models

Pancreatic ductal adenocarcinoma (PDAC) has one of the worst prognoses of all common solid cancers. For the large majority of PDAC patients, only systemic therapies with very limited efficacy are indicated. In addition, immunotherapies have not brought the advances seen in other cancer types. Several key characteristics of PDAC contribute to poor treatment outcomes, and in this review, we will discuss how these characteristics are best captured in currently available ex vivo or in vitro model systems. For instance, PDAC is hallmarked by a highly desmoplastic and immune-suppressed tumor microenvironment that impacts disease progression and therapy resistance. Also, large differences in tumor biology exist between and within tumors, complicating treatment decisions. Furthermore, PDAC has a very high propensity for locally invasive and metastatic growth. The use of animal models is often not desirable or feasible and several in vitro and ex vivo model systems have been developed, such as organotypic cocultures and tissue slices, among others. However, the absence of a full host organism impacts the ability of these models to accurately capture the characteristics that contribute to poor outcomes in PDAC. We will discuss the caveats and advantages of these model systems in the context of PDAC's key characteristics and provide recommendations on model choice and the possibilities for optimization. These considerations should be of use to researchers aiming to study PDAC in the in vitro setting.

Colorectal carcinoma organoid and cancer-associated fibroblasts co-culture system for drug evaluation

Patient-derived organoids (PDO) have the potential to be used as preclinical cancer models for testing anti-cancer drug efficiency. Cancer-associated fibroblasts (CAFs), which have been closely linked with colorectal carcinoma (CRC) progression and drug resistance, however, are generally not included (or gradually lost during culture) in the PDO models, leading to a major limitation in this cancer model. In this study, we established a new in vitro model with CRC organoids and co-cultured with CAFs and compared it with the organoid-only model. Through testing with anti-cancer drug, we demonstrated a significant difference in drug sensitivity between the two models, and the co-culture model showed higher drug resistance. RNA and whole exome sequencing were performed to reveal gene expression profiles in organoids and organoids co-culture with CAFs to assess interactions between drug sensitivity and gene copy number variation. We found that the expression levels of several pathway protein genes, which are highly expressed in original surgical specimens of colorectal carcinomas, were downregulated in organoids but restored in organoids by co-culturing with CAFs. In summary, the PDO-CAF joint model for CRC can recapitulate a more biomimetic tumor microenvironment and the drug resistance lead by changes in multiple signaling pathways that we discovered; thus, it could be a suitable model for future usage in drug discovery and precision medicine research.

The importance of preclinical models in cholangiocarcinoma

Cholangiocarcinoma (CCA) is an adenocarcinoma of the hepatobiliary system with a grim prognosis. Incidence is rising globally and surgery is currently the only curative treatment, but is only available for patients who are fit and diagnosed in an early-stage of disease progression. Great importance has been placed on developing preclinical models to help further our understanding of CCA and potential treatments to improve therapeutic outcomes. Preclinical models of varying complexity and cost have been established, ranging from more simplistic in vitro 2D CCA cell lines in culture, to more complex in vivo genetically engineered mouse models. Currently there is no single model that faithfully recaptures the complexities of human CCA and the in vivo tumour microenvironment. Instead a multi-model approach should be used when designing preclinical trials to study CCA and potential therapies.

Long-term maintenance of patient-specific characteristics in tumoroids from six cancer indications

Tumoroids, sometimes referred to as cancer organoids, are patient-derived cancer cells grown as 3D, self-organized multicellular structures that maintain key characteristics (e.g., genotype, gene expression levels) of the tumor from which they originated. These models have emerged as valuable tools for studying tumor biology, cytotoxicity, and response of patient-derived cells to cancer therapies. However, the establishment and maintenance of tumoroids has historically been challenging, labor intensive, and highly variable from lab to lab, hindering their widespread use. Here, we characterize the establishment and/or expansion of colorectal, lung, head and neck, breast, pancreas, and endometrial tumoroids using the standardized, serum-free Gibco OncoPro Tumoroid Culture Medium. Newly derived tumoroid lines (n = 20) were analyzed by targeted genomic profiling and RNA sequencing and were representative of tumor tissue samples. Tumoroid lines were stable for over 250 days in culture and freeze-thaw competent. Previously established tumoroid lines were also transitioned to OncoPro medium and exhibited, on average, similar growth rates and conserved donor-specific characteristics when compared to original media systems. Additionally, OncoPro medium was compatible with both embedded culture in extracellular matrix and growth in a suspension format for facile culture and scale up. An example application of these models for assessing the cytotoxicity of a natural killer cell line and primary natural killer cells over time and at various doses demonstrated the compatibility of these models with assays used in compound and cell therapy development. We anticipate that the standardization and versatility of this approach will have important benefits for basic cancer research, drug discovery, and personalized medicine and help make tumoroid models more accessible to the cancer research community.

Patient-Derived Organoid Models for NKT Cell-Based Cancer Immunotherapy

Invariant Natural Killer T (iNKT) cells are a unique subset of T cells that bridge innate and adaptive immunity, displaying potent anti-tumor properties through cytokine secretion, direct cytotoxicity, and recruitment of immune effector cells such as CD8+ T cells and NK cells. Despite their therapeutic potential, the immunosuppressive tumor microenvironment (TME), characterized by regulatory T cells, myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages (TAMs), limits iNKT cell efficacy. Patient-derived organoid (PDO) platforms provide an innovative model for dissecting these complex interactions and evaluating strategies to reinvigorate iNKT cell functionality within the TME. PDOs closely mimic the genetic, phenotypic, and structural characteristics of primary tumors, enabling the study of tumor-immune dynamics. Integrating iNKT cells into PDOs offers a robust platform for investigating CD1d-mediated interactions, Th1-biased immune responses driven by glycolipid analogs like α-GalCer, and combination therapies such as immune checkpoint inhibitors. Additionally, PDO systems can assess the effects of metabolic modulation, including reducing lactic acid accumulation or targeting glutamine pathways, on enhancing iNKT cell activity. Emerging innovations, such as organoid-on-a-chip systems, CRISPR-Cas9 gene editing, and multi-omics approaches, further expand the potential of PDO-iNKT platforms for personalized immunotherapy research. Although the application of iNKT cells in PDOs is still undeveloped, these systems hold immense promise for bridging preclinical studies and clinical translation. By addressing the challenges of the TME and optimizing therapeutic strategies, PDO-iNKT platforms offer a transformative avenue for advancing cancer immunotherapy and personalized medicine.

Trends in Colorectal Cancer Peritoneal Metastases Research: A Comprehensive Bibliometric Analysis

BACKGROUND

Colorectal cancer (CRC) stands as the third most prevalent malignancy globally and is recognized as the second leading cause of cancer-related mortality. Notably, nearly 50% of individuals diagnosed with CRC ultimately develop metastatic disease, with the peritoneum emerging as the second most frequent site for metastatic spread. Recent advancements in therapeutic frameworks have enhanced both survival rates and quality of life metrics for patients afflicted with colorectal cancer peritoneal metastases (CRCPM).

OBJECTIVE

This study endeavors to facilitate an in-depth review of the current scientific landscape surrounding CRCPM, ultimately aiming to delineate future avenues for investigative research in this realm.

METHODS

Employing R software through the Bibliometrix package, alongside analytical tools such as CiteSpace and VOSviewer, we performed a comprehensive bibliometric analysis. This enabled us to assess pivotal keywords, prominent authors, influential countries, notable institutions, relevant literature, and key journals pertinent to the field of CRCPM research.

RESULTS

Our findings illustrate a significant uptick in the volume of publications addressing CRCPM, with the USA leading in overall contribution, complemented by substantial input from distinguished scholars in the Netherlands and France. The author Ignace H. J. T. de Hingh emerged as the most prolific contributor. Current research endeavors have predominantly focused on the characterization of primary malignancies with peritoneal metastases, therapeutic interventions for CRCPM, and the orchestration of clinical trials.

CONCLUSION

This analysis culminates in a systematic encapsulation of the prevailing research findings concerning CRCPM, underscoring current hotspots and predicting future trends within the global research spectrum. The exploration of treatment modalities for CRCPM remains vibrant, and ongoing multicenter clinical trials are anticipated to further enrich our understanding and management of this challenging clinical issue.

Cellular Systems for Colorectal Stem Cancer Cell Research

Oncological diseases consistently occupy leading positions among the most life-threatening diseases, including in highly developed countries. At the same time, the second most common cause of cancer death is colorectal cancer. The current level of research shows that the development of effective therapy, in this case, requires a new grade of understanding processes during the emergence and development of a tumor. In particular, the concept of cancer stem cells that ensure the survival of chemoresistant cells capable of giving rise to new tumors is becoming widespread. To provide adequate conditions that reproduce natural processes typical for tumor development, approaches based on increasingly complex cellular systems are being improved. This review discusses the main strategies that allow for the study of the properties of tumor cells with an emphasis on colorectal cancer stem cells. The features of working with tumor cells and the advantages and disadvantages of 2D and 3D culture systems are considered.

Mesenchymal stromal cells promote the formation of lung cancer organoids via Kindlin-2

BACKGROUND

Patient-derived lung cancer organoids (PD-LCOs) demonstrate exceptional potential in preclinical testing and serve as a promising model for the multimodal management of lung cancer. However, certain lung cancer cells derived from patients exhibit limited capacity to generate organoids due to inter-tumor or intra-tumor variability. To overcome this limitation, we have created an in vitro system that employs mesenchymal stromal cells (MSCs) or fibroblasts to serve as a supportive scaffold for lung cancer cells that do not form organoids.

METHODS

We successfully established an MSCs/fibroblast co-culture system to form LCOs. We analyzed the morphological and histological similarities between LCOs co-cultured with fibroblast and primary lung cancer lesions through HE and IF staining. We evaluated whether LCOs co-cultured with fibroblast retained the original genetic mutations of their source tumors based on WES. RNA sequencing was used to analyze the differences in gene expression profiles between LCOs co-cultured with fibroblast and paracancerous organoids (POs). Importantly, we have successfully validated the impact of Kindlin-2 on the regulation of MSCs in organoid formation through lentiviral vector-mediated interference or overexpression of kindlin-2.

RESULTS

Our findings demonstrate that the addition of MSCs/fibroblasts to three tumor samples, initially incapable of forming organoids by traditional methods, successfully facilitated the cultivation of tumor organoids. Importantly, these organoids co-cultured with fibroblast faithfully recapitulate the tissue morphology of original lung tumors and replicate the genetic profile observed in the parental tumors even after prolonged in vitro culture. Moreover, drug responses exhibited by these organoids co-cultured with MSCs/fibroblasts are consistent with those observed in the original tumors. Mechanistically, we have also identified kindlin-2 as a crucial regulator linking extracellular matrix (ECM) and mitochondria that influence MSC/fibroblast-mediated support for tumor organoid formation.

CONCLUSION

The results obtained from our research enhance the understanding of the mechanisms implicated in the formation of tumor organoids and aid in creating stronger patient-specific tumor organoid models. This advancement supports the refinement of personalized drug response assessments for use in clinical settings.

OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft

Patient-derived models (PDMs, particularly organoids and xenografts) are irreplaceable tools for precision medicine, from target development to lead identification, then to preclinical evaluation, and finally to clinical decision-making. So far, PDM-based proteomics has emerged to be one of the cutting-edge directions and massive data have been accumulated. However, such PDM-based proteomic data have not been provided by any of the available databases, and proteomics profiles of all proteins in proteomic study are also completely absent from existing databases. Herein, an integrated database named 'OrgXenomics' was thus developed to provide the proteomic data for PDMs, which was unique in (a) explicitly describing the establishment detail for a wide array of models, (b) systematically providing the proteomic profiles (expression/function/interaction) for all proteins in studied proteomic analysis and (c) comprehensively giving the raw data for diverse organoid/xenograft-based proteomic studies of various diseases. Our OrgXenomics was expected to server as one good complement to existing proteomic databases, and had great implication for the practice of precision medicine, which could be accessed at: https://idrblab.org/orgxenomics/.

Establishment and characterization of a sigmoid colon cancer organoid with spinal metastasis

Background

Sigmoid colon cancer with spinal metastases is rare in distant metastasis. In addition, the prognosis of colon cancer patients with spinal metastases is extremely poor. In order to find effective therapeutic agents, we need to know the biological characteristics of such patients from related models.

Methods

We collected sigmoid colon cancer tissue from a young female subject who was diagnosed with sigmoid colon cancer with multiple spinal metastases. We successfully established a sigmoid colon cancer organoid using this tissue and investigated drug screening in the patient. HE staining, immunohistochemistry, and DNA sequencing were utilized to compare the biological characteristics between the original tumor and the organoid. Furthermore, we investigated the drug screening of the sigmoid colon cancer organoid in vitro.

Results

A colon cancer organoid from sigmoid colon cancer with spinal metastases was successfully established. The organoid culture maintained the morphological features, histological features, and genomic landscape of the corresponding sigmoid colon cancer cells. Moreover, we performed drug screening tests to evaluate the effects of chemotherapeutic drugs and targeted drugs.

Conclusion

The sigmoid colon cancer organoid with spinal metastases was a favorable preclinical model to explore the clinicopathologic characteristics of colon cancer patients with spinal metastases.

Direct visualization of emergent metastatic features within an ex vivo model of the tumor microenvironment

Ischemic conditions such as hypoxia and nutrient starvation, together with interactions with stromal cells, are critical drivers of metastasis. These conditions arise deep within tumor tissues, and thus, observing nascent metastases is exceedingly challenging. We thus developed the 3MIC-an ex vivo model of the tumor microenvironment-to study the emergence of metastatic features in tumor cells in a 3-dimensional (3D) context. Here, tumor cells spontaneously create ischemic-like conditions, allowing us to study how tumor spheroids migrate, invade, and interact with stromal cells under different metabolic conditions. Consistent with previous data, we show that ischemia increases cell migration and invasion, but the 3MIC allowed us to directly observe and perturb cells while they acquire these pro-metastatic features. Interestingly, our results indicate that medium acidification is one of the strongest pro-metastatic cues and also illustrate using the 3MIC to test anti-metastatic drugs on cells experiencing different metabolic conditions. Overall, the 3MIC can help dissecting the complexity of the tumor microenvironment for the direct observation and perturbation of tumor cells during the early metastatic process.

Patient-Derived Organoids: A Game-Changer in Personalized Cancer Medicine

Research on cancer therapies has benefited from predictive tools capable of simulating treatment response and other disease characteristics in a personalized manner, in particular three-dimensional cell culture models. Such models include tumor-derived spheroids, multicellular spheroids including organotypic multicellular spheroids, and tumor-derived organoids. Additionally, organoids can be grown from various cancer cell types, such as pluripotent stem cells and induced pluripotent stem cells, progenitor cells, and adult stem cells. Although patient-derived xenografts and genetically engineered mouse models replicate human disease in vivo, organoids are less expensive, less labor intensive, and less time-consuming, all-important aspects in high-throughput settings. Like in vivo models, organoids mimic the three-dimensional structure, cellular heterogeneity, and functions of primary tissues, with the advantage of representing the normal oxygen conditions of patient organs. In this review, we summarize the use of organoids in disease modeling, drug discovery, toxicity testing, and precision oncology. We also summarize the current clinical trials using organoids.

Patient-Derived Tumor Organoids: A Platform for Precision Therapy of Colorectal Cancer

Colorectal cancer (CRC) represents a significant cause of cancer-related mortality on a global scale. It is a highly heterogeneous cancer, and the response of patients to homogeneous drug therapy varies considerably. Patient-derived tumor organoids (PDTOs) represent an optimal preclinical model for cancer research. A substantial body of evidence from numerous studies has demonstrated that PDTOs can accurately predict a patient's response to different drug treatments. This article outlines the utilization of PDTOs in the management of CRC across a range of therapeutic contexts, including postoperative adjuvant chemotherapy, palliative chemotherapy, neoadjuvant chemoradiotherapy, targeted therapy, third-line and follow-up treatment, and the treatment of elderly patients. This article delineates the manner in which PDTOs can inform therapeutic decisions at all stages of CRC, thereby assisting clinicians in selecting treatment options and reducing the risk of toxicity and resistance associated with clinical drugs. Moreover, it identifies shortcomings of existing PDTOs, including the absence of consistent criteria for assessing drug sensitivity tests, the lack of vascular and tumor microenvironment models, and the high cost of the technology. In conclusion, despite their inherent limitations, PDTOs offer several advantages, including rapid culture, a high success rate, high consistency, and high throughput, which can be employed as a personalized treatment option for CRC. The use of PDTOs in CRC allows for the prediction of responses to different treatment modalities at various stages of disease progression. This has the potential to reduce adverse drug reactions and the emergence of resistance associated with clinical drugs, facilitate evidence-based clinical decision-making, and guide CRC patients in the selection of personalized medications, thereby advancing the individualized treatment of CRC.

Genetically modified organoids for tissue engineering and regenerative medicine

To date, genetically modified organoids are emerging as a promising 3D modeling tool aimed at solving genetically relevant clinical and biomedical problems for regenerative medicine and tissue engineering. As an optimal vehicle for gene delivery, genetically modified organoids can enhance or reduce the expression of target genes through virus and non-virus-based gene transfection methods to achieve tissue regeneration. Animal experiments and preclinical studies have demonstrated the beneficial role of genetically modified organoids in various aspects of organ regeneration, including thymus, lacrimal glands, brain, lung, kidney, photoreceptors, etc. Furthermore, the technology offers a potential treatment option for various diseases, such as Fabry disease, non-alcoholic steatohepatitis, and Lynch syndrome. Nevertheless, the uncertain safety of genetic modification, the risk of organoid application, and bionics of current genetically modified organoids are still challenging. This review summarizes the researches on genetically modified organoids in recent years, and describes the transfection methods and functions of genetically modified organoids, then introduced their applications at length. Also, the limitations and future development directions of genetically modified organoids are included.

Temporary Nanoencapsulation of Human Intestinal Organoids Using Silk Ionomers

Human intestinal organoids (HIOs) are vital for modeling intestinal development, disease, and therapeutic tissue regeneration. However, their susceptibility to stress, immunological attack, and environmental fluctuations limits their utility in research and therapeutic applications. This study evaluated the effectiveness of temporary silk protein-based layer-by-layer (LbL) nanoencapsulation technique to enhance the viability and functions of HIOs against common biomedical stressors, without compromising their native functions. Cell viability and differentiation capacity are assessed, finding that nanoencapsulation significantly improved HIO survival under the various environmental perturbations studied without compromising cellular functionality. Post-stress exposures, the encapsulated HIOs still successfully differentiated into essential intestinal cell types such as enterocytes, goblet cells, enteroendocrine cells, and Paneth cells. Moreover, the silk nanocoatings effectively protected against environmental stressors such as ultraviolet (UV) light exposure, protease degradation, antibody binding, and cytokine-induced inflammation. This nanoencapsulation technique shows promise for advancing HIO applications in disease modeling, drug testing, and potential transplantation therapies.

Development of a reliable method for human triple-negative breast cancer organotypic culture: Improving imaging and genomic studies in 3D cultures

Triple-negative breast cancer (TNBC) is highly aggressive and lacks targeted therapies, posing a major challenge in oncology. Traditional two-dimensional (2D) cell cultures fail to capture the tumor microenvironment's complexity, whereas three-dimensional (3D) cultures provide a more accurate model of tumor biology. We developed an advanced 3D culture system for TNBC cell lines BT-20 and MDA-MB-231, enhancing the hanging-drop method with Matrigel to restore essential extracellular matrix interactions. Confocal imaging showed MDA-MB-231 cells forming clusters typical of aggressive carcinoma, while BT-20 cells organized into duct-like structures. Molecular analysis of PI3K and β-catenin target genes revealed distinct expression patterns, with PI3K overexpressed and β-catenin downregulated in 3D cultures. Moreover, β-catenin distribution in the 3D cell culture closely resembles its pattern in tissue. These findings underscore the value of 3D models in understanding TNBC progression and in supporting the exploration of novel therapeutic strategies.

High Efficiency Lentiviral Transduction of Colon Organoids Using Reversible 2D/3D Culture Techniques

Organoids are a promising research tool for studying tissue development and disease in vitro. While organoids are frequently considered a replacement or complementary model for in vivo mouse experiments, exploiting their full potential often requires genetically engineered mice as a source of transgenic stem cells, also because genetic manipulation of organoids is rather inefficient and cumbersome. Here, we describe an alternative and optimized murine colon organoid manipulation protocol that reversibly and temporarily interrupts the 3D organoid structure for short-term 2D monolayer culture. This approach allows highly efficient viral transduction and genetic manipulation of stem cells in a 2D setting, followed by 3D stem cell embedding and restoration of the original organoid architecture. This method greatly improves the efficiency of lentiviral-mediated genetic manipulation of organoids and increases their potential applications in CRISPR/Cas9 and compound screens, immune-competent co-cultures, and disease modeling.

Novel research model for in vitro immunotherapy: co-culturing tumor organoids with peripheral blood mononuclear cells

Tumor organoids have emerged as powerful tools for in vitro cancer research due to their ability to retain the structural and genetic characteristics of tumors. Nevertheless, the absence of a complete tumor microenvironment (TME) limits the broader application of organoid models in immunological studies. Given the critical role of immune cells in tumor initiation and progression, the co-culture model of organoids and peripheral blood mononuclear cells (PBMCs) may provide an effective platform for simulating the interactions between immune and tumor cells in vitro. This model stands as a robust instrument for dissecting the TME, elucidating the molecular interactions, and exploring the therapeutic applications of chimeric antigen receptor (CAR)-engineered lymphocytes, as well as other cancer treatment modalities. This review systematically evaluates the advantages and disadvantages of the co-culture model, identifies its technical bottlenecks, and proposes corresponding optimization strategies. By summarizing the latest research advancements in this co-culture model, our goal is to provide valuable insights for further model optimization and clinical application, thereby promoting immunological research and bridging the gap between experimental outcomes and clinical practice.

Advancing precision medicine in esophageal squamous cell carcinoma using patient-derived organoids

BACKGROUND

Patient-derived organoids (PDOs) represent a promising approach for replicating the characteristics of original tumors and facilitating drug testing for personalized treatments across diverse cancer types. However, clinical evidence regarding their application to esophageal cancer remains limited. This study aims to evaluate the efficacy of implementing PDOs in clinical practice to benefit patients with esophageal squamous cell carcinoma (ESCC).

METHODS

Fresh surgical biopsies were obtained from patients with esophageal cancer for the establishment of PDOs. These PDOs were subsequently characterized through histological analysis. A customized drug panel, based on standard-of-care chemotherapy regimens, was applied to the PDOs. The resulting drug sensitivity profiles were then correlated with the clinical responses observed in individual patients undergoing actual treatment.

RESULTS

A total of 34 PDOs were successfully established with a 61.8% success rate. The classification method based on chemotherapy sensitivity closely corresponded to clinical responses. The paclitaxel plus cisplatin (TP)-sensitive group demonstrated significantly longer progression-free survival (PFS) compared to the resistant groups, Hazard ratio (HR), 5.12; 95% confidence intervals (CI 0.58-44.71; p < 0.05), thus illustrating the potential of this approach for guiding personalized treatment strategies.

CONCLUSION

Organoid biobanks were established across multiple institutes to facilitate PDOs-based functional precision medicine. The findings demonstrate that this framework offers robust predictive value in clinical settings, enhances precision therapeutics, and advances drug discovery for esophageal cancer.

Preliminary study of utilizing a patient derived tumor spheroid model to augment precision therapy in metastatic brain tumors

Treating metastatic brain tumors remains a significant challenge. This study introduces and applies the Patient-Derived Tumor Spheroid (PDTS) system, an ex vivo model for precision drug testing on metastatic brain tumor. The PDTS system utilizes a decellularized extracellular matrix (dECM) derived from adipose tissue, combined with the tumor cells, to form tumor spheroids. These spheroids were subsequently used to test anticancer drugs, with results compared to the clinical outcomes observed after administering these treatments to patients. To assess the validity of the data, the correlation between the drug responses observed in the PDTS model and actual patient outcomes was analyzed. Chi-square tests evaluated the significance of associations between lab predictions and clinical outcomes, using a significance threshold of p < 0.05. In preliminary data, 17 patients met the criteria for final analysis, which showed an overall 57% accuracy (p-value = 0.463), with improvements to 73% accuracy (p-value = 0.072) when patients receiving certain treatments were excluded. This PDTS offers real-time results within three weeks, simultaneous testing of multiple drugs, and the ability to culture and store tumor cells for reproducibility. Despite some limitations, further development of this model could enhance its clinical application and improve patient outcomes.

Carbonic anhydrase 2 facilitates sorafenib resistance by counteracting MCT4-mediated intracellular pH dysregulation in HCC

Sorafenib, the targeted therapy for hepatocellular carcinoma (HCC), has been utilized in clinics for over a decade. However, its effectiveness is severely hindered by acquired drug resistance, the mechanisms of which remain largely elusive. In this study, we identify that carbonic anhydrase 2 (CA2) is a key regulator of sorafenib resistance. Mechanistically, sorafenib treatment decreases intracellular pH (pHi) by suppressing monocarboxylate transporter 4 (MCT4) expression, while high levels of CA2 counteract MCT4-mediated pHi dysregulation upon sorafenib treatment, maintaining pHi homeostasis to facilitate cell survival and sorafenib resistance. Targeting CA2 re-sensitizes resistant HCC cells to sorafenib both in vitro and in vivo. Importantly, analysis of clinical samples shows a strong correlation between CA2 expression levels and the therapeutic efficacy of sorafenib in HCC patients. Our findings highlight the significance of CA2 in facilitating sorafenib resistance and propose targeting CA2 as a potential strategy for overcoming sorafenib resistance in HCC patients.

Current preclinical models of brain metastasis

Brain metastases (BMs) represent the most prevalent intracranial malignancy within the adult. They are identified in up to 20% of patients with solid tumors and this percentage varies between tumor types and age. Due to the selective permeability of the blood-brain barrier, most anticancer drugs can't reach significant concentrations in the brain, representing a major obstacle to the patients' survival. Furthermore, intra- and inter-patient heterogeneity and the unique brain microenvironment add a layer of complexity to the clinical management of BMs. In the perspective of finding new therapeutic approaches and better understanding the molecular mechanisms involved in brain metastasis, the use of appropriate preclinical models is essential. Here, we review current in vivo, in vitro and ex vivo models for the study of brain metastasis while outlining their advantages and limitations.

Matrix-free human lung organoids derived from induced pluripotent stem cells to model lung injury

BACKGROUND

Organoids, as near-physiological 3D culture systems, offer new opportunities to study the pathogenesis of various organs in mimicking the cellular complexity and functionality of human organs.

METHOD

Here we used a quite simple and very practicable method to successfully generate induced pluripotent stem cell (iPSC)-derived human lung organoids (LuOrg) in a matrix-free manner as an alternative to the widely used preclinical mouse models in order to investigate normal lung damage in detail and as close as possible to the patient. We performed detailed morphological and molecular analyses, including bulk and single cell RNA sequencing, of generated lung organoids and evaluated the quality and robustness of our model as a potential in vitro platform for lung diseases, namely radiation-induced lung injury.

RESULTS

A matrix-free method for differentiation of iPSCs can be used to obtain lung organoids that morphologically reflect the target tissue of the human lung very well, especially with regard to the cellular composition. The different cellular fates were investigated following the genotoxic stress induced by radiation and revealed further insights in the radiation-sensitivity of the different lung cells. Finally, we provide cellular gene sets found to be induced in the different lung organoid cellular subsets after irradiation, which could be used as additional RT response and particularly senescence gene sets in future studies.

CONCLUSION

By establishing these free-floating LuOrgs for the investigation of cancer therapeutic approaches as a new and patient-oriented in vitro platform particularly in experimental radiooncology, not only a reduction in the number of experimental animals, but also an adequately and meaningfully replacement of corresponding animal experiments can be achieved.

GO-CRISPR: A highly controlled workflow to discover gene essentiality in loss-of-function screens

Genome-wide CRISPR screens are an effective discovery tool for genes that underlie diverse cellular mechanisms that can be scored through cell fitness. Loss-of-function screens are particularly challenging compared to gain-of-function because of the limited dynamic range of decreased sgRNA sequence detection. Here we describe Guide-Only control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, Toolset for the Ranked Analysis of GO-CRISPR Screens (TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer and demonstrate superior performance to standard screening methods. The unique integration of the pooled sgRNA library quality and guide-only controls allows TRACS to identify novel molecular pathways that were previously unidentified in tumor dormancy and undetectable to analysis packages that lack the guide only controls. Together, GO-CRISPR and TRACS can robustly improve the discovery of essential genes in challenging biological scenarios such as growth arrested cells.

A High-Throughput and Logarithm-Serial-Dilution Microfluidic Chip for Combinational Drug Screening on Tumor Organoids

Tumor organoids are biological models for studying precision medicine. Microfluidic technology offers significant benefits for high throughput drug screening using tumor organoids. However, the range of concentrations achievable with traditional linear gradient generators in microfluidics is restricted, generating logarithmic drug concentration gradients by adjusting the channel ratio in the chip is confined to single-drug dilution chips, significantly restricting the application of microfluidics in drug screening. Here, we presented a microfluidic chip featuring continuous dilution capabilities, which generates logarithmic stepwise drug concentration gradients. We have devised a "mathematical-circuit-chip" model for designing such chips, and based on this model, we have developed and fabricated a device capable of providing 36 distinct drug concentration conditions for two types of drugs. The chip is composed of two structurally identical yet orthogonally arranged layers, each containing a dilution network capable of forming a 5-fold gradient and a tumor organoid culture module. Drug and culture medium delivery to the open culture chamber array is driven by syringe pumps. We have conducted drug screening experiments on patient-derived tumor organoids. This device facilitates high-throughput drug screening for patient-derived organoids, representing a significant stride toward the realization of precision medicine.