Potent Inhibition and Rapid Photoactivation of Endogenous Bruton's Tyrosine Kinase Activity in Native Cells via Opto-Covalent Modulators.

Naturally, kinases exert their activities in a highly regulated fashion. A number of ingenious approaches have been developed to artificially control kinase activity by external stimuli, such as the incorporation of unnatural amino acids or the fusion of additional protein domains; however, methods that directly modulate endogenous kinases in native cells are lacking. Herein, we present a facile and potent method that takes advantage of recent developments in targeted covalent inhibitors and rapid light-mediated uncaging chemistry. Using an important drug target, Bruton's tyrosine kinase (BTK), as an example, these opto-covalent modulators successfully blocked the activity of endogenous BTK in native cells after simple incubation and washout steps. However, upon a few minutes of light irradiation, BTK activity was cleanly restored, and could be blocked again by conventional inhibitors. Promisingly, this photoactivation strategy easily worked in human peripheral blood mononuclear cells (hPBMCs).

ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1.

Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type-B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling-mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling-mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26-LIKE INTRINSIC PROTEIN (NIP)-encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12-mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high-order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP-qPCR, EMSA, and transient dual-LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling-mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.

Predictive Modeling with Temporal Graphical Representation on Electronic Health Records.

Deep learning-based predictive models, leveraging Electronic Health Records (EHR), are receiving increasing attention in healthcare. An effective representation of a patient's EHR should hierarchically encompass both the temporal relationships between historical visits and medical events, and the inherent structural information within these elements. Existing patient representation methods can be roughly categorized into sequential representation and graphical representation. The sequential representation methods focus only on the temporal relationships among longitudinal visits. On the other hand, the graphical representation approaches, while adept at extracting the graph-structured relationships between various medical events, fall short in effectively integrate temporal information. To capture both types of information, we model a patient's EHR as a novel temporal heterogeneous graph. This graph includes historical visits nodes and medical events nodes. It propagates structured information from medical event nodes to visit nodes and utilizes time-aware visit nodes to capture changes in the patient's health status. Furthermore, we introduce a novel temporal graph transformer (TRANS) that integrates temporal edge features, global positional encoding, and local structural encoding into heterogeneous graph convolution, capturing both temporal and structural information. We validate the effectiveness of TRANS through extensive experiments on three real-world datasets. The results show that our proposed approach achieves state-of-the-art performance.

N-Methyl-d-Aspartate Receptor Antibody and Sensory Gating Deficits in Non-smoking, Minimal Antipsychotic Medication Exposure, and First-Episode Patients With Schizophrenia.

BACKGROUND AND HYPOTHESIS: Sensory gating deficit is considered a pathophysiological feature of schizophrenia, which has been linked to N-methyl-d-aspartate receptor (NMDAR) hypofunction as one of the potential underlying mechanisms. Here, we hypothesize that higher levels of NMDAR antibody (Ab) may contribute to the sensory gating deficits in schizophrenia. STUDY DESIGN: We enrolled 72 non-smoking inpatients with first-episode schizophrenia (FES), most of them with only a relatively short duration of exposure to antipsychotic medications, and 51 non-smoking healthy controls (HC). Sensory gating was measured by P50 evoked potentials ratio and the difference between the two stimuli in an auditory paired-stimuli paradigm and serum NMDAR Ab levels were quantified by enzyme-linked immunosorbent assay. STUDY RESULTS: The FES group showed higher serum NMDAR Ab levels [(9.23 ±â€…4.15) ng/mL vs. (7.08 ±â€…2.83) ng/mL; P = .002], higher P50 ratio (P = .002), and less P50 difference (P = .001) than HC. In partial correlation analysis, serum NMDAR Ab levels were positively correlated with the P50 ratio (r = 0.36, P = .003) and negatively with the P50 difference (r = -0.39, P = .001) in the FES group. The NMDAR Ab levels mediated the diagnosis of schizophrenia and P50 sensory gating deficits (P50 ratio and P50 difference). CONCLUSIONS: Autoimmunity targeting NMDAR is a crucial intermediate mechanism in impaired sensory gating in patients with schizophrenia. The findings support early intervention targeting NMDAR for patients with schizophrenia.

Prolongation of seed viability and grain quality in rice by editing OsLOX1 using CRISPR/Cas9.

Deterioration of rice (Oryza sativa L.) affects grain quality and seed viability during storage. Lipoxygenase (LOX), a key enzyme in lipid metabolism, directly affects the rate of ageing. Here, we found that knock-out of lipoxygenase gene OsLOX1 by CRISPR/Cas9 delayed loss of seed viability and quality. Transcriptome analysis showed that during storage, OsLOX1 affected transcription of multiple genes, including genes related to lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase, which may regulate the seed storability. The genes significantly down- and up-regulated only in Ningjing 4 after NA for 13 months and 3 days of AA suggesting that OsLOX1 likely promoted seed viability in rice by balancing ageing and storage related genes, and regulated the seed storability through the amino acid synthesis and metabolic pathways. Moreover, knock-out of OsLOX1 without CRISPR/Cas9 not only improved the seed viability, but also had little impact on agronomic traits. More importantly, the OsLOX1 knock-out lines were approved in 2019 (Agricultural Foundation of China Report No. 770). Collectively, our study showed that knock-out of OsLOX1 is beneficial for prolongation of seed viability and can be directly applied to agricultural production. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01506-4.

SepsisLab: Early Sepsis Prediction with Uncertainty Quantification and Active Sensing.

Sepsis is the leading cause of in-hospital mortality in the USA. Early sepsis onset prediction and diagnosis could significantly improve the survival of sepsis patients. Existing predictive models are usually trained on high-quality data with few missing information, while missing values widely exist in real-world clinical scenarios (especially in the first hours of admissions to the hospital), which causes a significant decrease in accuracy and an increase in uncertainty for the predictive models. The common method to handle missing values is imputation, which replaces the unavailable variables with estimates from the observed data. The uncertainty of imputation results can be propagated to the sepsis prediction outputs, which have not been studied in existing works on either sepsis prediction or uncertainty quantification. In this study, we first define such propagated uncertainty as the variance of prediction output and then introduce uncertainty propagation methods to quantify the propagated uncertainty. Moreover, for the potential high-risk patients with low confidence due to limited observations, we propose a robust active sensing algorithm to increase confidence by actively recommending clinicians to observe the most informative variables. We validate the proposed models in both publicly available data (i.e., MIMIC-III and AmsterdamUMCdb) and proprietary data in The Ohio State University Wexner Medical Center (OSUWMC). The experimental results show that the propagated uncertainty is dominant at the beginning of admissions to hospitals and the proposed algorithm outperforms state-of-the-art active sensing methods. Finally, we implement a SepsisLab system for early sepsis prediction and active sensing based on our pre-trained models. Clinicians and potential sepsis patients can benefit from the system in early prediction and diagnosis of sepsis.

CCR2+ monocytes are dispensable to resolve acute pulmonary Pseudomonas aeruginosa infections in WT and Cystic Fibrosis mice.

Extravasation of CCR2-positive monocytes into tissue and to the site of injury is a fundamental immunological response to infections. Nevertheless, exuberant recruitment and/or activity of these monocytes and monocyte-derived macrophages can propagate tissue damage, especially in chronic inflammatory disease conditions. We have previously shown that inhibiting the recruitment of CCR2-positive monocytes ameliorates lung tissue damage caused by chronic neutrophilic inflammation in cystic fibrosis (CF) mouse models. A potential concern with targeting monocyte recruitment for therapeutic benefit in CF, however, is whether they are essential for eradicating infections such as Pseudomonas aeruginosa (PA), a pathogen that commonly colonizes and damages the lungs of patients with CF. In this study, we investigated the role of CCR2-positive monocytes in the immune response to acute pulmonary PA infection. Our data show that the altered host immune response caused by the lack of monocyte recruitment to the lungs does not impact PA lung colonization, clearance, and the severity of the infection. These results also hold up in a CF mouse background, which have a hyper-inflammatory immune response, yet exhibit reduced bactericidal activity. Thus, we lay the groundwork for future studies to investigate the use of CCR2 inhibitors as a potential therapy to ameliorate lung tissue damage in CF. This could be given alone or as an adjunct therapy with CFTR modulators that significantly improve clinical outcomes for eligible patients, but do not completely resolve the persistent infection and inflammation that drive lung tissue damage.

Non-stationary Domain Generalization: Theory and Algorithm.

Although recent advances in machine learning have shown its success to learn from independent and identically distributed (IID) data, it is vulnerable to out-of-distribution (OOD) data in an open world. Domain generalization (DG) deals with such an issue and it aims to learn a model from multiple source domains that can be generalized to unseen target domains. Existing studies on DG have largely focused on stationary settings with homogeneous source domains. However, in many applications, domains may evolve along a specific direction (e.g., time, space). Without accounting for such non-stationary patterns, models trained with existing methods may fail to generalize on OOD data. In this paper, we study domain generalization in non-stationary environment. We first examine the impact of environmental non-stationarity on model performance and establish the theoretical upper bounds for the model error at target domains. Then, we propose a novel algorithm based on adaptive invariant representation learning, which leverages the non-stationary pattern to train a model that attains good performance on target domains. Experiments on both synthetic and real data validate the proposed algorithm.

Impact of exacerbation history on future risk and treatment outcomes in chronic obstructive pulmonary disease patients: A prospective cohort study based on Global Initiative for Chronic Obstructive Lung Disease (GOLD) A and B classifications.

Background: In this study, we aimed to explore the impact of exacerbation history on future exacerbation and mortality with different inhaled drugs in chronic obstructive pulmonary disease (COPD) patients based on a Global Initiative Chronic Obstructive Lung Disease (GOLD) A and B classifications. Methods: This observational study was based on the cohort study Real World Research of Diagnosis and Treatment of COPD (RealDTC). We collected data from COPD patients in China from 1 July 2017 to 31 December 2022. Patients were followed up until December 2023 or death. Further, we separated GOLD A and B patients into GOLD A0 and B0, who had no exacerbation during the previous year, and GOLD A1 and B1, who had only one exacerbation during the previous year. Study outcomes included moderate-to-severe exacerbation, hospitalisation, frequent exacerbation in the first year and all-cause mortality during total follow-up. Results: Of the 8318 eligible patients, GOLD E group of patients suffered from a greater risk of exacerbation in the first year and death than patients in the GOLD A and B groups. GOLD A1 group had a higher risk of moderate-to-severe exacerbation (hazard ratio (HR) = 2.087; 95% confidence interval (CI) = 1.419-3.068), hospitalisation (HR = 1.704; 95% CI = 1.010-2.705) and frequent exacerbation (HR = 1.983; 95% CI = 1.046-3.709) compared to GOLD A0. GOLD B1 group had a risk of moderate-to-severe exacerbation (HR = 1.321; 95% CI = 1.105-1.679) and mortality (HR = 1.362; 95% CI = 1.026-1.963) that exceeded the risk in GOLD B0 group. The treatment outcome of different inhaled drugs had no statistical differences in GOLD A0 group. In GOLD A1 group, only inhaled corticosteroids (ICS), in addition to long-acting ß-2 agonist (LABA) and long-acting muscarinic antagonist (LAMA), reduced the risk of moderate-to-severe exacerbation in the first year compared to only LAMA. As for the GOLD B0 group, LABA and LAMA decreased the odds of moderate-to-severe exacerbation, hospitalisation, frequent exacerbation and mortality compared to only LAMA. ICS, LABA, and LAMA in GOLD B0 also down-regulated the risk of frequent exacerbation, compared to only LAMA. In addition, GOLD B1 patients treated with LABA and LAMA or ICS, LABA, and LAMA had a lower risk of moderate-to-severe exacerbation and hospitalisation. Meanwhile, ICS, LABA, and LAMA also reduced the risk of frequent exacerbation and mortality, compared to only LAMA in the multivariate Cox analysis. Conclusions: Compared to the GOLD A or B group without exacerbation history, GOLD A patients with exacerbation history had a higher risk of future exacerbation, and GOLD B patients with exacerbation history had a higher risk of future exacerbation and mortality and benefited more from triple inhaler therapy.

DNMT1 silencing induces KIR2DL1/2/3 expression via methylation to alleviate graft-versus-host disease after allogeneic hematopoietic stem cell transplantation.

Natural killer (NK) cells are the promoters in graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT), while demethylation can regulate NK cell function. We explored the mechanism of demethylation regulating NK cell function to affect GVHD after allo-HSCT. BALB/c mice were transfused with C57BL/6 mouse-derived NK and bone marrow cells to establish GVHD models, followed by isolation and in-vitro expansion of NK cells. NK cell purity, cytokine levels, proliferation, and cytokine-producing NK cell levels were measured via flow cytometry. KIR2DL1/2/3 methylation was tested by Methylation-specific polymerase chain reaction (MSP), with determination of mouse survival and GVHD scores. KIR2DL1/2/3 and DNMT1 expression was detected through qRT-PCR and/or western blot. Methylation levels were upregulated and KIR2DL1/2/3 expression was downregulated in GVHD mouse model-derived NK cells following IL-2 stimulation. DNMT1 silencing promoted KIR2DL1/2/3 expression, proliferation, and the secretion of Granzyme, Perforin, and Interferon-γ (IFN-γ) in C57BL/6 mouse-derived NK cells. DNMT1 silencing also enhanced mouse survival, reduced GVHD scores, promoted KIR2DL1/2/3 expression on the NK cell surface, and increased the secretion of Granzyme, Perforin, IFN-γ, and the number of cytokine-producing NK cells in the spleen, liver, and lung tissues of the models. Collectively, DNMT1 silencing induced KIR2DL1/2/3 expression in NK cells through reducing methylation to alleviate GVHD after allo-HSCT.

Synthesis of an Ethylenediaminetetraacetic Acid-like Ligand Based on Sucrose Scaffold and Complexation and Proton Relaxivity Studies of Its Gadolinium(III) Complex in Solution.

Sucrose constitutes a non-toxic, biodegradable, low-cost and readily available natural product. To expand its utility, we developed total synthesis for a ligand based on a sucrose scaffold for potential use as a metal chelation agent. The designed target (compound 2) has a metal-chelating functionality at both the C-6 and C-6' positions, which can provide a first coordination sphere of eight valencies. The designed total synthesis was highly efficient. To demonstrate the utility of the ligand, we studied its complexation with Gd(III). Using potentiometric titration and high-resolution mass spectrometry, we confirmed the formation of a 1:1 complex with Gd(III), which has a respectable formation constant of ~1013.4. Further NMR relaxivity studies show that the Gd(III) complex has a relaxivity (r1) of 7.6958 mmol-1 s-1.

Based on electronic nose and multi-omics, investigate the dynamic changes of volatile and non-volatile organic compounds in waxy wheat Baijiu from different years.

Chinese baijiu is highly regarded for its unique flavor, and a variety of crops can be utilized as raw materials in its production. Waxy crops are essential ingredients in the brewing of high-quality baijiu; however, there is currently no comprehensive identification of volatile organic compounds (VOCs) and non-volatile compounds (N-VOCs) in waxy wheat baijiu (WWB). This study aims to investigate the dynamic changes of VOCs and N-VOCs in WWB during several important time periods from new to aged. A total of 25 amino acids underwent changes in the samples, with numerous physiologically active beneficial amino acids showing significant accumulation after aging. Additionally, 517 VOCs changed after aging, predominantly comprising esters and terpenoids, with 72 major VOCs being identified. A total of 718 metabolites were identified in the metabolome, primarily comprising alterations in lipids, amino acids, phenolic acids, organic acids, and alkaloids. These metabolites significantly influenced the levels of amino acids and VOCs. Our study is the first to provide a comprehensive examination of these aspects of WWB, highlighting its unique advantages over other crops. We believe that this research will establish a theoretical foundation for the application of waxy wheat in the baijiu industry, improve baijiu quality, and promote the development of functional baijius.

Association between ABO blood groups and hematological myeloid neoplasms in adolescents and adults.

Background: Prior research suggests a potential link between ABO blood types and susceptibility to various malignancies. The correlation between ABO blood types and hematological myeloid neoplasms, however, remains inadequately explored. Objective: This study investigates the association between ABO blood groups and the incidence of hematological myeloid neoplasms in adolescents and adults. Methods: In this retrospective clinical study, 1,022 adolescent and adult cases of myeloid neoplasms diagnosed at our institution were initially considered. After excluding conditions potentially linked to ABO blood types from prior studies, 792 eligible cases were analyzed. These cases were categorized based on disease subtypes and compared with a control group for blood type distribution. Results: Our findings reveal a significantly higher prevalence of blood type A in patients with myeloid neoplasms compared to the control group, except for chronic myelocytic leukemia and myeloproliferative neoplasms. Conversely, the prevalence of blood type AB in myeloid neoplasms was notably lower than in the control group. Conclusion: The study suggests a potential association between ABO blood types and the risk of developing hematological myeloid neoplasms in adolescents and adults. Further research is warranted to elucidate the underlying mechanisms of this relationship.

Thoracic Radiotherapy Improves the Survival in Patients With EGFR-Mutated Oligo-Organ Metastatic Non-Small Cell Lung Cancer Treated With Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors: A Multicenter, Randomized, Controlled, Phase III Trial.

PURPOSE: This multicenter, randomized, phase III clinical trial (Northern Radiation Oncology Group of China-002) focused on patients with oligo-organ metastatic non-small cell lung cancer (NSCLC) who have epidermal growth factor receptor (EGFR) mutations. We aimed to investigate whether first-line concurrent thoracic radiotherapy (TRT) and EGFR-tyrosine kinase inhibitors (TKIs), compared with TKIs alone, could achieve better survival. MATERIALS AND METHODS: The patients in the TKI plus TRT group received 60 Gy to primary lung tumor and positive regional lymph nodes. Radiotherapy for metastases to other sites was determined by clinicians. The primary end point was the progression-free survival (PFS). Secondary end points included overall survival (OS) and treatment-related adverse events (TRAEs). The first and second interim analyses were performed in March 2021 and March 2022. RESULTS: Between April 14, 2016, and February 25, 2022, a total of 118 patients were enrolled. Compared with the TKI alone group, the TKI plus TRT group achieved significantly better PFS (hazard ratio [HR], 0.57; P = .004) and OS (HR, 0.62; P = .029). The median PFS was 10.6 months in the TKI alone group and 17.1 months in the TKI plus TRT group. The median OS was 26.2 months and 34.4 months in the TKI alone group and TKI plus TRT group, respectively. The TKI plus TRT group showed better local control but was associated with a higher incidence of severe TRAEs (11.9% v 5.1%). CONCLUSION: For patients with EGFR-mutated oligo-organ metastatic NSCLC treated with first-line EGFR-TKIs, concurrent TRT improves the PFS and OS, and TRAEs are acceptable and tolerable.

Associations between plasma metals and hemoglobin in female college students with dysmenorrhea.

Background: Hemoglobin (HGB) was the most important factors which could cause dysmenorrhea in women. Metals exposure and hemoglobin level in dysmenorrhea female was unclear. We aimed to explore the associations of multi-metal exposure and HGB level in female college students with dysmenorrhea. Methods: 253 female students who had dysmenorrhea was included in our study. The Last Absolute Shrinkage and Selection Operator (LASSO) regression, generalized linear model (GLM), and Bayesian Kernel Machine Regression (BKMR) models were used to explore the associations of multi-metal exposure and HGB levels in female college students with dysmenorrhea. Results: GLM results showed that plasma Fe, Ni and Rb was positively associated with HGB and plasma Co was negatively associated with HGB. In menarche age ≤13 years old group, plasma Co and Rb only was negatively and positively associated with HGB level, respectively, and plasma Ni had positive association with HGB level in menarche age >13 years old group. BKMR results showed the reverse U-shaped relationship between the five metals mixture (Co, Fe, Ni, Cu and Rb) and HGB levels in overall and menarche age ≤13 years old group. However, there were positive association between the five metals mixture and HGB levels in menarche age >13 years old group. Conclusion: Our present study revealed that metals (Fe, Ni, Co, Rb, Cu) mixture exposure could effect HGB levels in female college students with dysmenorrhea. And the relationships were different during different menarche age in female college students.

Characterization of Trap States in AlGaN/GaN MIS-High-Electron-Mobility Transistors under Semi-on-State Stress.

Devices under semi-on-state stress often suffer from more severe current collapse than when they are in the off-state, which causes an increase in dynamic on-resistance. Therefore, characterization of the trap states is necessary. In this study, temperature-dependent transient recovery current analysis determined a trap energy level of 0.08 eV under semi-on-state stress, implying that interface traps are responsible for current collapse. Multi-frequency capacitance-voltage (C-V) testing was performed on the MIS diode, calculating that interface trap density is in the range of 1.37×1013 to 6.07×1012cm-2eV-1 from EC-ET=0.29 eV to 0.45 eV.

The bifunctional transcription factor NAC32 modulates nickel toxicity responses through repression of root-nickel compartmentalization and activation of auxin biosynthesis.

Nickel (Ni) is an important micronutrient, but excess Ni is toxic to many plant species. Currently, relatively little is known about the genetic basis of the plant responses to Ni toxicity. Here, we demonstrate that NAC32 transcription factor functions as a core genetic hub to regulate the Ni toxicity responses in Arabidopsis. NAC32 negatively regulates root-Ni concentration through the IREG2 (IRON REGULATED2) encoding a transporter. NAC32 also induces local auxin biosynthesis in the root-apex transition zone by upregulating YUCCA 7 (YUC7)/8/9 expression, which results in a local enhancement of auxin signaling in root tips, especially under Ni toxicity, thereby impaired primary root growth. By analyses of various combinations of nac32 and ireg2 mutants, as well as nac32 and yuc7/8/9 triple mutants, including high-order quadruple mutant, we demonstrated that NAC32 negatively regulates Ni stress tolerance by acting upstream of IREG2 and YUC7/8/9 to modulate their function in Ni toxicity responses. ChIPqPCR, EMSA (electrophoretic mobility shift assay) and transient dual-LUC reporter assays showed that NAC32 transcriptionally represses IREG2 expression but activates YUC7/8/9 expression by directly binding to their promoters. Our work demonstrates that NAC32 coordinates Ni compartmentation and developmental plasticity in roots, providing a conceptual framework for understanding Ni toxicity responses in plants.

Patient-derived organoids in precision cancer medicine.

Organoids are three-dimensional (3D) cultures, normally derived from stem cells, that replicate the complex structure and function of human tissues. They offer a physiologically relevant model to address important questions in cancer research. The generation of patient-derived organoids (PDOs) from various human cancers allows for deeper insights into tumor heterogeneity and spatial organization. Additionally, interrogating non-tumor stromal cells increases the relevance in studying the tumor microenvironment, thereby enhancing the relevance of PDOs in personalized medicine. PDOs mark a significant advancement in cancer research and patient care, signifying a shift toward more innovative and patient-centric approaches. This review covers aspects of PDO cultures to address the modeling of the tumor microenvironment, including extracellular matrices, air-liquid interface and microfluidic cultures, and organ-on-chip. Specifically, the role of PDOs as preclinical models in gene editing, molecular profiling, drug testing, and biomarker discovery and their potential for guiding personalized treatment in clinical practice are discussed.