The rapid emergence of multidrug-resistant Shigella dysenteriae strains necessitates new therapeutic approaches, such as phage therapy. Phages are considered a promising adjunct to antibiotics. The rapid emergence of phage-resistant bacterial mutants represents a major challenge in clinical practice. Nevertheless, this sometimes comes with fitness trade-offs. Thus, understanding the fitness trade-offs is crucial prior to phage clinical application. In the present study, a new lytic S. dysenteriae phage, Henu12, was isolated. Henu12 was assigned to the Caudoviricetes class and demonstrated good thermal, pH, and chloroform stability. The phage genome comprises a 69,779 bp linear double-stranded DNA with 90 open reading frames and has the highest similarity with Shigella phage Sf15 and Escherichia phage vB_EcoM_3HA14. Interestingly, the genome did not contain integrases, virulence, or antibiotic resistance genes. A time-kill assay demonstrated synergistic effects with polymyxin B, tetracycline, and ceftazidime. The phage-resistant mutant demonstrated impaired adsorption, downregulation of the tested lipopolysaccharide biosynthetic genes, enhanced sensitivity to polymyxin B and tetracycline, and environmental stressors, impaired biofilm, and diminished in vivo colonization compared to the wild-type strain. The whole-genome resequencing of the phage-resistant mutant identified a multi-base insertion in the waaH gene involved in the lipopolysaccharide biosynthesis pathway, potentially responsible for the phage resistance phenotype, along with other mutations related to the associated trade-offs. Together, these findings provide new insights into the evolutionary interactions between phage resistance and bacterial fitness that could potentially offer a novel approach to treat resistant Shigella dysenteriae infections. IMPORTANCE: Phage therapy is a promising approach to combat the rise of multidrug-resistant bacteria. The emergence of phage-resistant bacterial strains is a potential complication associated with the application of phages. In the current study, we demonstrated that the synergistic use of phage Henu12 in conjunction with antibiotics not only enhances the bactericidal efficacy but also postpones the development of resistant strains. In addition, we provide a better understanding of the fitness trade-off that might fill some gaps in the future success of phage therapies in combating resistant shigellosis in clinical settings.

Chronic kidney disease (CKD) has emerged as a critical public health challenge worldwide, and organ donor shortages underscore the urgent need for alternative therapeutic strategies. Advances in stem cell technologies have enabled the generation of kidney organoids, providing innovative platforms to model renal development, investigate disease mechanisms, support drug discovery, and explore applications in regenerative medicine. Yet, limitations such as immature tissue architecture, insufficient vascularisation, and unaddressed safety concerns still hinder their translation into regenerative medicine. In this review, we summarise the fundamentals of kidney development, current differentiation approaches, and the signalling and epigenetic mechanisms underlying organoid lineage specification. We further highlight the roles of bioengineering innovations and single‐cell transcriptomics in establishing evaluation frameworks and enhancing structural complexity. We finally emphasise that existing optimisation frameworks, primarily focused on improving differentiation efficiency and enforcing relatively restricted lineage specification, may prove inadequate for bridging the gap to clinical translation. Instead, the most promising paradigm shift involves the convergence of bioengineering modulation and high‐resolution functional assessment to facilitate the synchronised advancement of organoid complexity and physiological utility.

Background: Thymoma (THYM) is a rare epithelial tumor originating in the anterior mediastinum. Due to the lack of specific clinical manifestations and reliable molecular biomarkers, its diagnosis and treatment are often delayed until advanced stages. Although multi-omics technologies have provided new strategies for biomarker discovery, systematic integrative studies specifically focused on thymoma remain limited. Objectives: This study aimed to identify and validate potential diagnostic biomarkers for thymoma through the integration of multi-omics data and machine learning approaches. Methods: We integrated transcriptomic, proteomic, and epigenomic datasets and applied machine learning algorithms to screen for core candidate genes. The cell-type-specific expression patterns of the identified candidates were further evaluated using single-cell RNA sequencing (scRNA-seq), and their potential molecular functions were predicted via in silico perturbation analysis. In addition, immunohistochemistry (IHC) was performed to validate the differential expression of the candidate biomarker at the protein level. Results: Six core candidate genes—interferon regulatory factor 6 (IRF6), thyroid hormone receptor interactor 6 (TRIP6), plakophilin 1 (PKP1), cadherin 1 (CDH1), pre-B-cell leukemia transcription factor 1 (PBX1), and keratin 1 (KRT1)—were identified through machine learning. Among these, PKP1 demonstrated excellent diagnostic performance in both the training set (area under the receiver operating characteristic (ROC) curve, AUC: 0.83; sensitivity: 0.80; specificity: 0.875) and the validation set (AUC: 0.94; sensitivity: 0.93; specificity: 1.000). Single-cell RNA sequencing confirmed a significantly enriched expression pattern of PKP1 in thymoma tumor cells. In silico perturbation analysis suggested that PKP1 may be involved in cell adhesion and tumor progression through regulation of the extracellular matrix (ECM)–integrin–cytoskeleton axis. Immunohistochemistry further validated the significantly elevated protein expression level of PKP1 in thymoma tissues. Conclusions: This study identifies PKP1 as a potential diagnostic biomarker for thymoma with high diagnostic performance and tumor cell-enriched expression, providing new insights into the molecular mechanisms underlying thymoma progression and its potential clinical applications.