Radiotherapy is an important treatment for lung cancer. However, in the course of radiotherapy, treatment-related side effects and decreased radiosensitivity remain challenging issues. TGF-βR1 can induce radiation-induced bystander effect (RIBE) through the primary cilia; however, this mechanism needs to be further elucidated. At present, traditional Chinese medicine (TCM) shows great advantages in protecting against RIBE, in which Astragalus and its related formulations show good protective effects against radiation; however, the mechanisms by which Astragalus exerts these protective effects are unknown. Therefore, this study aims to investigate the molecular mechanisms by which TGF-βR1 exerts RIBE through the primary cilia, enhancing radiosensitivity, and to reveal the therapeutic effects of small molecules derived from Astragalus membranaceus via this pathway.

Tumorigenesis and progression are driven by immune dysregulation and escape, thus evaluating immune function is crucial for the identification of diseases or health conditions. Currently, there is a lack of non-invasive biomarkers in the overall management of PCa to assess a patient's immune status and immune response to different treatment regimens. Lymphocyte subsets are directly involved in the surveillance, defense and regulation of the human immune system, and are primarily composed of T cells, B cells and NK cells. The combined assay of lymphocyte subsets number, phenotype and function is currently a more accepted method of assessing immune function. Quantitative aspects are presented in terms of both absolute counts and relative percentages. Phenotypic molecules reflect host immunity mainly through markers such as HLA-DR, CD25, CD45RO, CD45RA, CCR7 and CD28. Markers, such as IFN-γ, Fas ligand, perforin, granzyme B, TCF-1 (marker for maintaining the stem cell nature, self-renewal and undifferentiated state), TOX (marker of T cells exhaustion) and immune checkpoint molecules (TIM-3, PD-1, LAG3) can be used to represent the functions of lymphocyte subsets. Nevertheless, existing research conclusions are miscellaneous and no studies have systematically reviewed the role of lymphocyte subsets in the diagnosis, treatment, and prognosis of PCa. In order to strengthen the comprehensive understanding and grasp of its role by urological surgeons, this review first introduced lymphocyte subsets in detail, and then condenses and summarizes the research progress of lymphocyte subsets in PCa from peripheral blood and tumor infiltration, respectively.

The thyroid gland is an endocrine organ responsible for production of triiodothyronine and thyroxine, essential hormones that regulate human metabolism. A wide range of conditions can impair its function, leading to potential life-threatening consequences such as myxedema coma. The standard treatment for hypothyroidism is lifelong levothyroxine supplementation, which, despite being a significant therapeutic breakthrough, has notable limitations and does not fully restore quality of life for many patients. Biomimetic thyroid gland has emerged as a promising alternative treatment strategy for patients with hypothyroidism. Most research to date has focused on generating thyroid organoids from primary thyroid cells or stem cells. However, there is growing interest in other approaches, including the use of biomaterials, bioreactors, and 3D bioprinting as potential alternatives or supplementary technologies to the organoids. While in vitro and preclinical studies have shown encouraging results, clinical application of biomimetic thyroid gland requires further studies in several key areas, including long-term functional validation, studies on large animal models, immunological compatibility and scaffold biodegradation, and absence of standardized good manufacturing practice (GMP)-compliant production protocols.

Tumor-associated macrophages (TAMs) are key contributors to the brain tumor microenvironment. However, their role in medulloblastoma (MB) progression and chemoresistance remains elusive.

Emerging evidence indicates that granzyme K expressing tumor infiltrating CD8 + T-cells play a critical role in mediating anti-tumor T-cell immunity and immunotherapy treatment response. However, precise characterization and cell surface markers for the viable isolation of these cells from tumor samples are lacking.

During weaning, the transition to solid food diversifies the gut microbiome, triggering a programmed immune response critical for long-lasting mucosal immunity. Previous work showed that the gut microbiome mediates epigenetic development in intestinal stem cells (ISCs) during suckling, but what happens during weaning is unclear. Here, genome-wide profiling revealed that weaning-driven microbiome changes shape the DNA methylome and transcriptome of murine ISCs in an IFNγ-dependent manner. Specifically, we observe demethylation of enhancer elements essential for MHC class II genes, which results in a transcriptional memory that persists through differentiation into adulthood. IFNγ blockade, or low-dose penicillin to target Gram-positive bacteria, in early life impaired microbiome-mediated epigenetic control and mucosal immunity, and exacerbated colitis. Murine organoids primed with IFNγ showed rapid, amplified transcriptional responses upon secondary stimulations. These findings reveal that early-life events alter the gut microbiome and these changes reprogramme ISC epigenetic memory to shape mucosal immunity.

Neural cells in the adult human central nervous system (CNS) display extensive transcriptional heterogeneity. How different layers of epigenetic regulation underpin this heterogeneity is poorly understood. Here we profile, at the single-nuclei epigenomic level, distinct regions of the adult human CNS, for chromatin accessibility and simultaneously for the histone modifications H3K27me3 and H3K27ac. We unveil a putative SOX10 enhancer and primed chromatin signatures at HOX loci in spinal-cord-derived human oligodendroglia (OLG) and astrocytes, but not microglia. These signatures in adult OLG were reminiscent of developmental profiles but were decoupled from robust gene expression. Moreover, using high-resolution Micro-C, we show that induced pluripotent stem-cell-derived human OLGs exhibit a HOX chromatin architecture compatible with the primed chromatin in adult OLGs, bearing a strong resemblance not only to OLG developmental architecture but also to high-grade pontine gliomas. Thus, epigenetic memory from developmental states in adult OLG not only enables them to promptly transcribe Hox family genes during regeneration but also makes them susceptible to gliomagenesis.

Ulcerative colitis (UC) is a debilitating, immune-mediated inflammatory disorder of the gastrointestinal (GI) tract with far-reaching consequences on distal organs, including the bone marrow. Here, we describe the molecular mechanisms that contribute to UC-induced abnormal hematopoiesis. We show that chronic UC drives HSPC differentiation toward myelopoiesis in an APE1/Ref-1/HIF-1α/IL-1r1-dependent manner. Blockade of the redox-activity of APE1/Ref-1 with APX3330 inhibits the elevated expression of HIF-1α in HSPCs and reverses the aberrant HSPC dynamics under the inflammatory milieu of UC, including suppression of pro-inflammatory Ly6Chi monocytes. Using echinomycin, we pharmacologically blocked HIF-1α activity and found that HIF-1α mediates inflammatory responses via downstream IL-1r1 signaling. Blockade of the redox activity of ref-1 rescues the abnormal HSPC function. Our data highlight the significance of the APE1/Ref-1/HIF-1α/IL-1r1 signaling cascade in aberrant hematopoiesis that contributes to the pathophysiology of chronic UC through a feed-forward loop.

The mammary gland serves as a pivotal model for studying stem cell dynamics and breast cancer, the most prevalent malignancy worldwide. Developing a long-term organoid culture system to study the normal physiology and pathophysiology of mammary glands in vitro is of paramount importance. However, current organoid systems lack the morphological and functional fidelity required to model its complex physiology. Here we present a detailed Protocol to establish a long-term, dynamic three-dimensional culture system for mouse mammary organoids, which we call 'mini-glands', that recapitulates in vivo morphogenesis and functional cycles. This method uses basal stem cells to generate organoids through sequential phases: sphere formation, polarity induction, symmetry breaking, branching morphogenesis and pseudoestrous cycle simulation. The resulting 'mini-glands' replicate the natural gland's branched architecture and undergo developmental stages mimicking puberty, pregnancy, lactation and involution. Furthermore, the system enables lineage tracing of cell fate transitions and oncogenic transformation studies via genetic manipulation. By bridging the gap between in vitro models and in vivo complexity, this platform advances studies in mammary gland biology, breast cancer initiation and therapeutic screening. The Protocol can be readily performed by researchers with basic experience in mammalian cell culture and requires no specialized instrumentation. A full culture cycle typically takes ~2 weeks to produce mature, highly branched 'mini-glands'.

Glioblastoma (GBM) is often complicated by venous thromboembolism (VTE), primarily driven by tissue factor (TF, F3) and podoplanin (PDPN). These factors promote local hypercoagulation and microthrombosis, thereby contributing to tumor progression by enhancing migration, invasion, and inflammation. Both TF and PDPN can be released via extracellular vesicles (EVs), which carry procoagulant and immunomodulatory cargo. We developed a translational workflow combining biobanked tumor samples, clinical data, ex vivo GBM cultures, and coagulation assays to investigate mechanisms of hypercoagulation. Intraoperative blood coagulation was profiled using ClotPro®. Gene expression of coagulation-related markers was analyzed in tumor tissues and cell lines, complemented by RNAseq-based profiling of coagulation–inflammation links. Functional coagulation assays included clotting time, platelet aggregation, and EV-based analysis of prothrombotic and immunomodulatory activity. Peripheral coagulation in GBM patients was largely unaltered. However, tumor tissues consistently showed high F3 and PDPN expression and markedly low tissue factor pathway inhibitor (TFPI) levels (p < 0.001), indicating a shift toward a procoagulant phenotype. Patient-derived GBM cell lines showed variable TF and PDPN expression, which correlated with clotting potential. Distinct procoagulant mechanisms were observed, with some cells engaging both TF-mediated thrombin generation and PDPN-driven platelet activation. EVs isolated from GBM patient plasma and culture media showed similar procoagulant characteristics, with activity proportional to TF expression, and immune-modulating effects. Notably, GBM-derived EVs modulated microglial behavior, induced senescence, and triggered immune polarization in a cell line-dependent manner, likely contributing to tumor microenvironment remodeling. GBM-associated hypercoagulability is shaped by heterogeneous tumor-intrinsic pathways and EV-mediated mechanisms. The dual role of EVs in promoting coagulation and modulating immune responses provides a mechanistic framework for further studies investigating EVs as potential biomarkers and therapeutic targets relevant to future thromboprophylactic strategies in GBM patients.

Breast cancer stem cells (BCSCs) have been proposed as the cause of resistance to conventional treatments and of breast cancer recurrence and metastasis. This study provides compelling evidence for the role of the transcription factor POU1F1 in the increase of BCSC-like. Using POU1F1-overexpressing and knock-down breast cancer cell lines, as well as immunodeficient mouse models, our data demonstrate that POU1F1 induces a BCSC-like phenotype in breast tumor cells by deregulating markers such as CD24, CD44, CD133, and ALDH. These phenotypic modifications correlate with functional changes, i.e., increased clonogenicity, mammosphere formation, and glycolysis. In addition, we found that a subpopulation of MCF-7 cells with overexpression of POU1F1 and elevated ALDH expression exhibits both a high tumor-initiating capacity and increased resistance to chemotherapy and radiotherapy treatments. Mechanistically, these features are mediated by POU1F1 activation of the IL-6/JAK2/STAT3 pathway and up-regulation of ALDH. Janus kinase inhibitors and monoclonal anti-IL6 receptor antibodies significantly decrease ALDH expression, colony, and mammosphere formation, suggesting possible use of pharmacological inhibitors of the IL-6/JAK2/STAT3 pathway in breast tumors with elevated POU1F1 levels.

Acute myeloid leukemia (AML) is a hematologic malignancy originating in the bone marrow and often progressing to extramedullary sites. Despite advances in molecularly targeted therapies and hematopoietic stem cell transplantation, clinical outcomes remain poor. Tyrosine kinase inhibitors (TKIs) provide benefit to a subset of AML patients harboring FLT3-ITD mutations; however, relapse and resistance remain common. These therapeutic failures are driven by both intrinsic properties of leukemic stem cells (LSCs)-a quiescent, self-renewing population-and extrinsic cues from the tumor microenvironment. We previously demonstrated that arteriolar endothelial cells (ECs) produce miR-126, which is transferred to LSCs, promoting quiescence, treatment resistance, and niche retention. During disease progression, TNF-α secreted by expanding blasts suppresses EC miR-126 production. Following TKI administration, blast reduction lowers TNF-ɑ levels, restoring EC miR-126 production, and this miR-126 expression enables LSCs to re-enter quiescence-thereby escaping therapy and facilitating relapse. To explore this dynamic, we developed an agent-based computational model of the AML bone marrow microenvironment, parameterized with in vitro and in vivo data. The model captures vascular niche remodeling and feedback between leukemic populations and endothelial signaling. Simulations reveal that LSC protection mediated by miR-126 can be disrupted by combining TKIs with miRisten, a miR-126 inhibitor. When administered on a defined schedule, this combination dismantles the protective niche and enhances LSC eradication. These findings underscore the therapeutic potential of targeting microenvironmental feedback to overcome resistance and prevent AML relapse.

We identified a new progeroid syndrome with severe neuropathy and intellectual deficits but its underlying cellular and molecular mechanism is unknown. Exome sequencing revealed a homozygous mutation in the IVNS1ABP gene, which encodes IVNS1ABP, an influenza virus non-structural protein-1 binding protein. To investigate disease mechanisms, we generated isogenic induced pluripotent stem cells (iPSCs) from patient fibroblasts and differentiated them into neural progenitor cells (NPCs). Mutant IVNS1ABP fibroblasts, iPSCs, and NPCs exhibited defective cytokinesis, increased DNA damage, and premature cellular senescence. Consistent with these findings, cerebral organoids showed early differentiation of NPCs into neurons. Molecular profiling as well as biochemical and cellular analysis revealed altered binding of mutant IVNS1ABP to actin / actin-associated proteins and dysregulated actin dynamics during cytokinesis. Taken together, we propose that mutant IVNS1ABP dysregulates actin polymerization and organization which is at least partly responsible for the cellular senescence phenotypes in this progeroid neuropathy.

In mouse cells, constitutive heterochromatin is associated with underlying arrays of A/T-rich DNA repeat elements, called the major satellite repeats (MaSat or MSR). We examine >18,000 MSR copies in mouse ES cells and identify that heterochromatin forms only at transcriptionally competent MSR units. To directly dissect the function of MSR DNA, we insert isolated MSR units into an inert genomic region that is repeat- and gene-free. Insertion of three or more intact MSR units induces heterochromatic histone marks, recruitment of HP1 and incorporation of histone H1. Only transcriptionally competent MSR units, but not permutated MSR variants or LINE1 5'UTR elements, nucleate de novo heterochromatin. MSR-derived transcription is bi-directional and MSR-originating transcripts are attenuated by the RNAPII-associated Integrator complex. Instructively, multi-copy intact MSR units impart an unwound DNA template that facilitates RNAPII engagement. Together, this study uncovers a DNA/RNA-based logic and transcription-coupled mechanism for the nucleation of heterochromatin.