搜索结果：Anatomy & cell biology

B cell maturation within the germinal center tissue microenvironment involves immunoglobulin gene diversification by somatic hypermutation (SHM). How three-dimensional (3D) genome architecture influences SHM is not fully understood. We leveraged sequencing-based and image-based 3D genomics and transcriptomics to map single-cell 3D genome organization and gene expression across cell types and states in human tonsils and in B cell lymphoma cell lines. These analyses revealed trajectories of compartment, looping, and nuclear position changes during the B cell immune response and activation of SHM. Targeted protein degradation of cohesin component RAD21 revealed its contribution to enabling SHM. Our results provide a single-cell 3D genome atlas of human tonsil cells and outline the links between the chromatin loop extrusion machinery and SHM.

Clinically relevant postoperative pancreatic fistula (CR-POPF) remains a major cause of morbidity after pancreatoduodenectomy, yet the biochemical composition of postoperative effluents and their effects on anastomotic healing remain poorly understood. We investigated whether CR-POPF effluents exhibit lipolysis-associated lipid signatures and induce defined responses in cellular model systems relevant to anastomotic healing. Drain effluents from 14 patients (7 CR-POPF, 7 non-POPF) underwent GC-MS lipid profiling. Metabolic viability assays (ATP-based readout of cellular stress responses) were performed in peritoneal mesothelial cells and human foreskin fibroblasts as stromal model systems relevant to anastomotic healing, as well as PanC-1 cells. Two CR-POPF effluents associated with reproducible reductions in metabolic viability were functionally selected for transcriptomic profiling. RNA sequencing was performed in mesothelial cells and fibroblasts after exposure to these effluents and monopalmitin. CR-POPF effluents showed coordinated enrichment of long-chain fatty acids and monoacylglycerides. Only a subset reproducibly impaired cellular metabolic viability. Transcriptomic profiling of the two functionally selected CR-POPF effluents revealed a lipid-responsive transcriptional signal across these biologically distinct effluent samples, characterized by induction of ANGPTL4, HMOX1, PLIN2, and PDK4 and consistent with a metabolic and stress-adaptive transcriptional response to lipid exposure. Activation followed a clear gradient (monopalmitin > AES1448 > GR1479) and was more pronounced in mesothelial cells than in fibroblasts. Functionally active CR-POPF effluent samples may carry lipid signals that are associated with a consistent transcriptional signal in peritoneal mesothelial cells and fibroblasts in functionally active effluent samples. The lipid-dependent amplitude and compartment-specific embedding of this signal support a hypothesis-generating framework derived from the two functionally selected CR-POPF effluents.

Spermatogenesis, the complex developmental process of male germ cell proliferation, differentiation, and maturation, is the basis of male fertility. In the seminiferous tubules of the testes, spermatozoa are constantly generated from spermatogonial stem cells through a stereotyped sequence of divisions. The basic physiological principles, however, that control seminiferous tubule function remain poorly, if at all, defined. Here, we address cell type-specific seminiferous tubule signaling in vitro and in vivo. By monitoring changes in cellular Ca2+ concentration at high spatiotemporal resolution, we show that the three cell types that build the seminiferous epithelium-Sertoli, peritubular, and germ cells-each display unique Ca2+ signaling patterns. We reveal the underlying mechanisms and demonstrate that Sertoli cell Ca2+ signals are under gonadotropin regulation. Together, our experimental findings provide insights into seminiferous tubule signaling, its mechanistic basis, and its endocrine control.

Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multiomic profiling of three-dimensional (3D) genome structure and DNA methylation for 86,689 single nuclei across 16 tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, which indicates that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers a reference for exploring gene regulation in human health and disease.

Small nucleolar RNA host genes (SNHGs) are a distinctive subgroup of long non-coding RNAs whose loci can generate both host lncRNA transcripts and intronic small nucleolar RNAs. In hepatocellular carcinoma (HCC), dysregulated SNHGs have been linked to tumor growth, epithelial-mesenchymal transition, metastasis, stemness, immune remodeling, extracellular vesicle communication, and therapeutic resistance. However, the clinical meaning of these associations remains uneven because many reported mechanisms are based on limited cell-line experiments, retrospective cohorts, or non-stratified HCC models. This structured narrative review examines SNHG biology in HCC through an evidence-weighted and etiology-aware framework. Rather than cataloguing individual SNHG-miRNA-mRNA axes, we distinguish mechanistically stronger pathways from preliminary or hypothesis-generating findings and separate diagnostic, prognostic, predictive, and therapeutic implications. We also emphasize non-ceRNA mechanisms, including nuclear epigenetic regulation, RNA-protein interaction, protein-stability control, extracellular-vesicle signaling, and the dual-output architecture of SNHG loci. Particular attention is given to quantitative constraints of ceRNA models, differences among HBV-, HCV-, alcohol-related, and MASLD/MASH-associated HCC, and the current barriers to clinical translation. Overall, SNHGs represent promising but not yet clinically mature biomarkers or therapeutic targets. Their future value will depend on prospective validation, standardized assays, etiology-defined models, isoform-aware targeting, and integration into multi-omic and functional precision oncology frameworks.

Colorectal cancer (CRC) can induce stresses on the immune system that can affect both the numbers and function of immune cells. Changes in immune cell functions can also occur during ageing and these may affect both the ability to fight infections and to protect against cancers. As the incidence of CRC is age-related, the aim of this work was to identify changes in immune cell subtypes that are specific to CRC and not merely due to age-related changes. Whole blood samples from 49 CRC patients about to undergo surgery and 22 healthy controls were collected. Samples were analysed by immunophenotyping, detection of HLA-DR on T-lymphocytes and monocytes, and senescent-like T-lymphocytes. CD4 staining intensity of monocytes was significantly increased in CRC patients and showed a positive correlation with their HLA-DR staining intensity. In most CRC patients, the numbers of helper T-lymphocytes were lower with the progression of the disease, while cytotoxic T-lymphocytes were higher (an opposite pattern to the immunophenotypes of the healthy ageing cohort). NKbright cells were higher while NKdim cells were lower in patients with large tumours. An increase in the T-lymphocytes to B-lymphocytes ratio correlated with the metastatic status. Complex changes in the immune phenotypes in CRC, distinct from those that occur during ageing were observed, that imply development of an immuno-suppressive phenotype that may aid tumour evasion of immunity.

Neuroblastoma (NB) is the most common extracranial solid tumour of childhood and remains a leading cause of paediatric cancer mortality, particularly in high-risk disease driven by MYCN amplification. Although MYCN is a central oncogenic driver, its role as a transcription factor has limited direct therapeutic targeting, shifting attention toward downstream metabolic and microenvironmental dependencies. Increasing evidence indicates that MYCN-driven metabolic rewiring extends beyond tumour-intrinsic processes to reshape the tumour microenvironment (TME), influencing immune composition and stromal dynamics. Recent advances in single-cell and spatial profiling technologies have revealed substantial heterogeneity within the NB TME, highlighting complex interactions between tumour cells, immune populations, and stromal components. Among these, cancer-associated fibroblasts (CAFs) have emerged as key regulators of extracellular matrix architecture, immune modulation, and metabolic crosstalk. However, CAF identity, functional diversity, and lineage relationships in NB remain incompletely defined, with significant overlap between tumour-intrinsic mesenchymal programs and stromal fibroblast signatures. In this review, we synthesise current understanding of MYCN-driven metabolic reprogramming and its impact on CAF heterogeneity and immune regulation. We integrate insights from adult cancers with emerging data in NB to critically evaluate CAF functional states, including inflammatory and myofibroblastic programs, and their roles in shaping tumour progression, immune exclusion, and therapeutic response. By framing NB as a MYCN-remodelled tumour ecosystem, this review identifies key knowledge gaps in stromal biology and highlights the need to resolve CAF heterogeneity and tumour-stroma interactions. These insights have broader implications for MYC-driven malignancies and support the development of integrated therapeutic strategies targeting both tumour cells and their supportive microenvironment.

Most genetic risk variants linked to ocular diseases are nonprotein coding and presumably contribute to disease through dysregulation of gene expression; however, understanding their mechanisms has been impeded by incomplete annotation of transcriptional regulatory elements across retinal cell types. To address this, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome, and three-dimensional (3D) chromatin architecture in human retina, macula, and retinal pigment epithelium/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 retinal cell types. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the advancements in deep-learning techniques, we developed sequence-based predictors to interpret noncoding risk variants of retinal diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases and provides a resource for studying the gene regulatory programs of the human retina and ocular diseases.

Mantle Cell Lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma, with frequent relapses and shorter responses with every subsequent treatment. MCL depends on growth factors and cytokines derived from microenvironmental cells for its growth and can alter the immune system to evade recognition and subsequent elimination. The soluble factors secreted by MCL can contribute to endothelial differentiation, lymphangiogenesis, and clonal selection under hypoxic conditions, thereby evading the DNA damage response. Targeting the tumor microenvironment and angiogenesis is an active area of research and development, as the angiogenic gene signatures in MCL remain poorly understood. To address this knowledge gap, we performed transcriptomic analyses of MCL patient cohorts and identified 10 key angiogenic genes upregulated in MCL. We focused on four receptors (FGFR1, VEGFR1, VEGFR2, and PDGFRB) that have receptor tyrosine kinase activity and are localized to the plasma membranes of MCL cells. These receptors were assessed for therapeutic targeting potential in four independent preclinical models, including patient-derived xenografts, cell-derived xenografts, bone marrow-derived xenografts, and a genetically engineered murine model of MCL. Our work establishes that simultaneous targeting of multiple kinases, such as FGFR1 and VEGFR2, is a promising therapeutic strategy for patients with MCL.

Five years after the emergence of SARS-CoV-2 and the declaration of the COVID-19 pandemic, the long-term implications of COVID-19 for cancer biology remain incompletely understood. Beyond the major disruptions in cancer screening, diagnosis, and treatment observed worldwide, increasing attention has focused on whether SARS-CoV-2 infection and post-acute sequelae of COVID-19 (Long COVID) may induce persistent biological alterations relevant to tumor progression or recurrence. Current evidence does not support SARS-CoV-2 as a classical oncogenic virus or demonstrate direct viral carcinogenesis. However, experimental, transcriptomic, and clinical studies suggest that SARS-CoV-2 infection can induce persistent inflammatory and immune alterations that overlap with pathways implicated in cancer biology. Among the most consistently reported findings are chronic activation of IL-6/STAT3 and NF-κB signaling, immune dysregulation, T-cell exhaustion, oxidative stress, mitochondrial dysfunction, and senescence-associated inflammatory programs. Additional proposed mechanisms include perturbation of tumor suppressor pathways, epigenetic remodeling, and microRNA alterations involving the let-7/LIN28B/STAT3 axis. Experimental models have further suggested that inflammatory remodeling induced by respiratory viral infection may influence dormant tumor cell behavior and tissue microenvironments under defined conditions. However, many of these observations derive from in vitro systems, animal models, or association studies, and their long-term relevance to human oncogenesis remains uncertain. Collectively, current evidence supports the existence of convergent biological mechanisms between SARS-CoV-2-induced inflammatory stress responses and pathways involved in cancer progression, rather than direct oncogenic transformation. Future longitudinal studies integrating immune profiling, inflammatory biomarkers, transcriptomic and epigenetic analyses, and clinical cancer outcomes will be essential to determine whether persistent post-infectious alterations contribute to tumor progression, recurrence, or susceptibility in selected patient populations.

Alzheimer's disease (AD) disrupts brain function through cell type-specific transcriptomic and epigenomic alterations, yet the contribution of three-dimensional (3D) genome organization to AD remains poorly understood. We applied GAGE-seq (genome architecture and gene expression by sequencing) to jointly profile gene expression and 3D chromatin structure in single cells from postmortem brain tissue from AD patients and age-matched individuals without AD, revealing chromatin reorganization linked to cell type-specific dysregulation. Integrations with spatial transcriptomics and chromatin accessibility data uncovered altered niches reflecting genome compartment remodeling and regulatory element reorganization. Hicformer, a deep learning framework, showed that 3D genome features are essential for predicting disease-relevant, cell type-specific gene expression changes. Our results establish higher-order chromatin alterations as a component of AD-associated molecular pathology, providing a multiscale view of transcriptional regulation and 3D genome organization in neurodegeneration.

Hepatocellular carcinoma (HCC) is associated with poor prognosis and limited responses to immunotherapy, partly due to the immunosuppressive tumor microenvironment (TME). Tumor-associated macrophages, especially M2-like macrophages, play important roles in HCC progression. Interleukin-4-induced gene 1 (IL4I1), a tryptophan-metabolizing enzyme, has been implicated in tumor immune regulation. However, the role and prognostic significance of IL4I1-expressing M2-like macrophages in HCC remain unclear. This study investigated the expression pattern, spatial distribution, functional association, and prognostic relevance of IL4I1-expressing M2-like macrophages in HCC and their association with patient outcomes. We analyzed public databases (TIMER, UALCAN, TISCH2) for gene expression and prognostic significance. An in vitro co-culture system was established using a Huh7 HCC cell line and THP-1-derived M2-like macrophages with and without IL4I1 knockout via CRISPR/Cas9. We assessed cell proliferation, migration, apoptosis, and cytokine profiles. Multiplex immunofluorescence (mIF) was performed on tissue microarrays from 92 HCC patients to analyze the spatial distribution of IL4I1+ M2-like macrophages. IL4I1 was highly expressed in HCC, predominantly within macrophages, and correlated with poor prognosis. In a THP-1-derived macrophage/Huh7 co-culture model, IL4I1 expression in M2-like macrophages was associated with increased Huh7 cell proliferation and migration and reduced apoptosis. This was associated with increased secretion of pro-inflammatory cytokines (e.g., CCL15, TNF-α) and decreased levels of IL-10 and TGF-β1. mIF analysis further showed that a high density of IL4I1+ M2-like macrophages in the epithelial/parenchymal tumor region was significantly associated with poorer overall survival (p = 0.033). IL4I1+ M2-like macrophages are associated with a pro-tumorigenic microenvironment and adverse patient outcomes in HCC. Our findings support IL4I1+ M2-like macrophages as a prognostically relevant macrophage subset, while further mechanistic validation, particularly of IL4I1-derived metabolites and AHR pathway activation, is required before IL4I1 can be considered a validated therapeutic target.

Satellite cells (SCs) are essential for skeletal muscle regeneration, but their function declines with aging, often associated with increased pro-apoptotic signaling. This study investigated the impact of in vitro serum starvation-as a model of acute microenvironmental and nutrient stress-on the apoptosis and differentiation potential of human SCs from young and aged donors. SCs were isolated from the Vastus Lateralis of young and aged subjects and cultured in serum-free medium for up to 72 h. We assessed apoptosis through Annexin V/PI staining, TUNEL assays, and caspase activity measurements, while transcriptional profiles were analyzed via RT-PCR. Aged SCs displayed a significantly higher susceptibility to stress-induced apoptosis compared to young controls, marked by the early upregulation of CASP9 and FOXO1. While typical nucleosomal DNA fragmentation was absent, we observed the activation of caspase-3 after 72 h of starvation. In aged cells, activated caspase-3 co-localized with myogenin and extranuclear DNA at sites of nuclear remodeling. Notably, treatment with a pan-caspase inhibitor (z-VAD-fmk) prevented the formation of micronuclei and myotubes, further highlighting a non-apoptotic role for these enzymes. Aged SCs also showed a distinct cell cycle profile characterized by an enlarged G0/G1 phase and altered expression of CDK and CCNB1 genes. Our findings suggest that in human aged SCs, caspase enzymes serve a dual role: mediating a heightened stress response and facilitating the nuclear remodeling necessary for myogenic differentiation. These results clarify how intrinsic aging shapes the response of muscle stem cells under severe environmental and metabolic resource deprivation.

Aging tissues gradually lose cellular diversity due to stem cell exhaustion. A new PLOS Biology study utilizes advanced lineage tracing to track intestinal stem cell lineages across the life span. The findings reveal clonal attrition happens in early ages.

Mechanical forces from blood flow are essential for production of hematopoietic stem and progenitor cells (HSPCs) during embryogenesis, but the molecular mechanisms by which hemodynamic cues are sensed and orchestrate endothelial-to-hematopoietic (EHT) transition remain incompletely defined. We previously identified YAP mechanotransduction as a key integrator of physical forces with EHT. Here we show that hemodynamic forces can activate YAP signaling via the mechanoresponsive ion channel Piezo1 in human iPSC-derived hemogenic endothelium (HE) and zebrafish embryos. Investigation of the Piezo1/YAP axis revealed shared and unique roles of YAP and its paralogue TAZ in EHT. Mechanistically, we find a requirement for the Tead DNA-binding co-factor in YAP/TAZ-dependent control of HSPC number, and note that TAZ uniquely augments transcriptional output of the hematopoietic master regulator Runx1 via direct protein-protein interactions. By comprehensive scRNA-sequencing of YAP/TAZ gain-of-function (GOF) and yap-deficient cells from zebrafish, we reveal that YAP/TAZ promotes HSC production by positively regulating gene programs for hematopoietic self-renewal, cell cycle, and glycolysis-to-oxidative phosphorylation switching, while preventing reversion to endothelial identity. Importantly, comparison of GOF transcriptomes and functional analyses suggest decoupling of metabolic/proliferative and endothelial gene regulatory modules between YAP and TAZ: while either can functionally compensate for loss of the other in EHT, indiscriminate overactivation of TAZ enhances an endothelial program over pro-hematopoietic fate, ultimately blunting progression of HSPC production. Given that hemodynamic cues are integrated simultaneously by arterial and HE cells in embryonic vessels in which EHT occurs, these findings have strong implications for strategies designed to introduce biomechanical cues to in vitro hematopoietic differentiation systems to drive HSC production.

Dysregulated pH homeostasis is a defining feature of tumor biology and a potential therapeutic vulnerability. Cancer cells maintain an alkaline intracellular pH, whereas the tumor microenvironment remains acidic and intracellular organelles preserve compartment-specific luminal acidity, together supporting tumor growth, metabolic adaptation, immune evasion, and therapeutic resistance. Recent studies show that modulation of pH regulation across the tumor microenvironment, cytoplasm, and intracellular organelles disrupts ionic balance, impairs organelle function, and triggers regulated cell death, including alkaliptosis and organelle stress-associated lethality. Beyond direct tumor killing, pH modulation also reshapes antitumor immunity by relieving extracellular acidosis, restoring immune-cell function, and inflammatory signaling. In this review, we summarize recent advances in compartmental pH regulation in cancer, with particular emphasis on the distinction between experimentally demonstrated mechanisms and emerging conceptual models. We discuss how alkalization-oriented interventions may suppress tumor growth in selected contexts, but may also produce neutral, adaptive, or even protumorigenic consequences depending on tumor type, buffering capacity, transporter activity, metabolic state, and immune composition. We further evaluate pH-dependent immune regulation, organelle alkalization, alkaliptosis, quantitative pH measurement, and monitoring technologies. Finally, we highlight major translational barriers. A more quantitative, compartment-resolved, and context-aware understanding of pH biology will be required before pH modulation can be reliably translated into clinically useful therapeutic strategies.

Malignant gliomas are lethal brain tumors characterized by profound local immunosuppression and a radically remodeled myeloid landscape. Although these tumors mobilize resident microglia and infiltrating monocyte-derived macrophages, the mechanisms governing their phenotypic convergence and diversification remain elusive. Here, we integrated single-cell profiling and spatial transcriptomics of glioma-associated microglia in the GL261 model. We identified distinct microglial states that aligned with tumor architecture, most notably Cst7-expressing disease-associated microglia (DAMs) that aggregated at the tumor invasive margin and exhibited a conserved transcriptional signature shared across various central nervous system pathologies. Interferon-γ and toll-like receptor signaling sequentially tuned stage-specific DAM features, including transient MHC-II expression and sustained PD-L1 upregulation, thereby recalibrating the local immune equilibrium by reshaping bidirectional DAM-T cell interactions during glioma progression. Our findings highlight microglial state transitions as a stage-specific layer of immune regulation in glioma that shapes T cell fate and support targeting microglial plasticity to rebalance anti-tumor immunity.

Immune checkpoint inhibitors (ICIs) combined with vascular endothelial growth factor tyrosine kinase inhibitors (VEGF-TKIs) have transformed the treatment landscape of advanced clear cell renal cell carcinoma (ccRCC). Current guidelines favour ICI plus VEGF-TKI (IO+TKI) combinations for favourable-risk disease (International Metastatic RCC Database Consortium [IMDC] score 0) based on improved objective response rates and progression-free survival. However, no IO+TKI combination has demonstrated a statistically significant overall survival (OS) benefit in this subgroup. A pooled analysis of four pivotal phase III trials (n = 839 favourable-risk patients) revealed no OS advantage for IO+TKI versus sunitinib monotherapy (hazard ratio [HR] 1.24; 95% CI 0.86-1.78) despite higher toxicity rates (71-82% Grade ≥ 3 adverse events vs. 63-72% with sunitinib) and substantially greater cost. The IMDC favourable-risk category represents approximately 20% of metastatic ccRCC cases and is often characterised by indolent disease biology. Emerging molecular classifications reveal distinct transcriptomic subgroups, including an angiogenic subtype (ccA/CC-e.2/clusters 1-2) enriched in favourable-risk patients, characterised by high hypoxia-inducible factor (HIF) pathway gene expression, frequent PBRM1 mutations, robust VEGF-TKI responsiveness, and comparatively lower benefit from immunotherapy. Current clinical risk stratification fails to capture this molecular heterogeneity, limiting optimal treatment selection. VEGF-TKI monotherapy (median OS 47.6-79.4 months) and active surveillance remain valid, evidence-based alternatives in carefully selected favourable-risk patients, particularly those with asymptomatic, metachronous, or otherwise indolent disease. Uncritical universal use of IO+TKI in this population may therefore represent overtreatment. The development and validation of predictive biomarkers, refinement of molecular risk stratification, and exploration of novel agents with more favourable toxicity profiles (e.g., HIF-2α inhibitors) are urgently required to personalise therapy and identify candidates for rational treatment de-escalation.

Schwann cells (SC) are responsible for myelination in the peripheral nervous system (PNS). Myelin allows saltatory transmission of action potentials along axons and functionally relies on its unique constitution. We previously reported that Cdk7, a regulator of cell cycle progression and transcription, regulates myelin gene expression in oligodendrocytes and contributes to myelin maintenance in the central nervous system. Using mice with conditional Cdk7 knock-out in SCs, we provide evidence that Cdk7 is dispensable for myelin initiation but needed for the correct myelin thickness of larger caliber fibers in young mice, as well as for myelin elongation and rapid nerve conduction throughout age. We report that Cdk7 loss results in disturbed myelin stoichiometry, with significant dysregulation of lipid-related genes in SCs and a reduction in myelin protein zero. Finally, we demonstrate that Rxrγ, a nuclear receptor involved in lipid metabolism, is significantly downregulated in the absence of Cdk7. However, although Cdk7 regulates myelin segment length, our results indicate that this effect occurs independently of Rxrγ in myelinating dorsal root ganglion explants.