An integrative approach to identifying NPC1 as a susceptibility gene for gestational diabetes mellitus

OBJECTIVE

The objective of this study was to identify a novel gene and its potential mechanisms associated with susceptibility to gestational diabetes mellitus (GDM) through an integrative approach.

METHODS

We analyzed data from genome-wide association studies (GWAS) of GDM in the FinnGen R11 dataset (16,802 GDM cases and 237,816 controls) and Genotype Tissue Expression v8 expression quantitative trait locus data. We used summary-data-based Mendelian randomization to determine associations between transcript levels and phenotypes, transcriptome-wide association studies to provide insights into gene-trait associations, multi-marker analysis of genomic annotation to perform gene-based analysis, genome-wide complex trait analysis-multivariate set-based association test-combo to determine gene prioritization, and polygenic priority scores to prioritize the causal genes to screen candidate genes. Subsequent Mendelian randomization analysis was performed to infer causality between the candidate genes and GDM and phenome-wide association study (PheWAS) analysis was used to explore the associations between selected genes and other characteristics. Furthermore, to gain a deeper understanding of the functional implications of these susceptibility genes, GeneMANIA analysis was used to determine the fundamental biological functions of the therapeutic targets and protein-protein interaction network analysis was performed to identify intracellular protein interactions.

RESULTS

We identified two novel susceptibility genes associated with GDM: NPC1 and KIAA1191. Magnetic resonance imaging revealed a strong correlation between NPC1 expression levels and a lower incidence of GDM (odds ratio: 0.922, 95% confidence interval: 0.866-0.981, p = 0.011). PheWAS at the gene level indicated that NPC1 was not associated with any other trait. The biological significance of this gene was evidenced by its strong association with sterol metabolism.

CONCLUSION

Our study identified NPC1 as a novel gene whose predicted expression level is linked to a reduced risk of GDM, providing new insights into the genetic framework of this disease.

Gut-brain axis and environmental factors in Parkinson's disease: bidirectional link between disease onset and progression

Parkinson's disease has long been considered a disorder that primarily affects the brain, as it is defined by the dopaminergic neurodegeneration in the substantia nigra and the brain accumulation of Lewy bodies containing α-synuclein protein. In recent decades, however, accumulating research has revealed that Parkinson's disease also involves the gut and uncovered an intimate and important bidirectional link between the brain and the gut, called the "gut-brain axis." Numerous clinical studies demonstrate that gut dysfunction frequently precedes motor symptoms in Parkinson's disease patients, with findings including impaired intestinal permeability, heightened inflammation, and distinct gut microbiome profiles and metabolites. Furthermore, α-synuclein deposition has been consistently observed in the gut of Parkinson's disease patients, suggesting a potential role in disease initiation. Importantly, individuals with vagotomy have a reduced Parkinson's disease risk. From these observations, researchers have hypothesized that α-synuclein accumulation may initiate in the gut and subsequently propagate to the central dopaminergic neurons through the gut-brain axis, leading to Parkinson's disease. This review comprehensively examines the gut's involvement in Parkinson's disease, focusing on the concept of a gut-origin for the disease. We also examine the interplay between altered gut-related factors and the accumulation of pathological α-synuclein in the gut of Parkinson's disease patients. Given the accessibility of the gut to both dietary and pharmacological interventions, targeting gut-localized α-synuclein represents a promising avenue for developing effective Parkinson's disease therapies.

Targeting myeloid cells with platelet-derived extracellular vesicles to overcome resistance of immune checkpoint blockade therapy

Immune checkpoint blockade (ICB) therapy is designed to boost antitumor immune responses, yet it may unintentionally alter the chemokine profile, which can attract suppressive myeloid cells to the tumor, leading to acquired immune resistance. To address this, we developed a platform that targets myeloid cells post-ICB therapy using platelet-derived extracellular vesicles (PEVs). Unlike free drug administration, this system selectively targets anti-PD-L1-treated tumors through the CXCL-CXCR2 axis, effectively redirecting myeloid cells and overcoming ICB resistance. Consequently, mice exhibited robust responses to subsequent ICB therapy cycles, resulting in significantly enhanced tumor clearance and prolonged survival. The PEVs' targeting capability was also effective in tumors treated with chemotherapy and radiotherapy, suggesting a wide range of potential applications. In summary, PEVs offer a versatile platform for targeted immunomodulation to counteract acquired immune resistance during ICB therapy.

Enteric tuft cell inflammasome activation drives NKp46+ILC3 IL22 via PGD2 and inhibits Salmonella

To distinguish pathogens from commensals, the intestinal epithelium employs cytosolic innate immune sensors. Activation of the NAIP-NLRC4 inflammasome initiates extrusion of infected intestinal epithelial cells (IEC) upon cytosolic bacterial sensing. We previously reported that activation of the inflammasome in tuft cells, which are primarily known for their role in parasitic infections, leads to the release of prostaglandin D2 (PGD2). We observe that NAIP-NLRC4 inflammasome activation in tuft cells leads to an antibacterial response with increased IL-22 and antimicrobial protein levels within the small intestine, which is dependent on PGD2 signaling. A NKp46+ subset of ILC3 expresses the PGD2 receptor CRTH2 and is the source of the increased IL-22. Inflammasome activation in tuft cells also leads to better control of Salmonella Typhimurium in the distal small intestine. However, tuft cells in the cecum and colon are dispensable for antibacterial immunity. These data support that intestinal tuft cells can also induce antibacterial responses, possibly in a tissue-specific manner.

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response

Intratumoral heterogeneity (ITH)-defined as genetic and cellular diversity within a tumor-is linked to failure of immunotherapy and an inferior anti-tumor immune response. We modeled heterogeneous tumors comprised of "hot" and "cold" tumor populations (giving rise to T cell-rich and T cell-poor tumors, respectively) and introduced fluorescent labels to enable precise spatial tracking. We found the cold tumor cell population exerted a "dominant cold" effect in mixed tumors. Strikingly, spatial analysis revealed that the tumor cells themselves created distinct local microenvironments within heterogeneous tumors: regions occupied by cold tumor cells showed pronounced immunosuppression, harboring increased CD206Hi macrophages and diminished local T cell function. This inferior T cell activity in cold regions persisted even after immunotherapy and mechanistically was mediated by CX3CL1 produced by the cold tumor cells. An immune cold tumor population within a heterogeneous tumor thus impairs tumor immunity on both a tumor-wide and a highly localized spatial scale.

Pdia3 deficiency exacerbates intestinal injury by disrupting goblet and Paneth cell function during ischemia/reperfusion

Intestinal ischemia/reperfusion (I/R) injury is a severe medical condition associated with high mortality rates due to its disruption of intestinal homeostasis and impairment of mucosal defenses. The intestinal epithelium, particularly goblet and Paneth cells, plays a critical role in maintaining gut barrier integrity. Protein disulfide isomerase A3 (PDIA3) is involved in protein folding within intestinal epithelial cells (IECs) and has been linked to the stress response during I/R injury. This study aims to explore the role of PDIA3 in preserving intestinal integrity and immune function during I/R injury. Our study employed both human and mouse models to investigate PDIA3's expression and function. The correlation between PDIA3 expression and disease severity was analyzed using statistical tests, including Pearson's correlation coefficient. An intestinal I/R model was established in intestinal epithelium-specific conditional knockout mice lacking the Pdia3 gene. Single-cell RNA sequencing, immunohistochemistry, and transcriptomic analysis were used to assess PDIA3 expression in various intestinal cell types and to evaluate its role in epithelial differentiation and immune responses. PDIA3 was found to be highly expressed in healthy IECs, especially in goblet and Paneth cells. Its expression was reduced in patients with mesenteric artery ischemia and Pdia3-deficient mice, leading to severe intestinal damage, including impaired goblet and Paneth cell function, reduced antimicrobial peptide production, and altered gut microbiota. Treatment with recombinant defensin α1, an antimicrobial peptide secreted by Paneth cells, significantly alleviated the adverse effects of Pdia3 deficiency, restoring gut microbiota balance and reducing inflammation in the intestinal I/R injury mice. Taken together, our findings suggest that Pdia3 plays a vital role in maintaining intestinal barrier function and immune defense. Its deficiency exacerbates I/R-induced intestinal damage by impairing epithelial differentiation, mucus production, and antimicrobial peptide secretion. Targeting Pdia3 and associated pathways offers promising therapeutic strategies for mitigating I/R injury and restoring intestinal homeostasis.

Sodium-Coupled Monocarboxylate Absorption in the Airway Epithelium Is Facilitated by the SLC5A8 Co-Transporter

AIM

Amino acids, sugars, short-chain fatty acids (SCFA), vitamins, and other small molecules compose the extracellular metabolome on the airway lumen surface, but how the airway epithelium deals with these molecules has not been deeply studied. Due to the broad spectrum of metabolites transported by SLC5A8 and SLC5A12, we aim to determine if they are functionally expressed and participate in the absorption of Na+, short-chain fatty acids, and monocarboxylates in mouse and human airway epithelium.

METHODS

Tracheas isolated from male or female mice and human bronchial epithelial cells (HBECs) were used for electrophysiological studies in the Ussing chamber and to detect members of the SLC16 family by RT-PCR and bulk RNAseq. Additionally, cell lines expressing the human and murine SLC5A8 transporter were employed for uptake studies using a fluorescent lactate probe.

RESULTS

We showed for the first time that human and murine airway epithelium express a functional SLC5A8 transporter, facilitating the absorption of glucose metabolites and SCFAs. The Na+-coupled monocarboxylate transport was not additive with ENaC-mediated Na+ absorption in mouse trachea. We observed that valproate acts as an inhibitor of the murine but not of the human SLC5A8 transporter.

CONCLUSIONS

Our results demonstrate that several metabolites derived from bacterial and cellular metabolism can be transported from the airway lumen into the epithelial cells, participating in a homeostatic relation of the tissue with its environment.

Precision medicine in the pediatric and neonatal intensive care units through genomics

PURPOSE OF REVIEW

Genome-wide sequencing technologies have revolutionized the understanding of human disorders and advanced precision medicine, especially for pediatric disorders. Here, we discuss the utility of genomic technologies in advancing the care of children admitted to the pediatric and neonatal intensive care units.

RECENT FINDINGS

Rapid molecular diagnosis permitted by genomic medicine has yielded clinically actionable findings that influence decision-making and facilitate timely therapeutic interventions. Identifying a genetic association provides a causal anchor to understanding disease biology at the single nucleotide resolution, revealing hidden biological heterogeneity that may be obscured by traditional imaging, laboratory, and pathological workup. The importance of a genetic diagnosis is further highlighted by the promise of gene therapy to correct the underlying genetic perturbation, as evidenced by the recent emergence of FDA-approved gene therapies for childhood genetic conditions.

SUMMARY

We predict that whole-genome sequencing, in conjunction with other omic technologies, will become critical diagnostic adjuncts in the clinical workup of critically ill children.

New LFA-1 inhibitor Orientin reduces angiotensin II-induced vascular remodeling

BACKGROUND

The interaction between monocytes and vascular endothelium often leads to inflammatory reactions and vascular remodeling. The lymphocyte function-associated antigen 1 (LFA1) plays a crucial role in promoting leukocyte adhesion and migration during inflammatory diseases. However, the role of LFA1 in angiotensin II (Ang II)-induced hypertension and vascular remodeling is not clear. Orientin (Ori) has antioxidant, anti-inflammatory, anticancer, and resistance to myocardial remodeling. However, the role of Orientin remains unclear in angiotensin II (Ang II)-induced hypertension and vascular remodeling.

METHODS

In this study, Ang II was used to induce hypertension in mice. We employed various techniques including blood pressure monitoring, pathological staining, Immunofluorescent and Immunohistochemical staining, real time-PCR, vasodilation analysis and other methods to study whether LFA1 antibody and Orientin can regulate vascular remoding.

RESULTS

Our results showed that LFA1 significantly improved Ang II-induced hypertension, inflammation, fibrosis, and oxidative stress. Furthermore, in vitro experiments have substantiated that the use of neutralizing antibodies targeting LFA1 can effectively hinder the migration of macrophages to endothelial cells, which is triggered by Ang II. Additionally, the antibodies also reduce the extent of DNA damage and oxidative stress. Orientin can interact with LFA-1. Then, it was proved by pathological staining that Orientin can inhibit Ang II-induced vascular remodeling.

CONCLUSION

Here, we identified Orientin as a small molecule inhibitor of LFA-1 with anti-vascular remodeling function. These findings not only suggest that Orientin is a promising compound for the clinical treatment of vascular injury and hypertension, but also provide strategies for the treatment of cardiovascular diseases.

A single cell atlas of the mouse seminal vesicle

During mammalian reproduction, sperm are delivered to the female reproductive tract bathed in a complex medium known as seminal fluid, which plays key roles in signaling to the female reproductive tract and in nourishing sperm for their onwards journey. Along with minor contributions from the prostate and the epididymis, the majority of seminal fluid is produced by a somewhat understudied organ known as the seminal vesicle. Here, we report the first single-cell RNA-seq atlas of the mouse seminal vesicle, generated using tissues obtained from 23 mice of varying ages, exposed to a range of dietary challenges. We define the transcriptome of the secretory cells in this tissue, identifying a relatively homogeneous population of the epithelial cells which are responsible for producing the majority of seminal fluid. We also define the immune cell populations-including large populations of macrophages, dendritic cells, T cells, and NKT cells-which have the potential to play roles in producing the various immune mediators present in seminal plasma. Together, our data provide a resource for understanding the composition of an understudied reproductive tissue, with potential implications for paternal control of offspring development and metabolism.

IsoalloLCA-intervened regulatory T cell exosomes alleviate inflammatory bowel disease by inhibiting NF-κB-associated inflammation in intestinal epithelial cells

Regulatory T cells (Tregs) are the principal immune cells that exert anti-inflammatory effects within the organism. Their exosomes exhibit therapeutic efficacy across a broad spectrum of diseases owing to their high stability, low immunogenicity, and substantial penetration capacity. Recent research have indicated that isoallolithocholic acid (isoalloLCA), a metabolite associated with bile acid metabolism, may enhance Treg activity by upregulating forkhead box protein3 (Foxp3) expression. Hence, metabolite-based strategies for reinforcing Tregs may offer novel intervention options for treating related diseases. In this study, tumor necrosis factor (TNF)-α and dextran sulfate sodium (DSS) were employed to establish cellular and animal models of inflammatory bowel disease (IBD), further evaluating the therapeutic efficacy of isoalloLCA-intervened regulatory T cell exosomes (isoalloLCA-Exo) within this model. Our findings demonstrated that isoalloLCA-Exo effectively inhibit colitis progression in a murine model, as indicated by reduced inflammation, decreased apoptosis of intestinal epithelial cells, and improved intestinal barrier function. Furthermore, in vitro analyses elucidated the molecular mechanisms underlying the anti-inflammatory effects of isoalloLCA-Exo, revealing that the intervention effectively reversed TNF-α-induced inflammation and apoptosis in intestinal epithelial cells by modulating the NF-κB pathway. In conclusion, isoalloLCA-Exo can decelerate inflammatory bowel disease progression and suppress inflammatory response in intestinal epithelial cells by inhibiting NF-κB pathway. Notably, isoalloLCA-Exo exhibit superior efficacy to the traditional drug mesalazine and conventional treg exosome(NC-Exo). These findings have significant implications for optimizing Treg-derived exosome-based therapies for inflammation-related diseases.

Impaired ketogenesis in Leydig Cells drives testicular aging

Testicular aging commonly leads to testosterone deficiency and impaired spermatogenesis, yet the underlying mechanisms remain elusive. Here, we show that Leydig cells are particularly vulnerable to aging processes in testis. Single-cell RNA sequencing identifies the expression of Hmgcs2, the gene encoding rate-limiting enzyme of ketogenesis, decreases significantly in Leydig cells from aged mice. Additionally, the concentrations of ketone bodies β-hydroxybutyric acid and acetoacetic acid in young testes are substantially higher than that in serum, but significantly diminish in aged testes. Silencing of Hmgcs2 in young Leydig cells drives cell senescence and accelerated testicular aging. Mechanistically, β-hydroxybutyric acid upregulates the expression of Foxo3a by facilitating histone acetylation, thereby mitigating Leydig cells senescence and promoting testosterone production. Consistently, enhanced ketogenesis by genetic manipulation or oral β-hydroxybutyric acid supplementation alleviates Leydig cells senescence and ameliorates testicular aging in aged mice. These findings highlight defective ketogenesis as a pivotal factor in testicular aging, suggesting potential therapeutic avenues for addressing age-related testicular dysfunction.

Mitochondrial gene SLC25A24 regulated anti-tumor immunity and inhibited the proliferation and metastasis of colorectal cancer by PKG1-dependent cGMP/PKG1 pathway

Colorectal cancer (CRC) is a leading cause of cancer-related mortality globally, with metastasis playing a key role in its unfavorable prognosis. Emerging research has emphasized the pivotal role of mitochondria in tumor immune regulation. Nevertheless, the clinical relevance and functional role of SLC25A24, a mitochondrial solute carrier, in CRC remain largely unexplored. Through bioinformatics analyses and validation in clinical cohorts, this study identifies SLC25A24 as an independent prognostic marker in CRC, significantly linked to immune infiltration in CRC tissues. Our findings demonstrated that SLC25A24 expression is markedly reduced in CRC cell lines and tissues. Kaplan-Meier survival analysis revealed that lower SLC25A24 expression is associated with worse overall survival and progression-free survival in CRC patients. Interestingly, SLC25A24 expression was higher in microsatellite instability (MSI) CRC, which shows greater responsiveness to immune checkpoint inhibitors (ICIs). Functional experiments indicated that SLC25A24 overexpression suppresses CRC cell proliferation, migration, and invasion. Mechanistic studies revealed that SLC25A24 positively regulates the cGMP/PKG1 signaling pathway in CRC, influencing mitochondrial potential, apoptosis, and proliferation-related markers. This research highlights the SLC25A24-PKG1 axis as a potential therapeutic target to bolster anti-tumor immunity and curb CRC progression.

Progress of personalized medicine of cystic fibrosis in the times of efficient CFTR modulators

BACKGROUND

Cystic fibrosis (CF) is a systemic disorder of exocrine glands that is caused by mutations in the CFTR gene.

MAIN BODY

The basic defect in people with CF (pwCF) leads to impaired epithelial transport of chloride and bicarbonate that can be assessed by CFTR biomarkers, i.e. the β-adrenergic sweat rate and sweat chloride concentration (SCC), chloride conductance of the nasal respiratory epithelium (NPD), urine secretion of bicarbonate, intestinal current measurements (ICM) of chloride secretory responses in rectal biopsies and in bioassays of chloride transport in organoids or cell cultures. CFTR modulators are a novel class of drugs that improve defective posttranslational processing, trafficking and function of mutant CFTR. By April 2025, triple combination therapy with the CFTR potentiator ivacaftor (IVA) and the CFTR correctors elexacaftor (ELX) and tezacaftor (TEZ) has been approved in Europe for the treatment of all pwCF who do not carry two minimal function CFTR mutations. Previous phase 3 and post-approval phase 4 studies in pwCF who harbour one or two alleles of the major mutation F508del consistently reported significant improvements of lung function and anthropometry upon initiation of ELX/TEZ/IVA compared to baseline. Normalization of SCC, NPD and ICM correlated with clinical outcomes on the population level, but the restoration of CFTR function was diverse and not predictive for clinical outcome in the individual patient. Theratyping of non-F508del CF genotypes in patient-derived organoids and cell cultures revealed for most cases clinically meaningful increases of CFTR activity upon exposure to ELX/TEZ/IVA. Likewise, every second CF patient with non-F508del genotypes improved in SCC and clinical outcome upon exposure to ELX/TEZ/IVA indicating that triple CFTR modulator therapy is potentially beneficial for all pwCF who do not carry two minimal function CFTR mutations. This group who is not eligible for CFTR modulators may opt for gene addition therapy in the future, as the first-in-human trial with a recombinant lentiviral vector is underway.

FUTURE DIRECTIONS

The upcoming generation of pwCF will probably experience a rather normal life in childhood and adolescence. To classify the upcoming personal signatures of CF disease in the times of efficient modulators, we need more sensitive CFTR biomarkers that address the long-term course of airway and gut microbiome, host defense, epithelial homeostasis and multiorgan metabolism.

Fate mapping in mouse demonstrates early secretory differentiation directly from Lgr5+ intestinal stem cells

The intestinal epithelium has a remarkably high turnover in homeostasis. It remains unresolved how this is orchestrated at the cellular level and how the behavior of stem and progenitor cells ensures tissue maintenance. To address this, we combined quantitative fate mapping in three complementary mouse models with mathematical modeling and single-cell RNA sequencing. Our integrated approach generated a spatially and temporally defined model of crypt maintenance based on two cycling populations: stem cells at the crypt-bottom and transit-amplifying (TA) cells above them. Subsequently, we validated the predictions from the mathematical model, demonstrating that fate decisions between the secretory and absorptive lineages are made within the stem cell compartment, whereas TA cell divisions contribute specifically to the absorptive lineage. These quantitative insights provide further direct evidence for crypt-bottom stem cells as the dominant driver of the intestinal epithelium replenishment.

Non-canonical Wnt signaling promotes epithelial fluidization in the repairing airway

Concerted migration of basal stem cells (BCs) in the airway, also known as epithelial fluidization, has been implicated in epithelial repair after injury. How BC migration is regulated, and how it influences the success of epithelial repair, remains unclear. Here we have identified non-canonical Wnt signaling through Ptk7, Fzd7, and YAP as a critical regulator of BC migration in the mouse trachea. Using live imaging and genetic studies in the mouse, we find that Ptk7 is required for the concerted movement of BCs after injury, and that this requirement extends to BC proliferation and subsequent restoration of epithelial homeostasis after injury. We demonstrate that Ptk7 exerts this function in conjunction with Wnt5a and Fzd7, and through YAP activation in BCs. Our data provide mechanistic insight into the regulation of epithelial repair in the airway.

Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment

The gut microbiota crucially regulates the efficacy of immune checkpoint inhibitor (ICI) based immunotherapy, but the underlying mechanisms remain unclear at the single-cell resolution. Using single-cell RNA sequencing and subsequent validations, we investigate gut microbiota-ICI synergy by profiling the tumor microenvironment (TME) and elucidating critical cellular interactions in mouse models. Our findings reveal that intact gut microbiota combined with ICIs may synergistically increase the proportions of CD8+, CD4+, and γδ T cells, reduce glycolysis metabolism, and reverse exhausted CD8+ T cells into memory/effector CD8+ T cells, enhancing antitumor response. This synergistic effect also induces macrophage reprogramming from M2 protumor Spp1+ tumor-associated macrophages (TAMs) to Cd74+ TAMs, which act as antigen-presenting cells (APCs). These macrophage subtypes show a negative correlation within tumors, particularly during fecal microbiota transplantation. Depleting Spp1+ TAMs in Spp1 conditional knockout mice boosts ICI efficacy and T cell infiltration, regardless of gut microbiota status, suggesting a potential upstream role of the gut microbiota and highlighting the crucial negative impact of Spp1+ TAMs during macrophage reprogramming on immunotherapy outcomes. Mechanistically, we propose a γδ T cell-APC-CD8+ T cell axis, where gut microbiota and ICIs enhance Cd40lg expression on γδ T cells, activating Cd40 overexpressing APCs (e.g., Cd74+ TAMs) through CD40-CD40L-related NF-κB signaling and boosting CD8+ T cell responses via CD86-CD28 interactions. These findings highlight the potential importance of γδ T cells and SPP1-related macrophage reprogramming in activating CD8+ T cells, as well as the synergistic effect of gut microbiota and ICIs in immunotherapy through modulating the TME.

Interleukin-11 expressed in the polyp-enriched fibroblast subset is a potential therapeutic target in Peutz-Jeghers syndrome

Peutz-Jeghers syndrome (PJS) is associated with early-onset gastrointestinal polyposis caused by hereditary inactivating pathogenic variants in the tumor suppressor gene STK11 (LKB1). Due to lack of prophylactic therapies, management of PJS polyps requires frequent surveillance. Interestingly, studies in mouse models have revealed that stromal cells drive the polyp formation, but detailed understanding of the cell types and interactions involved has been lacking. Using single-cell RNA sequencing of PJS mouse model polyps, we here identify a polyp-enriched crypt top fibroblast (pCTF) cluster characterized by a transcriptional signature also enriched in PJS patient polyps. The pCTF signature was also noted in primary fibroblasts in vitro following acute STK11 loss. Targeted deletion of Stk11 in crypt top fibroblasts using Foxl1-Cre led to upregulation of the pCTF signature genes and later to polyposis. pCTFs displayed similarity to inflammation-associated fibroblasts, and polyposis was exacerbated by inflammation. Cell-cell communication analysis identified interleukin 11 (IL-11) as a potential pCTF inducer, and consistent with this, IL-11 was required for fibroblast reprogramming toward pCTFs following STK11 loss. Importantly, a neutralizing IL-11 antibody efficiently reduced polyp formation in a PJS model indicating a key, targetable role for IL-11 in polyp development. Together the results characterize pCTFs as a PJS polyp-enriched fibroblast subset and identify IL-11 as a key mediator of fibroblast reprogramming and a potential therapeutic target in PJS. © 2025 The Pathological Society of Great Britain and Ireland.

Mechanistic insights into Wnt-β-catenin pathway activation and signal transduction

In multicellular organisms, Wnt proteins govern stem and progenitor cell renewal and differentiation to regulate embryonic development, adult tissue homeostasis and tissue regeneration. Defects in canonical Wnt signalling, which is transduced intracellularly by β-catenin, have been associated with developmental disorders, degenerative diseases and cancers. Although a simple model describing Wnt-β-catenin signalling is widely used to introduce this pathway and has largely remained unchanged over the past 30 years, in this Review we discuss recent studies that have provided important new insights into the mechanisms of Wnt production, receptor activation and intracellular signalling that advance our understanding of the molecular mechanisms that underlie this important cell-cell communication system. In addition, we review the recent development of molecules capable of activating the Wnt-β-catenin pathway with selectivity in vitro and in vivo that is enabling new lines of study to pave the way for the development of Wnt therapies for the treatment of human diseases.

PAR2 deficiency impairs antitumor immunity and attenuates anti-PD1 efficacy in colorectal cancer

A T cell-inflamed tumor microenvironment is predictive of better prognosis and clinical response to immunotherapy. Proteinase-activated receptor 2 (PAR2), a member of G-protein coupled receptors is involved in inflammatory process and the progression of various cancers. However, the role of PAR2 in modulating the tumor microenvironment remains unclear. Here, we found that PAR2 high-expression was associated with a favorable prognosis in patients with colorectal cancer. Intriguingly, PAR2 expression in human colorectal cancer was mainly confined to tumor cells and was significantly associated with CD8+ T cell infiltration. Tumor-intrinsic PAR2 deficiency blunted antitumor immune responses to promote tumor growth and attenuated the therapeutic efficacy of anti-PD1 in a mouse model of colon cancer. Tumors with downregulated PAR2 showed decreased CD8+ T cell infiltration and impaired effector function. Mechanistically, PAR2 activation in tumor cells induced CXCL9 and CXCL10 production via PI3K/AKT/mTOR signaling, thereby enhancing CD8+ T cell recruitment in the tumor microenvironment. In addition, PAR2 was essential for dendritic cell activation and differentiation towards conventional type 1 subset. PAR2 deficiency in dendritic cells markedly impaired their ability to prime CD8+ T cells and control tumor growth in vivo. Thus, our findings identify new roles for PAR2 in promoting antitumor immunity and provide a promising target to improve immunotherapy efficacy in colorectal cancer.

Translating premalignant biology to accelerate non-small-cell lung cancer interception

Over the past decade, substantial progress has been made in the development of targeted and immune-based therapies for patients with advanced non-small-cell lung cancer. To further improve outcomes for patients with lung cancer, identifying and intercepting disease at the earliest and most curable stages are crucial next steps. With the recent implementation of low-dose computed tomography scan screening in populations at high risk, there is an emerging unmet need for new diagnostic, prognostic and therapeutic tools to help treat patients suspected of harbouring premalignant lesions and minimally invasive non-small-cell lung cancer. Continued advances in the identification of the earliest drivers of lung carcinogenesis are poised to address these unmet needs. Employing multimodal approaches to chart the temporal and spatial maps of the molecular events driving lung premalignant lesion progression will refine our understanding of early carcinogenesis. Elucidating the molecular drivers of premalignancy is critical to the development of biomarkers to detect those incubating a premalignant lesion, to stratify risk for progression to invasive cancer and to identify novel therapeutic targets to intercept that process. In this Review, we summarize emerging insights into the earliest cellular and molecular events associated with lung squamous and adenocarcinoma carcinogenesis and highlight the growing opportunity for translating these insights into clinical tools for early detection and disease interception to transform the outcomes for those at risk for lung cancer.

Decoding functional hematopoietic progenitor cells in the adult human lung

ABSTRACT

Although the bone marrow is the main site of blood cell production in adults, rare pools of hematopoietic stem and progenitor cells have been found in extramedullary organs. In mice, we have previously shown that the lung contains hematopoietic progenitor cells and is a site of platelet production. Here, in the adult human lung, we show that functional hematopoietic precursors reside in the extravascular spaces with a frequency similar to the bone marrow and are capable of proliferation and engraftment in mice. The gene signature of pulmonary and medullary CD34+ hematopoietic progenitors indicates greater baseline activation of immune-, megakaryocyte/platelet-, and erythroid-related pathways in lung progenitors. Spatial transcriptomics mapped blood progenitors in the lung to an alveolar interstitium niche with only a few cells identified in an intravascular location. In human blood samples collected for stem cell transplantation, CD34+ cells with a lung signature enriched the mobilized pool of hematopoietic stem cells. These results identify the lung as a pool for uniquely programmed blood stem and progenitor cells with the potential to support hematopoiesis in humans.

Coordinated Regulation of Extrafollicular B Cell Responses by IL-12 and IFNγ

Upon activation, B cells undergo either the germinal center (GC) or extrafollicular (EF) response. While GC are known to generate high-affinity memory B cells and long-lived plasma cells, the role of the EF response is less well understood. Initially, it was thought to be limited to that of a source of fast but lower-quality antibodies until the GC can form. However, recent evidence strongly supports the EF response as an important component of the humoral response to infection. EF responses are now also recognized as a source of pathogenic B cells in autoimmune diseases. The EF response itself is dynamic and regulated by pathways that are only recently being uncovered. We have identified that the cytokine IL-12 acts as a molecular switch, enhancing the EF response and suppressing GC through multiple mechanisms. These include direct effects on both B cells themselves and the coordinated differentiation of helper CD4 T cells. Here, we explore this pathway in relation to other recent advancements in our understanding of the EF response's role and highlight areas for future research. A better understanding of how the EF response forms and is regulated is essential for advancing treatments for many disease states.

Enteric neuronal Piezo1 maintains mechanical and immunological homeostasis by sensing force

The gastrointestinal (GI) tract experiences a myriad of mechanical forces while orchestrating digestion and barrier immunity. A central conductor of these processes, the enteric nervous system (ENS), detects luminal pressure to regulate peristalsis independently of extrinsic input from the central and peripheral nervous systems. However, how the ∼500 million enteric neurons that reside in the GI tract sense and respond to force remains unknown. Herein, we establish that the mechanosensor Piezo1 is functionally expressed in cholinergic enteric neurons. Optogenetic stimulation of Piezo1+ cholinergic enteric neurons drives colonic motility, while Piezo1 deficiency reduces cholinergic neuronal activity and slows peristalsis. Additionally, Piezo1 deficiency in cholinergic enteric neurons abolishes exercise-induced acceleration of GI motility. Finally, we uncover that enteric neuronal Piezo1 function is required for motility alterations in colitis and acts to prevent aberrant inflammation and tissue damage. This work uncovers how the ENS senses and responds to mechanical force.

Emerging clinical applications of single-cell RNA sequencing in oncology

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of complex tissues both in health and in disease. Over the past decade, scRNA-seq has been applied to tumour samples obtained from patients with cancer in hundreds of studies, thereby advancing the view that each tumour is a complex ecosystem and uncovering the diverse states of both cancer cells and the tumour microenvironment. Such studies have primarily investigated and provided insights into the basic biology of cancer, although considerable research interest exists in leveraging these findings towards clinical applications. In this Review, we summarize the available data from scRNA-seq studies investigating samples from patients with cancer with a particular focus on findings that are of potential clinical relevance. We highlight four main research objectives of scRNA-seq studies and describe some of the most relevant findings towards such goals. We also describe the limitations of scRNA-seq, as well as future approaches in this field that are anticipated to further advance clinical applicability.

miR-143-3p boosts extracellular vesicles to improve the dermal fibrosis of localized scleroderma

Localized scleroderma (LoSc) is an autoimmune disease that features extensive fibrosis of the skin. Due to its severity and limited understanding, no effective treatments have been developed to date. Bone marrow mesenchymal stem cells (BMSCs) derived extracellular vesicles (EVs) have been demonstrated promising therapeutic effects on the LoSc mouse model in our previous study. However, identifying the targets and underlying mechanisms of EVs remains a significant challenge for therapeutic applications. miR-143-3p, a critical and abundant factor in BMSC-EVs identified through miRNA sequencing, mediates antifibrotic effects in a LoSc mouse model and is significantly lacking in the dermis of LoSc patients. This microRNA inhibits myofibroblast formation and collagen synthesis, contributing to the therapeutic effects of BMSC-EVs in the LoSc mouse model. Moreover, miR-143-3p-reinforced BMSC-EVs demonstrated enhanced therapeutic efficacy compared to normal BMSC-EVs, reducing dermal thickening, collagen deposition, fibroblast differentiation into myofibroblasts, and promoting skin tissue remodeling. IGF1R, highly expressed in the skin of LoSc, was identified as a potential target of miR-143-3p and was inhibited by miR-143-3p-reinforced EVs, thereby modulating the IGF1/IGF1R-AKT/MAPK pathway. In conclusion, miR-143-3p-enriched EVs could be a more efficient candidate for treating dermal fibrosis in LoSc.

Recent strategies for enhanced delivery of mRNA to the lungs

mRNA-based therapies have emerged as a transformative tool in modern medicine, gaining significant attention following their successful use in COVID-19 vaccines. Delivery to the lungs offers several compelling advantages for mRNA delivery. The lungs are one of the most vascularized organs in the body, which provides an extensive surface area that can facilitate efficient drug transport. Local delivery to the lungs bypasses gastrointestinal degradation, potentially enhancing therapeutic efficacy. In addition, the extensive capillary network of the lungs provides an ideal target for systemic delivery. However, developing effective mRNA therapies for the lungs presents significant challenges. The complex anatomy of the lungs and the body's immune response to foreign particles create barriers to delivery. This review discusses key approaches for overcoming these challenges and improving mRNA delivery to the lungs. It examines both local and systemic delivery strategies aimed at improving lung delivery while mitigating off-target effects. Although substantial progress has been made in lung-targeted mRNA therapies, challenges remain in optimizing cellular uptake and achieving therapeutic efficacy within pulmonary tissues. The continued refinement of delivery strategies that enhance lung-specific targeting while minimizing degradation is critical for the clinical success of mRNA-based pulmonary therapies.

Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome

Microbial genome-wide association studies (GWAS) have uncovered numerous host genetic variants associated with gut microbiota. However, links between host genetics, the gut microbiome and specific cellular contexts remain unclear. Here we use a computational framework, scBPS (single-cell Bacteria Polygenic Score), to integrate existing microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs, including the liver, pancreas, lung and intestine, to identify host tissues and cell types relevant to gut microbes. Analysing 207 microbial taxa and 254 host cell types, scBPS-inferred cellular enrichments confirmed known biology such as dominant communications between gut microbes and the digestive tissue module and liver epithelial cell compartment. scBPS also identified a robust association between Collinsella and the central-veinal hepatocyte subpopulation. We experimentally validated the causal effects of Collinsella on cholesterol metabolism in mice through single-nuclei RNA sequencing on liver tissue to identify relevant cell subpopulations. Mechanistically, oral gavage of Collinsella modulated cholesterol pathway gene expression in central-veinal hepatocytes. We further validated our approach using independent microbial GWAS data, alongside single-cell and bulk transcriptomic analyses, demonstrating its robustness and reproducibility. Together, scBPS enables a systematic mapping of the host-microbe crosstalk by linking cell populations to their interacting gut microbes.

SPP1 + macrophages in colorectal cancer: Markers of malignancy and promising therapeutic targets

SPP1+ macrophages have been identified as key players in the colorectal cancer (CRC) tumor microenvironment, but their function remains unclear. This study integrated single-cell and spatial transcriptomics with bulk sequencing to investigate the roles and mechanisms of SPP1 + macrophages in CRC. Our findings revealed a pronounced elevation of SPP1 + macrophages in CRC, especially within tumor territories. These macrophages served as markers for CRC initiation, progression, metastasis, and potential prognosis. Furthermore, they showed heightened transcriptional activity in genes linked to angiogenesis, epithelial-mesenchymal transition, glycolysis, hypoxia, and immunosuppression. SPP1 protein amplified CRC cell migration and invasion, potentially mediating cellular crosstalk via the SPP1-CD44, SPP1-PTGER4, and SPP1-a4b1 complex axes. Patients with a high proportion of SPP1 + macrophages could benefit more from immune checkpoint blockade therapy. Interestingly, CSF1R expression was significantly enriched in C1QC + macrophages versus SPP1 + macrophages, possibly explaining limited anti-CSF1R monotherapy effects. In conclusion, we propose an SPP1 + macrophage model in CRC, highlighting such macrophages as a promising therapeutic target due to their malignancy markers.

Cancer immune evasion, immunoediting and intratumour heterogeneity

Cancers can avoid immune-mediated elimination by acquiring traits that disrupt antitumour immunity. These mechanisms of immune evasion are selected and reinforced during tumour evolution under immune pressure. Some immunogenic subclones are effectively eliminated by antitumour T cell responses (a process known as immunoediting), which results in a clonally selected tumour. Other cancer cells arise to resist immunoediting, which leads to a tumour that includes several distinct cancer cell populations (referred to as intratumour heterogeneity (ITH)). Tumours with high ITH are associated with poor patient outcomes and a lack of responsiveness to immune checkpoint blockade therapy. In this Review, we discuss the different ways that cancer cells evade the immune system and how these mechanisms impact immunoediting and tumour evolution. We also describe how subclonal antigen presentation in tumours with high ITH can result in immune evasion.

Multiomic spatial atlas shows deleted in malignant brain tumors 1 (DMBT1) glycoprotein is lost in colonic dysplasia

Colorectal cancer (CRC) is responsible for over 900,000 annual deaths worldwide. Emerging evidence supports pro-carcinogenic bacteria in the colonic microbiome are at least promotional in CRC development and may be causal. We previously showed toxigenic C. difficile from human CRC-associated bacterial biofilms accelerates tumorigenesis in ApcMin/+ mice, both in specific pathogen-free mice and in gnotobiotic mice colonized with a defined consortium of bacteria. To further understand host-microbe interactions during colonic tumorigenesis, we combined single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics, and immunofluorescence to define the molecular spatial organization of colonic dysplasia in our consortium model with or without C. difficile. Our data show a striking bipartite regulation of Deleted in Malignant Brain Tumors 1 (DMBT1) in the inflamed versus dysplastic colon. From scRNA-seq, differential gene expression analysis of normal absorptive colonocytes at 2 weeks postinoculation showed DMBT1 upregulated by C. difficile compared to colonocytes from mice without C. difficile exposure. In contrast, our spatial transcriptomic analysis showed DMBT1 dramatically downregulated in dysplastic foci compared with normal-adjacent tissue. We further integrated our datasets to generate custom colonic dysplasia scores and ligand-receptor mapping. Validation with immunofluorescence showed DMBT1 protein downregulated in dysplastic foci from three mouse models of colonic tumorigenesis and in adenomatous dysplasia from human samples. Finally, we used mouse and human organoids to implicate WNT signaling in the downregulation of DMBT1 mRNA and protein. Together, our data reveal cell type-specific regulation of DMBT1, a potential mechanistic link between bacteria and colonic tumorigenesis. Published 2025. This article is a U.S. Government work and is in the public domain in the USA. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Differential cellular origins of the extracellular matrix of tumor and normal tissues according to colorectal cancer subtypes

BACKGROUND

Understanding the proteomic-level heterogeneity of the tumor microenvironment (TME) in colorectal cancer (CRC) is crucial due to its well-known heterogeneity. While heterogenous CRC has been extensively characterized at the molecular subtype level, research into the functional heterogeneity of fibroblasts, particularly their relationship with extracellular matrix (ECM) alterations, remains limited. Addressing this gap is essential for a comprehensive understanding of CRC progression and the development of targeted therapies.

METHODS

24 tissue samples from 21 CRC patients, along with adjacent normal tissues (NAT), were collected and decellularized using a detergent-based method to enrich the ECM component. Proteomic analysis of ECM-enriched samples was performed using tandem mass tag (TMT) spectrometry, followed by statistical analysis including differential expression protein (DEP) analysis. Single-cell RNA sequencing (scRNA-Seq) data from public datasets were integrated and analyzed to delineate cell states within the TME. Bulk tissue RNA-Seq and bioinformatics analysis, including consensus molecular subtype (CMS) classification and single-cell level deconvolution of TCGA bulk RNA-seq data, were conducted to further explore gene expression patterns and TME composition.

RESULTS

Differential cellular origin of the NAT and tumorous ECM proteins were identified, revealing 110 ECM proteins enriched in NAT and 28 ECM proteins in tumor tissues. Desmoplastic and WNT5A+ inflammatory fibroblasts were indicated as the sources of tumor-enriched ECM proteins, while ADAMDEC1+ expressing fibroblasts and PI16+ expressing fibroblast were identified as the sources of NAT-enriched ECM proteins. Deconvolution of bulk RNA-seq of CRC tissues discriminated CMS-specific fibroblast state, reflecting the biological traits of each CMS subtype. Specially, seven ECM genes specific to mesenchymal subtype (CMS4), including PI16+ fibroblast-related 4 genes (SFRP2, PRELP, OGN, SRPX) and desmoplastic fibroblast-related 3 genes (THBS2, CTHRC1, BGN), showed a significant association with poorer survival in patient with CRC.

CONCLUSION

We conducted an extracellular matrix (ECM)-focused profiling of the TME by integrating quantitative proteomics with single-cell RNA sequencing (scRNA-seq) data from CRC patients. We identified the ECM proteins of NAT and tumor tissue, and established a cell-matrisome database. We defined mesenchymal subtype-specific molecules associated with specific fibroblast subtypes showing a significant association with poorer survival in patients with CRC. Our ECM-focused profiling of tumor stroma provides new insights as indicators for biological processes and clinical endpoints.

BRAF mutation cancer, colorectal cancer, tumor associated lymph node structure and immune microenvironment study: MAPK protein kinase molecular action and SIRPG-CD47 protein signaling pathway

BRAF mutation affects the biological characteristics and microenvironment of the tumor during the development of colorectal cancer. Tumor-associated lymph nodes are the key sites of immune response. This study aimed to systematically evaluate the impact of BRAF gene mutations on the remodeling of the CRC immune microenvironment, with a particular focus on their effects on the maturation and function of TLS·In this study, clinical samples of CRC patients were collected, and immune cell subsets were analyzed by single-cell RNA sequencing, and pseudo-temporal locus analysis and spatial transcriptome analysis were performed to explore intercellular communication and functional enrichment analysis. The distribution and maturity of TLS were evaluated by immunohistochemistry and multiple fluorescence staining techniques, and statistical analysis was performed.The results showed that BRAF mutation significantly affected the number and maturity of lymphatic structures infiltrated by tumors, and was negatively correlated with patient prognosis. BRAF mutations lead to alterations in T cell subsets, particularly the dual role of CD4+ CXCL13 cells in TLS maturation. B-cell subpopulation analysis revealed functional deficits in CRC patients with BRAF mutations, which further drove the remodeling of the tumor immune microenvironment.

ACKR3 in Skin Homeostasis, an Overlooked Player in the CXCR4/CXCL12 Axis

CXCL12 and its receptor CXCR4 emerge as critical regulators within the intricate network of processes ensuring skin homeostasis. In this review, we discuss their spatial distribution and function in steady-state skin; delve into their role in acute wound healing, with emphasis on fibrotic and regenerative responses; and explore their relevance in skin responses to commensals and pathogens. Given the lack of knowledge surrounding ACKR3, the atypical receptor of CXCL12, we speculate whether and how it might be involved in the processes mentioned earlier. Is ACKR3 the (a)typical friend who enjoys missing the party, or do we need to take a closer look?

Aberrant basal cell clonal dynamics shape early lung carcinogenesis

Preinvasive squamous lung lesions are precursors of lung squamous cell carcinoma (LUSC). The cellular events underlying lesion formation are unknown. Using a carcinogen-induced model of LUSC with no added genetic hits or cell type bias, we find that carcinogen exposure leads to non-neutral competition among basal cells, aberrant clonal expansions, and basal cell mobilization along the airways. Ultimately, preinvasive lesions develop from a few highly mutated clones that dominate most of the bronchial tree. Multi-site sequencing in human patients confirms the presence of clonally related preinvasive lesions across distinct airway regions. Our work identifies a transition in basal cell clonal dynamics, and an associated shift in basal cell fate, as drivers of field cancerization in the lung.

Vagal pathway activation links chronic stress to decline in intestinal stem cell function

Chronic stress adversely affects intestinal health, but the specific neural pathways linking the brain to intestinal tissue are not fully understood. Here, we show that chronic stress-induced activation of the central amygdala-dorsal motor nucleus of the vagus (CeA-DMV) pathway accelerates premature aging and impairs the stemness of intestinal stem cells (ISCs). This pathway influences ISC function independently of the microbiota, the hypothalamic-pituitary-adrenal (HPA) axis, the immune response, and the sympathetic nervous system (SNS). Under chronic stress, DMV-mediated vagal activation prompts cholinergic enteric neurons to release acetylcholine (ACh), which engages ISCs via the M3 muscarinic acetylcholine receptor (CHRM3). This interaction activates the p38 mitogen-activated protein kinase (MAPK) pathway, triggering growth arrest and mitochondrial fragmentation, thereby accelerating an aging-like decline in ISCs. Together, our findings provide insights into an alternative neural mechanism that links stress to intestinal dysfunction. Strategies targeting the DMV-associated vagal pathway represent potential therapeutic approaches for stress-induced intestinal diseases.

Granzyme K activates the entire complement cascade

Granzymes are a family of serine proteases that are mainly expressed by CD8+ T cells, natural killer cells and innate-like lymphocytes1. Although their primary function is thought to be the induction of cell death in virally infected cells and tumours, accumulating evidence indicates that some granzymes can elicit inflammation by acting on extracellular substrates1. We previously found that most tissue CD8+ T cells in rheumatoid arthritis synovium, and in inflamed organs for some other diseases, express granzyme K (GZMK)2, a tryptase-like protease with poorly defined function. Here, we show that GZMK can activate the complement cascade by cleaving the C2 and C4 proteins. The nascent C4b and C2b fragments form a C3 convertase that cleaves C3, enabling the assembly of a C5 convertase that cleaves C5. The resulting convertases generate all the effector molecules of the complement cascade: the anaphylatoxins C3a and C5a, the opsonins C4b and C3b, and the membrane attack complex. In rheumatoid arthritis synovium, GZMK is enriched in regions with abundant complement activation, and fibroblasts are the main producers of complement proteins that serve as substrates for GZMK-mediated complement activation. Furthermore, Gzmk-deficient mice are significantly protected from inflammatory disease, exhibiting reduced arthritis and dermatitis, with concomitant decreases in complement activation. Our findings describe the discovery of a previously unidentified mechanism of complement activation that is driven entirely by lymphocyte-derived GZMK. Given the widespread abundance of GZMK-expressing T cells in tissues in chronic inflammatory diseases, GZMK-mediated complement activation is likely to be an important contributor to tissue inflammation in multiple disease contexts.

Tritrichomonas muris sensitizes the intestinal epithelium to doxorubicin-induced apoptosis

Doxorubicin (DXR) is a widely used chemotherapy drug that can induce severe intestinal mucositis. Although the influence of gut bacteria on DXR-induced damage has been documented, the role of eukaryotic commensals remains unexplored. We discovered Tritrichomonas muris (Tmu) in one of our mouse colonies exhibiting abnormal tuft cell hyperplasia, prompting an investigation into its impact on DXR-induced intestinal injury. Mice from Tmu-colonized and Tmu-excluded facilities were injected with DXR. Tissue morphology and gene expression were evaluated at acute injury (6 h) and regenerative (72 h and 120 h) phases. Changes to crypt and villus morphology were more subtle than previously reported and region-specific, with significantly shorter jejunal villi in Tmu+ mice at 72 h post-DXR compared with Tmu- controls. Most notably, we observed elevated rates of DXR-induced apoptosis, measured by cleaved caspase 3 (CC3) staining, in Tmu+ intestinal crypts at 6 h post-DXR. Tmu+ mice also exhibited reduced expression of active intestinal stem cell (aISC) marker Lgr5 and facultative ISC (fISC) marker Ly6a at 6 h post-DXR compared with Tmu- controls. Tmu, but not DXR, was associated with increased inflammation and expression of type 2 cytokines IL-5 and IL-13. Tmu+ mice also exhibited a decreased fecal abundance of Lactobacillus, which promotes gut barrier integrity, and reduced claudin expression, indicating potential barrier dysfunction that could explain the increase in DXR-induced apoptosis. These findings highlight the significant influence of commensal microbiota, particularly eukaryotic organisms like Tmu, on intestinal biology and response to chemotherapy, underscoring the complexity of gut microbiota interactions in drug-induced mucositis.NEW & NOTEWORTHY Our study found that the eukaryotic commensal Tritrichomonas muris (Tmu) significantly increases DXR-induced intestinal apoptosis in mice. Tmu also reduces Lgr5 expression post-DXR injury and elevates inflammation and type 2 cytokine expression in the absence of injury. 16S sequencing identifies decreased abundance of protective Lactobacillus in Tmu colonized mice, as well as decreased expression of barrier-forming claudins, which may explain increased apoptosis. These findings emphasize the complex role of microbiota in drug-induced intestinal damage.

Human Enteric Glia Diversity in Health and Disease: New Avenues for the Treatment of Hirschsprung Disease

BACKGROUND & AIMS

The enteric nervous system (ENS), which is composed of neurons and glia, regulates intestinal motility. Hirschsprung disease (HSCR) results from defects in ENS formation; however, although neuronal aspects have been studied extensively, enteric glia remain disregarded. This study aimed to explore enteric glia diversity in health and disease.

METHODS

Full-thickness intestinal resection material from pediatric controls and patients with HSCR was collected, dissociated, and enriched for the ENS population through fluorescence-activated cell sorting. Single-cell RNA sequencing was performed to uncover the transcriptomic diversity of the ENS in controls and HSCR patients, as well as in wild-type and ret mutant zebrafish. Immunofluorescence and fluorescence in situ hybridization confirmed the presence of distinct subtypes.

RESULTS

Two major enteric glial classes emerged in the pediatric intestine: Schwann-like enteric glia, which are reminiscent of Schwann cells, and enteric glia expressing classical glial markers. Comparative analysis with previously published datasets confirmed our classification and revealed that although classical enteric glia are predominant prenatally, Schwann-like enteric glia become more abundant postnatally. In HSCR, ganglionic segments mirrored controls and aganglionic segments featured only Schwann-like enteric glia. Leveraging the regenerative potential of Schwann cells, we explored therapeutic options using a ret mutant zebrafish. Prucalopride, a serotonin-receptor (5-HT) agonist, induced neurogenesis partially rescuing the HSCR phenotype in ret+/- mutants.

CONCLUSIONS

Two major enteric glial classes were identified in the pediatric intestine, highlighting the significant postnatal contribution of Schwann-like enteric glia to glial heterogeneity. Crucially, these glial subtypes persist in aganglionic segments of patients with HSCR, offering a new target for their treatment using 5-HT agonists.

Organoid-Guided Precision Medicine: From Bench to Bedside

Organoid technology, as an emerging field within biotechnology, has demonstrated transformative potential in advancing precision medicine. This review systematically outlines the translational trajectory of organoids from bench to bedside, emphasizing their construction methodologies, key regulatory factors, and multifaceted applications in personalized healthcare. By recapitulating physiological architectures and disease phenotypes through three-dimensional culture systems, organoids leverage natural and synthetic scaffolds, stem cell sources, and spatiotemporal cytokine regulation to model tissue-specific microenvironments. Diverse organoid types-including skin, intestinal, lung, and tumor organoids-have facilitated breakthroughs in modeling tissue development, drug efficacy and toxicity screening, disease pathogenesis studies, and patient-tailored diagnostics. For instance, patient-derived tumor organoids preserve tumor heterogeneity and genomic profiles, serving as predictive platforms for individualized chemotherapy responses. In precision medicine, organoid-guided multiomics analyses identify actionable biomarkers and resistance mechanisms, while clustered regularly interspaced short palindromic repeats-based functional screens optimize therapeutic targeting. Despite preclinical successes, challenges persist in standardization, vascularization, and ethical considerations. Future integration of artificial intelligence, microfluidics, and spatial transcriptomics will enhance organoid scalability, reproducibility, and clinical relevance. By bridging molecular insights with patient-specific therapies, organoids are poised to revolutionize precision medicine, offering dynamic platforms for drug development, regenerative strategies, and individualized treatment paradigms.

Beyond circulating B cells: Characteristics and role of tissue-infiltrating B cells in systemic sclerosis

B cells play a key role in the pathophysiology of systemic sclerosis (SSc). While they are less characterized than their circulating counterparts, tissue-infiltrating B cells may have a more direct pathological role in tissues. In this review, we decipher the multiple evidence of B cells infiltration in the skin and lungs of SSc patients and animal models of SSc but also of other chronic fibrotic diseases with similar pathological mechanisms such as chronic graft versus host disease, idiopathic pulmonary fibrosis or morphea. We also recapitulate the current knowledge about mechanisms of B cells infiltration and their functions in tissues. Finally, we discuss B cell targeted therapies, and their specific impact on infiltrated B cells. Understanding the local consequences of infiltrating B cells is an important step for a better management of patients and the improvement of therapies in SSc.

Tissue mechanics in tumor heterogeneity and aggression

Tumorigenesis ensues within a heterogeneous tissue microenvironment that promotes malignant transformation, metastasis and treatment resistance. A major feature of the tumor microenvironment is the heterogeneous population of cancer-associated fibroblasts and myeloid cells that stiffen the extracellular matrix. The heterogeneously stiffened extracellular matrix in turn activates cellular mechanotransduction and creates a hypoxic and metabolically hostile microenvironment. The stiffened extracellular matrix and elevated mechanosignaling also drive tumor aggression by fostering tumor cell growth, survival, and invasion, compromising antitumor immunity, expanding cancer stem cell frequency, and increasing mutational burden, which promote intratumor heterogeneity. Delineating the molecular mechanisms whereby tissue mechanics regulate these phenotypes should help to clarify the basis for tumor heterogeneity and cancer aggression and identify novel therapeutic targets that could improve patient outcome. Here, we discuss the role of the extracellular matrix in driving cancer aggression through its impact on tumor heterogeneity.

Insights into Modeling Inflammatory Bowel Disease from Stem Cell Derived Intestinal Organoids

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial, immune-mediated condition marked by chronic gastrointestinal inflammation. This condition significantly impairs patients' quality of life and represents a major public health challenge globally. Pathogenesis of IBD arises from complex interplay among genetic predisposition, environmental factors, immune dysregulation, and microbial dysbiosis. Although significant strides have been made in unraveling these mechanisms, existing therapeutic options remain inadequate in addressing the full spectrum of clinical needs, underscoring the urgent demand for innovative strategies. Regenerative medicine has emerged as a promising frontier, offering novel tools for therapeutic development. We briefly consolidated current knowledge on IBD pathogenesis and treatments, emphasized the pivotal potential of human intestinal organoids (including adult stem cell-derived organoids and pluripotent stem cell- derived organoids) as a robust platform for mechanistic studies and treatment exploration. Leveraging this technology, we aim to advance personalized and next-generation therapies for IBD.

Bioinspired Claw-Engaged Adhesive Microparticles Armed with γGC Alleviate Ulcerative Colitis via Targeted Suppression of Macrophage Ferroptosis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease, characterized by focal iron overload. Herein, we reported that γ-glutamylcysteine (γGC) deletion in UC lesions intensified the disease by depleting intracellular GSH to induce macrophage ferroptosis, leading to macrophage M1 reprogramming and eventually exacerbating inflammation. To counteract this, the advanced microparticles (MPs)-based delivery system is selected to encapsulate γGC. The resulting γGC-MPs displayed the same porous and spiky morphology as their substrate's natural pollens, resulting in improved intestinal adhesion and enhanced lesion contact of γGC-MPs. Our results demonstrated that exogenous γGC supplementation could inhibit macrophage M1 polarization by restraining ferroptosis, as well as suppressing the PI3K/AKT pathway and TNF signaling pathway. Compared with free γGC, γGC-MPs significantly alleviated typical UC symptoms in dextran sulfate sodium (DSS)-induced colitis, evidenced by reduced intestinal inflammation, restored intestinal barrier function, and improved microbiota composition. Consequently, this study addressed critical gaps in understanding the causes of ferroptosis and its impact on macrophage reprogramming in UC, offering a novel synergistic therapeutic strategy for UC.

Integrated multimodel analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD

BACKGROUND

IBD is a chronic inflammatory condition driven by complex genetic and immune interactions, yet preclinical models often fail to fully recapitulate all aspects of the human disease. A systematic comparison of commonly used IBD models is essential to identify conserved molecular mechanisms and improve translational relevance.

OBJECTIVE

We performed a multimodel transcriptomic analysis of 13 widely used IBD mouse models to uncover coregulatory gene networks conserved between preclinical colitis/ileitis and human IBD and to define model-specific and conserved cellular, subcellular and molecular signatures.

DESIGN

We employed comparative transcriptomic analyses with curated and a priori statistical correlative methods between mouse models versus IBD patient datasets at both bulk and single-cell levels.

RESULTS

We identify IBD-related pathways, ontologies and cellular compositions that are translatable between mouse models and patient cohorts. We further describe a conserved core inflammatory signature of IBD-associated genes governing T-cell homing, innate immunity and epithelial barrier that translates into the new mouse gut Molecular Inflammation Score (mMIS). Moreover, specific mouse IBD models have distinct signatures for B-cell, T-cell and enteric neurons. We discover that transcriptomic relatedness of models is a function of the mode of induction, not the canonical immunotype (Th1/Th2/Th17). Moreover, the model compendium database is made available as a web explorer (http://trr241.hosting.rrze.uni-erlangen.de/SEPIA/).

CONCLUSION

This integrated multimodel approach provides a framework for systematically assessing the molecular landscape of intestinal inflammation. Our findings reveal conserved inflammatory circuits, refine model selection, offering a valuable resource for the IBD research community.

Genetic determinants of proteomic aging

Changes in the proteome and its dysregulation have long been known to be a hallmark of aging. We derived a proteomic aging trait using data on 1459 plasma proteins from 44,435 UK Biobank individuals measured using an antibody-based assay. This metric is strongly associated with four age-related disease outcomes, even after adjusting for chronological age. Survival analysis showed that one-year older proteomic age, relative to chronological age, increases all-cause mortality hazard by 13 percent. We performed a genome-wide association analysis of proteomic age acceleration (proteomic aging trait minus chronological age) to identify its biological determinants. Proteomic age acceleration showed modest genetic correlations with four epigenetic clocks (Rg = 0.17 to 0.19) and telomere length (Rg = -0.2). Once we removed associations that were explained by a single pQTL, we were left with three signals mapping to BRCA1, POLR2A and TET2 with apparent widespread effects on plasma proteomic aging. Genetic variation at these three loci has been shown to affect other omics-related aging measures. Mendelian randomisation analyses showed causal effects of higher BMI and type 2 diabetes on faster proteomic age acceleration. This supports the idea that obesity and other features of metabolic syndrome have an adverse effect on the processes of human aging.

ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction

With the development of single-cell RNA-sequencing (scRNA-seq) technology, scRNA-seq data analysis suffers huge challenges due to large scale, high dimensionality, high noise, and high sparsity. To achieve accurately embedded representation in the large-scale scRNA-seq data, we try to design a novel graph convolutional network with an adaptive aggregation mechanism. Based on the assumption that the aggregation order of different cells would be different, a graph convolutional network with an adaptive aggregation-based dimensionality reduction algorithm for scRNA-seq data is developed, named scAGCN. In scAGCN, a preprocessing consisting of quality control and feature selection is implemented. Then, an approximate nearest neighbor graph is rapidly constructed. Finally, a graph convolutional network with an adaptive aggregation mechanism is constructed, in which the neighborhood selection strategy based on node distribution and similarity boxplots is designed, and the aggregation function is optimized by defining a similarity measurement between neighborhood nodes and the central node. The results show that scAGCN outperforms existing dimensionality reduction methods on 15 real scRNA-seq datasets, especially in 10 large-scale scRNA-seq datasets.