Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics

Studies of the avian gastrointestinal tract, where nutrient absorption and key host-pathogen interactions occur, have been strongly enabled by the development of intestinal organoid models. Here we report a single cell transcriptomic atlas of intestinal organoid cells derived from embryos of broiler and layer chickens, capturing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. Eight inferred mesenchymal subpopulations reflect anatomically distinct intestinal layers, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal. Identified heterogeneity within the epithelial lineage included enterocytes, goblet cells, Paneth cells, tuft cells, and diverse enteroendocrine cell subtypes. Additionally, we identified candidate macrophages, monocytes, γδ T cells, NK cells and granulocytes. Layer and broiler organoids showed significant differences in cell-specific transcriptome, most pronounced in epithelial cells, pointing to divergent selection on intestinal physiology. Our analysis finally provides a catalogue of novel cell marker genes to enable future research of chicken intestinal organoids.

There's no place like home: How local tissue microenvironments shape the function of innate lymphoid cells

Innate lymphoid cells (ILC) have emerged as critical immune effectors with key roles in orchestrating the wider immune response. While ILC are relatively rare cells they are found enriched within discrete microenvironments, predominantly within barrier tissues. An emerging body of evidence implicates complex and multi-layered interactions between cell types, tissue structure and the external environment as key determinants of ILC function within these niches. In this review we will discuss the specific components that constitute ILC-associated microenvironments and consider how they act to determine health and disease. The development of holistic, integrated models of ILC function within complex tissue environments will inform new understanding of the contextual cues and mechanisms that determine the protective versus disease-causing roles of this immune cell family.

Sodium Houttuyfonate Ameliorates DSS-induced Colitis Aggravated by Candida albicans through Dectin-1/NF-κB/miR-32-5p/NFKBIZ Axis Based on Intestinal microRNA Profiling

Our previous research indicated that Sodium houttuyfonate (SH) can effectively ameliorate dextran sulfate sodium (DSS)-induced colitis exacerbated by Candida albicans. However, the underlying protective mechanism of SH remains unclear. Therefore, in this study, a mice colitis model was infected with C. albicans, and the total colonic miRNAs were assessed. Furthermore, the differentially expressed miRNAs were enriched, clustered, and analyzed. Moreover, based on the dual luciferase analysis of NFKBIZ modulation by miR-32-5p, the in vitro and in vivo therapeutic effects of SH on inflammatory response, fungal burden, oxidative stress, and apoptosis were assessed at transcriptional and translational levels in the presence of agonist and antagonist. A total of 1157 miRNAs were identified, 84 of which were differentially expressed. Furthermore, qRT-PCR validated that SH treatment improved 17 differentially expressed miRNAs with > fourfold upregulation or > sixfold downregulation. Similar to most differentially altered miRNA, C. albicans significantly increased Dectin-1, NF-κB, TNF-α, IL-1β, IL-17A, and decreased miR-32-5p which negatively targeted NFKBIZ. In addition, SH treatment reduced inflammatory response and fungal burden in a colitis model with C. albicans infection. Further analyses indicated that in C. albicans infected Caco2 cells, SH inhibited fungal growth, oxidative stress, and apoptosis by increasing Dectin-1, NF-κB, NFKBIZ, TNF-α, IL-1β, IL-17A, and decreasing miR-32-5p. Therefore, SH can ameliorate the severity of colitis aggravated by C. albicans via the Dectin-1/NF-κB/miR-32-5p/NFKBIZ axis.

Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation

The tuft cell-group 2 innate lymphoid cell (ILC2) circuit orchestrates rapid type 2 responses upon detecting microbially derived succinate and luminal helminths. Our findings delineate key mechanistic steps involving IP3R2 engagement and Ca2+ flux, governing interleukin-25 (IL-25) production by tuft cells triggered by succinate detection. While IL-17RB has a pivotal intrinsic role in ILC2 activation, it exerts a regulatory function in tuft cells. Tuft cells exhibit constitutive Il25 expression, placing them in an anticipatory state that facilitates rapid production of IL-25 protein for ILC2 activation. Tuft cell IL-17RB is crucial for restraining IL-25 bioavailability, preventing excessive tonic ILC2 stimulation due to basal Il25 expression. Supraoptimal ILC2 stimulation by IL-25 resulting from tuft cell Il17rb deficiency or prolonged succinate exposure induces a state of hypoproliferation in ILC2s, also observed in chronic helminth infection. Our study offers critical insights into the regulatory dynamics of IL-25 in this circuit, highlighting the delicate tuning required for responses to diverse luminal states.

The multi-organ landscape of B cells highlights dysregulated memory B cell responses in Crohn's disease

Crohn's disease (CD) is a prevalent type of inflammatory bowel disease (IBD) with dysregulated antibody responses. However, there is a lack of comprehensive analysis of B cell responses in CD. Here, we collected B cells from the small intestine, colon and blood of CD patients and control subjects. Through the coupled analysis of transcriptome and immunoglobulin (Ig) gene in individual cells, we characterized the cellular composition, transcriptome and Ig clonotype in different B cell subtypes. We observed shared disruptions in plasma cell (PC) responses between different IBD subtypes. We revealed heterogeneity in memory B cells (MBCs) and showed a positive correlation between gut resident-like MBCs and disease severity. Furthermore, our clonotype analysis demonstrated an increased direct differentiation of MBCs into PCs in CD patients. Overall, this study demonstrates significantly altered B cell responses associated with chronic inflammation during CD and highlights the potential role of mucosal MBCs in CD pathogenesis.

Cross-ancestry genome-wide association study and systems-level integrative analyses implicate new risk genes and therapeutic targets for depression

Deciphering the genetic architecture of depression is pivotal for characterizing the associated pathophysiological processes and development of new therapeutics. Here we conducted a cross-ancestry genome-wide meta-analysis on depression (416,437 cases and 1,308,758 controls) and identified 287 risk loci, of which 49 are new. Variant-level fine mapping prioritized potential causal variants and functional genomic analysis identified variants that regulate the binding of transcription factors. We validated that 80% of the identified functional variants are regulatory variants, and expression quantitative trait loci analysis uncovered the potential target genes regulated by the prioritized risk variants. Gene-level analysis, including transcriptome and proteome-wide association studies, colocalization and Mendelian randomization-based analyses, prioritized potential causal genes and drug targets. Gene prioritization analyses highlighted likely causal genes, including TMEM106B, CTNND1, AREL1 and so on. Pathway analysis indicated significant enrichment of depression risk genes in synapse-related pathways. Finally, knockdown of Tmem106b in mice resulted in depression-like behaviours, supporting the involvement of Tmem106b in depression. Our study identified new risk loci, likely causal variants and genes for depression, providing important insights into the genetic architecture of depression and potential therapeutic targets.

Spatially resolved transcriptomic analysis of the adult human prostate

The prostate is an organ characterized by significant spatial heterogeneity. To better understand its intricate structure and cellular composition, we constructed a comprehensive single-cell atlas of the adult human prostate. Our high-resolution mapping effort identified 253,381 single cells and 34,876 nuclei sampled from 11 patients who underwent radical resection of bladder cancer, which were categorized into 126 unique subpopulations. This work revealed various new cell types in the human prostate and their specific spatial localization. Notably, we discovered four distinct acini, two of which were tightly associated with E-twenty-six transcription factor family (ETS)-fusion-negative prostate cancer. Through the integration of spatial, single-cell and bulk-seq analyses, we propose that two specific luminal cell types could serve as the common origins of prostate cancer. Additionally, our findings suggest that zone-specific fibroblasts may contribute to the observed heterogeneity among luminal cells. This atlas will serve as a valuable reference for studying prostate biology and diseases such as prostate cancer.

Sargassum fusiforme polysaccharides protect mice against Citrobacter rodentium infection via intestinal microbiota-driven microRNA-92a-3p-induced Muc2 production

Sargassum fusiforme, widely consumed in Asian countries, has been proven to have various biological activities. However, the impacts and mechanisms of Sargassum fusiforme polysaccharides (SFPs) on intestinal bacterial infection are not yet fully understood. Our findings indicate that SFPs pretreatment ameliorates intestinal inflammation by reducing C. rodentium colonization, increasing colon length and levels of IL-10 and IL-22, decreasing IL-1β, IL-6, TNF-α, and IL-17 levels, inhibiting colonic crypt elongation and hyperplasia, and enhancing the intestinal mucosal barrier. The protective effects against intestinal bacterial infection are linked to enhanced clearance of C. rodentium and improvements in the intestinal mucosal barrier and C. rodentium-induced intestinal microbiota dysbiosis. Fecal microbiota transplantation experiments were conducted to evaluate the functional impact of microbiota induced by SFPs. The results suggest that intestinal microbiota modified by SFPs effectively countered C. rodentium infection. In addition, our study identified that miRNA-92a-3p is partially complementary to the 3'-UTR of the Notch1 gene, thereby repressing the Notch1-Hes1 signaling pathway and enhancing Muc2 secretion. Taken together, these findings reveal that SFPs protect mice from C. rodentium infection by activating the miR-92a-3p/Notch1-Hes1 regulatory axis driven by the intestinal microbiota, which stimulates Muc2 production to maintain intestinal barrier homeostasis.

Maladaptive Peripheral Ketogenesis in Schwann Cells Mediated by CB1R Contributes to Diabetic Neuropathy

Diabetic peripheral neuropathy (DPN) is the most common complication of diabetes. Although studies have previously investigated metabolic disruptions in the peripheral nervous system (PNS), the exact metabolic mechanisms underlying DPN remain largely unknown. Herein, a specific form of metabolic remodeling involving aberrant ketogenesis within Schwann cells (SCs) in streptozotocin (STZ)-induced type I diabetes mellitus is identified. The PNS adapts poorly to such aberrant ketogenesis, resulting in disrupted energy metabolism, mitochondrial damage, and homeostatic decompensation, ultimately contributing to DPN. Additionally, the maladaptive peripheral ketogenesis is highly dependent on the cannabinoid type-1 receptor (CB1R)-Hmgcs2 axis. Silencing CB1R reprogrammed the metabolism of SCs by blocking maladaptive ketogenesis, resulting in rebalanced energy metabolism, reduced histopathological changes, and improved neuropathic symptoms. Moreover, this metabolic reprogramming can be induced pharmacologically using JD5037, a peripheral CB1R blocker. These findings revealed a new metabolic mechanism underlying DPN, and promoted CB1R as a promising therapeutic target for DPN.

Mycoplasma ovipnuemoniae impairs the immune response of sheep and suppresses neutrophil function by inhibiting S100A9

Mycoplasma pneumonia is a chronic respiratory disease that seriously affects the health of sheep. To date, little information is available about the damage caused by Mycoplasma ovipneumoniae (MO) pneumonia to host lungs. Here, after sheep were infected with MO for 28 days, severe inflammatory reactions and pathological damage occurred. By using single-cell RNA sequencing (scRNA-seq), all the transcriptome changes in 11 cell types in sheep lung tissue were systematically analyzed, and the key biological processes regulating inflammation and immunity were identified. Moreover, we constructed both intercellular communication models and differential expression maps of key regulatory genes for each cell subgroup. We also specifically focused on the response of T cell subpopulations and neutrophils to MO infection. Long-term infection may affect an organism's immune response, inhibit intercellular communication, and highlight the important role of the cyclophilin A (CypA) and macrophage migration inhibitory factor (MIF) pathways in intercellular communication. Notably, MO infection decreased the toxicity of CD8 effector T cells and depleted regulatory T cells, thus inhibiting normal cell function. Subsequently, emphasis was placed on the important role of the neutrophil marker gene S100A9 in promoting neutrophil clearance of MO through activation of the ERK signaling pathway and reactive oxygen species (ROS) burst in vitro. These results contribute to understanding the progression of MO infection in the lungs and provide a rich database on the molecular basis of the response to different cell types in MO infection.

Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial

Adoptive transfer of unselected autologous tumor-infiltrating lymphocytes (TILs) has mediated meaningful clinical responses in patients with metastatic melanoma but not in cancers of gastrointestinal epithelial origin. In an evolving single-arm phase 2 trial design, TILs were derived from and administered to 91 patients with treatment-refractory mismatch repair proficient metastatic gastrointestinal cancers in a schema with lymphodepleting chemotherapy and high-dose interleukin-2 (three cohorts of an ongoing trial). The primary endpoint of this study was the objective response rate as measured using Response Evaluation Criteria in Solid Tumors 1.0; safety was a descriptive secondary endpoint. In the pilot phase, no clinical responses were observed in 18 patients to bulk, unselected TILs; however, when TILs were screened and selected for neoantigen recognition (SEL-TIL), three responses were seen in 39 patients (7.7% (95% confidence interval (CI): 2.7-20.3)). Based on the high levels of programmed cell death protein 1 in the infused TILs, pembrolizumab was added to the regimen (SEL-TIL + P), and eight objective responses were seen in 34 patients (23.5% (95% CI: 12.4-40.0)). All patients experienced transient severe hematologic toxicities from chemotherapy. Seven (10%) patients required critical care support. Exploratory analyses for laboratory and clinical correlates of response were performed for the SEL-TIL and SEL-TIL + P treatment arms. Response was associated with recognition of an increased number of targeted neoantigens and an increased number of administered CD4+ neoantigen-reactive TILs. The current strategy (SEL-TIL + P) exceeded the parameters of the trial design for patients with colorectal cancer, and an expansion phase is accruing. These results could potentially provide a cell-based treatment in a population not traditionally expected to respond to immunotherapy. ClinicalTrials.gov identifier: NCT01174121 .

Integrative analysis of single-cell transcriptomics and genetic associations identify cell states associated with vascular disease

BACKGROUND

Vascular diseases are accompanied by alterations in cellular phenotypes which underlie disease pathogenesis, with single-cell technologies aiding in the discovery of cellular heterogeneity among endothelial cell (EC) and vascular smooth muscle cell (VSMC) populations. In atherosclerotic disease, VSMCs are hypothesized to transition between contractile and synthetic states; however, the specific vascular subpopulations and intermediate cell states responsible for early vascular dysfunction remain unclear.

METHODS

We integrated newly generated and published single-nuclear RNA-sequencing (snRNA-seq) datasets to analyze normal (n = 7), aneurysmal (n = 9), and atherosclerotic (n = 2) flash-frozen human ascending thoracic aortas. Cell types and subtypes were defined using both top marker genes and canonical gene markers. Disease enrichment and relevant cell types were identified using newly developed computational tools to integrate GWAS data from multiple vascular disease-relevant studies with the single nuclei aortic expression profiles.

RESULTS

Nuclear dissociation and snRNA-seq identified ten distinct transcriptomic clusters from the integrated analysis representing all major vascular cell populations. Three distinct VSMC populations emerged that exhibited differential expression of extracellular matrix, contractile and pro-proliferative genes. Aneurysmal specimens were enriched for one fibroblast and one VSMC subpopulation compared to healthy tissue. RNA-trajectory analysis inferred a phenotypic continuum of gene expression between VSMC A and VSMC B or C and between two of the identified fibroblast types. VSMCs and Fibroblast C exhibited the greatest cell type-specific enrichment of genes mapped to GWAS loci for coronary artery disease (CAD), blood pressure, and migraine. Cell type-specific enrichment scores were more robust among the transcriptional profiles from non-diseased vascular tissue.

CONCLUSIONS

Our use of single-cell isolation and new computational methods prioritizes the cell types that most contribute to vascular disease pathogenesis. Specifically, tissue dissociation and single-nuclear transcriptomics better represent all vascular cell types, from which we demonstrate enrichment of pro-proliferative VSMCs in TAA and further implicate phenotypic switching as a likely pathologic mechanism. Integrated analysis of cell-specific gene expression and vascular disease GWAS data implicate genes and pathways associated with fibroblast and VSMC cell-state transitions.

Single-cell omics technologies - Fundamentals on how to create single-cell looking glasses for reproductive health

Over the last decade, in line with the goals of precision medicine to offer individualized patient care, various single-cell technologies measuring gene and proteomic expression in various tissues have rapidly advanced to study health and disease at the single cell level. Precisely understanding cell composition, position within tissues, signaling pathways, and communication can reveal insights into disease mechanisms and systemic changes during development, pregnancy, and gynecologic disorders across the lifespan. Single-cell technologies dissect the complex cellular compositions of reproductive tract tissues, providing insights into mechanisms behind reproductive tract dysfunction which impact wellness and quality of life. These technologies aim to understand basic tissue and organ functions and, clinically, to develop novel diagnostics, early disease biomarkers, and cell-targeted therapies for currently suboptimally-treated disorders. Increasingly, they are applied to pregnancy and pregnancy disorders, gynecologic malignancies, and uterine and ovarian physiology and aging, which are discussed in more detail in manuscripts in this special issue of AJOG. Here, we review recent applications of single-cell technologies to the study of gynecologic disorders and systemic biological adaptations during fetal development, pregnancy, and across a woman's lifespan. We discuss sequencing- and proteomic-based single-cell methods, as well as spatial transcriptomics and high-dimensional proteomic imaging, describing each technology's mechanism, workflow, quality control, and highlighting specific benefits, drawbacks, and utility in the context of reproductive medicine. We consider analytical methods for the high-dimensional single-cell data generated, highlighting statistical constraints and recent computational techniques for downstream clinical translation. Overall, current and evolving single-cell "looking glasses", or perspectives, have the potential to transform fundamental understanding of women's health and reproductive disorders and alter the trajectory of clinical practice and patient outcomes in the future.

Cross-ancestry genome-wide association study identifies new susceptibility genes for preeclampsia

BACKGROUND

Preeclampsia (PE) is a heterogeneous, multi-organ pregnancy disorder that poses a significant health burden globally, with its pathogenesis remaining unclear. This study aimed to identify novel susceptibility genes for PE through a cross-ancestry genome-wide association study (GWAS).

METHODS

We performed meta-analysis to summarize the PE GWAS data from the United Kingdom, Finland, and Japan. Subsequently, the multi-ancestry sum of the single-effects model was used to perform cross-ancestry fine-mapping. The functional mapping and annotation (FUMA)-expression quantitative trait loci (eQTL) mapping method, transcriptome-wide association study (TWAS)- functional summary-based imputation (FUSION) method, genome-wide complex trait analysis (GCTA)-multivariate set-based association test (mBAT)-combo method, and polygenic priority score (PoPS) method were employed to screen for candidate genes. We utilized biomarker expression level imputation using summary-level statistics (BLISS), based on summary-level protein quantitative trait loci (pQTL) data, to conduct a multi-ancestry proteome-wide association study (PWAS) analysis, followed by candidate drug prediction.

RESULTS

Six novel susceptibility genes associated with PE risk were identified: NPPA, SWAP70, NPR3, FGF5, REPIN1, and ACAA1. High expression of the NPPA and SWAP70 and low expression of the remaining genes were associated with a reduced risk of PE. Furthermore, we identified drugs that target NPPA, NPR3, and REPIN1.

CONCLUSIONS

Our study identified NPPA, SWAP70, NPR3, FGF5, REPIN1, and ACAA1 as novel genes whose predicted expression was linked to the risk of PE, offering new insights into the genetic framework of this condition.

scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data

It is a significant step for single cell analysis to identify cell types through clustering single-cell RNA sequencing (scRNA-seq) data. However, great challenges still remain due to the inherent high-dimensionality, noise, and sparsity of scRNA-seq data. In this study, scPEDSSC, a deep sparse subspace clustering method based on proximity enhancement, is put forward. The self-expression matrix (SEM), learned from the deep auto-encoder with two part generalized gamma (TPGG) distribution, are adopted to generate the similarity matrix along with its second power. Compared with eight state-of-the-art single-cell clustering methods on twelve real biological datasets, the proposed method scPEDSSC can achieve superior performance in most datasets, which has been verified through a number of experiments.

The Type III Secretion System (T3SS) of Escherichia Coli Promotes Atherosclerosis in Type 2 Diabetes Mellitus

Large-scale studies indicate a strong relationship between the gut microbiome, type 2 diabetes mellitus (T2DM), and atherosclerotic cardiovascular disease (ASCVD). Here, a higher abundance of the type III secretion system (T3SS) virulence factors of Enterobacteriaceae/Escherichia-Shigella in patients with T2DM-related-ASCVD, which correlates with their atherosclerotic stenosis is reported. Overexpression of T3SS via Citrobacter rodentium (CR) infection in Apoe-/- T2DM mice exacerbated atherosclerotic lesion formation and increased gut permeability. Non-targeted metabolomic and proteomic analysis of mouse serum showed that T3SS caused abnormal glycerophospholipid metabolism in mice. Proteomics, RNA sequencing, and functional analyses showed that T3SS induced ferroptosis in intestinal epithelial cells, partly due to increased expression of ferritin heavy chains (FTH1). This findings first demonstrated that T3SS increases ferroptosis in intestinal epithelial cells, via disrupting the intestinal barrier and upregulation of phosphatidylcholine, thereby exacerbating T2DM-related ASCVD.

Quantitative characterization of tissue states using multiomics and ecological spatial analysis

The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.

An SSTR2-somatostatin chemotactic axis drives T cell progenitor homing to the intestines

Progenitors of intraepithelial T cells (IELps) migrate from the thymus to the intestines after birth where they develop into unconventional TCRγδ and TCRαβ lymphocytes in a process of extrathymic lymphopoiesis within cryptopatches. Mechanisms of IELp migration have remained unclear. Here we show that thymic IELps express the somatostatin receptor SSTR2, which contributes to their homing to the gut. IELp homing is Sstr2 dependent and correlates with neonatal induction of Sst encoding somatostatin in neuroendocrine and lamina propria stromal cells. The SSTR2 ligands somatostatin and cortistatin attract IELps in chemotaxis assays and somatostatin triggers IELp binding to the mucosal vascular addressin MAdCAM1. T cell transduction with Sstr2 confers homing to the neonatal colon. Human fetal thymic IELp-like cells express SSTR2 and intestinal stromal cells express SST at the time of initial T cell population, suggesting conserved mechanisms of progenitor seeding of the developing intestines. These results reveal an unexpected role for the SSTR2-somatostatin axis in early immune system development and describe a new role for a small peptide hormone G-protein-coupled receptor in developmental lymphocyte trafficking.

FGF21 Ameliorates Fibroblasts Activation and Systemic Sclerosis by Inhibiting CK2α/GLI2 Signaling Axis

Systemic sclerosis is a typical fibrotic disease of unknown etiology that is characterized by abnormal fibroblast activation and excessive deposition of extracellular matrix. Unfortunately, effective therapeutic approaches are lacking. FGF21 plays a key role in mediating a variety of biological activities. However, its specific function in systemic sclerosis is unclear. In this study, we found that the expression of FGF21 was significantly downregulated in fibrotic skin tissue and in TGF-β-stimulated fibroblasts. Furthermore, our studies demonstrated that treatment with recombinant FGF21 in the skin significantly alleviated bleomycin-induced and TBRI-activated fibrosis and inhibited the activation of fibroblasts, whereas skin fibrosis was exacerbated by deletion of FGF21. Mechanistically, FGF21 inhibits the activity of CK2α and promotes the degradation of GLI2. In conclusion, these results indicate that FGF21 attenuates skin fibrosis through the CK2α/GLI2 signaling pathway and therefore may be a potential therapeutic target for systemic sclerosis.

Tolerogenic dendritic cell-mediated regulatory T cell differentiation by Chinese herbal formulation attenuates colitis progression

INTRODUCTION

Ulcerative colitis (UC) is a chronic inflammatory disease characterized by loss of immune tolerance to luminal antigens and progressive intestinal tissue injury. Thus, the re-establishment of immune tolerance is crucial for suppressing aberrant immune responses and UC progression.

OBJECTIVES

This study aimed to investigate the mechanisms underlying the action of CDD-2103 and its bioactive compounds in mediating immune regulation in mouse models of colitis.

METHODS

Two experimental colitis models, chronic 2,4,6-trinitrobenzene sulfonic acid (TNBS)- and T-cell transfer-induced Rag1-/- mice, were used to determine the effects of CDD-2103 on colitis progression. Single-cell transcriptome analysis was used to profile the immune landscape and its interactions after CDD-2103 treatment. Liquid chromatography-mass spectrometry (LC-MS) was used to analyze the major components interacting with lymphoid cells. A primary cell co-culture system was used to confirm the effects of bioactive component.

RESULTS

CDD-2103 dose-dependently suppresses the progression of colitis induced by chemicals or T cell transplantation in Rag1-/- mice. The effect of CDD-2103 is primarily attributable to an increase in the de novo generation of regulatory T cells (Tregs) in the lamina propria (LP). Single-cell transcriptomic analysis revealed that CDD-2103 treatment increased the number of tolerogenic dendritic cells (DCs). Mechanistically, CDD-2103 promoted tolerogenic DCs accumulation and function by upregulating several genes in the electron transport chain related to oxidative phosphorylation, leading to increased differentiation of Tregs. Further LC-MS analysis identified several compounds in CDD-2103, particularly those distributed within the mesenteric lymph nodes of mice. Subsequent studies revealed that palmatine and berberine promoted tolerogenic bone marrow-derived dendritic cells (BMDC)-mediated Treg differentiation.

CONCLUSION

Overall, our study demonstrated that the clinically beneficial effect of CDD-2103 in the treatment of UC is based on the induction of immune tolerance. In addition, this study supports berberine and palmatine as potential chemical entities in CDD-2103 that modulate immune tolerance.

Lactate controls cancer stemness and plasticity through epigenetic regulation

Tumors arise from uncontrolled cell proliferation driven by mutations in genes that regulate stem cell renewal and differentiation. Intestinal tumors, however, retain some hierarchical organization, maintaining both cancer stem cells (CSCs) and cancer differentiated cells (CDCs). This heterogeneity, coupled with cellular plasticity enabling CDCs to revert to CSCs, contributes to therapy resistance and relapse. Using genetically encoded fluorescent reporters in human tumor organoids, combined with our machine-learning-based cell tracker, CellPhenTracker, we simultaneously traced cell-type specification, metabolic changes, and reconstructed cell lineage trajectories during tumor organoid development. Our findings reveal distinctive metabolic phenotypes in CSCs and CDCs. We find that lactate regulates tumor dynamics, suppressing CSC differentiation and inducing dedifferentiation into a proliferative CSC state. Mechanistically, lactate increases histone acetylation, epigenetically activating MYC. Given that lactate's regulation of MYC depends on the bromodomain-containing protein 4 (BRD4), targeting cancer metabolism and BRD4 inhibitors emerge as a promising strategy to prevent tumor relapse.

The Direct and Indirect Role of IgE on Airway Epithelium in Asthma

Asthma is a chronic airway inflammatory disorder, affecting over 350 million people worldwide, with allergic asthma being the most common form of the disease. Allergic asthma is characterized by a type 2 (T2) inflammatory response triggered by numerous allergens beginning in the airway epithelium, which acts as a physical barrier to allergens as well as other external irritants including infectious agents, and atmospheric pollutants. T2 inflammation is propagated by several key cell types including T helper 2 (Th2) cells, eosinophils, mast cells, and B cells. Immunoglobulin E (IgE), produced by B cells, is a key molecule in allergic airway disease and plays an important role in T2 inflammation, as well as being central to remodeling processes within the airway epithelium. Blocking IgE with omalizumab has been shown to be efficacious in treating allergic asthma however, the role of IgE on airway epithelial cells is less communicated. Developing a deeper explanation of the complex network of interactions between IgE and the airway epithelium will facilitate an improved understanding of asthma pathophysiology. This review discusses the indirect and direct roles of IgE on airway epithelial cells, with a focus on allergic asthma disease.

Age-Stratified Treg Responses During Viral Infections of the Central Nervous System: A Literature Review

Regulatory T cells (Tregs) play a vital role in limiting inflammation and resolving the immune response after a viral infection. Within the central nervous system (CNS), Tregs are especially important for the protection of neurons, which have limited regenerative capacity, and the preservation of myelin sheaths, which support neuronal function and survival. Nevertheless, viral infections of the CNS often result in enduring neurological dysfunction, especially in more vulnerable age groups such as newborns and the elderly. Although it is appreciated that Treg activity changes with age, it is unclear how these age-dependent changes impact viral CNS infections. In this review, we explore Treg development over the life of the host and discuss evidence for age-dependent Treg responses to peripheral viral infections. We also discuss the CNS-specific roles of Tregs, where both immunomodulatory and neuroprotective functions can contribute to preservation of brain cells. Finally, we examine the current evidence for Treg activity in neurotropic infections in the context of age, and highlight gaps in our understanding of Treg function in younger and older hosts. Overall, a better understanding of age-dependent Treg activity in the CNS may reveal opportunities for therapeutic interventions tailored to the most vulnerable ages.

Integrated microbiome and metabolomic analysis of Spodoptera litura under Metarhizium flavoviride qc1401 stress

Metarhizium spp. have emerged as an alternative to chemical pesticides for protecting crops from insect pest. Here, we investigated midgut microbial community and metabolites of Spodoptera litura at three different timepoints after infection with Metarhizium flavoviride. The innate immune system of S. litura was activated with levels of polyphenol oxidase, carboxylesterase, multifunctional oxidase, and glutathione S-transferase activity significantly increasing. Exposure to the fungal pathogen also altered bacterial abundance and diversity in host's midgut, and these changes varied depending on the time elapsed since exposure. We identified more operational taxonomic units in the treated samples as compared to the control samples at all tested time points. A total of 372 metabolites were identified, and 88, 149, and 142 differentially accumulated metabolites (DAMs) were identified between the treatment and control groups at 3 timepoints after treatment, respectively. Based on the changes of DAMs in response to M. flavoviride infection at different timepoints and significantly enriched KEGG pathways, we speculated that "tyrosine metabolism," "galactose metabolism," "ATP-binding cassette transporters," "neuroactive ligand-receptor interaction," "purine metabolism," "arginine and proline metabolism," "beta-alanine metabolism," "lysosome," and "carbon metabolism" may participate in the metabolic-level defense response. An integrated pathway-level analysis of the 16S-rDNA and metabolomic data illustrated the connections and interdependencies between the metabolic responses of S. litura and the midgut microorganisms to M. flavoviride infection. This work emphasizes the value of integrated analyses of insect-pathogen interactions, provides a framework for future studies of critical microorganisms and metabolic determinants of these interactions, establishes a theoretical basis for the sustainable use of M. flavoviride.

Perspectives on photodynamic therapy combined with immunotherapy in treatment of colorectal cancer: An overview based on experimental studies

Colorectal cancer (CRC) is one of the major cancers threatening human health, with high mortality, tumor drug resistance and metastasis. Due to its advantages of non-invasive, strongly targeted and limited side effects, Photodynamic therapy (PDT) has become a promising treatment for CRC. Remarkably, PDT has been shown to activate T cell-adaptive immune response and induce immunogenic cell death (ICD). Used in combination with other treatment techniques, PDT has considerable promise in the management of colorectal cancer. In particular, the combination of PDT and tumor immunotherapy, the systemic anti-tumor immune response was enhanced more significantly. This strategy is expected to achieve a synergistic anti-tumor effect by inducing tumor cell apoptosis, regulating tumor immune microenvironment and effectively activating anti-tumor immunity during treatment process. This review focuses on the research of PDT combined with immunotherapy to improve the treatment of CRC. In most studies, a positive effect was observed for combination therapy, experimentally indicating new therapeutic opportunities for CRC.

Toxoplasma GRA15 expression on dendritic cells inhibits B cell differentiation and antibody production

One of the dense granule proteins named GRA15 in Toxoplasma gondii (T. gondii), is known to support an innate immune response in host through activation of NF-κB. However, little is known about advantages of GRA15 for parasites. By examining the role of GRA15 in the host-parasite interactions, it was clarified that GRA15 in T. gondii suppressed acquired immune responses in host. Wild-type parasite infection to C57BL/6 mice resulted in lower titers of T. gondii antibody and lower plasma cell counts compared to Δgra15 T. gondii. To identify host cells in which GRA15 acts to suppress antibody production, we generated conditional knock-in mice that express GRA15 in specific cell lineages. Anti-T. gondii antibodies were not reduced in macrophages of conditional knock-in mice after infection with Δgra15 T. gondii, while the production of T. gondii antibody was suppressed in dendritic cells of the conditional knock-in mice (CD11c-Cre/GRA15cKI). In the CD11c-Cre/GRA15cKI immunized with ovalbumin (OVA), the titers of anti-OVA antibody were reduced compared to control mice. Furthermore, the number of OVA antigen-specific T cells was also decreased in CD11c-Cre/GRA15cKI. These data showed that GRA15 in dendritic cells suppressed T cell-mediated humoral immunity. These findings might implicate the pathological significance of GRA15 and facilitate Toxoplasma vaccines production.

TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice

Intestinal immune homeostasis relies on intestinal epithelial cells (IECs), which provide an efficient barrier, and warrant a state of tolerance between the microbiome and the mucosal immune system. Thus, proper epithelial microbial sensing and handling of microbes is key to preventing excessive immunity, such as seen in patients with inflammatory bowel disease (IBD). To date, the molecular underpinnings of these processes remain incompletely understood. This study identifies TIFA as a driver of intestinal inflammation and an epithelial signaling hub between the microbiome and mucosal immune cells. TIFA was constitutively expressed in crypt epithelial cells and was highly induced in the intestine of mice and IBD patients with intestinal inflammation. We further identified IL-22 signaling via STAT3 as key mechanism driving TIFA expression in IECs. At the molecular level, we demonstrate that TIFA expression is essential for IEC responsiveness to the bacterial metabolite ADP-heptose. Most importantly, ADP-heptose-induced TIFA signaling orchestrates an inflammatory cellular response in the epithelium, with NF-κB and inflammasome activation, and high levels of chemokine production. Finally, mice lacking TIFA were protected from intestinal inflammation when subjected to a model of experimental colitis. In conclusion, our study implicates that targeting TIFA may be a strategy for future IBD therapy.

Maintained homeostasis: LGYD facilitated the restoration of ISCs following radiation exposure by activating Hes1

BACKGROUND

Radiation-induced Intestinal Injury (RIII) affects quality of life in radiotherapy patients; Liangxue Guyuan Yishen Decoction (LGYD) offers protection but requires further study on its mechanism.

PURPOSE

The aim of this study was to investigate the heterogeneity of cellular responses in the intestine at a single-cell level following radiation and LGYD treatment.

STUDY DESIGN

This study's design includes in vivo and in vitro assessments to evaluate LGYD's effects on intestinal cells post-radiation, targeting survival, recovery, and molecular pathways.

METHODS

Mice were categorized into four groups: LGYD group, NC group, IR group, and Am group. Each group received daily drug administrations. All groups, except for the NC group, were subjected to a single whole-body irradiation at a dose rate of 70 R/min with a source-to-skin distance of 250 cm. Subsequent experiments were conducted following the irradiation, which led to severe survival impairments in the mice.

RESULTS

Our findings demonstrate that LGYD intervention substantially improves survival rates following lethal doses (8.5 Gy, 70R/min) of whole-body irradiation. Moreover, LGYD expedites the recovery period for intestinal injury on the fifth day after radiation by promoting repair mechanisms within intestinal tissue, with particular focus on mitigating intestinal stem cells (ISCs) damage and immune disorders. Through both in vivo and in vitro experiments, we have discovered that LGYD effectively treats RIII by activating Hes1 transcription factor activity through its key active ingredients in drug-containing serum. This activation further upregulates the downstream Stat3 and Akt gene, thereby facilitating repair processes within intestinal stem cells.

CONCLUSION

In this study, we discovered that LGYD can enhance the downstream expression and phosphorylation pathways of Stat3 and Akt by upregulating the expression of Hes1 gene following high-dose radiation exposure.

Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell

Enterocytes and four classic secretory cell types derive from intestinal epithelial stem cells. Based on morphology, location, and canonical markers, goblet and Paneth cells are considered distinct secretory types. Here, we report high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of their enteroendocrine or tuft cell siblings. Mouse and human goblet and Paneth cells express extraordinary fractions of few antimicrobial genes, which reflect specific responses to local niches. Wnt signaling retains some ATOH1+ secretory cells in crypt bottoms, where the absence of BMP signaling potently induces Paneth features. Cells that migrate away from crypt bottoms encounter BMPs and thereby acquire goblet properties. These phenotypes and underlying accessible cis-elements interconvert in post-mitotic cells. Thus, goblet and Paneth properties represent alternative phenotypic manifestations of a common signal-responsive terminal cell type. These findings reveal exquisite niche-dependent cell plasticity and cis-regulatory dynamics in likely response to antimicrobial needs.

Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes

Heart failure (HF) is a major contributor to global morbidity and mortality. While distinct clinical subtypes, defined by etiology and left ventricular ejection fraction, are well recognized, their genetic determinants remain inadequately understood. In this study, we report a genome-wide association study of HF and its subtypes in a sample of 1.9 million individuals. A total of 153,174 individuals had HF, of whom 44,012 had a nonischemic etiology (ni-HF). A subset of patients with ni-HF were stratified based on left ventricular systolic function, where data were available, identifying 5,406 individuals with reduced ejection fraction and 3,841 with preserved ejection fraction. We identify 66 genetic loci associated with HF and its subtypes, 37 of which have not previously been reported. Using functionally informed gene prioritization methods, we predict effector genes for each identified locus, and map these to etiologic disease clusters through phenome-wide association analysis, network analysis and colocalization. Through heritability enrichment analysis, we highlight the role of extracardiac tissues in disease etiology. We then examine the differential associations of upstream risk factors with HF subtypes using Mendelian randomization. These findings extend our understanding of the mechanisms underlying HF etiology and may inform future approaches to prevention and treatment.

Immune Regulation of Goblet Cell and Mucus Functions in Health and Disease

The mucosal surfaces of the body are the most vulnerable points for infection because they are lined by single or multiple layers of very active epithelial cells. The main protector of these cells is the mucus system generated by the specialized goblet cell secreting its main components, the gel-forming mucins. The organization of the mucus varies from an attached mucus that is impenetrable to bacteria in the large intestine to a nonattached, more penetrable mucus in the small intestine. The respiratory tract mucus system clears particles and microorganisms from healthy lungs but causes disease if reorganized to an attached mucus that cannot be efficiently transported. Similarly, transformation of large intestine mucus from impenetrable to penetrable causes chronic inflammation directed toward the intestinal microbiota. Mucus-producing goblet cells are regulated by and responsive to signals from immune cells, and at the same time signal back to the immune system. In this review we focus on the relationship of immune cells with intestinal goblet cells and mucus, making parallels to the respiratory tract.

A Lgr5-independent developmental lineage is involved in mouse intestinal regeneration

Collagenase and dispase treatment of intestinal tissue from adult mice generates cells growing in matrigel as stably replatable cystic spheroids, in addition to differentiated organoids. Contrary to classical EDTA-derived organoids, these spheroids display poor intestinal differentiation and grow independently of Rspondin, noggin and EGF. Their transcriptome strikingly resembles that of fetal intestinal spheroids, with downregulation of crypt base columnar cell (CBC) markers (Lgr5, Ascl2, Smoc2 and Olfm4). In addition, they display upregulation of inflammatory and mesenchymal genetic programs, together with robust expression of YAP target genes. Lineage tracing, cell-sorting and single cell RNA sequencing experiments demonstrate that adult spheroid-generating cells belong to a hitherto undescribed developmental lineage, independent of Lgr5-positive CBCs, and are involved in regeneration of the epithelium following CBC ablation.

Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones

Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.

IL-1β+ macrophages and the control of pathogenic inflammation in cancer

While highlighting the complexity and heterogeneity of tumor immune microenvironments, the application of single-cell analyses in human cancers has identified recurrent subsets of tumor-associated macrophages (TAMs). Among these, interleukin (IL)-1β+ TAMs - cells with high levels of expression of inflammatory response and tissue repair genes, but with limited capacity to stimulate cytotoxic immunity - are emerging as key drivers of pathogenic inflammation in cancer. In this review we discuss recent literature defining the phenotypical, molecular, and functional properties of IL-1β+ TAMs, as well as their temporal dynamics and spatial organization. Elucidating the biology of these cells across tumor initiation, progression, metastasis, and therapy could inform the design and interpretation of clinical trials targeting IL-1β and/or other inflammatory factors in cancer immunotherapy.

Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms

MOTIVATION

Modern single-cell omics data are key to unraveling the complex mechanisms underlying risk for complex diseases revealed by genome-wide association studies (GWAS). Phenotypic screens in model organisms have several important parallels to GWAS which the author explores in this essay.

RESULTS

The author provides the historical context of such screens, comparing and contrasting similarities to association studies, and how these screens in model organisms can teach us what to look for. Then the author considers how the results of GWAS might be exhaustively interrogated to interpret the biological mechanisms underpinning disease processes. Finally, the author proposes a general framework for tackling this problem computationally, and explore the data, mechanisms, and technology (both existing and yet to be invented) that are necessary to complete the task.

AVAILABILITY AND IMPLEMENTATION

There are no data or code associated with this article.

Canine genome-wide association study identifies DENND1B as an obesity gene in dogs and humans

Obesity is a heritable disease, but its genetic basis is incompletely understood. Canine population history facilitates trait mapping. We performed a canine genome-wide association study for body condition score-a measure of obesity-in 241 Labrador retrievers. Using a cross-species approach, we showed that canine obesity genes are also associated with rare and common forms of obesity in humans. The lead canine association was within the gene DENN domain containing 1B (DENND1B). Each copy of the alternate allele was associated with ~7.5% greater body fat. We demonstrate a role for this gene in regulating signaling and trafficking of melanocortin 4 receptor, a critical controller of energy homeostasis. Thus, canine genetics identified obesity genes and mechanisms relevant to both dogs and humans.

Integrated promoter-capture Hi-C and Hi-C analysis reveals fine-tuned regulation of the 3D chromatin architecture in colorectal cancer

Introduction

Hi-C is a widely used technique for mapping chromosomal interactions within a 3D genomic framework, however, its resolution is often constrained by sequencing depth, making it challenging to detect fine-scale interactions. To overcome this limitation, Promoter-Capture Hi-C (PCHi-C), as it selectively enriches for promoter-associated interactions, was employed. This study integrates PCHi-C and Hi-C datasets from colorectal cancer (CRC) models investigate chromosomal interaction dynamics across various regulatory levels, from cis-regulatory elements to topologically associated domains (TADs). The primary goal is to examine how genomic structural alterations shape the epigenomic landscape in CRC and to assess their potential role in colorectal cancer susceptibility.

Methods

PCHi-C and Hi-C datasets from multiple colorectal cancer (CRC) studies were integrated to enhance the resolution of chromatin interaction mapping. The analysis focused on identifying fine-scale interactions within topologically associated domains (TADs) while incorporating histone modification landscapes (H3K27ac, H3K4me3) and transcriptomic signatures from CRC cell lines and the TCGA database. For experimental validation, ChIP-quantitative PCR was performed at the promoters of target genes using the highly malignant colorectal cell line HT29 and compared it to an embryonic cell line NT2D1.

Results

Our integrated analysis revealed significant genomic structural instability in CRC cells, closely associated with tumor-suppressive transcriptional programs. We identified nine dysregulated genes, including long non-coding RNAs (MALAT1, NEAT1, FTX, and PVT1), small nucleolar RNAs (SNORA26 and SNORA71A), and protein-coding genes (TMPRSS11D, TSPEAR, and DSG4), all of which exhibited a substantial increase in expression in CRC cell lines compared to human embryonic stem cells (hESCs). Additionally, we observed enriched activation-associated histone modifications (H3K27ac and H3K4me3) at the potential enhancer regions of these genes, indicating possible transcriptional activation. ChIP-quantitative PCRs conducted using in the highly malignant CRC cell line HT29, compared to the embryonic cell line NT2D1, further validated these findings, reinforcing the link between altered chromosomal interactions and gene dysregulation in CRC.

Discussion

This study sheds light on the dynamic 3D genome organization in CRC, highlighting critical structural changes associated with disease-associated loci. The identification of nine dysregulated genes points to potential biomarkers for colorectal cancer, with implications for diagnostic and therapeutic strategies. The combination of Hi-C and PCHi-C offers a refined approach for detecting chromosomal interactions at a higher resolution, laying the foundation for future studies on cancer-associated chromatin architecture.

Different fibroblast subtypes propel spatially defined ileal inflammation through TNFR1 signalling in murine ileitis

Crohn's disease (CD) is a persistent inflammatory disorder primarily affecting the terminal ileum. The TnfΔΑRE mice, which spontaneously develop CD-like ileitis due to TNF overexpression, represent a faithful model of the human disease. Here, via single-cell RNA sequencing in TnfΔΑRE mice, we show that murine TNF-dependent ileitis is characterized by cell expansion in tertiary lymphoid organs (TLO), T cell effector reprogramming, and accumulation of activated macrophages in the submucosal granulomas. Within the stromal cell compartment, fibroblast subsets (telocytes, trophocytes, PdgfraloCd81- cells) are less abundant while lymphatic endothelial cells (LEC) and fibroblastic reticular cells (FRC) show relative expansion compared to the wild type. All three fibroblast subsets show strong pro-inflammatory signature. TNFR1 loss or gain of function experiments in specific fibroblast subsets suggest that the TnfΔΑRE-induced ileitis is initiated in the lamina propria via TNF pathway activation in villus-associated fibroblasts (telocytes and PdgfraloCd81- cells), which are responsible for the organization of TLOs. Trophocytes drive disease progression in the submucosal layer, accompanied by the excessive formation of granulomas. These findings provide evidence for spatial regulation of inflammation by fibroblast subsets and underscore the pivotal role of fibroblasts in the inception and advancement of ileitis.

Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders

Genome-wide association studies (GWASs) have identified thousands of genetic loci associated with cardiometabolic disorders. However, the functional interpretation of these loci remains a daunting challenge. This is particularly true for adipose tissue, a critical organ in systemic metabolism and the pathogenesis of various cardiometabolic diseases. We discuss how variant-to-function (V2F) approaches are used to elucidate the mechanisms by which GWAS loci increase the risk of cardiometabolic disorders by directly influencing adipose tissue. We outline GWAS traits most likely to harbor adipose-related variants and summarize tools to pinpoint the putative causal variants, genes, and cell types for the associated loci. We explain how large-scale perturbation experiments, coupled with imaging and multi-omics, can be used to screen variants' effects on cellular phenotypes and how these phenotypes can be tied to physiological mechanisms. Lastly, we discuss the challenges and opportunities that lie ahead for V2F research and propose a roadmap for future studies.

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

The Ulcerative Colitis-Associated Gene NXPE1 Catalyzes Glycan Modifications on Colonic Mucin

Colonic mucus forms a first line of defense against bacterial invasion while providing nutrition to support coinhabiting microbes in the gut. Mucus is composed of polymeric networks of mucin proteins, which are heavily modified post-translationally. The full compendium of enzymes responsible for these modifications and their roles in health and disease remain incompletely understood. Herein, we determine the biochemical function of NXPE1, a gene implicated in ulcerative colitis (UC), and demonstrate that it encodes an acetyltransferase that modifies mucin glycans. Specifically, NXPE1 utilizes acetyl-CoA to regioselectively modify the mucus sialic acid, 5-N-acetylneuraminic acid (Neu5Ac), at the 9-OH group to generate 9-O-acetylated Neu5Ac (Neu5,9Ac2). We further demonstrate that colonic organoids derived from donors harboring the missense variant NXPE1 G353R, which is protective against UC, exhibit severely impaired acetylation of Neu5Ac on mucins. Together, our findings support a model in which NXPE1 masks the alcohols of mucus sialoglycans via acetylation, which is important for modulating mucus barrier properties that limit interactions with commensal microbes.

Airway epithelial cells as drivers of severe asthma pathogenesis

Our understanding of the airway epithelium's role in driving asthma pathogenesis has evolved over time. From being regarded primarily as a physical barrier that could be damaged via inflammation, the epithelium is now known to actively contribute to asthma development through interactions with the immune system. The airway epithelium contains multiple cell types with specialized functions spanning barrier action, mucociliary clearance, immune cell recruitment, and maintenance of tissue homeostasis. Environmental insults may cause direct or indirect injury to the epithelium leading to impaired barrier function, epithelial remodelling, and increased release of inflammatory mediators. In severe asthma, the epithelial barrier repair process is inhibited and the response to insults is exaggerated, driving downstream inflammation. Genetic and epigenetic mechanisms also maintain dysregulation of the epithelial barrier, adding to disease chronicity. Here, we review the role of the airway epithelium in severe asthma and how targeting the epithelium can contribute to asthma treatment.

The balance between IFN-γ and ERK/MAPK signaling activities ensures lifelong maintenance of intestinal stem cells

While the intestinal epithelium has the highest cellular turnover rates in the mammalian body, it is also considered one of the tissues most resilient to aging-related disorders. Here, we reveal an innate protective mechanism that safeguards intestinal stem cells (ISCs) from environmental conditions in the aged intestine. Using in vivo phenotypic analysis, transcriptomics, and in vitro intestinal organoid studies, we show that age-dependent activation of interferon-γ (IFN-γ) signaling and inactivation of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling are responsible for establishing an equilibrium of Lgr5+ ISCs-between active and quiescent states-to preserve the ISC pool during aging. Furthermore, we show that differentiated cells have different sensitivities to each of the two signaling pathways, which may induce aging-related, functional, and metabolic changes in the body. Thus, our findings reveal an exquisitely balanced, age-dependent signaling mechanism that preserves stem cells at the expense of differentiated cells.

Shared Genetics in Celiac Disease and Inflammatory Bowel Disease Specify a Greater Role for Intestinal Epithelial Cells

The contribution of genetics to the development of gut-related autoimmune diseases such as celiac disease (CeD) and inflammatory bowel diseases (IBDs) is well-established, especially in immune cells, but pinpointing the significance of genetic variants to other cell types is more elusive. Increasing evidence indicates that intestinal epithelial cells are active players in modulating the immune response, suggesting that genetic variants affecting these cells could change cell behavior during disease. Moreover, fine-mapping genetic variants and causal genes to relevant cell types can help to identify drug targets and develop personalized targeted therapies. In this context, we reviewed the functions of genes in disease-associated loci shared by CeD and IBD that are expressed in epithelial cells and explored their potential impacts.

The m6A reader HNRNPC is a key regulator in DSS-induced colitis by modulating macrophage phenotype

m6A regulators were demonstrated to modulate the functions of intestinal epithelial and immune cells in the ulcerative colitis. This study aimed to elucidate whether and how the m6A reader heterogeneous nuclear ribonucleoprotein C (HNRNPC) regulates macrophage function in the colitis. We observed elevated HNRNPC in the inflammatory Raw264.7 cells and macrophages in the dextran sodium sulfate (DSS)-induced colitis. Knocking down HNRNPC can mitigate LPS-induced activation of macrophages in vitro. Furthermore, adoptive transfer of macrophages with HNRNPC knockdown significantly alleviated colitis compared to those transfected with negative control siRNA. Additionally, RNA sequencing illuminated that HNRNPC regulated functions of macrophages by inhibiting alternative mRNA slicing, involving adjusting acute inflammatory response, and promoting cell chemotaxis and migration. Besides, HNRNPC can govern the stability of Itgb7, and Itgb7 might be an effective target for HNRNPC in macrophages. Our findings highlight the crucial role and therapeutic potential of HNRNPC inhibition in macrophages in alleviating colitis.

scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis

Discovering a lower-dimensional embedding of single-cell data can improve downstream analysis. The embedding should encapsulate both the high-level features and low-level variations. While existing generative models attempt to learn such low-dimensional representations, they have limitations. Here, we introduce scVAEDer, a scalable deep-learning model that combines the power of variational autoencoders and deep diffusion models to learn a meaningful representation that retains both global structure and local variations. Using the learned embeddings, scVAEDer can generate novel scRNA-seq data, predict perturbation response on various cell types, identify changes in gene expression during dedifferentiation, and detect master regulators in biological processes.

Characterizing macrophage diversity in colorectal malignancies through single-cell genomics

Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract, with increasing incidence and mortality rates, posing a significant burden on human health. Its progression relies on various mechanisms, among which the tumor microenvironment and tumor-associated macrophages (TAMs) have garnered increasing attention. Macrophage infiltration in various solid tumors is associated with poor prognosis and is linked to chemotherapy resistance in many cancers. These significant biological behaviors depend on the heterogeneity of macrophages. Tumor-promoting TAMs comprise subpopulations characterized by distinct markers and unique transcriptional profiles, rendering them potential targets for anticancer therapies through either depletion or reprogramming from a pro-tumoral to an anti-tumoral state. Single-cell RNA sequencing technology has significantly enhanced our research resolution, breaking the traditional simplistic definitions of macrophage subtypes and deepening our understanding of the diversity within TAMs. However, a unified elucidation of the nomenclature and molecular characteristics associated with this diversity remains lacking. In this review, we assess the application of conventional macrophage polarization subtypes in colorectal malignancies and explore several unique subtypes defined from a single-cell omics perspective in recent years, categorizing them based on their potential functions.

The Intestinal Macrophage-Intestinal Stem Cell Axis in Inflammatory Bowel Diseases: From Pathogenesis to Therapy

The gut plays a crucial role in digestion and immunity, so its balance is essential to overall health. This balance relies on dynamic interactions between intestinal epithelial cells, immune cells, and crypt stem cells. Inflammatory bowel disease (IBD), which consists of ulcerative colitis and Crohn's disease, is a chronic relapsing inflammatory disease of the gastrointestinal tract closely related to immune dysfunction. Stem cells, known for their ability to self-renew and differentiate, play an important role in repairing damaged intestinal epithelium and maintaining homeostasis in vivo. Macrophages are key gatekeepers of intestinal immune homeostasis and have a significant impact on IBD. Current research has focused on the link between epithelial cells and stem cells, but interactions with macrophages, which have been recognized as attractive targets for the development of new therapeutic approaches to disease, have been less explored. Recently, the developing field of immunometabolism has reinforced that metabolic reprogramming is a key determinant of macrophage function and subsequent disease progression. The aim of this review is to explore the role of the macrophage-stem cell axis in the maintenance of intestinal homeostasis and to summarize potential approaches to treating IBD by manipulating the cellular metabolism of macrophages, as well as the main opportunities and challenges faced. In summary, our overview provides a framework for understanding the critical role of macrophage immunometabolism in maintaining gut health and potential therapeutic targets.

The Regulation of Cellular Senescence in Cancer

Cellular senescence is a stable state of cell cycle arrest caused by telomere shortening or various stresses. After senescence, cells cease dividing and exhibit many age-related characteristics. Unlike the halted proliferation of senescence cells, cancer cells are considered to have unlimited growth potential. When cells display senescence-related features, such as telomere loss or stem cell failure, they can inhibit tumor development. Therefore, inducing cells to enter a senescence state can serve as a barrier to tumor cell development. However, many recent studies have found that sustained senescence of tumor cells or normal cells under certain circumstances can exert environment-dependent effects of tumor promotion and inhibition by producing various cytokines. In this review, we first introduce the causes and characteristics of induced cellular senescence, analyze the senescence process of immune cells and cancer cells, and then discuss the dual regulatory role of cell senescence on tumor growth and senescence-induced therapies targeting cancer cells. Finally, we discuss the role of senescence in tumor progression and treatment opportunities, and propose further studies on cellular senescence and cancer therapy.