Fast, sensitive and accurate integration of single-cell data with Harmony

Prognostic significance of neutrophil extracellular trap-related genes in childhood acute lymphoblastic leukemia: insights from multi-omics and in vitro experiment

BACKGROUND

This study aimed to develop a prognostic model based on extracellular trap-related genes (NETRGs) for patients with cALL.

METHODS

Data from the TARGET-ALL-P2 and TARGET-ALL-P3 cohorts in the Genomic Data Commons database, the transcriptome dataset GSE26713, the single-cell transcriptome dataset GSE130116 from the Gene Expression Omnibus database and 306 NETRGs identified were analysed. Differentially expressed genes (DEGs) were identified from GSE26713 and differentially expressed NETRGs (DE-NETRGs) were obtained by overlapping DEGs with NETRGs. Functional analyses were conducted. Key feature genes were identified through univariate and least absolute shrinkage and selection operator (LASSO) regression. Prognostic genes were determined via multivariate Cox regression analysis, followed by the construction and validation of a risk model and nomogram. Additional analyses included immune profiling, drug sensitivity, functional differences, cell-type-specific expression, enrichment analysis and RT-qPCR.

RESULTS

A total of 1,270 DEGs were identified in GSE26713, of which 74 overlapped with NETRGs. Seven prognostic genes were identified using univariate, LASSO and multivariate Cox regression analyses. Survival analysis revealed lower survival rates in the high-risk group. Independent prognostic analysis identified risk scores and primary diagnosis as independent predictors of prognosis. Immune cell profiling showed significant differences in cell populations such as aDCs, eosinophils and Th2 cells between risk groups. Six cell subtypes were annotated, with prognostic genes predominantly expressed in myeloid cells. RT-qPCR revealed that PTAFR, FCGR2A, RETN and CAT were significantly downregulated, while TLR2 and S100A12 were upregulated in cALL.

CONCLUSION

TLR2, PTAFR, FCGR2A, RETN, S100A12 and CAT may serve as potential therapeutic targets.

Comprehensive profiling of cell type-specific expression and distribution of complement genes in mouse and human kidneys: insights into normal physiology and response to kidney transplantations

BACKGROUND

Recent studies innovatively revealed the localized expression of complement genes in kidneys and shed light on the vital roles of the intracellular complement system in the physiologic function and pathological conditions. However, a comprehensive analysis of the expression of complement genes in the context of the evolving cellular landscape of the kidney is not available.

METHODS

We analyzed single-cell RNA sequencing data from healthy human subjects, C57BL/6 mice, and kidney transplant-rejected mice. The data were sourced from the NCBI Gene Expression Omnibus and processed using quality control measures and unsupervised clustering. Differential gene analyses were based on expression levels.

RESULTS

In total, 50 complement genes were categorized into pattern recognition molecules, proteases, complement components, receptors, and regulators. In normal mice kidneys, complement genes were expressed at relatively low levels. Among different complement gene categories, receptor genes were most widely expressed in kidney cells. Comparatively, macrophages and mesangial cells are the most abundant immune and nonimmune cell types for complement gene expression. A comparison of human and mouse data showed similar expression patterns, but human kidney complement gene expression was more abundant. Comparative analysis between mouse transplant-rejected and normal kidneys demonstrated stronger complement gene expression in transplant-rejected kidneys.

CONCLUSIONS

This study illustrated significant similarities in complement gene expression between murine and human kidneys and highlighted the responsive nature of complement genes to kidney injury, underscoring the dynamic nature of local complement regulation. These findings enhance our understanding of the complex regulation of the complement system within the kidney, offering insights into its role in renal disease pathogenesis.

Immune infiltration landscape and potential drug-targeted implications for hepatocellular carcinoma with 'progression/hyper-progression' recurrence

BACKGROUND AND AIMS

Hepatocellular carcinoma (HCC) recurrence was previously characterized into four types, and patients with progression/hyper-progression recurrence (type III-IV) have an extremely poor prognosis. However, the immune background of resectable HCC, particularly in patients who experience recurrence, remains underexplored. Therefore, this study aimed to describe the immune landscape of resectable HCC, especially postoperative type III-IV recurrent HCC, and explore potential immune-targeted anti-relapse strategies for treated populations.

METHODS

The differences in gene expression in patients with recurrent HCC (type I-II (solitary or multi-intrahepatic oligo recurrence) vs. type III-IV) were investigated using bulk sequencing. Multiple immune infiltration methods (single-sample gene set enrichment analysis (GSEA), Microenvironment Cell Populations-counter and ESTIMATE) were used, and patients were divided into four groups to identify four distinct immune subtypes: immune-enrichment/matrix-poor (IE1), immune-enrichment/matrix-rich (IE2), immune intermediate/matrix-rich (ITM) and immune desert/matrix-poor (ID). Co-expression and protein interaction analyses were used to identify characteristic genes in ITM closely associated with type III-IV recurrence, which was matched with drug targets for Huaier granules (HG) and lenvatinib. Virtual docking was used to identify potential therapeutic targets, and the results were verified using single-nuclei RNA sequencing and histological analysis.

RESULTS

ITM was closely related to type III-IV recurrence and exhibited immunotherapy potential. The potential efficacy of inhibiting CCNA2, VEGFA, CXCL8, PLK2, TIMP1, ITGB2, ALDOA, ANXA5 and CSK in ITM reversal was determined. Molecular docking demonstrated that the proteins of these genes could bind to HG or lenvatinib. The immunohistochemical findings demonstrated differential VEGFA (p < .01) and PLK2 (p < .001) expression in ITM type and ID in type III-IV recurrent HCC.

CONCLUSIONS

Three primary immunotypes of resectable HCC (IE2, ITM and ID) were identified, and HG and lenvatinib could potentially overcome immune checkpoint blockade (ICB) resistance in ITM patients with HCC, particularly those classified as type III-IV.

The pancreatic tumor microenvironment of treatment-naïve patients causes a functional shift in γδ T cells, impairing their anti-tumoral defense

Pancreatic ductal adenocarcinoma (PDAC) presents a unique challenge for researchers due to its late diagnosis caused by vague symptoms and lack of early detection markers. Additionally, PDAC is characterized by an immunosuppressive microenvironment (TME), making it a difficult tumor to treat. While γδ T cells have shown potential for anti-tumor activity, conflicting studies exist regarding their effectiveness in pancreatic cancer. This study aims to explore the hypothesis that the PDAC TME hinders the anti-tumor capabilities of γδ T cells through blockade of cytotoxic functions. For this reason, we chose to enroll PDAC treatment-naive patients to avoid the possibility of therapy modifying the TME. By flow cytometry, our research findings indicate that the presence of γδ T cells among CD45+ cells in tumor tissue is lower compared to CD66+ cells, but higher than in blood. Circulating Vδ1 T cells exhibit a terminal effector memory phenotype (TEMRA) more than Vδ2 T cells. Interestingly, Vδ1 and Vδ2 T cells appear to be more prevalent at different stages of tumor development. In our in vitro culture using conditioned medium derived from Patient-derived organoids ;(PDOs), we observed a shift in expression markers in γδ T cells of healthy individuals toward an activation and exhaustion phenotype, as confirmed by scRNA-seq analysis extracted from a public database. A deeper understanding of γδ T cells in PDAC could be valuable for developing novel therapies aimed at mitigating the impact of the pancreatic tumor microenvironment on this cell population.

Dynamic development of microglia and macrophages after spinal cord injury

JOURNAL/nrgr/04.03/01300535-202512000-00029/figure1/v/2025-01-31T122243Z/r/image-tiff Secondary injury following spinal cord injury is primarily characterized by a complex inflammatory response, with resident microglia and infiltrating macrophages playing pivotal roles. While previous studies have grouped these two cell types together based on similarities in structure and function, an increasing number of studies have demonstrated that microglia and macrophages exhibit differences in structure and function and have different effects on disease processes. In this study, we used single-cell RNA sequencing and spatial transcriptomics to identify the distinct evolutionary paths of microglia and macrophages following spinal cord injury. Our results showed that microglia were activated to a pro-inflammatory phenotype immediately after spinal cord injury, gradually transforming to an anti-inflammatory steady state phenotype as the disease progressed. Regarding macrophages, our findings highlighted abundant communication with other cells, including fibroblasts and neurons. Both pro-inflammatory and neuroprotective effects of macrophages were also identified; the pro-inflammatory effect may be related to integrin β2 ( Itgb2 ) and the neuroprotective effect may be related to the oncostatin M pathway. These findings were validated by in vivo experiments. This research underscores differences in the cellular dynamics of microglia and macrophages following spinal cord injury, and may offer new perspectives on inflammatory mechanisms and potential therapeutic targets.

Reading of human acute immune dynamics in omicron SARS-CoV-2 breakthrough infection

The dynamics of the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infections remain unclear, particularly when compared to responses in naive individuals. In this longitudinal prospective cohort study, 13 participants were recruited. Peripheral blood samples were collected every other day until day 7 after symptom onset. Transcriptome sequencing, single-cell sequencing, T-cell receptor (TCR) sequencing, B-cell receptor (BCR) sequencing, Olink proteomics, and antigen-antibody binding experiments were then performed. During the incubation periods of breakthrough infections, peripheral blood exhibited type 2 cytokine response, which shifted to type 1 cytokine response upon symptom onset. Plasma cytokine levels of C-X-C motif chemokine ligand 10, monocyte chemoattractant protein-1, interferon-γ, and interleukin-6 show larger changes in breakthrough infections than naïve infections. The inflammatory response in breakthrough infections rapidly subsided, returning to homeostasis by day 5 after symptom onset. Notably, the levels of monocyte-derived S100A8/A9, previously considered a marker of severe disease, physiologically significantly increased in the early stages of mild cases and persisted until day 7, suggesting a specific biological function. Longitudinal tracking also revealed that antibodies anti-Receptor Binding Domain (anti-RBD) in breakthrough infections significantly increased by day 7 after symptom onset, whereas cytotoxic T lymphocytes appeared by day 5. This study presents a reference for interpreting the immunological response to breakthrough infectious disease in humans.

Deficiency of FUN14 domain-containing 1 enhances the migration and invasion of fibroblast-like synoviocytes in rheumatoid arthritis through mitochondrial dysregulation

BACKGROUND

Fibroblast-like synoviocytes (FLS) display aggressive phenotypes contributing to synovitis and joint destruction in rheumatoid arthritis (RA). Disrupted mitochondrial homeostasis has been proposed to aggravate the RA pathogenesis, however, the underlying mechanism remains to be elucidated. This study aimed to elucidate the role of mitophagy receptor FUN14 domain-containing 1 (FUNDC1) on RA-FLS migration and invasion.

METHODS

We analyzed the correlation of synovial FUNDC1 expression with joint destruction and disease activity in RA patients. Single cell sequencing data analysis combined with immunofluorescence indicated the specific expression and localization of FUNDC1 in synovial tissue and RA-FLS. The roles of FUNDC1 in the migration, invasion, and cytokine secretion of RA-FLS were examined by patient-derived primary culture as well as SCID mouse models. We investigated the effects and mechanism of FUNDC1 on mitophagy and mitochondrial quality control network in primary RA-FLS.

RESULTS

We found that the FUNDC1 was mainly expressed in FLS and exhibited a decreased level in RA synovium, which was correlated with severe joint destruction. Deficiency of FUNDC1 enhanced migration, invasion as well as secretion of matrix metalloproteinases in RA-FLS. On the contrary, overexpression of FUNDC1 in RA-FLS with low FUNDC1 inhibited the migration, invasion and secretion capacity of RA-FLS. Mechanistically, repressed FUNDC1 level in RA-FLS impaired mitophagy, imbalanced mitochondrial quality control, and increased mitochondrial reactive oxygen species (mtROS) production, leading to the overactivation of the MAPK pathway. Treatment with mtROS scavenger mtTEMPO can reverse this process and diminish the invasiveness of RA-FLS.

CONCLUSIONS

Deficiency of FUNDC1 dysregulates mitochondrial quality-control system and induces aggressive phenotype of RA-FLS, resulting in joint destruction during RA progression.

Single-cell transcriptomic reveals network topology changes of cancer at the individual level

Network biology facilitates a better understanding of complex diseases. Single-sample networks retain individual information and have the potential to distinguish disease status. Previous studies mainly used bulk RNA sequencing data to construct single-sample networks, but different cell types in the tissue microenvironment perform significantly different functions. In this study, we investigated whether network topology features of cell-type-specific networks varied in different pathological states at the individual level. Protein-protein interaction network (PPI) and co-expression network of cancer and ulcerative colitis were established using four publicly single-cell RNA sequencing (scRNA-seq) datasets. We analyzed cell-cell interactions of epithelial cells and immune cells using CellChat R package. Network topology changes between normal tissues and pathological tissues were analyzed using Cytoscape software and QUACN R package. Results showed cell-cell interactions of epithelial cells were enhanced in carcinoma and adenoma. The average number of neighbors and graphindex of co-expression network increased in epithelial cells of adenoma, carcinoma and paracancer compared with normal tissues. The co-expression network density of T cells in tumors was significantly higher than that in normal tissues. The co-expression network complexity of epithelial cells in the benign tissues was associated with the grade group of paired tumors. This study suggests topological properties of cell-type-specific individual network vary in different pathological states, providing an insight into understanding complex diseases.

Prenatally derived macrophages support choroidal health and decline in age-related macular degeneration

Hallmark findings in age-related macular degeneration (AMD) include the accumulation of extracellular lipid and vasodegeneration of the choriocapillaris. Choroidal inflammation has long been associated with AMD, but little is known about the immune landscape of the human choroid. Using 3D multiplex immunofluorescence, single-cell RNA sequencing, and flow cytometry, we unravel the cellular composition and spatial organization of the human choroid and the immune cells within it. We identify two populations of choroidal macrophages with distinct FOLR2 expression that account for the majority of myeloid cells. FOLR2+ macrophages predominate in the nondiseased eye, express lipid-handling machinery, uptake lipoprotein particles, and contain high amounts of lipid. In AMD, FOLR2+ macrophages are decreased in number and exhibit dysfunctional lipoprotein metabolism. In mice, FOLR2+ macrophages are negative for the postnatal fate-reporter Ms4a3, and their depletion causes an accelerated AMD-like phenotype. Our results show that prenatally derived resident macrophages decline in AMD and are implicated in multiple hallmark functions known to be compromised in the disease.

Plasmodium falciparum infection induces T cell tolerance that is associated with decreased disease severity upon re-infection

Immunity to severe malaria is acquired quickly, operates independently of pathogen load, and represents a highly effective form of disease tolerance. The mechanism that underpins tolerance remains unknown. We used a human rechallenge model of falciparum malaria in which healthy adult volunteers were infected three times over a 12 mo period to track the development of disease tolerance in real-time. We found that parasitemia triggered a hardwired innate immune response that led to systemic inflammation, pyrexia, and hallmark symptoms of clinical malaria across the first three infections of life. In contrast, a single infection was sufficient to reprogram T cell activation and reduce the number and diversity of effector cells upon rechallenge. Crucially, this did not silence stem-like memory cells but instead prevented the generation of cytotoxic effectors associated with autoinflammatory disease. Tolerized hosts were thus able to prevent collateral tissue damage in the absence of antiparasite immunity.

Therapeutic potential of Da Cheng Qi Decoction and its ingredients in regulating ferroptosis via the NOX2-GPX4 signaling pathway to alleviate and predict severe acute pancreatitis

OBJECTIVE

This study aimed to elucidate the protective effects of Da Cheng Qi Decoction (DCQD) on severe acute pancreatitis (SAP) by targeting ferroptosis in pancreatic acinar cells and to establish a predictive signature and nomogram for acute pancreatitis (AP) risk assessment.

METHODS

We utilized microarray analysis to delineate gene expression patterns among 32 healthy controls and 87 AP patients stratified by severity. Employing SAP models and NOX2-deficient cells, we investigated the molecular underpinnings of ferroptosis. The impact of DCQD and the ferroptosis inhibitor Fer-1 on gene expression, oxidative stress, and inflammation was assessed. Machine learning algorithms identified differentially expressed genes (DEGs) sensitive to DCQD, SAP, and ferroptosis (DSNFGs), which were validated across multiple datasets. A predictive nomogram integrating DSNFGs was developed, and single-cell analysis provided a comprehensive view of the cellular dynamics.

RESULTS

The microarray analysis revealed upregulation of NOX2 and downregulation of GPX4 in AP, with expression patterns correlating with disease severity. DCQD ameliorated SAP-induced pancreatic acinar cell damage and ferroptosis by reducing inflammatory markers and enhancing GPX4 expression. NOX2 knockout mitigated ferroptosis in SAP models, suggesting a key role in the disease process. DCQD and Fer-1 differentially regulated the expression of ferroptosis-related genes, reduced reactive oxygen species (ROS) and high-mobility group box 1 (HMGB1) levels, and suppressed the inflammatory response in a SAP mouse model. The HPLC analysis of DCQD constituents indicated eight components (aloe-emodin, rhein, emodin, chrysophanol, naringin, hesperidin, magnolol, and honokiol) with the capacity to modulate ferroptosis. Venn analysis identified 48 DSNFGs, with a subset of five genes demonstrating significant predictive value. The developed nomogram, based on LASSO regression, showed high accuracy in validation cohorts. Single-cell RNA sequencing (scRNA-seq) and CellChat analysis uncovered heterogeneity and cell-cell communication networks in the pancreas during recovery from pancreatitis, implicating several signaling pathways.

CONCLUSION

DCQD and its eight ingredients exert its protective effect in SAP by inhibiting ferroptosis through the NOX2/GPX4 pathway. The DCQD-SAP-ferroptosis-related signature and nomogram offer a novel tool for AP risk assessment, prognosis prediction, and personalized therapeutic strategies in SAP management.

Fibroblast-derived versican exacerbates periodontitis progression by regulating macrophage migration and inflammatory cytokine secretion

OBJECTIVE

Versican (VCAN), a prominent extracellular matrix component upregulated in inflammatory diseases, demonstrates context-specific regulatory mechanisms. Periodontitis, a chronic inflammatory disease leading to periodontal tissue destruction and tooth loss, the pathological role of it remains poorly defined. Our study aims to examine VCAN-mediated mechanisms in periodontitis.

METHODS

We conducted a comprehensive analysis of bulk RNA sequencing and single-cell RNA sequencing data to examine VCAN expression level and source in periodontitis. Functional and correlation analyses were used to explore its biological functions. We then validated VCAN expression using quantitative real-time polymerase chain reaction, immunohistochemical staining, and immunofluorescence staining in animal models and investigated its biological functions in inflammation through in vitro experiments.

RESULTS

Our findings reveal that VCAN is mainly generated by fibroblast in periodontitis, and its expression significantly upregulated at both mRNA and protein levels. Using VCAN-overexpressing L929 cells, we demonstrated enhanced proliferative capacity and inflammatory potential. Co-culture experiments with RAW264.7 cells showed promoted migration, adhesion, M1 polarization, and mitogen-activated protein kinase (MAPK) pathway activation.

CONCLUSION

VCAN enhances fibroblast proliferation and migration, and upregulates inflammatory cytokines expression. Furthermore, fibroblast-derived VCAN not only induces macrophage chemotaxis, migration, adhesion, and polarization toward the proinflammatory M1 phenotype, but also activates MAPK signaling of macrophage, which may amplify inflammatory cascades to exacerbate periodontal tissue destruction. Targeted regulation of VCAN expression may become a promising precision treatment strategy for periodontitis.

Nicotinamide metabolism affects the prognosis of hepatocellular carcinoma by influencing the tumor microenvironment

In this study, we utilized the public database along with single-cell genomics techniques to systematically analyze the expression patterns and clinical significance of key genes in the nicotinamide metabolism pathway in liver cancer samples. The findings indicate that differential nicotinamide metabolism-related key genes are expressed in liver cancer samples. The liver cancer samples were put into separate subgroups using consistency clustering analysis based on differential gene expression levels observed. Additionally, immune infiltration and drug sensitivity analysis also revealed differences between the two subgroups. Survival analysis suggested that the key genes were associated with prognosis. Finally, a prognostic model was established using the key genes, offering a fresh viewpoint on the molecular mechanism investigating liver cancer. This study demonstrated the significant correlation between key genes in the nicotinamide metabolism pathway and the occurrence and progression of liver cancer and indicated that these key genes could serve as prognostic markers and tailored treatment targets for liver cancer.

Single-cell RNA sequencing indicates AP-1 as a potential therapeutic target for autoimmune uveitis

Autoimmune uveitis (AU) is a sight-threatening eye disease, marked by a complex pathogenesis and limited treatment options. Herein, we conducted single-cell RNA sequencing (scRNA-seq) on the spleen and cervical draining lymph nodes (CDLNs) of both normal and experimental autoimmune uveitis (EAU) mice and found common alterations in celluar composition and transcriptional regulation occurred throughout the EAU process. Moreover, we identified activator protein-1 (AP-1) as a pivotal disease-related molecule in the pathogenesis of EAU. Inhibiting AP-1 alleviated symptoms of EAU and reduced the retina infiltration of T helper 17 cells (Th17) and Th1 cells. Additionally, following treatment with the AP-1 inhibitor, both the spleen and CDLNs showed decreased Th17 and Th1 cell proportions. Meanwhile, in vitro studies revealed that treatment with AP-1 inhibitor reduced the level of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-23 (IL-23), two pivotal molecules implicated in the Th17 cell pathogenicity, during EAU. The adoptive transfer experiment also showed that inhibiting AP-1 in CD4+ T cells suppressed their ability to elicit EAU. Altogether, our study demonstrates that AP-1 might involved in EAU pathogenesis by supporting Th17 cell pathogenicity via the GM-CSF/IL-23 feedback loop. Thus, AP-1 inhibition might be a novel treatment strategy for uveitis.

Reproductive adaptation of Astyanax mexicanus under nutrient limitation

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetra Astyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, lower biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identified insulin-like growth factor 1a receptor (igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies in Astyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.

Single-cell transcriptomic analysis identifies tissue-specific fibroblasts as the main modulators of myeloid cells in peritoneal metastasis of different origin

Colorectal cancer (CRC) peritoneal metastasis (CPM) is related to limited therapy options and poor prognosis. Although stromal cells heavily infiltrate most CPMs, interactions between different cell types in their microenvironment remain unclear. Here, we investigated tumor and distant normal tissue from CPM and CRC patients using single-cell RNA sequencing. Investigating the incoming and outgoing signals between cells revealed that fibroblasts dominate the CPM signaling landscape with myeloid cells as their strongest interaction partner. Using immunohistochemistry, we confirmed that fibroblasts co-localize with macrophages in the CPM microenvironment. A fibroblast sub-population detected only in CPM and normal peritoneum demonstrated immunoregulatory properties in co-culture experiments, and was further detected in additional peritoneal malignancies derived from ovarian and gastric origin. This novel fibroblast type and its communication with macrophages could be attractive targets for therapeutic interventions in CPM and potentially peritoneal surface malignancies in general.

Transcriptome analysis reveals the potential role of neural factor EN1 for long-terms survival in estrogen receptor-independent breast cancer

Breast cancer patients with estrogen receptor-negative (ERneg) status, encompassing triple negative breast cancer (TNBC) and human epidermal growth factor receptor 2 positive breast cancer, are confronted with a heightened risk of drug resistance, often leading to early recurrence; the biomarkers and biological processes associated with recurrence is still unclear. In this study, we analyzed bulk RNA sequencing (RNA-seq) data from 285 cancer and paracancerous samples from 155 TNBC patients, along with transcriptome data from 11 independent public cohorts comprising 7,449 breast cancer patients and 26 single-cell RNA-seq datasets. Our results revealed differential enrichment of nerve-related pathways between TNBC patients with and without 10-year recurrence-free survival. We developed an early recurrence index (ERI) using a machine learning model and constructed a nomogram that accurately predicts the 10-year survival of ERneg patients (area under the curve [AUC]Training = 0.79; AUCTest = 0.796). Further analysis linked ERI to enhanced neural function and immunosuppression. Additionally, we identified EN1, the most significant ERI gene, as a potential biomarker that may regulate the tumor microenvironment and sensitize patients to immunotherapy.

The upregulation of TNKS1 drives the phenotypic switching of vascular smooth muscle cells in aortic dissection through the activation of ferroptosis

OBJECTIVE

Aortic dissection (AD) is a life-threatening disease. Tankyrase1 (TNKS1), a PARylating ADP-ribosyl transferase, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration.This study explores the impact of TNKS1 on the transformation of human aortic smooth muscle cells (HASMCs) in AD.

METHODS AND RESULTS

Single-cell RNA sequencing was performed and clusters were used for between-disease differential gene expression analyses. In the AD aorta, WB, immunofluorescence and RT-q-PCR revealed that TNKS1 expression was elevated, accompanied by a disorganized cell phenotype. Further examination like WB，immunofluorescence,Scratch-Wound Assay confirmed the upregulation of TNKS1 triggers phenotypic switching.Subsequent studies revealed that ferroptosis played a key role in TNKS1-induced phenotypic switching. Increased ferroptosis markers, such as elevated iron content,ROS and lipid peroxidation, were observed in HASMCs overexpressing TNKS1, while inhibition of ferroptosis restored the contractile phenotype.Co-IP assay demonstrated a direct protein-protein interaction between TNKS1 and SLC7A11 at the molecular level. In vivo, the upregulation of TNKS1 not only activated ferroptosis but also triggered phenotypic transformation.

CONCLUSION

This study demonstrates that TNKS1 is a key regulator of AD pathogenesis, driving HASMC phenotypic switching through ferroptosis activation, ultimately leading to aortic wall destabilization and dissection. Targeting TNKS1 or the ferroptosis pathway may offer novel therapeutic strategies for AD prevention and treatment.

Response of astrocytes and their interaction with surrounding brain cells after acute ischemia-reperfusion analyzed by single-cell transcriptome sequencing

Astrocytes play a key role in the occurrence and development of ischemic stroke. However, reactive astrocytes have both detrimental and protective roles in ischemic stroke. Regrettably, the stimulation signals associated with the transformation of astrocytes into different subclusters lack systemic analysis, and the mechanism by which astrocytes produce multiple effects is not entirely clear. We investigated the heterogeneity of mouse astrocytes 12 h after cerebral ischemia-reperfusion via Single-cell RNA sequencing and verified gene expressions by reverse transcription-polymerase chain reaction. We acquired astrocyte subclusters' transcriptional characteristics involved in diversified functions. To explore what stimulus signals cause astrocyte heterogeneity, we present a blueprint for cellular communication between astrocyte subclusters and other surrounding brain cells 12 h after ischemia-reperfusion, and identified 9 genes which are potential and promising for being therapeutic targets and 6 genes were specific to astrocyte subcluster 2 that tend to resist ischemia-reperfusion injury. At 12 h after ischemia-reperfusion, each subcluster of astrocytes is characteristic in terms of function and communication with surrounding cells, which is based on the activation genes and transcription molecules that we have revealed with subcluster characteristics. Our results provide a basis for revealing the anti-injury response of astrocytes to cerebral ischemia-reperfusion, which involves coordination of different subclusters and the coordination of astrocytes with surrounding brain cells.

Developmental landscape and asymmetric gene expression in the leaf vasculature of Brassica rapa revealed by single-cell transcriptome

Leaf vasculature not only acts as a channel for nutrients and signaling information but also influences leaf morphology. It consists of several distinct cell types with specialized functions. Cell type-specific characterizations based on single-cell RNA sequencing technology could aid in understanding the identities of vascular tissues and their roles in leaf morphogenesis in Brassica rapa. Here, we generated a single-cell transcriptome landscape of the Chinese cabbage leaf vasculature. A total of 12 cell clusters covering seven known cell types were identified. Different vascular cell types were characterized by distinct identities. The xylem parenchyma and companion cells exhibited an active expression pattern of amino acid metabolism genes. Tracheary elements and sieve elements were enriched in many genes related to cell wall biosynthesis, and the phloem parenchyma was enriched in many sugar transporter-encoding genes. Pseudo-time analyses revealed the developmental trajectories of the xylem and phloem and the potential roles of auxin and ethylene in xylem development. Furthermore, we identified key candidate regulators along the differentiation trajectory of the sieve elements and companion cells. Most of the homoeologous genes in the syntenic triads from the three subgenomes showed asymmetric gene expression patterns in different vascular cell types. Collectively, our study revealed that Chinese cabbage leaf vasculature cells had highly heterogeneous transcriptomes, providing new insights into the complex processes of leaf vasculature development in B. rapa leafy vegetables and other Brassica crops.

Transcriptional reprogramming triggered by neonatal UV radiation or Lkb1 loss prevents BRAFV600E-induced growth arrest in melanocytes

The mechanisms behind UVB-initiated, neonatal-specific melanoma linked to BRAFV600E are not well understood, particularly regarding its role in growth arrest. We found that, beyond mutations, neonatal UV irradiation or Lkb1 loss promotes a cell-autonomous transcriptional reprogramming that prevents BRAFV600E-induced growth arrest, leading to melanoma development. Using UVB-dependent and independent mouse models, genomic analyses, clinical data, and single-cell transcriptomics, we identified a transcriptional program that bypasses growth arrest, promoting melanoma. In humans, many of these genes are linked to poor survival and are upregulated in melanoma progression and other RAS pathway-driven tumors. Reconstitution experiments showed these genes cooperate with BRAFV600E in melanocyte transformation, dedifferentiation, and drug resistance. Depleting gene products like UPP1 highlights their potential as therapeutic targets. Our findings reveal that BRAFV600E-mutated melanomas can develop independently of nevus progression and identify novel targets for treatment.

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.

Characterizing the Cellular Constituents of Proximal Airway Disease in Granulomatosis With Polyangiitis

OBJECTIVE

Granulomatosis with polyangiitis (GPA) is a rare multisystem autoimmune vasculitis. 10-20% of patients suffer life-threatening obstruction of their proximal airways. Although progress has been made in the treatment of systemic disease, ameliorating airway disease in GPA remains an unmet need arising from limited understanding of disease pathogenesis. We sought to characterize the cellular constituents of the affected proximal airway mucosa in GPA airway scar.

STUDY DESIGN

Basic/translational study.

SETTING

Single tertiary care center.

METHODS

Using single-cell RNA sequencing, we profiled the cellular constituents of proximal airway samples from GPA and disease comparators (GPA; n = 9, idiopathic subglottic stenosis: iSGS; n = 7, post-intubation proximal stenosis: PIPS; n = 5, and control; n = 10). We report transcriptomes for subglottic epithelial, immune, endothelial, and stromal cell types and map expression of GPA risk genes to tissue types present in the proximal airway. We compared differential gene expression across immune cell populations and performed pseudotime analysis using Monocle 3.

RESULTS

Similar to iSGS and PIPS, the subglottic mucosa of GPA patients demonstrated an abundant immune infiltrate. 71% of the established GPA risk genes (10 of 14) localized to T cells and macrophages. Differential gene expression and pseudotime analysis revealed a sub-population of CD4-/CD8- inflammatory T cells that only originated from GPA.

CONCLUSION

We characterized the cellular composition of GPA airway disease and demonstrated that the expression of GPA risk alleles is predominantly localized to immune cell populations. We also identified a subset of inflammatory T cells that is unique to GPA.

Single-cell RNA sequencing and spatial transcriptomics reveal unique subpopulations of infiltrating macrophages and dendritic cells following AKI

Kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) are strongly associated with inflammation and fibrosis in acute kidney injury (AKI) and chronic kidney disease (CKD). Contrary to kidney resident macrophages (KRMs), which are self-renewing and present in the kidney prior to injury, KIMs are bone-marrow derived F4/80int, CD11bhigh macrophages that infiltrate the kidney during AKI. Here, we combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, and cellular indexing of transcriptomes and epitopes (CITE)-sequencing to elucidate temporal, spatial, and transcriptional characteristics of unique subpopulations of KIMs and KDCs in ischemia-induced AKI. scRNAseq revealed three KIM, two KDC, and one proliferative macrophage subpopulation. All six clusters were localized in unique, spatially constrained microenvironments and their locations were dynamically regulated following bilateral ischemia reperfusion injury. We showed that a specific Arginase 1-expressing KIM cluster infiltrates the kidney cortex at day 1 after ischemia. We also identified a macrophage subpopulation that expresses genes specific to cell proliferation that resides in the cortex in uninjured states and in the medulla at day 6 during the reparative phase of AKI. Gene ontology analysis revealed functional characteristics that distinguish each KIM and KDC population. By day 28 after ischemia, the transcriptional profiles of KIMs upregulate C1q, Cd81, and Cd74, markers normally limited to KRMs in quiescence and early AKI. Since KIMs and KDCs are profoundly involved in AKI, it is paramount that we understand their dynamics-temporally and spatially-and identify their key genes and surface protein markers to develop macrophage-specific therapeutics aimed toward targeting kidney disease.NEW & NOTEWORTHY In this work, we fully characterized both single cell and spatial transcriptomes of kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) following bilateral ischemia reperfusion injury. We also discovered distinct markers that differentiate KIMs from one another and kidney resident macrophages (KRMs). Finally, we show evidence suggesting that KIMs may reprogram and express genes previously limited to KRMs by day 28 following injury resolution.

FOXM1 cooperates with ERα to regulate functional β-cell mass

The transcription factor forkhead box (FOX)M1 regulates β-cell proliferation and insulin secretion. Our previous work demonstrates that expressing a constitutively active form of FOXM1 (FOXM1*) in β-cells increases β-cell function, proliferation, and mass in male mice. However, in contrast to what is observed in males, we demonstrate here that in female mice expression of FOXM1* in β-cells does not affect β-cell proliferation or glucose tolerance. Similarly, FOXM1* transduction of male but not female human islets enhances insulin secretion in response to elevated glucose. We therefore examined the mechanism behind this sexual dimorphism. Estrogen contributes to diabetes susceptibility differences between males and females, and estrogen receptor (ER)α is the primary mediator of β-cell estrogen signaling. Moreover, in breast cancer cells, ERα and FOXM1 work together to drive gene expression. We therefore examined whether FOXM1 and ERα functionally interact in β-cells. FOXM1* rescued elevated fasting glucose, glucose intolerance, and homeostatic model assessment of β-cell function (HOMA-B) in female mice with a β-cell-specific ERα deletion. Furthermore, in the presence of estrogen, the FOXM1 and ERα cistromes exhibit significant overlap in βTC6 β-cells. In addition, FOXM1 and ERα binding sites frequently occur in complex enhancers co-occupied by other islet transcription factors. These data indicate that FOXM1 and nuclear ERα cooperate to regulate β-cell function and suggest a general mechanism contributing to the lower incidence of diabetes observed in women.NEW & NOTEWORTHY Here we investigate why the effects of increasing FOXM1 activity in β-cells observed in male mice are not seen in female mice. ERα likely collaborates with FOXM1 and other transcription factors to enhance gene expression related to β-cell function. Higher estrogen levels in females may contribute to their increased insulin secretion and the more severe consequences of losing transcription factors like FOXM1 in males. Overall, these findings shed light on sex differences in diabetes susceptibility.

MAP4K4 aggravates microvascular anomalies in diabetic retinopathy in a YTHDF2-dependent manner

AIMS/HYPOTHESIS

Signalling pathways that regulate endothelial cell (EC) dysfunction, ischaemia and inflammation play a crucial role in retinal microangiopathy such as diabetic retinopathy. MAP4K4 is highly expressed in ECs. However, the involvement of MAP4K4 in retinal vasculopathy of diabetic retinopathy remains unclear.

METHODS

We analysed publicly available single-cell RNA sequencing (scRNA-seq) data from fibrovascular membranes (FVMs) from eight individuals with proliferative diabetic retinopathy (PDR) and normal retinas from 11 individuals without diabetes. Using db/db mice and human primary retinal endothelial cells (HRMECs), we further investigated the effects of MAP4K4 on retinal microangiopathy and endothelial dysfunction to explore the underlying regulatory mechanisms.

RESULTS

The scRNA-seq analysis revealed that MAP4K4 was predominantly expressed in retinal ECs, with elevated expression in FVMs from individuals with PDR compared with normal retinas from individuals without diabetes. This finding was confirmed at the protein level, with MAP4K4 expression and activity being upregulated in both the FVMs of individuals with PDR and the retinas of db/db mice. Inhibition of MAP4K4 using DMX-5804 alleviated retinal microvascular leakage by enhancing the expression and integrity of junctional proteins in both ECs from db/db mice and HRMECs. Additionally, DMX-5804 reduced retinal angiogenesis by inhibiting EC migration and vascular sprouting. Mechanistically, MAP4K4 regulated EC characteristics through NF-κB signalling pathway activity. The exacerbating effect of recombinant MAP4K4 on diabetic retinopathy in db/db mice was mitigated by a p65 inhibitor, confirming the involvement of NF-κB. Moreover, MAP4K4 expression was regulated by YTH N6-methyladenosine RNA-binding protein 2 (YTHDF2), which modulates the stability of MAP4K4 mRNA.

CONCLUSIONS/INTERPRETATION

Our study highlights the critical role of MAP4K4 in EC dysfunction and diabetic retinal microangiopathy, providing new insights into its molecular pathogenesis. Targeting MAP4K4, particularly through modulation of the YTHDF2/MAP4K4/NF-κB axis, may provide a novel therapeutic strategy for diabetic retinopathy.

Integration of Bulk RNA and Single-Cell Analyses Reveal Distinct Expression Patterns of Anoikis-Related Genes and the Immunosuppressive Role of NQO1+ Macrophages in Hepatocellular Carcinoma

Anoikis resistance plays a crucial role in the proliferation, metastasis, and invasion of hepatocellular carcinoma (HCC). However, the key genes involved remain to be identified. This study aimed to investigate the prognostic value and impact of anoikis-related genes (ARGs) on the immunosuppressive microenvironment in HCC patients through the integration of bulk RNA and single-cell RNA sequencing (scRNA-seq) bioinformatic analysis. An anoikis-related gene risk score model (ARGRS) comprising 11 ARGs was established via machine learning. scRNA-seq was performed to assess the heterogeneity of ARGs in HCC. In vitro experiments were conducted to investigate the effects of NAD(P)H: quinone oxidoreductase 1 (NQO1) on the polarization, phenotype, and function of macrophages. Bioinformatics analysis demonstrated that ARGRS had perfect efficiency in predicting the prognosis of HCC patients and that ARGs potentially play a role in maintaining the invasion and metastasis of malignant cells. Notably, NQO1+ macrophages presented features consistent with alternatively activated macrophages (M2) and displayed a powerful immunosuppressive effect, particularly in close interaction with T cells within the tumor immune microenvironment. Moreover, inhibition of NQO1 expression via dicoumarol resulted in reduced expression of the M2-associated markers CD206 and CD163, as well as the immunosuppressive cytokines IL-10 and TGF-β. Strikingly, this treatment effectively mitigated the immunosuppressive impact of macrophages on T cells. Collectively, ARGs are closely associated with the poor prognosis of HCC patients, and NQO1+ macrophages may have an immunosuppressive effect on HCC, suggesting that intervention in anoikis may represent a potential strategy for HCC treatment.

Bronchopulmonary dysplasia with pulmonary hypertension associates with semaphorin signaling loss and functionally decreased FOXF1 expression

Lung injury in preterm infants leads to structural and functional respiratory deficits, with a risk for bronchopulmonary dysplasia (BPD) that in its most severe form is accompanied by pulmonary hypertension (PH). To identify potential cellular and molecular drivers of BPD in humans, we performed single-cell RNA sequencing of preterm infant lungs with evolving BPD and BPD + PH compared to term infants. Examination of endothelial cells reveals a unique, aberrant capillary cell-state in BPD + PH defined by ANKRD1 expression. Within the alveolar parenchyma in infants with BPD/BPD + PH, predictive signaling analysis identifies surprising deficits in the semaphorin guidance-cue pathway, with decreased expression of pro-angiogenic transcription factor FOXF1. Loss of semaphorin signaling is replicated in a murine BPD model and in humans with causal FOXF1 mutations for alveolar capillary dysplasia (ACDMPV), suggesting a mechanistic link between developmental programs underlying BPD and ACDMPV and uncovering a critical role for semaphorin signaling in normal lung development.

Single-cell and spatial transcriptome analyses reveal tumor heterogeneity and immune remodeling involved in pituitary neuroendocrine tumor progression

Pituitary neuroendocrine tumors (PitNETs) can be invasive or aggressive, yet the mechanisms behind these behaviors remain poorly understood, impeding treatment advancements. Here, we integrat single-cell RNA sequencing and spatial transcriptomics, analyzing over 177,000 cells and 35,000 spots across 57 tissue samples. This comprehensive approach facilitates the identification of PitNETs tumor populations and characterizes the reconfiguration of the tumor microenvironment (TME) as PitNETs progress and invade. We trace the trajectory of TPIT-lineage PitNETs and identify an aggressive tumor cluster marked by elevated p53-mediated proliferation and a higher Trouillas classification, both associated with tumor progression. Additionally, we document the heterogeneity of immune stromal cells within PitNETs, particularly noting the enrichment of SPP1+ tumor associated macrophages (TAMs) in invasive tumors. These TAMs facilitate tumor invasion through the SPP1-ITGAV/ITGB1 signaling pathway. Our in-depth single-cell and spatial analysis of PitNETs uncovers the molecular dynamics within the TME, suggesting potential targets for therapeutic intervention.

An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation

With rapid advancements in single-cell RNA sequencing (scRNA-seq) technologies, exploration of the systemic coordination of critical physiological processes has entered a new era. Here, we generated a comprehensive Arabidopsis single-nucleus transcriptomic atlas using over 1 million nuclei from 20 tissues encompassing multiple developmental stages. Our analyses identified cell types that have not been characterized in previous single-protoplast studies and revealed cell-type conservation and specificity across different organs. Through time-resolved sampling, we revealed highly coordinated onset and progression of senescence among the major leaf cell types. We originally formulated two molecular indexes to quantify the aging state of leaf cells at single-cell resolution. Additionally, facilitated by weighted gene co-expression network analysis, we identified hundreds of promising hub genes that may integratively regulate leaf senescence. Inspired by the functional validation of identified hub genes, we built a systemic scenario of carbon and nitrogen allocation among different cell types from source leaves to sink organs.

Translational disease modeling of peripheral blood identifies type 2 diabetes biomarkers predictive of Alzheimer's disease

Type 2 diabetes (T2D) is a significant risk factor for Alzheimer's disease (AD). Despite multiple studies reporting this connection, the mechanism by which T2D exacerbates AD is poorly understood. It is challenging to design studies that address co-occurring and comorbid diseases, limiting the number of existing evidence bases. To address this challenge, we expanded the applications of a computational framework called Translatable Components Regression (TransComp-R), initially designed for cross-species translation modeling, to perform cross-disease modeling to identify biological programs of T2D that may exacerbate AD pathology. Using TransComp-R, we combined peripheral blood-derived T2D and AD human transcriptomic data to identify T2D principal components predictive of AD status. Our model revealed genes enriched for biological pathways associated with inflammation, metabolism, and signaling pathways from T2D principal components predictive of AD. The same T2D PC predictive of AD outcomes unveiled sex-based differences across the AD datasets. We performed a gene expression correlational analysis to identify therapeutic hypotheses tailored to the T2D-AD axis. We identified six T2D and two dementia medications that induced gene expression profiles associated with a non-T2D or non-AD state. We next assessed our blood-based T2DxAD biomarker signature in post-mortem human AD and control brain gene expression data from the hippocampus, entorhinal cortex, superior frontal gyrus, and postcentral gyrus. Using partial least squares discriminant analysis, we identified a subset of genes from our cross-disease blood-based biomarker panel that significantly separated AD and control brain samples. Finally, we validated our findings using single cell RNA-sequencing blood data of AD and healthy individuals and found erythroid cells contained the most gene expression signatures to the T2D PC. Our methodological advance in cross-disease modeling identified biological programs in T2D that may predict the future onset of AD in this population. This, paired with our therapeutic gene expression correlational analysis, also revealed alogliptin, a T2D medication that may help prevent the onset of AD in T2D patients.

Early mucosal responses following a randomised controlled human inhaled infection with attenuated Mycobacterium bovis BCG

The development of an effective vaccine against Mycobacterium tuberculosis is hampered by an incomplete understanding of immunoprotective mechanisms. We utilise an aerosol human challenge model using attenuated Mycobacterium bovis BCG, in BCG-naïve UK adults. The primary endpoint of this study (NCT03912207) was to characterise the early immune responses induced by aerosol BCG infection, the secondary endpoint was to identify immune markers associated with in-vitro protection. Blinded volunteers were randomised to inhale 1 × 107 CFU aerosolised BCG or 0.9% saline (20:6); and sequentially allocated to bronchoscopy at day 2 or 7 post-inhalation (10 BCG, 3 saline each timepoint). In the bronchoalveolar lavage post-aerosol BCG infection, there was an increase in frequency of eosinophils, neutrophils, NK cells and Donor-Unrestricted T cells at day 7, and the frequency of antigen presenting cells decreased at day 7 compared with day 2. The frequency of interferon-gamma+ BCG-specific CD4+ T cells increased in the BAL and peaked in the blood at day 7 post-BCG infection compared to day 2. BAL cells at day 2 and day 7 upregulated gene pathways related to phagocytosis, MHC-II antigen loading, T cell activation and proliferation. BCG's lack of key virulence factors and its failure to induce granulomas, may mean the observed immune responses do not fully recapitulate Mycobacterium tuberculosis infection. However, human infection models can provide unique insights into early immune mechanisms, informing vaccine design for complex pathogens.

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links

Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our understanding of cell functions and disease mechanisms from various omics perspectives. As these technologies evolve rapidly and data resources expand, there is a growing need for computational methods that can integrate information from different modalities to facilitate joint analysis of single-cell multi-omics data. However, integrating single-cell omics datasets presents unique challenges due to varied feature correlations and technology-specific limitations. To address these challenges, we introduce scMODAL, a deep learning framework tailored for single-cell multi-omics data alignment using feature links. scMODAL integrates datasets with limited known positively correlated features, leveraging neural networks and generative adversarial networks to align cell embeddings and preserve feature topology. Our experiments demonstrate scMODAL's effectiveness in removing unwanted variation, preserving biological information, and accurately identifying cell subpopulations across diverse datasets. scMODAL not only advances integration tasks but also supports downstream analyses such as feature imputation and feature relationship inference, offering a robust solution for advancing single-cell multi-omics research.

Single-cell RNA sequencing reveals the role of GTF2F2 in ovarian cancer oncogenesis and progression

BACKGROUND

Ovarian cancer is one of the most common malignancies of the female reproductive system and is associated with poor prognosis. This study aimed to utilize single-cell RNA sequencing to investigate the heterogeneity of malignant epithelial cells in ovarian cancer, focusing on their potential functions and the implications for treatment and prognosis.

METHODS

Single-cell RNA sequencing data were clustered using a single-cell transcriptome clustering method, and malignant epithelial cells were identified through copy number variation analysis. The interaction patterns between different malignant subpopulations and immune/stromal cells were analyzed using cell-to-cell communication analysis. A risk score (URS) model based on the UBE2C + epithelial subpopulation was then constructed through LASSO and multivariable Cox regression. High and low URS groups were compared in terms of tumor mutational burden (TMB), survival outcomes, and drug sensitivity. Finally, the role of GTF2F2 in ovarian cancer progression was validated through gene knockdown experiments in an ovarian cancer cell line (ES-2).

RESULTS

Three major malignant epithelial cell subpopulations were identified (TMSB4X + Epi, TSC22D1 + Epi, and UBE2C + Epi). The UBE2C + Epi subpopulation exhibited higher stemness and greater invasive potential. The constructed URS model effectively stratified patients into high- and low-risk groups, with the high-risk group displaying a higher TMB level (p = 0.00011). Drug sensitivity predictions indicated that osimertinib, rapamycin, and dihydrorotenone might have stronger inhibitory effects in the high-risk group, whereas ERK inhibitors were more effective in the low-risk group. Functional assays demonstrated that GTF2F2 knockdown significantly suppressed ovarian cancer cell migration and invasion. Western blot analyses further showed elevated E-cadherin and reduced N-cadherin expression, suggesting that GTF2F2 may promote epithelial-mesenchymal transition (EMT).

CONCLUSION

The risk score model established in this study offers a novel framework for patient stratification and personalized therapy. Notably, the identification of the UBE2C + Epi subpopulation and key genes such as GTF2F2 highlights potential diagnostic and therapeutic targets, shedding light on the pathogenesis of ovarian cancer and paving the way for precision medicine approaches.

Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics

Cervical cancer represents a significant global health challenge, with complex cellular and molecular mechanisms driving its progression from HPV infection to invasive malignancy. This study employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) to comprehensively characterize the tumor microenvironment (TME) across different stages of cervical cancer development. Through analysis of samples from normal cervix, HPV-infected normal cervix, high-grade squamous intraepithelial lesions (HSIL), and invasive cervical cancer, we identified distinct cellular populations and their dynamic changes during disease progression. Our findings revealed significant heterogeneity in immune cell populations, particularly highlighting the role of SPP1+ macrophages that were substantially enriched in cervical cancer compared to precancerous and normal tissues. Cell-cell communication networks and spatial mapping demonstrated that SPP1+ macrophages interact extensively with immune cells through the SPP1-CD44 signaling axis. This interaction contributes to an immunosuppressive microenvironment through modulation of T cell function and promotion of tumor cell survival. Furthermore, high expression of SPP1 correlated with advanced tumor stages and poor overall survival in cervical cancer patients, highlighting its potential as a prognostic biomarker. Our comprehensive characterization of the cellular landscape and intercellular communication networks in cervical cancer progression provides valuable insights for the development of targeted therapeutic strategies aimed at modulating the TME, particularly through disruption of the SPP1-CD44 axis. These findings establish a foundation for more effective personalized approaches to improve clinical outcomes in cervical cancer patients.

Radiation Exposure Induced Blood-Brain Barrier Injury via Mitochondria-Mediated Sterile Inflammation

Radiation-induced brain injury (RIBI) is caused by exposure to high doses of ionizing radiation and characterized by severe cognitive dysfunction and brain necrosis. However, the pathogenesis of RIBI is not fully understood, and no effective intervention is available. This work describes a blood-brain barrier (BBB) microphysiological system (MPS), that allowed to explore the responses of BBB and distinct brain cells to radiation exposure. Following acute exposure to radiation of X-ray or γ-ray, characteristic RIBI-associated pathological responses are observed, including BBB compromise, DNA breaks, inhibited cell proliferation, cell hypertrophy, and proinflammatory cytokine release. Among the distinctive types of cells, brain endothelial cells show the highest radiosensitivity as compared to other cells in the MPS. Intriguingly, X-ray and γ-ray radiation consistently induce prominent sterile inflammation responses, especially type I interferon response, in the BBB MPS. These responses are mediated by radiation-induced mitochondrial DNA release and subsequent activation of cGAS-STING signaling pathway. Furthermore, it is found abrocitinib (JAK1 inhibitor) and idebenone (mitochondrial protectant) can attenuate radiation-induced inflammation and ameliorate injuries in the BBB MPS. These findings reveal the involvement of mitochondria-mediated sterile inflammation in RIBI pathogenesis, identifying mitochondria as a potential target for new radioprotective measures.

Cancer-associated fibroblast-derived SEMA3C facilitates colorectal cancer liver metastasis via NRP2-mediated MAPK activation

Liver metastasis remains the predominant cause of mortality in patients with colorectal cancer (CRC). Nevertheless, the mechanisms underlying the initiation of colorectal cancer liver metastasis remain poorly elucidated. During the metastatic process of CRC cells from the primary site to the liver, we performed time-resolved analyses and identified a subset of tumor cells spatially located in the primary tumor and temporally distributed in the early stages of liver metastasis. These cells were termed liver metastasis-initiating cells (LMICs). LMICs exhibit high stemness, low proliferation, active interaction with surrounding stromal components, and a close association with liver metastasis. Notably, we found significant interactions between cancer-associated fibroblasts (CAFs) and LMICs via the SEMA3C-NRP2 receptor-ligand pair. Further in vivo and in vitro experiments confirmed that CAF-secreted SEMA3C could bind to the NRP2 receptor, which activates the MAPK pathway and promotes colorectal cancer liver metastasis. Our findings suggest potential therapeutic strategies for the early prevention of colorectal cancer liver metastasis.

A CD4+ T cell-intrinsic complement C5aR2-prostacyclin-IL-1R2 axis orchestrates Th1 cell contraction

T helper 1 (Th1) cell initiation pathways are well characterized; however, those regulating their contraction are less understood. Here, we define a CD4+ T cell-autonomous pathway in which complement C5 orchestrated a shift from prostaglandin E2 (PGE2) dominance to enhanced prostacyclin (PGI2) production via activation of C5a receptor 2 (C5aR2). This pivot in lipid mediators induced autocrine signaling through the PGI2 receptor and expression of the interleukin-1 (IL-1) decoy IL-1 receptor type 2 (IL-1R2), which sequestered Th1 cell-driving intrinsic IL-1β, facilitating Th1 cell contraction. Disruption of this C5aR2-PGI2-R axis was a hallmark of pathologically persistent Th1 cell activity in inflammatory conditions, including cryopyrin-associated periodic syndromes (CAPS), Crohn's disease, and rheumatoid arthritis. Rebalancing this axis through selective PGE2 synthase inhibition rectified the hyperactive Th1 cell phenotype in vitro in T cells from individuals with CAPS. Therefore, complement is a key controller of prostanoid metabolism, and the latter is an intrinsic-and potentially druggable-checkpoint for the cessation of Th1 cell effector responses.

Fibroblast reprogramming in the dura mater of NTG-induced migraine-related chronic hypersensitivity model drives monocyte infiltration via Angptl1-dependent stromal signaling

BACKGROUND

Migraine, characterized by recurrent episodes of severe headache, remains mechanistically enigmatic. While traditional theories emphasize trigeminovascular activation, the role of meningeal stromal-immune crosstalk in disease chronicity is poorly understood.

METHODS

A migraine-related chronic hypersensitivity model was utilized via intermittent intraperitoneal nitroglycerin (NTG, 10 mg/kg, every other day for 9 days) and peripheral mechanical hypersensitivity was assessed using von Frey filaments. Single-cell RNA sequencing (scRNA-seq) was performed on dura tissues to construct a cellular atlas of NTG-induced remodeling. These data were then integrated with migraine genome-wide association study (GWAS) risk genes, cell-cell interaction networks, and transcriptional regulation analysis to dissect NTG-driven meningeal remodeling.

RESULTS

The NTG-induced migraine-related chronic hypersensitivity model demonstrated sustained mechanical allodynia, as evidenced by significantly decreased paw withdrawal thresholds (p < 0.0001). Single-cell profiling of the dura mater revealed a 2.4-fold expansion of a pro-inflammatory fibroblast subpopulation (Fibro_c5: 1.9% in Vehicle vs. 4.6% in NTG group), which exhibited marked activation of TNF-α/NF-κB signaling pathways (normalized enrichment score [NES] = 1.83). Concomitantly, we observed an 82% increase in meningeal monocytes (5.7-10.4%) that showed preferential interaction with Fibro_c5 fibroblasts through Angptl1-mediated stromal-immune crosstalk (log2 fold change = 1.41). Regulatory network analysis identified Mafk as the upstream transcriptional regulator orchestrating Angptl1 expression in this pathological communication axis.

CONCLUSION

Our study reveals that NTG reprograms meningeal fibroblasts to expand a pro-inflammatory fibroblast subtype, which drives migraine-related chronic hypersensitivity through TNF-α/NF-κB signaling and Angptl1-mediated monocyte crosstalk. The identified Mafk-Angptl1 axis presents a potential therapeutic target, though human validation remains essential.

FOXA2 promotes metastatic competence in small cell lung cancer

Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compare gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identifies FOXA2 as a transcription factor strongly associated with SCLC metastasis. Subsequent analyses in experimental models demonstrates that FOXA2 induces a fetal neuroendocrine gene expression program and promotes multi-site metastasis. Moreover, we identify ASCL1, a transcription factor known for its initiating role in SCLC tumorigenesis, as a direct binder of the FOXA2 promoter and regulator of FOXA2 expression. Taken together, these data define the ASCL1-FOXA2 axis as a critical driver of multiorgan SCLC metastasis.

Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions

Embryonal tumor with multilayered rosettes (ETMR) is a pediatric brain tumor with dismal prognosis. Characteristic alterations of the chromosome 19 microRNA cluster (C19MC) are observed in most ETMR; however, the ramifications of C19MC activation and the complex cellular architecture of ETMR remain understudied. Here we analyze 11 ETMR samples from patients using single-cell transcriptomics and multiplexed spatial imaging. We reveal a spatially distinct cellular hierarchy that spans highly proliferative neural stem-like cells and more differentiated neuron-like cells. C19MC is predominantly expressed in stem-like cells and controls a transcriptional network governing stemness and lineage commitment, as resolved by genome-wide analysis of microRNA-mRNA binding. Systematic analysis of receptor-ligand interactions between malignant cell types reveals fibroblast growth factor receptor and Notch signaling as oncogenic pathways that can be successfully targeted in preclinical models and in one patient with ETMR. Our study provides fundamental insights into ETMR pathobiology and a powerful rationale for more effective targeted therapies.

Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer's disease and a cumulative effects model for risk liability

Genome-wide association studies (GWAS) on Alzheimer's disease (AD) have predominantly focused on identifying common variants in Europeans. Here, we performed whole-genome sequencing (WGS) of 1,559 individuals from a Korean AD cohort to identify various genetic variants and biomarkers associated with AD. Our GWAS analysis identified a previously unreported locus for common variants (APCDD1) associated with AD. Our WGS analysis was extended to explore the less-characterized genetic factors contributing to AD risk. We identified rare noncoding variants located in cis-regulatory elements specific to excitatory neurons associated with cognitive impairment. Moreover, structural variation analysis showed that short tandem repeat expansion was associated with an increased risk of AD, and copy number variant at the HPSE2 locus showed borderline statistical significance. APOE ε4 carriers with high polygenic burden or structural variants exhibited severe cognitive impairment and increased amyloid beta levels, suggesting a cumulative effects model of AD risk.

Revealing a novel Decorin-expressing tumor stromal subset in hepatocellular carcinoma via integrative analysis single-cell RNA sequencing

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, emphasizing the need for novel therapeutic strategies. Decorin (DCN), a chondroitin sulfate proteoglycan (CSPG), has been proposed as a tumor suppressor, yet its precise role in HCC and the tumor microenvironment (TME) remains underexplored. Through integrated analyses of bulk RNA and single-cell RNA sequencing datasets, we identified a distinct tumor stromal subset highly expressing DCN and associated chondroitin sulfate (CS) synthases. Our findings revealed that DCN expression is significantly downregulated in HCC tissue, but upregulated in peri-tumor stroma, where it correlates with better prognosis and reduced capsular invasion. Western blot analysis demonstrated that CS-DCN, the glycosylated form of DCN, plays a dominant role in this context. Single-cell clustering analysis identified a unique stromal subset in HCC characterized by elevated expression of DCN, CSPGs, and CS synthases, associated with extracellular matrix (ECM) remodeling and protective barrier functions. A six-gene DCN-associated signature derived from this subset, including DCN, BGN, SRPX, CHSY3, CHST3, and CHPF, was validated as a prognostic marker for HCC. Furthermore, functional assays demonstrated that CS-DCN significantly inhibited HCC cell proliferation and invasion. Our study highlights the critical role of DCN in HCC TME and provides insights into its therapeutic potential. Modulating CSPG pathways, particularly on CS-DCN-expressing stromal cells, may offer a promising approach for improving HCC treatment and patient outcomes.

Efficacy, safety and exploratory analysis of neoadjuvant tislelizumab (a PD-1 inhibitor) plus nab-paclitaxel followed by epirubicin/cyclophosphamide for triple-negative breast cancer: a phase 2 TREND trial

The optimal chemotherapy backbone and specific population of triple-negative breast cancer (TNBC) patients that benefit from neoadjuvant immunotherapy are not well established. This prospective, single-arm, phase II TREND trial assessed the efficacy and safety of tislelizumab plus nab-paclitaxel and epirubicin/cyclophosphamide-based chemotherapy as a neoadjuvant treatment for TNBC (ChiCTR2000035262). The primary endpoint was pathological complete response (pCR), with the secondary endpoints including safety assessment and objective response rate (ORR). ScRNA-seq, bulk RNA-seq, TCR-seq, cyTOF and WES were performed on pre-treatment and post-treatment samples. Among 53 total enrolled patients, 44 completed the combined neoadjuvant therapy, and 30 of 44 patients (68.18%) achieved pCR. Additionally, 14 out of 44 patients had a complete response (31.82%), with an ORR of 93.18%. The most commonly observed treatment-related adverse events (TRAEs) were alopecia, nausea and liver injury with 6 cases classified as grade 3 or higher adverse events. Immune response-related pathways, including TNF signaling pathway, T cell receptor signaling pathway, were enriched in pCR group. Pre-treatment model was identified and construct to predict response to immunotherapy. CDKN1A+ CD8 T lymphocytes were enriched in pCR group after neoadjuvant immunotherapy. Dynamic change of immune-related pathways at an early stage during the neoadjuvant immunotherapy may be associated with the treatment efficacy. In conclusion, neoadjuvant treatment of tislelizumab with nab-paclitaxel and anthracycline-based chemotherapy showed promising clinical activity and was well-tolerated among TNBC patients, without high incidence of TRAEs. These findings provide evidence supporting neoadjuvant tislelizumab with chemotherapy as an effective rational approach for treating TNBC.

Comprehensive analysis of the critical role of the epithelial mesenchymal transition subtype - TAGLN-positive fibroblasts in colorectal cancer progression and immunosuppression

Epithelial-mesenchymal transition (EMT) plays a pivotal role in tumor metastasis and immune suppression in colorectal cancer (CRC). However, the specific mechanisms of EMT and its relationship with the clinical prognosis and immunotherapy response in CRC patients remain unclear. In this study, we identified TAGLN-positive fibroblasts (TAGLN⁺Fib) as a cancer-associated fibroblast (CAF) subtype within the tumor microenvironment (TME) that promotes tumor metastasis and immune evasion. High EMT scores, strongly associated with TAGLN expression, were correlated with advanced tumor stages, poor prognosis, and resistance to immunotherapy. Functional experiments demonstrated that TAGLN knockdown significantly reduced CRC cell proliferation, migration, and EMT phenotypes in vitro and suppressed tumor growth in vivo. Furthermore, TAGLN⁺Fib closely interacted with MMP7-positive tumor epithelial cells and SPP1-positive macrophages, forming a pro-metastatic and immunosuppressive network. An EMT-TME risk model constructed using TAGLN⁺Fib exhibited robust predictive power for CRC prognosis and immunotherapy response. This study reveals the association of EMT scores with CRC prognosis and immunotherapy response, highlights TAGLN⁺Fib's critical role in tumor progression, and develops an EMT-TME risk model, offering insights for personalized CRC treatment and precision medicine.

Control of alveolar bone development, homeostasis, and socket healing by salt-inducible kinases

Alveolar bone supports and anchors teeth. The parathyroid hormone-related protein (PTHrP) pathway plays a key role in alveolar bone biology. Salt-inducible kinases (SIKs) are important downstream regulators of PTH/PTHrP signaling in the appendicular skeleton, where SIK inhibition increases bone formation and trabecular bone mass. However, the function of these kinases in alveolar bone remains unknown. Here, we report a critical role for SIK2/SIK3 in alveolar bone development, homeostasis, and socket healing after tooth extraction. Inducible SIK2/SIK3 (Ubq-creERt;Sik2f/f;Sik3f/f) deletion led to dramatic alveolar bone defects without changes in tooth eruption. Ablating these kinases impairs alveolar bone formation due to disrupted osteoblast maturation, a finding associated with ectopic periostin expression by fibrous cells in regions of absent alveolar bone at steady state and following molar extraction. Notably, this phenotype is the opposite of the increased trabecular bone mass observed in long bones following SIK2/SIK3 deletion. Distinct phenotypic consequences of SIK2/SIK3 deletion in appendicular versus craniofacial bones prompted us to identify a specific transcriptomic signature in alveolar versus long bone osteoblasts. Thus, SIK2/SIK3 deletion illuminates a key role for these kinases in alveolar bone biology and highlights the emerging concept that different osteoblast subsets utilize unique genetic programs.

CDC34 suppresses macrophage phagocytic activity and predicts poor response to immune checkpoint inhibitor in cancers

The cell division cycle 34 (CDC34) is an E2 ubiquitin-conjugating enzyme that is required for proteasomal degradation of substrate proteins, and is able to stabilize proteins including the epidermal growth factor receptor to promote lung carcinogenesis. Here, we conducted a pan-cancer analysis of CDC34 in The Cancer Genome Atlas datasets, and found its high expression in breast cancer and negative association with patient outcomes. Analysis of single-cell RNA-sequencing data revealed a negative role of CDC34 in macrophage phagocytotic activity for cancer cells. CDC34 stabilized hypoxia-inducible factor 1α (HIF1α) and transcriptionally upregulated CD47 in cancer cells to evade phagocytosis by macrophages. Inhibition of CDC34 inhibited tumor growth and synergized with anti-PD-L1 antibody in murine models. CDC34 was positively associated with CD47 and negatively associated with CD8+ granzyme B+ T-cell infiltration in patient samples, and patients with co-overexpression of CDC34 and CD47 had markedly poorer prognosis compared to those with high expression of either marker alone. In pre-treatment tumor samples, non-responders to immunotherapy exhibited significantly higher CDC34 levels and reduced CD8+ T-cell infiltration compared to responders. These findings indicated that CDC34 is critical to immune evasion and could be a potential therapeutic target for those resistant to immune checkpoint inhibitors.

Single cell analysis identified IFN signaling activation contributes to the pathogenesis of pediatric steroid-sensitive nephrotic syndrome

BACKGROUND

Idiopathic nephrotic syndrome (INS) is a prevalent condition whose recurrence leads to multiple adverse effects. Previous studies on INS pathogenesis primarily focused on immune dysregulation, particularly T-cell changes and their correlation with cytokine shifts. Accumulating evidence suggests that B-cell dysfunction also plays a role. Nevertheless, a comprehensive understanding of the mechanisms and effective treatment strategies remains incomplete.

METHODS

This study investigates changes in gene expressions and cellular interactions of immune cells at a single-cell level using peripheral blood mononuclear cells (PBMCs). And subsequently validated through quantitative PCR (qPCR), enzyme-linked immunosorbent assay (ELISA), and flow cytometry.

RESULTS

We identified seven main clusters using unsupervised clustering of 103,213 high-quality single cells. Through unsupervised clustering, patient-specific T cells (IFI44L + CD4 + T cells) that exhibited a pronounced elevation of interferon-stimulated genes (ISGs) is identified. Activation of ISGs and interferon (IFN)-related pathways are also observed in other clusters. Specifically, this study demonstrates that interferon-γ (IFN-γ) plays a crucial role by promoting the interaction between B-cell activating factor (BAFF) and receptors on B cells. This interaction triggers the release of autoantibodies, thereby initiating INS pathogenesis. Furthermore, telitacicept has shown efficacy in treating pediatric patients with frequent relapse NS(FRNS).

CONCLUSIONS

Overall, our findings underscore the role of interferon and its related pathways in INS pathogenesis, providing novel therapeutic interventions for NS.

Analyses of single-cell RNA sequencing uncover the role of intratumoral Helicobacter pylori in shaping tumor progression and immunity in gastric cancer

The intratumoral microbiota is closely associated with tumor initiation and progression in multiple solid tumors, including gastric cancer (GC). Single-cell analysis of host-microbiome interactions (SAHMI) is a pipeline used to systematically recover and denoise microbial signals in human clinical tissues and examine tumor-microbiome interactions at the single-cell transcriptome level. In a large GC cohort, we used SAHMI to detect 12 bacteria, among which Helicobacter pylori (H. pylori) was widely present in multiple tumor and normal samples. Meanwhile, we verified the presence of H. pylori in GC tissues via fluorescence in situ hybridization and immunohistochemistry. We performed single-cell RNA sequencing to analyze 11 cell populations, including B cells, T cells, and epithelial cells, and these cell types contained large numbers of H. pylori. We detected obvious enrichment of H. pylori in cancer cells and identified 13 upregulated differentially expressed genes exhibiting significantly negative correlations with patient survival in the H. pylori-positive tumor group compared with the findings in the other groups, indicating that these genes could represent prognostic biomarkers or therapeutic targets for H. pylori-infected patients with GC. Moreover, H. pylori-enriched immune cells, including T cells, B cells, and macrophages, were associated with cell-type-specific gene expression and pathway activities, including cell fate and immune signaling. In summary, tumor-microbiome interactions might reflect or influence tumorigenesis in GC, which has implications for clinical practice.

Combined analysis of somatic mutations and gene expression reveals nuclear speckles-associated enhanced stemness in gingivobuccal carcinoma under DNA damage response

Smokeless tobacco chewing habits in India lead to a high prevalence of Gingivobuccal oral squamous cell carcinoma (OSCC-GB). Cancer stem cells (CSCs) are a sub-population of cancer cells within a tumor with stem-like properties and are believed to contribute to tumor initiation, progression, increased resistance to drug therapy, and promote post-therapeutic cancer relapse. An RNA-sequencing data-based combined analysis of somatic mutations and gene expression was performed to explore the role of CSCs in disease progression using the novel Indian-origin OSCC-GB cell line 'IIOC019' from a patient with tobacco-chewing habit. The identified DNA damage-related known mutational signature (1 bp T/(A) nucleotide insertions and C>T mutations) indicates the impact of smokeless tobacco-related carcinogens in the IIOC019 cell line. The differentially expressed somatic variants, functional impact predictions, and survival analysis reveal the role of DNA damage response (DDR)-related genes in OSCC-GB, with the SON gene as a significant player. The study suggests that the loss-of-function in a somatic variant of the SON gene is linked to nuclear speckles-associated enhanced stemness and increased risk of disease progression in OSCC-GB under DDR conditions. The newly identified CSC-associated somatic variants appear to promote cancer spread, local recurrence, and resistance to chemotherapy or radiotherapy, contributing to the high mortality rates among Indian OSCC-GB patients.