decoupleR: ensemble of computational methods to infer biological activities from omics data

A diagnostic signatures for intervertebral disc degeneration using TNFAIP6 and COL6A2 based on single-cell RNA-seq and bulk RNA-seq analyses

OBJECTIVES

Intervertebral disc degeneration (IVDD) is a prevalent degenerative condition associated with a high incidence rate of low back pain and disability. This study aimed to identify potential biomarkers and signaling pathways associated with IVDD.

METHODS

Biomarkers were discerned through bulk-RNA and single-cell RNA sequencing (scRNA-Seq) investigations of IVDD cases from the Gene Expression Omnibus (GEO) database. Following this, two central genes were identified. Furthermore, gene set enrichment analysis (GSEA) and receiver operating characteristic (ROC) curve analysis were conducted. The transcriptional factor (TF) derived from nucleus pulposus (NP) cells was examined through the DoRothEA R package. RT-qPCR and IHC techniques were employed to confirm the expression of the two hub genes and their associated genes in tissue samples.

RESULTS

The proteins Tumor necrosis factor-inducible gene 6 protein (TNFAIP6) and collagen VI-α2 (COL6A2) were frequently analyzed using a combination of DEGs from datasets GSE70362, GSE124272, and scRNA-seq. Examination of gene expression across multiple datasets indicated significant differences in TNFAIP6 and COL6A2 levels in IVDD compared to control or normal groups (p < 0.05). These two central genes demonstrated strong diagnostic utility in the training cohort and reliable predictive value in the validation datasets. Our study verified the potential role of ZEB2 as a TF in regulating two key genes associated with IVDD. Furthermore, qPCR and IHC confirmed elevated expression levels of the hub genes and transcription factor.

CONCLUSION

We identified biomarkers, specifically TNFAIP6 and COL6A2, that have the potential to predict disease activity and aid in the diagnosis of IVDD.

Dominant interfering CARD11 variants disrupt JNK signaling to promote GATA3 expression in T cells

Several "primary atopic disorders" are linked to monogenic defects that attenuate TCR signaling, favoring T helper type 2 (TH2) cell differentiation. Patients with CARD11-associated atopy with dominant interference of NF-κB signaling (CADINS) disease suffer from severe atopy, caused by germline loss-of-function/dominant interfering (LOF/DI) CARD11 variants. The CARD11 scaffold enables TCR-induced activation of NF-κB, mTORC1, and JNK signaling, yet the function of CARD11-dependent JNK signaling in T cells remains nebulous. Here we show that CARD11 is critical for TCR-induced activation of JNK1 and JNK2, as well as canonical JUN/FOS AP-1 family members. Patient-derived CARD11 DI variants attenuated WT CARD11 JNK signaling, mirroring effects on NF-κB. Transcriptome profiling revealed JNK inhibition upregulated TCR-induced expression of GATA3 and NFATC1, key transcription factors for TH2 cell development. Further, impaired CARD11-JNK signaling was linked to enhanced GATA3 expression in CADINS patient T cells. Our findings reveal a novel intrinsic mechanism connecting impaired CARD11-dependent JNK signaling to enhanced GATA3/NFAT2 induction and TH2 cell differentiation in CADINS patients.

Antigen presentation potential is variable among human ovarian tumour and syngeneic murine models and dictates pre-clinical outcomes of immunotherapy

High grade serous ovarian carcinoma (HGSC) is a fatal gynaecological malignancy with limited therapeutic options. Immunotherapies targeting MHC-I-dependent antigen presentation offer potential. Currently, the antigen presentation machinery (APM) of widely used syngeneic murine HGSC models remains poorly characterised, limiting translational relevance. Here, we systematically evaluate APM gene expression in syngeneic murine and patient samples. Tap1 and Psmb8 were identified as critical APM markers, deficient in murine models and strongly correlating with MHC-I expression. Hierarchical clustering correlation analysis using these markers revealed that ID8-p53⁻/⁻BRCA1⁻/⁻ was the most strongly correlated model and aligned with the largest patient subset. Moreover, ID8-ip1 correlated to the smaller second patient subset strongly. The low MHC-I expressing IG10 model was unique clustering alongside patient derived LP28 tumour and not fitting either patient subset. In vivo test of a novel combination immune therapy consisting of Flt3L, Poly(I:C), and paclitaxel therapy demonstrated significantly reduced tumour burden in high APM models (p53⁻/⁻BRCA1⁻/⁻, ID8-ip1; p < 0.01), but not IG10. Furthermore, high expressing MHC-I models were linked to enhanced DC expansion, CD8⁺ T-cell infiltration, and effector differentiation (131 % increase in ID8-ip1), alongside improved CD8⁺ T-cell activation and CD86⁺ B-cell co-stimulation. These findings establish MHC-I as a predictive biomarker for immunotherapy response and underscore the need for APM-enhancing strategies in antigen-poor tumours. By bridging murine models to human APM heterogeneity, this work provides a framework for optimising preclinical immunotherapy evaluation and patient stratification, advancing tailored therapeutic approaches for HGSC.

The transcriptional landscape of atrial fibrillation: A systematic review and meta-analysis

BACKGROUND

Despite advances in understanding atrial fibrillation (AF) pathophysiology, there is limited agreement on the key genes driving its pathophysiology. To understand the genome-wide transcriptomic landscape, we performed a meta-analysis from studies reporting gene expression patterns in atrial heart tissue from patients with AF and controls in sinus rhythm (SR).

METHODS

Bibliographic databases and data repositories were systematically searched for studies reporting gene expression patterns in atrial heart auricle tissue from patients with AF and controls in sinus rhythm. We calculated the pooled differences in individual gene expression from fourteen studies comprising 534 samples (353 AF and 181 SR) to create a consensus signature (CS), from which we identified differentially regulated pathways, estimated transcription factor activity, and evaluated its performance in classifying validation samples as AF or SR.

RESULTS

Despite heterogeneity in the top differentially expressed genes across studies, the AF-CS in both chambers were robust, showing a better performance in classifying AF status than individual study signatures. Functional analysis revealed commonality in the dysregulated cellular processes between chambers, including extracellular matrix remodeling (highlighting epithelial mesenchymal transition, actin filament organization, and actin binding hallmark pathways), cardiac conduction (including cardiac muscle cell action potential, gated channel activity, and cation channel activity pathways), metabolic derangements (highlighting oxidative phosphorylation and asparagine n linked glycosylation), and innate immune system activity (mainly neutrophil degranulation, and TNFα signaling pathways). Finally, the AF-CS showed a good performance differentiating AF from controls in three validation datasets (two from peripheral blood and one from left ventricle samples).

CONCLUSIONS

Despite variability in individual studies, this meta-analysis elucidated conserved molecular pathways involved in AF pathophysiology across its phenotypes and the potential of a transcriptomic signature in identifying AF from peripheral blood samples. Our work highlights the value of integrating published transcriptomics data in AF and the need for better data deposition practices.

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Intracerebral hemorrhage (ICH) is a prevalent disease with high mortality. Despite advances in clinical care, the prognosis of ICH remains poor due to an incomplete understanding of the complex pathological processes. To address this challenge, we generated single-cell-resolution spatiotemporal transcriptomic maps of the mouse brain following ICH. This dataset is the most extensive resource available, providing detailed information about the temporal expression of genes along with a high-resolution cellular profile and preserved cellular organization. We identified 100 distinct cell subclasses, 17 of which were found to play significant roles in the pathophysiology of ICH. We also report similarities and differences between two experimental ICH models and human postmortem ICH brain tissue. This study advances the understanding of the local and global responses of brain cells to ICH. It provides a valuable resource that can facilitate future research and aid the development of novel therapies for this devastating condition.

Differential activation of the inositol 5-phosphatase SHIP2 by EGF and insulin signaling pathways

The importance of phosphatidylinositol 3,4,5- trisphosphate (PIP3) in cell signaling has been well established. Despite phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] emerging as an actor independent of PIP3, its exact signaling role remains poorly understood and the precise dynamics of PI(3,4)P2 and PIP3 upon receptor tyrosine kinase (RTK) stimulation are still inadequately investigated. In this study, we employed bioluminescence resonance energy transfer (BRET) sensors to monitor plasma membrane phosphoinositide (PIP) dynamics in HEK293-derived and HeLa cells following stimulation with epidermal growth factor (EGF) and insulin. Our findings reveal significant differences in PIP regulation: the increase in PI(3,4)P2 compared to PIP3 was larger with EGF stimulation relative to insulin. Using siRNA-mediated knockdown, we identified SH2-domain containing inositol polyphosphate 5-phosphatase 2 (SHIP2) as the key enzyme responsible for PI(3,4)P2 production in the EGF pathway, which was further supported by a bioinformatics analysis. Moreover, we detected increased phosphorylation at two tyrosine sites in SHIP2 upon EGF stimulation which was shown to be dependent on PI3K activation and PLC-induced calcium signal. These findings help refine our understanding of receptor-specific phosphoinositide dynamics and the enzymatic machinery involved as well as their potential influence on downstream cellular responses.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active or inactive kinases. We used benchmarKIN to evaluate kinase-substrate libraries, inference algorithms and the potential of adding predicted kinase-substrate interactions to overcome the coverage limitations. Our evaluation shows most computational methods perform similarly, but the choice of library impacts the inferred activities with a combination of manually curated libraries demonstrating superior performance in recapitulating kinase activities. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance. We then demonstrate how kinase activity inference aids characterize kinase inhibitor responses in cell lines. Overall, benchmarKIN helps researchers to select reliable methods for identifying deregulated kinases.

Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity

Glioblastoma is the most common and aggressive primary brain cancer and shows minimal response to therapies. The immunosuppressive tumour microenvironment in glioblastoma contributes to the limited therapeutic response. Astrocytes are abundant in the central nervous system and have important immunoregulatory roles. However, little is known about their role in the immune response to glioblastoma1. Here we used single-cell and bulk RNA sequencing of clinical glioblastoma samples and samples from preclinical models, multiplexed immunofluorescence, in vivo CRISPR-based cell-specific genetic perturbations and in vitro mouse and human experimental systems to address this gap in knowledge. We identified an astrocyte subset that limits tumour immunity by inducing T cell apoptosis through the death receptor ligand TRAIL. Moreover, we identified that IL-11 produced by tumour cells is a driver of STAT3-dependent TRAIL expression in astrocytes. Astrocyte signalling through STAT3 and TRAIL expression were associated with a shorter time to recurrence and overall decreased survival in patients with glioblastoma. Genetic inactivation of the IL-11 receptor or TRAIL in astrocytes extended survival in mouse models of glioblastoma and enhanced T cell and macrophage responses. Finally, treatment with an oncolytic HSV-1 virus engineered to express a TRAIL-blocking single-chain antibody in the tumour microenvironment extended survival and enhanced tumour-specific immunity in preclinical models of glioblastoma. In summary, we establish that IL-11-STAT3-driven astrocytes suppress glioblastoma-specific protective immunity by inducing TRAIL-dependent T cell apoptosis, and engineered therapeutic viruses can be used to target this mechanism of astrocyte-driven tumour immunoevasion.

TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoids

Cancer cells infiltrating surrounding tissue frequently undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and interconnected remains underexplored. Here, we used intestinal organoids with colorectal cancer (CRC) driver mutations as model system to investigate the mechanistic basis of TGF-β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype of human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor gene whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF-β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated SOX11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.

Single-cell transcriptomic analysis deciphers the inflammatory microenvironment characterized by CXCL9+ fibroblasts and ACKR1+ endothelial cells in immune-related myocarditis

BACKGROUND

Immune-related myocarditis induced by immune checkpoint inhibitors (ICIs) is a rare immune-related adverse event (irAE) but is characterized by a high mortality rate. However, the specific pathological mechanisms underlying immune-related myocarditis remain largely unclear. In this study, we aimed to elucidate the inflammatory microenvironment within cardiac tissues affected by immune-related myocarditis at the single-cell level to identify potential therapeutic targets.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) on an endomyocardial biopsy specimen obtained from a patient with pancreatic neuroendocrine carcinoma who developed immune-related myocarditis following treatment with ICIs. Additionally, the scRNA-seq data of heart specimens from deceased donors without cardiovascular diseases were collected and applied as normal control. To validate our findings and assess their specificity to ICI-related pathology, we analyzed mouse scRNA-seq data, including controls, ICI-related myocarditis, viral myocarditis, and autoimmune myocarditis.

RESULTS

We found elevated proportions of lymphocytes, myeloid cells, and fibroblasts in the irAE group, suggesting an intensified inflammatory microenvironment in human immune-related myocarditis. Within the lymphocyte compartment, increased proportions of CD8 + T exhausted cells and CD8 + T proliferative cells were observed in the irAE group. The upregulated differentially expressed genes in myeloid cells in the irAE group were enriched in pro-inflammatory pathways, consistent with the observed metabolic shift from oxidative phosphorylation to glycolysis. CXCL9 + fibroblasts, characterized by the production of multiple pro-inflammatory cytokines and enriched in the JAK-STAT and TNFα signaling pathways, were predominantly found in the irAE group. Venous endothelial cells specifically expressing atypical chemokine receptor-1 (ACKR1) interacted with myeloid cells and CXCL9 + fibroblasts through the CXCL signaling pathway, facilitating chemokine transcytosis and leukocyte recruitment. Analysis of murine scRNA-seq data further supported these findings, revealing that exhausted CD8 + T cells and pro-inflammatory fibroblasts were uniquely enriched in ICI-related myocarditis, reflecting its distinct inflammatory microenvironment.

CONCLUSIONS

We elucidated the unique inflammatory microenvironment of immune-related myocarditis at the single-cell level. Our work revealed key cell subpopulations that were significantly implicated in inflammation, thus offering potential therapeutic targets.

FGFR2-RUNX2 activation: An unexplored therapeutic pathway in luminal breast cancer related to tumor progression

Overcoming luminal breast cancer (BrCa) progression remains a critical challenge for improved overall patient survival. RUNX2 has emerged as a protein related to aggressiveness in triple-negative BrCa, however its role in luminal tumors remains elusive. We have previously shown that active FGFR2 (FGFR2-CA) contributes to increased tumor growth and that RUNX2 expression was high in hormone-independent mouse mammary carcinomas. To elucidate the interaction between FGFR2 and RUNX2 in human BrCa, we investigated their roles in tumor progression and treatment responsiveness. Increased FGFR2 activity resulted in higher RUNX2 expression, cell proliferation, and metastasis. In contrast, silencing FGFR2 reduced these parameters. Overexpression of RUNX2 in FGFR2-silenced cells rescued the inhibitory effects, promoting a more aggressive phenotype, even if compared with the wt RUNX2-transfected cells, which also had increased aggressiveness compared with naïve-transfected cells. RUNX2-overexpressing tumors were insensitive to endocrine- or FGFR inhibitor treatments. Notably, the CBFβ-RUNX complex inhibitor, AI-14-91, demonstrated great effectiveness in vitro. In a small cohort of luminal BrCa patients, nuclear RUNX2 expression was associated with tumor recurrence. Transcriptomic analysis strongly supported these data showing that patients with luminal carcinomas with high RUNX2 activity score have a worse progression-free interval than those with low RUNX2 activity. Our findings suggest a complex interplay between FGFR2 and RUNX2 in regulating tumor aggressiveness. This study underscores the significance of RUNX2 in luminal BrCa progression and posits RUNX2 as a promising therapeutic target and as a potential prognostic biomarker in luminal BrCa patients.

HDAC6 inhibition by ITF3756 modulates PD-L1 expression and monocyte phenotype: insights for a promising immune checkpoint blockade co-treatment therapy

Introduction

Tumor immunotherapy has revolutionized cancer treatment, particularly through the use of immune checkpoint inhibitors targeting the PD-L1/PD-1 axis. While PD-L1 expression on tumor cells is an established predictive biomarker for therapeutic response, emerging evidence highlights the importance of PD-L1 expression on myeloid cells, both in the periphery and within the tumor microenvironment (TME). This study explores the immunomodulatory effects of the selective HDAC6 inhibitor ITF3756 on monocytes and dendritic cells (DCs).

Methods

Monocytes were stimulated with the pro-inflammatory cytokine TNF-α and treated with ITF3756. PD-L1 and CD40 expression levels were assessed by flow cytometry. Transcriptomic and proteomic analyses were performed to characterize changes in gene and protein expression profiles. T cell proliferation was evaluated in co-culture assays. Additionally, the impact of ITF3756 was assessed in an in vivo murine model of colon cancer.

Results

ITF3756 effectively downregulated PD-L1 expression in TNF-α-activated monocytes and enhanced their costimulatory capacity by increasing CD40 expression. Transcriptomic and proteomic analyses revealed that ITF3756 counteracted TNF-α pathway activation and downregulated multiple inhibitory immune checkpoint molecules, promoting a less immunosuppressive phenotype. In co-culture assays, ITF3756-treated monocytes and DCs significantly enhanced T cell proliferation. In vivo, ITF3756 treatment led to reduced tumor growth in a colon cancer model.

Discussion

These findings demonstrate that selective HDAC6 inhibition by ITF3756 modulates myeloid cell functionality by diminishing inhibitory signals and promoting T cell activation. Thus, ITF3756 represents a promising immunomodulatory agent that could enhance the efficacy of immune checkpoint blockade in cancer immunotherapy.

Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4+ T cells in head and neck cancer

Tumor tertiary lymphoid structures (TLS), especially mature TLS (mTLS), have been associated with better prognosis and improved responses to immune checkpoint blockade (ICB), but the underlying mechanisms remain incompletely understood. Here, by performing single-cell RNA, antigen receptor sequencing and spatial transcriptomics on tumor tissue from head and neck squamous cell carcinoma (HNSCC) patients with different statuses of TLS, we observe that mTLS are enriched with stem-like T cells, and B cells at various maturation stages. Notably, progenitor exhausted CD4+ T cells, with features resembling follicular helper T cells, support these responses, by activating B cells to produce plasma cells in the germinal center, and interacting with DC-LAMP+ dendritic cells to support CD8+ T cell activation. Conversely, non-mTLS tumors do not promote local anti-tumor immunity which is abundant of immunosuppressive cells or a lack of stem-like B and T cells. Furthermore, patients with mTLS manifest improved overall survival and response to ICB compared to those with non-mTLS. Overall, our study provides insights into mechanisms underlying mTLS-mediated intra-tumoral immunity events against cancer.

EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer

Inhibition of the epidermal growth factor receptor (EGFR) shows clinical benefit in metastatic colorectal cancer (CRC) patients, but KRAS-mutations are known to confer resistance. However, recent reports highlight EGFR as a crucial target to be co-inhibited with RAS inhibitors for effective treatment of KRAS mutant CRC. Here, we investigated the tumor cell-intrinsic contribution of EGFR in KRASG12D tumors by establishing murine CRC organoids with key CRC mutations (KRAS, APC, TP53) and inducible EGFR deletion. Metabolomic, transcriptomic, and scRNA-analyses revealed that EGFR deletion in KRAS-mutant organoids reduced their phenotypic heterogeneity and activated a distinct cancer-stem-cell/WNT signature associated with reduced cell size and downregulation of major signaling cascades like MAPK, PI3K, and ErbB. This was accompanied by metabolic rewiring with a decrease in glycolytic routing and increased anaplerotic glutaminolysis. Mechanistically, following EGFR loss, Smoc2 was identified as a key upregulated target mediating these phenotypes that could be rescued upon additional Smoc2 deletion. Validation in patient-datasets revealed that the identified signature is associated with better overall survival of RAS mutant CRC patients possibly allowing to predict therapy responses in patients.

Fermented chrysanthemum stem as a source of natural phenolic compounds to alleviate tomato bacterial wilt disease

Natural antimicrobial compounds (NACs) in the plant stem are crucial for replacing conventional synthetic pesticides in the control of soil-borne diseases, and microbial fermentation can enhance their concentration and bioactivity. In this study, the stems of 10 plant species were collected for fermentation by probiotic bacteria Bacillus amyloliquefaciens T-5 to identify the most effective plant resource for controlling tomato bacterial wilt disease and discover key NACs. Chrysanthemum stem was identified as an optimal fermentation substrate, as its water-soluble extracts (WSEs) significantly inhibited the growth of pathogenic Ralstonia solanacearum and effectively alleviated tomato wilt under greenhouse conditions. Key metabolites, primarily phenolic acids including 2-hydroxy-3-phenylpropanoic acid (PLA), 3-(4-hydroxyphenyl)-propionic acid (HPPA), and mandelic acid (MA), were determined by metabolomics, all of which significantly inhibited the growth of R. solanacearum at a concentration of 0.2 mM, with only HPPA effectively controlling tomato wilt. Thus, fermented chrysanthemum stem contains NACs that are effective against bacterial wilt, providing a green option for controlling soil-borne diseases.

Direct cell interactions potentially regulate transcriptional programmes that control the responses of high grade serous ovarian cancer patients to therapy

The tumour microenvironment is composed of a complex cellular network involving cancer, stromal and immune cells in dynamic interactions. A large proportion of this network relies on direct physical interactions between cells, which may impact patient responses to clinical therapy. Doublets in scRNA-seq are usually excluded from analysis. However, they may represent directly interacting cells. To decipher the physical interaction landscape in relation to clinical prognosis, we inferred a physical cell-cell interaction (PCI) network from 'biological' doublets in a scRNA-seq dataset of approximately 18,000 cells, obtained from 7 treatment-naive ovarian cancer patients. Focusing on cancer-stromal PCIs, we uncovered molecular interaction networks and transcriptional landscapes that stratified patients in respect to their clinical responses to standard therapy. Good responders featured PCIs involving immune cells interacting with other cell types including cancer cells. Poor responders lacked immune cell interactions, but showed a high enrichment of cancer-stromal PCIs. To explore the molecular differences between cancer-stromal PCIs between responders and non-responders, we identified correlating gene signatures. We constructed ligand-receptor interaction networks and identified associated downstream pathways. The reconstruction of gene regulatory networks and trajectory analysis revealed distinct transcription factor (TF) clusters and gene modules that separated doublet cells by clinical outcomes. Our results indicate (i) that transcriptional changes resulting from PCIs predict the response of ovarian cancer patients to standard therapy, (ii) that immune reactivity of the host against the tumour enhances the efficacy of therapy, and (iii) that cancer-stromal cell interaction can have a dual effect either supporting or inhibiting therapy responses.

Benchmarking foundation cell models for post-perturbation RNA-seq prediction

Accurately predicting cellular responses to perturbations is essential for understanding cell behaviour in both healthy and diseased states. While perturbation data is ideal for building such predictive models, its availability is considerably lower than baseline (non-perturbed) cellular data. To address this limitation, several foundation cell models have been developed using large-scale single-cell gene expression data. These models are fine-tuned after pre-training for specific tasks, such as predicting post-perturbation gene expression profiles, and are considered state-of-the-art for these problems. However, proper benchmarking of these models remains an unsolved challenge. In this study, we benchmarked two recently published foundation models, scGPT and scFoundation, against baseline models. Surprisingly, we found that even the simplest baseline model-taking the mean of training examples-outperformed scGPT and scFoundation. Furthermore, basic machine learning models that incorporate biologically meaningful features outperformed scGPT by a large margin. Additionally, we identified that the current Perturb-Seq benchmark datasets exhibit low perturbation-specific variance, making them suboptimal for evaluating such models. Our results highlight important limitations in current benchmarking approaches and provide insights into more effectively evaluating post-perturbation gene expression prediction models.

CMV serostatus is associated with improved survival and delayed toxicity onset following anti-PD-1 checkpoint blockade

Cytomegalovirus (CMV) is a globally endemic latent herpes virus that profoundly impacts T cell immunity. We investigated the oncological consequences of CMV infection across 341 prospectively recruited patients receiving immune checkpoint blockade (ICB) for melanoma. CMV+ patients with metastatic melanoma (MM) have higher lymphocyte counts, reduced neutrophil to lymphocyte ratio and divergent CD8+ T cell gene expression. Combination anti-CTLA-4/anti-PD-1 ICB, but not single-agent anti-PD-1 ICB, induces cytotoxicity and CMV-associated gene expression in CD8+ T cells from CMV- patients. Correspondingly, overall survival was independent of CMV serostatus in combination anti-CTLA-4/anti-PD-1 ICB recipients (CMV+ hazard ratio for death: 1.02, P = 0.92), whereas CMV+ single-agent anti-PD-1 ICB recipients had improved overall survival (CMV+ hazard ratio for death: 0.37, P < 0.01), a finding also seen in CMV+ adjuvant single-agent anti-PD-1 ICB recipients (CMV+ hazard ratio for recurrence: 0.19, P = 0.03). We identify TBX21, encoding T-bet, as a transcriptional driver of CMV-associated CD8+ T cell gene expression, finding that TBX21 expression is predictive of overall survival (hazard ratio: 0.62, P = 0.026). CMV+ patients unexpectedly show reduced cumulative incidence of grade 3+ immune-related adverse events at 6 months (0.30 versus 0.52, P = 2.2 × 10-5), with lower incidence of colitis (P = 7.8 × 10-4) and pneumonitis (P = 0.028), an effect replicated in non-melanoma ICB recipients (n = 58, P = 0.044). Finally, we find reduced CMV seropositivity rates in patients with MM compared with UK Biobank controls (odds ratio: 0.52, P = 1.8 × 10-4), indicating CMV seropositivity may protect against MM. Specifically, patients with BRAF-mutated MM are less likely to be CMV+ (odds ratio = 2.2, P = 0.0054), while CMV- patients present 9 yr earlier with BRAF wild-type MM (P = 1.3 × 10-4). This work reveals an interaction between CMV infection, MM development according to BRAF status and response to ICB, while demonstrating CMV infection is protective against severe ICB immune-related adverse events, highlighting the potential importance of previous infection history and chronic immune activation in MM development and immunotherapy outcomes.

Identification of SURF4 and RALGAPA1 as promising therapeutic targets in glioblastoma and pan-cancer through integrative multi-omics, CRISPR-Cas9 screening and prognostic meta-analysis

Glioblastoma (GBM) is the most aggressive and malignant type of primary brain tumor, with a median survival time of less than two years and a uniformly poor prognosis, despite multimodal therapeutic approaches, which highlights an urgent need for novel therapeutic targets. In this study, by integrative multi-omics analysis from CPTAC database, DepMap database and seven independent GBM cohorts, four hub genes (CD44, SURF4, IGSF3 and RALGAPA1) were identified as essential genes regulated by cancer driver genes with robust prognostic value. GBM multi-omics data from public and in-house cohorts validated that CD44 and SURF4 might be synthetic lethal partners of loss-of-function tumor suppressor genes. Analysis for immune-related pathway activity revealed complex regulation relationships of the four hub genes in tumor microenvironment (TME). Further investigation on SURF4 in pathway activity, immune therapy response and drug sensitivity proposed that SURF4 emerged as a promising therapeutic target for GBM, even for pan-cancer. Pan-cancer multi-omics exploration suggested that RALGAPA1 may be a tumor suppressor gene. By screening the first-generation and second-generation DepMap database, four genes (CCDC106, GAL3ST1, GDI2 and HSF1) might be considered as synthetic targets after mutation of RALGAPA1 as a tumor suppressor gene.

KLRG1 re-defines a leukemic clone of CD8 effector T cells sensitive to PI3K inhibitor in T cell large granular lymphocytic leukemia

T cell large granular lymphocytic leukemia (T-LGLL) is a clonal lymphoproliferative disorder, originated from mature effector memory CD8+ T cells. It is a challenge to define the leukemic T cell clones due to the lack of definite markers. Here, we decipher the heterogeneity of CD8+ T cells using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and T cell receptor (TCR) profiling in T-LGLL patients. A CD8+ terminal effector subset is identified, marked by reduced KLRG1 expression. Remarkably, high fidelity of leukemic clonality was specially limited in KLRG1- large granular lymphocytes (LGLs), not seen in KLRG1+ LGLs in T-LGLL patients or in KLRG1- LGLs in healthy controls. KLRG1- leukemic LGLs show upregulated PI3K signaling with enhanced cytotoxicity and exhaustion, persisting after conventional treatment. In a pilot trial of linperlisib (a PI3Kδ inhibitor) for refractory cases, 7 of 8 participants quickly respond with satisfactory safety. This study is registered at ClinicalTrials.gov (NCT05676710).

Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution

Tendon ruptures in humans have often been studied during the chronic phase of injury, particularly in the context of rotator cuff disease. However, the early response to acute tendon ruptures remains less investigated. Quadriceps tendons, which require prompt surgical treatment, offer a model to investigate this early response. Therefore, this study aimed to explore the early cellular changes in ruptured compared to healthy human quadriceps tendons. Quadriceps tendon samples were collected from patients undergoing fracture repair (healthy) or tendon repair surgery (collected 7-8 days post-injury). Nuclei were isolated for single-nucleus RNA sequencing, and comprehensive transcriptomic analysis was conducted. The transcriptomes of 12,808 nuclei (7268 from healthy and 5540 from ruptured quadriceps tendons) were profiled, revealing 12 major cell types and several cell subtypes and states. Rupture samples showed increased expression of genes related to extracellular matrix organisation and cell cycle signalling, and a decrease in expression of genes in lipid metabolism pathways. These changes were predominantly driven by gene expression changes in the fibroblast, vascular endothelial cell (VEC), mural cell, and macrophage populations: fibroblasts shift to an activated phenotype upon rupture and there is an increase in the proportion of capillary and dividing VECs. A diverse immune environment was observed, with a shift from homeostatic to activated macrophages following rupture. Cell-cell interactions increased in number and diversity in rupture, and primarily involved fibroblast and VEC populations. Collectively, this transcriptomic analysis suggests that fibroblasts and endothelial cells are key orchestrators of the early injury response within ruptured quadriceps tendon. KEY POINTS: Tendon ruptures in humans have regularly been studied during the chronic phase of injury, but less is known about the early injury response after acute tendon ruptures. This study explored the early cellular changes in ruptured compared to healthy human quadriceps tendons at single-cell resolution. Fibroblasts and endothelial cells seem to be the key orchestrators of the early injury response within ruptured quadriceps tendon. Therefore, these cell types are obvious targets for interventions to enhance tendon healing. Overall, this study highlights that the development of more effective therapeutic options for tendon injury requires better understanding of the cellular, extracellular, and mechanical landscape of tendon tissue.

SMAD4 and KRAS Status Shapes Cancer Cell-Stromal Cross-Talk and Therapeutic Response in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) contains an extensive stroma that modulates response to therapy, contributing to the dismal prognosis associated with this cancer. Evidence suggests that PDAC stromal composition is shaped by mutations within malignant cells, but most previous work has focused on preclinical models driven by KrasG12D and mutant Trp53. Elucidation of the contribution of additional known oncogenic drivers, including KrasG12V mutation and Smad4 loss, is needed to increase the understanding of malignant cell-stromal cell cross-talk in PDAC. In this study, we used single-cell RNA sequencing to analyze the cellular landscape of Trp53-mutant mouse models driven by KrasG12D or KrasG12V, in which Smad4 was wild type or deleted. KrasG12DSmad4-deleted PDAC developed a fibro-inflammatory rich stroma with increased malignant JAK/STAT cell signaling and enhanced therapeutic response to JAK/STAT inhibition. SMAD4 loss in KrasG12V PDAC differently altered the tumor microenvironment compared with KrasG12D PDAC, and the malignant compartment lacked JAK/STAT signaling dependency. Thus, malignant cell genotype affects cancer cell and stromal cell phenotypes in PDAC, directly affecting therapeutic efficacy. Significance: SMAD4 loss differentially impacts malignant cell-stromal cell signaling and treatment sensitivity of pancreatic tumors driven by KRASG12D or KRASG12V, highlighting the importance of understanding genotype-phenotype relationships for precision therapy.

IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases

Multi-omic and multimodal datasets with detailed clinical annotations offer significant potential to advance our understanding of inflammatory bowel diseases (IBD), refine diagnostics, and enable personalized therapeutic strategies. In this multi-cohort study, we performed an extensive multi-omic and multimodal analysis of 1,002 clinically annotated patients with IBD and non-IBD controls, incorporating whole-exome and RNA sequencing of normal and inflamed gut tissues, serum proteomics, and histopathological assessments from images of H&E-stained tissue sections. Transcriptomic profiles of normal and inflamed tissues revealed distinct site-specific inflammatory signatures in Crohn's disease (CD) and ulcerative colitis (UC). Leveraging serum proteomics, we developed an inflammatory protein severity signature that reflects underlying intestinal molecular inflammation. Furthermore, foundation model-based deep learning accurately predicted histologic disease activity scores from images of H&E-stained intestinal tissue sections, offering a robust tool for clinical evaluation. Our integrative analysis highlights the potential of combining multi-omics and advanced computational approaches to improve our understanding and management of IBD.

Context-specific eQTLs provide deeper insight into causal genes underlying shared genetic architecture of COVID-19 and idiopathic pulmonary fibrosis

Most genetic variants identified through genome-wide association studies (GWASs) are suspected to be regulatory in nature, but only a small fraction colocalize with expression quantitative trait loci (eQTLs, variants associated with expression of a gene). Therefore, it is hypothesized but largely untested that integration of disease GWAS with context-specific eQTLs will reveal the underlying genes driving disease associations. We used colocalization and transcriptomic analyses to identify shared genetic variants and likely causal genes associated with critically ill COVID-19 and idiopathic pulmonary fibrosis. We first identified five genome-wide significant variants associated with both diseases. Four of the variants did not demonstrate clear colocalization between GWAS and healthy lung eQTL signals. Instead, two of the four variants colocalized only in cell type- and disease-specific eQTL datasets. These analyses pointed to higher ATP11A expression from the C allele of rs12585036, in monocytes and in lung tissue from primarily smokers, which increased risk of idiopathic pulmonary fibrosis (IPF) and decreased risk of critically ill COVID-19. We also found lower DPP9 expression (and higher methylation at a specific CpG) from the G allele of rs12610495, acting in fibroblasts and in IPF lungs, and increased risk of IPF and critically ill COVID-19. We further found differential expression of the identified causal genes in diseased lungs when compared to non-diseased lungs, specifically in epithelial and immune cell types. These findings highlight the power of integrating GWASs, context-specific eQTLs, and transcriptomics of diseased tissue to harness human genetic variation to identify causal genes and where they function during multiple diseases.

HuTAge: a comprehensive human tissue- and cell-specific ageing signature atlas

Summary

Ageing is a complex process that involves interorgan and intercellular interactions. To obtain a clear understanding of ageing, cross-tissue single-cell data resources are required. However, a complete resource for humans is not available. To bridge this gap, we developed HuTAge, a comprehensive resource that integrates cross-tissue age-related information from The Genotype-Tissue Expression project with cross-tissue single-cell information from Tabula Sapiens to provide human tissue- and cell-specific ageing molecular information.

Availability and implementation

HuTAge is implemented within an R Shiny application and can be freely accessed at https://igcore.cloud/GerOmics/HuTAge/home. The source code is available at https://github.com/matsui-lab/HuTAge.

Quantitative characterization of cell niches in spatially resolved omics data

Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass' scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.

Evolutionary fingerprints of epithelial-to-mesenchymal transition

Mesenchymal plasticity has been extensively described in advanced epithelial cancers; however, its functional role in malignant progression is controversial1-5. The function of epithelial-to-mesenchymal transition (EMT) and cell plasticity in tumour heterogeneity and clonal evolution is poorly understood. Here we clarify the contribution of EMT to malignant progression in pancreatic cancer. We used somatic mosaic genome engineering technologies to trace and ablate malignant mesenchymal lineages along the EMT continuum. The experimental evidence clarifies the essential contribution of mesenchymal lineages to pancreatic cancer evolution. Spatial genomic analysis, single-cell transcriptomic and epigenomic profiling of EMT clarifies its contribution to the emergence of genomic instability, including events of chromothripsis. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross-species analysis of pancreatic and other human solid tumours. Mechanistically, we identified that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, in turn resulting in delayed mitosis and catastrophic cell division. Thus, EMT favours the emergence of genomic-unstable, highly fit tumour cells, which strongly supports the concept of cell-state-restricted patterns of evolution, whereby cancer cell speciation is propagated to progeny within restricted functional compartments. Restraining the evolutionary routes through ablation of clones capable of mesenchymal plasticity, and extinction of the derived lineages, halts the malignant potential of one of the most aggressive forms of human cancer.

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.

Natural genetic variation in wild-derived mice controls host survival and transcriptional responses during endotoxic shock

Innate immune cells sense microbial danger signals, resulting in dynamic transcriptional reprogramming and rapid inflammatory responses. If not properly regulated, such responses can be detrimental to the host, as is seen in septic shock. A better understanding of the genetic regulation of responses during endotoxemia could provide potential therapeutic insights. However, the majority of animal model studies have been performed using classic inbred laboratory strains of mice, capturing limited genetic diversity. Here, we compared classic inbred C57BL/6 (B6) mice with wild-derived and genetically divergent PWD/PhJ (PWD) mice using in vivo and in vitro models of endotoxemia. Compared with B6 mice, PWD mice were markedly resistant to bacterial lipopolysaccharide (LPS)-induced endotoxic shock. Using LPS stimulation of bone marrow derived dendritic cells (BMDC) and RNA sequencing, we demonstrate that B6 and PWD BMDCs exhibit partially overlapping yet highly divergent transcriptional responses, with B6 skewed toward stereotypical proinflammatory pathway activation, and PWD engaging regulatory or developmental pathways. To dissect genetic regulation of inflammatory responses by allelic variants, we used BMDCs from a sub-consomic strain carrying a ∼50 Mb PWD-derived portion of chromosome 11 on the B6 background. This identified a subset of cis-regulated and a large number of trans-regulated genes. Bioinformatic analyses identified candidate trans regulators encoded in the chromosome 11 locus as transcription factors Irf1, Ncor1, and Srebf1. Our results demonstrate that natural genetic variation controls host survival and transcriptional reprogramming during endotoxemia, suggesting possibilities for prediction of sepsis risk and/or personalized therapeutic interventions.

Intercellular signaling reinforces single-cell level phenotypic transitions and facilitates robust re-equilibrium of heterogeneous cancer cell populations

Background

Cancer cells within tumors exhibit a wide range of phenotypic states driven by non-genetic mechanisms in addition to extensively studied genetic alterations. Conversions among cancer cell states can result in intratumoral heterogeneity which contributes to metastasis and development of drug resistance. However, mechanisms underlying the initiation and/or maintenance of such phenotypic plasticity are poorly understood. In particular, the role of intercellular communications in phenotypic plasticity remains elusive.

Methods

In this study, we employ a multiscale inference-based approach using single-cell RNA sequencing (scRNA-seq) data to explore how intercellular interactions influence phenotypic dynamics of cancer cells, particularly cancers undergoing epithelial-mesenchymal transition. In addition, we use mathematical models based on our data-driven findings to interrogate the roles of intercellular communications at the cell populations from the viewpoint of dynamical systems.

Results

Our inference approach reveals that signaling interactions between cancerous cells in small cell lung cancer (SCLC) result in the reinforcement of the phenotypic transition in single cells and the maintenance of population-level intratumoral heterogeneity. Additionally, we find a recurring signaling pattern across multiple types of cancer in which the mesenchymal-like subtypes utilize signals from other subtypes to support its new phenotype, further promoting the intratumoral heterogeneity. Our models show that inter-subtype communication both accelerates the development of heterogeneous tumor populations and confers robustness to their steady state phenotypic compositions.

Conclusions

Our work highlights the critical role of intercellular signaling in sustaining intratumoral heterogeneity, and our approach of computational analysis of scRNA-seq data can infer inter- and intra-cellular signaling networks in a holistic manner.

Not all controls are made equal: Definition of human kidney reference samples by single cell gene expression profiles

Identifying kidney disease mechanisms often requires comparing samples from disease states with healthy reference tissues. However, the effect of variations in sample procurement, storage and donor baseline characteristics of reference samples has thus far not been evaluated. Three distinct kidney reference sample types were evaluated for integrity and injury biomarkers and in their ability to define differentially expressed genes (DEGs) when compared to three different diabetic kidney disease (DKD) states. Unaffected parts of tumor nephrectomies (TN), pre-transplant living donor biopsies (LD), and percutaneous kidney research biopsies from healthy volunteers (HC) served as sources for reference tissue. Single cell gene expression profiles showed differences in the expression of injury or disease markers and the proportion of immune and proximal cell states. TN exhibited the highest expression of early stress response genes. A gene set associated with procurement effect in post-operative biopsies (LD and TN) was identified. An age-associated transcriptional signature was extracted from the reference data. Providing these tools to control for age and tissue procurement effects, immune-related pathways were found to be most enriched in DKD when compared to HC. Energy-related processes were enriched in DEGs from DKD versus LD. TN samples exhibited more underlying pathology than LD. The pathway analyses using the DEGs underscore the importance of accounting for appropriate confounding factors in differential expression analyses between disease and reference samples. Comparable controls are essential for appropriate molecular evaluation of pathologic tissues.

TRANSLATIONAL STATEMENT

Integrated single-cell data analysis of three reference sample types-needle biopsy from young healthy kidney tissue, pre-perfusion biopsy from transplant kidneys, and cancer-free tissue from tumor-nephrectomies-revealed distinct transcriptional profiles influenced by the biopsy procurement method and age. These differences impacted findings in diabetes-related kidney disease versus reference comparisons highlighting the need and providing the tools to account for these differences in interpreting analyses and identifying disease mechanisms.

Cell-type-specific roles of FOXP1 in the excitatory neuronal lineage during early neocortical murine development

Forkhead box protein P1 (FOXP1), a transcription factor enriched in the neocortex, is associated with autism spectrum disorders (ASDs) and FOXP1 syndrome. Emx1Cre/+;Foxp1fl/fl conditional deletion (Foxp1 conditional knockout [cKO]) in the mouse cortex leads to overall reduced cortex thickness, alterations in cortical lamination, and changes in the relative thickness of cortical layers. However, the developmental and cell-type-specific mechanisms underlying these changes remained unclear. We find that Foxp1 deletion results in accelerated pseudo-age during early neurogenesis, increased cell cycle exit during late neurogenesis, altered gene expression and chromatin accessibility, and selective migration deficits in a subset of upper-layer neurons. These data explain the postnatal differences observed in cortical layers and relative cortical thickness. We also highlight genes regulated by FOXP1 and their enrichment with high-confidence ASD or synaptic genes. Together, these results underscore a network of neurodevelopmental-disorder-related genes that may serve as potential modulatory targets for postnatal modification relevant to ASDs and FOXP1 syndrome.

Comparative analysis of transcriptomic profiles of mesenchymal stem cells at the onset of senescence and after exposure to acute exogenous oxidative stress

Cellular senescence can be triggered by a wide range of stress-inducing factors, including environmental and internal damaging events, such as oxidative stress. Moreover, stressed and senescent cells exhibit modifications in their transcriptional expression profile, but little is known regarding the common genes and pathways regulating these processes. Here, we analyzed the effects of long-term culture as well as exogenous acute oxidative stress on the transcriptional program of Wharton's jelly mesenchymal stem cells (WJ-MSCs). We demonstrate that, exposure to H2O2 compromised genomic stability and mitochondrial function in early passage WJ-MSCs, potentially initiating senescence to prevent cellular transformation. On the other hand, prolonged in vitro expansion of WJ-MSCs activated processes linked to integrins and extracellular matrix organization, possibly indicating the unfavorable consequences that senescence has on tissue integrity. Additionally, cells entering senescence and oxidative stressed young WJ-MSCs over-activated transcription factors related to permanent proliferative arrest and suppressed anti-senescence factors. Common differentially expressed genes in the late passage and H2O2-treated WJ-MSCs were implicated in DNA damage response and cell cycle arrest, which are known to trigger a senescent phenotype. Notably, the TP53INP1 gene emerged as a significantly upregulated gene in both late passage and H2O2-treated young WJ-MSCs, marking it as a potent senescence indicator. Silencing TP53INP1 mitigated the senescent phenotype, a role that appeared to be facilitated by autophagy regulation. Taken together, our results shed light on how transcriptomic changes govern MSCs' senescence program and identify key molecular drivers that could prove crucial for WJ-MSCs-based clinical applications.

CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data

Cell-cell communication is essential for tissue development, function and regeneration. The revolution of single-cell genomics technologies offers an unprecedented opportunity to uncover how cells communicate in vivo within their tissue niches and how disruption of these niches can lead to diseases and developmental abnormalities. CellPhoneDB is a bioinformatics toolkit designed to infer cell-cell communication by combining a curated repository of bona fide ligand-receptor interactions with methods to integrate these interactions with single-cell genomics data. Here we present a protocol for the latest version of CellPhoneDB (v5), offering several new features. First, the repository has been expanded by one-third with the addition of new interactions, including ~1,000 interactions mediated by nonpeptidic ligands such as steroidogenic hormones, neurotransmitters and small G-protein-coupled receptor (GPCR)-binding ligands. Second, we outline a new way of using the database that allows users to tailor queries to their experimental designs. Third, the update incorporates novel strategies to prioritize specific cell-cell interactions, leveraging information from other modalities such as tissue microenvironments derived from spatial transcriptomics technologies or transcription factor activities derived from a single-cell assay for transposase accessible chromatin assays. Finally, we describe the new CellPhoneDBViz module to interactively visualize and share results. Altogether, CellPhoneDB v5 enhances the precision of cell-cell communication inference, offering new insights into tissue biology in physiological microenvironments. This protocol typically takes ~15 min and requires basic knowledge of python.

Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP) complexes

For genome editing, the use of CRISPR ribonucleoprotein (RNP) complexes is well established and often the superior choice over plasmid-based or viral strategies. RNPs containing dCas9 fusion proteins, which enable the targeted manipulation of transcriptomes and epigenomes, remain significantly less accessible. Here, we describe the production, delivery, and optimization of second generation CRISPRa RNPs (dRNPs). We characterize the transcriptional and cellular consequences of dRNP treatments in a variety of human target cells and show that the uptake is very efficient. The targeted activation of genes demonstrates remarkable potency, even for genes that are strongly silenced, such as developmental master transcription factors. In contrast to DNA-based CRISPRa strategies, gene activation is immediate and characterized by a sharp temporal precision. We also show that dRNPs allow very high-target multiplexing, enabling undiminished gene activation of multiple genes simultaneously. Applying these insights, we find that intensive target multiplexing at single promoters synergistically elevates gene transcription. Finally, we demonstrate in human stem and differentiated cells that the preferable features of dRNPs allow to instruct and convert cell fates efficiently without the need for DNA delivery or viral vectors.

Spatial Transcriptomics Identifies Immune-Stromal Niches Associated with Cancer in Adult Dermatomyositis

Adult-onset dermatomyositis (DM) is an autoimmune inflammatory myopathy with distinct cutaneous manifestations and a strong malignancy association. Through comparative analysis with cutaneous lupus erythematosus (CLE), our integrated spatial and single-cell transcriptomics analysis revealed unique immune and stromal niches associated with DM subtypes. Unexpectedly, we found an association between cancer-associated DM skin lesions and the presence of dispersed immune infiltrates enriched with macrophages, CD8+ T cells, plasma cells, and B cells with preserved vascular architecture. In contrast, non-cancer associated DM skin exhibited dense myeloid cell infiltrates, including neutrophils, monocytes, and macrophages, with elevated expression of IL1B and CXCL10 localized near injured vascular endothelia. Cytokines produced by these myeloid infiltrates together with local tissue hypoxia triggered dramatic stromal remodeling, leading to loss of vascular-associated fibroblasts. In addition to the CXCL10+ myeloid signature, non-cancer-associated DM skin with pDC presence showed the emergence of specific cellular pairs: PD-L1-expressing mregDCs and activated Tregs expressing NFKB2 and TNF receptors. While both DM and CLE showed strong interferon signatures, DM uniquely displayed IFN-β expression. Together, our study provides the first comprehensive spatial mapping of immune and stromal cells in adult-onset DM.

Immune-featured stromal niches associate with response to neoadjuvant immunotherapy in oral squamous cell carcinoma

Tumor stromal cells (TSCs) play a crucial yet underexplored role in the tumor microenvironment (TME). This study uses single-cell sequencing and spatial transcriptomics on paired tumor specimens from 22 patients with oral squamous cell carcinoma (OSCC) enrolled in a randomized two-arm phase 2 trial, receiving neoadjuvant anti-PD-1 mono-immunotherapy or anti-PD-1 plus docetaxel-cisplatin-5-fluorouracil (TPF) immunochemotherapy. Single-cell analysis reveals increased TSCs within the TME of responders in immunochemotherapy. Notably, significant post-treatment upregulation of SELP+ high endothelial venules (HEVs) and APOD+ myofibroblastic cancer-associated fibroblasts (myCAFs), alongside a decline in STMN1+ capillary endothelial cells (cECs), is specific to the immunochemotherapy cohort. In contrast, MYF5+ muscle satellite cells (MSCs) are upregulated in non-responders to mono-immunotherapy. SELP+ HEVs and APOD+ myCAFs foster favorable immunomodulatory stromal niches for improved outcomes, while STMN1+ cECs and MYF5+ MSCs form immunosuppressive niches in tumor invasion regions, highlighting therapeutic targets. The trial was registered at ClinicalTrials.gov, and the registration number is NCT04649476.

Total body irradiation primes CD19-directed CAR T cells against large B-cell lymphoma

CD19-targeting chimeric antigen receptor T cells (CART19) have demonstrated significant effectiveness in treating relapsed or refractory large B-cell lymphoma (LBCL). However, they often fail to sustain durable remissions in more than half of all treated patients. Therefore, there is an urgent need to identify approaches to enhance CART19 efficacy. Here, we studied the impact of low-dose radiation on CART19 activity in vitro and find that radiation enhances the cytotoxicity of CART19 against LBCL by upregulating death receptors. Disrupting the FAS receptor diminishes this benefit, indicating that this pathway plays an important role in enhancing the cytotoxic effects of CAR T cells. To further validate these findings, we conducted in vivo studies using a lymphoma syngeneic mouse model delivering total body irradiation (TBI). We observed that delivering TBI at a single dose of 1Gy prior to CAR T cell infusion significantly improved CART19-mediated tumor elimination and increased overall survival rates. Importantly, we characterized several important effects of TBI, including enhanced lymphodepletion, improved T cell expansion and persistence, better intra-tumoral migration, and a more favorable, anti-tumor phenotypic composition of the T cells. In summary, for the first time, we have demonstrated preclinically that administering TBI before CART19 infusion significantly accelerates tumor elimination and improves overall survival. This approach holds promise for translation into clinical practice and serves as a valuable foundation for further research to enhance outcomes for patients receiving CART19 treatment.

IL-1 protects from fatal systemic candidiasis in mice by inhibiting oxidative phosphorylation and hypoxia

Invasive C. albicans infections result in high mortality rates. While IL-1 is important to combat C. albicans infections, the underlying mechanisms remain unclear. Using global and conditional Il1r1 knockouts in mice, here we show that IL-1R signaling in non-hematopoietic cells in the kidney and brain is crucial for a protective response. In the kidney, endothelial IL-1R contributes to fungal clearance independent of neutrophil recruitment, while IL-1R in hematopoietic cells is dispensable. IL-1R signaling indirectly recruits neutrophils and monocytes in the brain by regulating chemokines and adhesion molecules. Single-nucleus-RNA-sequencing data implicates excessive metabolic activity and oxidative phosphorylation across all cell types in the kidney of Il1r1-deficient mice within a few hours upon infection, with associated, localized hypoxia at infection foci. Lastly, we find that hypoxia promotes fungal growth and pathogenicity. In summary, our results show that IL-1R-signaling in non-hematopoietic cells is required to prevent fatal candidiasis by inhibiting a metabolic shift, including excessive oxidative phosphorylation and hypoxia.

CelEst: a unified gene regulatory network for estimating transcription factor activities in C. elegans

Transcription factors (TFs) play a pivotal role in orchestrating critical intricate patterns of gene regulation. Although gene expression is complex, differential expression of hundreds of genes is often due to regulation by just a handful of TFs. Despite extensive efforts to elucidate TF-target regulatory relationships in Caenorhabditis elegans, existing experimental datasets cover distinct subsets of TFs and leave data integration challenging. Here, I introduce CelEst, a unified gene regulatory network designed to estimate the activity of 487 distinct C. elegans TFs-∼58% of the total-from gene expression data. To integrate data from ChIP-seq, DNA-binding motifs, and eY1H screens, optimal processing of each data type was benchmarked against a set of TF perturbation RNA-seq experiments. Moreover, I showcase how leveraging TF motif conservation in target promoters across genomes of related species can distinguish highly informative interactions, a strategy which can be applied to many model organisms. Integrated analyses of data from commonly studied conditions including heat shock, bacterial infection, and sex differences validates CelEst's performance and highlights overlooked TFs that likely play major roles in coordinating the transcriptional response to these conditions. CelEst can infer TF activity on a standard laptop computer within minutes. Furthermore, an R Shiny app with a step-by-step guide is provided for the community to perform rapid analysis with minimal coding required. I anticipate that widespread adoption of CelEsT will significantly enhance the interpretive power of transcriptomic experiments, both present and retrospective, thereby advancing our understanding of gene regulation in C. elegans and beyond.

Systematic Identification of Mitochondrial Signatures in Alzheimer's Disease and Inflammatory Bowel Disease

Mitochondrial dysfunction is increasingly recognized as a shared feature of Alzheimer's disease (AD) and inflammatory bowel disease (IBD), linked through overlapping pathways of hypoxia and immune dysregulation. Our study integrated transcriptomic and genetic analyses to uncover mitochondria-related mechanisms underlying these diseases. By analyzing multiple AD and IBD datasets through differential expression gene (DEG) analyses, biological pathway enrichment, and co-expression module construction, we identified hypoxia-induced mitochondrial dysfunction as a central risk factor for both conditions. Key findings revealed several mitochondrial-related genes shared between AD and IBD, including BCL6, PFKFB3, NDUFS3, and COX5B, which serve as critical regulators bridging mitochondrial and immune pathways. Drug enrichment analyses using Drug Signatures Database (DsigDB) and the Connectivity Map (cMAP) identified promising therapeutic candidates, including decitabine, DMOG, and estradiol, targeting shared regulators such as BCL6, PFKFB3, MAFF, and TGFBI. These drugs demonstrated potential to modulate mitochondrial autophagy and oxidative phosphorylation (OXPHOS), pathways enriched in the constructed interaction network with BCL6 and PFKFB3 as central nodes. Mendelian randomization (MR) analysis further identified MAP1LC3A as significantly associated with increased risk for both AD and IBD, while NME1 emerged as strongly protective, suggesting their roles as therapeutic targets. Our findings underscore hypoxia-induced mitochondrial dysfunction as a unifying mechanism in AD and IBD, mediated by hypoxia-inducible factor-1α (HIF-1α). By identifying key mitochondria-associated genes and pathways, this study highlights innovative therapeutic targets and contributes to a deeper understanding of the gut-brain interplay in neurodegeneration and chronic inflammation. These insights pave the way for precision medicine strategies targeting mitochondrial dysfunction in AD and IBD.

Shaping early neural development by timed elevated tissue oxygen tension: Insights from multiomic analysis on human cerebral organoids

Oxygen plays a critical role in early neural development in brains, particularly before establishment of complete vasculature; however, it has seldom been investigated due to technical limitations. This study uses an in vitro human cerebral organoid model with multiomic analysis, integrating advanced microscopies and single-cell RNA sequencing, to monitor tissue oxygen tension during neural development. Results reveal a key period between weeks 4 and 6 with elevated intra-organoid oxygen tension, altered energy homeostasis, and rapid neurogenesis within the organoids. The timed oxygen tension elevation can be suppressed by hypoxia treatment or silencing of neuroglobin gene. This study provides insights into the role of oxygen in early neurogenesis from functional, genotypic, phenotypic, and proteomic aspects. These findings highlight the significance of the timed tissue oxygen tension elevation in neurogenesis and provide insights into the role of neuroglobin in neural development, with potential implications for understanding neurodegenerative diseases and therapeutic strategies.

Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis

BACKGROUND

Pulmonary fibrosis is a relentless and ultimately fatal lung disorder. Despite a wealth of research, the intricate molecular pathways that contribute to the onset of PF, especially the aspects related to epigenetic modifications and chromatin dynamics, continue to be elusive and not fully understood.

METHODS

Utilizing a bleomycin-induced pulmonary fibrosis model, we conducted a comprehensive analysis of the interplay between chromatin structure, chromatin accessibility, gene expression patterns, and cellular heterogeneity. Our chromatin structure analysis included 5 samples (2 control and 3 bleomycin-treated), while accessibility and expression analysis included 6 samples each (3 control and 3 bleomycin-treated).

RESULTS

We found that chromatin architecture, with its alterations in compartmentalization and accessibility, is positively correlated with genome-wide gene expression changes during fibrosis. The importance of immune system inflammation and extracellular matrix reorganization in fibrosis is underscored by these chromatin alterations. Transcription factors such as PU.1, AP-1, and IRF proteins, which are pivotal in immune regulation, are associated with an increased abundance of their motifs in accessible genomic regions and are correlated with highly expressed genes.

CONCLUSIONS

We identified 14 genes that demonstrated consistent changes in their expression, accessibility, and compartmentalization, suggesting their potential as promising targets for the development of treatments for lung fibrosis.

Thor: a platform for cell-level investigation of spatial transcriptomics and histology

Spatial transcriptomics integrates transcriptomics data with histological tissue images, offering deeper insights into cellular organization and molecular functions. However, existing computational platforms mainly focus on genomic analysis, leaving a gap in the seamless integration of genomic and image analysis. To address this, we introduce Thor, a comprehensive computational platform for multi-modal analysis of spatial transcriptomics and histological images. Thor utilizes an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptomes from spot-level data, effectively integrating cell morphology with spatial transcriptomics. The platform features 10 modules designed for cell-level genomic and image analysis. Additionally, we present Mjolnir, a web-based tool for interactive tissue analysis using vivid gigapixel images that display information on histology, gene expression, pathway enrichment, and immune response. Thor's accuracy was validated through simulations and ISH, MERFISH, Xenium, and Stereo-seq datasets. To demonstrate its versatility, we applied Thor for joint genomic-histology analysis across various datasets. In in-house heart failure patient samples, Thor identified a regenerative signature in heart failure, with protein presence confirmed in blood vessels through immunofluorescence staining. Thor also revealed the layered structure of the mouse olfactory bulb, performed unbiased screening of breast cancer hallmarks, elucidated the heterogeneity of immune responses, and annotated fibrotic regions in multiple heart failure zones using a semi-supervised approach. Furthermore, Thor imputed high-resolution spatial transcriptomics data in an in-house bladder cancer sample sequenced using Visium HD, uncovering stronger spatial patterns that align more closely with histology. Bridging the gap between genomic and image analysis in spatial biology, Thor offers a powerful tool for comprehensive cellular and molecular analysis.

Aging activates escape of the silent X chromosome in the female mouse hippocampus

Women live longer than men and exhibit less cognitive aging. The X chromosome contributes to sex differences, as females harbor an inactive X (Xi) and active X (Xa), in contrast to males with only an Xa. Thus, reactivation of silent Xi genes may contribute to sex differences. We use allele-specific, single-nucleus RNA sequencing to show that aging remodels transcription of the Xi and Xa across hippocampal cell types. Aging preferentially changed gene expression on the X's relative to autosomes. Select genes on the Xi underwent activation, with new escape across cells including in the dentate gyrus, critical to learning and memory. Expression of the Xi escapee Plp1, a myelin component, was increased in the aging hippocampus of female mice and parahippocampus of women. AAV-mediated Plp1 elevation in the dentate gyrus of aging male and female mice improved cognition. Understanding how the Xi may confer female advantage could lead to novel targets that counter brain aging and disease in both sexes.

Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points

Alzheimer's disease (AD) is the most common form of dementia and is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-β plaques and intracellular neurofibrillary tangles of phosphorylated tau, along with neuronal loss. Although neuronal loss is an AD hallmark, cell-cell communication between neuronal and non-neuronal cell populations maintains neuronal health and brain homeostasis. To study changes in cell-cell communication during disease progression, we performed snRNA-sequencing of the hippocampus from female 3xTg-AD and wild-type littermates at 6 and 12 months. We inferred differential cell-cell communication between 3xTg-AD and wild-type mice across time points and between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) of interest. We also assessed the downstream effects of altered glia-neuron communication using pseudobulk differential gene expression, functional enrichment, and gene regulatory analyses. We found that glia-neuron communication is increasingly dysregulated in 12-month 3xTg-AD mice. We also identified 23 AD-associated ligand-receptor pairs that are upregulated in the 12-month-old 3xTg-AD hippocampus. Our results suggest increased AD association of interactions originating from microglia. Signaling mediators were not significantly differentially expressed but showed altered gene regulation and transcription factor activity. Our findings indicate that altered glia-neuron communication is increasingly dysregulated and affects the gene regulatory mechanisms in neurons of 12-month-old 3xTg-AD mice.

Targeting YAP/TAZ-TEAD signaling as a therapeutic approach in head and neck squamous cell carcinoma

Genetic alterations in Hippo pathway and the consequent activation of YAP/TAZ-TEAD are frequently observed in HPV-negative head and neck squamous cell carcinoma (HNSCC) patients. These include loss-of-function mutation and/or copy number loss of FAT1, and amplification of YAP1 and WWTR1 (encoding TAZ), thus raising the possibility that HNSCC cells may be dependent on YAP/TAZ-TEAD-mediated transcriptional programs. In this regard, the recent development of small molecule TEAD inhibitors (smTEADi) provides an opportunity to therapeutically target Hippo pathway dysregulation in human malignancies. This prompted us to explore the potential benefit of pharmacologically targeting the YAP/TAZ-TEAD axis in this disease. Here, we provide the pre-clinical evidence for the antitumor activity of novel smTEADi, SW-682 in HPV-negative HNSCC. By the use of multiple complementary experimental approaches, including siRNA knockdown, expression of a genetically encoded TEAD inhibitor peptide (pTEADi), and SW-682, we revealed that disruption of YAP/TAZ-TEAD interaction suppresses YAP/TAZ-TEAD-dependent target gene transcription and growth of HNSCC tumors. HNSCC cells with genetic alterations in FAT1 were more sensitive to TEADi compared to FAT1-wild type cells. Mechanistically, TEADi suppressed cell cycle progression and promoted the expression of terminal differentiation gene programs, resulting in tumor growth inhibition. A HNSCC-specific TEADi target gene set was defined from RNA-seq data, which is highly expressed in HNSCC tissues and predicts poor prognosis of HPV-negative HNSCC patients. Our results underscore that YAP/TAZ-TEAD-mediated growth-promoting programs represent a vulnerability in HPV-negative HNSCC, thus providing a pre-clinical rationale for the future evaluation of YAP/TAZ-TEAD targeting strategies as a therapeutic approach for HPV-negative HNSCC patients.

Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness

Tissue remodeling and cell plasticity in the mammary gland are activated by multilineage communications; however, the dynamic signaling promoting breast cancer remains unclear. Here, by RNA sequencing of single cells and physically interacting cells (PICs) along mammary gland development and carcinogenesis, we uncovered that neutrophils appear transiently during early development and re-emerge in physical interaction with tumor cells in advanced carcinoma. Neutrophil heterogeneity analysis characterized transcriptional states linked to age and cancer stage. Integrating ligand-receptor and PIC sequencing analyses with various functional experiments unveiled a physical and secreted protumorigenic signaling niche. This approach revealed that neutrophils are recruited by tumor-activated macrophages and physically interact with tumor cells, increasing tumor cell proliferative and invasive properties, as well as endothelial proliferation and angiogenesis. The molecular program upregulated in neutrophil-PICs correlates with lower survival in advanced breast cancer patients. Our interaction-driven perspective highlights potential molecular targets and biomarkers for breast cancer treatment.

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs

Understanding the role of transcription and transcription factors (TFs) in cellular identity and disease, such as cancer, is essential. However, comprehensive data resources for cell line-specific TF-to-target gene annotations are currently limited. To address this, we employed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels. By integrating cellular transcriptome and TF binding data, we generated regulons for 40 common cell lines comprising both proximal and distal cell line-specific regulatory events. Through systematic benchmarking involving TF knockout experiments, we demonstrated performance on par with state-of-the-art methods, with our method being easily applicable to other cell types of interest. We present case studies using three cancer single-cell datasets to showcase the utility of these cell-type-specific regulons in exploring transcriptional dysregulation. In summary, this study provides a valuable pipeline and a resource for systematically exploring cell line-specific transcriptional regulations, emphasizing the utility of network analysis in deciphering disease mechanisms.

Pig jejunal single-cell RNA landscapes revealing breed-specific immunology differentiation at various domestication stages

Background

Domestication of wild boars into local and intensive pig breeds has driven adaptive genomic changes, resulting in significant phenotypic differences in intestinal immune function. The intestine relies on diverse immune cells, but their evolutionary changes during domestication remain poorly understood at single-cell resolution.

Methods

We performed single-cell RNA sequencing (scRNA-seq) and marker gene analysis on jejunal tissues from wild boars, a Chinese local breed (Jinhua), and an intensive breed (Duroc). Then, we developed an immune cell evaluation system that includes immune scoring, gene identification, and cell communication analysis. Additionally, we mapped domestication-related clustering relationships, highlighting changes in gene expression and immune function.

Results

We generated a single-cell atlas of jejunal tissues, analyzing 26,246 cells and identifying 11 distinct cell lineages, including epithelial and plasma cells, and discovered shared and unique patterns in intestinal nutrition and immunity across breeds. Immune cell evaluation analysis confirmed the conservation and heterogeneity of immune cells, manifested by highly conserved functions of immune cell subgroups, but wild boars possess stronger immune capabilities than domesticated breeds. We also discovered four patterns of domestication-related breed-specific genes related to metabolism, immune surveillance, and cytotoxic functions. Lastly, we identified a unique population of plasma cells with distinctive antibody production in Jinhua pig population.

Conclusions

Our findings provide valuable single-cell insights into the cellular heterogeneity and immune function evolution in the jejunum during pig at various domestication stages. The single-cell atlas also serves as a resource for comparative studies and supports breeding programs aimed at enhancing immune traits in pigs.