Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is critical to understanding the mechanism of action of TFs. With the development of high-throughput sequencing techniques, a large amount of TF-related data has accumulated, which can be used to identify their target genes. In this study, we developed TFTG (Transcription Factor and Target Genes) database ( http://tf.liclab.net/TFTG ), which aimed to provide a large number of available human TF-target gene resources by multiple strategies, besides performing a comprehensive functional and epigenetic annotations and regulatory analyses of TFs. We identified extensive available TF-target genes by collecting and processing TF-associated ChIP-seq datasets, perturbation RNA-seq datasets and motifs. We also obtained experimentally confirmed relationships between TF and target genes from available resources. Overall, the target genes of TFs were obtained through integrating the relevant data of various TFs as well as fourteen identification strategies. Meanwhile, TFTG was embedded with user-friendly search, analysis, browsing, downloading and visualization functions. TFTG is designed to be a convenient resource for exploring human TF-target gene regulations, which will be useful for most users in the TF and gene expression regulation research.

Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological processes, scRNA-seq datasets are accumulating rapidly, highlighting the urgent need for collecting and processing these data to support comprehensive and effective annotation and analysis. Here, we have developed a comprehensive S ingle- C ell transcriptome inte gration database fo r human and mouse (SCInter, https://bio.liclab.net/SCInter/index.php), which aims to provide a manually curated database that supports the provision of gene expression profiles across various cell types at the sample level. The current version of SCInter includes 115 integrated datasets and 1016 samples, covering nearly 150 tissues/cell lines. It contains 8016,646 cell markers in 457 identified cell types. SCInter enabled comprehensive analysis of cataloged single-cell data encompassing quality control (QC), clustering, cell markers, multi-method cell type automatic annotation, predicting cell differentiation trajectories and so on. At the same time, SCInter provided a user-friendly interface to query, browse, analyze and visualize each integrated dataset and single cell sample, along with comprehensive QC reports and processing results. It will facilitate the identification of cell type in different cell subpopulations and explore developmental trajectories, enhancing the study of cell heterogeneity in the fields of immunology and oncology.

Consensus molecular subtype 4 (CMS4) colorectal cancer (CRC) is associated with an aggressive clinical course and poor survival, yet the biological basis of heterogeneity within this subtype remains incompletely understood. DNA methylation is an epigenetic mechanism involved in transcriptional regulation, cellular differentiation, and colorectal tumorigenesis. Here, we integrated single-cell RNA sequencing (scRNA-seq), bulk data, and promoter DNA methylation data to characterize CMS4-associated cancer cell states and methylation-related features. Using the scAB algorithm, we integrated scRNA-seq with bulk CMS4 data and identified CMS4-related cells distributed across multiple patients. Single-cell analyses of cell–cell communication and transcriptional regulation revealed a CMS4-related cancer cell population characterized by macrophage migration inhibitory factor (MIF)-centered intercellular communication, enhanced caudal type homeobox 1 (CDX1) and Kruppel-like factor 5 (KLF5) regulon activity, and gene modules enriched in differentiation-related pathways. CytoTRACE analysis further stratified CMS4 cancer cells into poorly and well-differentiated states, yielding 802 differentially expressed genes (DEGs). Linking these differentiation-associated DEGs with bulk expression and promoter methylation data identified 218 methylation-associated DEGs showing significant inverse methylation expression correlations, suggesting a link between differentiation-related heterogeneity and promoter methylation. Univariable Cox regression followed by LASSO regression further prioritized eight genes for construction of the methylation and differentiation-related prognostic model (MeDiff-PM). MeDiff-PM consistently stratified overall survival in the TCGA CMS4 cohort and two independent validation cohorts, with cutoff-independent continuous Cox analyses further supporting its prognostic association across cohorts. And MeDiff-PM remained prognostically significant after adjustment for available clinical variables. High MeDiff-PM risk scores were associated with activation of P53, WNT, and ubiquitin-mediated proteolysis pathways and with consistent predicted drug response differences for compounds across three CMS4 cohorts. While individual in silico knockout analysis suggested links between MeDiff-PM genes and metallothionein-related and immune-associated transcriptional responses. Collectively, these findings indicate that methylation-associated differentiation features represent a molecular dimension of intra-CMS4 heterogeneity and provide a biologically informed framework for prognostic stratification within CMS4 CRC.

Breast cancer (BRCA) is one of the most common malignancies and a leading cause of cancer-related mortality in women. We integrated predicted compound targets of Fufang Banmao Capsules with BRCA-associated genes and prioritized candidates using LASSO regression, correlation analysis, and ROC analysis. Single-cell RNA sequencing analysis then characterized their expression patterns, endothelial heterogeneity, and inferred endothelial–macrophage communication. The four key genes CAV1, CES1, PPARG, and RUNX1T1 showed the highest AUCell scores in endothelial cells. Cell–cell communication analysis inferred MIF signaling involving CD74-containing receptor complexes between endothelial cells and macrophages. Virtual knockout analysis identified CD74 among the genes predicted to be perturbed following CAV1, CES1, or RUNX1T1 knockout in endothelial cells. Further analysis revealed heterogeneous CAV1 expression across endothelial subpopulations, with relatively higher expression in ACKR1-positive and metabolic endothelial cells. Pseudotime analysis characterized variation in CAV1 expression along inferred trajectories, while regulon analysis identified distinct regulatory programs across endothelial subpopulations. Together, these findings prioritize candidate genes linked to the predicted targets of Fufang Banmao Capsules and generate hypotheses concerning their cellular context in BRCA.

Double negative T cells (DNT cells) are a rare T cell population involved in immune regulation, inflammation, autoimmunity, transplantation, and tumor immunity. However, their low abundance and dispersed distribution across tissues have limited a systematic understanding of their cellular organization and transcriptional diversity. To address this problem, we developed an integrative single cell framework to reconstruct the mouse DNT cell landscape across tissues using multiple public single cell RNA sequencing datasets. Using transcriptomic criteria, we identified and integrated 7984 mouse RNA defined DNT cells. The integrated population was resolved into multiple transcriptionally distinct clusters. These clusters were organized into naive like, proinflammatory, cytotoxic, proliferative, and myeloid associated states, revealing that mouse RNA defined DNT cells constitute a highly heterogeneous yet structured transcriptional compartment. Integrated downstream analyses indicated transcriptional relationships among these subsets. Naive like populations showed inferred transcriptional relationships with inflammatory and cytotoxic programs, while virtual knockout and intercellular communication analyses identified distinct predicted regulatory and signaling features across states. To place these mouse DNT associated genes in a human disease context, selected genes were mapped to their corresponding human homologs and examined using TCGA pan cancer transcriptomic data. Together, these findings define a cross tissue transcriptional framework for mouse RNA defined DNT cells and provide a basis for further evaluating the conservation and relevance of these transcriptional programs in human DNT biology. More broadly, this study provides a generalizable integrative strategy for reconstructing and characterizing rare immune cell populations that are insufficiently represented in individual single cell datasets.

Colorectal cancer (CRC) is a highly aggressive cancer, with its treatment and prognosis particularly challenging due to metastasis. The immune response is involved in the whole process of CRC development, and immunotherapy has increasingly become a part of CRC patients’ treatment. However, comprehensive research on the immune microenvironment driving CRC metastasis remains limited. Given this limitation, we proposed a bioinformatics method to construct a metastasis–based immune prognostic model (MIPM) by integrating CRC single–cell RNA sequencing (scRNA–seq) and bulk data. Our study identified several MIPM genes significantly associated with CRC metastasis and progression. MIPM reliably predicted overall survival (OS) and tumor recurrence in CRC across eleven bulk validation datasets. Notably, MIPM could independently predict outcomes beyond traditional clinical factors such as age, sex, and stage. It showed high predictive accuracy in CRC patients treated with chemotherapy. Drug sensitivity and multifaceted immune analyses further underscored the importance of MIPM in therapeutic and immunotherapy response modulation. In conclusion, our findings have profound implications for the illustration of MIPM, which could serve as a new plausible prognostic marker for CRC patients and provide new insights for treatment strategies. The further evaluation and investigation of MIPM will enhance the prognosis and precision therapy of CRC patients.