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Single-cell landscape of peripheral and tumor-infiltrating immune cells in HPV-negative HNSCC.
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, arising in diverse upper airway mucosal niches, is particularly aggressive, with poor 5-y survival and a limited response to immune…
FULLTEXT: Spatial transcriptome -
Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma.
Diffuse large B-cell Lymphoma (DLBCL) is the most prevalent subtype of non-Hodgkin's lymphoma for which current therapeutic strategies remain insufficient, in part owing to heterogeneity in tumor biology and the immune microenvironment. The…
FULLTEXT: Spatial transcriptome -
Whole transcriptome sequencing reveals differences in the pathogenesis of myelodysplastic syndromes and acute myeloid leukemia.
[OBJECTIVES] Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are closely related hematologic malignancies. However, the transcriptomic distinctions between them are not fully elucidated. This study aimed to identify transcri…
FULLTEXT: Spatial transcriptome -
DA-LUNGNET: a multi-stage deep framework with adaptive attention for early detection of subcentimeter pulmonary nodules.
Early and reliable detection of subcentimeter pulmonary nodules remains a major bottleneck in low-dose CT-based lung cancer screening due to high miss rates, vascular-adhesion-induced false positives, and insufficient multi-scale feature fu…
FULLTEXT: Spatial transcriptome -
Advancing the understanding of the immune escape in lung cancer immunotherapy: Global trends, collaborations, and future directions.
Immune escape mechanisms critically restrict the efficacy of immunotherapy in lung cancer (LC), with only 20%-30% of patients responding to checkpoint inhibitors. To systematically map global trends and identify emerging hotspots, this stud…
FULLTEXT: Spatial transcriptome -
A data fusion deep learning approach for accurate organelle-based classification of cancer cells.
[PURPOSE] Microscopy-based cancer cell classification traditionally relies on cell-based morphological features, while subcellular organelle organization remains underutilized. Existing machine learning methods often require manual preproce…
FULLTEXT: Spatial transcriptome -
Costs and benefits of whole-exome, whole-transcriptome sequencing versus 50-gene panels for genomic profiling in solid tumors.
[AIMS] The rapid development of therapies linked to molecular biomarkers has increased the importance of next-generation sequencing (NGS)-based tumor profiling to guide treatment decisions. Technology has enabled more comprehensive clinical…
FULLTEXT: Spatial transcriptome -
A system-level metastable model of cancer evolution: integrating replication stress, cell cycle deregulation and chromosomal instability.
[INTRODUCTION] Cancer cell proliferation occurs within the context of persistent genomic instability. In this review, we propose the RS-CCD-CIN axis as a systems-level framework in which replication stress (RS), cell cycle deregulation (CCD…
FULLTEXT: Spatial transcriptome -
Spatial confinement-enhanced CHA system based on tetrahedral DNA nanostructures for sensitive in situ mRNA analysis.
Sensitive and efficient detection of tumor-related mRNA is essential for the early diagnosis of cancer yet remains challenging due to low biomarker abundance and methodological limitations. Here, we developed a three-dimensional DNA nanomac…
FULLTEXT: Spatial transcriptome -
Integrated network pharmacology, metabolomics, and transcriptomics of Lianpuyin Jiawei decoction in Helicobacter pylori induced chronic gastritis.
[ETHNOPHARMACOLOGICAL RELEVANCE] Helicobacter pylori (H. pylori) infection represents the most significant pathogenetic factor for chronic gastritis (CG) and is also the most critical controllable risk factor for the prevention of gastric c…
FULLTEXT: Spatial transcriptome -
Targeting the NSUN5-circPPAP2A axis reverses immunosuppression and sensitizes renal cell carcinoma to anti-PD-1 therapy.
[BACKGROUND] The role of 5-methylcytosine (m5C) RNA modification in clear cell renal cell carcinoma (ccRCC) is recognized, yet its function and regulation on circular RNAs (circRNAs) remain uncharted. This study aims to identify key m5C reg…
FULLTEXT: Spatial transcriptome -
Protein 4.1R regulates CCDC26 and impacts myeloid leukemia progression.
Myeloid leukemia is a malignant hematologic disorder characterized by abnormal proliferation and differentiation arrest of myeloid progenitor cells, and its molecular mechanisms remain incompletely understood. Protein 4.1R (EPB41) is a cyto…
FULLTEXT: Spatial transcriptome -
AEG-1 3'UTR functions as a ceRNA to facilitate Helicobacter pylori-induced gastric cancer EMT by regulating the miR-375-3p/JAK2 axis.
Helicobacter pylori (H. pylori) infection is a major risk factor for gastric cancer (GC), but the molecular mechanisms driving H. pylori-induced gastric carcinogenesis remain incompletely understood. This study investigates the role of the …
FULLTEXT: Spatial transcriptome -
Integration of deep learning and radiomic features from multiplex immunohistochemistry images for reproducible Multi-Outcome prediction in a Multi-Center study of colorectal cancer.
[OBJECTIVE] To develop and validate a robust, multimodal machine learning framework integrating radiomic and deep learning features from multiplex immunohistochemistry (mIHC) images for comprehensive outcome prediction in colorectal cancer …
FULLTEXT: Spatial transcriptome -
Cross-species single-cell and spatial transcriptomic mapping reveals EFNA1-EPHA4-mediated stem-like epithelial-macrophage crosstalk driving colorectal cancer progression.
Colorectal cancer (CRC) typically follows the "normal-adenoma-carcinoma" (NAC) progression, with approximately 70-90% of cases driven by an adenomatous polyposis coli (APC) mutation-dependent pathway. The Apc-mutant (Min) mouse, valuable fo…
FULLTEXT: Spatial transcriptome -
The Yin and Yang of tertiary lymphoid structures in primary liver cancer.
Tertiary lymphoid structures (TLSs) have emerged as key regulators of anti-tumor immunity and biomarkers for immunotherapy response in liver cancer, including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), and combi…
FULLTEXT: Spatial transcriptome -
Fueling the fatal voyage: How metabolic plasticity empowers every step of cancer metastasis.
Metastasis is the primary cause of cancer mortality, a complex cascade driven by intertwined cellular adaptability and microenvironmental reprogramming. Although its mechanistic origins are multifactorial and context-dependent, metabolic pl…
FULLTEXT: Spatial transcriptome -
The CXCL12-CXCR4/CXCR7 axis as a therapeutic target in liver cancer: Enhancing immune evasion and the future of combination therapies.
Liver cancer remains one of the leading causes of cancer-related death worldwide, and its immunologically "cold" tumor microenvironment continues to undermine the efficacy of immunotherapy. Among the many stroma-derived factors, C-X-C motif…
FULLTEXT: Spatial transcriptome -
Multi-omic profiling reveals SMAD4 drives linoleic acid-arachidonic acid metabolism to mediate PDAC radiosensitivity via the SLC27A3/FADS2 axis.
[BACKGROUND] Pancreatic ductal adenocarcinoma (PDAC) is characterized by frequent SMAD4 inactivation and extensive lipid metabolic rewiring, yet the mechanistic crosstalk between these processes remains poorly elucidated. [METHODS] Multi-o…
FULLTEXT: Spatial transcriptome -
Integrated transcriptomic analysis reveals a lncRNA-miRNA-TF-mRNA regulatory network underlying quercetin's anti-hepatocellular carcinoma effects.
[BACKGROUND] Quercetin (QUR) exhibits multiple pharmacological activities against hepatocellular carcinoma (HCC). Competing endogenous RNA (ceRNA) networks and transcription factors (TFs) play critical roles in oncogenesis and cancer progre…
FULLTEXT: Spatial transcriptome