Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.

  PMID 41710887 · PMC12909565 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  Higher EZH2 expression is associated with adverse clinical outcomes in bulk PCa/CRPC cohorts

  tcga-prad su2c gse264573 gse137829 bulk scrna-seq ligand-receptor

• DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

  PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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  Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

  tcga-luad tcga luad dendritic-cell bulk survival pan-cancer

• Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

  PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

  oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk

• Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

  PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

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  SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

  pdac bulk ssgsea differential

• pmid-42092126

  PMID 42092126 · PMC13234301 · 8 claims · 8 setups

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  IMIREG, a 14-regulon transcriptional signature, robustly predicts clinical benefit from ICB across 50 immunotherapy cohorts (52 treatment arms) spanning 16 cancer types with mean AUROC = 0.71

  imvigor210 matched gtex healthy bulk scrna-seq pathway

• Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

  PMID 41701761 · PMC12928580 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  Driver2Comm is a computational framework that identifies intrinsic-extrinsic (IE) pathways functionally connecting cancer cell driver genes with their associated CCC signatures in the TME using single-cell transcriptomics data.

  pdac genes tcga single-cell copy fisher's

• A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

  PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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  MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

  crc epithelial rcrc tcga-read scrna-seq copy gene

• PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer.

  PMID 41932868 · PMC13172513 · Cell death & disease · 2026 · 8 claims · 8 setups

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  PMEPA1 is a pivotal EMT regulator in BTC; its high expression correlates with adverse prognosis and distant metastasis

  btc tcga hucct1 scrna-seq cnmf bulk

• Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

  PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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  MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

  gastric epithelial stomach nod-scid single-cell cnv differential

• pmid-42074506

  PMID 42074506 · PMC13116210 · 7 claims · 8 setups

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  γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

  crc γδt epithelial c4_cxcl13 single-cell differential pseudotime

• An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

  PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

  nsclc epithelial macrophage caf scrna-seq copy gene-set

• pmid-42074110

  PMID 42074110 · PMC13115843 · 8 claims · 8 setups

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  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

  PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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  Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

  luad pan-cancer tumor scrna-seq spatial bulk

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

  PMID 41850291 · PMC13030954 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Metapipeline-DNA automates germline and somatic DNA sequencing analysis end-to-end, from raw reads through preprocessing, feature detection, QC, and visualization.

  pcawg giab pcawg-5 tumor-normal whole-genome germline somatic

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

  PMID 41840060 · PMC13125306 · Scientific reports · 2026 · 8 claims · 7 setups

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  IDC exhibits significantly higher CNV burden than DCIS, supporting progressive genomic instability during tumor evolution

  her2-positive epithelial malignant tcga-brca single-cell spatial infercnv

• Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

  PMID 41958675 · PMC13056825 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  scRNA-seq identifies five CRC tumor cell subtypes, with the C4 BCL2L1+ subtype predominantly enriched in liver metastases and showing enhanced proliferation, metabolic reprogramming, and anti-apoptotic activity

  crc epcs malignant tcga scrna-seq infercnv cytotrace

• Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

  PMID 41975179 · PMC13250061 · Nature communications · 2026 · 8 claims · 8 setups

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  Epithelial cells in mLNs and matched mLN+ primary tumors (mLN+PTs) show enhanced cancer stemness (higher CytoTRACE scores) compared to mLN-negative and normal samples.

  patient-matched mln epithelial tcga-luad scrna-seq spatial cytotrace