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).

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 45

  Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

  tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson

• Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data.

  PMID 41758825 · PMC12948085 · PloS one · 2026 · 8 claims · 6 setups

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  AI-based predictive models built on unannotated scRNA-seq data (cell-by-gene expression matrices) can classify melanoma patients as ICI responders vs. non-responders

  cd45+ scrna-seq independent scrna-seq single-gene-level pathway-level

• TOPK Suppresses the CD8(+) T Cell Antitumor Immunity via Modulation of IRF5 Expression.

  PMID 41868885 · PMC13003159 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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  A TOPK+ subset of tumor-infiltrating CD8+ T cells exists in melanoma at higher frequency than in normal lymph nodes and shows suppressed cytotoxic/cytokine programs.

  tumor-infiltrating melanoma b16-f10 unspecified scrna-seq flow multiplex

• A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential.

  PMID 41781391 · PMC13077004 · Nature communications · 2026 · 8 claims · 7 setups

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  Prrx1 is a master regulator of dissemination that, beyond promoting invasion, represses proliferation (via Ccnd1/2, Cdkn2a/b/c) and activates a dormancy program (Gas6, Mme, Ogn)

  infiltrating metabric facs-sorted pymt immunohistochemistry bioinformatic rt-qpcr

• Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

  PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

  Has reproduction · 71

  A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

  luad tumor a549 single-cell infercnv pseudotime

• Host-derived interleukin-1α drives tumor immunosuppression by reprogramming tumor-associated myeloid cells.

  PMID 41547846 · PMC12910057 · NPJ breast cancer · 2026 · 8 claims · 8 setups

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  Deletion of host Il1α causes rejection/regression of transplanted breast tumors

  h605 pymt tumor-infiltrating two-week orthotopic flow single-cell

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

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  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• pmid-42032669

  PMID 42032669 · PMC13261971 · 7 claims · 8 setups

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  BCG training induces pan-anti-tumor activity across multiple mouse tumor models, mediated predominantly by tumor-associated macrophages (TAMs)

  llc tumor-infiltrating macrophage raw264.7 tumor flow antibody-mediated

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

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  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• Fibroblast-associated CTHRC1 as a key indicator of recurrence risk in prostate cancer.

  PMID 41832493 · PMC13101373 · World journal of surgical oncology · 2026 · 7 claims · 8 setups

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  Pathological T stage, N stage, Gleason score, and TP53 mutation are associated with higher PRAD recurrence risk

  tcga geo prad scrna-seq bulk single-cell cell-cell

• Lymphodepleting preconditioning impairs host antitumor immunity induced by adoptive T cell therapy in mouse models.

  PMID 41912536 · PMC13172322 · Nature communications · 2026 · 8 claims · 8 setups

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  ACT with TCR-transgenic (OTI) CD8+ T cells eradicates established B16F10-OTI tumors and expands host CD8+ T cells with tumor-reactive (PD-1+GzmB-/PD-1+GzmB+, Tpex/Tex) and tissue-resident phenotypes

  b16f10-oti draining ragko c57bl flow tumor antibody

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy

• Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

  PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 88

  APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

  tcga tcga-luad beas-2b rna-seq somatic gene

• PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

  PMID 41951588 · PMC13237225 · Nature communications · 2026 · 8 claims · 6 setups

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  Progenitor-exhausted CD8+ T cells (CD8-Tpex, TCF7+PDCD1+) are enriched in proximal lymph nodes and proliferate at a high rate after ICI treatment

  esophagogastric cancer surgically tcga scrna-seq scrna reanalysis

• Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

  PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups

  Has reproduction · 48

  A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

  tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating gene

• The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

  PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

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  EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

  ehf facs-sorted dss-induced lethal cd4+

• 5-HT reuptake blockade induces pyroptosis in BRAF(V600E)-mutated melanomas via remodeling histone serotonylation.

  PMID 41494533 · PMC12866116 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Has reproduction · 40

  High-throughput screening of 90 FDA-approved antidepressants identifies PH as an alternative therapeutic for BRAF V600E-mutated melanoma

  braf a375 gfp-tph1-overexpressing yumm1.7 high-throughput ic50 xenograft

• CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.

  PMID 41652996 · PMC12881829 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  Grouping genes into pathway-defined gene sets as Transformer input tokens (instead of using individual genes or discretized bins) mitigates the long-sequence problem and improves representation learning of scRNA-Seq gene expression profiles.

  tabula tumor-infiltrating scrna-seq

• Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

  PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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  Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

  hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna

• ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

  PMID 41896465 · PMC13043298 · Nature immunology · 2026 · 8 claims · 8 setups

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  ZFP148 is enriched in CD8+ T progenitor (T PRO) cells and its expression declines during differentiation into effector (T EFF) and exhausted (T EX) cells

  p14 splenic cd8+ b16-gp scrna-seq flow tcr