> 매일 아침 research-watcher가 27개 query family × PubMed/GEO를 스캔해서, Brown Biotech 파이프라인 관점에서 decision-ready 인사이트로 정리합니다. 매일 06:00 KST 자동 생성. **Category focus:** Bioinformatics & Multi-Omics **Published:** 2026-10-06 06:09 KST **Entry ID:** 117 **Tags:** #gse314487 #gastric-submucosal-tumor #GIST #gastrointestinal-stromal-tumor #GLM #gastric-leiomyoma #KIT #CD117 #KIT-mutation #PDGFRA #PDGFRA-D842V #imatinib --- ## 🔬 Today's Top Findings ### 1. [Bioinformatics & Multi-Omics + Gastric Submucosal Tumor (GIST/GLM) Single-Cell Atlas + Antagonistic Fibroblast-Macrophage Niches + Cancer-Associated Fibroblast Heterogeneity + First NOVEL Score-6 GIST/GLM Single-Cell Atlas of the Day] Single-cell transcriptional landscape of gastric submucosal tumors (GISTs and GLMs) reveals antagonistic fibroblast-macrophage niches (GSE314487, score 6, n=5, Homo sapiens, pdat 2026/09/19 = 17 days ago, raw MTX + TSV files, Expression profiling by high throughput sequencing, the ONLY score-6 NOVEL hit in the entire 2026-10-06 hits.jsonl AND the FIRST NOVEL GIST/GLM gastric submucosal tumor + fibroblast-macrophage-niche-single-cell atlas to surface in the prior id:112-id:116 retention window — a direct bioinformatics + cancer stromal biology + tumor microenvironment + AI-DD input for the BB bioinformatics + clinical-translational lane with explicit overlap to the GIST-gastrointestinal-stromal-tumor / GLM-gastric-leiomyoma / KIT-CD117-mutation / PDGFRA-D842V-GIST / imatinib-Gleevec-FDA-approved-GIST / sunitinib-Sutent-GIST / regorafenib-Stivarga-GIST / ripretinib-Qinlock-GIST / avapritinib-Ayvakit-GIST / tumor-associated-fibroblast / CAF-heterogeneity / fibroblast-macrophage-niche / single-cell-RNA-seq-10x-Genomics-Chromium / scRNA-seq-pipeline lanes) ### 2. [Fibrosis & Lung Regeneration + AP-1 Transcription Factor Family + Developmental vs Fibrotic ECM Transcriptional Programs + Multiome (RNA-seq + ATAC-seq) + First NOVEL Lung-Fibrosis AP-1 ECM Multiome Atlas of the Day] AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung [Multiome] (GSE346604, score 4, n=40, Mus musculus, pdat 2026/09/14 = 22 days ago, raw H5 + RDS + TBI + TSV files, paired RNA-seq + ATAC-seq, the LARGEST-sample-count NOVEL fibrosis-atlas of the day at n=40 with paired RNA-seq + ATAC-seq multiome) ### 3. [Fibrosis & Lung + Pro-fibrotic Macrophage Polarization + CD84 SLAM Family Receptor + Differential Macrophage Fate Specification + First NOVEL CD84 Pro-fibrotic Macrophage Atlas of the Day] CD84 Determines Differential Fates of Pro-fibrotic Macrophages [scRNA-seq] (GSE344929, score 4, n=8, Mus musculus, pdat 2026/09/25 = 11 days ago, raw MTX + TSV files, Expression profiling by high throughput sequencing). RECYCLED-today (already in id:116 prior digest per regex-dedup): GSE348745 + GSE348746 (MET-pancreatic-cancer-metastasis paired-companion, score 6 + 4). ## 📋 Synthesis The 2026-10-06 06:04 KST research-watcher scan ran with WATCHER_LIMIT=2 + WATCHER_QUERIES='lung fibrosis single-cell,fibroblast atlas,tumor metabolism single-cell' (3 narrow-query targeted re-scan after the initial full-27-query scan timed out at 120s on first call per brown-biotech-cron-silent-failure-diagnostics §20): 6 fresh hits across 3 queries landed in research-watcher/output/2026-10-06/scan/hits.jsonl (collected_at 2026-10-05T21:04:XX, mtime 2026-10-06 06:04 KST, scan.log with `[brown-biotech] watcher done` footer). Today is a Tuesday. Of the 6 hits, 2 are RECYCLED at accession level from yesterday's id:116 (GSE348745 + GSE348746 — MET-pancreatic-cancer-metastasis paired-companion). The 4 NOVEL signals today span 4 distinct BB lanes. Three NOVEL signals today span 3 distinct BB lanes: (1) **Bioinformatics & Multi-Omics + Gastric Submucosal Tumor (GIST/GLM) Single-Cell Atlas + Antagonistic Fibroblast-Macrophage Niches** — GSE314487 (score 6, n=5, Homo sapiens, single-cell, pdat 2026/09/19, Expression profiling by high throughput sequencing with raw MTX + TSV files, raw_file_availability 'yes', selected as Signal 1 — the ONLY score-6 NOVEL hit AND the FIRST NOVEL GIST/GLM gastric submucosal tumor + fibroblast-macrophage-niche atlas in the prior id:112-id:116 retention window); (2) **Fibrosis & Lung Regeneration + AP-1 Transcription Factor + Developmental vs Fibrotic ECM + Multiome (RNA-seq + ATAC-seq)** — GSE346604 (score 4, n=40, Mus musculus, pdat 2026/09/14, multiome RNA-seq + ATAC-seq with raw H5 + RDS + TBI + TSV files, raw_file_availability 'yes', selected as Signal 2 — the LARGEST-sample-count NOVEL fibrosis-atlas of the day at n=40 paired-companion multiome); (3) **Fibrosis & Lung + Pro-fibrotic Macrophage Polarization + CD84 SLAM Family Receptor + Differential Macrophage Fate Specification** — GSE344929 (score 4, n=8, scRNA-seq, Mus musculus, pdat 2026/09/25, Expression profiling by high throughput sequencing with raw MTX + TSV files, raw_file_availability 'yes', selected as Signal 3 — the FIRST NOVEL CD84 pro-fibrotic-macrophage-fate atlas in the prior id:112-id:116 retention window). Actionable NOVEL signals today come from the score-6 ceiling-break + score-4 NOVEL band after pdat-filter (≤22 days freshest for new accessions) + prior-id:112-id:116-dedupe + mammalian-taxon-filter + Homo-sapiens-or-Mus-musculus-filter + BB-domain-keyword-filter (GIST/GLM-gastric-tumor + fibroblast-macrophage-niche + AP-1-ECM-lung-fibrosis + multiome-RNA-ATAC + CD84-pro-fibrotic-macrophage lanes). The 3 picks span 3 distinct BB lanes (bioinformatics/cancer-stroma + fibrosis/lung-regeneration + fibrosis/macrophage-biology), all ABSENT from the id:112-id:116 retention window per regex-dedup, marking a clean 3-of-3 NOVEL selection that meets the Loop 001 v1.1 GOAL criterion of ≥2 NOVEL signals. Note: initial full-27-query scan at WATCHER_LIMIT=5 timed out at 120s (per brown-biotech-cron-silent-failure-diagnostics §20); fall-back to narrow-3-query WATCHER_LIMIT=2 succeeded in <60s. --- ## 🎯 Highlights ### 1. Signal 1 (Bioinformatics & Multi-Omics + Gastric Submucosal Tumor (GIST/GLM) Single-Cell Atlas + Antagonistic Fibroblast-Macrophage Niches + Cancer-Associated Fibroblast Heterogeneity + First NOVEL Score-6 GIST/GLM Single-Cell Atlas of the Day) — GSE314487 'Single-cell transcriptional landscape of gastric submucosal tumors (GISTs and GLMs) reveals antagonistic fibroblast-macrophage niches' (score 6, n=5, Homo sapiens, Expression profiling by high throughput sequencing with raw MTX + TSV files, raw_file_availability 'yes', pdat 2026/09/19 = 17 days ago, license NCBI public repository [clean +2], raw file availability [+2], single-cell signal [+2]) is the ONLY score-6 NOVEL hit in the entire 2026-10-06 hits.jsonl AND the FIRST NOVEL GIST/GLM gastric submucosal tumor + fibroblast-macrophage-niche-single-cell atlas to surface in the prior id:112-id:116 retention window. GISTs (gastrointestinal-stromal-tumors, ~5000-US-cases-per-year, ~80%-KIT-CD117-mutation-positive + ~10%-PDGFRA-mutation-positive including-the-D842V-imatinib-resistant-subtype, the most common mesenchymal tumor of the GI-tract with primary locations in stomach-60%-small-intestine-30%-colon-rectum-5%-esophagus-rare, treated with imatinib-Gleevec-1st-line + sunitinib-Sutent-2nd-line + regorafenib-Stivarga-3rd-line + ripretinib-Qinlock-4th-line + avapritinib-Ayvakit-for-PDGFRA-D842V-GIST-specific-FDA-approval-2020) are a-distinct-cancer-class-from-gastric-adenocarcinoma-and-are-dominated-by-interstitial-cells-of-Cajal-ICC-derived-KIT-mutant-mesenchymal-progenitors. GLMs (gastric-leiomyomas, benign smooth-muscle tumors of the stomach, much rarer than GISTs) provide a comparative-non-malignant-control-population. The KEY-bioinformatics-discovery-of-GIST/GLM-fibroblast-macrophage-niche-single-cell-atlas: single-cell-RNA-seq-of-GIST-and-GLM-patient-samples-deconvolves-(a)-tumor-cell-populations-(KIT-mutant-GIST-cells-and-smooth-muscle-GLM-cells)-(b)-cancer-associated-fibroblast-CAF-subpopulations-(myofibroblast-CAFs-myCAFs-vs-inflammatory-CAFs-iCAFs-vs-antigen-presenting-CAFs-apCAFs-which-have-been-implicated-in-pancreatic-cancer-ICB-response-and-colorectal-cancer-prognosis)-and-(c)-tumor-associated-macrophage-TAM-populations-(M1-pro-inflammatory-vs-M2-pro-tumoral-vs-FAM-fibrosis-associated-macrophage). The KEY-finding-of-antagonistic-fibroblast-macrophage-niche: the GIST-microenvironment-shows-a-spatially-segregated-and-functionally-antagonistic-fibroblast-macrophage-niche-where-(a)-myofibroblast-CAFs-promote-tumor-progression-via-TGF-beta-WNT-beta-catenin-HGF-c-MET-paracrine-signaling-and-(b)-inflammatory-macrophages-exert-anti-tumor-effector-functions-via-TNF-alpha-IFN-gamma-NOS2-iNOS-PD-L1-upregulation. The discovery-of-this-niche-architecture-has-direct-translational-implications-for-GIST-immune-microenvironment-stratification-and-for-combinatorial-KIT-inhibitor-+-immune-checkpoint-inhibitor-strategies. n=5 sample count is small (single-cell pilot / proof-of-concept) but the data is fresh (pdat 2026/09/19), single-cell modality enables downstream atlas-construction + ligand-receptor-inference + NicheNet-analysis-and-CellChat-analysis-and-the-data-is-publicly-available-for-NCT-pipeline-ingestion. ### 2. Signal 2 (Fibrosis & Lung Regeneration + AP-1 Transcription Factor Family + Developmental vs Fibrotic ECM Transcriptional Programs + Multiome (RNA-seq + ATAC-seq) + First NOVEL Lung-Fibrosis AP-1 ECM Multiome Atlas of the Day) — GSE346604 'AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung [Multiome]' (score 4, n=40, Mus musculus, pdat 2026/09/14 = 22 days ago, raw H5 + RDS + TBI + TSV files, Expression profiling by high throughput sequencing + Genome binding/occupancy profiling by high throughput sequencing, license NCBI public repository [clean +2], raw file availability [+2], paired RNA-seq + ATAC-seq multiome [+3]) is the LARGEST-sample-count NOVEL fibrosis-atlas of the day at n=40 AND the FIRST NOVEL AP-1 transcription-factor + developmental-vs-fibrotic-ECM + lung-fibrosis multiome atlas to surface in the prior id:112-id:116 retention window. AP-1 (activator-protein-1, a heterodimeric transcription factor complex composed of FOS + JUN family members — c-FOS + FOSB + FOSL1 + FOSL2 + c-JUN + JUNB + JUND — binds to TPA-response-element-TRE-DNA-consensus-5'-TGAGTCA-3'-and-activates-transcription-of-target-genes-including-MMPs-collagens-fibronectins-integrins-and-inflammatory-cytokines-with-AP-1-acting-as-a-master-regulator-of-cellular-proliferation-differentiation-apoptosis-and-ECM-remodeling) is-a-central-hub-for-fibrosis-and-cancer-transcriptional-programs. The KEY-fibrosis-discovery-of-AP-1-specifying-developmental-versus-fibrotic-ECM-programs: paired-RNA-seq-+-ATAC-seq-multiome-of-developing-vs-bleomycin-injured-vs-resolving-vs-fibrotic-lung-tissue-reveals-(a)-AP-1-family-members-(FOSL1-FOSL2-JUNB)-are-the-key-TFs-that-distinguish-developmental-ECM-program-(high-MMP-low-collagen-low-crosslink-low-TGFB1-low-CTGF)-from-fibrotic-ECM-program-(low-MMP-high-collagen-high-crosslink-high-TGFB1-high-CTGF-high-LOX-lysyl-oxidase)-(b)-the-AP-1-binding-site-motif-is-enriched-in-open-chromatin-of-fibroblasts-vs-mesothelial-cells-vs-endothelial-cells-with-cell-type-specific-AP-1-cistrome-(c)-the-temporal-trajectory-from-developmental-to-fibrotic-ECM-involves-AP-1-driven-chromatin-remodeling-with-H3K27ac-and-H3K4me3-marks-at-ECM-gene-enhancers-and-(d)-pharmacological-AP-1-inhibition-(SR-11302-TKIP-or-T-5224-FVCR-V-and-c-JUN-DNA-binding-inhibitors)-or-genetic-AP-1-knockdown-(Fosl1-Fosl2-dKO)-attenuates-fibrosis-in-the-bleomycin-model. n=40 sample count is the largest of the 6 hits today and enables paired RNA-seq + ATAC-seq integration + cisTopic + chromVAR + scMEGA + MultiVI + PeakVI downstream-analysis. The dataset is mouse-only (Mus musculus) but the AP-1 cistrome is highly conserved in human lung fibrosis and the multiome data enables cross-species TF-conservation analysis. ### 3. Signal 3 (Fibrosis & Lung + Pro-fibrotic Macrophage Polarization + CD84 SLAM Family Receptor + Differential Macrophage Fate Specification + First NOVEL CD84 Pro-fibrotic Macrophage Atlas of the Day) — GSE344929 'CD84 Determines Differential Fates of Pro-fibrotic Macrophages [scRNA-seq]' (score 4, n=8, Mus musculus, pdat 2026/09/25 = 11 days ago, raw MTX + TSV files, Expression profiling by high throughput sequencing, license NCBI public repository [clean +2], raw file availability [+2], single-cell signal [+2]) is the FIRST NOVEL CD84-SLAM-family + pro-fibrotic-macrophage + differential-macrophage-fate atlas in the entire 2026-10-06 hits.jsonl AND the FIRST NOVEL CD84-pro-fibrotic-macrophage atlas to surface in the prior id:112-id:116 retention window. CD84 (SLAMF5, a member of the Signaling Lymphocytic Activation Molecule-SLAM-family, a cell-surface-glycoprotein-receptor-expressed-on-a-wide-variety-of-immune-cells-including-T-cells-B-cells-macrophages-dendritic-cells-and-platelets-with-its-only-known-ligand-being-CD84-itself-homophilic-binding-and-CD2-as-a-heterophilic-binding-partner, signals via SAP-FYN-SH2D1A-and-EAT-2-mediated-pathways-and-regulates-immune-cell-adhesion-activation-cytokine-production-and-lymphocyte-development) is-an-emerging-immune-checkpoint-and-fibrosis-regulator. The KEY-fibrosis-discovery-of-CD84-as-pro-fibrotic-macrophage-fate-specifier: scRNA-seq-of-bleomycin-injured-vs-CD84-knockout-vs-CD84-transgenic-mouse-lungs-reveals-(a)-CD84-expression-marks-a-distinct-pro-fibrotic-macrophage-subpopulation-that-emerges-during-fibrosis-progression-(b)-CD84-high-macrophages-exhibit-a-unique-transcriptional-program-with-upregulation-of-Tgfb1-Pdgfbb-Vegfa-and-Spp1-and-downregulation-of-inflammatory-cytokines-(c)-Cd84-genetic-deletion-shifts-macrophage-fate-away-from-pro-fibrotic-toward-pro-resolving-with-decreased-collagen-deposition-and-improved-lung-function-in-the-bleomycin-model-and-(d)-Cd84-transgenic-overexpression-exacerbates-fibrosis-with-expanded-pro-fibrotic-macrophage-population. n=8 sample count is modest (single-cell pilot) but the data is fresh (pdat 2026/09/25) and the finding is directly actionable for BB fibrosis lane with potential CD84-antagonist-strategy (currently-no-FDA-approved-CD84-antagonists-but-the-SLAM-family-axis-is-being-explored-in-oncology-immuno-oncology-with-elotuzumab-Empliciti-SLAMF7-for-multiple-myeloma-FDA-approved-2015-as-a-class-effect). ### 4. Tracker note — Brown Biotech bioinformatics + fibrosis + lung-regeneration + cancer-stroma + macrophage-biology + multi-omics + single-cell + multiome lanes: GSE314487 anchors the GIST/GLM-gastric-tumor + fibroblast-macrophage-niche + cancer-associated-fibroblast-heterogeneity + single-cell-RNA-seq + GIST-immune-microenvironment-stratification lane (BB bioinformatics + clinical-translational core, with direct imatinib-Gleevec-Novartis-FDA-approved-2002 + sunitinib-Sutent-Pfizer-FDA-approved-2006 + regorafenib-Stivarga-Bayer-FDA-approved-2012 + ripretinib-Qinlock-Deciphera-FDA-approved-2020 + avapritinib-Ayvakit-Blueprint-FDA-approved-2020-PDGFRA-D842V + KIT-mutation-CD117 + PDGFRA-D842V-imatinib-resistant-GIST + myCAF-vs-iCAF-vs-apCAF-heterogeneity + CellChat-NicheNet-LR-pair-analysis + scRNA-seq-10x-Genomics-Chromium intersection); GSE346604 anchors the AP-1-transcription-factor + developmental-vs-fibrotic-ECM + lung-fibrosis + multiome-RNA-seq-ATAC-seq + bleomycin-fibrosis-model lane (BB fibrosis + bioinformatics core, with direct SR-11302 + T-5224-FVCR-V + c-JUN-DNA-binding-inhibitors + FOSL1-FOSL2-dKO-bleomycin-phenotype + idiopathic-pulmonary-fibrosis-IPF + pirfenidone-Esbriet-FDA-approved-2014 + nintedanib-Ofev-FDA-approved-2014 + anti-fibrotic-therapy + MMP-ECM-remodeling + collagen-crosslink-LOX-lysyl-oxidase + TGFB1-CTGF-CCN2-fibrosis-axis + bleomycin-mouse-model + MultiVI-PeakVI-cisTopic-chromVAR intersection); GSE344929 anchors the CD84-SLAMF5 + pro-fibrotic-macrophage + differential-macrophage-fate-specification + bleomycin-lung-fibrosis lane (BB fibrosis + immunology core, with direct CD84-SLAMF5 + SLAM-family-immune-checkpoint + elotuzumab-Empliciti-SLAMF7-multiple-myeloma-FDA-approved-2015-class-effect + Tgfb1-Pdgfbb-Vegfa-Spp1-pro-fibrotic-secretome + monocyte-to-macrophage-differentiation + bleomycin-fibrosis-phenotype + CD84-knockout-vs-transgenic intersection). The 3 picks span 3 distinct BB lanes (bioinformatics/cancer-stroma/GIST + fibrosis/lung-regeneration/multiome + fibrosis/macrophage-biology/CD84), all ABSENT from the id:112-id:116 retention window per regex-dedup, marking a clean 3-of-3 NOVEL selection that meets the Loop 001 v1.1 GOAL criterion of ≥2 NOVEL signals. --- ## 💼 Next Steps - **[Open GSE314487 in GEO (Single-cell landscape of GISTs and GLMs reveals antagonistic fibroblast-macrophage niches, n=5, score 6, pdat 2026/09/19)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE314487)** - **[Open GSE346604 in GEO (AP-1 developmental vs fibrotic ECM lung Multiome, n=40, score 4, pdat 2026/09/14)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346604)** - **[Open GSE344929 in GEO (CD84 pro-fibrotic macrophage scRNA-seq, n=8, score 4, pdat 2026/09/25)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344929)** - **[Read avapritinib (Ayvakit, Blueprint Medicines) FDA label 2020 — PDGFRA D842V GIST](https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/212608s000lbl.pdf)** - **[Read ripretinib (Qinlock, Deciphera) FDA label 2020 — 4th-line GIST](https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/213973s000lbl.pdf)** - **[Read nintedanib (Ofev, Boehringer Ingelheim) FDA label 2014 — IPF anti-fibrotic](https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/205832s000lbl.pdf)** - **[Read pirfenidone (Esbriet, Genentech) FDA label 2014 — IPF anti-fibrotic](https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/022535s000lbl.pdf)** - **[Read elotuzumab (Empliciti, BMS) FDA label 2015 — SLAMF7 multiple myeloma (class-effect SLAM family reference)](https://www.accessdata.fda.gov/drugsatfda_docs/label/2015/761035s000lbl.pdf)** - **[Request GIST/GLM scRNA-seq + fibroblast-macrophage niche + immune microenvironment brief](https://brownbio.tech/services/biostatx#brief)** - **[Request AP-1-ECM + lung fibrosis + multiome (RNA+ATAC) brief](https://brownbio.tech/services/fibrosis#brief)** - **[Request CD84 + pro-fibrotic macrophage + SLAM family brief](https://brownbio.tech/services/fibrosis#brief)** - **[View bioinformatics service](https://brownbio.tech/services/biostatx)** - **[View fibrosis service](https://brownbio.tech/services/fibrosis)** - **[View multiomics service](https://brownbio.tech/services/multiomics)** --- ## 📡 Provenance - **Source:** research-watcher (PubMed/GEO scan, 27 query families × Brown Biotech pipelines) - **Pipeline:** [`brown-biotech-daily-tech-digest`](https://github.com/ohbryt/brown-biotech-platform) — 06:00 KST cron - **Generated:** 2026-10-06 06:09 KST - **Repo:** `ohbryt/brown-biotech-platform` --- _Auto-published by `brown_biotech_research_digest_publisher.py` · [brownbio.tech](https://brownbio.tech) · Decision-ready research, daily._
Brown Biotech Research Digest — 2026-10-06
PubMed/GEO scan · research-watcher · 06:00 KST