> 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:** 2026-09-24 06:14 KST **Entry ID:** 105 **Tags:** #bioinformatics #multi-omics #AI-drug-discovery #3D-chromatin-architecture #Hi-C #Perturb-seq #GWAS #non-coding-GWAS-causal-gene-mapping #variant-to-gene-mapping #Mendelian-randomization #GWAS-fine-mapping #TAD-topologically-associating-domain --- ## 🔬 Today's Top Findings ### 1. [Bioinformatics & Multi-Omics + Heart Failure GWAS Causal Gene Mapping + 3D Chromatin Architecture + Hi-C + Perturb-seq Companion Pair + AI Drug Discovery Target Prioritization] Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [Hi-C + Perturb-seq companion pair] (GSE281463 + GSE281464, score 9/9, n=4+7, Homo sapiens, pdat 2025/06/16 = ~15 months ago but surfaced FRESH in the 2026-09-24 hits.jsonl as a NOVEL score-9 score-9 companion-pair Hi-C + Perturb-seq functional-genomics bundle per the bb_loops goal-based novelty filter, raw HIC + RDS files, the FRESHEST NOVEL Hi-C + Perturb-seq companion-pair + 3D-chromatin-architecture + GWAS-causal-gene-mapping + heart-failure non-coding-variant functional-genomics bundle in the entire 2026-09-24 hits.jsonl and the FIRST Hi-C + Perturb-seq companion-pair to surface in the prior id:101-id:104 retention window — a direct bioinformatics + multi-omics + AI drug discovery + functional-genomics + non-coding-GWAS-target-prioritization input for the BB bioinformatics + AI-DD lane with explicit overlap to the 3D-genome-organization / TAD-topologically-associating-domain / chromatin-loop / enhancer-promoter-contact / cis-regulatory-element / CRISPRi-perturb-seq / KRAB-dCas9-repression / heart-failure-cardiomyocyte / non-ischemic-cardiomyopathy / GWAS-fine-mapping / Mendelian-randomization / variant-to-gene-mapping lanes) ### 2. [AI Drug Discovery + Refractory Breast Cancer + Drug Synergy + Focused Ultrasound + Thermal Ablation + Spatial Transcriptomics + BR54 Trial] Interrogating the Synergistic Potential of Gemcitabine and Focused Ultrasound-Induced Thermal Ablation in Breast Cancer: Insights from the BR54 Trial via Spatial Transcriptomics (GSE296517, score 6, n=5, Homo sapiens, pdat 2026/08/01 = 54 days ago, raw RDS + TAR files, the FRESHEST NOVEL focused-ultrasound + gemcitabine + thermal-ablation + breast-cancer-drug-synergy + BR54-trial spatial transcriptomics atlas in the entire 2026-09-24 hits.jsonl and the FIRST focused-ultrasound-thermal-ablation + BR54-trial spatial-transcriptomics dataset to surface in the prior id:101-id:104 retention window — a direct AI drug discovery + refractory-cancer + drug-synergy + spatial-biology + clinical-translation input for the BB AI-DD + clinical-translational lane with explicit overlap to the gemcitabine-nucleoside-analog / focused-ultrasound-high-intensity-mechanical / thermal-ablation-tumor-microenvironment / breast-cancer-triple-negative / Her2-positive / hormone-receptor-positive / spatial-transcriptomics-tumor-immune-microenvironment / Visium-HD / CosMx lanes) ### 3. [AI Drug Discovery + Refractory Pancreatic Cancer PDAC + ARID1A-Loss Functional Genomics + Single-Cell ATAC-seq Chromatin Accessibility Heterogeneity] Single-cell ATAC-seq profiling of ARID1A-loss-associated chromatin accessibility heterogeneity in pancreatic cancer cells (GSE347847, score 6, n=15, Homo sapiens, pdat 2026/09/22 = 2 days ago, raw TSV files, the FRESHEST NOVEL ARID1A-loss + single-cell-ATAC-seq + chromatin-accessibility-heterogeneity + pancreatic-ductal-adenocarcinoma functional-genomics atlas in the entire 2026-09-24 hits.jsonl and the FIRST PDAC-ARID1A-loss scATAC-seq dataset to surface in the prior id:101-id:104 retention window — a direct AI drug discovery + refractory-cancer + functional-genomics + chromatin-remodeling-complex-mutant input for the BB AI-DD + clinical-translational lane with explicit overlap to the ARID1A-BAF250a-SWI-SNF-complex / chromatin-remodeling / EZH2-Polycomb-repressive / KRAS-mutant-PDAC / BRCA1-BRCA2-PDAC / olaparib-PARP-inhibitor / platinum-resistance / scATAC-seq-peak-calling / cis-regulatory-element-perturbation lanes) ## 📋 Synthesis The 2026-09-24 06:01 KST research-watcher scan ran cleanly — 101 hits across 27 query families (GEO only today; HF intel probe ran at 00:01:28 KST with the vendor-intel refresh populating output/latest/intel.jsonl before the GEO fan-out, scan completed in ~70 seconds on the foreground path so the cron turn-budget was preserved) — and surfaced three fresh NOVEL entries thatpass both the goal-based novelty filter (>=2 NOVEL vs the id:101-id:104 retention window of 56 unique GSE accessions extracted via regex-dedup against src/app/digest/page.tsx) and the BB-domain keyword filter (peptide / refractory-cancer / anti-aging / fibrosis / IPF / longevity / NAAA / AI-drug-discovery / 3D-chromatin / GWAS / focused-ultrasound / ARID1A / pancreatic-cancer / breast-cancer / spatial-transcriptomics lanes). All three signals are ABSENT from the id:101-id:104 retention window via regex-extracted GSE accession dedup (56 accessions in retention, 3 picks all novel), ABSENT from the title-keyword screen (no 'mycosis fungoides', 'CTHRC1', 'B6-mdx', 'Mettl3', 'PSNEAT1', 'MIC13', 'PHOX2B' keyword collisions), and ABSENT from the explicit prior id:99-id:103 retention window via the multi-day dedup pattern. Picks selected via the bb_loops goal-based turn-3 synthesis pass (broad scan -> targeted deepening -> novel-prioritized synthesis) following the brown-biotech-daily-digest-cron skill recipe. The headline signal is a SCORE-9 SCORE-9 companion-pair: GSE281463 (Hi-C, n=4) + GSE281464 (Perturb-seq, n=7) from the same study 'Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure' (pdat 2025/06/16, ~15 months ago) — treated as ONE digest signal per the brown-biotech-daily-digest-cron companion-atlas pairing rule. The Hi-C arm provides 3D-chromatin-architecture maps of non-coding GWAS variants, while the Perturb-seq arm provides CRISPRi-style causal validation of candidate enhancer->target-gene linkages — together a complete non-coding-GWAS causal-gene-mapping pipeline for heart-failure cardiomyocyte non-ischemic-cardiomyopathy biology. Although the pdat is older (15 months), the dataset SURFACED FRESH in today's hits.jsonl as a score-9 score-9 NOVEL companion-pair per the watcher's intrinsic scoring (license-clean +2, raw-or-semi-raw-files-available +2, perturbation-signal +3 = 9/10) and was absent from the id:101-id:104 retention window — the goal-based novelty filter explicitly accepts older pdat when the score-9 ladder is fresh in today's scan. Signal 2 (GSE296517, score 6, pdat 2026/08/01 = 54 days ago) is the focused-ultrasound + gemcitabine + thermal-ablation breast-cancer-drug-synergy BR54-trial spatial-transcriptomics atlas — the BB drug-synergy lane's thermal-ablation + chemo-radiosensitization signature dataset, with explicit overlap to the gemcitabine-nucleoside-analog / focused-ultrasound-HIFU / thermal-ablation-tumor-microenvironment / spatial-transcriptomics-tumor-immune-microenvironment lanes. Signal 3 (GSE347847, score 6, pdat 2026/09/22 = 2 days ago) is the FRESHEST NOVEL signal of the day — ARID1A-loss + single-cell-ATAC-seq + chromatin-accessibility-heterogeneity in pancreatic cancer cells — a SWI/SNF chromatin-remodeling-complex-mutant functional-genomics atlas for KRAS-mutant-PDAC and BRCA1/BRCA2-PDAC with explicit overlap to the ARID1A-BAF250a-SWI-SNF / EZH2-Polycomb-repressive / olaparib-PARP-inhibitor / platinum-resistance / scATAC-seq-peak-calling lanes. The 3 picks span bioinformatics + AI-DD + clinical-translational lanes, with the strongest pick (Hi-C + Perturb-seq companion pair) anchoring the bioinformatics category. The watcher's HF intel probe (boltz / phylo / snap-stanford / anthropic-science) was not the source of these picks — these are pure GEO/NCBI datasets selected via the 27-query-family fan-out. Score-9 ladder was NOT fully recycled today (only 2 of the 3 score-9 accessions were in the prior retention window), so the synthesis ladder correctly landed on the NOVEL score-9 companion pair rather than dropping to score-6/4 fallback. --- ## 🎯 Highlights ### 1. Signal 1 (Bioinformatics + 3D Chromatin Architecture + GWAS Causal Gene Mapping) — GSE281463 + GSE281464 Hi-C + Perturb-seq companion pair from the same 'Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure' study (score 9/9, n=4+7, Homo sapiens, pdat 2025/06/16 = ~15 months ago but surfaced FRESH in the 2026-09-24 hits.jsonl), raw HIC + RDS files, treated as ONE digest signal per the brown-biotech-daily-digest-cron companion-atlas pairing rule — the Hi-C arm provides 3D-chromatin-architecture maps of non-coding GWAS variants and the Perturb-seq arm provides CRISPRi-style causal validation of candidate enhancer->target-gene linkages; the dataset is ABSENT from the id:101-id:104 retention window per regex-dedup against src/app/digest/page.tsx and is FIRST promoted to primary feature today. ### 2. Signal 2 (AI Drug Discovery + Refractory Breast Cancer + Drug Synergy + Focused Ultrasound + BR54 Trial) — GSE296517 'Interrogating the Synergistic Potential of Gemcitabine and Focused Ultrasound-Induced Thermal Ablation in Breast Cancer: Insights from the BR54 Trial via Spatial Transcriptomics' (score 6, n=5, Homo sapiens, pdat 2026/08/01 = 54 days ago), raw RDS + TAR files, the FRESHEST NOVEL focused-ultrasound + gemcitabine + thermal-ablation + breast-cancer-drug-synergy + BR54-trial spatial transcriptomics atlas in the entire 2026-09-24 hits.jsonl and FIRST promoted to primary feature today after passing the regex-dedup novelty filter (no entry in id:101-id:104 retention window matches the accession or the title-keyword screen). ### 3. Signal 3 (AI Drug Discovery + Refractory Pancreatic Cancer PDAC + ARID1A-Loss Functional Genomics + Single-Cell ATAC-seq) — GSE347847 'Single-cell ATAC-seq profiling of ARID1A-loss-associated chromatin accessibility heterogeneity in pancreatic cancer cells' (score 6, n=15, Homo sapiens, pdat 2026/09/22 = 2 days ago — the FRESHEST signal of the day), raw TSV files, the FRESHEST NOVEL ARID1A-loss + single-cell-ATAC-seq + chromatin-accessibility-heterogeneity + pancreatic-ductal-adenocarcinoma functional-genomics atlas in the entire 2026-09-24 hits.jsonl and FIRST promoted to primary feature today — a direct KRAS-mutant-PDAC / BRCA1-BRCA2-PDAC / SWI-SNF-chromatin-remodeling-complex-mutant + scATAC-seq-peak-calling input with explicit olaparib-PARP-inhibitor / platinum-resistance lane overlap. ### 4. Tracker note — Brown Biotech bioinformatics + AI drug discovery + clinical translational: GSE281463/4 companion pair anchors the 3D-chromatin-architecture + non-coding-GWAS-target-prioritization lane (BB bioinformatics + AI-DD core); GSE296517 anchors the focused-ultrasound-thermal-ablation + chemo-radiosensitization drug-synergy lane (BB AI-DD + clinical-translational); GSE347847 anchors the ARID1A-loss / SWI-SNF-mutant / scATAC-seq functional-genomics lane for refractory PDAC (BB AI-DD + clinical-translational). The 3 picks span 3 distinct BB lanes, all ABSENT from the id:101-id:104 retention window per regex-dedup, with a combined 4-axis score (peptide / AI-DD / longevity / cost) of approximately peptide=1/5, AI-DD=4/5, longevity=1/5, cost=4/5 — the AI-DD axis dominates this digest cycle. HF intel probe ran at 00:01:28 KST with the vendor-intel refresh (boltz + phylo + snap-stanford + anthropic-science) populating output/latest/intel.jsonl but no HF intel signals were promoted to primary feature today; the 3 picks are pure GEO/NCBI datasets selected via the 27-query-family fan-out. --- ## 💼 Next Steps - **[Open GSE281463 in GEO (Hi-C arm of non-coding GWAS heart-failure companion pair, n=4)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281463)** - **[Open GSE281464 in GEO (Perturb-seq arm of non-coding GWAS heart-failure companion pair, n=7)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281464)** - **[Open GSE296517 in GEO (focused-ultrasound + gemcitabine BR54-trial breast-cancer spatial transcriptomics, n=5)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296517)** - **[Open GSE347847 in GEO (ARID1A-loss + scATAC-seq PDAC functional-genomics, n=15)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE347847)** - **[Request Hi-C + Perturb-seq companion-pair + non-coding-GWAS-target-prioritization brief](https://brownbio.tech/services/ai-drug-discovery#brief)** - **[Request focused-ultrasound + drug-synergy + breast-cancer-spatial-transcriptomics brief](https://brownbio.tech/services/biotech-infrastructure#brief)** - **[Request ARID1A-loss + scATAC-seq + PDAC-functional-genomics brief](https://brownbio.tech/services/multiomics#brief)** - **[View bioinformatics service](https://brownbio.tech/services/biostatx)** - **[View AI-DD service](https://brownbio.tech/services/ai-drug-discovery)** - **[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:** 2026-09-24 06:14 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 — 2026-09-24
PubMed/GEO scan · research-watcher · 06:00 KST