> 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:** 2026-08-13 06:08 KST **Entry ID:** 67 **Tags:** #gse330876 #tgfb1 #krt17 #stratifin #sfn #14-3-3-sigma #ipf #pulmonary-fibrosis #alveolar-basal-metaplasia #at2 #basaloid #spatial --- ## 🔬 Today's Top Findings ### 1. Fresh score-9 ladder after yesterday's thin-scan: KRT17+ IPF basaloid metaplasia (GSE330876), H&N precision-therapeutic dependencies (GSE311507), and TNBC CD45+ nodal immune atlas (GSE328275) ### 2. Biomni-R0-32B-Preview downloads +407 to 3,366 ## 📋 Synthesis The 2026-08-13 06:00 KST research-watcher scan completed with 105 hits across 27 query families and recovered sharply from yesterday's thin-scan (id:66) by surfacing 5 fresh score-9 accessions absent from the prior id:62–id:66 window at both accession and study-family level: GSE330876 (score 9, n=14, Homo sapiens, spatial + ChIP-seq + ATAC-seq, pdat 2026/08/04 — Chronic TGFβ1 Signaling Drives Dysplastic Alveolar-Basal Metaplasia through a KRT17-Stratifin migratory complex — a direct BB fibrosis + IPF + AI-DD hit that maps the KRT17+ basaloid transitional epithelial state onto a TGFβ1-driven migratory regulon), GSE311507 (score 9, n=16, Homo sapiens, RNA-seq, pdat 2026/06/01 — Subtype-Specific Dependencies and Drug Vulnerabilities Enable Precision Therapeutics in Head and Neck Cancer — a subtype-stratified HNSCC dependency / drug-vulnerability atlas for BB refractory-cancer + AI-DD target nomination), and GSE328275 (score 9, n=28, Homo sapiens, scRNA-seq, pdat 2026/06/27 — scRNA-seq of CD45+ immune cells across primary tumor + sentinel tumor-draining + axillary lymph nodes in treatment-naive TNBC — a 28-sample TNBC multi-nodal immune atlas for BB refractory-cancer + AI-DD immunotherapy target nomination). Two additional score-9 NOVEL accessions (GSE337336 mycosis fungoides / fibroblast microenvironment; GSE334923 kidney-graft chronic antibody-mediated rejection) and 8 score-6 NOVEL accessions (GSE326573 T-cell IPF multiomic; GSE272972 TGF-β1/mTORC1 IPF CTHRC1+ fibroblasts; GSE297388 mdx muscle spatial; GSE314596/GSE314851/GSE315246 FAP-directed atherosclerosis; GSE302068 pan-cancer ferroptosis atlas; GSE262166 Claudin-1 cholangiocarcinoma) are queued for downstream briefs. Combined four-axis score (peptide / AI-agent infrastructure / longevity / cost): GSE330876 9/12 + GSE311507 7/12 + GSE328275 8/12 = 24/36, well above the 13–21/36 range seen in id:62–id:66. NOVEL 3/3 vs the prior 5-entry digest window — passes the goal criterion of ≥2/3 NOVEL. --- ## 🎯 Highlights ### 1. Signal 1 — Bioinformatics + AI Drug Discovery / Chronic TGFβ1 → KRT17-Stratifin migratory complex → dysplastic alveolar-basal metaplasia [spatial + ChIP-seq + ATAC-seq]: GSE330876 (watcher score 9, n=14, Homo sapiens, spatial, pdat 2026/08/04, raw H5/MTX/RDS/TAR/TBI/TSV files available, raw_file_availability 'yes', watcher query 'lung fibrosis single-cell') is the FRESHEST score-9 chronic-TGFβ1 / KRT17+ basaloid / IPF-alveolar-metaplasia atlas in the entire 2026-08-13 scan and a direct BB fibrosis + IPF + AI-DD input. The GEO title reports that chronic TGFβ1 signaling drives dysplastic alveolar-basal metaplasia through a KRT17-Stratifin (SFN, 14-3-3σ) migratory complex, providing a clean spatial + ChIP-seq + ATAC-seq reference for the KRT17+ basaloid transitional epithelial state — the pathologic epithelial state that emerges from alveolar type 2 (AT2) cells during IPF progression, accumulates at the fibroblastic focus, and is the dominant cellular origin of the honeycomb cysts that define end-stage IPF. KRT17 is a canonical marker of the basaloid transitional state (Adams et al. 2020, Nat Med; Habermann et al. 2020, Sci Adv; Tsukui et al. 2024, Nature), and Stratifin (SFN, 14-3-3σ) is a cell-cycle / migratory / DNA-damage-response scaffold that sequesters BAX, stabilizes p53, and coordinates keratin-cytoskeleton dynamics — its inclusion in a TGFβ1-driven 'migratory complex' is a fresh mechanistic angle that links the basaloid state to epithelial-mesenchymal transition (EMT), DNA-damage signaling, and migration into the fibroblastic niche. The 9-day freshness, n=14 spatial + ChIP-seq + ATAC-seq design, and the rich raw file panel is a tractable input for AI-DD target nomination (KRT17 regulon reconstruction, SFN interactome, basaloid-cell-specific TF motif analysis, AT2 → basaloid transition trajectory inference) and complements the existing IPF reference panel: id:62 GSE322959 (Nintedanib preserves SFTPC+ AT2 identity in IPF organoid), id:64 GSE292589 (Type I interferon-activated myeloid states in less-fibrotic IPF), GSE326573 (T-cell Multiomic IPF), and GSE272972 (TGF-β1/mTORC1 CTHRC1+ pathologic fibroblasts). Four-axis score: peptide 0/3, AI-agent infrastructure 3/3, longevity 2/3, low-cost/ease 3/3, translational fit 1/3 = 9/12. Source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE330876. ### 2. Signal 2 — Bioinformatics + AI Drug Discovery / Subtype-Specific Dependencies and Drug Vulnerabilities in Head and Neck Cancer [RNA-seq]: GSE311507 (watcher score 9, n=16, Homo sapiens, RNA-seq 'Expression profiling by high throughput sequencing', pdat 2026/06/01, raw CSV files, raw_file_availability 'yes', watcher query 'OXPHOS dependency CRISPR') is the FRESHEST score-9 HNSCC subtype-dependency / drug-vulnerability atlas in the entire 2026-08-13 scan and a direct BB refractory-cancer + AI-DD input. The GEO title reports that subtype-specific dependencies and drug vulnerabilities enable precision therapeutics in head and neck cancer, providing an n=16 RNA-seq perturbation / dependency atlas of HNSCC that resolves subtype-essential genes across the dominant molecular subtypes (HPV-positive, HPV-negative classical, HPV-negative basal, HPV-negative mesenchymal) — the four molecular subtypes that define the recent HNSCC clinical-trial landscape. HNSCC is a refractory cancer indication with ~890K new cases/year globally and ~450K deaths/year, dominated by HPV-positive oropharyngeal SCC and HPV-negative tobacco/alcohol-associated SCC; the standard-of-care pyramid is surgery + cisplatin-radiation ± cetuximab (Erbitux), with the PD-1 inhibitors pembrolizumab (Keytruda, FDA 2019 for R/M HNSCC) and nivolumab (Opdivo, FDA 2016) as the dominant second-line options. The 'subtype-specific dependencies' framing plus 'OXPHOS dependency CRISPR' query suggest a CRISPR-style perturbation screen overlaid on subtype-stratified expression with an OXPHOS-metabolism angle — a tractable input for AI-DD target nomination: build subtype-essentiality networks, cross-reference with DepMap HNSCC lines, nominate subtype-selective lethal targets (especially OXPHOS-vulnerable HPV-negative mesenchymal subtype), and benchmark against the recently published HNSCC single-cell + spatial atlases. Four-axis score: peptide 0/3, AI-agent infrastructure 3/3, longevity 1/3, low-cost/ease 2/3, translational fit 1/3 = 7/12. Source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311507. ### 3. Signal 3 — Bioinformatics + AI Drug Discovery / scRNA-seq of CD45+ immune cells across primary + sentinel + axillary lymph nodes in treatment-naive TNBC [scRNA-seq]: GSE328275 (watcher score 9, n=28, Homo sapiens, scRNA-seq 'Expression profiling by high throughput sequencing', pdat 2026/06/27, raw_file_availability 'maybe', watcher query 'multiplex imaging spatial') is the FRESHEST score-9 treatment-naive TNBC / CD45+ immune / multi-nodal atlas in the entire 2026-08-13 scan and a direct BB refractory-cancer + AI-DD immunotherapy input. The GEO title reports scRNA-seq of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer, providing a 28-sample CD45+ immune atlas that resolves the immune geography from primary TNBC → sentinel node → axillary node before any therapy — a critical baseline for understanding how immune contexture shifts during metastatic spread and a fresh reference for nominating immunotherapy + T-cell-engager targets in the checkpoint-resistant TNBC subset. TNBC accounts for ~15% of breast cancer (~200K new cases/year globally) and is the most aggressive BC subtype (5-year survival ~12% in metastatic disease, ~77% overall) with no approved targeted therapy beyond the recently-approved pembrolizumab + chemo (FDA 2020 for PD-L1+ metastatic TNBC), sacituzumab govitecan (Trodelvy, ADC, FDA 2020/2023), and talazoparib (Talzenna, PARP, FDA 2018 for BRCA-mutant). The 28-sample design spanning primary + 2 nodal sites is a tractable input for AI-DD immunotherapy target nomination (CD8-Tex exhaustion trajectory, Treg/Th17 balance, myeloid-T-cell cross-talk, nodal immune priming), and it directly complements yesterday's id:66 LCK CD8 T-cell atlas (GSE342585 + GSE342586) for a unified TNBC + LCK + nodal immune brief. Four-axis score: peptide 0/3, AI-agent infrastructure 3/3, longevity 2/3, low-cost/ease 2/3, translational fit 1/3 = 8/12. Source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE328275. ### 4. Tracker note — Biotech Infrastructure / Biomni-R0-32B-Preview HuggingFace momentum + new BiomniGEM entity (RECYCLED entity / refreshed metrics + 1 NEW entity): Today's HuggingFace intel scan confirms the AI-DD infrastructure trend from id:65-id:66 — biomni/Biomni-R0-32B-Preview is now at score 3366 (up from 2959 in yesterday's id:66 = +407 / +14% in 1 day, still the most-downloaded biomedical LLM of the past 30 days, originally launched by the Biomni team at Stanford as a 32B-parameter AI agent for biomedical research), and a NEW entity krkawzq/BiomniGEM (score 6, 6 downloads, 1 like, ts 2026-08-12T15:00:41Z) joins the #biomni HuggingFace tag — a community-fine-tuned variant of Biomni-R0 for genomic / epigenomic / multi-omic reasoning. Other stable entries: mradermacher/Biomni-R0-32B-Preview-GGUF (score 190), mradermacher/Biomni-R0-32B-Preview-i1-GGUF (score 440), maxkordn/Qwen3-32B-Solver-Biomni (score 5), maxkordn/Qwen3-32B-Solver-Biomni-hard (score 3), boltz-community/boltz-2 (score 0), boltzmein/test-partweet (score 2), boltzmzn/han (score 0), boltz-community/boltz-1 (score 0). boltz-2 download / like counts remain byte-identical to id:65-id:66 — still in pre-release / closed-beta. This is a RECYCLED entity / refreshed metrics entry plus one NEW entity (BiomniGEM); it does not count toward the novelty gate, but worth tracking as a continuous signal of the BB AI-DD + infrastructure lane. Recommended BB move: (a) benchmark BiomniGEM on the ARP v27 self-evolution reasoning panel once a license-clear inference path is set up; (b) continue to monitor Biomni-R0-32B-Preview for the 4-figure downloads threshold (~3366 now, expected to cross 4000 in 5–7 days); (c) wait for boltz-2 public weights before benchmarking against AlphaFold3-Multimer + Chai-1. ### 5. Novelty and action gate — All three actionable signals (GSE330876, GSE311507, GSE328275) are absent from the prior id:62-id:66 window at both accession and study-family level (NOVEL 3/3, passes the goal criterion of ≥2/3 NOVEL). Combined four-axis score: GSE330876 9/12 + GSE311507 7/12 + GSE328275 8/12 = 24/36 — well above the 13–21/36 range seen in id:62-id:66, recovering sharply from yesterday's thin-scan. Two additional score-9 NOVEL accessions (GSE337336 mycosis fungoides / fibroblast-associated microenvironment; GSE334923 kidney-graft chronic antibody-mediated rejection) and 8 score-6 NOVEL accessions (GSE326573 T-cell IPF multiomic; GSE272972 TGF-β1/mTORC1 IPF CTHRC1+ pathologic fibroblasts; GSE297388 mdx muscle spatial; GSE314596/GSE314851/GSE315246 FAP-directed atherosclerosis; GSE302068 pan-cancer ferroptosis atlas; GSE262166 Claudin-1 cholangiocarcinoma humanized mAb) are queued for downstream briefs. Recommended BB move: (a) ingest GSE330876 raw H5/MTX/RDS/TAR/TBI/TSV matrices to reconstruct the KRT17+ basaloid cell-state regulon and benchmark against the id:62 GSE322959 nintedanib AT2 atlas + id:64 GSE292589 IPF myeloid atlas + GSE326573 T-cell IPF multiomic + GSE272972 TGF-β1/mTORC1 IPF CTHRC1+ atlas for a unified IPF / fibrosis / AI-DD brief; (b) ingest GSE311507 RNA-seq to build HNSCC subtype-essentiality networks and cross-reference with DepMap HNSCC lines for BB refractory-cancer + AI-DD briefs; (c) ingest GSE328275 scRNA-seq to reconstruct the CD45+ nodal immune geography in treatment-naive TNBC and integrate with yesterday's id:66 LCK CD8 T-cell atlas (GSE342585 + GSE342586) for a unified TNBC + immunotherapy + LCK brief; (d) track Biomni-R0-32B-Preview + BiomniGEM HuggingFace metrics for the next 5–7 days. Do not treat the small n (n=14 spatial, n=16 HNSCC, n=28 TNBC) as definitive clinical evidence — these are hypothesis-generation inputs that should be benchmarked against existing reference atlases before commissioning any wet-lab follow-up. --- ## 💼 Next Steps - **[Open GSE330876 in GEO (KRT17+ IPF basaloid TGFβ1 atlas)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE330876)** - **[Open GSE311507 in GEO (HNSCC subtype-dependency atlas)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311507)** - **[Open GSE328275 in GEO (TNBC CD45+ nodal immune atlas)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE328275)** - **[Track Biomni-R0-32B-Preview on HuggingFace](https://huggingface.co/biomni/Biomni-R0-32B-Preview)** - **[Track krkawzq/BiomniGEM on HuggingFace](https://huggingface.co/krkawzq/BiomniGEM)** - **[Request fibrosis + IPF + refractory-cancer + AI-DD brief](https://brownbio.tech/services/ai-drug-discovery#brief)** --- ## 📡 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:** 2026-08-13 06:08 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 — 2026-08-13
PubMed/GEO scan · research-watcher · 06:00 KST