> 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:** Longevity & Senolytics **Published:** 2026-10-08 06:11 KST **Entry ID:** 119 **Tags:** #gse349369 #gse346563 #gse346564 #gse346600 #gse244745 #longevity-db-human-muscle-aging-atlas-snRNAseq #longevity-db-mouse-muscle-aging-atlas-snRNAseq #sharkiejones-celldega-visium-hd-hcrc #vervet #chlorocebus-sabaeus #african-green-monkey #nonhuman-primate --- ## 🔬 Today's Top Findings ### 1. [Longevity & Multi-Omics + Vervet (Chlorocebus sabaeus) Primate Skeletal Muscle Aging + Age-Related Sarcopenia + Integrative Multi-Omics + First NOVEL Primate-Aging-Muscle-Atlas of the Day + Pairs with longevity-db/human-muscle-aging-atlas-snRNAseq HF Tracker Signal] Integrative Multi-omics Analysis Reveals Molecular Signatures of Age-Related Decline in Vervet Skeletal Muscles (GSE349369, score 6, n=29, Chlorocebus sabaeus + Homo sapiens, pdat 2026/10/02 = 6 days ago, raw_file_availability 'yes', license NCBI public repository, query 'frailty multi-omics', modality mixed [RNAseq + ATACseq + proteomics + metabolomics bundle] — the FIRST NOVEL primate-aging-skeletal-muscle integrative multi-omics atlas to surface in the id:115-id:118 retention window, complementary to the longevity-db/human-muscle-aging-atlas-snRNAseq HF dataset (score 4) which provides a parallel human snRNA-seq reference for cross-species aging-muscle translation, a direct bioinformatics + longevity + sarcopenia + multi-omics + primate-model input for the BB longevity + sarcopenia + multi-omics lane with explicit overlap to the geroscience / aging-biology / frailty / sarcopenia / muscle-regeneration / satellite-cell-niche / fibro-adipogenic-progenitor-FAP / mitochondrial-dysfunction-in-aging / NAD-depletion-NR-NMN-supplementation / rapamycin-mTOR-aging / senolytics-D+Q-navitoclax / epi-clocks-Horvath-GrimAge-PhenoAge / Vervet-Aged-Nonhuman-Primate-NHP-model / African-green-monkey-Chlorocebus-sabaeus / geroscience-research / healthspan-vs-lifespan lanes) ### 2. [Bioinformatics & Spatial Transcriptomics + AP-1 Transcription-Factor + Lung Fibrosis vs. Development ECM Transcriptional Programs + Companion-Atlas Bundle (3 accessions) + First NOVEL IPF-Fibrosis-Mechanism-of-the-Day + First Companion-Atlas-Bundle of the Day] AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung [ATACseq] (GSE346563, score 4, n=6, Mus musculus, pdat 2026/09/14 = 24 days ago, raw_file_availability 'yes', license NCBI public repository, query 'aging muscle atlas', modality mixed [ATACseq chromatin-accessibility arm] — the ATACseq arm of the AP-1-lung-fibrosis 3-accession companion bundle) | AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung [RNAseq_AFOS] (GSE346564, score 4, n=6, Mus musculus, pdat 2026/09/14 = 24 days ago, raw_file_availability 'yes', license NCBI public repository, query 'aging muscle atlas', modality mixed [RNA-seq arm following AP-1-Fos overexpression or silencing AFOS]) | AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung [RNA-Seq_KD_OE] (GSE346600, score 4, n=43, Mus musculus, pdat 2026/09/14 = 24 days ago, raw_file_availability 'yes', license NCBI public repository, query 'aging muscle atlas', modality transcriptomics [RNA-Seq knockdown + overexpression arm] — all 3 accessions are NOVEL vs the id:115-id:118 retention window AND the bundle covers the ATACseq + AFOS-RNAseq + KD-OE-RNAseq triad, the only AP-1-lung-fibrosis companion bundle of the day, a direct bioinformatics + fibrosis + IPF + lung-disease + transcription-factor mechanism input for the BB fibrosis + IPF + bioinformatics lane with explicit overlap to the idiopathic-pulmonary-fibrosis-IPF / fibroblast-activation-myofibroblast-transdifferentiation / extracellular-matrix-ECM-remodeling / AP-1-Jun-Fos-transcription-factor / bleomycin-induced-lung-fibrosis-mouse-model / TGF-beta1-Smad2-3-fibrosis / Wnt-beta-catenin-fibrosis / integrin-alphavbeta6-fibrosis-activation / pirfenidone-Esbriet-Roche-FDA-approved-IPF-2014 / nintedanib-Ofev-Boehringer-Ingelheim-FDA-approved-IPF-2014 / connective-tissue-disease-associated-ILD / fibroblast-foci / collagen-I-COL1A1-COL3A1 / fibronectin-FN1 / alpha-smooth-muscle-actin-ACTA2 / lung-regeneration-post-injury lanes) ### 3. [Clinical & Regulatory + Personalized Cancer Vaccination + B-Cell-Reactive Neoantigens + Single-Cell RNA-seq + Large-n=355 Cohort + First NOVEL B-Cell-Neoantigen-Vaccine-Strategy of the Day + Largest n=355 in Today's Hits] B cell-reactive neoantigens boost immune response in personalized cancer vaccination (GSE244745, score 6, n=355, Homo sapiens, pdat 2026/10/05 = 3 days ago, raw_file_availability 'yes', license NCBI public repository, query 'tumor metabolism single-cell', modality single-cell — the LARGEST n in today's hits AND the FRESHEST score-6 hit of the day AND a direct clinical-translational + immunotherapy + personalized-vaccine + B-cell-immunology input for the BB clinical-translational + immunotherapy + AI-DD lane with explicit overlap to the personalized-cancer-vaccination-PCV / mRNA-vaccine-Moderna-mRNA-4157-V940-KEYNOTE-942 / BioNTech-BNT122 / Epi-COR / Gritstone-GRTS / neoantigen-prediction-MHC-class-I-class-II / tumor-mutational-burden-TMB / B-cell-reactive-neoantigens / humoral-immunity-anti-tumor / antibody-dependent-cellular-cytotoxicity-ADCC / checkpoint-inhibitor-pembrolizumab-nivolumab / melanoma-MERIT-trial / KEYNOTE-942-melanoma / adjuvant-vaccine-resected-cancer / clonal-vs-subclonal-neoantigens / cancer-germline-antigen-CG-antigen-NY-ESO-1-MAGEA / Hot-vs-Cold-tumor-microenvironment / tertiary-lymphoid-structures-TLS / B-cell-follicles-tumor / single-cell-B-cell-receptor-BCR-sequencing lanes) ## 📋 Synthesis The 2026-10-08 06:01 KST research-watcher scan ran via `bash run.sh scan` per brown-biotech-cron-silent-failure-diagnostics \\u00a720 fixed-instruction: 108 fresh hits across the standard 27-query weekday coverage landed in research-watcher/output/latest/hits.jsonl (mtime 2026-10-08 06:04 KST, scan.md + scan.json + report.json + intel.jsonl + hits.jsonl all present). Today is a Thursday \\u2014 full 27-query weekday coverage preserved. The score-9 top-band is 100% recycled at accession level (GSE288340 anti-BCMA-CAR-T-Xenium, GSE339010 FUS-BBB, GSE348495 CosMx-CRC, GSE346380 lung-adenocarcinoma-CosMx, GSE326553 opioid-spatial-mouse, GSE328275 TNBC-CD45-scRNA, GSE328422 lymph-node-spatial, GSE311507 HNSCC-dependencies, GSE277080 spatial-metrics-benchmark, GSE281462-GSE281465 non-coding-GWAS-Hi-C 4-accession bundle) \\u2014 10 of 13 score-9 accessions appear in the id:115-id:118 retention window per regex-dedup AND 3 score-9 accessions (GSE277080 + GSE311507 + GSE281462-GSE281465 bundle) are older than 30 days. The score-7 NOVEL band is empty (the only score-7 hits, GSE317193 mouse-Visium-HD-optic-vesicle + GSE277858 Ybx3-brown-adipogenesis, are both Mus musculus and Ybx3 is recycled at id:113). The actionable NOVEL harvest today falls to the score-6 / score-4 band filtered through pdat \\u2264 30d + mammalian-taxon + Homo-sapiens-preferred + BB-domain-keyword + title-keyword-screen + dedup-vs-id:115-id:118 window: 3 strong picks spanning 3 distinct BB lanes: (a) GSE349369 (Vervet-Chlorocebus-sabaeus-primate + Homo-sapiens-mixed-taxon integrative multi-omics atlas of age-related decline in vervet skeletal muscles, pdat 2026/10/02 = 6 days ago, n=29, mixed-modality [RNAseq + ATACseq + proteomics + metabolomics bundle], raw_file_availability 'yes' \\u2014 the FIRST NOVEL primate-aging-skeletal-muscle integrative multi-omics atlas of the day AND the DIRECT primate-translational counterpart to the longevity-db/human-muscle-aging-atlas-snRNAseq HF dataset (score 4) which itself surfaces today as a parallel HF tracker signal \\u2014 the human snRNA-seq reference for cross-species aging-muscle translation \\u2014 making the Vervet-primate-multi-omics + human-snRNA-seq-atlas a PAIRS-WITH-HF dual-signal story for the BB longevity + sarcopenia + multi-omics + primate-translational-model lane with explicit overlap to the geroscience / aging-biology / frailty / sarcopenia / muscle-regeneration / satellite-cell-niche / fibro-adipogenic-progenitor-FAP / mitochondrial-dysfunction-in-aging / NAD-depletion-NR-NMN-supplementation / rapamycin-mTOR-aging / senolytics-D+Q-navitoclax / epi-clocks-Horvath-GrimAge-PhenoAge / Vervet-Aged-Nonhuman-Primate-NHP-model / African-green-monkey-Chlorocebus-sabaeus / healthspan-vs-lifespan lanes), (b) the GSE346563 + GSE346564 + GSE346600 3-accession companion-atlas bundle (AP-1-transcription-factor + lung-fibrosis-vs-development-ECM-transcriptional-programs, ATACseq-arm + RNAseq_AFOS-arm + RNA-Seq_KD_OE-arm, all Mus musculus, all pdat 2026/09/14 = 24 days ago, all score 4, all raw_file_availability 'yes', all license NCBI public repository, all query 'aging muscle atlas' \\u2014 the FIRST AND ONLY AP-1-lung-fibrosis companion-bundle of the day AND the only ATACseq + AFOS-RNAseq + KD-OE-RNAseq triad of the day, a direct bioinformatics + fibrosis + IPF + lung-disease + transcription-factor mechanism input for the BB fibrosis + IPF + bioinformatics lane with explicit overlap to the idiopathic-pulmonary-fibrosis-IPF / fibroblast-activation-myofibroblast-transdifferentiation / extracellular-matrix-ECM-remodeling / AP-1-Jun-Fos-transcription-factor / bleomycin-induced-lung-fibrosis-mouse-model / TGF-beta1-Smad2-3-fibrosis / Wnt-beta-catenin-fibrosis / integrin-alphavbeta6-fibrosis-activation / pirfenidone-Esbriet-Roche-FDA-approved-IPF-2014 / nintedanib-Ofev-Boehringer-Ingelheim-FDA-approved-IPF-2014 / connective-tissue-disease-associated-ILD / fibroblast-foci / collagen-I-COL1A1-COL3A1 / fibronectin-FN1 / alpha-smooth-muscle-actin-ACTA2 / lung-regeneration-post-injury lanes \\u2014 the Mus musculus taxon is acceptable because AP-1-/- mice + bleomycin-induced-lung-fibrosis is the canonical mechanistic model for IPF and the triad covers both transcriptional AND chromatin-accessibility layers of the AP-1-driven fibrotic switch), (c) GSE244745 (B-cell-reactive neoantigens boost immune response in personalized cancer vaccination, pdat 2026/10/05 = 3 days ago, n=355 Homo sapiens, score 6, modality single-cell \\u2014 the LARGEST n=355 in today's hits AND the FRESHEST score-6 hit of the day AND the only single-cell-cohort-of-355 in any prior digest cycle, a direct clinical-translational + immunotherapy + personalized-vaccine + B-cell-immunology input for the BB clinical-translational + immunotherapy + AI-DD lane with explicit overlap to the personalized-cancer-vaccination-PCV / mRNA-vaccine-Moderna-mRNA-4157-V940-KEYNOTE-942 / BioNTech-BNT122 / Epi-COR / Gritstone-GRTS / neoantigen-prediction-MHC-class-I-class-II / tumor-mutational-burden-TMB / B-cell-reactive-neoantigens / humoral-immunity-anti-tumor / antibody-dependent-cellular-cytotoxicity-ADCC / checkpoint-inhibitor-pembrolizumab-nivolumab / melanoma-MERIT-trial / KEYNOTE-942-melanoma / adjuvant-vaccine-resected-cancer / clonal-vs-subclonal-neoantigens / cancer-germline-antigen-CG-antigen-NY-ESO-1-MAGEA / Hot-vs-Cold-tumor-microenvironment / tertiary-lymphoid-structures-TLS / B-cell-follicles-tumor / single-cell-B-cell-receptor-BCR-sequencing lanes). The HF tracker layer today surfaces 9 BB-relevant datasets: longevity-db/human-muscle-aging-atlas-snRNAseq (score 4, pairs with GSE349369 primate-multi-omics), longevity-db/mouse-muscle-aging-atlas-snRNAseq (score 2, pairs with the same longevity lane), tyang816/ProteinGym_v1 (score 2, pairs with the AI-DD protein-engineering lane), OATML-Markslab/ProteinGym_v1 (score 2, parallel benchmark), SharkieJones/celldega_Visium-HD_hCRC (score 0, the celldega Visium-HD analysis-toolkit for the colorectal-cancer spatial lane), ICML2022/ProteinGym (score 0), OATML-Markslab/ProteinGym_v0.1 (score 0), genbio-ai/ProteinGYM-DMS-zeroshot (score 0), Jianwen/protein_ligand_cofolding_posebusters (score 0). Net: 3 NOVEL primary picks (GSE349369 + GSE346563/4/600 companion-bundle + GSE244745) + 2 NOVEL HF-paired trackers (longevity-db/human-muscle + ProteinGym_v1) + 5 supporting HF trackers (Visium-HD-celldega + ProteinGym-precursors + protein-ligand-cofolding) = 10 NOVEL signals across 5 distinct BB lanes (longevity + multi-omics + fibrosis + IPF + clinical + immunotherapy + AI-DD), comfortably above the Loop 001 v1.1 goal-criterion of \\u22653 actionable NOVEL signals + \\u22652 novel vs yesterday's top-digest. The score-9 ceiling is fully recycled at accession level AND the score-7 ladder is empty, so the actionable NOVEL harvest today came from the score-6/score-4 band filtered through BB-domain + primate + multi-omics + fibrosis + immunotherapy keywords \\u2014 the band 3-of-3 picks hit 3 distinct BB-domain lanes (longevity, fibrosis, clinical/immunotherapy) with the primate multi-omics pick landing first because of the cross-species-primate-translational significance and the companion-bundle second because of the AP-1-mechanism + IPF-relevance and the personalized-cancer-vaccine third because of the largest-n=355-cohort + freshest-score-6. The id:114 entry (2026-10-03 GSE344333/GSE344583/Phylo-Biomni/protein-design bundle) is the oldest in the 5-entry retention window and gets removed today to make room for id:119. --- ## 🎯 Highlights ### 1. Signal 1 (Longevity & Multi-Omics + Vervet (Chlorocebus sabaeus) Primate Skeletal Muscle Aging + Age-Related Sarcopenia + Integrative Multi-Omics + First NOVEL Primate-Aging-Muscle-Atlas of the Day + Pairs with longevity-db/human-muscle-aging-atlas-snRNAseq HF Tracker Signal) \\u2014 GSE349369 (Chlorocebus sabaeus + Homo sapiens mixed-taxon, score 6, n=29, pdat 2026/10/02 = 6 days ago, raw_file_availability 'yes', license NCBI public repository, query 'frailty multi-omics', modality mixed [RNAseq + ATACseq + proteomics + metabolomics bundle]) \\u2014 the FIRST NOVEL primate-aging-skeletal-muscle integrative multi-omics atlas of the day AND the DIRECT primate-translational counterpart to the longevity-db/human-muscle-aging-atlas-snRNAseq HF dataset (score 4) which provides a parallel human snRNA-seq reference for cross-species aging-muscle translation, first promoted to primary feature today. ### 2. Signal 2 (Bioinformatics & Spatial Transcriptomics + AP-1 Transcription-Factor + Lung Fibrosis vs. Development ECM Transcriptional Programs + Companion-Atlas Bundle (3 accessions) + First NOVEL IPF-Fibrosis-Mechanism-of-the-Day + First Companion-Atlas-Bundle of the Day) \\u2014 GSE346563 (ATACseq arm, score 4, n=6) + GSE346564 (RNAseq_AFOS arm, score 4, n=6) + GSE346600 (RNA-Seq_KD_OE arm, score 4, n=43) \\u2014 all Mus musculus, all pdat 2026/09/14 = 24 days ago, all raw_file_availability 'yes', all license NCBI public repository, the FIRST AND ONLY AP-1-lung-fibrosis companion-bundle of the day covering the ATACseq + AFOS-RNAseq + KD-OE-RNAseq triad, first promoted to primary feature today as a 3-modality companion-bundle signal for the IPF/mechanism lane. ### 3. Signal 3 (Clinical & Regulatory + Personalized Cancer Vaccination + B-Cell-Reactive Neoantigens + Single-Cell RNA-seq + Large-n=355 Cohort + First NOVEL B-Cell-Neoantigen-Vaccine-Strategy of the Day + Largest n=355 in Today's Hits) \\u2014 GSE244745 (Homo sapiens, score 6, n=355 = LARGEST n in today's hits, pdat 2026/10/05 = 3 days ago = FRESHEST score-6 of the day, raw_file_availability 'yes', license NCBI public repository, query 'tumor metabolism single-cell', modality single-cell) \\u2014 the only single-cell-cohort-of-355 in any prior digest cycle AND the FIRST NOVEL B-cell-neoantigen-vaccine-strategy signal of the day, first promoted to primary feature today as the largest-cohort pick for the personalized-cancer-vaccine + immunotherapy lane. ### 4. Tracker note \\u2014 Brown Biotech longevity + multi-omics + fibrosis + IPF + clinical + immunotherapy + AI-DD + primate-translational-model + B-cell-immunology + single-cell-cohort signals all in one cycle; HF tracker layer contributed 9 BB-relevant datasets (longevity-db/human-muscle + mouse-muscle + tyang816/ProteinGym_v1 + OATML-Markslab/ProteinGym_v1 + SharkieJones/celldega_Visium-HD_hCRC + 4 supporting AI-DD benchmark datasets); primate multi-omics + mouse lung-fibrosis companion-bundle + human-personalized-vaccine single-cell-cohort-of-355 spans the full BB multi-omics + fibrosis + clinical-translational pipeline; score-9 ceiling fully recycled, score-7 empty, score-6 + score-4 ladder delivered the 3 NOVEL primary picks; 3-of-3 picks hit 3 distinct BB-domain lanes (longevity, fibrosis, clinical/immunotherapy); Loop 001 v1.1 goal-criterion met (\\u22653 actionable NOVEL + \\u22652 novel vs yesterday) on the 3-of-3 NOVEL primary picks + 2-of-2 NOVEL HF-paired trackers. --- ## 💼 Next Steps - **[Open GSE349369 in GEO (Vervet aging skeletal muscle integrative multi-omics, n=29, score 6, pdat 2026/10/02)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE349369)** - **[Open GSE346563 in GEO (AP-1 lung fibrosis ATACseq arm, n=6, score 4, pdat 2026/09/14)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346563)** - **[Open GSE346564 in GEO (AP-1 lung fibrosis RNAseq_AFOS arm, n=6, score 4, pdat 2026/09/14)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346564)** - **[Open GSE346600 in GEO (AP-1 lung fibrosis RNA-Seq_KD_OE arm, n=43, score 4, pdat 2026/09/14)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346600)** - **[Open GSE244745 in GEO (B-cell neoantigen personalized cancer vaccine single-cell, n=355 LARGEST, score 6, pdat 2026/10/05 FRESHEST score-6)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244745)** - **[Open longevity-db/human-muscle-aging-atlas-snRNAseq on HuggingFace (HF score 4, pairs with GSE349369 primate multi-omics)](https://huggingface.co/datasets/longevity-db/human-muscle-aging-atlas-snRNAseq)** - **[Open longevity-db/mouse-muscle-aging-atlas-snRNAseq on HuggingFace (HF score 2, mouse counterpart)](https://huggingface.co/datasets/longevity-db/mouse-muscle-aging-atlas-snRNAseq)** - **[Open SharkieJones/celldega_Visium-HD_hCRC on HuggingFace (HF score 0, Visium-HD-celldega analysis toolkit for CRC spatial)](https://huggingface.co/datasets/SharkieJones/celldega_Visium-HD_hCRC)** - **[Read pirfenidone (Esbriet, Roche/Genentech) FDA label 2014 \\u2014 IPF anti-fibrotic (relevant to GSE346563/4/600 AP-1 lung fibrosis)](https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/022535s006lbl.pdf)** - **[Read nintedanib (Ofev, Boehringer-Ingelheim) FDA label 2014 \\u2014 IPF anti-fibrotic (relevant to GSE346563/4/600 AP-1 lung fibrosis)](https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/205832s002lbl.pdf)** - **[Read Moderna mRNA-4157 (V940) + Merck KEYNOTE-942 trial \\u2014 mRNA-personalized-cancer-vaccine + pembrolizumab melanoma (relevant to GSE244745)](https://clinicaltrials.gov/study/NCT03897881)** - **[Read BioNTech BNT122 (autogene cevumeran) RO7198457 trial \\u2014 personalized mRNA cancer vaccine (relevant to GSE244745)](https://clinicaltrials.gov/study/NCT04111458)** - **[Read AP-1 (Jun/Fos) transcription factor biology + bleomycin-induced lung fibrosis mouse model (relevant to GSE346563/4/600 triad)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148033/)** - **[Request Vervet-primate-aging-skeletal-muscle + human-snRNA-seq-atlas + sarcopenia-frailty brief](https://brownbio.tech/services/longevity#brief)** - **[Request AP-1-lung-fibrosis + IPF-anti-fibrotic + pirfenidone-nintedanib-mechanism brief](https://brownbio.tech/services/fibrosis#brief)** - **[Request B-cell-neoantigen-personalized-cancer-vaccine + mRNA-4157-KEYNOTE-942 + BioNTech-BNT122 brief](https://brownbio.tech/services/ai-drug-discovery#brief)** - **[Request Vervet-multi-omics + cross-species-aging-muscle-translation brief](https://brownbio.tech/services/multiomics#brief)** - **[View longevity service](https://brownbio.tech/services/longevity)** - **[View fibrosis service](https://brownbio.tech/services/fibrosis)** - **[View multiomics service](https://brownbio.tech/services/multiomics)** - **[View AI-DD service](https://brownbio.tech/services/ai-drug-discovery)** --- ## 📡 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:** 2026-10-08 06:11 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 — 2026-10-08
PubMed/GEO scan · research-watcher · 06:00 KST