Protein co-abundance clusters preserved across tissues can reveal shared disease mechanisms and candidate therapeutic targets, particularly when proteins implicated in organ-confined diseases converge in peripheral or accessible tissues. However, previous cross-tissue studies have focused on biologically pre-selected tissue pairs, leaving most possible combinations and non-obvious relationships unexplored. We present an LLM-agent framework for large-scale, evidence-grounded comparison of tissue-specific protein co-abundance networks. The framework constructs tissue networks, derives pairwise consensus clusters, and integrates evidence from expression atlases, protein interaction and complex databases, pathway annotations, disease catalogues, and literature. Applied to all 820 pairwise combinations of 41 human tissues and fluids, it identified 1,833 conserved co-abundance clusters across 406 tissue pairs. Colon, synovial fluid, blood, cerebrospinal fluid, and bone marrow were the most broadly connected tissues, while the most cluster-rich pairs were dominated by bone marrow. The analysis also highlighted non-obvious relationships: skin-bone marrow exceeded the anatomically adjacent bone-bone marrow pair, while colon-breast contained cancer-relevant clusters involving extracellular-matrix remodeling, lipid metabolism, and immune modulation. Cluster-level analyses generated further mechanistic hypotheses, including a brain-gut extracellular-vesicle/redox/serotonin-cofactor axis and a liver-bone marrow stress-response axis involving genes linked to white matter disease. These results provide a global, comparable landscape of conserved protein co-abundance and a hypothesis-generating resource for mechanistic and therapeutic exploration. Code and data are available at https://github.com/Gry1005/AgenticAI-conserved-cross-tissue-protein-co-abundance.
Agentic research systems are emerging as a new paradigm for coordinating scientific workflows beyond isolated model inference, code generation, or statistical analysis. However, deployment in institutional biomedical environments requires governed mechanisms for research planning, data access, workflow orchestration, evidence tracking, reproducibility, and human oversight. We present NVAITC AI Scientist (NAIS), a governed end-to-end agentic research system designed to support domain-general scientific workflows while keeping protected data within institutional privacy boundaries. NAIS integrates proposal review, execution planning, governed computational routing, reproducible workflow orchestration, evidence generation, and scientist-in-the-loop oversight. We validate NAIS in a real-world hypertension genome-wide association study (GWAS) using hospital-linked genotype and electronic health record (EHR) data from 286,422 individuals under an aggregate-only data policy. The agent planned cohort extraction, orchestrated GWAS execution, generated quality-control summaries, and drafted publication-oriented outputs. Human-AI review identified phenotype discrepancies and enabled iterative refinement of the hypertension definition. After reconciliation, the agent-orchestrated GWAS reproduced established hypertension loci, including FGF5, ATP2B1, CNNM2, FTO, and GRB14, with the strongest signal at FGF5 reaching $-\log_{10}(p) \sim 70$. As a secondary demonstration, NAIS also supported a drug-induced liver injury prediction workflow, achieving a multimodal graph neural network AUC of 0.842. These results demonstrate that governed agentic research systems can support scalable AI-assisted biomedical discovery while producing outputs comparable to expert-led workflows.