bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.09.05.674444

Therapeutic Monoclonal Antibodies Repurposing in Oncology via IMGT/mAb-KG Embeddings

Sanou, G.·Manso, T.·Todorov, K.·Giudicelli, V.·Duroux, P.·Kossida, S.
View original source ↗Export metadata ↓

Abstract

BackgroundCancer remains one of the leading causes of mortality world-wide, accounting for approximately 9.7 million deaths in 2022. Faced with this significant public health challenge, therapeutic monoclonal antibodies (mAbs) have emerged as promising alternatives that may minimize the side effects associated with conventional treatments such as radiotherapy and chemotherapy. To support mAb research and development, IMGT(R), the international ImMuno-GeneTics information system, has established two standardized data sources namely IMGT/mAb-DB, a comprehensive database for mAbs, and, more recently, IMGT/mAb-KG, a dedicated knowledge graph for mAbs. Despite these advances, the development of therapeutic mAbs remains both time-consuming and financially burdensome--costs can reach up to $2.8 billion. To address this challenge and accelerate cancer treatment, mAb repurposing represents a promising alternative. ResultsIn this study, we leveraged a subset of IMGT/mAb-KG, dedicated to the oncology domain, to develop a scientific hypothesis generation application for mAb repurposing. This application, based on knowledge graph embedding techniques, is designed to suggest potential mAb candidates for novel oncology applications. A user-friendly web interface provides access to the tool, incorporating visual support to facilitate the interpretation of generated hypotheses. This application is a decision support tool aiming to accelerate the discovery of new therapeutic applications for existing mAbs. ConclusionOur application demonstrates the potential of knowledge graph embedding techniques in the oncology domain by enabling the repurposing of existing mAbs for new therapeutic uses. Using this tool, we have identified two novel mAbs, loncastuximab tesirine and glofitamab, both currently undergoing clinical trials for the treatment of chronic lymphocytic leukemia. This decision-support tool thus facilitates the discovery of new therapeutic opportunities by effectively repositioning existing mAbs for oncological indications, potentially accelerating the development of cancer therapies and addressing critical public health needs.

Source connections

Explore related subjects

bioinformaticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sanou, G., Manso, T., Todorov, K., Giudicelli, V., Duroux, P., Kossida, S.. 2025-09-10. Therapeutic Monoclonal Antibodies Repurposing in Oncology via IMGT/mAb-KG Embeddings. https://doi.org/10.1101/2025.09.05.674444

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease

Aims: Premature coronary artery disease (PCAD) lacks specific molecular drivers, and the role of immunosenescence is unclear. We investigated whether aging-related gene dysregulation in T cells contributes to PCAD. Methods: We combined bulk transcriptomics of PBMCs from 12 PCAD patients and 21 controls, single-cell RNA sequencing of PBMCs and human atherosclerotic plaques, weighted gene co-expression network analysis, gene perturbation network analysis, and molecular docking. Results: KRAS was identified as a hub gene intersecting PCAD-associated genes and aging-related genes. Single-cell analysis showed KRAS upregulation predominantly in effector CD8+ T cells, which exhibited the highest senescence scores that were further elevated in disease. Network perturbation of KRAS strongly impacted the cell killing pathway. KRAS-high effector CD8+ T cells were detected in coronary and carotid plaques, displaying enhanced cytotoxicity, exhaustion, and senescence features. Additionally, a candidate small molecule was computationally predicted to bind inactive KRAS. Conclusions: Elevated KRAS expression in senescent, cytotoxic CD8+ T cells is associated with PCAD, bridging immunosenescence and premature atherosclerosis. This finding provides a novel biomarker candidate and potential therapeutic entry point, awaiting further functional validation.

bioinformatics↗
bioRxiv2026

Targeted finetuning enables co-folding models to learn ligand-induced protein conformational states

Advances in protein structure prediction have enabled all-atom protein-ligand co-folding models that predict bound conformations directly from sequence and small-molecule structure. However, these models often fail to generalize to novel binding sites or alternative protein conformational states, limiting their utility for chemical biology and drug discovery. Here we show this limitation reflects training data bias rather than architectural constraints and can be overcome through targeted finetuning. Using ten previously unseen X-ray structures of Werner (WRN) helicase from a drug discovery program, we finetune Boltz-1 to learn both an allosteric binding site and a large conformational change locking the enzyme in an inactive state, while preserving accuracy on the ATP-bound state. The finetuned model generalizes to different chemical series and transfers the conformational logic across RecQ-family helicases in a binding-site sequence-dependent manner. This approach provides a blueprint for adapting foundation models as new structural and mechanistic data emerge, enabling co-folding networks to capture ligand-induced conformational switches and binding poses absent from their training data but central to biological regulation and therapeutic intervention.

bioinformatics↗
bioRxiv2026

Benchmarking single-cell foundation models for aging biology

Single cell foundation models (scFMs) provide representations of cellular states, but their utility across biological questions in aging research remains unclear. We established a benchmark of cellular representations for aging research, evaluating ten general-purpose scFMs, three aging-specific models and conventional methods across five biological questions using more than 2.5 million single cell transcriptomes. Using frozen pretrained representations, Geneformer performed best among scFMs for chronological age prediction and age pseudotime concordance, although 2,000 highly variable genes achieved higher mean performance. Several scFMs captured positive molecular age shifts across three disease contexts, consistent with reported aging-associated changes. SCimilarity performed well for rare cellular state identification across out-of-distribution datasets, exceeding aging specific models and conventional baselines. At the gene level, scGPT showed the highest recovery of reference TF target interactions, including aging-related regulatory hubs. Overall, scFMs supported diverse aging analyses, but performance depended on the biological question, highlighting their utility for rare cellular state identification and regulatory analysis.

bioinformatics↗