Bioengineering

Bioengineering at the interface between materials, cells, and computation requires the careful pairing of wet-lab experimentation with omics-scale analysis. Our contribution here is computational and analytic: we partner with synthetic biology, biomaterials, and clinical teams to interpret transcriptomic, metabolomic, and structural data from engineered biological systems, patient-derived models, and human studies. The distinctive angle is to bring the same ontology-aware, multi-omics integration that underpins our diagnostic and functional-genomics work to bear on bioengineered constructs and their physiological consequences.

A central line of collaboration has been the analysis of cells cultured in biomimetic peptide scaffolds. In The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds, we characterised how three-dimensional, chemically defined matrices reshape fibroblast metabolism and gene expression relative to two-dimensional culture, providing quantitative evidence that mechanical context alters cellular state in ways that 2D models cannot capture. This work has extended into clinical bioengineering through Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study and Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling, which build patient-derived organoid systems in defined peptide matrices and use them as substrates for disease modelling and therapeutic screening.

A second strand applies omics analysis to human physiological extremes and to the molecular biophysics of disease-relevant proteins. Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke and Age-related differences in gene expression and pathway activation following heatstroke dissect the transcriptomic signatures of heat stroke in peripheral blood mononuclear cells across sex and age, identifying differential pathway activation that is directly relevant to climate-health risk in hot regions. At the protein level, Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates characterises how the kinase-FAT linker region of PYK2 drives cytoplasmic phase separation and sequesters paxillin, linking biomolecular condensation to focal-adhesion signalling. Complementing these analyses, Nanodesigner: resolving the complex-CDR interdependency with iterative refinement develops a generative model for nanobody design that resolves the interdependence between target-antigen complex and complementarity-determining region geometry through iterative refinement, supporting the rational engineering of single-domain antibodies.

Together these contributions support an expanding bioengineering programme that links engineered microenvironments and engineered biomolecules to measurable cellular and clinical outcomes. The peptide-scaffold and organoid work is moving towards precision-medicine pipelines in which patient-derived constructs are profiled at multi-omics depth and matched to therapeutic options. The transcriptomic studies of heat stroke connect bioengineering to climate-health priorities relevant to KAUST and the wider region. The nanobody and condensate work places computational design and analysis squarely alongside biomaterials and protein engineering, ensuring that our collaborators can interpret the molecular consequences of the systems they build.

Publications (7)