Engineering Biology Beyond Single Genes: Advances and Challenges in Multiplex Genome Editing

ABSTRACT Complex traits and disease phenotypes typically arise from the regulation of intricate genetic networks rather than single genes. Multiplex genome editing has therefore become central to trait engineering and therapeutic cell design. This review dissects the technological foundations and limiting factors of multiplex genome editing, focusing on guide RNA (gRNA) array engineering, delivery constraints, and scale‐dependent safety risks. We further examine the growing role of artificial intelligence (AI) in gRNA design and the engineering of clustered regularly interspaced short palindromic repeats (CRISPR)‐associated proteins (Cas proteins) and auxiliary editing modules. Despite rapid progress, delivery bottlenecks and nonlinear genomic and cellular risks remain the principal barriers to scalable and translational multiplex genome editing.