One Size Does Not Fit All: A Comparative Framework for Optimizing RNA Transfection Across AML Cell Lines

Abstract Robust transient knockdown strategies are critical to oligonucleotide therapeutic development, yet ineffective and variable RNA delivery across experimental models continues to limit target validation. Efficient delivery of nucleic acids into acute myeloid leukemia (AML) cells is particularly challenging due to their immature, suspension phenotype. Here, we performed a head-to-head benchmarking comparison of commonly used chemical transfection reagents (Lipofectamine 3000, Lipofectamine 2000, RNAiMAX, INTERFERin) alongside a physical electroporation approach (Lonza nucleofection) across four genetically distinct AML cell lines (THP-1, OCI-AML3, MV4-11, MOLM-14). To establish recommended RNA delivery strategies, we used small-interfering RNA (siRNA) and quantified functional knockdown by RT-qPCR, with protein-level validation and paired assessment of post-transfection viability. Lipid-based formulations were most effective in more differentiated AML cell lines (for example, THP-1 and OCI-AML3), whereas more immature lines (MV4-11 and MOLM-14) were poorly responsive to chemical transfection but efficiently transfected by electroporation. A short serum-free incubation period enhanced lipid-mediated delivery in permissive lines and produced measurable gains in more resistant models. Transfection-associated cytotoxicity was strongly method-dependent, with lipid-based reagents producing minimal to modest viability losses and nucleofection causing substantially greater short-term reductions in viable cell numbers. Based on this systematic comparison, most chemical reagents supported efficient delivery in THP-1 and, to a lesser extent, OCI-AML3, while MV4-11 and MOLM-14 demonstrated strict dependence on electroporation for meaningful intracellular uptake. Together, our results define a concise, qPCR-guided workflow, validated at the protein level, that provides a replicable, decision-oriented framework for selecting efficient and fit-for-purpose short RNA delivery strategies in AML cell lines.