CRISPR-based gene drive systems alter the transcriptome in Anopheles gambiae mosquitoes

CRISPR-based gene drive systems have emerged as promising strategies for mosquito population control to reduce the impact of vector-borne diseases such as malaria. However, their broader molecular impact on the mosquito transcriptome remains poorly understood. Here, we performed a comprehensive RNA sequencing analysis of Anopheles gambiae gene drive (GD) mosquitoes under three conditions: males fed with sugar, females fed with sugar, and females fed with blood. Principal component analyses distinguished samples by sex and diet, while differential expression analysis revealed genotype-specific transcriptional alterations. Most importantly, several changes were unique to the GD mosquitoes, indicating that these alterations stem from the gene drive cassette itself rather than target gene disruption. The mRNA transcripts encoded by genes such as histone H1, ficolin-1, and E3 ubiquitin-protein ligase XIAP were present in increased abundance across all conditions tested, suggesting a potential impact on chromatin structure, immune function, and protein degradation pathways. These results highlight molecular responses resulting from the engineered gene drive alleles, offering relevant insights into their biological effects and potential implications for field implementation.