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. We performed an 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 identified sex and diet as the major drivers of transcriptomic variation, although differential expression analyses identified a subset of genes displaying genotype-specific transcriptional alterations. Several changes were unique to the GD mosquitoes across conditions, consistent with a potential contribution of the gene drive cassette beyond target gene disruption. The mRNA transcripts encoded by genes such as histone H1 , ficolin-1 , and E3 ubiquitin-protein ligase XIAP were present in decreased abundance, 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 while offering relevant insights into their biological effects and potential implications for field implementation.