The key feature of Huntington disease (HD) pathology is the accumulation of soluble mutant huntingtin (Htt) protein into micrometer-sized inclusion bodies. There is increasing evidence that soluble mutant Htt states are most proteotoxic and trigger an enhanced risk of death prior to aggregation1. Whereas inclusions confer different changes to cellular health, possibly adapting the cell to stress with the toxicity becoming nullified as the soluble states are sequestered into visible aggregates. Yet the molecular mechanisms underpinning these changes remain unclear. This is primarily due to the difficulty in separating the cells based on their aggregation states. Using the flow cytometry method of pulse-shape analysis (PulSA)2 to sort neuroblastoma (Neuro2a) cells enriched with mutant or wild-type Htt into different aggregation states, we clarified which transcriptional signatures were specifically attributable to discrete steps in the aggregation process. Dampened CREB signalling invoked specifically by soluble mutant Httex1 states was the most striking change seen overall. Toxicity could be rescued by stimulation of CREB signalling. Other biological processes mapped to different steps of aggregation included transcription regulation by HDACs and HATs - BRD4, altered NF-kB signalling, autophagy, SUMOylation, NAD+ biosynthesis, ribosome biogenesis and altered HIF-1 signalling. These findings could lead the way for therapeutic strategies targeting key molecular changes before and after pathological protein aggregation.