Lejeune et al. BMC Genomics 2012, 13:91 http://www.biomedcentral.com/1471-2164/13/91 approach confirmed the trends observed in gene set enrichment analysis, namely the detection of pathways involved in metabolism, immune response and develop- ment. Additionally, it provided insights into the possible mechanisms of how RNAi hits potentially interact to modify 128Q-neuron dysfunction. We notably detected modules seeded by RNAi hits that were annotated for ‘Huntington’s disease’, ‘Parkinson’s disease’ and ‘pantho- tenate kinase activity’, the latter previously associated with neurodegeneration [45]. More largely, we detected modules annotated for biological processes established or strongly suspected (see [3] for review of HD mechan- isms) to have a role in neurodegenerative disease patho- genesis such as ‘oxidative phosphorylation’, ‘cholesterol biosynthesis’ and ‘cell cycle’. Interestingly, several mod- ules were annotated for cell differentiation and survival pathways such as ‘Wnt signaling’, a pathway suspected to have a role in HD pathogenesis [46], ‘apoptosis sig- naling’ and ‘integrin signaling’, suggesting that such pathways might be targeted for therapeutic intervention in HD. Annotations for metabolic pathways such as ‘sucrose metabolism’, ‘pentose phosphate pathway’ and ‘cholesterol biosynthesis’ were also detected, consistent with the notion that metabolic pathways may be tar- geted for therapeutic intervention in HD [3,47]. Addi- tionally, several modules were annotated for genes of interest in HD such as druggable genes (as notably observed in the modules for suppression of 128Q-neu- ron dysfunction by RNAi; see Additional file 9: Table S8), htt partners, and genes involved in autophagy, mito- chondrial function and synaptic activity, which further illustrated the relevance of our dataset to neuroprotec- tive target discovery in HD. Modifiers of 128Q-neuron dysfunction in C. elegans are dysregulated in the striatum of either CHL2 knock-in mice or R6/2 transgenic mice To further assess the relevance of our RNAi data to can- didate target profiling and discovery in HD, we next compared our dataset to striatal gene expression data collected from mouse models of HD. Given that 128Q nematodes recapitulate progressive neuron dysfunction, which may occur in HD before cell loss, we compared our RNAi data to striatal gene expression data collected from the CHL2(Q150/Q150) knock-in mice, a model that may recapitulate progressive neuronal injury similar to that found early in the course of HD [48]. To reach a more specific level of comparison, we also compared our data to striatal gene expression data collected from the R6/2 transgenic mice, a model that exhibits rapid phenotypic changes as induced by a short N-terminal fragment of mutant htt [10]. Among the 662 modifiers of 128Q-neuron dysfunction in C. elegans, 239 genes were conserved in the mouse. Forty-nine genes were Page 10 of 14 found at the intersection of the C. elegans RNAi data and gene dysregulation data in HD mice (Figure 4). Six of these 49 genes including Acy1, Sh3gl3, Snw1, Aars, Ppp5 and Gpi1 were oppositely dysregulated in the CHL2 mice compared to R6/2 mice (Figure 4), illustrat- ing the differences that may exist between these two models at the molecular level. In contrast, genes that are involved in a variety of biological processes and that modulate 128Q-neuron dysfunction when knocked- down by RNAi were dysregulated in either the CHL2 or R6/2 mice (Figure 4), illustrating how data comparison using substractive analysis may be useful for target prioritisation. Notably, 12 genes that suppress 128Q- neuron dysfunction when knocked-down by RNAi in C. elegans were observed to be up-regulated in either the CHL2 or R6/2 mice, suggesting that inhibiting these genes might elicit neuroprotection in HD. One of them, the phenylalanine-4-hydroxylase Pah, appeared to be particularly interesting since it is a druggable gene that acts upstream of tyrosine-dopamine biosynthesis and since increased dopamine levels were previously asso- ciated with early HD phenotypes such as hyperkinesia [49]. Discussion The aim of our study was to collect information on the genes and pathways that may act as modifiers of the early stage of mutant htt toxicity in HD such as neuron dysfunction. To this end, we used an in vivo model to screen for gene inactivations that modulate the neuronal dysfunction induced by expanded-polyQ expression in C. elegans, and we used network-boosted analysis to enhance the identification of candidate pathways that may be further evaluated in mammalian systems. We identified 662 hits from the evaluation of 6034 genes. Compared to RNAi screens based on biochemical pro- cesses such as protein aggregation [38-40], the relatively high number of hits in our study is likely to reflect the multigenic nature of behavioral phenotypes such as response to touch rather than changes in polyQ- expanded htt expression levels. Previously-identified modulators of neuron dysfunction in expanded-polyQ nematodes do not change transgene expression levels [14,18], further suggesting most RNAi effects are not due to changes in htt expression levels. In contrast to 128Q-neuron dysfunction, neuronal dysfunction produced by normal polyQ expression in our trangenic nematodes is not directly relevant to HD pathogenesis. Microarray analysis of gene expression in touch receptor cells isolated by fluorescence-activated cell sorting indeed indicated that only 18 out of 2000 genes dysregulated by 128Q expression are also dysregu- lated by 19Q expression (submitted elsewhere), and sev- eral of the expanded-polyQ cytotoxicity that we