Uninterrupted Mutant Huntingtin CAG-repeat but Not Polyglutamine Length Predicts Striatal Nuclear Pathogenesis and Transcriptionopathy in HD Mice
Huntington's disease (HD) is caused by CAG repeat expansion at the N-terminal region of huntingtin (HTT) gene and characterize by neuronal cell loss and neuroinflammation transcriptional profile change in striatum, cortex and other brain regions.  Here we reported generation and characterization of BAC-CAG, a novel full length human HD mouse model host over 120 uninterrupted CAG repeats. we performed RNA-seq analysis of the striatum and cortex of BAC-CAG mice at 2m, 6m and 12m of age (N=6 per genotype, sex balanced). We observed an age-dependent transcriptionopathy in the striatum of BAC-CAG mice, with only 7 and 36 significant DE genes in 2m and 6m striatum respectively (FDR<0.1), but 820 DE genes (538 downregulated and 282 upregulated genes) at 12m of age (FDR<0.1). The transcriptomic deficits in this model are highly striatum-selective, as we only detected 4, 3 and 14 DE genes (FDR<0.1) at 2m, 6m and 12m respectively in BAC-CAG cortices compared to WT controls. Remarkably, we found a highly significant positive transcriptome-wide correlation (r=0.62) of DE Z statistics between BAC-CAG vs WT at 12m and Q140 vs WT at 6m (p<1e-200). This result demonstrates a high concordance of both upregulated and downregulated genes in the BAC-CAG striatum compared to that of allelic series KI mice; but RNA-seq studies of BACHD mice at 12m and found only 50 genes significantly differentially expressed (DE) genes (FDR<0.1) in the striatum at 12m of age compared to WT littermates, 31 downregulated and 19 upregulated genes. In the cortex at 12m of age, BACHD only showed 6  significantly downregulated genes and 7 upregulated genes comapred to WT controls (FDR<0.1). Overall design: Three males and three females BAC-CAG mice and their WT littermates from 2, 6 and 12m age groups, respectively, were perfused with PBS and striatum, cortex and cerebellum were dissected out immediately. The samples were fresh frozen and kept at -80°C. Total RNA was extracted using Qiagen (Valencia, CA) RNeasy kit with QIA shredder columns. cDNA libraries were generated using Illumina TruSeq RNA Library Prep Kit v2 and sequenced using an Illumina Illumina HiSeq 4000 sequencer with strand-specific, paired-end, 69-mer sequencing protocols to a minimum read depth of 37.5 million reads per sample. In another experiment, 4 BACHD and 4 WT littermate control mice (both 2 males and 2 females) at 12 months age were used. Their cortical and striatal tissues were dissected and assayed as above.