Journal: Acta Neuropathologica Communications
Article Title: Pathobiology of the autophagy-lysosomal pathway in the Huntington’s disease brain
doi: 10.1186/s40478-025-02131-8
Figure Lengend Snippet: Correlation between marker expression levels and HD progression stages across different brain regions, grouped by marker category. The heatmap illustrates Spearman’s rank correlation coefficients (ρ) between the relative mRNA expression levels from qPCR of selected molecular markers and Huntington’s disease (HD) severity. Analyses were performed on human post-mortem brain tissue from control (Ctl) and HD patients (grades HD2, HD3, HD4), with severity numerically encoded for correlation (Ctl = 0, HD2 = 1, HD3 = 2, HD4 = 3). Correlations are shown for STR, CTX, and CBM). Markers are grouped into functional categories, displayed from top to bottom: Induction Markers (Autophagy induction): ATG7, LC3, p62. Lysosomal Markers (Lysosomal biogenesis, hydrolases and structural elements): TFEB, TFE3, CTSB, CTSD, HEXA, LAMP1, LAMP2. Cellular Markers (cellular processes): ENO2, TUBB3, GFAP, AIF1, MBP. The color of each cell represents the Spearman ρ value, with a continuous gradient from blue (strong negative correlation, ρ = −1) through white (no correlation, ρ = 0) to red (strong positive correlation, ρ = + 1). Nominal p-values for the correlations are indicated by asterisks: * p < 0.05, ** p < 0.01, *** p < 0.001.
Article Snippet: Antibodies for immunohistochemistry (IHC), western blotting (WB): The following primary antibodies were used in this study. (1) from Cell Signaling Technology: tHTT rabbit mAb (clone D7F7, #5656, targeting residues surrounding Pro1220 of human HTT and detecting total HTTs), p70S6K pAb (#9202), p-p70S6K (T389) pAb (#9205), ULK1 pAb (#4773), p-ULK1 (S757) pAb (#6888, #14202; detecting S757 or S758 of mouse or human ULK1, respectively), ATG5 rabbit mAb (#12994), ATG7 pAb (#2631), ATG13 rabbit mAb (#13273), p-ATG13 (S355) rabbit mAb (#26839), VPS34 rabbit mAb (#81453), TRAF6 rabbit mAb (#8028), Calnexin rabbit mAb (#2679). (2) from Millipore-Sigma: ntHTT mAb (N-Terminus-specific, mEM48, #MAB5374, preferentially recognizing aggregated HTT) , ATG5 pAb (#ABC14), K48- or K63-specific ubiquitin mAb (#05–1307, #05–1308, respectively), βIII-tubulin mAb (#SAB4700544), β–actin mAb (#A1978). (3) from other vendors: BECN1 mAb (BD Biosciences, #612113); LC3 pAb (Novus Biologics, #NB100-2220), ATG9 (Novus Biologics, #B-110–56893); p62 mAb (BD Biosciences, #610832) or C-term-specific p62 Guinea Pig pAb (Progen Biotechnik, #C-1620); total ubiquitin pAb (Dako Agilent, #Z0458), LAMP1 or LAMP2 rat mAb (Developmental Studies Hybridoma Bank, University of Iowa, #H4A3 or #H4B4, respectively); CTSD sheep pAb (D-2–3, in-house made) ( ); CTSD pAb (Scripps Laboratories, #RC245), CTSD mAb (CD1.1, in-house made) ( ); CTSB pAb (Cortex Biochemicals, #CR6009RP), CTSB goat pAb (Neuromics, #GT15047).
Techniques: Marker, Expressing, Control, Functional Assay