Additional file 1 of Plasma apolipoprotein E levels, isoform composition, and dimer profile in relation to plasma lipids in racially diverse patients with Alzheimer’s disease and mild cognitive impairment
Creators: name: Giannisis, Andreas
name: Al-Grety, Asma
name: Carlsson, Henrik
name: Howell, Jennifer C.
name: Hu, William T.
name: Kultima, Kim
name: Nielsen, Henrietta M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 111714
subject: Mental Health
subject: Hematology

description: Additional file 1: Table S1. Spiked amount of the heavy labeled peptides in each sample. Table S2. Endogenous peptides in the different APOE genotypes. Table S3. Mass-spectrometry determined plasma apoE phenotypes. Table S4A. Distribution of plasma apoE in monomers, dimers and multimers. Table S4B. Plasma apoE monomers/dimer/multimer profile in Black/African-Americans. Table S4C. Plasma apoE monomers/dimer/multimer profile in Non-Hispanic whites. Table S5. Non-significant correlations between plasma total apoE levels with cognition and CSF AD biomarkers. Table S6. Non-significant correlations between plasma total apoE levels and CSF AD biomarkers. Table S7. Correlations between plasma apoE monomers and dimers in APOE ε3/ε3 and APOE ε3/ε4 subjects. Table S8. Associations between plasma apoE3 monomers and dimers, plasma lipids and age in APOE ε3/ε3 and APOE ε3/ε4 subjects. Table S9. Significant associations between plasma lipids, age, cognition and CSF markers. Fig. S1. Quantification of apoE isoforms. (a) Equation used for the quantification of endogenous apoE peptides LGPLVEQGR, LGADMEDVCGR, LGADMEDVR, LAVYQAGAR and CLAVYQAGAR. (b) Correlation between the peptides LAVYQAGAR and LGPLVEQGR in APOE ε3/ε3 (open dots), APOE ε3/ε4 (open rhombus) and APOE ε4/ε4 (black dots) studied subjects. (c) Correlation between apoE3 isoform levels directly quantified by the peptide LGADMEVCGR or calculated by subtracting the levels of apoE4 peptide LGADMEDVR from the peptide LAVYQAGAR in individuals with APOE ε3/ε4 genotype. (d) Correlation between apoE4 isoform levels quantified by the peptide LGADMEVR or calculated by subtracting the levels of apoE3 peptide LGADMEDVCGR from the peptide LAVYQAGAR in subjects with APOE ε3/ε4 genotype. (e) Correlation between the levels of plasma apoE quantified by the peptide LGPLVEQGR which is common for all apoE isoforms and by adding the apoE isoforms in individuals with APOE ε2/ε3 (open triangles), APOE ε2/ε4 (x-shape), APOE ε3/ε3 (open dots), APOE ε3/ε4 (open rhombus) and APOE ε4/ε4 (black dots). Fig. S2. Calibration curves for the peptides LGPLVEQGR (a), LGADMEDVCGR (b), LAVYQAGAR (c), and CLAVYQAGAR (d). Increasing amount of heavy labeled peptide added in a plasma pool containing all apoE variants plotted against the ratio of heavy to the corresponding endogenous variant. The linearity of the curves was assessed by the weighted sum of squares (1/X2) in non-log transformed data and both axes are shown in logarithmic scale. Fig. S3. Plasma apoE molecular species. (a-d) Western blot analysis under non-reducing conditions to visualize plasma apoE monomers (36 kDa), heterodimers (43 kDa) and homodimers (95 kDa) in the plasma of Black/African-Americans (B/AAs) and Non-Hispanic whites (NHWs) with APOE ε3/ε3 (a), APOE ε3/ε4 (b) as well as with APOE ε2/ε3 (c) and APOE ε2/ε4 (d) genotypes. An upper band at 100 kDa corresponding to apoE2 multimeric molecular species was found in APOE ε2 plasma (c-d). (e-f) In assayed plasma from APOE ε2/ε3 Black/African-Americans (B/AAs) and Non-Hispanic whites (NHWs) a band at 55 kDa corresponding to apoA-II-apoE2-apoA-II heterotrimeric structure was detected when the membrane was imaged for 2 minutes (e), this band was not detected in APOE ε2/ε4 plasma (f). (g) Only apoE monomers were detected in APOE ε4/ε4 plasma samples. ApoE molecular species were detected using the mouse pan-apoE antibody WUE-4 (Novus Biologicals). Molecular weight was determined using the protein ladder (PL) PageRuler™ Prestained Protein Ladder, 10 to 180 kDa (Thermo Fisher Scientific). Color differences for B/AAs or NHWs correspond to clinical diagnosis, with black color indicating controls, while blue and red correspond to MCI and AD patients. Fig. S4. Effect of gender and race/ethnicity on the levels of plasma lipids. (a-d) Levels of plasma total cholesterol (a), HDL (b), LDL (c) and triglycerides (d) in males and females of combined racial/ethnic groups as well as with different races/ethnicities. Data is presented as median (minimum – maximum). p-values acquired using Student’s t-test. ns: non-significant, B/AA: Black/African-Americans, NHW: Non-Hispanic whites, *:p-value for data after log transformation. :p-value obtained after including the APOE genotype of the studied subjects as a covariate in the analysis.