Additional file 1 of Magnetic transferrin nanoparticles (MTNs) assay as a novel isolation approach for exosomal biomarkers in neurological diseases
Creators: name: Jang, Yoon Ok
name: Ahn, Hee-Sung
name: Dao, Thuy Nguyen Thi
name: Hong, JeongYeon
name: Shin, Wangyong
name: Lim, Young-Min
name: Chung, Sun Ju
name: Lee, Jae-Hong
name: Liu, Huifang
name: Koo, Bonhan
name: Kim, Myoung Gyu
name: Kim, Kyunggon
name: Lee, Eun-Jae
name: Shin, Yong
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 1: Supplementary Fig. S1. Characterization of MTNs assay. (a) Washing buffer testing either with ethanol or distilled water for effectiveness on the Fe3O4@SiO2-NH2 MNPs. (b) Testing of various transferrin concentrations and determined the optimal concentration via the zeta potential analysis. (c) Performance of MTNs depends on incubation time (24 h or 3 h) with either 10 mL HCT-116 cell culture medium (1-2 &amp; 5-6) or 500 µL human normal serum sample (3-4 &amp; 7-8) using Coomassie blue staining. (d) Western blot result from 24 h incubation with either 10 mL HCT-116 cell culture medium (1-2) or 500 µL human normal serum sample (3-4). Supplementary Fig. S2. Characterization of the isolated exosomes. (a−c) Representative SEM images and NTA of the exosomes isolated from colon cancer CCM using (a and b) MTNs, (c and d) UC, and (e and f) TEI. Supplementary Fig. S3. Validation of exosome isolation. (a and b) Representative (a) SEM image and (b) zeta-potential of the exosomes isolated from colon cancer CCM using MTNs. Supplementary Fig. S4. Flowchart of statistical analysis and batch effect correction (a) From the first 746 quantified proteins, 550 proteins that were quantified at least 70% in at least one of the three groups were selected, log2-transformed, and normalized by the width adjustment method. Then, missing values were estimated from a normal distribution with an area of 0.3 minus 1.8 from the protein distribution for each sample, and batch 1 and batch 2 were adjusted for the batch effect with the protein average. Principal component analysis plot (b) before batch correction and (c) after batch correction. Circle (batch 1 samples), filled rectangle (batch 2 samples), green (Parkinson’s disease), blue (multiple sclerosis), orange (dementia). Supplementary Fig. S5. Distribution of normalized protein abundances based on label-free quantification. (a) Mapping proteins to exosomes public database, Vesiclepedia. Exosome top 100 proteins are highlighted in red. Proteins belonging to Vesiclepedia are shown in blue. The remaining proteins are shown in gray. (b) Mapping proteins to brain-elevated protein in the Human Protein Atlas. Brain-elevated proteins are highlighted in red. The remaining proteins are shown in gray. Supplementary Fig. S6. Boxplots of 20 proteins with top 10 and bottom 10 proteins with loadings of principal component 1. (a) Top 10 proteins (b) Bottom 10 proteins. Green (Parkinson’s disease), blue (multiple sclerosis), orange (dementia); * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, **** p &lt; 0.0001, n.s., not significant. Supplementary Fig. S7. Boxplots of 21 proteins highly expressed in the brain in the HPA or annotated in SYNGO. Green (Parkinson’s disease), blue (multiple sclerosis), orange (dementia); * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, **** p &lt; 0.0001, n.s., not significant. Supplementary Fig. S8. Principal component analysis (PCA) of plasma exosome proteins and assessment of the relative quality of clustering by silhouette method. (a) PCA by the three sample groups (Parkinson’s disease (PD; N = 10), multiple sclerosis (MS; N = 10), dementia (Dem; N = 10)) and silhouette plot of the groups. (b) PCA by sex (female (N = 16) and male (N = 14)) and silhouette plot of sex. (c) PCA by age groups based on age 65 (age&gt;65 (N = 15) and age≤65 (N = 15)) and silhouette plot of the age groups. Supplementary Table S1. Baseline characteristics of the patients.