Journal: Scientific Reports

Article Title: Comprehensive antigen profiling predicts post-surgical neuropathic pain in women treated for breast cancer

doi: 10.1038/s41598-026-41637-6

Figure Lengend Snippet: Characterization of antibody epitope profiles from the serum of patients with CPSNP ( n = 27) and non-CPSNP ( n = 30) by MVA. ( a ) Clinical study design. Samples from 57 patients with breast cancer (BC) diagnosis were analyzed. Each patient had given two samples: one before (timepoint 1, T1) and another after (timepoint 2, T2) surgery. The period between T1 and T2 varied between 4 and 9 years. The control group (CTRL) included serum samples derived from T1 and T2 timepoints from six patients from the same cohort without ICBN injury and without pain. ( b ) Age distribution of the 63 patients at T1 and T2. ( c ) Antibody epitope profiling with MVA. MVA workflow comprised different sequential steps: (i) immunocapture of IgG-phage complexes from a sample using the phage library (random 12-mer peptide M13 phage library); (ii) high-throughput Illumina HiSeq2500 short DNA sequencing of bar-coded phage DNA; (iii) bioinformatical data analysis resulting in antibody epitope identification. The sequenced DNA reads obtained were quality-checked, translated to peptide sequences, and sample- and cohort-specific epitopes from peptide sets were developed by the SPEXS2 pattern search algorithm. Schematic presentation was created with biorender.com ( d ) Highly individual immunoreactive epitope profiles shared similar features in paired sera (T1 and T2) samples, as observed from MVA. The 5000 most IgG-bound (abundant) peptide values (read counts) from each sample were taken into immunoprofile similarity analysis. For all sample pairs, the normalized scalar products of peptide count vectors were calculated for the cosine similarity index (CSI, R package lsa). The CSI values depicted are 0.70 and above (color-coded scale on the right), showing highly correlated immune profiles. Based on CSI analysis, the data of one CPSNP, one non-CPSNP and two CTRL samples were removed from quantitative analyses (Table ). Group sizes: Paired samples n = 59, Unpaired sample pairs = 6844. Sample pairs were combined from timepoint samples of cohort patients: CPSNP n = 26, non-CPSNP n = 29 and CTRL n = 4 (Table ). BC: breast cancer; CPSNP: chronic post-surgical neuropathic pain; CSI: cosine similarity index; CTRL: control; MVA: mimotope variance analysis; NGS: next generation sequencing; NP: neuropathic pain; T1: timepoint 1; T2: timepoint 2.

Article Snippet: In brief, plasma samples ( n = 126, 2 μl of plasma per analysis) were incubated with Escherichia coli M13 phage library displaying random 12-mer peptides (complexity 1 × 10 9 peptides; NEB, E8111L).

Techniques: Biomarker Discovery, Control, Derivative Assay, High Throughput Screening Assay, DNA Sequencing, Next-Generation Sequencing

Journal:

Article Title: Immune-Directed Gene Therapeutic Development for Alzheimer's, Prion, and Parkinson's Diseases

doi: 10.1007/s11481-008-9133-3

Figure Lengend Snippet: Immunotherapy for neurodegenerative diseases. AD, TSE, and PD share a common hallmark pathobiologic feature of misfolded toxic proteins. In this review, we discuss the use of both active and passive vaccination approaches to decrease the amount of the toxic moieties. a Active vaccination utilizing HSV amplicon delivery of Aβ and IL-4 shaped the immune response toward TH2 in a mouse model of AD decreasing the Aβ plaque levels (Frazer et al. 2008). b Passive vaccination of scrapie-challenged mice with rAAVscFvPrPC decreased the PrPSc burden and improved clinical and behavioral outcome measurements (Wuertzer et al. 2008). c Anti-SYN scFv have been identified with preferential binding to monomeric and/or protofibrillar SYN conformers (Emadi et al. 2004, 2007; Zhou et al. 2004; Maguire-Zeiss et al. 2006; Lynch et al. 2008). Subsets of these scFv have demonstrable efficacy in preventing SYN aggregation (Emadi et al. 2004; Zhou et al. 2004; Emadi et al. 2007; Lynch et al. 2008). In this schematic, we also consider scFv that may accelerate the formation of toxic oligomers to larger nontoxic aggregates

Article Snippet: Using monomeric, aggregated, and dopamine-modified SYN, we interrogated a human scFv phage display library for sequence and conformation-specific anti-SYN binders ( Maguire-Zeiss et al. 2006 ).

Techniques: Amplification, Binding Assay