Journal: iScience

Article Title: Multiplexed protein profiling reveals spatial subcellular signaling networks

doi: 10.1016/j.isci.2022.104980

Figure Lengend Snippet: Expression and spatial signaling analysis on tissue microarray from diverse lung cancers (A) Multiplexed protein images of lung tissue samples at normal, malignant stages IB, IIA, and IIIA were presented. The tissue was masked based on pan-cytokeratin-positive staining. (B) The normalized total intensity of each marker per cell was provided in pan-cytokeratin-negative (false) and -positive (true) regions. Asterisk indicates the statistical significance for pairwise comparison; p-value calculated using Wilcoxon rank-sum test (ns: 0.05 < p, ∗: 0.01 < p ≤ 0.05, ∗∗: 0.001 < p ≤ 0.01 ∗∗∗: 0.0001 < p ≤ 0.001, ∗∗∗∗: p<=0.0001). Boxplot showing the distribution of the data with minimum, first quartile (Q1), median, third quartile (Q3), and maximum. (C) The comparison of signaling expression profiles of 24 markers was provided. The tissue cores were classified by stages and pan-cytokeratin expression. Classification of signaling maps was demonstrated for 21 patients and 55 tissue cores using the average linkage method based on Euclidean distance to cluster cores and markers along the x and y axis. Data are represented as mean expression per core. (D) Heatmap of 19 clusters on a Z score scale was shown. Each cluster represented one distinct expression profile of 17 protein markers in lung microarray, excluding segmentation and epigenetic markers. Data are represented as mean expression per cluster. (E) Multiplexed signaling protein images from tissue cores were analyzed by single-cell level clustering of 17 protein markers in four stages of tumor. The expression profile was clustered in pan-cytokeratin-positive regions. Each stage contained three images from the same patient.

Article Snippet: FFPE lung cancer microarray tissue blocks were purchased from Biomax with 61 cores and 21 cases (BS04081a).

Techniques: Expressing, Microarray, Staining, Marker, Comparison

Journal: iScience

Article Title: Multiplexed protein profiling reveals spatial subcellular signaling networks

doi: 10.1016/j.isci.2022.104980

Figure Lengend Snippet:

Article Snippet: FFPE lung cancer microarray tissue blocks were purchased from Biomax with 61 cores and 21 cases (BS04081a).

Techniques: Software

Journal: Laboratory Investigation; a Journal of Technical Methods and Pathology

Article Title: Accelerated instability testing reveals quantitative mass spectrometry overcomes specimen storage limitations associated with PD-L1 immunohistochemistry

doi: 10.1038/s41374-019-0366-y

Figure Lengend Snippet: Representative PD-L1 expression assessed by E1L3N IHC in FFPE gastric carcinoma under normal atmospheric conditions ( a – c ) and in NSCLC under acceleration conditions ( d – f ). a Day 0, b 4.5 months, c 24 months; d Day 0, e Day 9, f Day 28. PD-L1 programmed-death-ligand-1, IHC immunohistochemistry, FFPE formalin-fixed, paraffin embedded, NSCLC non-small cell lung cancer.

Article Snippet: FFPE tissue blocks of non-small cell lung carcinoma (NSCLC), gastric carcinoma, placenta, and tonsil tissue were commercially acquired from Asterand Bioscience (Detroit, MI, USA), US Biomax (Rockville, MD, USA), Tristar Technology Group (Washington, DC, USA), and Indiana University Health Methodist Hospital biobank (Indianapolis, IN, USA) in either tissue microarray (TMA) or whole section format.

Techniques: Expressing, Immunohistochemistry, Formalin-fixed Paraffin-Embedded

Journal: Laboratory Investigation; a Journal of Technical Methods and Pathology

Article Title: Accelerated instability testing reveals quantitative mass spectrometry overcomes specimen storage limitations associated with PD-L1 immunohistochemistry

doi: 10.1038/s41374-019-0366-y

Figure Lengend Snippet: Bars represent number of cases in series with PD-L1 expression equal or above TPS clinical cutoff thresholds. PD-L1 programmed-death-ligand-1, TPS tumor proportion score, TC tumor cell, NSCLC non-small cell lung cancer, FFPE formalin-fixed, paraffin embedded.

Article Snippet: FFPE tissue blocks of non-small cell lung carcinoma (NSCLC), gastric carcinoma, placenta, and tonsil tissue were commercially acquired from Asterand Bioscience (Detroit, MI, USA), US Biomax (Rockville, MD, USA), Tristar Technology Group (Washington, DC, USA), and Indiana University Health Methodist Hospital biobank (Indianapolis, IN, USA) in either tissue microarray (TMA) or whole section format.

Techniques: Expressing, Formalin-fixed Paraffin-Embedded

Journal: Laboratory Investigation; a Journal of Technical Methods and Pathology

Article Title: Accelerated instability testing reveals quantitative mass spectrometry overcomes specimen storage limitations associated with PD-L1 immunohistochemistry

doi: 10.1038/s41374-019-0366-y

Figure Lengend Snippet: Placenta and tonsil FFPE sections incubated in the acceleration chamber under different environmental conditions at day 28; a – d : 100% oxygen and 80% humidity at either 20 °C or 37 °C, then stained for PD-L1 (E1L3N) or pan-CK (AE1/AE3): a Placenta PD-L1, b Tonsil PD-L1, c Placenta pan-CK, d Tonsil pan-CK. 100% oxygen and 37 °C at either 45% or 80% humidity at day 28, e Placenta PD-L1, f Tonsil PD-L1. Control conditions: 20 °C, atmospheric humidity and oxygen. Bar represents mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001. PD-L1 programmed-death-ligand-1, CK cytokeratin, FFPE formalin-fixed, paraffin embedded.

Article Snippet: FFPE tissue blocks of non-small cell lung carcinoma (NSCLC), gastric carcinoma, placenta, and tonsil tissue were commercially acquired from Asterand Bioscience (Detroit, MI, USA), US Biomax (Rockville, MD, USA), Tristar Technology Group (Washington, DC, USA), and Indiana University Health Methodist Hospital biobank (Indianapolis, IN, USA) in either tissue microarray (TMA) or whole section format.

Techniques: Incubation, Staining, Formalin-fixed Paraffin-Embedded