Journal: Nature Communications

Article Title: Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer

doi: 10.1038/s41467-022-34407-1

Figure Lengend Snippet: a Upset plot presenting the intersection of differentially abundant proteins associated with lymph node metastasis in the multiple sites (pN+ vs. pN0; p ≤ 0.05; two-sided unpaired Student’s t -test or proteins detected exclusively in one group; primary tumor – malignant: n = 11 pN+, 14 pN0 patients; primary tumor and lymph node – non-malignant: n = 13 pN+, 14 pN0; buffy coat: n = 11 pN+, 13 pN0; saliva cells: n = 13 pN+, 11 pN0). b Combined view of the top-10 GO biological processes overrepresented for tissues and fluids considering differentially abundant proteins between pN+ and pN0 from a (Enrichment FDR ≤ 0.01; hypergeometric test followed by FDR correction). c Abundance of 23 proteins significantly associated with lymph node metastasis in multiple sites (pN+ vs. pN0; p ≤ 0.05; two-sided unpaired Student’s t -test or proteins detected exclusively in one group). d Relationship between GO biological processes significantly enriched for the 23 common proteins listed in c (Enrichment FDR ≤ 0.05; hypergeometric test followed by FDR correction). Darker nodes are more significantly enriched gene sets, bigger nodes represent larger gene sets and thicker edges represent more overlapped genes. e Differentially abundant proteins from proteomics data identified as cluster markers of cells from the lymph node microenvironment (upper), the tumor microenvironment (bottom left), and PBMC (bottom right). The size of the circles indicates the percentage of cells expressing the clusters markers in the scRNASeq external dataset . Colors represent the LFQ intensity of the metastasis-associated proteins herein evidenced from the proteomes of lymph nodes or primary tumor non-malignant cells or buffy coat. Higher LFQ levels in pN+ are represented in red and higher LFQ levels in pN0 are in blue. f Immune cell count/mm 3 from 9 pN+ and 16 pN0 HNSCC patients. Lymphocyte cell count/mm 3 was significantly associated with lymph node metastasis (pN+ vs. pN0; p = 0.0261; two-sided unpaired Student’s t -test). The results obtained for basophils and eosinophils were not plotted to improve visualization (low cell count), and the values were not statistically different between pN+ and pN0 samples. Data are expressed as mean ± standard deviation. * p ≤ 0.05. Source data are provided as a Source Data file.

Article Snippet: Subsequently, public scRNASeq datasets comprised of 18 HNSCC tissue samples and a human peripheral blood mononuclear cell (PBMC) sample from a healthy donor ( https://www.10xgenomics.com ) were used to generate signatures that were further employed as reference matrices in this study (Supplementary Fig. ; Methods section ‘scRNASeq processing and differential expression’).

Techniques: Expressing, Cell Counting, Standard Deviation

Journal: Nature Communications

Article Title: Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer

doi: 10.1038/s41467-022-34407-1

Figure Lengend Snippet: a Expression of the six selected targets (SRSF1, SRSF2, SRSF3, SRSF5, TRA2A, and CD209) in immune populations from HNSCC that were identified by scRNASeq public data in lymph node pN+ microenvironment. b Average fold change (y axis) and adjusted p (x axis) between pN+ and pN0 tumor microenvironments for the six targets evaluated in individual immune populations (two-sided Wilcoxon test followed by Benjamini-Hochberg correction). The dashed lines represent a p threshold of 0.05 and significant results are indicated by arrows. The differences could not be tested for plasma and CD8+ T exhausted cells because there were not enough cells for comparison. c Heat-map representing the average fold change for GO splicing genes differentially expressed between pN+ and pN0 immune populations from tumor microenvironments (pN+ vs. pN0; adjusted p ≤ 0.05; two-sided Wilcoxon test followed by Benjamini-Hochberg correction). Blank cells indicate transcripts without difference between pN+ and pN0. d Proportion of up- and downregulated genes from ( c ) that are expressed by the immune cells. Gene expression (up- and downregulation in pN+ when compared to pN0) was significantly associated with the immune cell types ( p = 0.0210; two-sided Fisher’s exact test). * p ≤ 0.05. e Heat-map representing the average ratio for GO splicing proteins differentially expressed between pN+ and pN0 multisites (pN+ vs. pN0; p ≤ 0.05; two-sided unpaired Student’s t -test). The log2 LFQ ratios are shown for the statistically significant proteins. Blank cells indicate proteins that were not differentially abundant between pN+ and pN0. f Proportion of up- and downregulated proteins from ( e ) expressed in the multisites. Protein abundance (up- and downregulation in pN+ when compared to pN0) was significantly associated with the environments ( p = 0.0008; two-sided Fisher’s exact test). LN: lymph node; PT: primary tumor. *** p ≤ 0.001. Source data are provided as a Source Data file.

Article Snippet: Subsequently, public scRNASeq datasets comprised of 18 HNSCC tissue samples and a human peripheral blood mononuclear cell (PBMC) sample from a healthy donor ( https://www.10xgenomics.com ) were used to generate signatures that were further employed as reference matrices in this study (Supplementary Fig. ; Methods section ‘scRNASeq processing and differential expression’).

Techniques: Expressing, Clinical Proteomics, Comparison, Gene Expression, Quantitative Proteomics