Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma

<p>Data supporting the findings of the paper &quot;<a href="https://doi.org/10.1038/s41698-022-00253-z">Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma</a>.&quot; Files include output of multiplex immunohistochemistry computational&nbsp;image processing workflow for each tumor region&nbsp;and survival data for each patient. The code used to produce the results of this study is available at: <a href="https://github.com/kblise/HNSCC_mIHC_paper">https://github.com/kblise/HNSCC_mIHC_paper</a>.</p> <p>Notes about data files:</p> <ul> <li>clinicalData.csv = Contains the following columns for each tumor region: <ul> <li>sample = tumor region ID</li> <li>dtr = Progression free survival (days to recurrence)</li> <li>tnm = TNM stage</li> <li>anatomy = anatomic site of resection</li> <li>tx = therapy administered</li> <li>area = area in mm²&nbsp;of tissue region</li> </ul> </li> <li>pt .csv files&nbsp;= Matrix of single cells (rows) and marker expression&nbsp;(columns). One file per tumor region (n=47).&nbsp;Other columns include: <ul> <li>class = Cell phenotype assigned via hierarchical gating strategy (see below for classes)</li> <li>Location_Center_X&nbsp;and Location_Center_Y&nbsp;= Cartesian coordinates of cell center</li> <li>Cellsp_PD1p = PD-1 expression; 1 = PD-1⁺, 0 = PD-1^-</li> <li>Cellsp_PDL1p = PD-L1 expression; 1 = PD-L1⁺, 0 = PD-L1^-</li> <li>Cellsp_KI67p = Ki-67 expression; 1 = Ki-67⁺, 0 = Ki-67^-</li> </ul> </li> </ul> <p>Classes, corresponding cell phenotype, and gating strategy used:</p> <ul> <li>A = CD8⁺ T Cell (CD45⁺&nbsp;CD20^-&nbsp;CD3⁺&nbsp;CD8⁺)</li> <li>B = CD4⁺ T Helper&nbsp;(CD45⁺&nbsp;CD20^-&nbsp;CD3⁺&nbsp;CD8^-&nbsp;FOXP3^-)</li> <li>C = B Cell (CD45⁺&nbsp;CD20⁺)</li> <li>D = Macrophage&nbsp;(CD45⁺&nbsp;CD20^-&nbsp;CD3^-&nbsp;CD66B^-&nbsp;CD68⁺)</li> <li>E = Other Immune (CD45⁺&nbsp;CD20^-&nbsp;CD3^-&nbsp;CD66B^-&nbsp;CD68^-&nbsp;MHCII^-&nbsp;CD8^-&nbsp;FOXP3^-)</li> <li>F = Other Non-Immune (CD45^-&nbsp;PANCK^-&nbsp;&alpha;SMA^-) - excluded from analysis</li> <li>G = Noise - excluded from analysis</li> <li>H = Neoplastic Tumor&nbsp;(CD45^-&nbsp;PANCK⁺)</li> <li>J = Granulocyte (CD45⁺&nbsp;CD20^-&nbsp;CD3^-&nbsp;CD66B⁺)</li> <li>K = CD4⁺ Regulatory T Cell&nbsp;(CD45⁺&nbsp;CD20^-&nbsp;CD3⁺&nbsp;CD8^-&nbsp;FOXP3⁺)</li> <li>N =&nbsp;&alpha;SMA⁺ Mesenchymal&nbsp;(CD45^-&nbsp;PANCK^-&nbsp;&alpha;SMA⁺)</li> <li>X = Antigen Presenting Cell&nbsp;(CD45⁺&nbsp;CD20^-&nbsp;CD3^-&nbsp;CD66B^-&nbsp;CD68^-&nbsp;MHCII⁺)</li> </ul>