Case Study / Tutorial
Analyze Cell Identity
In this example, we demonstrate how to use CellSeekr to characterize immune cell composition in GBM patients who responded to PD-1 blockade therapy.
Goal: Determine the proportion of myeloid cells in PD-1 blockade-responsive GBM patients relative to newly diagnosed GBM patients.
Steps
1
Navigate to analyze.cellseekr.com. Select “Targeted” analysis by clicking on the box. The analysis page will open.
2
For immune cell expression analysis, select “Standard.”
3
In order to analyze the glioblastoma (GBM) dataset, select “Glioblastoma (GBM)” in the “Tumor / Dataset” drop box.
4
The name of the corresponding GEO study (GSE235676) will populate automatically. Under ‘Select Pairwise Comparison,’ choose the group comparison you wish to analyze. For this example, select ‘New Diagnosis vs. Responders.’
5
Under “Select a Cell Type (Phenoype 1)“, select “Myeloid.” This designates myeloid cells as the numerator population to be quantified in the analysis.
6
Under “Denominator for percentage calculation,” select “Immune (UBC+ & PTPRC+).” This sets the total immune cell population as the denominator, enabling calculation of myeloid cells as a proportion of all immune cells identified in the sample.
7
Click “Apply Filter & Run Analysis” to initiate the computation. A progress bar will indicate the status of the analysis. Depending on dataset size, the analysis may take up to several minutes to complete.
Results
CellSeekr will generate two primary outputs: a table titled ‘Filtered Cells per Patient,’ containing raw per-patient data including cell counts and percentages for each condition, and a bar graph titled ‘Percent Plot for Selected Pairwise Groups.’
The bar graph will display one bar per pairwise condition — in this example, one representing the proportion of myeloid cells among all immune cells in newly diagnosed patients, and one representing the same proportion in PD-1 blockade responders.
An asterisk (*) indicates a statistically significant difference in immune cell proportion between the two patient groups (*p<0.05).
Bar Graph
The bar graph serves as the primary data output, providing a visual summary of the selected pairwise comparison alongside its corresponding statistical analysis.
Results
Analysis of myeloid cell composition in GBM patients reveals a marked reduction in myeloid cell proportion following PD-1 blockade therapy. Myeloid cells comprised approximately 70% of total immune cells in newly diagnosed patients (n=7), compared to approximately 38% in treatment responders (n=7), suggesting that effective immunotherapy response is associated with a substantial remodeling of the immunosuppressive myeloid compartment in GBM.
New diagnosis
Myeloid: 69.967% (SD 10.248%)
N = 7 patients
Responders
Myeloid: 37.890% (SD 17.665%)
N = 7 patients
Notes:
- Custom myeloid phenotype: In the example above, we utilized the pre-computed myeloid cell identity available in CellSeekr. To incorporate additional genes into the myeloid definition, select ‘Other’ in Step 3 instead of ‘Myeloid,’ and construct a custom gene signature tailored to your analysis.
- Using the raw data table: The raw data table is provided for downstream use and can be copied directly from the platform for further analysis in software such as GraphPad Prism, Microsoft Excel, or other statistical tools.