Reference genes for M2 Macrophages

[jakesleighton]

Hello,
I really enjoyed your paper (great method!), and I am applying spaCET for deconvolution of a lung cancer ST Visium data set. For validation, I would like to know how to find the marker genes spaCET uses to differentiate M1 and M2 macrophages (or any cell type). In the spaCET paper, you reference the paper (https://www.sciencedirect.com/science/article/pii/S0092867418307232?via%3Dihub#cebib0010) for the M1 and M2 marker genes used by spaCET. However, when I create the spaCET object I see different gene lists in the (SpaCET_obj@results[["deconvolution"]][["Ref"]][["sigGenes"]][["Macrophage M2"]]) and (SpaCET_obj@results[["deconvolution"]][["Ref"]][["refProfiles"]]), and none of these genes seem to overlap the marker genes from the paper. If you could please help me understand what markers are used for each cell type (especially the M1/M2 macrophages), I would really appreciate it! Thanks!

Best,
Jake

[beibeiru]

Hi, Jake,

I am happy that our tool can help with your data analysis!
Please see the following analysis, they do have several overlapped markers.

However, they are not the same completely.
Because the M1 or M2 markers from our tool were generated by these steps.

1. use the M1 or M2 markers from the paper to separate macrophages from scRNA-seq datasets into two groups, i.e., M1 high and M2 high clusters.
2. do differential expression analysis between these two groups to identify differentially expressed genes (DEGs) for each scRNA-seq dataset
3. find frequently observed DEGs across 10 scRNA-seq datasets as the M1 or M2 markers for our tool.

Please let me know if this is clear for you!

# M1 markers from the paper
M1
 [1] "CCL5"   "CCR7"   "CD40"   "FCGR1A" "CD80"   "CD86"   "CXCL10"
 [8] "CXCL11" "CXCL9"  "IDO1"   "IL12A"  "IL12B"  "IL1A"   "IL1B"  
[15] "IL23A"  "IL6"    "IRF1"   "IRF5"   "KYNU"   "TNF" 

# overlap between M1 markers from the paper and SpaCET_obj@results[["deconvolution"]][["Ref"]][["sigGenes"]][["Macrophage M1"]]
intersect(SpaCET_obj@results[["deconvolution"]][["Ref"]][["sigGenes"]][["Macrophage M1"]], M1)
## [1] "CD40"   "CD80"   "CXCL10" "CXCL11" "CXCL9"  "FCGR1A" "IDO1"  
## [8] "IL1A"   "IL1B"   "IRF1"   "TNF" 


# M2 markers from the paper
M2
 [1] "ARG1"     "ARG2"     "CCL13"    "CCL17"    "CCL18"    "CCL20"   
 [7] "CCL22"    "CCL24"    "CCL4"     "CD163"    "CD200R1"  "MRC1"    
[13] "FCER2"    "CD276"    "FCGR2A"   "CLEC7A"   "CSF1R"    "CTSA"    
[19] "CTSB"     "CTSD"     "EGF"      "FASLG"    "FN1"      "IL10"    
[25] "IL1R2"    "IL1RN"    "IL4R"     "IRF4"     "LYVE1"    "MMP14"   
[31] "MMP19"    "MMP9"     "MSR1"     "PDCD1LG2" "CD274"    "TGFB1"   
[37] "TGFB2"    "TGFB3"    "TNFSF12"  "TNFSF8"   "VEGFA"    "VEGFB"   
[43] "VEGFC"    "FIGF"     "VTCN1"    "WNT7B" 

# overlap between M2 markers from the paper and SpaCET_obj@results[["deconvolution"]][["Ref"]][["sigGenes"]][["Macrophage M2"]]
intersect(SpaCET_obj@results[["deconvolution"]][["Ref"]][["sigGenes"]][["Macrophage M2"]], M2)
## [1] "CCL13"   "CCL18"   "CD163"   "CSF1R"   "CTSD"    "FCGR2A"  "LYVE1"  
## [8] "MMP19"   "MRC1"    "MSR1"    "TNFSF12"

Best,
Beibei