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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 18, 2020 |
| Title |
Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted therapies in colon cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Single cell RNA sequencing (scRNA-seq) is a powerful tool for defining cellular diversity in tumors, but its application towards dissecting mechanisms underlying immune-modulating therapies is scarce. We performed scRNA-seq analyses on immune and stromal populations from colorectal cancer patients, identifying specific macrophage and conventional dendritic cell (cDC) subsets as key mediators of cellular cross-talk in the tumor microenvironment. Defining comparable myeloid populations in mouse tumors enabled characterization of their response to myeloid-targeted immunotherapy. Treatment with anti-CSF1R preferentially depleted macrophages with an inflammatory signature but spared macrophage populations that in mouse and human expresses pro-angiogenic/tumorigenic genes. Treatment with a CD40 agonist antibody preferentially activated a conventional dendritic cell population and increased Bhlhe40+ Th1-like cells and CD8+ memory T cells. Our comprehensive analysis of key myeloid subsets in human and mouse identifies critical cellular interactions regulating tumor immunity and defines mechanisms underlying myeloid-targeted immunotherapies currently undergoing clinical testing.
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| Overall design |
For Patient P0104, P0305, P0309, P0411, P0720, P0728, P1212, P1228, P0413, and P0825, single-cell RNA-seq were performed by the SMART-seq2 platform. Single cell suspensions collected from CRC samples were stained with antibodies against CD45 for FACS sorting, performed on a BD Aria III instrument. To enrich myeloid cells, single cells were further enriched either by gating CD3-, CD3-CD19-/CD79A- or CD3-CD19-CD56- cells to exclude lymphoid cells. For B cells and NK cells, single cells were enriched by gating 7AAD-CD45+CD3-CD19+CD56- and 7AAD-CD45+CD3-CD19-CD56+. For non-immune cells, single cells were enriched by gating 7AAD-CD45-.
For Patient P0104, P0123, P0202, P0305, P0323, P0408, P0410, P0613, P1025, P1026, single-cell RNA-seq were performed by the 10x Genomic single cell 3’ library platform. Single cell suspensions collected from CRC samples were stained with antibodies against CD45 for FACS sorting, performed on a BD Aria III instrument. To enrich myeloid cells, single cells were further enriched either by gating CD3- or CD3-CD19-/CD79A-CD56-, cells to exclude lymphoid cells. For T and monocyte-lineage cells, single cells were enriched by gating 7AAD-CD45+CD3+ and 7AAD-CD45+CD3-CD14+ cells, respectively.
*** Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (under accession HRA000056 https://bigd.big.ac.cn/gsa-human/browse/HRA000056).
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| Contributor(s) |
Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, O’Brien SA, He Y, Wang L, Zhang Q, Kim A, Gao R, Orf J, Wang T, Sawant D, Kang J, Bhatt D, Lu D, Li C, Rapaport A, Perez K, Ye Y, Wang S, Hu X, Ren X, Ouyang W, Shen Z, Egen JG, Zhang Z, Yu X |
| Citation(s) |
32302573 |
| Submission date |
Mar 11, 2020 |
| Last update date |
Apr 06, 2021 |
| Contact name |
ZIyi Li |
| E-mail(s) |
liziyie@pku.edu.cn
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| Phone |
13269475795
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| Organization name |
Peking University
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| Street address |
No.5 Yiheyuan Road Haidian District
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| City |
Beijing |
| State/province |
- |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA611928 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE146771_CRC.Leukocyte.10x.Metadata.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE146771_CRC.Leukocyte.10x.TPM.txt.gz |
433.5 Mb |
(ftp)(http) |
TXT |
| GSE146771_CRC.Leukocyte.Smart-seq2.Metadata.txt.gz |
794.1 Kb |
(ftp)(http) |
TXT |
| GSE146771_CRC.Leukocyte.Smart-seq2.TPM.txt.gz |
388.2 Mb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data are available on Series record |
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