Gene expression profile at single cell level from the colorectal cancer (CRC)
Download from source ↗Dataset overview
Oncogenic KRAS Drives Lipofibrogenesis to Promote Angiogenesis and Colon Cancer Progression.
Abstract
Oncogenic KRAS (KRAS*) contributes to many cancer hallmarks. In colorectal cancer, KRAS* suppresses antitumor immunity to promote tumor invasion and metastasis. Here, we uncovered that KRAS* transforms the phenotype of carcinoma-associated fibroblasts (CAF) into lipid-laden CAFs, promoting angiogenesis and tumor progression. Mechanistically, KRAS* activates the transcription factor CP2 (TFCP2) that upregulates the expression of the proadipogenic factors BMP4 and WNT5B, triggering the transformation of CAFs into lipid-rich CAFs. These lipid-rich CAFs, in turn, produce VEGFA to spur angiogenesis. In KRAS*-driven colorectal cancer mouse models, genetic or pharmacologic neutralization of TFCP2 reduced lipid-rich CAFs, lessened tumor angiogenesis, and improved overall survival. Correspondingly, in human colorectal cancer, lipid-rich CAF and TFCP2 signatures correlate with worse prognosis. This work unveils a new role for KRAS* in transforming CAFs, driving tumor angiogenesis and disease progression, providing an actionable therapeutic intervention for KRAS*-driven colorectal cancer.<h4>Significance</h4>This study identified a molecular mechanism contributing to KRAS*-driven colorectal cancer progression via fibroblast transformation in the tumor microenvironment to produce VEGFA driving tumor angiogenesis. In preclinical models, targeting the KRAS*-TFCP2-VEGFA axis impaired tumor progression, revealing a potential novel therapeutic option for patients with KRAS*-driven colorectal cancer. This article is featured in Selected Articles from This Issue, p. 2489.
doi:10.1158/2159-8290.cd-22-1467 ↗ PMID 37768068 ↗ PMC10807546 ↗
Study facts
- Organism
- Homo sapiens
- Platform
- NextSeq 500
- Age group
- —
- Disease groups
- —
- Anatomical sites
- colon, liver
Data availability
- Processed matrix
File types
MTXTSV
Files and samples
- filelist.txt ↗
- GSE231559_RAW.tar ↗
- GSM7290760_SC10_21N_barcodes.tsv.gz ↗
- GSM7290760_SC10_21N_features.tsv.gz ↗
- GSM7290760_SC10_21N_matrix.mtx.gz ↗
- GSM7290761_SC10_22T_barcodes.tsv.gz ↗
- GSM7290761_SC10_22T_features.tsv.gz ↗
- GSM7290761_SC10_22T_matrix.mtx.gz ↗
- GSM7290762_SC10_23N_barcodes.tsv.gz ↗
- GSM7290762_SC10_23N_features.tsv.gz ↗
- GSM7290762_SC10_23N_matrix.mtx.gz ↗
- GSM7290763_SC10_24T_barcodes.tsv.gz ↗
- GSM7290763_SC10_24T_features.tsv.gz ↗
- GSM7290763_SC10_24T_matrix.mtx.gz ↗
- GSM7290764_SC10_25N_barcodes.tsv.gz ↗
- GSM7290764_SC10_25N_features.tsv.gz ↗
- GSM7290764_SC10_25N_matrix.mtx.gz ↗
- GSM7290765_SC10_26N_barcodes.tsv.gz ↗
- GSM7290765_SC10_26N_features.tsv.gz ↗
- GSM7290765_SC10_26N_matrix.mtx.gz ↗
- GSM7290766_SC10_27N_barcodes.tsv.gz ↗
- GSM7290766_SC10_27N_features.tsv.gz ↗
- GSM7290766_SC10_27N_matrix.mtx.gz ↗
- GSM7290767_SC10_28T_barcodes.tsv.gz ↗
- GSM7290767_SC10_28T_features.tsv.gz ↗
- GSM7290767_SC10_28T_matrix.mtx.gz ↗
- GSM7290768_SC10_29N_barcodes.tsv.gz ↗
- GSM7290768_SC10_29N_features.tsv.gz ↗
- GSM7290768_SC10_29N_matrix.mtx.gz ↗
- GSM7290769_SC10_30T_barcodes.tsv.gz ↗
- GSM7290769_SC10_30T_features.tsv.gz ↗
- GSM7290769_SC10_30T_matrix.mtx.gz ↗
- GSM7290770_SC10_35N_barcodes.tsv.gz ↗
- GSM7290770_SC10_35N_features.tsv.gz ↗
- GSM7290770_SC10_35N_matrix.mtx.gz ↗
- GSM7290771_SC10_37N_barcodes.tsv.gz ↗
- GSM7290771_SC10_37N_features.tsv.gz ↗
- GSM7290771_SC10_37N_matrix.mtx.gz ↗
- GSM7290772_SC10_38T_barcodes.tsv.gz ↗
- GSM7290772_SC10_38T_features.tsv.gz ↗
- GSM7290772_SC10_38T_matrix.mtx.gz ↗
- GSM7290773_SC10_5_barcodes.tsv.gz ↗
- GSM7290773_SC10_5_features.tsv.gz ↗
- GSM7290773_SC10_5_matrix.mtx.gz ↗
- GSM7290774_SC10_7_barcodes.tsv.gz ↗
- GSM7290774_SC10_7_features.tsv.gz ↗
- GSM7290774_SC10_7_matrix.mtx.gz ↗
- GSM7290775_SC10_8_barcodes.tsv.gz ↗
- GSM7290775_SC10_8_features.tsv.gz ↗
- GSM7290775_SC10_8_matrix.mtx.gz ↗
- GSM7290776_SC143_17_barcodes.tsv.gz ↗
- GSM7290776_SC143_17_features.tsv.gz ↗
- GSM7290776_SC143_17_matrix.mtx.gz ↗
- GSM7290777_SC143_7_barcodes.tsv.gz ↗
- GSM7290777_SC143_7_features.tsv.gz ↗
- GSM7290777_SC143_7_matrix.mtx.gz ↗
- GSM7290778_SC173_1_barcodes.tsv.gz ↗
- GSM7290778_SC173_1_features.tsv.gz ↗
- GSM7290778_SC173_1_matrix.mtx.gz ↗
- GSM7290779_SC173_2_barcodes.tsv.gz ↗
- GSM7290779_SC173_2_features.tsv.gz ↗
- GSM7290779_SC173_2_matrix.mtx.gz ↗
- GSM7290780_SC216_1_barcodes.tsv.gz ↗
- GSM7290780_SC216_1_features.tsv.gz ↗
- GSM7290780_SC216_1_matrix.mtx.gz ↗
- GSM7290781_SC216_2_barcodes.tsv.gz ↗
- GSM7290781_SC216_2_features.tsv.gz ↗
- GSM7290781_SC216_2_matrix.mtx.gz ↗
- GSM7290782_SC216_3_barcodes.tsv.gz ↗
- GSM7290782_SC216_3_features.tsv.gz ↗
- GSM7290782_SC216_3_matrix.mtx.gz ↗
- GSM7290783_SC216_5_barcodes.tsv.gz ↗
- GSM7290783_SC216_5_features.tsv.gz ↗
- GSM7290783_SC216_5_matrix.mtx.gz ↗
- GSM7290784_SC216_6_barcodes.tsv.gz ↗
- GSM7290784_SC216_6_features.tsv.gz ↗
- GSM7290784_SC216_6_matrix.mtx.gz ↗
- GSM7290785_SC216_7_barcodes.tsv.gz ↗
- GSM7290785_SC216_7_features.tsv.gz ↗
- GSM7290785_SC216_7_matrix.mtx.gz ↗
- index.html ↗
- Liver tumor9
- Liver normal8
- Colon tumor6
- Colon normal3
| Accession | Sample | Tissue | Molecule |
|---|---|---|---|
GSM7290760 |
L1N | Liver normal | total RNA |
GSM7290761 |
L1T | Liver tumor | total RNA |
GSM7290762 |
C1N | Colon normal | total RNA |
GSM7290763 |
C1T | Colon tumor | total RNA |
GSM7290764 |
L2N | Liver normal | total RNA |
GSM7290765 |
L3N | Liver normal | total RNA |
GSM7290766 |
L4N | Liver normal | total RNA |
GSM7290767 |
L4T | Liver tumor | total RNA |
GSM7290768 |
C2N | Colon normal | total RNA |
GSM7290769 |
C2T | Colon tumor | total RNA |
GSM7290770 |
L5N | Liver normal | total RNA |
GSM7290771 |
C3N | Colon normal | total RNA |
GSM7290772 |
C3T | Colon tumor | total RNA |
GSM7290773 |
C4T | Colon tumor | total RNA |
GSM7290774 |
C5T | Colon tumor | total RNA |
GSM7290775 |
L6T | Liver tumor | total RNA |
GSM7290776 |
L7N | Liver normal | total RNA |
GSM7290777 |
C6T | Colon tumor | total RNA |
GSM7290778 |
L8T1 | Liver tumor | total RNA |
GSM7290779 |
L8T2 | Liver tumor | total RNA |
GSM7290780 |
L9N | Liver normal | total RNA |
GSM7290781 |
L9T | Liver tumor | total RNA |
GSM7290782 |
L10T | Liver tumor | total RNA |
GSM7290783 |
L11T | Liver tumor | total RNA |
GSM7290784 |
L11N | Liver normal | total RNA |
GSM7290785 |
L12T | Liver tumor | total RNA |
Strengths & limitations for reuse
Strengths
- Raw reads are advertised
- Processed matrices are advertised
Limitations
- Not documented: raw counts are advertised
- Not documented: cell metadata are advertised
- Not documented: participant counts are documented
Extraction evidence & provenance
Each extracted field is shown with the source excerpt and location used to resolve it.
Assay
| Field | Value | Evidence |
|---|---|---|
assay.library_chemistry |
10x Genomics single cell 3' v3 |
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Section |
assay.platform |
NextSeq 500 |
NextSeq 500 Section |
assay.reference_genome |
GRCh38-3.0.0 |
Assembly: GRCh38-3.0.0 Section |
assay.sequencing_type |
scrna_seq |
We used single cell RNAsequencing (scRNA-seq) to analyze the diversity of CRC. Section |
Data_Assets
| Field | Value | Evidence |
|---|---|---|
data_assets.open_access |
True |
Public on Sep 25 2023 Section |
data_assets.processed_matrix |
True |
Supplementary files format and content: Tab-separated values files and matrix files Section |
data_assets.raw_reads |
True |
GSE231559_RAW.tar Section |
Specimens
| Field | Value | Evidence |
|---|---|---|
specimens.anatomical_sites |
['colon', 'liver'] |
Fresh colorectal cancer tissues and adjucent normal tissues from primary and liver/peritnoeum-Met patients were collected for scRNA-seq. Section |
specimens.number_of_samples |
26 |
"n_samples": 26 Section |