Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma

Zhaohui Chen, Lijie Zhou, Lilong Liu, Yaxin Hou, Ming Xiong, Yu Yang, Junyi Hu, Ke Chen

Study ID

chen_et_al_2020_all

Total cells

52,721

Abtract
Although substantial progress has been made in cancer biology and treatment, clinical outcomes of bladder carcinoma (BC) patients are still not satisfactory. The tumor microenvironment (TME) is a potential target. Here, by single-cell RNA sequencing on 8 BC tumor samples and 3 para tumor samples, we identify 19 different cell types in the BC microenvironment, indicating high intra-tumoral heterogeneity. We find that tumor cells down regulated MHC-II molecules, suggesting that the downregulated immunogenicity of cancer cells may contribute to the formation of an immunosuppressive microenvironment. We also find that monocytes undergo M2 polarization in the tumor region and differentiate. Furthermore, the LAMP3 + DC subgroup may be able to recruit regulatory T cells, potentially taking part in the formation of an immunosuppressive TME. Through correlation analysis using public datasets containing over 3000 BC samples, we identify a role for inflammatory cancer-associated fibroblasts (iCAFs) in tumor progression, which is significantly related to poor prognosis. Additionally, we characterize a regulatory network depending on iCAFs. These results could help elucidate the protumor mechanisms of iCAFs. Our results provide deep insight into cancer immunology and provide an essential resource for drug discovery in the future.

Age (years)

70
9320 cells
63
8597 cells
59
8226 cells
72
7565 cells
67
6362 cells
75
4579 cells
57
4218 cells
77
3854 cells

Author's cell type

Epithelial
31850 cells
Endothelial
7245 cells
iCAF
3662 cells
mCAF
3630 cells
B cell
2235 cells
Myeloid
2228 cells
T cell
1701 cells
Mast cell
170 cells

Author's sub cell type

Epithelial
31850 cells
Endothelial
7245 cells
iCAF (inflammatory cancer-associated fibroblasts)
3662 cells
mCAF (myo-cancer-associated fibroblasts)
3630 cells
B cell
2307 cells
T cell
1701 cells
TAM
986 cells
CD1C+ DC
449 cells
Monocyte
234 cells
Mast cell
170 cells
Proliferating myeloid
150 cells
Cross-presenting DC
102 cells
Doublets (Epithelial)
96 cells
LAMP3+ DC
71 cells
Doublets (Endothelial)
68 cells

Condition

bladder urothelial carcinoma
52721 cells

Developmental stage

old adult
52721 cells

Gender

male
36930 cells
female
15791 cells

Invasiveness

Noninvasive
24015 cells
Invasive
17455 cells
Unassigned
11251 cells

Louvain clustering

Cluster 5
8655 cells
Cluster 7
6831 cells
Cluster 4
6011 cells
Cluster 9
5581 cells
Cluster 1
4419 cells
Cluster 6
4126 cells
Cluster 10
3933 cells
Cluster 2
3843 cells
Cluster 8
3495 cells
Cluster 3
3229 cells
Cluster 11
2457 cells
Cluster 12
141 cells

Quantification

CellRanger 2.2.0
52721 cells

Sample ID

L-T2 (11)
9320 cells
H-T2 (8)
8226 cells
H-I-T4 (7)
7565 cells
N3 (2)
5134 cells
H-I-T1 (4)
4218 cells
H-I-T3 (6)
3854 cells
H-T1 (1)
3463 cells
N1 (9)
3356 cells
L-T1 (10)
3006 cells
N2 (3)
2761 cells
H-I-T2 (5)
1818 cells

Samples

2 - Tumor
9320 cells
4 - Tumor
8226 cells
8 - Tumor
7565 cells
3 - Normal
5134 cells
5 - Tumor
4218 cells
7 - Tumor
3854 cells
3 - Tumor
3463 cells
1 - Normal
3356 cells
1 - Tumor
3006 cells
6 - Normal
2761 cells
6 - Tumor
1818 cells

Sequencing platform

Chromium v3
52721 cells

Storage technique

fresh
52721 cells

Subject ID

2
9320 cells
3
8597 cells
4
8226 cells
8
7565 cells
1
6362 cells
6
4579 cells
5
4218 cells
7
3854 cells

Tissue

bladder
52721 cells

Treatment

no treatment
52721 cells

Tumor grade

High grade
29144 cells
Low grade
12326 cells
Normal
11251 cells

Tumor size (centimeter)

Unassigned
11251 cells
2.5
9320 cells
4.7
8226 cells
4.1
7565 cells
5.1
4218 cells
4.5
3854 cells
3.5
3463 cells
1.9
3006 cells
4.3
1818 cells

Type of surgery

Cystectomy
37039 cells
Transurethral resection of bladder tumor
15682 cells