Mapping the single-cell landscape of acral melanoma and analysis of the molecular regulatory network of the tumor microenvironments

Abstract
Data availability
Article and author information
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Abstract

Acral melanoma (AM) exhibits a high incidence in Asian patients with melanoma, and it is not well treated with immunotherapy. However, little attention has been paid to the characteristics of the immune microenvironment in AM. Therefore, in this study, we collected clinical samples from Chinese patients with AM and conducted single-cell RNA sequencing to analyze the heterogeneity of its tumour microenvironments (TMEs) and the molecular regulatory network . Our analysis revealed that genes, such as TWIST1, EREG, TNFRSF9, and CTGF could drive the deregulation of various TME components. The molecular interaction relationships between TME cells, such as MIF-CD44 and TNFSF9-TNFRSF9, might be an attractive target for developing novel immunotherapeutic agents.

Data availability

Sequencing data have been deposited in GSA under accession codes HRA001804.

The following data sets were generated

1. Hua Zhao
(2022) Mapping the single-cell landscape of acral melanoma and analysis of the molecular regulatory network of the tumor microenvironment
GSA for Human, HRA001804.

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001804

The following previously published data sets were used

1. Jerby-Arnon L
2. Shah P
3. Cuoco MS
4. Rodman C
5. Su MJ
6. Melms JC
7. Leeson R
8. Kanodia A
9. Mei S
10. Lin JR
11. Wang S
12. Rabasha B
13. Liu D
14. Zhang G
15. Margolais C
16. Ashenberg O
17. Ott PA
18. Buchbinder EI
19. Haq R
20. Hodi FS
21. Boland GM
22. Sullivan RJ
23. Frederick DT
24. Miao B
25. Moll T
26. Flaherty KT
27. Herlyn M
28. Jenkins RW
29. Thummalapalli R
30. Kowalczyk MS
31. Cañadas I
32. Schilling B
33. Cartwright AN
34. Luoma AM
35. Malu S
36. Hwu P
37. Bernatchez C
38. Forget MA
39. Barbie DA
40. Shalek AK
41. Tirosh I
42. Sorger PK
43. Wucherpfennig K
44. Van Allen EM
45. Schadendorf D
46. Johnson BE
47. Rotem A
48. Rozenblatt-Rosen O
49. Garraway LA
50. Yoon CH
51. Izar B
52. Regev A
(2018) Single-cell RNA-seq of melanoma ecosystems reveals sources of T cells exclusion linked to immunotherapy clinical outcomes
NCBI Gene Expression Omnibus, GSE115978.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115978
1. Tirosh I
2. Izar B
(2016) Single cell RNA-seq analysis of melanoma
NCBI Gene Expression Omnibus, GSE72056.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056

Article and author information

Author details

Zan He

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Zijuan Xin

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Qiong Yang

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Chen Wang

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Meng Li

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Wei Rao

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Zhimin Du

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Jia Bai

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Zixuan Guo

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Xiuyan Ruan

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Zhaojun Zhang

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Xiangdong Fang

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

For correspondence
fangxd@big.ac.cn

Competing interests
The authors declare that no competing interests exist.
Hua Zhao

Department of Dermatology, General Hospital of People's Liberation Army, Beijing, China

For correspondence
hualuck301@163.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7139-1844

Funding

National Natural Science Foundation of China (81672698)

Hua Zhao

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: All samples were obtained from the General Hospital of the People's Liberation Army, Beijing, China. All volunteers signed informed consent prior to sample acquisition. Four primary AM tissues, three paracancerous tissues, and a metastatic lymph gland sample were included in this cohort. This study was approved by the Ethics Committee of Chinese PLA General Hospital and complied with all relevant ethical regulations(Approval No. S2021-626).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.