Single-Cell RNA Sequencing Reveals Cellular Heterogeneity in an Acral Amelanotic Melanoma After Immunotherapy Treatment

Le Zhuang; Jie Tian; Binbin Lai; Guohong Zhang; Hang Li

doi:10.2147/CCID.S404381

Single-Cell RNA Sequencing Reveals Cellular Heterogeneity in an Acral Amelanotic Melanoma After Immunotherapy Treatment

Clin Cosmet Investig Dermatol. 2023 Apr 13:16:1009-1018. doi: 10.2147/CCID.S404381. eCollection 2023.

Authors

Le Zhuang^#^{1

2

3

4

5

6}, Jie Tian^#^{1

2

3

4

7}, Binbin Lai^{1

2

3

4

7}, Guohong Zhang^{1

2

3

4}, Hang Li^{1

2

3

4}

Affiliations

¹ Department of Dermatology, Peking University First Hospital, Beijing, People's Republic of China.
² National Clinical Research Center for Skin and Immune Diseases, Peking University First Hospital, Beijing, People's Republic of China.
³ Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People's Republic of China.
⁴ NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Peking University First Hospital, Beijing, People's Republic of China.
⁵ Dermatology Hospital, Southern Medical University, Guangzhou, People's Republic of China.
⁶ Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, People's Republic of China.
⁷ Institute of Medical Technology, Peking University Health Science Center, Beijing, People's Republic of China.

^# Contributed equally.

Abstract

Background: Anti-programmed cell death ligand-1 (anti-PD-L1) immunotherapy is often used for advanced urothelial carcinoma and melanoma, including amelanotic melanoma, a relatively rare subtype with little to no pigment in the tumor cells. However, cellular heterogeneity of amelanotic melanoma during or after anti-PD-L1 immunotherapy treatments has not been described.

Purpose: To investigate cellular heterogeneity in acral amelanotic melanoma after immunotherapy exposure.

Methods: We evaluated subtle visual changes of the melanoma by dermoscopy and performed a pathological examination to analyze the heterogeneity of microscopic morphological and immunohistochemistry changes. The cellular transcriptional heterogeneity and corresponding biological function profiles of the melanoma were determined by single-cell RNA sequencing (scRNA-seq).

Results: The dermoscopic examination revealed black globules and scar-like depigmentation areas against a homogeneous red background. Pigmented and amelanotic melanoma cells were observed microscopically. The pigmented cells were large and contained melanin granules expressing Melan-A and HMB45; the amelanotic cells were small and did not express HMB45. Ki-67 immunohistochemical staining revealed that the pigmented melanoma cells had a higher proliferative ability than the amelanotic cells. scRNA-seq identified three cell clusters: amelanotic cell cluster 1, amelanotic cell cluster 2, and pigmented cell cluster. Furthermore, a pseudo-time trajectory analysis showed that amelanotic cell cluster 2 originated from amelanotic cell cluster 1 and transformed into the pigmented melanoma cell cluster. The expression pattern of melanin synthesis-related and lysosome-endosome-related genes in different cell clusters supported the cell cluster transformation results. Also, upregulated expression of cell cycle genes indicated that the pigmented melanoma cells had a high proliferative ability.

Conclusion: Coexisting amelanotic and pigmented melanoma cells indicated cellular heterogeneity in an acral amelanotic melanoma from a patient who underwent immunotherapy treatment. Additionally, the pigmented melanoma cells acquired a higher proliferative ability than the amelanotic melanoma cells.

Keywords: acral melanoma; amelanotic; cellular heterogeneity; drug resistance; immunotherapy.

Grants and funding

This work was supported by the National Key Research and Development Program of China (2019YFC0840706), the National Natural Science Foundation of China (82073015), and the Shandong Province Natural Science Foundation (ZR2020QH138).