In‐depth proteomic analysis reveals unique subtype‐specific signatures in human small‐cell lung cancer

Abstract

Background Small‐cell lung cancer (SCLC) molecular subtypes have been primarily characterized based on the expression pattern of the following key transcription regulators: ASCL1 (SCLC‐A), NEUROD1 (SCLC‐N), POU2F3 (SCLC‐P) and YAP1 (SCLC‐Y). Here, we investigated the proteomic landscape of these molecular subsets with the aim to identify novel subtype‐specific proteins of diagnostic and therapeutic relevance. Methods Pellets and cell media of 26 human SCLC cell lines were subjected to label‐free shotgun proteomics for large‐scale protein identification and quantitation, followed by in‐depth bioinformatic analyses. Proteomic data were correlated with the cell lines’ phenotypic characteristics and with public transcriptomic data of SCLC cell lines and tissues. Results Our quantitative proteomic data highlighted that four molecular subtypes are clearly distinguishable at the protein level. The cell lines exhibited diverse neuroendocrine and epithelial–mesenchymal characteristics that varied by subtype. A total of 367 proteins were identified in the cell pellet and 34 in the culture media that showed significant up‐ or downregulation in one subtype, including known druggable proteins and potential blood‐based markers. Pathway enrichment analysis and parallel investigation of transcriptomics from SCLC cell lines outlined unique signatures for each subtype, such as upregulated oxidative phosphorylation in SCLC‐A, DNA replication in SCLC‐N, neurotrophin signalling in SCLC‐P and epithelial–mesenchymal transition in SCLC‐Y. Importantly, we identified the YAP1‐driven subtype as the most distinct SCLC subgroup. Using sparse partial least squares discriminant analysis, we identified proteins that clearly distinguish four SCLC subtypes based on their expression pattern, including potential diagnostic markers for SCLC‐Y (e.g. GPX8, PKD2 and UFO). Conclusions We report for the first time, the protein expression differences among SCLC subtypes. By shedding light on potential subtype‐specific therapeutic vulnerabilities and diagnostic biomarkers, our results may contribute to a better understanding of SCLC biology and the development of novel therapies.

Clinical insights into small cell lung cancer: Tumor heterogeneity, diagnosis, therapy, and future directions

“…Indeed, recent genomic and proteomic data suggest that several putative targets in patients with SCLC representing subtype‐specific vulnerabilities might exist (Figure 2C). 30,97,103 Among others, DLL3, a target of multiple SCLC therapeutics now in clinical development, is reported to be highly expressed in SCLC‐A tumors 6,92 . Likewise, BCL‐2 is also preferentially expressed in this subtype 71,104,105 .…”

“…Because certain tumor‐associated proteins are of diagnostic importance, in‐depth proteomic profiling might also offer new insights into subtype‐specific biomarkers. In total, 367 subtype‐specific proteins were identified recently by mass spectrometry‐based proteomics that were differentially expressed in a given subtype compared with all other subtypes 103 . Considering that the cell pellet and culture media were analyzed separately, the results can also be interpreted as potential tissue‐based and blood‐based biomarkers.…”

“…In total, 367 subtype-specific proteins were identified recently by mass spectrometry-based proteomics that were differentially expressed in a given subtype compared with all other subtypes. 103 Considering that the cell pellet and culture media were analyzed separately, the results can also be interpreted as potential tissue-based and blood-based biomarkers. However, that study 103 was conducted on SCLC cell lines; therefore, the clinical utility and applicability of these proteins warrant further validation using human tissue and blood samples.…”

“…103 Considering that the cell pellet and culture media were analyzed separately, the results can also be interpreted as potential tissue-based and blood-based biomarkers. However, that study 103 was conducted on SCLC cell lines; therefore, the clinical utility and applicability of these proteins warrant further validation using human tissue and blood samples.…”

“… Major discoveries and therapeutic advancements in SCLC. ASCL1 indicates achaete‐scute homolog 1; IHC, immunohistochemistry; NEUROD1, neurogenic differentiation factor 1; NFIB, nuclear factor IB; POU2F3, POU class 2 homeobox 3; RB1, retinoblastoma 1; SCLC, small cell lung cancer; SVV, Seneca Valley virus; YAP1, yes‐associated protein 1 3,6,8,9,11,15–17,19,20,50,51,53,66,67,74,75,77,78,88,89,95,97,103,104,110,224,312–316 . Created with http://BioRender.com.…”