Česká společnost pro hmotnostní spektrometrii

(13. ročník České konference hmotnostní spektrometrie a 11. Neformální proteomické setkání - ThS-09)
Integrated proteogenomic analysis identifies synuclein gamma as a key target of the mesenchymal stem-like subtype of triple negative breast cancer

Jan Šimoník ^1 *, Pavla Bouchalova ¹, Petr Lapcik ¹, Katerina Juraskova ², David Potesil ³, Milos Holanek ^4,5, Vojtech Bystry ², Rudolf Nenutil ⁶, Roman Hrstka ⁷, Pavel Bouchal ¹

1. Department of Biochemistry, Faculty of Science, Masaryk University, Brno
2. Core Facility Bioinformatics, CEITEC, Masaryk University, Brno
3. Proteomics Core Facility, CEITEC, Masaryk University, Brno
4. Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno
5. Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Brno
6. Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Brno
7. Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno

Abstrakt

Triple-negative breast cancer (TNBC) is an aggressive BC subtype that represents ~15% of cases and is primarily treated with systemic chemotherapy. To identify novel therapeutic targets, we performed a multiomics study using LC-DIA-MS/MS based proteomics, RNA sequencing, and whole-exome sequencing in a set of fresh frozen TNBC tissues, generating an integrated dataset for 96 samples. Hierarchical clustering utilizing the proteomics data for 1,223 most correlated transcript–protein pairs stratified TNBC into seven clusters. Of these, cluster 1 was designated as Mesenchymal stem-like (MSL) based on Gene set enrichment analysis and TNBCtype tool outputs. Within MSL subtype, synuclein gamma (SNCG) emerged as a key protein target, originating from significant upregulation in MSL subtype compared to others (log₂FC=1.64, padj=0.0023), its core pathway enrichment, and association with both poor progression-free survival of the patients (PFS; HR=2.542, p=0.005, Cox; p=0.004, log-rank test) and overall survival (OS; HR=2.425, p=0.008, Cox; p=0.006, log-rank test). Functional SNCG validation via CRISPR/Cas9 knockout in MDA-MB-231 cells showed reduced proliferation in SNCG⁻/⁻ clones in the CCK8 proliferation assay (parental vs. G10, padj=2x10-13; vs. B1, padj=9.08x10-4; vs. B3, padj=4.04x10-9). However, no effect on cell migration capacity has been observed in the scratch assay. This is in good agreement with a previous SNCG association with breast cancer progression and recurrence¹ and with promoting proliferation in oral squamous cell carcinoma². In summary, proteomics-driven, multiomics analysis of TNBC patients identified SNCG as a key protein in the MSL subtype linked to poor PFS and OS, and its association with cancer cell proliferation and growth was functionally validated.

* Korespondující autor: simonikjan@mail.muni.cz

Literatura

1. Wu K. et al.: Breast Cancer Res Treat 2007, 101 (3), 259–267.
2. Yang J. et al.: Am J Cancer Res 2024, 14 (5), 2408–2423

Poděkování:

Supported by the Ministry of Health of the Czech Republic in cooperation with the Czech Health Research Council under project No. NU22-08-00230. Supported by the project National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102)—Funded by the European Union—Next Generation EU.