Response to neoadjuvant chemotherapy according to molecular subtypes in muscle-invasive bladder carcinoma.
Authors: Pinto Alvaro , Trilla-Fuertes Lucía , Pedregosa-Barbas Jorge , García-Fernández Eugenia , Wisultschew-Puigdellivol Alma L , Zambrana Francisco , Martinez Imanol , Gajate Pablo , Dittmann Antje , Lopez Vacas Rocio , Kunz Laura , Rubio Gustavo , Nieto-Torrero Sandra , Lalanda-Delgado Pedro , Pertejo Ana , Saiz Ana , González-Peramato María Pilar , Fresno-Vara Juan Angel , Gámez-Pozo Angelo 
Published: June 2024

e16605

Background: Cisplatin-based neoadjuvant chemotherapy (NACT) is the current standard treatment for non-metastatic muscle-invasive bladder carcinoma (MIBC). However, benefit of this treatment significantly differs between patients, and we lack predictive factors to tailor therapy. Methods: Fifty-eight FFPE samples from MIBC patients obtained from transurethral resection (TURB) were analyzed. Proteins were isolated using 2% SDS and digested with trypsin. Proteins extracts were analyzed using data-independent acquisition mass-spectrometry. Proteomics data was preprocessing using Perseus software. A probabilistic graphical model (PGM) was built using protein data without any a priori information and grapHD R package. The resulting network was divided into functional nodes with an overrepresented function using DAVID webtool. To make comparisons between groups, functional node activities were calculated as the mean of the protein expression of the proteins of each functional node related to the overrepresented function. Statistical analyses were performed in GraphPad Prism v6. Results: 5532 proteins were identified and quantified in DIA mass-spectrometry experiments. After applying quality criteria, 3399 proteins were used for the subsequent analyses. Three groups with different proteomics profiles were identified using a hierarchical clustering. Cluster 1 was characterized by a higher expression of KRT20, a luminal-papillary biomarker. Cluster 2 was characterized by a higher expression of KRT5, KRT6A, KRT14, and CD44, all basal MIBC biomarkers. Finally, Cluster 3 had a higher expression of PGM5, DES, and SGDC proteins, biomarkers of luminal-infiltrated and luminal. Therefore, cluster 1 was reassigned as Luminal-papillary, cluster 2 as basal-squamous, and cluster 3 as Luminal-infiltrated+Luminal. Using PGMs, several differential biological processes were identified between the three subtypes, being Luminal-papillary more metabolic and mitochondria active, basal group presented a higher activity of DNA replication and cell cycle, and Luminal-infiltrated+Luminal had a higher adhesion and collagen activity. Regarding the number of pCRs in each group, Luminal-papillary tumors had a lower number of pCR (only 20% of the Luminal-papillary tumors respond to NACT), in Luminal-infiltrated+Luminal the number of pCR sligthy increases (40% of these tumors responde to NACT), and in the basal-squamous group a 45% of patients did respond to NACT. Conclusions: MIBC molecular subtypes defined using transcriptomics also showed different protein profiles. Luminal-papillary are more metabolic tumors whereas basal group had a higher activity of DNA replication and cell cycle. Finally, Luminal-infiltrated+Luminal had a higher adhesion. Additionally, rates of complete responses to NACT varies according to MIBC molecular subtype.