Proteotype classification of metastatic and localized renal
cell carcinomas for prognosis and therapy response

a 2023

Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response

ŠIMONÍK, Jan; Pavla BOUCHALOVÁ; Richard ŠTEFANÍK; Petr LAPČÍK; David POTĚŠIL et. al.

Základní údaje

Originální název

Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response

Autoři

ŠIMONÍK, Jan (203 Česká republika, domácí); Pavla BOUCHALOVÁ (203 Česká republika, domácí); Richard ŠTEFANÍK (203 Česká republika, domácí); Petr LAPČÍK (203 Česká republika, domácí); David POTĚŠIL (203 Česká republika, domácí); Vlad POPOVICI (642 Rumunsko, domácí); Ján PODHOREC (703 Slovensko, domácí); Milan HORA (203 Česká republika, domácí); Alexandr POPRACH (203 Česká republika, domácí); Ondřej FIALA a Pavel BOUCHAL (203 Česká republika, domácí)

Vydání

Abstract Book of XVIII. Czech Annual Cancer Research Meeting, Olomouc, CZ, 20.-22.11.2023, 2023

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Kód RIV

RIV/00216224:14310/23:00132860

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-80-908348-2-8

ISSN

Klíčová slova anglicky

localized RCC; metastatic RCC; therapy response; tyrosin kinase inhibitors; prognosis; relapse; proteomics; LC-DIA-MS/MS

Změněno: 5. 4. 2024 09:49, Mgr. Tereza Miškechová

Anotace

V originále

Renal cell carcinoma (RCC) represents a serious oncological disease with the second highest incidence in the Czech Republic across the world. Reliable molecular predictive and prognostic biomarkers for RCC are mostly unavailable, namely at protein level. To quantify proteins associated with pro-tumorigenic and pro-metastatic mechanisms in RCC, we first generated a comprehensive RCC-specific spectral library of targeted proteomic assays for 7960 protein groups (FDR=1%) [1]. Second, we have applied data independent acquisition mass spectrometry (DIA-MS) on QExactive HF-X LC-MS system and analyzed a well-characterized set of metastatic RCC tumors (training cohort n=53, validation cohort n=22) and adjacent non-cancerous tissues (n=17) a part of which responded and a part did not respond to tyrosine kinase inhibitor (TKI) treatment. We have identified and validated single protein biomarker with a poor response to TKI but not with tumor grade. Functional assays using CRISPR/Cas9 knockdown confirmed its role in metastatic potential of 786-0 cells. Third, we analyzed a well-characterized set of initially localized RCC tumors (n=86) of which a half exhibited a relapse in <5 years after diagnosis. We have identified a single potential biomarker as well as protein classifiers able to predict the relapse, for which we have developed targeted proteomics assays for further validation and routine quantification. CRISPR/Cas9 knockdown confirmed the role of the key protein in cell migration in 786-0 cells, supporting its role in metastatic potential of RCC. In a summary, next generation proteomics based on DIA-MS is a powerful tool to classify RCC tissues, to identify prognostic biomarkers and alternative therapeutic targets. Supported by Ministry of Health of the Czech Republic, project No. NV19-08-00250, all rights reserved. CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2018127, is gratefully acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. Supported by the project National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union - Next Generation EU.

Návaznosti

LM2018127, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

LX22NPO5102, projekt VaV

Název: Národní ústav pro výzkum rakoviny (Akronym: NÚVR)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní ústav pro výzkum rakoviny, 5.1 EXCELES

NV19-08-00250, projekt VaV

Název: Proteotypová klasifikace renálního karcinomu ve vztahu k prognóze a terapeutické odpovědi

Investor: Ministerstvo zdravotnictví ČR, Proteotypová klasifikace renálního karcinomu ve vztahu k prognóze a terapeutické odpovědi

Citovat

ŠIMONÍK, Jan; Pavla BOUCHALOVÁ; Richard ŠTEFANÍK; Petr LAPČÍK; David POTĚŠIL; Vlad POPOVICI; Ján PODHOREC; Milan HORA; Alexandr POPRACH; Ondřej FIALA a Pavel BOUCHAL. Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response. In Abstract Book of XVIII. Czech Annual Cancer Research Meeting, Olomouc, CZ, 20.-22.11.2023. 2023. ISBN 978-80-908348-2-8.

@proceedings{2358159,
   author = {Šimoník, Jan and Bouchalová, Pavla and Štefaník, Richard and Lapčík, Petr and Potěšil, David and Popovici, Vlad and Podhorec, Ján and Hora, Milan and Poprach, Alexandr and Fiala, Ondřej and Bouchal, Pavel},
   booktitle = {Abstract Book of XVIII. Czech Annual Cancer Research Meeting, Olomouc, CZ, 20.-22.11.2023},
   keywords = {localized RCC; metastatic RCC; therapy response; tyrosin kinase inhibitors; prognosis; relapse; proteomics; LC-DIA-MS/MS},
   language = {eng},
   isbn = {978-80-908348-2-8},
   title = {Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response},
   url = {https://cancermeeting.cz/},
   year = {2023}
}

TY  - CONF
ID  - 2358159
AU  - Šimoník, Jan - Bouchalová, Pavla - Štefaník, Richard - Lapčík, Petr - Potěšil, David - Popovici, Vlad - Podhorec, Ján - Hora, Milan - Poprach, Alexandr - Fiala, Ondřej - Bouchal, Pavel
PY  - 2023
TI  - Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response
SN  - 9788090834828
KW  - localized RCC
KW  - metastatic RCC
KW  - therapy response
KW  - tyrosin kinase inhibitors
KW  - prognosis
KW  - relapse
KW  - proteomics
KW  - LC-DIA-MS/MS
UR  - https://cancermeeting.cz/
N2  - Renal cell carcinoma (RCC) represents a serious oncological disease with the second highest incidence in the Czech Republic across the world. Reliable molecular predictive and prognostic biomarkers for RCC are mostly unavailable, namely at protein level. To quantify proteins associated with pro-tumorigenic and pro-metastatic mechanisms in RCC, we first generated a comprehensive RCC-specific spectral library of targeted proteomic assays for 7960 protein groups (FDR=1%) [1]. Second, we have applied data independent acquisition mass spectrometry (DIA-MS) on QExactive HF-X LC-MS system and analyzed a well-characterized set of metastatic RCC tumors (training cohort n=53, validation cohort n=22) and adjacent non-cancerous tissues (n=17) a part of which responded and a part did not respond to tyrosine kinase inhibitor (TKI) treatment. We have identified and validated single protein biomarker with a poor response to TKI but not with tumor grade. Functional assays using CRISPR/Cas9 knockdown confirmed its role in metastatic potential of 786-0 cells. Third, we analyzed a well-characterized set of initially localized RCC tumors (n=86) of which a half exhibited a relapse in <5 years after diagnosis. We have identified a single potential biomarker as well as protein classifiers able to predict the relapse, for which we have developed targeted proteomics assays for further validation and routine quantification. CRISPR/Cas9 knockdown confirmed the role of the key protein in cell migration in 786-0 cells, supporting its role in metastatic potential of RCC. In a summary, next generation proteomics based on DIA-MS is a powerful tool to classify RCC tissues, to identify prognostic biomarkers and alternative therapeutic targets. Supported by Ministry of Health of the Czech Republic, project No. NV19-08-00250, all rights reserved. CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2018127, is gratefully acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. Supported by the project National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union - Next Generation EU.
ER  -

ŠIMONÍK, Jan; Pavla BOUCHALOVÁ; Richard ŠTEFANÍK; Petr LAPČÍK; David POTĚŠIL; Vlad POPOVICI; Ján PODHOREC; Milan HORA; Alexandr POPRACH; Ondřej FIALA a Pavel BOUCHAL. Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response. In \textit{Abstract Book of XVIII. Czech Annual Cancer Research Meeting, Olomouc, CZ, 20.-22.11.2023}. 2023. ISBN~978-80-908348-2-8.

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