1
|
Romanovsky E, Kluck K, Ourailidis I, Menzel M, Beck S, Ball M, Kazdal D, Christopoulos P, Schirmacher P, Stiewe T, Stenzinger A, Budczies J. Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by transcriptome analysis. Cell Death Discov 2023; 9:126. [PMID: 37059713 PMCID: PMC10104808 DOI: 10.1038/s41420-023-01413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
TP53 is the most frequently mutated gene in human cancer. While no TP53-targeting drugs have been approved in the USA or Europe so far, preclinical and clinical studies are underway to investigate targeting of specific or all TP53 mutations, for example, by restoration of the functionality of mutated TP53 (TP53mut) or protecting wildtype TP53 (TP53wt) from negative regulation. We performed a comprehensive mRNA expression analysis in 24 cancer types of TCGA to extract (i) a consensus expression signature shared across TP53 mutation types and cancer types, (ii) differential gene expression patterns between tumors harboring different TP53 mutation types such as loss of function, gain of function or dominant-negative mutations, and (iii) cancer-type-specific patterns of gene expression and immune infiltration. Analysis of mutational hotspots revealed both similarities across cancer types and cancer type-specific hotspots. Underlying ubiquitous and cancer type-specific mutational processes with the associated mutational signatures contributed to explaining this observation. Virtually no genes were differentially expressed between tumors harboring different TP53 mutation types, while hundreds of genes were over- and underexpressed in TP53mut compared to TP53wt tumors. A consensus list included 178 genes that were overexpressed and 32 genes that were underexpressed in the TP53mut tumors of at least 16 of the investigated 24 cancer types. In an association analysis of immune infiltration with TP53 mutations in 32 cancer subtypes, decreased immune infiltration was observed in six subtypes, increased infiltration in two subtypes, a mixed pattern of decreased and increased immune cell populations in four subtypes, while immune infiltration was not associated with TP53 status in 20 subtypes. The analysis of a large cohort of human tumors complements results from experimental studies and supports the view that TP53 mutations should be further evaluated as predictive markers for immunotherapy and targeted therapies.
Collapse
Affiliation(s)
- Eva Romanovsky
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Iordanis Ourailidis
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Michael Menzel
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
- Center for Personalized Medicine (ZPM) Heidelberg, 69120, Heidelberg, Germany
| | - Susanne Beck
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Markus Ball
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor Diseases (NCT) Heidelberg, member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
- Center for Personalized Medicine (ZPM) Heidelberg, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg partner site, Heidelberg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, member of the German Center for Lung Research (DZL), Philipps-University, 35037, Marburg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
- Center for Personalized Medicine (ZPM) Heidelberg, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg partner site, Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM) Heidelberg, 69120, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg partner site, Heidelberg, Germany.
| |
Collapse
|
2
|
Budczies J, Romanovsky E, Kluck K, Ourailidis I, Menzel M, Beck S, Ball M, Kazdal D, Christopoulos P, Schirmacher P, Stiewe T, Stenzinger A. Abstract 2607: Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
TP53 mutations are the most common single gene alteration in human cancer with diagnostic and prognostic implications in some cancer types. While no TP53-targeting therapeutics have been approved in the USA or Europe yet, drugs tailored to specific TP53 mutations, restoring the functionality of mutated TP53 (TP53mut), and protecting TP53 from negative regulation are being explored in preclinical studies and clinical trials. We performed a comprehensive mRNA expression analysis in 24 cancer types of the TCGA to extract (i) a consensus expression signature shared across TP53 mutation types and cancer types, (ii) differential gene expression patterns between different TP53 mutation types such as LOF, GOF, as well as dominant-negative mutations, and (iii) cancer types specific gene expression patterns. Mutational hotspots showed a similar pattern across cancer types, but at the same time prevalence was significantly different between cancer types for about half of the most prevalent hotspots. Both can be explained in part by the mutational processes operational for example the clock-like process behind SBS1 that is operational across cancer types and aflatoxin exposure assocated with SBS24 that ist operational in liver hepatocellular carcinoma. Virtually no genes were differential between tumors harboring different types of TP53 mutations in none of the cancer types, while hundreds of genes were over- and underexpressed in TP53mut compared to TP53wt tumors. A consensus gene list of 178 common over- and 32 common underexpressed genes was shared between at least two-thirds of the 24 cancer types. Analysis of the immune tumor microenvironment revealed exclusively decreased immune cell populations in the TP53mut tumors in six, a mixed pattern in four, exclusively increased immune cell populations in two, and no significant alterations in 20 cancer subtypes. The analysis of a large cohort of human tumors complements results from experimental studies and support the development of novel strategies for therapeutic targeting of TP53mut.
Citation Format: Jan Budczies, Eva Romanovsky, Klaus Kluck, Iordanis Ourailidis, Michael Menzel, Susanne Beck, Markus Ball, Daniel Kazdal, Petros Christopoulos, Peter Schirmacher, Thorsten Stiewe, Albrecht Stenzinger. Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2607.
Collapse
Affiliation(s)
- Jan Budczies
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | - Eva Romanovsky
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | - Klaus Kluck
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | | | - Michael Menzel
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | - Susanne Beck
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | - Markus Ball
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | - Daniel Kazdal
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | | | | | | | | |
Collapse
|
3
|
Budczies J, Pfarr N, Romanovsky E, Endris V, Stenzinger A, Denkert C. Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data. BMC Bioinformatics 2018; 19:157. [PMID: 29699497 PMCID: PMC5921540 DOI: 10.1186/s12859-018-2159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. RESULTS Ioncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR. CONCLUSIONS Ioncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls.
Collapse
Affiliation(s)
- Jan Budczies
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany. .,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany.
| | - Nicole Pfarr
- Institute of Pathology, Technical University Munich (TUM), Munich, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
| | - Eva Romanovsky
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
| |
Collapse
|