1
|
Yaacov A, Ben Cohen G, Landau J, Hope T, Simon I, Rosenberg S. Cancer mutational signatures identification in clinical assays using neural embedding-based representations. Cell Rep Med 2024; 5:101608. [PMID: 38866015 PMCID: PMC11228799 DOI: 10.1016/j.xcrm.2024.101608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
While mutational signatures provide a plethora of prognostic and therapeutic insights, their application in clinical-setting, targeted gene panels is extremely limited. We develop a mutational representation model (which learns and embeds specific mutation signature connections) that enables prediction of dominant signatures with only a few mutations. We predict the dominant signatures across more than 60,000 tumors with gene panels, delineating their landscape across different cancers. Dominant signature predictions in gene panels are of clinical importance. These included UV, tobacco, and apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) signatures that are associated with better survival, independently from mutational burden. Further analyses reveal gene and mutation associations with signatures, such as SBS5 with TP53 and APOBEC with FGFR3S249C. In a clinical use case, APOBEC signature is a robust and specific predictor for resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). Our model provides an easy-to-use way to detect signatures in clinical setting assays with many possible clinical implications for an unprecedented number of cancer patients.
Collapse
Affiliation(s)
- Adar Yaacov
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Gil Ben Cohen
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jakob Landau
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tom Hope
- School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Rosenberg
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
2
|
Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with survival and gene expression in urological carcinomas. Neoplasia 2023; 44:100933. [PMID: 37678146 PMCID: PMC10495641 DOI: 10.1016/j.neo.2023.100933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Different sources of mutagenesis cause consistently identifiable patterns of mutations and mutational signatures that mirror the various carcinogenetic processes. We used publicly available data from the Cancer Genome Atlas to evaluate the associations between the activity of the mutational signatures and various survival endpoints in six types of urological cancers after adjusting for established prognostic factors. The predictive power of the signatures was evaluated with dynamic area under curve models. In addition, links between mutational signature activities and differences in gene expression patterns were analysed. APOBEC-related signature SBS2 was associated with improved overall survival (OS) and disease-specific survival (DSS) in bladder carcinomas in the multivariate analysis, while clock-like signature SBS1 predicted shortened DSS and progression-free interval (PFI) in clear cell renal cell carcinomas (ccRCC). In papillary renal cell carcinomas (pRCC), SBS45 was a predictor of improved outcomes, and APOBEC-related SBS13 was a predictor of worse outcomes. Gene expression analyses revealed various enriched pathways between the low- and high-signature groups. Interestingly, in both the ccRCC and pRCC cohorts, the genes of several members of the melanoma antigen (MAGE) family were highly upregulated in the signatures, which predicted poor outcomes, and downregulated in signatures, which were associated with improved survival. To summarize, SBS signatures provide substantial prognostic value compared with just the traditional prognostic factors in certain cancer types. APOBEC-related SBS2 and SBS13 seem to provide robust prognostic information for particular urological cancers, maybe driven by the expression of specific groups of genes, including the MAGE gene family.
Collapse
Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki FI-00290, Finland.
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki FI-00014, Finland; Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki FI-00014, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu FI-90220, Finland
| |
Collapse
|
3
|
Yang S, Zhu G, He R, Fang D, Feng J. Advances in transcriptomics and proteomics in differentiated thyroid cancer: An updated perspective (Review). Oncol Lett 2023; 26:396. [PMID: 37600346 PMCID: PMC10433702 DOI: 10.3892/ol.2023.13982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/25/2023] [Indexed: 08/22/2023] Open
Abstract
Thyroid cancer (TC) is a broad classification of neoplasms that includes differentiated thyroid cancer (DTC) as a common histological subtype. DTC is characterized by an increased mortality rate in advanced stages, which contributes to the overall high mortality rate of DTC. This progression is mainly attributed to alterations in molecular driver genes, resulting in changes in phenotypes such as invasion, metastasis and dedifferentiation. Clinical management of DTC is challenging due to insufficient diagnostic and therapeutic options. The advent of-omics technology has presented a promising avenue for the diagnosis and treatment of DTC. Identifying molecular markers that can predict the early progression of DTC to a late adverse outcome is essential for precise diagnosis and treatment. The present review aimed to enhance our understanding of DTC by integrating big data with biological systems through-omics technology, specifically transcriptomics and proteomics, which can shed light on the molecular mechanisms underlying carcinogenesis.
Collapse
Affiliation(s)
- Shici Yang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Gaohong Zhu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Rui He
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Dong Fang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jiaojiao Feng
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| |
Collapse
|
4
|
Maria AG, Azevedo B, Settas N, Hannah-Shmouni F, Stratakis CA, Faucz FR. USP13 genetics and expression in a family with thyroid cancer. Endocrine 2022; 77:281-290. [PMID: 35583846 PMCID: PMC9462409 DOI: 10.1007/s12020-022-03068-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE Papillary thyroid carcinoma (PTC) is the most common type of thyroid carcinoma and its incidence has greatly increased in the last 30 years. Ubiquitin-specific protease 13 (USP13) is a class of deubiquitinating enzymes (DUBs) and plays an important role in cellular functions such as cell cycle regulation, DNA damage repair, and different cell signaling pathways. Studies regarding the role of USP13 in cancer development and progression are divergent and there are no previous data regarding the role of USP13 gene in PTCs. In this study, we investigated the genetic cause of PTC diagnosed in multiple members of a Brazilian family. METHODS Whole exome sequencing (WES) was performed to identify the genetic cause of PTC. Cycloheximide chase assay and clonogenic assay were performed to study USP13 stability and function in vitro. RESULTS WES analysis identified a heterozygous missense variant c.1483G > A (p.V495M) in the USP13 gene that fully segregates with the disease. In silico modeling suggests that this variant may cause protein structural perturbations. USP13 overexpression increased the potential of a single cell to form colonies. The USP13 c.1483G > A variant enhanced the effects seen in USP13 overexpression and preserved protein stability for longer hours compared to the non-mutated USP13 protein. CONCLUSION Our study suggests that USP13 overexpression may play a role in tumorigenesis of PTCs; and that the USP13 p.V495M (c.1483G > A) variant enhances USP13 estability.
Collapse
Affiliation(s)
- Andrea G Maria
- Section on Endocrinology & Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Bruna Azevedo
- Group for Advanced Molecular Investigation (NIMA), Graduate Program in Health Sciences (PPGCS), School of Medicine (EM), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil
| | - Nikolaos Settas
- Section on Endocrinology & Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Fady Hannah-Shmouni
- Section on Endocrinology & Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Constantine A Stratakis
- Section on Endocrinology & Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Fabio R Faucz
- Group for Advanced Molecular Investigation (NIMA), Graduate Program in Health Sciences (PPGCS), School of Medicine (EM), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil
| |
Collapse
|
5
|
Landa I. Advances in Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14122908. [PMID: 35740572 PMCID: PMC9221251 DOI: 10.3390/cancers14122908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
"Thyroid cancer" encompasses a heterogeneous group of tumors that range from the predominant papillary thyroid cancer (PTC) subtype, which shows excellent survival rates, to the poorly differentiated (PDTC) and anaplastic thyroid cancer (ATC) forms, accounting for most of the disease-related morbidity and mortality [...].
Collapse
Affiliation(s)
- Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|