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Chen C, Dettman EJ, Zhou W, Gozman A, Jin F, Lee LC, Ren Y, Zhou H, Cristescu R, Shao C. Prevalence of homologous recombination biomarkers in multiple tumor types: an observational study. Future Oncol 2024:1-14. [PMID: 39011875 DOI: 10.1080/14796694.2024.2367957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/11/2024] [Indexed: 07/17/2024] Open
Abstract
Aim: To determine the prevalence of deleterious mutations in BRCA1 and BRCA2 and in 13 genes involved in homologous recombination repair (HRR), the prevalence of genomic loss of heterozygosity and the allelic and hereditary status of BRCA1, BRCA2 and other HRR gene mutations in multiple solid tumor types. Patients & methods: This was a retrospective observational study of patients with an advanced/metastatic diagnosis in one of 15 solid tumor types, who were identified in a real-world clinico-genomic database. Results: Tumor tissue samples from 9457 patients were analyzed, among which 4.7% had known or suspected deleterious BRCA1/2 mutations. The prevalence (range) of mutations in HRR genes was 13.6% (2.4%-26.0%) and genomic loss of heterozygosity ≥16% was 20.6% (2.6-34.4%) across all tumor types. Conclusion: The prevalence of mutations varied significantly depending on the type of tumor.
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Affiliation(s)
- Cai Chen
- Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Wei Zhou
- Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Fan Jin
- Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Liam C Lee
- Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Yixin Ren
- Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Heng Zhou
- Merck & Co., Inc., Rahway, NJ 07065, USA
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Wang X, Sun J, Liu Y, Lin Z, Jiang X, Ye Y, Lv C, Lian X, Xu W, Luo S, Liao S, Chen Z, Wang S. Trps1 predicts poor prognosis in advanced high grade serous ovarian carcinoma. Int J Cancer 2024; 154:1639-1651. [PMID: 38212905 DOI: 10.1002/ijc.34844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
TRPS1 is aberrantly expressed in a variety of tumors, including breast, prostate, and gastric cancers, and is strongly associated with tumorigenesis or prognosis. However, the role of TRPS1 in high grade serous ovarian carcinoma (HGSC) is unknown. We investigated the relationship between TRPS1 expression and clinicopathology in HGSC patients. The tumor-related regulatory mechanisms of TRPS1 was explored through in vivo and vitro experiments. The results showed that TRPS1 was highly expressed in HGSC compared to normal tissues. It was also linked to the cell proliferation index Ki67 and poor prognosis. In vivo experiments showed that knockdown of TRPS1 could inhibit tumor growth. In vitro experiments, knockdown of TRPS1 inhibited the proliferation of ovarian cancer cells. TRPS1 exerted its regulatory role as a transcription factor, binding to the PSAT1 promoter and promoting the expression of PSAT1 gene. Meanwhile, PSAT1 was positively correlated with CCND1 expression. These results suggest that TRPS1 affects HGSC proliferation and cell cycle by regulating PSAT1 and thus CCND1 expression.
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Affiliation(s)
- Xiaojiang Wang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Molecular Pathology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiandong Sun
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yue Liu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zihang Lin
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xia Jiang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yuhong Ye
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chengyu Lv
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiuli Lian
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Weiwei Xu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shanshan Luo
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shumin Liao
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zhangting Chen
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shie Wang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
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