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Lebedeva A, Veselovsky E, Kavun A, Belova E, Grigoreva T, Orlov P, Subbotovskaya A, Shipunov M, Mashkov O, Bilalov F, Shatalov P, Kaprin A, Shegai P, Diuzhev Z, Migiaev O, Vytnova N, Mileyko V, Ivanov M. Untapped Potential of Poly(ADP-Ribose) Polymerase Inhibitors: Lessons Learned From the Real-World Clinical Homologous Recombination Repair Mutation Testing. World J Oncol 2024; 15:562-578. [PMID: 38993246 PMCID: PMC11236374 DOI: 10.14740/wjon1820] [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: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 07/13/2024] Open
Abstract
Background Testing for homologous recombination deficiency (HRD) mutations is pivotal to assess individual risk, to proact preventive measures in healthy carriers and to tailor treatments for cancer patients. Increasing prominence of poly(ADP-ribose) polymerase (PARP) inhibitors with remarkable impact on molecular-selected patient survival across diverse nosologies, ingrains testing for BRCA genes and beyond in clinical practice. Nevertheless, testing strategies remain a question of debate. While several pathogenic BRCA1/2 gene variants have been described as founder pathogenic mutations frequently found in patients from Russia, other homologous recombination repair (HRR) genes have not been sufficiently explored. In this study, we present real-world data of routine HRR gene testing in Russia. Methods We evaluated clinical and sequencing data from cancer patients who had germline/somatic next-generation sequencing (NGS) HRR gene testing in Russia (BRCA1/2/ATM/CHEK2, or 15 HRR genes). The primary objectives of this study were to evaluate the frequency of BRCA1/2 and non-BRCA gene mutations in real-world unselected patients from Russia, and to determine whether testing beyond BRCA1/2 is feasible. Results Data of 2,032 patients were collected from February 2021 to February 2023. Most had breast (n = 715, 35.2%), ovarian (n = 259, 12.7%), pancreatic (n = 85, 4.2%), or prostate cancer (n = 58, 2.9%). We observed 586 variants of uncertain significance (VUS) and 372 deleterious variants (DVs) across 487 patients, with 17.6% HRR-mutation positivity. HRR testing identified 120 (11.8%) BRCA1/2-positive, and 172 (16.9%) HRR-positive patients. With 51 DVs identified in 242 formalin-fixed paraffin-embedded (FFPE), testing for variant origin clarification was required in one case (0.4%). Most BRCA1/2 germline variants were DV (121 DVs, 26 VUS); in non-BRCA1/2 genes, VUS were ubiquitous (53 DVs, 132 VUS). In silico prediction identified additional 4.9% HRR and 1.2% BRCA1/2/ATM/CHEK2 mutation patients. Conclusions Our study represents one of the first reports about the incidence of DV and VUS in HRR genes, including genes beyond BRCA1/2, identified in cancer patients from Russia, assessed by NGS. In silico predictions of the observed HRR gene variants suggest that non-BRCA gene testing is likely to result in higher frequency of patients who are candidates for PARP inhibitor therapy. Continuing sequencing efforts should clarify interpretation of frequently observed non-BRCA VUS.
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Affiliation(s)
- Alexandra Lebedeva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russia
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Orlov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Anna Subbotovskaya
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Maksim Shipunov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Oleg Mashkov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Fanil Bilalov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Peter Shatalov
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Andrey Kaprin
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Peter Shegai
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | | | | | | | - Vladislav Mileyko
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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Zhang P, Yang Q, Chen X, Chen X, Wang Q, Chen K, An Y, Jiang K, Sun F. CENPW knockdown inhibits progression of bladder cancer through inducing cell cycle arrest and apoptosis. J Cancer 2024; 15:858-870. [PMID: 38213721 PMCID: PMC10777039 DOI: 10.7150/jca.90449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Purpose: The objective of this study was to examine the expression and role of Centromere protein W (CENPW) in bladder cancer (BLCA), as well as its potential mechanistic impact on the progression of BLCA. Methods: In this study, we conducted a comparative analysis of the mRNA expression level of CENPW in BLCA tissues and adjacent normal tissues using data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Additionally, we investigated the association between CENPW expression and patient prognosis. Furthermore, we performed in vitro and in vivo experiments to assess the impact of CENPW knockdown on various tumor biological phenotypes in BLCA. Finally, we conducted an analysis to elucidate the underlying mechanisms responsible for the observed phenotypic alterations in BLCA. Results: The expression of CENPW was found to be upregulated in BLCA, and its higher expression was associated with a poorer disease-specific survival (DSS). CENPW was found to have close associations with the cell cycle, mitosis, and DNA replication. In vitro and in vivo experiments demonstrated that the inhibition of CENPW led to a suppression of BLCA progression. Specifically, the knockdown of CENPW resulted in cell cycle arrest phase and induced apoptosis in BLCA by potentially inactivating the signal transducer and activator of transcription3 (STAT3) signaling pathway. Conclusion: CENPW has the potential to function as a molecular marker indicating an unfavorable prognosis in BLCA. Additionally, CENPW exhibits promise as a novel therapeutic target for BLCA.
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Affiliation(s)
- Peng Zhang
- Guizhou Medical University, Guiyang, China
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Qian Yang
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Guiyang, China
| | | | - Xiaolong Chen
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Qing Wang
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Kun Chen
- Department of Medical Genetics, Guizhou Provincial People's Hospital, Guiyang, China
| | - Yu An
- NHC Key Laboratory of Pulmonary Immune-Related Diseases, Guizhou Provincial People's Hospital, Guiyang, China
| | - Kehua Jiang
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Fa Sun
- Guizhou Medical University, Guiyang, China
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
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Jiang XF, Zhang BM, Du FQ, Guo JN, Wang D, Li YE, Deng SH, Cui BB, Liu YL. Exploring biomarkers for prognosis and neoadjuvant chemosensitivity in rectal cancer: Multi-omics and ctDNA sequencing collaboration. Front Immunol 2022; 13:1013828. [PMID: 36569844 PMCID: PMC9780298 DOI: 10.3389/fimmu.2022.1013828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction This study aimed to identified the key genes and sequencing metrics for predicting prognosis and efficacy of neoadjuvant chemotherapy (nCT) in rectal cancer (RC) based on genomic DNA sequencing in samples with different origin and multi-omics association database. Methods We collected 16 RC patients and obtained DNA sequencing data from cancer tissues and plasma cell-free DNA before and after nCT. Various gene variations were analyzed, including single nucleotide variants (SNV), copy number variation (CNV), tumor mutation burden (TMB), copy number instability (CNI) and mutant-allele tumor heterogeneity (MATH). We also identified genes by which CNV level can differentiate the response to nCT. The Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database were used to further evaluate the specific role of therapeutic relevant genes and screen out the key genes in multi-omics levels. After the intersection of the screened genes from differential expression analysis, survival analysis and principal components analysis dimensionality reduction cluster analysis, the key genes were finally identified. Results The genes CNV level of principal component genes in baseline blood and cancer tissues could significantly distinguish the two groups of patients. The CNV of HSP90AA1, EGFR, SRC, MTOR, etc. were relatively gained in the better group compared with the poor group in baseline blood. The CNI and TMB was significantly different between the two groups. The increased expression of HSP90AA1, EGFR, and SRC was associated with increased sensitivity to multiple chemotherapeutic drugs. The nCT predictive score obtained by therapeutic relevant genes could be a potential prognostic indicator, and the combination with TMB could further refine prognostic prediction for patients. After a series of analysis in multi-omics association database, EGFR and HSP90AA1 with significant differences in multiple aspects were identified as the key predictive genes related to prognosis and the sensitivity of nCT. Discussion This work revealed that effective combined application and analysis in multi-omics data are critical to search for predictive biomarkers. The key genes EGFR and HSP90AA1 could serve as an effective biomarker to predict prognose and neoadjuvant chemosensitivity.
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Affiliation(s)
- Xiu-Feng Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bo-Miao Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fen-Qi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jun-Nan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dan Wang
- Department of Neurology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Yi-En Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shen-Hui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
| | - Yan-Long Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
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Fernández-Orth D, Rueda M, Singh B, Moldes M, Jene A, Ferri M, Vasallo C, Fromont LA, Navarro A, Rambla J. A quality control portal for sequencing data deposited at the European genome-phenome archive. Brief Bioinform 2022; 23:6570012. [PMID: 35438138 PMCID: PMC9116225 DOI: 10.1093/bib/bbac136] [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: 12/21/2021] [Revised: 03/01/2022] [Accepted: 03/23/2022] [Indexed: 11/15/2022] Open
Abstract
Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability of the stored data, as of now, data submitters are not mandated to perform any quality control (QC) before uploading their data and associated metadata information. Here, we present a new File QC Portal developed at EGA, along with QC reports performed and created for 1 694 442 files [Fastq, sequence alignment map (SAM)/binary alignment map (BAM)/CRAM and variant call format (VCF)] submitted at EGA. QC reports allow anonymous EGA users to view summary-level information regarding the files within a specific dataset, such as quality of reads, alignment quality, number and type of variants and other features. Researchers benefit from being able to assess the quality of data prior to the data access decision and thereby, increasing the reusability of data (https://ega-archive.org/blog/data-upcycling-powered-by-ega/).
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Affiliation(s)
- Dietmar Fernández-Orth
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Manuel Rueda
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Babita Singh
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Mauricio Moldes
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Aina Jene
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Marta Ferri
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Claudia Vasallo
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Lauren A Fromont
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Arcadi Navarro
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Jordi Rambla
- European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain
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Poloznikov A, Nikulin S, Bolotina L, Kachmazov A, Raigorodskaya M, Kudryavtseva A, Bakhtogarimov I, Rodin S, Gaisina I, Topchiy M, Asachenko A, Novosad V, Tonevitsky A, Alekseev B. 9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. Front Pharmacol 2021; 12:777114. [PMID: 34955846 PMCID: PMC8696016 DOI: 10.3389/fphar.2021.777114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and lethal types of cancer. Although researchers have made significant efforts to study the mechanisms underlying CRC drug resistance, our knowledge of this disease is still limited, and novel therapies are in high demand. It is urgent to find new targeted therapy considering limited chemotherapy options. KRAS mutations are the most frequent molecular alterations in CRC. However, there are no approved K-Ras targeted therapies for these tumors yet. GSK-3β is demonstrated to be a critically important kinase for the survival and proliferation of K-Ras–dependent pancreatic cancer cells. In this study, we tested combinations of standard-of-care therapy and 9-ING-41, a small molecule inhibitor of GSK-3β, in CRC cell lines and patient-derived tumor organoid models of CRC. We demonstrate that 9-ING-41 inhibits the growth of CRC cells via a distinct from chemotherapy mechanism of action. Although molecular biomarkers of 9-ING-41 efficacy are yet to be identified, the addition of 9-ING-41 to the standard-of-care drugs 5-FU and oxaliplatin could significantly enhance growth inhibition in certain CRC cells. The results of the transcriptomic analysis support our findings of cell cycle arrest and DNA repair deficiency in 9-ING-41–treated CRC cells. Notably, we find substantial similarity in the changes of the transcriptomic profile after inhibition of GSK-3β and suppression of STK33, another critically important kinase for K-Ras–dependent cells, which could be an interesting point for future research. Overall, the results of this study provide a rationale for the further investigation of GSK-3 inhibitors in combination with standard-of-care treatment of CRC.
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Affiliation(s)
- Andrey Poloznikov
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Larisa Bolotina
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Andrei Kachmazov
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Rodin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Irina Gaisina
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL, United States
| | - Maxim Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Victor Novosad
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,Scientific Research Centre Bioclinicum, Moscow, Russia.,Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Boris Alekseev
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
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