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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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Hou Y, Meng XY, Zhou X. Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308243. [PMID: 38881520 DOI: 10.1002/advs.202308243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Indexed: 06/18/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.
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Affiliation(s)
- Yuying Hou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang-Yu Meng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Health Science Center, Hubei Minzu University, Enshi, 445000, China
- Hubei Provincial Clinical Medical Research Center for Nephropathy, Hubei Minzu University, Enshi, 445000, China
| | - Xionghui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
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3
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Gao ZJ, Fang H, Sun S, Liu SQ, Fang Z, Liu Z, Li B, Wang P, Sun SR, Meng XY, Wu Q, Chen CS. Single-cell analyses reveal evolution mimicry during the specification of breast cancer subtype. Theranostics 2024; 14:3104-3126. [PMID: 38855191 PMCID: PMC11155410 DOI: 10.7150/thno.96163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024] Open
Abstract
Background: The stem or progenitor antecedents confer developmental plasticity and unique cell identities to cancer cells via genetic and epigenetic programs. A comprehensive characterization and mapping of the cell-of-origin of breast cancer using novel technologies to unveil novel subtype-specific therapeutic targets is still absent. Methods: We integrated 195,144 high-quality cells from normal breast tissues and 406,501 high-quality cells from primary breast cancer samples to create a large-scale single-cell atlas of human normal and cancerous breasts. Potential heterogeneous origin of malignant cells was explored by contrasting cancer cells against reference normal epithelial cells. Multi-omics analyses and both in vitro and in vivo experiments were performed to screen and validate potential subtype-specific treatment targets. Novel biomarkers of identified immune and stromal cell subpopulations were validated by immunohistochemistry in our cohort. Results: Tumor stratification based on cancer cell-of-origin patterns correlated with clinical outcomes, genomic aberrations and diverse microenvironment constitutions. We found that the luminal progenitor (LP) subtype was robustly associated with poor prognosis, genomic instability and dysfunctional immune microenvironment. However, the LP subtype patients were sensitive to neoadjuvant chemotherapy (NAC), PARP inhibitors (PARPi) and immunotherapy. The LP subtype-specific target PLK1 was investigated by both in vitro and in vivo experiments. Besides, large-scale single-cell profiling of breast cancer inspired us to identify a range of clinically relevant immune and stromal cell subpopulations, including subsets of innate lymphoid cells (ILCs), macrophages and endothelial cells. Conclusion: The present single-cell study revealed the cellular repertoire and cell-of-origin patterns of breast cancer. Combining single-cell and bulk transcriptome data, we elucidated the evolution mimicry from normal to malignant subtypes and expounded the LP subtype with vital clinical implications. Novel immune and stromal cell subpopulations of breast cancer identified in our study could be potential therapeutic targets. Taken together, Our findings lay the foundation for the precise prognostic and therapeutic stratification of breast cancer.
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Affiliation(s)
- Zhi-Jie Gao
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huan Fang
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Si-Qing Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Fang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bei Li
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei. China
| | - Ping Wang
- Medical College, Anhui University of Science and Technology, Huainan, AnHui. China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sheng-Rong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiang-Yu Meng
- Health Science Center, Hubei Minzu University, Enshi, Hubei, China
| | - Qi Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ce-Shi Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, Yunnan, China
- The Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
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4
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Chaudhry KA, Bianchi-Smiraglia A. The aryl hydrocarbon receptor as a tumor modulator: mechanisms to therapy. Front Oncol 2024; 14:1375905. [PMID: 38807762 PMCID: PMC11130384 DOI: 10.3389/fonc.2024.1375905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is widely recognized to play important, but complex, modulatory roles in a variety of tumor types. In this review, we comprehensively summarize the increasingly controversial role of AhR as a tumor regulator and the mechanisms by which it alters tumor progression based on the cancer cell type. Finally, we discuss new and emerging strategies to therapeutically modulate AhR, focusing on novel agents that hold promise in current human clinical trials as well as existing FDA-approved drugs that could potentially be repurposed for cancer therapy.
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Affiliation(s)
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, NY, United States
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5
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Liu YT, Meng XY. The underexplored role of APOBEC3 enzymes in autoimmune diseases. Rheumatology (Oxford) 2024; 63:e166-e167. [PMID: 38060252 DOI: 10.1093/rheumatology/kead663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Affiliation(s)
- Yi-Tong Liu
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Diseases, Hubei Minzu University, Enshi, China
- Health Science Center, Hubei Minzu University, Enshi, China
| | - Xiang-Yu Meng
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Diseases, Hubei Minzu University, Enshi, China
- Health Science Center, Hubei Minzu University, Enshi, China
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6
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Congues F, Wang P, Lee J, Lin D, Shahid A, Xie J, Huang Y. Targeting aryl hydrocarbon receptor to prevent cancer in barrier organs. Biochem Pharmacol 2024; 223:116156. [PMID: 38518996 PMCID: PMC11144369 DOI: 10.1016/j.bcp.2024.116156] [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: 10/31/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
The skin, lung, and gut are important barrier organs that control how the body reacts to environmental stressors such as ultraviolet (UV) radiation, air pollutants, dietary components, and microorganisms. The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that plays an important role in maintaining homeostasis of barrier organs. AhR was initially discovered as a receptor for environmental chemical carcinogens such as polycyclic aromatic hydrocarbons (PAHs). Activation of AhR pathways by PAHs leads to increased DNA damage and mutations which ultimately lead to carcinogenesis. Ongoing evidence reveals an ever-expanding role of AhR. Recently, AhR has been linked to immune systems by the interaction with the development of natural killer (NK) cells, regulatory T (Treg) cells, and T helper 17 (Th17) cells, as well as the production of immunosuppressive cytokines. However, the role of AhR in carcinogenesis is not as straightforward as we initially thought. Although AhR activation has been shown to promote carcinogenesis in some studies, others suggest that it may act as a tumor suppressor. In this review, we aim to explore the role of AhR in the development of cancer that originates from barrier organs. We also examined the preclinical efficacy data of AhR agonists and antagonists on carcinogenesis to determine whether AhR modulation can be a viable option for cancer chemoprevention.
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Affiliation(s)
- Francoise Congues
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Pengcheng Wang
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; Department of Stomatology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Joshua Lee
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Daphne Lin
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Ayaz Shahid
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Jianming Xie
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Ying Huang
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA.
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7
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Groeneveld CS, Sanchez-Quiles V, Dufour F, Shi M, Dingli F, Nicolle R, Chapeaublanc E, Poullet P, Jeffery D, Krucker C, Maillé P, Vacherot F, Vordos D, Benhamou S, Lebret T, Micheau O, Zinovyev A, Loew D, Allory Y, de Reyniès A, Bernard-Pierrot I, Radvanyi F. Proteogenomic Characterization of Bladder Cancer Reveals Sensitivity to Apoptosis Induced by Tumor Necrosis Factor-related Apoptosis-inducing Ligand in FGFR3-mutated Tumors. Eur Urol 2024; 85:483-494. [PMID: 37380559 DOI: 10.1016/j.eururo.2023.05.037] [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: 12/13/2022] [Revised: 04/26/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Molecular understanding of muscle-invasive (MIBC) and non-muscle-invasive (NMIBC) bladder cancer is currently based primarily on transcriptomic and genomic analyses. OBJECTIVE To conduct proteogenomic analyses to gain insights into bladder cancer (BC) heterogeneity and identify underlying processes specific to tumor subgroups and therapeutic outcomes. DESIGN, SETTING, AND PARTICIPANTS Proteomic data were obtained for 40 MIBC and 23 NMIBC cases for which transcriptomic and genomic data were already available. Four BC-derived cell lines harboring FGFR3 alterations were tested with interventions. INTERVENTION Recombinant tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), second mitochondrial-derived activator of caspases mimetic (birinapant), pan-FGFR inhibitor (erdafitinib), and FGFR3 knockdown. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Proteomic groups from unsupervised analyses (uPGs) were characterized using clinicopathological, proteomic, genomic, transcriptomic, and pathway enrichment analyses. Additional enrichment analyses were performed for FGFR3-mutated tumors. Treatment effects on cell viability for FGFR3-altered cell lines were evaluated. Synergistic treatment effects were evaluated using the zero interaction potency model. RESULTS AND LIMITATIONS Five uPGs, covering both NMIBC and MIBC, were identified and bore coarse-grained similarity to transcriptomic subtypes underlying common features of these different entities; uPG-E was associated with the Ta pathway and enriched in FGFR3 mutations. Our analyses also highlighted enrichment of proteins involved in apoptosis in FGFR3-mutated tumors, not captured through transcriptomics. Genetic and pharmacological inhibition demonstrated that FGFR3 activation regulates TRAIL receptor expression and sensitizes cells to TRAIL-mediated apoptosis, further increased by combination with birinapant. CONCLUSIONS This proteogenomic study provides a comprehensive resource for investigating NMIBC and MIBC heterogeneity and highlights the potential of TRAIL-induced apoptosis as a treatment option for FGFR3-mutated bladder tumors, warranting a clinical investigation. PATIENT SUMMARY We integrated proteomics, genomics, and transcriptomics to refine molecular classification of bladder cancer, which, combined with clinical and pathological classification, should lead to more appropriate management of patients. Moreover, we identified new biological processes altered in FGFR3-mutated tumors and showed that inducing apoptosis represents a new potential therapeutic option.
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Affiliation(s)
- Clarice S Groeneveld
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Centre de Recherche des Cordeliers, AP-HP, Université Paris Cité, Paris, France
| | - Virginia Sanchez-Quiles
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Florent Dufour
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Inovarion, Paris, France
| | - Mingjun Shi
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Florent Dingli
- Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Rémy Nicolle
- Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, Université Paris Cité, Paris, France
| | - Elodie Chapeaublanc
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Patrick Poullet
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Clémentine Krucker
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Pascale Maillé
- Département de Pathologie, Hôpital Henri Mondor, APHP, Créteil, France
| | | | - Dimitri Vordos
- Service d'Urologie, Hôpital Henri Mondor, APHP, Créteil, France
| | | | - Thierry Lebret
- Service d'Urologie, Hôpital Foch, UVSQ, Université Paris-Saclay, Suresnes, France
| | - Olivier Micheau
- INSERM, LNC UMR1231, Université Bourgogne Franche-Comté, Dijon, France
| | - Andrei Zinovyev
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Yves Allory
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Department of Pathology, Institut Curie, UVSQ, Université Paris-Saclay, Saint-Cloud, France
| | - Aurélien de Reyniès
- Centre de Recherche des Cordeliers, AP-HP, Université Paris Cité, Paris, France
| | - Isabelle Bernard-Pierrot
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - François Radvanyi
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France.
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8
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Nakauma-González JA, Rijnders M, Noordsij MTW, Martens JWM, van der Veldt AAM, Lolkema MPJ, Boormans JL, van de Werken HJG. Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature. CELL GENOMICS 2024; 4:100528. [PMID: 38552621 PMCID: PMC11019362 DOI: 10.1016/j.xgen.2024.100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes mutate specific DNA sequences and hairpin-loop structures, challenging the distinction between passenger and driver hotspot mutations. Here, we characterized 115 whole genomes of metastatic urothelial carcinoma (mUC) to identify APOBEC mutagenic hotspot drivers. APOBEC-associated mutations were detected in 92% of mUCs and were equally distributed across the genome, while APOBEC hotspot mutations (ApoHMs) were enriched in open chromatin. Hairpin loops were frequent targets of didymi (twins in Greek), two hotspot mutations characterized by the APOBEC SBS2 signature, in conjunction with an uncharacterized mutational context (Ap[C>T]). Next, we developed a statistical framework that identified ApoHMs as drivers in coding and non-coding genomic regions of mUCs. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UCs and 3,744 samples of 17 metastatic cancers, identifying cancer-type-specific drivers. Our study highlights the role of APOBEC in cancer development and may contribute to developing novel targeted therapy options for APOBEC-driven cancers.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Minouk T W Noordsij
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
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9
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Pukhta IR, Rout RK. Identification and segregation of genes with improved recurrent neural network trained with optimal gene level and mutation level features. Comput Methods Biomech Biomed Engin 2024:1-16. [PMID: 38424698 DOI: 10.1080/10255842.2024.2311322] [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: 07/04/2023] [Accepted: 01/20/2024] [Indexed: 03/02/2024]
Abstract
Even though many different approaches have been employed to address the complex mutational heterogeneity of cancer, finding driver genes is still problematic since other genomic factors cannot be fully integrated for combined analyses. This research paper presents a novel gene identification and segregation model with five key processes (a) pre-processing, (b) treatment of class imbalances, (c) feature extraction, (d) feature selection, and (e) gene classification. To increase the data quality, the gathered initial information is first pre-processed utilizing data cleaning and data normalization. This turns the raw data into something that is both useful and effective. In actuality, the sample is skewed against drivers because passenger mutation markers appear in proportionally less instances than drivers do. To address the Class Imbalance Problem, improved K-Means + SMOTE are applied to the preprocessed data. The most crucial characteristics, including those at the gene and mutation levels, are then extracted from the balanced dataset. To lessen the computational load in terms of time, the best features from the retrieved features are selected using Forensic interpretation tailored hunger food search optimization (FIHFSO). The ideal features are used to train the deep learning classifier that conducts the separation procedure. In this research, an Improved Recurrent Neural Network (I-RNN) is used to make a final decision about genes. At 90% of learning percentage, the accuracy of the proposed method achieves 0.98% of 0.83, 0.81, 0.65, 0.80, 0.92 and 0.63% which is compared to the other methods like HGS, FBIO, AOA, AO, GOA and PRO respectively.
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Affiliation(s)
- Irfan Rashid Pukhta
- Assistant Professor, Department of Computer Science and Engineering National Institute of Technology, Srinagar, Jammu and Kashmir 190006, India
| | - Ranjeet Kumar Rout
- Assistant Professor, Department of Computer Science and Engineering National Institute of Technology, Srinagar, Jammu and Kashmir 190006, India
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10
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Okato A, Utsumi T, Ranieri M, Zheng X, Zhou M, Pereira LD, Chen T, Kita Y, Wu D, Hyun H, Lee H, Gdowski AS, Raupp JD, Clark-Garvey S, Manocha U, Chafitz A, Sherman F, Stephens J, Rose TL, Milowsky MI, Wobker SE, Serody JS, Damrauer JS, Wong KK, Kim WY. FGFR inhibition augments anti-PD-1 efficacy in murine FGFR3-mutant bladder cancer by abrogating immunosuppression. J Clin Invest 2024; 134:e169241. [PMID: 38226620 PMCID: PMC10786699 DOI: 10.1172/jci169241] [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: 01/30/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
The combination of targeted therapy with immune checkpoint inhibition (ICI) is an area of intense interest. We studied the interaction of fibroblast growth factor receptor (FGFR) inhibition with ICI in urothelial carcinoma (UC) of the bladder, in which FGFR3 is altered in 50% of cases. Using an FGFR3-driven, Trp53-mutant genetically engineered murine model (UPFL), we demonstrate that UPFL tumors recapitulate the histology and molecular subtype of their FGFR3-altered human counterparts. Additionally, UPFL1 allografts exhibit hyperprogression to ICI associated with an expansion of T regulatory cells (Tregs). Erdafitinib blocked Treg proliferation in vitro, while in vivo ICI-induced Treg expansion was fully abrogated by FGFR inhibition. Combined erdafitinib and ICI resulted in high therapeutic efficacy. In aggregate, our work establishes that, in mice, co-alteration of FGFR3 and Trp53 results in high-grade, non-muscle-invasive UC and presents a previously underappreciated role for FGFR inhibition in blocking ICI-induced Treg expansion.
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Affiliation(s)
- Atsushi Okato
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Takanobu Utsumi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michela Ranieri
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Xingnan Zheng
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Luiza D. Pereira
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Ting Chen
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Yuki Kita
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Di Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyesun Hyun
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyojin Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Andrew S. Gdowski
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - John D. Raupp
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sean Clark-Garvey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alison Chafitz
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Fiona Sherman
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Janaye Stephens
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Tracy L. Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Matthew I. Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Sara E. Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine
| | - Jonathan S. Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Pathology and Laboratory Medicine
- Department of Microbiology and Immunology
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - William Y. Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Genetics, and
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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11
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Arnedo-Pac C, Muiños F, Gonzalez-Perez A, Lopez-Bigas N. Hotspot propensity across mutational processes. Mol Syst Biol 2024; 20:6-27. [PMID: 38177930 PMCID: PMC10883281 DOI: 10.1038/s44320-023-00001-w] [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: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis.
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Affiliation(s)
- Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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12
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Meng XY. Comments on "Methylation scores for smoking, alcohol consumption and body mass index and risk of seven types of cancer". Int J Cancer 2023; 153:1543-1544. [PMID: 37387394 DOI: 10.1002/ijc.34645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023]
Affiliation(s)
- Xiang-Yu Meng
- Health Science Center, Hubei Minzu University, Enshi, China
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13
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Meng XY, Wang QL, Shi MJ, Zhang HY. Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility. Bladder Cancer 2023; 9:211-216. [PMID: 38993187 PMCID: PMC11181760 DOI: 10.3233/blc-230010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2024]
Abstract
BACKGROUND The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences. METHODS We calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs. RESULTS We validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution. CONCLUSIONS It is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.
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Affiliation(s)
- Xiang-Yu Meng
- Health Science Center, Hubei Minzu University, Enshi, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Qiao-Li Wang
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ming-Jun Shi
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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14
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Boll LM, Perera-Bel J, Rodriguez-Vida A, Arpí O, Rovira A, Juanpere N, Vázquez Montes de Oca S, Hernández-Llodrà S, Lloreta J, Albà MM, Bellmunt J. The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer. Sci Rep 2023; 13:15287. [PMID: 37714872 PMCID: PMC10504302 DOI: 10.1038/s41598-023-42495-2] [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: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the treatment. To better understand which factors drive clinical benefit, we have generated whole exome and RNA sequencing data from 27 advanced urothelial carcinoma patients treated with anti-PD-(L)1 monoclonal antibodies. We assessed the influence on the response of non-synonymous mutations (tumor mutational burden or TMB), clonal and subclonal mutations, neoantigen load and various gene expression markers. We found that although TMB is significantly associated with response, this effect can be mostly explained by clonal mutations, present in all cancer cells. This trend was validated in an additional cohort. Additionally, we found that responders with few clonal mutations had abnormally high levels of T and B cell immune markers, suggesting that a high immune cell infiltration signature could be a better predictive biomarker for this subset of patients. Our results support the idea that highly clonal cancers are more likely to respond to ICI and suggest that non-additive effects of different signatures should be considered for predictive models.
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Affiliation(s)
| | | | - Alejo Rodriguez-Vida
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | - Oriol Arpí
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Ana Rovira
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | | | | | | | - Josep Lloreta
- Hospital del Mar Research Institute, Barcelona, Spain
- Department of Medicine and Life Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Joaquim Bellmunt
- Hospital del Mar Research Institute, Barcelona, Spain.
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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15
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Grant SR, Tang L, Wei L, Foster BA, Paragh G, Huss WJ. Mutation Hotspots Found in Bladder Cancer Aid Prediction of Carcinogenic Risk in Normal Urothelium. Int J Mol Sci 2023; 24:ijms24097852. [PMID: 37175559 PMCID: PMC10177765 DOI: 10.3390/ijms24097852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/11/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
More than 80,000 new cases of bladder cancer are estimated to be diagnosed in 2023. However, the 5-year survival rate for bladder cancer has not changed in decades, highlighting the need for prevention. Numerous cancer-causing mutations are present in the urothelium long before signs of cancer arise. Mutation hotspots in cancer-driving genes were identified in non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) tumor samples. Mutation burden within the hotspot regions was measured in normal urothelium with a low and high risk of cancer. A significant correlation was found between the mutation burden in normal urothelium and bladder cancer tissue within the hotspot regions. A combination of measured hotspot burden and personal risk factors was used to fit machine learning classification models. The efficacy of each model to differentiate between adjacent benign urothelium from bladder cancer patients and normal urothelium from healthy donors was measured. A random forest model using a combination of personal risk factors and mutations within MIBC hotspots yielded the highest AUC of 0.9286 for the prediction of high- vs. low-risk normal urothelium. Currently, there are no effective biomarkers to assess subclinical field disease and early carcinogenic progression in the bladder. Our findings demonstrate novel differences in mutation hotspots in NMIBC and MIBC and provide the first evidence for mutation hotspots to aid in the assessment of cancer risk in the normal urothelium. Early risk assessment and identification of patients at high risk of bladder cancer before the clinical presentation of the disease can pave the way for targeted personalized preventative therapy.
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Affiliation(s)
- Sydney R Grant
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Li Tang
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Lei Wei
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Barbara A Foster
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Gyorgy Paragh
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Wendy J Huss
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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16
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Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F. Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks. Oncogene 2023; 42:1524-1542. [PMID: 36944729 PMCID: PMC10162941 DOI: 10.1038/s41388-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2, respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.
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Affiliation(s)
- Hélène Neyret-Kahn
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France.
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France.
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France.
| | - Jacqueline Fontugne
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Xiang Yu Meng
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- College of Basic Medical Sciences, Medical School, Hubei Minzu University, Enshi, 445000, China
| | - Clarice S Groeneveld
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Université de Paris, Centre de Recherche des Cordeliers, Paris, France
| | - Luc Cabel
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg,1 rue Laurent Fries, 67404, Illkirch, France
| | - Elodie Guyon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Clémentine Krucker
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Florent Dufour
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Elodie Chapeaublanc
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Audrey Rapinat
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Laura Tanguy
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Victoria Dixon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Yann Neuzillet
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - Thierry Lebret
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - David Gentien
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genétique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, 67404, Illkirch Cedex, France
| | - Yves Allory
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Isabelle Bernard-Pierrot
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - François Radvanyi
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
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17
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Liu Y, Wu X, d'Aubenton-Carafa Y, Thermes C, Chen CL. OKseqHMM: a genome-wide replication fork directionality analysis toolkit. Nucleic Acids Res 2023; 51:e22. [PMID: 36629249 PMCID: PMC9976876 DOI: 10.1093/nar/gkac1239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
During each cell division, tens of thousands of DNA replication origins are co-ordinately activated to ensure the complete duplication of the human genome. However, replication fork progression can be challenged by many factors, including co-directional and head-on transcription-replication conflicts (TRC). Head-on TRCs are more dangerous for genome integrity. To study the direction of replication fork movement and TRCs, we developed a bioinformatics toolkit called OKseqHMM (https://github.com/CL-CHEN-Lab/OK-Seq, https://doi.org/10.5281/zenodo.7428883). Then, we used OKseqHMM to analyse a large number of datasets obtained by Okazaki fragment sequencing to directly measure the genome-wide replication fork directionality (RFD) and to accurately predict replication initiation and termination at a fine resolution in organisms including yeast, mouse and human. We also successfully applied our analysis to other genome-wide sequencing techniques that also contain RFD information (e.g. eSPAN, TrAEL-seq). Our toolkit can be used to predict replication initiation and fork progression direction genome-wide in a wide range of cell models and growth conditions. Comparing the replication and transcription directions allows identifying loci at risk of TRCs, particularly head-on TRCs, and investigating their role in genome instability by checking DNA damage data, which is of prime importance for human health.
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Affiliation(s)
- Yaqun Liu
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Xia Wu
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Yves d'Aubenton-Carafa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
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18
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Properties of non-coding mutation hotspots as urinary biomarkers for bladder cancer detection. Sci Rep 2023; 13:1060. [PMID: 36658180 PMCID: PMC9852567 DOI: 10.1038/s41598-023-27675-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Mutations at specific hotspots in non-coding regions of ADGRG6, PLEKHS1, WDR74, TBC1D12 and LEPROTL1 frequently occur in bladder cancer (BC). These mutations could function as biomarkers for the non-invasive detection of BC but this remains largely unexplored. Massively-parallel sequencing of non-coding hotspots was applied to 884 urine cell pellet DNAs: 591 from haematuria clinic patients (165 BCs, 426 non-BCs) and 293 from non-muscle invasive BC surveillance patients (29 with recurrence). Urine samples from 142 non-BC haematuria clinic patients were used to optimise variant calling. Non-coding mutations are readily detectable in the urine of BC patients and undetectable, or present at much lower frequencies, in the absence of BC. The mutations can be used to detect incident BC with 66% sensitivity (95% CI 58-75) at 92% specificity (95% CI 88-95) and recurrent disease with 55% sensitivity (95% CI 36-74) at 85% specificity (95% CI 80-89%) using a 2% variant allele frequency threshold. In the NMIBC surveillance setting, the detection of non-coding mutations in urine in the absence of clinically detectable disease was associated with an increased relative risk of future recurrence (RR = 4.62 (95% CI 3.75-5.48)). As urinary biomarkers, non-coding hotspot mutations behave similarly to driver mutations in BC-associated genes and could be included in biomarker panels for BC detection.
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19
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In-depth analysis of the interactions of various aryl hydrocarbon receptor ligands from a computational perspective. J Mol Graph Model 2023; 118:108339. [PMID: 36183684 DOI: 10.1016/j.jmgm.2022.108339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/01/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that acts as a machinery that controls the expression of many genes, including cytochrome P450 CYP1A1, CYP1A2 and CYP1B1. It plays a principal role in numerous biological and toxicological functions, making it a promising target for developing therapeutic agents. Several novel small molecules targeting the AhR signaling pathway are currently under investigation as antitumor agents. Some have already advanced into clinical trials in patients with various tumors. Activation of AhR by diverse chemicals either endogenous or exogenous is initiated by the binding of these ligands to the PAS-B domain, which modulates AhR functions. There is, however, limited information about how various ligands interact with the PAS-B domain for activating or inhibiting the AhR. To better understand the mode of action of AhR agonists/antagonists. The current work proposes a combination of several computational tools to build dynamical models for the PAS-B domain bound to different ligands in mouse and human. Our findings reveal the essential roles of specific PAS-B residues (e.g., S365, V381& Q383), which mediate the AhR ligand-binding process. Our results also explain how these residues regulate the promiscuity of AhR in accommodating various chemicals in its binding PAS-B ligand-binding pocket.
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20
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [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] [Indexed: 11/09/2022]
Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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21
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Cisneros LH, Vaske C, Bussey KJ. Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer. Front Genet 2022; 13:932763. [PMID: 36147501 PMCID: PMC9488704 DOI: 10.3389/fgene.2022.932763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. Bacteria deploy SIM when faced with DNA double-strand breaks in the presence of conditions that elicit an SOS response. SIM employs DinB, the evolutionary precursor to human trans-lesion synthesis (TLS) error-prone polymerases, and results in mutations concentrated around DNA double-strand breaks with an abundance that decays with distance. We performed a quantitative study on single nucleotide variant calls for whole-genome sequencing data from 1950 tumors, non-inherited mutations from 129 normal samples, and acquired mutations in 3 cell line models of stress-induced adaptive mutation. We introduce statistical methods to identify mutational clusters, quantify their shapes and tease out the potential mechanism that produced them. Our results show that mutations in both normal and cancer samples are indeed clustered and have shapes indicative of SIM. Clusters in normal samples occur more often in the same genomic location across samples than in cancer suggesting loss of regulation over the mutational process during carcinogenesis. Additionally, the signatures of TLS contribute the most to mutational cluster formation in both patient samples as well as experimental models of SIM. Furthermore, a measure of cluster shape heterogeneity was associated with cancer patient survival with a hazard ratio of 5.744 (Cox Proportional Hazard Regression, 95% CI: 1.824–18.09). Our results support the conclusion that the ancient and evolutionary-conserved adaptive mutation response found in bacteria is a source of genomic instability in cancer. Biological adaptation through SIM might explain the ability of tumors to evolve in the face of strong selective pressures such as treatment and suggests that the conventional ‘hit it hard’ approaches to therapy could prove themselves counterproductive.
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Affiliation(s)
- Luis H. Cisneros
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
| | | | - Kimberly J. Bussey
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
- Precision Medicine, Midwestern University, Glendale, AZ, United States
- *Correspondence: Kimberly J. Bussey,
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22
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Transcriptional and genetic alterations of cuproptosis-related genes correlated to malignancy and immune-infiltrate of esophageal carcinoma. Cell Death Dis 2022; 8:370. [PMID: 35995782 PMCID: PMC9395517 DOI: 10.1038/s41420-022-01164-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023]
Abstract
Esophageal carcinoma (ESCA) is a common type of cancer with high mortality. Cuproptosis is a new type of cell death and is characterized by the dependence on mitochondrial respiration and protein lipoylation. However, the potential roles of cuproptosis-related genes (CRGs) in ESCA remain elusive. Here, we systematically assessed the transcriptional and genetic alterations of CRGs in ESCA. We identified a CRGs signature for ESCA patients. A 6-CRGs signature was constructed by the least absolute shrinkage and selection operator (LASSO) regression analysis along with the univariate cox regression analysis and differential genes analysis. The CRGs score could significantly stratify ESCA patients’ survival and a high CRGs score was significantly correlated with worse overall survival. Moreover, higher CRGs score indicated higher pathology grades and aberrant cell adhesion, possibly via the PI3K-AKT pathway, which could also underly their increased sensitivity to PI3K-AKT pathway inhibitors. In addition, patients with high CRGs tend to hold more mutation load and abnormal APOBEC mutation. Notably, a higher CRGs score was anomalously associated with more immune infiltration, which could explain its malignancy by increased PD-L1 stability and a higher proportion of bystander T cells. In conclusion, our report revealed the significance of cuproptosis in ESCA and may have therapeutic potential in activating the bystander T cells.
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23
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Vlaar JM, Borgman A, Kalkhoven E, Westland D, Besselink N, Shale C, Faltas BM, Priestley P, Kuijk E, Cuppen E. Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer. Sci Rep 2022; 12:10081. [PMID: 35710704 PMCID: PMC9203531 DOI: 10.1038/s41598-022-14256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Bladder cancer has a high recurrence rate and low survival of advanced stage patients. Few genetic drivers of bladder cancer have thus far been identified. We performed in-depth structural variant analysis on whole-genome sequencing data of 206 metastasized urinary tract cancers. In ~ 10% of the patients, we identified recurrent in-frame deletions of exons 8 and 9 in the aryl hydrocarbon receptor gene (AHRΔe8-9), which codes for a ligand-activated transcription factor. Pan-cancer analyses show that AHRΔe8-9 is highly specific to urinary tract cancer and mutually exclusive with other bladder cancer drivers. The ligand-binding domain of the AHRΔe8-9 protein is disrupted and we show that this results in ligand-independent AHR-pathway activation. In bladder organoids, AHRΔe8-9 induces a transformed phenotype that is characterized by upregulation of AHR target genes, downregulation of differentiation markers and upregulation of genes associated with stemness and urothelial cancer. Furthermore, AHRΔe8-9 expression results in anchorage independent growth of bladder organoids, indicating tumorigenic potential. DNA-binding deficient AHRΔe8-9 fails to induce transformation, suggesting a role for AHR target genes in the acquisition of the oncogenic phenotype. In conclusion, we show that AHRΔe8-9 is a novel driver of urinary tract cancer and that the AHR pathway could be an interesting therapeutic target.
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Affiliation(s)
- Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Denise Westland
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Charles Shale
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Bishoy M Faltas
- Department of Medicine and Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Peter Priestley
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands. .,Hartwig Medical Foundation, Amsterdam, The Netherlands.
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24
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Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes. Genome Med 2022; 14:59. [PMID: 35655252 PMCID: PMC9164468 DOI: 10.1186/s13073-022-01056-4] [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] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Three-quarters of bladder cancer patients present with early-stage disease (non-muscle-invasive bladder cancer, NMIBC, UICC TNM stages Ta, T1 and Tis); however, most next-generation sequencing studies to date have concentrated on later-stage disease (muscle-invasive BC, stages T2+). We used exome and transcriptome sequencing to comprehensively characterise NMIBCs of all grades and stages to identify prognostic genes and pathways that could facilitate treatment decisions. Tumour grading is based upon microscopy and cellular appearances (grade 1 BCs are less aggressive, and grade 3 BCs are most aggressive), and we chose to also focus on the most clinically complex NMIBC subgroup, those patients with grade 3 pathological stage T1 (G3 pT1) disease. METHODS Whole-exome and RNA sequencing were performed in total on 96 primary NMIBCs including 22 G1 pTa, 14 G3 pTa and 53 G3 pT1s, with both exome and RNA sequencing data generated from 75 of these individual samples. Associations between genomic alterations, expression profiles and progression-free survival (PFS) were investigated. RESULTS NMIBCs clustered into 3 expression subtypes with different somatic alteration characteristics. Amplifications of ARNT and ERBB2 were significant indicators of worse PFS across all NMIBCs. High APOBEC mutagenesis and high tumour mutation burden were both potential indicators of better PFS in G3pT1 NMIBCs. The expression of individual genes was not prognostic in BCG-treated G3pT1 NMIBCs; however, downregulated interferon-alpha and gamma response pathways were significantly associated with worse PFS (adjusted p-value < 0.005). CONCLUSIONS Multi-omic data may facilitate better prognostication and selection of therapeutic interventions in patients with G3pT1 NMIBC. These findings demonstrate the potential for improving the management of high-risk NMIBC patients and warrant further prospective validation.
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25
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EpisomiR, a New Family of miRNAs, and Its Possible Roles in Human Diseases. Biomedicines 2022; 10:biomedicines10061280. [PMID: 35740302 PMCID: PMC9220071 DOI: 10.3390/biomedicines10061280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are synthesized through a canonical pathway and play a role in human diseases, such as cancers and cardiovascular, neurodegenerative, psychiatric, and chronic inflammatory diseases. The development of sequencing technologies has enabled the identification of variations in noncoding miRNAs. These miRNA variants, called isomiRs, are generated through a non-canonical pathway, by several enzymes that alter the length and sequence of miRNAs. The isomiR family is, now, expanding further to include episomiRs, which are miRNAs with different modifications. Since recent findings have shown that isomiRs reflect the cell-specific biological function of miRNAs, knowledge about episomiRs and isomiRs can, possibly, contribute to the optimization of diagnosis and therapeutic technology for precision medicine.
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26
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Gnan S, Josephides JM, Wu X, Spagnuolo M, Saulebekova D, Bohec M, Dumont M, Baudrin LG, Fachinetti D, Baulande S, Chen CL. Kronos scRT: a uniform framework for single-cell replication timing analysis. Nat Commun 2022; 13:2329. [PMID: 35484127 PMCID: PMC9050662 DOI: 10.1038/s41467-022-30043-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
Mammalian genomes are replicated in a cell type-specific order and in coordination with transcription and chromatin organization. Currently, single-cell replication studies require individual processing of sorted cells, yielding a limited number (<100) of cells. Here, we develop Kronos scRT, a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform or cell sorting, which allows investigating large datasets obtained from asynchronous cells. By applying our tool to published data as well as droplet-based single-cell whole-genome sequencing data generated in this study, we exploit scRT from thousands of cells for different mouse and human cell lines. Our results demonstrate that although genomic regions are frequently replicated around their population average RT, replication can occur stochastically throughout S phase. Altogether, Kronos scRT allows fast and comprehensive investigations of the RT programme at the single-cell resolution for both homogeneous and heterogeneous cell populations. A scalable approach to explore DNA replication in single cells reveals that although aneuploidy does not have a major impact on the pattern of replication, different cell types and sub-populations display distinguished replication paths.
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Affiliation(s)
- Stefano Gnan
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France
| | - Joseph M Josephides
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France
| | - Xia Wu
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France.,Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Manuela Spagnuolo
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France
| | - Dalila Saulebekova
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France
| | - Mylène Bohec
- Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University, 75005, Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS UMR144, Cell Biology and Cancer, 75005, Paris, France
| | - Laura G Baudrin
- Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University, 75005, Paris, France
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS UMR144, Cell Biology and Cancer, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University, 75005, Paris, France
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75005, Paris, France.
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27
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Chen H, Zhao L, Liu J, Zhou H, Wang X, Fang X, Xia X. Bioinformatic Analyzes of the Association Between Upregulated Expression of JUN Gene via APOBEC-Induced FLG Gene Mutation and Prognosis of Cervical Cancer. Front Med (Lausanne) 2022; 9:815450. [PMID: 35510248 PMCID: PMC9058067 DOI: 10.3389/fmed.2022.815450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/15/2022] [Indexed: 02/01/2023] Open
Abstract
Globally, cervical cancer (CC) is the most common malignant tumor of the female reproductive system and its incidence is only second after breast cancer. Although screening and advanced treatment strategies have improved the rates of survival, some patients with CC still die due to metastasis and drug resistance. It is considered that cancer is driven by somatic mutations, such as single nucleotide, small insertions/deletions, copy number, and structural variations, as well as epigenetic changes. Previous studies have shown that cervical intraepithelial neoplasia is associated with copy number variants (CNVs) and/or mutations in cancer-related genes. Further, CC is also related to genetic mutations. The present study analyzed the data on somatic mutations of cervical squamous cell carcinoma (CESC) in the Cancer Genome Atlas database. It was evident that the Apolipoprotein B mRNA editing enzyme-catalyzed polypeptide-like (APOBEC)-related mutation of the FLG gene can upregulate the expression of the JUN gene and ultimately lead to poor prognosis for patients with CC. Therefore, the findings of the current study provide a new direction for future treatment of CC.
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Affiliation(s)
- Huan Chen
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Liyun Zhao
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Jiaqiang Liu
- Laboratory Medicine Center, Zhu Zhou Hospital Affiliated to Xiangya School of Medicine, Central South University (CSU), Zhuzhou, China
| | - Housheng Zhou
- Department of Obstetrics and Gynecology, Zhu Zhou Hospital Affiliated to Xiangya School of Medicine, CSU, Zhuzhou, China
| | - Xi Wang
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Xiaomeng Xia
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
- *Correspondence: Xiaomeng Xia
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28
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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29
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Bos MK, Smid M, Sleijfer S, Martens JWM. Apolipoprotein B mRNA-Editing Catalytic Polypeptide-Like-Induced Protein Changes in Estrogen Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer Throughout Disease Progression. JCO Precis Oncol 2022; 6:e2100190. [PMID: 35050709 PMCID: PMC8789213 DOI: 10.1200/po.21.00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Apolipoprotein B mRNA-Editing Catalytic Polypeptide-like (APOBEC) enzymes are mutagenic factors contributing to tumor progression and therapy resistance. However, the effects of APOBEC-induced protein changes have not been systematically assessed. Here, we describe the effects of APOBEC on the coding sequence in primary and metastatic estrogen receptor–positive (ER+)/human epidermal growth factor receptor 2–negative (HER2–) breast cancer (BC). METHODS We determined the enrichment of amino acid (AA) changes resulting from APOBEC mutagenesis in 323 primary BC tumors and 424 metastatic breast cancer (mBC) lesions via comparison with a simulated mutational genomic landscape not under selection pressure. We subsequently explored genes with recurrent APOBEC-associated AA changes and investigated the clonality of individual APOBEC-associated mutations. Using public sequencing data from an independent primary BC and mBC cohort, we further confirm our findings by reporting genes having these enriched AA changes in an APOBEC context. RESULTS Our analysis demonstrated that several APOBEC-derived AA changes are significantly enriched compared with a simulated AA change distribution drawn at random. Among the enriched AA changes, Glutamate(E)>Lysine(K) and Glutamate(E)>Glutamine(Q) were mostly found at hotspots in oncogenes, whereas termination codons (Glutamine[Q]>STOP[X] and Serine[S]>STOP[X]) occurred in tumor suppressor genes and, mostly, not at hotspot locations. These mutations are found in genes contributing to BC initiation, eg, introduction of termination codons in TP53, MAP3K1, and CDH1 (in lobular BC) and two oncogenic hotspots in PIK3CA (p.E542K and p.E545K). In endocrine-resistant BC, we observed APOBEC-induced termination codons at ER-modulating genes, KMT2C, ARID1A, NF1, and ZFHX3. Finally, in mBC, compared with single PIK3CA mutations, dual PIK3CA mutations occurred more frequently in an APOBEC context (Fisher's exact P < .001). CONCLUSION Our results show that APOBEC mutagenesis recurrently targets various known drivers of BC initiation, progression, and endocrine resistance. APOBEC drives early, metastatic and endocrine resistant disease in ER+/HER2- breast cancer![]()
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Affiliation(s)
- Manouk K Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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30
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Pálinkás HL, Pongor L, Balajti M, Nagy Á, Nagy K, Békési A, Bianchini G, Vértessy BG, Győrffy B. Primary Founder Mutations in the PRKDC Gene Increase Tumor Mutation Load in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020633. [PMID: 35054819 PMCID: PMC8775830 DOI: 10.3390/ijms23020633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
The clonal composition of a malignant tumor strongly depends on cellular dynamics influenced by the asynchronized loss of DNA repair mechanisms. Here, our aim was to identify founder mutations leading to subsequent boosts in mutation load. The overall mutation burden in 591 colorectal cancer tumors was analyzed, including the mutation status of DNA-repair genes. The number of mutations was first determined across all patients and the proportion of genes having mutation in each percentile was ranked. Early mutations in DNA repair genes preceding a mutational expansion were designated as founder mutations. Survival analysis for gene expression was performed using microarray data with available relapse-free survival. Of the 180 genes involved in DNA repair, the top five founder mutations were in PRKDC (n = 31), ATM (n = 26), POLE (n = 18), SRCAP (n = 18), and BRCA2 (n = 15). PRKDC expression was 6.4-fold higher in tumors compared to normal samples, and higher expression led to longer relapse-free survival in 1211 patients (HR = 0.72, p = 4.4 × 10-3). In an experimental setting, the mutational load resulting from UV radiation combined with inhibition of PRKDC was analyzed. Upon treatments, the mutational load exposed a significant two-fold increase. Our results suggest PRKDC as a new key gene driving tumor heterogeneity.
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Affiliation(s)
- Hajnalka Laura Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Lőrinc Pongor
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
| | - Máté Balajti
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
| | - Ádám Nagy
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
| | - Kinga Nagy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Giampaolo Bianchini
- Department of Medical Oncology, San Raffaele Scientific Institute, via Olgettina 60, 20132 Milan, Italy;
| | - Beáta G. Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
- Correspondence: (B.G.V.); (B.G.)
| | - Balázs Győrffy
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
- Correspondence: (B.G.V.); (B.G.)
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Zhu Z, Ji X, Zhu W, Cai T, Xu C, Huang C, He S, Gong Y, Li X, Lin J, Zhou L. Comprehensive bioinformatics analyses of APOBECs family and identification of APOBEC3D as the unfavorable prognostic biomarker in clear cell renal cell carcinoma. J Cancer 2021; 12:7101-7110. [PMID: 34729111 PMCID: PMC8558646 DOI: 10.7150/jca.61972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/03/2021] [Indexed: 01/22/2023] Open
Abstract
Purpose: At present, how early screening for ccRCC is still a thorny issue for urologists. Probing the mechanisms underlying the development of ccRCC and finding relevant prognostic biomarkers remains crucial. Therefore, we systematically analyzed the APOBEC family in this study and identified APOBEC3D as a prognostic biomarker. Methods: In this study, based on the TCGA database, we systematically assessed the expression and prognosis of the APOBEC family and analyzed potential bioinformatic pathways. We then constructed nomograms to predict the prognosis of ccRCC patients better. Afterward, we further focused on APOBEC3D in our data on ccRCC specimens. The APOBEC3D should be extensively studied in ccRCC in the future. Results: The results showed that the APOBEC family showed the most significant changes in expression in ccRCC. The pathway enrichment analysis showed that APOBEC3 family members mainly regulated cytidine and cytosine-related processes. Subsequently, the Cox regression was used to construct prognostic signature, and validated in ICGC and GEO databases. Next, a nomogram was created integrating clinical parameters showing good predictive performance. Finally, we screened for APOBEC3D and found in our clinical sample that patients with high expression of APOBEC3D had a worse prognosis. Conclusion: Based on these results, APOBEC family members play important roles in the development of ccRCC, and APOBEC3D could serve as the biomarker for predicting patient prognosis.
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Affiliation(s)
- Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xing Ji
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Weijie Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Tianyu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Cong Huang
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
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32
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Review of Experimental Studies to Improve Radiotherapy Response in Bladder Cancer: Comments and Perspectives. Cancers (Basel) 2020; 13:cancers13010087. [PMID: 33396795 PMCID: PMC7795454 DOI: 10.3390/cancers13010087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
Bladder cancer is among the top ten most common cancer types in the world. Around 25% of all cases are muscle-invasive bladder cancer, for which the gold standard treatment in the absence of metastasis is the cystectomy. In recent years, trimodality treatment associating maximal transurethral resection and radiotherapy combined with concurrent chemotherapy is increasingly used as an organ-preserving alternative. However, the use of this treatment is still limited by the lack of biomarkers predicting tumour response and by a lack of targeted radiosensitising drugs that can improve the therapeutic index, especially by limiting side effects such as bladder fibrosis. In order to improve the bladder-preserving treatment, experimental studies addressing these main issues ought to be considered (both in vitro and in vivo studies). Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews, we conducted a literature search in PubMed on experimental studies investigating how to improve bladder cancer radiotherapy with different radiosensitising agents using a comprehensive search string. We made comments on experimental model selection, experimental design and results, formulating the gaps of knowledge still existing: such as the lack of reliable predictive biomarkers of tumour response to chemoradiation according to the molecular tumour subtype and lack of efficient radiosensitising agents specifically targeting bladder tumour cells. We provided guidance to improve forthcoming studies, such as taking into account molecular characteristics of the preclinical models and highlighted the value of using patient-derived xenografts as well as syngeneic models. Finally, this review could be a useful tool to set up new radiation-based combined treatments with an improved therapeutic index that is needed for bladder preservation.
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