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Zhang C, Liu J, Wu J, Ranjan K, Cui X, Wang X, Zhang D, Zhu S. Key molecular DNA damage responses of human cells to radiation. Front Cell Dev Biol 2024; 12:1422520. [PMID: 39050891 PMCID: PMC11266142 DOI: 10.3389/fcell.2024.1422520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Our understanding of the DNA damage responses of human cells to radiation has increased remarkably over the recent years although some notable signaling events remain to be discovered. Here we provide a brief account of the key molecular events of the responses to reflect the current understanding of the key underlying mechanisms involved.
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Affiliation(s)
- Chencheng Zhang
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
| | - Jibin Liu
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
| | - Jun Wu
- Nantong Tumor Hospital, Nantong, China
| | - Kamakshi Ranjan
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Xiaopeng Cui
- Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong, China
| | - Xingdan Wang
- Department of Radiotherapy, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Shudong Zhu
- Cancer Research Center, Nantong Tumor Hospital, Nantong, China
- Cancer Research Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, China
- Cancer Research Center, Nantong, China
- Argus Pharmaceuticals, Changsha, China
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2
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Peng X, Huang X, Zhang S, Zhang N, Huang S, Wang Y, Zhong Z, Zhu S, Gao H, Yu Z, Yan X, Tao Z, Dai Y, Zhang Z, Chen X, Wang F, Claret FX, Elkabets M, Ji N, Zhong Y, Kong D. Sequential Inhibition of PARP and BET as a Rational Therapeutic Strategy for Glioblastoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2307747. [PMID: 38896791 DOI: 10.1002/advs.202307747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 05/20/2024] [Indexed: 06/21/2024]
Abstract
PARP inhibitors (PARPi) hold substantial promise in treating glioblastoma (GBM). However, the adverse effects have restricted their broad application. Through unbiased transcriptomic and proteomic sequencing, it is discovered that the BET inhibitor (BETi) Birabresib profoundly alters the processes of DNA replication and cell cycle progression in GBM cells, beyond the previously reported impact of BET inhibition on homologous recombination repair. Through in vitro experiments using established GBM cell lines and patient-derived primary GBM cells, as well as in vivo orthotopic transplantation tumor experiments in zebrafish and nude mice, it is demonstrated that the concurrent administration of PARPi and BETi can synergistically inhibit GBM. Intriguingly, it is observed that DNA damage lingers after discontinuation of PARPi monotherapy, implying that sequential administration of PARPi followed by BETi can maintain antitumor efficacy while reducing toxicity. In GBM cells with elevated baseline replication stress, the sequential regimen exhibits comparable efficacy to concurrent treatment, protecting normal glial cells with lower baseline replication stress from DNA toxicity and subsequent death. This study provides compelling preclinical evidence supporting the development of innovative drug administration strategies focusing on PARPi for GBM therapy.
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Affiliation(s)
- Xin Peng
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
- Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xin Huang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Shaolu Zhang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Naixin Zhang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Shengfan Huang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Yingying Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Zhenxing Zhong
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Shan Zhu
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Haiwang Gao
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Zixiang Yu
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Xiaotong Yan
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Zhennan Tao
- Department of Neurosurgery, the Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, 210008, China
| | - Yuxiang Dai
- Department of Neurosurgery, the Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, 210008, China
| | - Zhe Zhang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
| | - Xi Chen
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, 300020, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Francois X Claret
- Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Moshe Elkabets
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Ning Ji
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Yuxu Zhong
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Dexin Kong
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
- Key Laboratory of Immune Microenvironment and Diseases (Ministry of Education), International Joint Laboratory of Ocular Diseases (Ministry of Education), Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin, 300052, China
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3
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Mariella E, Grasso G, Miotto M, Buzo K, Reilly NM, Andrei P, Vitiello PP, Crisafulli G, Arena S, Rospo G, Corti G, Lorenzato A, Cancelliere C, Barault L, Gionfriddo G, Linnebacher M, Russo M, Di Nicolantonio F, Bardelli A. Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer. Mol Oncol 2024; 18:1460-1485. [PMID: 38468448 PMCID: PMC11161737 DOI: 10.1002/1878-0261.13622] [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: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.
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Affiliation(s)
- Elisa Mariella
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Gaia Grasso
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Martina Miotto
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Kristi Buzo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | | | - Pietro Andrei
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | - Pietro Paolo Vitiello
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | | | - Sabrina Arena
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Giuseppe Rospo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Present address:
Boehringer Ingelheim RCV GmbH & Co KGViennaAustria
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | | | - Ludovic Barault
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | | | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and ImmunotherapyUniversity of RostockGermany
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Federica Di Nicolantonio
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
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4
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Battuello P, Corti G, Bartolini A, Lorenzato A, Sogari A, Russo M, Di Nicolantonio F, Bardelli A, Crisafulli G. Mutational signatures of colorectal cancers according to distinct computational workflows. Brief Bioinform 2024; 25:bbae249. [PMID: 38783705 PMCID: PMC11116831 DOI: 10.1093/bib/bbae249] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
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Affiliation(s)
- Paolo Battuello
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giovanni Crisafulli
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
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5
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Aubert L, Bastien E, Renoult O, Guilbaud C, Özkan K, Brusa D, Bouzin C, Richiardone E, Richard C, Boidot R, Léonard D, Corbet C, Feron O. Tumor acidosis-induced DNA damage response and tetraploidy enhance sensitivity to ATM and ATR inhibitors. EMBO Rep 2024; 25:1469-1489. [PMID: 38366255 PMCID: PMC10933359 DOI: 10.1038/s44319-024-00089-7] [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: 10/08/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Tumor acidosis is associated with increased invasiveness and drug resistance. Here, we take an unbiased approach to identify vulnerabilities of acid-exposed cancer cells by combining pH-dependent flow cytometry cell sorting from 3D colorectal tumor spheroids and transcriptomic profiling. Besides metabolic rewiring, we identify an increase in tetraploid cell frequency and DNA damage response as consistent hallmarks of acid-exposed cancer cells, supported by the activation of ATM and ATR signaling pathways. We find that regardless of the cell replication error status, both ATM and ATR inhibitors exert preferential growth inhibitory effects on acid-exposed cancer cells. The efficacy of a combination of these drugs with 5-FU is further documented in 3D spheroids as well as in patient-derived colorectal tumor organoids. These data position tumor acidosis as a revelator of the therapeutic potential of DNA repair blockers and as an attractive clinical biomarker to predict the response to a combination with chemotherapy.
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Affiliation(s)
- Léo Aubert
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium.
| | - Estelle Bastien
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Ophélie Renoult
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Céline Guilbaud
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Kübra Özkan
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Davide Brusa
- CytoFlux-Flow Cytometry and Cell Sorting Platform, Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Caroline Bouzin
- Imaging Platform 2IP, Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Elena Richiardone
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Corentin Richard
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges‑François Leclerc Cancer Center‑UNICANCER, 21079, Dijon, France
| | - Romain Boidot
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges‑François Leclerc Cancer Center‑UNICANCER, 21079, Dijon, France
| | - Daniel Léonard
- Institut Roi Albert II, Department of Digestive Surgery, Cliniques Universitaires St-Luc, and Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Cyril Corbet
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium
| | - Olivier Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, B-1200, Brussels, Belgium.
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Department, WEL Research Institute, B-1300, Wavre, Belgium.
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6
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Mavroeidi D, Georganta A, Panagiotou E, Syrigos K, Souliotis VL. Targeting ATR Pathway in Solid Tumors: Evidence of Improving Therapeutic Outcomes. Int J Mol Sci 2024; 25:2767. [PMID: 38474014 DOI: 10.3390/ijms25052767] [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: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The DNA damage response (DDR) system is a complicated network of signaling pathways that detects and repairs DNA damage or induces apoptosis. Critical regulators of the DDR network include the DNA damage kinases ataxia telangiectasia mutated Rad3-related kinase (ATR) and ataxia-telangiectasia mutated (ATM). The ATR pathway coordinates processes such as replication stress response, stabilization of replication forks, cell cycle arrest, and DNA repair. ATR inhibition disrupts these functions, causing a reduction of DNA repair, accumulation of DNA damage, replication fork collapse, inappropriate mitotic entry, and mitotic catastrophe. Recent data have shown that the inhibition of ATR can lead to synthetic lethality in ATM-deficient malignancies. In addition, ATR inhibition plays a significant role in the activation of the immune system by increasing the tumor mutational burden and neoantigen load as well as by triggering the accumulation of cytosolic DNA and subsequently inducing the cGAS-STING pathway and the type I IFN response. Taken together, we review stimulating data showing that ATR kinase inhibition can alter the DDR network, the immune system, and their interplay and, therefore, potentially provide a novel strategy to improve the efficacy of antitumor therapy, using ATR inhibitors as monotherapy or in combination with genotoxic drugs and/or immunomodulators.
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Affiliation(s)
- Dimitra Mavroeidi
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Anastasia Georganta
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Emmanouil Panagiotou
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Konstantinos Syrigos
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Vassilis L Souliotis
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
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7
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Sogari A, Rovera E, Grasso G, Mariella E, Reilly NM, Lamba S, Mauri G, Durinikova E, Vitiello PP, Lorenzato A, Avolio M, Piumatti E, Bonoldi E, Aquilano MC, Arena S, Sartore-Bianchi A, Siena S, Trusolino L, Donalisio M, Russo M, Di Nicolantonio F, Lembo D, Bardelli A. Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells. Cell Rep Med 2024; 5:101376. [PMID: 38228147 PMCID: PMC10897517 DOI: 10.1016/j.xcrm.2023.101376] [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: 04/16/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024]
Abstract
The bacterial genotoxin colibactin promotes colorectal cancer (CRC) tumorigenesis, but systematic assessment of its impact on DNA repair is lacking, and its effect on response to DNA-damaging chemotherapeutics is unknown. We find that CRC cell lines display differential response to colibactin on the basis of homologous recombination (HR) proficiency. Sensitivity to colibactin is induced by inhibition of ATM, which regulates DNA double-strand break repair, and blunted by HR reconstitution. Conversely, CRC cells chronically infected with colibactin develop a tolerant phenotype characterized by restored HR activity. Notably, sensitivity to colibactin correlates with response to irinotecan active metabolite SN38, in both cell lines and patient-derived organoids. Moreover, CRC cells that acquire colibactin tolerance develop cross-resistance to SN38, and a trend toward poorer response to irinotecan is observed in a retrospective cohort of CRCs harboring colibactin genomic island. Our results shed insight into colibactin activity and provide translational evidence on its chemoresistance-promoting role in CRC.
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Affiliation(s)
- Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Emanuele Rovera
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Gaia Grasso
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Elisa Mariella
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | - Simona Lamba
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Gianluca Mauri
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Pietro Paolo Vitiello
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Marco Avolio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Eleonora Piumatti
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Emanuela Bonoldi
- Department of Pathology, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Sabrina Arena
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Division of Clinical Research and Innovation, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, University of Torino, 10043 Orbassano, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Torino, 10060 Candiolo, Italy
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Torino, 10043 Orbassano, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy.
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8
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Zeng WJ, Li XR, Liu W, Yuan R, Liang WB, Zhuo Y. AND Logic Gate-Regulated DNAzyme Nanoflower for Monitoring the Activity of Multiple DNA Repair Enzymes. Anal Chem 2024; 96:2117-2123. [PMID: 38268109 DOI: 10.1021/acs.analchem.3c04807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Despite the progress that has been made in diverse DNA-based nanodevices to in situ monitor the activity of the DNA repair enzymes in living cells, the significance of improving both the sensitivity and specificity has remained largely neglected and understudied. Herein, we propose a regulatable DNA nanodevice to specifically monitor the activity of DNA repair enzymes for early evaluation of cancer mediated by genomic instability. Concretely, an AND logic gate-regulated DNAzyme nanoflower was rationally designed by the self-assembly of the DNA duplex modified with both apurinic/apyrimidinic (AP) site and methyl lesion site. The DNAzyme nanoflower could be reconfigured under the repair of AP sites and O6-methylguanine sites by apurinic/apyrimidinic endonuclease 1 (APE1) and O6-methylguanine methyltransferase (MGMT) to produce a fluorescent signal, realizing the sensitive monitoring of the activity of APE1 and MGMT. Compared to the free DNAzyme duplex, the fluorescent response of the DNAzyme nanoflower increased by 60%, due to the effective enrichment of the DNA probes by the nanoflower structure. More importantly, we have demonstrated that the dual-enzyme activated strategy allows imaging of specific cancer cells in the AND logic gate manner using MCF-7 as a cancer cell model, improving the specificity of cancer cell imaging. This AND logic gate-regulated multifunctional DNAzyme nanoflower provides a simple tool for simultaneously visualizing multiple DNA repair enzymes, holding great potential in early clinical diagnosis and drug discovery.
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Affiliation(s)
- Wei-Jia Zeng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xiao-Ran Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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9
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Khamidullina AI, Abramenko YE, Bruter AV, Tatarskiy VV. Key Proteins of Replication Stress Response and Cell Cycle Control as Cancer Therapy Targets. Int J Mol Sci 2024; 25:1263. [PMID: 38279263 PMCID: PMC10816012 DOI: 10.3390/ijms25021263] [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: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Replication stress (RS) is a characteristic state of cancer cells as they tend to exchange precision of replication for fast proliferation and increased genomic instability. To overcome the consequences of improper replication control, malignant cells frequently inactivate parts of their DNA damage response (DDR) pathways (the ATM-CHK2-p53 pathway), while relying on other pathways which help to maintain replication fork stability (ATR-CHK1). This creates a dependency on the remaining DDR pathways, vulnerability to further destabilization of replication and synthetic lethality of DDR inhibitors with common oncogenic alterations such as mutations of TP53, RB1, ATM, amplifications of MYC, CCNE1 and others. The response to RS is normally limited by coordination of cell cycle, transcription and replication. Inhibition of WEE1 and PKMYT1 kinases, which prevent unscheduled mitosis entry, leads to fragility of under-replicated sites. Recent evidence also shows that inhibition of Cyclin-dependent kinases (CDKs), such as CDK4/6, CDK2, CDK8/19 and CDK12/13 can contribute to RS through disruption of DNA repair and replication control. Here, we review the main causes of RS in cancers as well as main therapeutic targets-ATR, CHK1, PARP and their inhibitors.
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Affiliation(s)
- Alvina I. Khamidullina
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Yaroslav E. Abramenko
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
| | - Alexandra V. Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Victor V. Tatarskiy
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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10
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Feng Y, Jiang Y, Liu J, Liu J, Shi M, Chen J, Zhang J, Tian Y, Yang X, Liu H. Targeting RPA promotes autophagic flux and the antitumor response to radiation in nasopharyngeal carcinoma. J Transl Med 2023; 21:738. [PMID: 37858134 PMCID: PMC10585929 DOI: 10.1186/s12967-023-04574-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Autophagy is involved in nasopharyngeal carcinoma (NPC) radioresistance. Replication protein A 1 (RPA1) and RPA3, substrates of the RPA complex, are potential therapeutic targets for reversing NPC radioresistance. Nevertheless, the role of RPA in autophagy is not adequately understood. This investigation was performed to reveal the cytotoxic mechanism of a pharmacologic RPA inhibitor (RPAi) in NPC cells and the underlying mechanism by which RPAi-mediated autophagy regulates NPC radiosensitivity. METHODS AND RESULTS We characterized a potent RPAi (HAMNO) that was substantially correlated with radiosensitivity enhancement and proliferative inhibition of in vivo and in NPC cell lines in vitro. We show that the RPAi induced autophagy at multiple levels by inducing autophagic flux, AMPK/mTOR pathway activation, and autophagy-related gene transcription by decreasing glycolytic function. We hypothesized that RPA inhibition impaired glycolysis and increased NPC dependence on autophagy. We further demonstrated that combining autophagy inhibition with chloroquine (CQ) treatment or genetic inhibition of the autophagy regulator ATG5 and RPAi treatment was more effective than either approach alone in enhancing the antitumor response of NPC to radiation. CONCLUSIONS Our study suggests that HAMNO is a potent RPAi that enhances radiosensitivity and induces autophagy in NPC cell lines by decreasing glycolytic function and activating autophagy-related genes. We suggest a novel treatment strategy in which pharmacological inhibitors that simultaneously disrupt RPA and autophagic processes improve NPC responsiveness to radiation.
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Affiliation(s)
- Yanchun Feng
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yingming Jiang
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Department of General Surgery (Department of Gastric Surgery Section 2, ), The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Jun Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Jiaqi Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Mengchen Shi
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Junxiong Chen
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Jingdan Zhang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yu Tian
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Xiangling Yang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China.
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| | - Huanliang Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Guangdong Institute of Gastroenterology, Guangzhou, 510655, China.
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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11
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Thapa R, Afzal O, Bhat AA, Goyal A, Alfawaz Altamimi AS, Almalki WH, Alzarea SI, Kazmi I, Singh SK, Dua K, Thangavelu L, Gupta G. New horizons in lung cancer management through ATR/CHK1 pathway modulation. Future Med Chem 2023; 15:1807-1818. [PMID: 37877252 DOI: 10.4155/fmc-2023-0164] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Molecular profiling has contributed to a new classification of lung cancer, driving advancements in research and therapy. The ataxia telangiectasia and rad3/checkpoint kinase 1 (ATR/CHK1) pathway plays a crucial role in maintaining genomic stability, and its activation has been linked to the development of lung cancer, drug resistance and poor prognosis. Clinical and preclinical studies have demonstrated promising results in targeting this pathway. ATR and CHK1 are proteins that collaborate to repair DNA damage caused by radiation or chemotherapy. ATR/CHK1 inhibitors are currently under investigation in preclinical and clinical trials. This article explores the ATR/CHK1 pathway and its potential for treating lung cancer.
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Affiliation(s)
- Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, 11942, Saudi Arabia
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, U.P., India
| | | | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, 144411, India
- Faculty of Health, Australian Research Centre in Complementary & Integrative Medicine, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary & Integrative Medicine, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Ultimo-NSW, 2007, Australia
| | - Lakshmi Thangavelu
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical & Technical Sciences, Saveetha University, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
- School of Pharmacy, Graphic Era Hill University Dehradun, 248007, India
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12
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Liu T, Wang H, Chen Y, Wan Z, Du Z, Shen H, Yu Y, Ma S, Xu Y, Li Z, Yu N, Zhang F, Cao K, Cai J, Zhang W, Gao F, Yang Y. SENP5 promotes homologous recombination-mediated DNA damage repair in colorectal cancer cells through H2AZ deSUMOylation. J Exp Clin Cancer Res 2023; 42:234. [PMID: 37684630 PMCID: PMC10486113 DOI: 10.1186/s13046-023-02789-9] [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: 02/10/2023] [Accepted: 08/06/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Neoadjuvant radiotherapy has been used as the standard treatment of colorectal cancer (CRC). However, radiotherapy resistance often results in treatment failure. To identify radioresistant genes will provide novel targets for combined treatments and prognostic markers. METHODS Through high content screening and tissue array from CRC patients who are resistant or sensitive to radiotherapy, we identified a potent resistant gene SUMO specific peptidase 5 (SENP5). Then, the effect of SENP5 on radiosensitivity was investigated by CCK8, clone formation, comet assay, immunofluorescence and flow cytometric analysis of apoptosis and cell cycle to investigate the effect of SENP5 on radiosensitivity. SUMO-proteomic mass spectrometry combined with co-immunoprecipitation assay were used to identify the targets of SENP5. Patient-derived organoids (PDO) and xenograft (PDX) models were used to explore the possibility of clinical application. RESULTS We identified SENP5 as a potent radioresistant gene through high content screening and CRC patients tissue array analysis. Patients with high SENP5 expression showed increased resistance to radiotherapy. In vitro and in vivo experiments demonstrated that SENP5 knockdown significantly increased radiosensitivity in CRC cells. SENP5 was further demonstrated essential for efficient DNA damage repair in homologous recombination (HR) dependent manner. Through SUMO mass spectrometry analysis, we characterized H2AZ as a deSUMOylation substrate of SENP5, and depicted the SUMOylation balance of H2AZ in HR repair and cancer resistance. By using PDO and PDX models, we found targeting SENP5 significantly increased the therapeutic efficacy of radiotherapy. CONCLUSION Our findings revealed novel role of SENP5 in HR mediated DNA damage repair and cancer resistance, which could be applied as potent prognostic marker and intervention target for cancer radiotherapy.
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Affiliation(s)
- Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Hang Wang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Zhijie Wan
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Zhipeng Du
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hui Shen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yue Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shengzhe Ma
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Ying Xu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Zhuqing Li
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Nanxi Yu
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fangxiao Zhang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wei Zhang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China.
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China.
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China.
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Cao J, Tao X, Shi B, Wang J, Ma R, Zhao J, Tian J, Huang Q, Yu J, Wang L. NKD1 targeting PCM1 regulates the therapeutic effects of homoharringtonine on colorectal cancer. Mol Biol Rep 2023; 50:6543-6556. [PMID: 37338734 DOI: 10.1007/s11033-023-08572-5] [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: 03/29/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the most common primary malignancy. Recently, antineoplastic attributes of homoharringtonine (HHT) have attracted lots of attention. This study investigated the molecular target and underlying mechanism of HHT in the CRC process by using a cellular and animal models. METHODS This study first detected the effects of HHT on the proliferation, cell cycle and apoptosis ability of CRC cells using CCK-8, Edu staining, flow cytometry and Western blotting assay. In vitro recovery experiment and in vivo tumorigenesis experiment were used to detect the targeted interaction between HHT and NKD1. After that, the downstream target and mechanism of action of HHT targeting NKD1 was determined using quantitative proteomics combined with co-immunoprecipitation/immunofluorescence assay. RESULTS HHT suppressed CRC cells proliferation by inducing cell cycle arrest and apoptosis in vitro and vivo. HHT inhibited NKD1 expression in a concentration and time dependent manner. NKD1 was overexpressed in CRC and its depletion enhanced the therapeutic sensitivity of HHT on CRC, which indicating that NKD1 plays an important role in the development of CRC as the drug delivery target of HHT. Furthermore, proteomic analysis revealed that PCM1 participated the process of NKD1-regulated cell proliferation and cell cycle. NKD1 interacted with PCM1 and promoted PCM1 degradation through the ubiquitin-proteasome pathway. The overexpression of PCM1 effectively reversed the inhibition of siNKD1 on cell cycle. CONCLUSIONS The present findings revealed that HHT blocked NKD1 expression to participate in inhibiting cell proliferation and inducing cell apoptosis, ultimately leading to obstruction of CRC development through NKD1/PCM1 dependent mechanism. Our research provide evidence for clinical application of NKD1-targeted therapy in improving HHT sensitivity for CRC treatment.
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Affiliation(s)
- Jia Cao
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Xiang Tao
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Bin Shi
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jia Wang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Rong Ma
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jufen Zhao
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jinhai Tian
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Qi Huang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jingjing Yu
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Libin Wang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China.
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China.
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Voutsadakis IA. KRAS mutated colorectal cancers with or without PIK3CA mutations: Clinical and molecular profiles inform current and future therapeutics. Crit Rev Oncol Hematol 2023; 186:103987. [PMID: 37059275 DOI: 10.1016/j.critrevonc.2023.103987] [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: 11/18/2022] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Colorectal cancer is one of the most prevalent malignancies and its molecular pathogenesis has been intensely investigated for several decades. As a result, great progress has been made and targeted therapies have been introduced in the clinic. This paper examines colorectal cancers based on two of the most common molecular alterations, KRAS and PIK3CA mutations as a basis for therapeutic targeting. METHODS Two publicly available genomic series with clinical data were evaluated for prevalence and characteristics of cases with and without KRAS and PIK3CA mutations and the literature was reviewed for relevant information on the therapeutic implication of these alterations as well as other coincident alterations to derive therapeutic individualized options of targeted treatments. RESULTS Colorectal cancers without KRAS and PIK3CA mutations represent the most prevalent group (48% to 58% of patients) and present therapeutic targeted opportunities with BRAF inhibitors and immune checkpoint inhibitors in the subsets with BRAF mutations (15% to 22%) and Microsatellite Instability (MSI, 14% to 16%), respectively. The second most prevalent sub-set, with KRAS mutations and PIK3CA wild type, representing 20% to 25% of patients, has currently few targeted options, besides specific KRAS G12C inhibitors for the small percentage of cases (9%-10%) that bear this mutation. Cancers with KRAS wild type and PIK3CA mutations are observed in 12% to 14% of colorectal cancer patients, harbor the highest percentage of cases with BRAF mutations and Microsatellite Instability (MSI), and are candidates for the respective targeted therapies. New targeted therapies in development, such as ATR inhibitors could be effective in cases with ATM mutations and ARID1A mutations that are also most prevalent in this sub-group (14% to 22% and 30%, respectively). KRAS and PIK3CA double mutant cancers have also few targeted options currently and could benefit from combination therapies with PI3K inhibitors and new KRAS inhibitors in development. CONCLUSION The backbone of common KRAS and PIK3CA mutations is a rational frame for development of therapeutic algorithms in colorectal cancer and can help guide new drug therapies development. In addition, the prevalence of different molecular groups presented here may help with planning of combination clinical trials by providing estimations of sub-sets with more than one alteration.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada, and Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada.
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15
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Wang S, Deng S, Jin X, Chen W, Wang X, Zhan H, Fang X, Fu J. Dissecting the heterogeneities of the tumor microenvironment between metastatic and nonmetastatic primary colorectal cancer patients by single-cell RNA sequencing. Life Sci 2023; 320:121576. [PMID: 36933827 DOI: 10.1016/j.lfs.2023.121576] [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: 01/04/2023] [Revised: 03/05/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023]
Abstract
AIMS One of the main factors hampering the long-term prognosis of colorectal cancer (CRC) patients is distant metastasis. However, the driving factors of CRC metastasis have not been clarified at the single-cell level, which limits the in-depth study of accurate prediction and prevention of CRC metastasis to improve the prognosis. MATERIALS AND METHODS Heterogeneities in the tumor microenvironment (TME) between metastatic and nonmetastatic CRC were investigated by single-cell RNA (scRNA) sequencing data. In detail, 50,462 single cells from 20 primary CRC samples, including 40,910 cells from nonmetastatic CRC (M0 group) and 9552 cells from metastatic CRC (M1 group), were systematically analyzed in this study. KEY FINDINGS Based on the single-cell atlas, we revealed that cancer cells and fibroblasts accounted for relatively high proportions in metastatic CRC compared with nonmetastatic CRC. Moreover, two specific cancer cell subtypes (FGGY+SLC6A6+ and IGFBP3+KLK7+ cancer cells) and three specific fibroblast subtypes (ADAMTS6+CAPG+, PIM1+SGK1+ and CA9+UPP1+ fibroblasts) in metastatic CRC were identified. The functional and differentiation characteristics of these specific cell subclusters were elucidated by enrichment and trajectory analyses. SIGNIFICANCE These results provide fundamental knowledge for future in-depth research to screen effective methods and drugs to predict and prevent CRC metastasis to improve prognosis.
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Affiliation(s)
- Sixue Wang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shuangya Deng
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoxin Jin
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Weidong Chen
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaobo Wang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haiyan Zhan
- Department of General Surgery, The Second People's Hospital of Xiangtan City, Xiangtan, China
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - Jie Fu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China.
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Reitsam NG, Märkl B, Dintner S, Waidhauser J, Vlasenko D, Grosser B. Concurrent loss of MLH1, PMS2 and MSH6 immunoexpression in digestive system cancers indicating a widespread dysregulation in DNA repair processes. Front Oncol 2022; 12:1019798. [PMID: 36387226 PMCID: PMC9643848 DOI: 10.3389/fonc.2022.1019798] [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: 08/15/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Immunohistochemical analysis of mismatch repair (MMR) protein expression is widely used to identify tumors with a deficient MMR (dMMR). MMR proteins (MLH1/PMS2 and MSH2/MSH6) work as functional heterodimers, which usually leads to the loss of expression in only one functional MMR heterodimer. Recently, there have been studies showing the simultaneous loss of immunoexpression in proteins of both heterodimers. Yet, this phenomenon has been rarely investigated. In this study, we retrospectively considered cases of different digestive system cancers (gastric cancer, ampullary cancer, small bowel cancer, colorectal cancer), which were immunohistochemically tested for dMMR within a 4-year period at our university hospital (n=352). Of the 103 cases showing dMMR, 5 cases (1.4% of all, 5.1% of dMMR cases) showed a concurrent loss of MLH1, PMS2 and MSH6 immunoexpression, whereas in the other 98 dMMR cases only one MMR heterodimer was affected. MLH1-/PMS2-/MSH6- cancer cases almost arose throughout the entire digestive tract: from the gastric antrum to the left colic flexur. To provide a comprehensive molecular characterization of this MLH1-/PMS2-/MSH6- immunophenotype, tumors were analyzed for microsatellite instability, MLH1 promotor hypermethylation and BRAF exon 15 status. Furthermore, we performed next-generation sequencing focusing on genes related to DNA repair. Here, we could detect pathogenic germline variants as well as multiple sporadic mutations in different genes involved in MMR and homologous recombination repair (HRR) respectively. The affected MMR/HRR-related genes were: ATM, BARD1, BRCA1, CDK12, CHEK1, CHEK2, FANCA, MLH1, MSH6, PALB2, TP53. Considering the biologic function of HRR/MMR proteins as potential drug targets and the low frequency of most of these mutations in digestive system cancers in general, their common occurrence in our MLH1-/PMS2-/MSH6- cases seems to be even more noteworthy, highlighting the need for recognition, awareness and further investigation of this unusual IHC staining pattern.
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Affiliation(s)
- Nic Gabriel Reitsam
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
- *Correspondence: Nic Gabriel Reitsam, ;
| | - Bruno Märkl
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Sebastian Dintner
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Johanna Waidhauser
- Department of Hematology and Oncology, University Medical Center Augsburg / University Hospital of Augsburg, Augsburg, Germany
| | - Dmytro Vlasenko
- General, Visceral and Transplantation Surgery, University Hospital of Augsburg, Augsburg, Germany
| | - Bianca Grosser
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
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