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Aumer T, Däther M, Bergmayr L, Kartika S, Zeng T, Ge Q, Giorgio G, Hess AJ, Michalakis S, Traube FR. The type of DNA damage response after decitabine treatment depends on the level of DNMT activity. Life Sci Alliance 2024; 7:e202302437. [PMID: 38906675 PMCID: PMC11192838 DOI: 10.26508/lsa.202302437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
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Affiliation(s)
- Tina Aumer
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Maike Däther
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Linda Bergmayr
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Stephanie Kartika
- Department of Biochemistry, University of Munich (LMU), München, Germany
| | - Theodor Zeng
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Qingyi Ge
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Grazia Giorgio
- Department of Ophthalmology, University Hospital LMU Munich, München, Germany
| | - Alexander J Hess
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | | | - Franziska R Traube
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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Xiang H, Luo R, Wang Y, Yang B, Xu S, Huang W, Tang S, Fang R, Chen L, Zhu N, Yu Z, Akesu S, Wei C, Xu C, Zhou Y, Gu J, Zhao J, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pan-melanoma. Cell Discov 2024; 10:78. [PMID: 39039072 PMCID: PMC11263678 DOI: 10.1038/s41421-024-00688-7] [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: 08/04/2023] [Accepted: 05/03/2024] [Indexed: 07/24/2024] Open
Abstract
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.
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Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Na Zhu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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3
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Nguyen TPX, Roytrakul S, Buranapraditkun S, Shuangshoti S, Kitkumthorn N, Keelawat S. Proteomics profile in encapsulated follicular patterned thyroid neoplasms. Sci Rep 2024; 14:16343. [PMID: 39013964 PMCID: PMC11252349 DOI: 10.1038/s41598-024-67079-6] [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: 03/12/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Diagnosing encapsulated follicular-patterned thyroid tumors like Invasive Encapsulated Follicular Variant of Papillary Thyroid Carcinoma (IEFVPTC), Non-invasive Follicular Thyroid Neoplasm with Papillary-like Nuclear Features (NIFTP), and Well-Differentiated Tumor of Uncertain Malignant Potential (WDT-UMP) remains challenging due to their morphological and molecular similarities. This study aimed to investigate the protein distinctions among these three thyroid tumors and discover biological tumorigenesis through proteomic analysis. We employed total shotgun proteome analysis allowing to discover the quantitative expression of over 1398 proteins from 12 normal thyroid tissues, 13 IEFVPTC, 11 NIFTP, and 10 WDT-UMP. Principal component analysis revealed a distinct separation of IEFVPTC and normal tissue samples, distinguishing them from the low-risk tumor group (NIFTP and WDT-UMP). IEFVPTC exhibited the highest number of differentially expressed proteins (DEPs) compared to the other tumors. No discriminatory proteins between NIFTP and WDT-UMP were identified. Moreover, DEPs in IEFVPTC were significantly associated with thyroid tumor progression pathways. Certain hub genes linked to the response of immune checkpoint inhibitor therapy, revealing the potential predictor of prognosis. In conclusion, the proteomic profile of IEFVPTC differs from that of low-risk tumors. These findings may provide valuable insights into tumor biology and offer a basis for developing novel therapeutic strategies for follicular-patterned thyroid neoplasms.
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Affiliation(s)
- Truong Phan-Xuan Nguyen
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Supranee Buranapraditkun
- Division of Allergy and Clinical Immunology, Department of Medicine, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence in Thai Pediatric Gastroenterology, Hepatology and Immunology (TPGHAI), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Shanop Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, 10330, Thailand.
| | - Somboon Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Precision Pathology of Neoplasia Research Group, Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Ng YB, Akincilar SC. Shaping DNA damage responses: Therapeutic potential of targeting telomeric proteins and DNA repair factors in cancer. Curr Opin Pharmacol 2024; 76:102460. [PMID: 38776747 DOI: 10.1016/j.coph.2024.102460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 05/25/2024]
Abstract
Shelterin proteins regulate genomic stability by preventing inappropriate DNA damage responses (DDRs) at telomeres. Unprotected telomeres lead to persistent DDR causing cell cycle inhibition, growth arrest, and apoptosis. Cancer cells rely on DDR to protect themselves from DNA lesions and exogenous DNA-damaging agents such as chemotherapy and radiotherapy. Therefore, targeting DDR machinery is a promising strategy to increase the sensitivity of cancer cells to existing cancer therapies. However, the success of these DDR inhibitors depends on other mutations, and over time, patients develop resistance to these therapies. This suggests the need for alternative approaches. One promising strategy is co-inhibiting shelterin proteins with DDR molecules, which would offset cellular fitness in DNA repair in a mutation-independent manner. This review highlights the associations and dependencies of the shelterin complex with the DDR proteins and discusses potential co-inhibition strategies that might improve the therapeutic potential of current inhibitors.
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Affiliation(s)
- Yu Bin Ng
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Semih Can Akincilar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore.
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Yedla P, Bhamidipati P, Syed R, Amanchy R. Working title: Molecular involvement of p53-MDM2 interactome in gastrointestinal cancers. Cell Biochem Funct 2024; 42:e4075. [PMID: 38924101 DOI: 10.1002/cbf.4075] [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: 02/16/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
The interaction between murine double minute 2 (MDM2) and p53, marked by transcriptional induction and feedback inhibition, orchestrates a functional loop dictating cellular fate. The functional loop comprising p53-MDM2 axis is made up of an interactome consisting of approximately 81 proteins, which are spatio-temporally regulated and involved in DNA repair mechanisms. Biochemical and genetic alterations of the interactome result in dysregulation of the p53-mdm2 axis that leads to gastrointestinal (GI) cancers. A large subset of interactome is well known and it consists of proteins that either stabilize p53 or MDM2 and proteins that target the p53-MDM2 complex for ubiquitin-mediated destruction. Upstream signaling events brought about by growth factors and chemical messengers invoke a wide variety of posttranslational modifications in p53-MDM2 axis. Biochemical changes in the transactivation domain of p53 impact the energy landscape, induce conformational switching, alter interaction potential and could change solubility of p53 to redefine its co-localization, translocation and activity. A diverse set of chemical compounds mimic physiological effectors and simulate biochemical modifications of the p53-MDM2 interactome. p53-MDM2 interactome plays a crucial role in DNA damage and repair process. Genetic aberrations in the interactome, have resulted in cancers of GI tract (pancreas, liver, colorectal, gastric, biliary, and esophageal). We present in this article a review of the overall changes in the p53-MDM2 interactors and the effectors that form an epicenter for the development of next-generation molecules for understanding and targeting GI cancers.
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Affiliation(s)
- Poornachandra Yedla
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Pharmacogenomics, Institute of Translational Research, Asian Healthcare Foundation, Hyderabad, Telangana, India
| | - Pranav Bhamidipati
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Life Sciences, Imperial College London, London, UK
| | - Riyaz Syed
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
| | - Ramars Amanchy
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
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6
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Pan Y, Zhu Q, Hong T, Cheng J, Tang X. Targeting PRKDC activates the efficacy of antitumor immunity while sensitizing to chemotherapy and targeted therapy in liver hepatocellular carcinoma. Aging (Albany NY) 2024; 16:9047-9071. [PMID: 38787389 PMCID: PMC11164487 DOI: 10.18632/aging.205855] [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: 11/22/2023] [Accepted: 04/09/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) ranks among the malignancies with the highest mortality rates, primarily due to chemoresistance culminating in treatment failure. Despite its impact, predictive models addressing disease progression, tumor microenvironment, and drug sensitivity remain elusive for LIHC patients. Recognizing the significant influence of various programmed cell death (PCD) modes on tumor evolution, this study investigates PCD genes to elucidate their implications on the prognosis and immune landscape of LIHC. METHODS To develop the classification and model, we employed a total of 17 genes associated with PCD patterns. To collect data, we acquired gene expression profiles, somatic mutation information, copy number variation data, and corresponding clinical data from the TCGA database, specifically from LIHC patients. Moreover, we obtained spatial transcriptome data and additional bulk datasets from the Gene Expression Omnibus (GEO) database to conduct further analysis. Various experiments were conducted to validate the role of the PCD gene PRKDC in proliferation, migration, invasion, EMT, cell cycle, therapeutic sensitivity, and antitumor immunity. RESULTS A novel LIHC classification based on these genes divided patients into two clusters, C1 and C2. The C2 cluster exhibited characteristics indicative of poor prognosis and an immune-activated microenvironment. This group showed greater response potential to immune checkpoint inhibitors, displaying higher levels of certain immune signatures and receptors. A programmed cell death index (PCDI) was constructed using 17 selected PCD genes. This index could effectively predict patient prognosis, with higher PCDI indicating poorer survival rates and a more pro-tumor microenvironment. Immune landscapes revealed varying interactions with PCDI, suggesting therapeutic targets and insights into treatment resistance. Moreover, experiments results suggested that PRKDC can augment the invasive nature and growth of malignant cells and it can serve as a potential target for therapy, offering hope for ameliorating the prognosis of LIHC patients. CONCLUSIONS The study uncovers the insights of programmed cell death in the prognosis and potential therapeutic interventions. And we found that PRKDC can serve as a target for enhancing the efficacy of antitumor immunity while sensitizing chemotherapy and targeted therapy in liver hepatocellular carcinoma.
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Affiliation(s)
- Yitong Pan
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha 410013, Hunan, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiyao Zhu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha 410013, Hunan, China
| | - Ting Hong
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha 410013, Hunan, China
| | - Jun Cheng
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xinhui Tang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha 410013, Hunan, China
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Mansueto G, Fusco G, Colonna G. A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms. Biomolecules 2024; 14:541. [PMID: 38785948 PMCID: PMC11118181 DOI: 10.3390/biom14050541] [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: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.
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Affiliation(s)
- Gelsomina Mansueto
- Dipartimento di Scienze Mediche e Chirurgiche Avanzate, Università della Campania, L. Vanvitelli, 80138 Naples, Italy;
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Giovanni Colonna
- Medical Informatics AOU, Università della Campania, L. Vanvitelli, 80138 Naples, Italy
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Ngubo M, Moradi F, Ito CY, Stanford WL. Tissue-Specific Tumour Suppressor and Oncogenic Activities of the Polycomb-like Protein MTF2. Genes (Basel) 2023; 14:1879. [PMID: 37895228 PMCID: PMC10606531 DOI: 10.3390/genes14101879] [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: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a conserved chromatin-remodelling complex that catalyses the trimethylation of histone H3 lysine 27 (H3K27me3), a mark associated with gene silencing. PRC2 regulates chromatin structure and gene expression during organismal and tissue development and tissue homeostasis in the adult. PRC2 core subunits are associated with various accessory proteins that modulate its function and recruitment to target genes. The multimeric composition of accessory proteins results in two distinct variant complexes of PRC2, PRC2.1 and PRC2.2. Metal response element-binding transcription factor 2 (MTF2) is one of the Polycomb-like proteins (PCLs) that forms the PRC2.1 complex. MTF2 is highly conserved, and as an accessory subunit of PRC2, it has important roles in embryonic stem cell self-renewal and differentiation, development, and cancer progression. Here, we review the impact of MTF2 in PRC2 complex assembly, catalytic activity, and spatiotemporal function. The emerging paradoxical evidence suggesting that MTF2 has divergent roles as either a tumour suppressor or an oncogene in different tissues merits further investigations. Altogether, our review illuminates the context-dependent roles of MTF2 in Polycomb group (PcG) protein-mediated epigenetic regulation. Its impact on disease paves the way for a deeper understanding of epigenetic regulation and novel therapeutic strategies.
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Affiliation(s)
- Mzwanele Ngubo
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Fereshteh Moradi
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caryn Y. Ito
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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9
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Lee DJ, Kim Y, Dinh PTN, Chung Y, Lee D, Kim Y, Lee SH, Choi I, Lee SH. Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding. Genes (Basel) 2023; 14:1839. [PMID: 37895191 PMCID: PMC10606632 DOI: 10.3390/genes14101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 commercial Hanwoo. We found 33, 2, 1, and 3 significant SNPs associated with carcass weight (CW), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS), respectively. In CW and EMA, the most significant missense SNP was identified at 19,524,263 on BTA14 and involved the PRKDC. A missense SNP in the ZFAND2B, located at 107,160,304 on BTA2 was identified as being involved in BFT. For MS, missense SNP in the ACVR2B gene, located at 11,849,704 in BTA22 was identified as the most significant marker. The contribution of the most significant missense SNPs to genetic variance was confirmed to be 8.47%, 2.08%, 1.73%, and 1.19% in CW, BFT, EMA, and MS, respectively. We generated favorable and unfavorable haplotype combinations based on the significant SNPs for CW. Significant differences in GEBV (Genomic Estimated Breeding Values) were observed between groups with each favorable and unfavorable haplotype combination. In particular, the missense SNPs in PRKDC, MRPL9, and ANKFN1 appear to significantly affect the protein's function and structure, making them strong candidates as causal mutations. These missense SNPs have the potential to serve as valuable markers for improving carcass traits in Hanwoo commercial farms.
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Affiliation(s)
- Dong Jae Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Yoonsik Kim
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
| | - Phuong Thanh N. Dinh
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
| | - Yoonji Chung
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Dooho Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Yeongkuk Kim
- Quantomic Research & Solution, Daejeon 34134, Republic of Korea;
| | - Soo Hyun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Inchul Choi
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Seung Hwan Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
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Anzar I, Malone B, Samarakoon P, Vardaxis I, Simovski B, Fontenelle H, Meza-Zepeda LA, Stratford R, Keung EZ, Burgess M, Tawbi HA, Myklebost O, Clancy T. The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition. Front Immunol 2023; 14:1226445. [PMID: 37799721 PMCID: PMC10548483 DOI: 10.3389/fimmu.2023.1226445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/10/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Sarcomas are comprised of diverse bone and connective tissue tumors with few effective therapeutic options for locally advanced unresectable and/or metastatic disease. Recent advances in immunotherapy, in particular immune checkpoint inhibition (ICI), have shown promising outcomes in several cancer indications. Unfortunately, ICI therapy has provided only modest clinical responses and seems moderately effective in a subset of the diverse subtypes. Methods To explore the immune parameters governing ICI therapy resistance or immune escape, we performed whole exome sequencing (WES) on tumors and their matched normal blood, in addition to RNA-seq from tumors of 31 sarcoma patients treated with pembrolizumab. We used advanced computational methods to investigate key immune properties, such as neoantigens and immune cell composition in the tumor microenvironment (TME). Results A multifactorial analysis suggested that expression of high quality neoantigens in the context of specific immune cells in the TME are key prognostic markers of progression-free survival (PFS). The presence of several types of immune cells, including T cells, B cells and macrophages, in the TME were associated with improved PFS. Importantly, we also found the presence of both CD8+ T cells and neoantigens together was associated with improved survival compared to the presence of CD8+ T cells or neoantigens alone. Interestingly, this trend was not identified with the combined presence of CD8+ T cells and TMB; suggesting that a combined CD8+ T cell and neoantigen effect on PFS was important. Discussion The outcome of this study may inform future trials that may lead to improved outcomes for sarcoma patients treated with ICI.
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Affiliation(s)
- Irantzu Anzar
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | | | - Leonardo A. Meza-Zepeda
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | | | - Emily Z. Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Melissa Burgess
- Department of Medical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ola Myklebost
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
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11
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More P, Ngaffo JAM, Goedtel-Armbrust U, Hähnel PS, Hartwig UF, Kindler T, Wojnowski L. Transcriptional Response to Standard AML Drugs Identifies Synergistic Combinations. Int J Mol Sci 2023; 24:12926. [PMID: 37629110 PMCID: PMC10455220 DOI: 10.3390/ijms241612926] [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: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Unlike genomic alterations, gene expression profiles have not been widely used to refine cancer therapies. We analyzed transcriptional changes in acute myeloid leukemia (AML) cell lines in response to standard first-line AML drugs cytarabine and daunorubicin by means of RNA sequencing. Those changes were highly cell- and treatment-specific. By comparing the changes unique to treatment-sensitive and treatment-resistant AML cells, we enriched for treatment-relevant genes. Those genes were associated with drug response-specific pathways, including calcium ion-dependent exocytosis and chromatin remodeling. Pharmacological mimicking of those changes using EGFR and MEK inhibitors enhanced the response to daunorubicin with minimum standalone cytotoxicity. The synergistic response was observed even in the cell lines beyond those used for the discovery, including a primary AML sample. Additionally, publicly available cytotoxicity data confirmed the synergistic effect of EGFR inhibitors in combination with daunorubicin in all 60 investigated cancer cell lines. In conclusion, we demonstrate the utility of treatment-evoked gene expression changes to formulate rational drug combinations. This approach could improve the standard AML therapy, especially in older patients.
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Affiliation(s)
- Piyush More
- Department of Pharmacology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; (J.A.M.N.); (U.G.-A.); (L.W.)
| | - Joëlle Aurelie Mekontso Ngaffo
- Department of Pharmacology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; (J.A.M.N.); (U.G.-A.); (L.W.)
- Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
| | - Ute Goedtel-Armbrust
- Department of Pharmacology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; (J.A.M.N.); (U.G.-A.); (L.W.)
| | - Patricia S. Hähnel
- University Cancer Center (UCT) Mainz, Johannes Gutenberg-University, 55131 Mainz, Germany; (P.S.H.); (T.K.)
- Department of Hematology & Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany;
| | - Udo F. Hartwig
- Department of Hematology & Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany;
- Research Center of Immunotherapy, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Thomas Kindler
- University Cancer Center (UCT) Mainz, Johannes Gutenberg-University, 55131 Mainz, Germany; (P.S.H.); (T.K.)
- Department of Hematology & Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany;
| | - Leszek Wojnowski
- Department of Pharmacology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; (J.A.M.N.); (U.G.-A.); (L.W.)
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12
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Chen D, Ren H, Zhao N, Hao J. Expression and prognostic value of DNA sensors in hepatocellular carcinoma. J Leukoc Biol 2023; 114:68-78. [PMID: 37171016 DOI: 10.1093/jleuko/qiad055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
DNA sensor proteins play an important role in transducing DNA signals to induce immune responses that initiate inflammation or clear pathogens. It has been previously shown that several DNA sensors are involved in regulating tumor biology and/or cancer immunology. However, a systemic analysis of DNA sensor expression and its correlation with prognosis has not been conducted. Here, we analyzed messenger RNA expression and protein abundance in liver cancer databases and found that the genes of 5 DNA sensors (POLR3A, PRKDC, DHX9, cGAS, and MRE11) were consistently upregulated in tumor tissue. Moreover, the expression of these DNA sensor genes correlated with patient survival. Using a gene alterations analysis, we discovered that patients with genetically altered DNA sensors had significantly lower survival compared with an unaltered group. Furthermore, receiver-operating characteristic curves confirmed that the signatures of the 5 DNA sensors were independent prognostic factors in hepatocellular carcinoma. Tumor-infiltrating immune cell analysis revealed that expression of all 5 DNA sensors correlated with the amount of B cells, CD8 T cells, CD4 T cells, Tregs, DCs, Mϕs, and neutrophils. Surprisingly, 4 of the DNA sensors (POLR3A, PRKDC, DHX9, and MRE11) were inversely correlated with the amount of γδ T cells. Gene set enrichment analysis showed that all 5 DNA sensor genes were enriched for oxidative phosphorylation and xenobiotic metabolism. These results suggest that expression of these DNA sensors is associated with a unique immune profile and metabolic regulation in hepatocellular carcinoma.
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Affiliation(s)
- Danchun Chen
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, Guangdong, China
| | - He Ren
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 157 Baojian Road, Harbin 150076, Heilongjiang, China
| | - Na Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, Tianjin, China
| | - Jianlei Hao
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, 79 Kangning Road, Zhuhai 519000, Guangdong, China
- Fuda Cancer Hospital, Jinan University, 2 Tangdexi Road, Guangzhou 510399, Guangdong, China
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, 601 W Huangpu Ave, Guangzhou 510632, Guangdong, China
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13
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Qin S, Kitty I, Hao Y, Zhao F, Kim W. Maintaining Genome Integrity: Protein Kinases and Phosphatases Orchestrate the Balancing Act of DNA Double-Strand Breaks Repair in Cancer. Int J Mol Sci 2023; 24:10212. [PMID: 37373360 DOI: 10.3390/ijms241210212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most lethal DNA damages which lead to severe genome instability. Phosphorylation is one of the most important protein post-translation modifications involved in DSBs repair regulation. Kinases and phosphatases play coordinating roles in DSB repair by phosphorylating and dephosphorylating various proteins. Recent research has shed light on the importance of maintaining a balance between kinase and phosphatase activities in DSB repair. The interplay between kinases and phosphatases plays an important role in regulating DNA-repair processes, and alterations in their activity can lead to genomic instability and disease. Therefore, study on the function of kinases and phosphatases in DSBs repair is essential for understanding their roles in cancer development and therapeutics. In this review, we summarize the current knowledge of kinases and phosphatases in DSBs repair regulation and highlight the advancements in the development of cancer therapies targeting kinases or phosphatases in DSBs repair pathways. In conclusion, understanding the balance of kinase and phosphatase activities in DSBs repair provides opportunities for the development of novel cancer therapeutics.
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Affiliation(s)
- Sisi Qin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Ichiwa Kitty
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
| | - Yalan Hao
- Analytical Instrumentation Center, Hunan University, Changsha 410082, China
| | - Fei Zhao
- College of Biology, Hunan University, Changsha 410082, China
| | - Wootae Kim
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
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14
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Wang H, Yang L, Li Q, Song H, Ji H. Case report: Composite mantle cell lymphoma and classical Hodgkin lymphoma. Pathol Oncol Res 2023; 29:1611051. [PMID: 37006439 PMCID: PMC10064289 DOI: 10.3389/pore.2023.1611051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Composite mantle cell lymphoma and classical Hodgkin lymphoma is very rare and the actual origin of it is still unclear. Here we reported a new case of composite mantle cell lymphoma and classical Hodgkin lymphoma and analyzed its molecular changes. Eight mutations were identified in its Hodgkin component through next-generation sequencing. In addition, we reviewed the published cases of composite mantle cell lymphoma and classical Hodgkin lymphoma and summarized the molecular changes of reported cases as well as the current case to explore the possible pathway of histogenesis.
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Affiliation(s)
- Hongyu Wang
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Liqun Yang
- Huayin Health Hematopathology Comprehensive Diagnostic Center, Chengdu Huayin Medical Laboratory Center, Chengdu, China
| | - Qiuyao Li
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Haiyun Song
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Hong Ji
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- *Correspondence: Hong Ji,
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15
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Wang C, Chan DW, Hendrickson EA. Kinome-wide screening uncovers a role for Bromodomain Protein 3 in DNA double-stranded break repair. DNA Repair (Amst) 2023; 122:103445. [PMID: 36608404 PMCID: PMC10353298 DOI: 10.1016/j.dnarep.2022.103445] [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: 07/12/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Double-stranded breaks (DSBs) are toxic DNA damage and a serious threat to genomic integrity. Thus, all living organisms have evolved multiple mechanisms of DNA DSB repair, the two principal ones being classical-non homologous end joining (C-NHEJ), and homology dependent recombination (HDR). In mammals, C-NHEJ is the predominate DSB repair pathway, but how a cell chooses to repair a particular DSB by a certain pathway is still not mechanistically clear. To uncover novel regulators of DSB repair pathway choice, we performed a kinome-wide screen in a human cell line engineered to express a dominant-negative C-NHEJ factor. The intellectual basis for such a screen was our hypothesis that a C-NHEJ-crippled cell line might need to upregulate other DSB repair pathways, including HDR, in order to survive. This screen identified Bromodomain-containing Protein 3 (BRD3) as a protein whose expression was almost completely ablated specifically in a C-NHEJ-defective cell line. Subsequent experimentation demonstrated that BRD3 is a negative regulator of HDR as BRD3-null cell lines proved to be hyper-recombinogenic for gene conversion, sister chromatid exchanges and gene targeting. Mechanistically, BRD3 appears to be working at the level of Radiation Sensitive 51 (RAD51) recruitment. Overall, our results demonstrate that BRD3 is a novel regulator of human DSB repair pathway choice.
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Affiliation(s)
- Chen Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Doug W Chan
- Department of Systems Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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16
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Jiang G, Wu Q, Li B. Evaluation of immunotherapy efficacy in gynecologic cancer. Front Immunol 2023; 14:1061761. [PMID: 36793735 PMCID: PMC9922993 DOI: 10.3389/fimmu.2023.1061761] [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: 10/05/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Various immunotherapies have demonstrated remarkable success over the past few decades, and have been approved for the treatment of different cancer types. However, patient responses to immunotherapy are variable, and approximately 50% of cases are refractory to these agents. Tumor biomarker-based stratification of cases may therefore help identify subpopulations that are sensitive/resistant to immunotherapy; it may also improve prediction of response in various cancers including gynecologic cancer. These biomarkers include the tumor mutational burden, microsatellite instability, mismatch repair deficiency, T cell-inflamed gene expression profile, programmed cell death protein 1 ligand 1, tumor-infiltrating lymphocytes, and numerous other genomic alterations. Future directions in the treatment of gynecologic cancer include the utilization of these biomarkers to select ideal candidates. This review focused on recent advances in the predictive ability of molecular biomarkers in patients with gynecologic cancer who undergo immunotherapy. The most recent developments in combined immunotherapy and targeted therapy strategies and novel immune interventions against gynecologic cancers have also been discussed.
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Affiliation(s)
- Genyi Jiang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qianhua Wu
- School of Medicine, Tongji University, Shanghai, China
| | - Bilan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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17
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Chen J, Wu F, Hou E, Zeng J, Li F, Gao H. Exosomal microRNA Therapy for Non-Small-Cell Lung Cancer. Technol Cancer Res Treat 2023; 22:15330338231210731. [PMID: 37936417 PMCID: PMC10631355 DOI: 10.1177/15330338231210731] [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: 04/21/2023] [Revised: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
With the progress of molecular diagnosis research on non-small cell lung cancer (NSCLC) cells, four identified categories of microRNAs have been found to be related to disease diagnosis, diagnosis of treatment resistance, prediction of prognosis, and drugs for treatment. To date, nine target mRNA/signal pathways have been confirmed for microRNA drug therapy both in vitro and in vivo. When microRNA drugs enter blood vessels, they target the tumor site and play a similar role to that of targeted drugs. However, whether they will produce serious off-target effects remains unknown, and further clinical research is needed. This review provides the first summary of microRNA therapy for NSCLC.
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Affiliation(s)
- Jibing Chen
- Jinan University, Guangzhou, Guangdong, China
- Fuda Cancer Hospital Affiliated to Jinan University, Guangzhou, Guangdong, China
- Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Fasheng Wu
- Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Encun Hou
- Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Jianying Zeng
- Jinan University, Guangzhou, Guangdong, China
- Fuda Cancer Hospital Affiliated to Jinan University, Guangzhou, Guangdong, China
| | - Fujun Li
- Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Hongjun Gao
- Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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18
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Wang X, Huang Z, Li L, Yang Y, Zhang J, Wang L, Yuan J, Li Y. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients. Genes (Basel) 2022; 14:genes14010039. [PMID: 36672781 PMCID: PMC9858704 DOI: 10.3390/genes14010039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA damage response is a key signal transduction pathway in triggering ageing and tumor progression. Abnormal alternative splicing (AS) is associated with tumors and ageing. However, the role of AS factors associated with DNA damage repair and ageing in stomach adenocarcinoma (STAD) remains unclear. We downloaded the percentage of splicing (PSI) values for AS in STAD from the TCGA SpliceSeq database. The PSI values of DNA repair gene AS events were integrated with STAD patient survival data for Cox regression analysis. The prediction model for the overall survival (OS) was constructed by the clinical traits. The tumor immune microenvironment was analyzed by CIBERSORT and ESTIMATE. We detected 824 AS events originating from 166 DNA repair genes. Cox regression analysis provided 21 prognostic AS events connected with OS statistically, and a prognostic prediction model was constructed. The expression of these AS factors was higher in STAD tumors. DDB2 high senescence levels were associated with active immune responses and better survival in STAD patients. We built a novel prognostic model founded on DNA repair genes with AS events and identified that DDB2 may be a potential biomarker to apply in clinics.
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Affiliation(s)
- Xinshu Wang
- Postgraduate Training Base of Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Zhiyuan Huang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Yuntong Yang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jiyuan Zhang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Li Wang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Ji’an Hospital, Shanghai East Hospital, Ji’an 343000, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
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19
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Lan B, Zeng S, Zhang S, Ren X, Xing Y, Kutschick I, Pfeffer S, Frey B, Britzen-Laurent N, Grützmann R, Cordes N, Pilarsky C. CRISPR-Cas9 Screen Identifies DYRK1A as a Target for Radiotherapy Sensitization in Pancreatic Cancer. Cancers (Basel) 2022; 14:cancers14020326. [PMID: 35053488 PMCID: PMC8773906 DOI: 10.3390/cancers14020326] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Pancreatic cancer is the fourth leading cause of cancer-related death in Western countries. Although several therapeutic strategies have been developed for pancreatic cancer, radiation therapy has not yet yielded satisfactory results. Unraveling the mechanism of radioresistance in pancreatic cancer and developing new therapeutic targets has become a major challenge. Therefore, we applied kinome-wide CRISPR-Cas9 loss-of-function screening combined with the 3D cell culture method and identified DYRK1A as a sensitive target for radiotherapy. Additionally, we confirmed that DYRK1A-targeted inhibitors could enhance the efficacy of radiotherapy. Our results further support the use of CRISPR-Cas9 screening to identify novel therapeutic targets and develop new strategies to enhance radiotherapy efficacy in pancreatic cancer. Abstract Although radiation therapy has recently made great advances in cancer treatment, the majority of patients diagnosed with pancreatic cancer (PC) cannot achieve satisfactory outcomes due to intrinsic and acquired radioresistance. Identifying the molecular mechanisms that impair the efficacy of radiotherapy and targeting these pathways are essential to improve the radiation response of PC patients. Our goal is to identify sensitive targets for pancreatic cancer radiotherapy (RT) using the kinome-wide CRISPR-Cas9 loss-of-function screen and enhance the therapeutic effect through the development and application of targeted inhibitors combined with radiotherapy. We transduced pancreatic cancer cells with a protein kinase library; 2D and 3D library cells were irradiated daily with a single dose of up to 2 Gy for 4 weeks for a total of 40 Gy using an X-ray generator. Sufficient DNA was collected for next-generation deep sequencing to identify candidate genes. In this study, we identified several cell cycle checkpoint kinases and DNA damage related kinases in 2D- and 3D-cultivated cells, including DYRK1A, whose loss of function sensitizes cells to radiotherapy. Additionally, we demonstrated that the harmine-targeted suppression of DYRK1A used in conjunction with radiotherapy increases DNA double-strand breaks (DSBs) and impairs homologous repair (HR), resulting in more cancer cell death. Our results support the use of CRISPR-Cas9 screening to identify new therapeutic targets, develop radiosensitizers, and provide novel strategies for overcoming the tolerance of pancreatic cancer to radiotherapy.
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Affiliation(s)
- Bin Lan
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Siyuan Zeng
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Shuman Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Xiaofan Ren
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Yuming Xing
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Isabella Kutschick
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Susanne Pfeffer
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Nathalie Britzen-Laurent
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
| | - Nils Cordes
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus Technische Universität Dresden, 01307 Dresden, Germany;
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
- German Cancer Consortium, Partner Site Dresden: German Cancer Research Center, 69120 Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Christian Pilarsky
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (B.L.); (S.Z.); (S.Z.); (X.R.); (Y.X.); (I.K.); (S.P.); (N.B.-L.); (R.G.)
- Correspondence:
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Shevyrev D, Tereshchenko V, Kozlov V, Sennikov S. Phylogeny, Structure, Functions, and Role of AIRE in the Formation of T-Cell Subsets. Cells 2022; 11:194. [PMID: 35053310 PMCID: PMC8773594 DOI: 10.3390/cells11020194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
It is well known that the most important feature of adaptive immunity is the specificity that provides highly precise recognition of the self, altered-self, and non-self. Due to the high specificity of antigen recognition, the adaptive immune system participates in the maintenance of genetic homeostasis, supports multicellularity, and protects an organism from different pathogens at a qualitatively different level than innate immunity. This seemingly simple property is based on millions of years of evolution that led to the formation of diversification mechanisms of antigen-recognizing receptors and later to the emergence of a system of presentation of the self and non-self antigens. The latter could have a crucial significance because the presentation of nearly complete diversity of auto-antigens in the thymus allows for the "calibration" of the forming repertoires of T-cells for the recognition of self, altered-self, and non-self antigens that are presented on the periphery. The central role in this process belongs to promiscuous gene expression by the thymic epithelial cells that express nearly the whole spectrum of proteins encoded in the genome, meanwhile maintaining their cellular identity. This complex mechanism requires strict control that is executed by several transcription factors. One of the most important of them is AIRE. This noncanonical transcription factor not only regulates the processes of differentiation and expression of peripheral tissue-specific antigens in the thymic medullar epithelial cells but also controls intercellular interactions in the thymus. Besides, it participates in an increase in the diversity and transfer of presented antigens and thus influences the formation of repertoires of maturing thymocytes. Due to these complex effects, AIRE is also called a transcriptional regulator. In this review, we briefly described the history of AIRE discovery, its structure, functions, and role in the formation of antigen-recognizing receptor repertoires, along with other transcription factors. We focused on the phylogenetic prerequisites for the development of modern adaptive immunity and emphasized the importance of the antigen presentation system.
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Affiliation(s)
- Daniil Shevyrev
- Research Institute for Fundamental and Clinical Immunology (RIFCI), 630099 Novosibirsk, Russia; (V.T.); (V.K.); (S.S.)
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Ray S, Chaturvedi NK, Bhakat KK, Rizzino A, Mahapatra S. Subgroup-Specific Diagnostic, Prognostic, and Predictive Markers Influencing Pediatric Medulloblastoma Treatment. Diagnostics (Basel) 2021; 12:diagnostics12010061. [PMID: 35054230 PMCID: PMC8774967 DOI: 10.3390/diagnostics12010061] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/11/2021] [Accepted: 12/18/2021] [Indexed: 12/24/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant central nervous system tumor in pediatric patients. Mainstay of therapy remains surgical resection followed by craniospinal radiation and chemotherapy, although limitations to this therapy are applied in the youngest patients. Clinically, tumors are divided into average and high-risk status on the basis of age, metastasis at diagnosis, and extent of surgical resection. However, technological advances in high-throughput screening have facilitated the analysis of large transcriptomic datasets that have been used to generate the current classification system, dividing patients into four primary subgroups, i.e., WNT (wingless), SHH (sonic hedgehog), and the non-SHH/WNT subgroups 3 and 4. Each subgroup can further be subdivided on the basis of a combination of cytogenetic and epigenetic events, some in distinct signaling pathways, that activate specific phenotypes impacting patient prognosis. Here, we delve deeper into the genetic basis for each subgroup by reviewing the extent of cytogenetic events in key genes that trigger neoplastic transformation or that exhibit oncogenic properties. Each of these discussions is further centered on how these genetic aberrations can be exploited to generate novel targeted therapeutics for each subgroup along with a discussion on challenges that are currently faced in generating said therapies. Our future hope is that through better understanding of subgroup-specific cytogenetic events, the field may improve diagnosis, prognosis, and treatment to improve overall quality of life for these patients.
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Affiliation(s)
- Sutapa Ray
- Department of Pediatrics, University of Nebraska Medical Center, 601 S Saddle Creek Road, Omaha, NE 68198, USA; (S.R.); (N.K.C.)
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68105, USA; (K.K.B.); (A.R.)
| | - Nagendra K. Chaturvedi
- Department of Pediatrics, University of Nebraska Medical Center, 601 S Saddle Creek Road, Omaha, NE 68198, USA; (S.R.); (N.K.C.)
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68105, USA; (K.K.B.); (A.R.)
| | - Kishor K. Bhakat
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68105, USA; (K.K.B.); (A.R.)
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angie Rizzino
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68105, USA; (K.K.B.); (A.R.)
- Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sidharth Mahapatra
- Department of Pediatrics, University of Nebraska Medical Center, 601 S Saddle Creek Road, Omaha, NE 68198, USA; (S.R.); (N.K.C.)
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68105, USA; (K.K.B.); (A.R.)
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: ; Tel.: +1-(402)-599-7754
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