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Thote V, Dinesh S, Sharma S. Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach. Syst Biol Reprod Med 2024; 70:101-112. [PMID: 38630598 DOI: 10.1080/19396368.2024.2325699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024]
Abstract
MDC1 (Mediator of DNA damage Checkpoint protein 1) functions to facilitate the localization of numerous DNA damage response (DDR) components to DNA double-strand break sites. MDC1 is an integral component in preserving genomic stability and appropriate DDR regulation. There haven't been systematic investigations of MDC1 mutations that induce cancer and genomic instability. Variations in nsSNPs have the potential to modify the protein chemistry and their function. Describing functional SNPs in disease-associated genes presents a significant conundrum for investigators, it is possible to assess potential functional SNPs before conducting larger population examinations. Multiple sequences and structure-based bioinformatics strategies were implemented in the current in-silico investigation to discern potential nsSNPs of the MDC1 genes. The nsSNPs were identified with SIFT, SNAP2, Align GVGD, PolyPhen-2, and PANTHER, and their stability was determined with MUpro. The conservation, solvent accessibility, and structural effects of the mutations were identified with ConSurf, NetSurfP-2.0, and SAAFEC-SEQ respectively. Cancer-related analysis of the nsSNPs was conducted using cBioPortal and TCGA web servers. The present study appraised five nsSNPs (P1426T, P69S, P194R, P203L, and H131Y) as probably mutilating due to their existence in highly conserved regions and propensity to deplete protein stability. The nsSNPs P194R, P203L, and H131Y were concluded as deleterious and possibly damaging from the 5 prediction tools. The functional nsSNP P194R mutation is associated with skin cutaneous melanoma while no significant records were found for other nsSNPs. The present study concludes that the highly deleterious P194R mutations can potentially induce genomic instability and contribute to various cancers' pathogenesis. Developing drugs targeting these mutations can undoubtedly be advantageous in large population-based studies, particularly in the development of precision medicine.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, India
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Wang Y, Liu X, Zuo X, Wang C, Zhang Z, Zhang H, Zeng T, Chen S, Liu M, Chen H, Song Q, Li Q, Yang C, Le Y, Xing J, Zhang H, An J, Jia W, Kang L, Zhang H, Xie H, Ye J, Wu T, He F, Zhang X, Li Y, Zhou G. NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors. CELL GENOMICS 2024; 4:100550. [PMID: 38697125 PMCID: PMC11099347 DOI: 10.1016/j.xgen.2024.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, including NRDE2, RANBP17, RTEL1, and STEAP3. Using NRDE2 (index rs199890497 [p.N377I], p = 1.19 × 10-9) as an exemplary candidate, we demonstrated that it promotes homologous recombination (HR) repair and suppresses HCC. Mechanistically, NRDE2 binds to the subunits of casein kinase 2 (CK2) and facilitates the assembly and activity of the CK2 holoenzyme. This NRDE2-mediated enhancement of CK2 activity increases the phosphorylation of MDC1 and then facilitates the HR repair. These functions are eliminated almost completely by the NRDE2-p.N377I variant, which sensitizes the HCC cells to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with chemotherapy. Collectively, our findings highlight the relevance of the rare variants to genetic susceptibility to HCC, which would be helpful for the precise treatment of this malignancy.
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Affiliation(s)
- Yahui Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Xinyi Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Xianbo Zuo
- Department of Dermatology, Department of Pharmacy, China-Japan Friendship Hospital, Beijing, P.R. China
| | - Cuiling Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Zheng Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Haitao Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Tao Zeng
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Shunqi Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Mengyu Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Hongxia Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Qingfeng Song
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning City, Guangxi Province, P.R. China
| | - Qi Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Department of Neurosciences, School of Medicine, University of South China, Hengyang City, Hunan Province, P.R. China
| | - Chenning Yang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Yi Le
- Department of Hepatobiliary Surgery, the 5th Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Experimental Teaching Center of Basic Medicine, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Hongxin Zhang
- Department of Pain Treatment, Tangdu Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Weihua Jia
- State Key Laboratory of Oncology in Southern China, Guangzhou City, Guangdong Province, P.R. China; Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang City, Shaanxi Province, P.R. China
| | - Hongxing Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Hui Xie
- Department of Interventional Oncology, the Fifth Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jiazhou Ye
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Tianzhun Wu
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China.
| | - Xuejun Zhang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, Anhui Province, P.R. China.
| | - Yuanfeng Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.
| | - Gangqiao Zhou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, P.R. China.
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Rajpurohit YS, Sharma DK, Lal M, Soni I. A perspective on tumor radiation resistance following high-LET radiation treatment. J Cancer Res Clin Oncol 2024; 150:226. [PMID: 38696003 PMCID: PMC11065934 DOI: 10.1007/s00432-024-05757-8] [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: 02/24/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
High-linear energy transfer (LET) radiation is a promising alternative to conventional low-LET radiation for therapeutic gain against cancer owing to its ability to induce complex and clustered DNA lesions. However, the development of radiation resistance poses a significant barrier. The potential molecular mechanisms that could confer resistance development are translesion synthesis (TLS), replication gap suppression (RGS) mechanisms, autophagy, epithelial-mesenchymal transition (EMT) activation, release of exosomes, and epigenetic changes. This article will discuss various types of complex clustered DNA damage, their repair mechanisms, mutagenic potential, and the development of radiation resistance strategies. Furthermore, it highlights the importance of careful consideration and patient selection when employing high-LET radiotherapy in clinical settings.
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Affiliation(s)
- Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India.
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Mitu Lal
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Ishu Soni
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India
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Pandya K, Singh N. In silico study reveals unconventional interactions between MDC1 of DDR and Beclin-1 of autophagy. Mol Divers 2023; 27:2789-2802. [PMID: 36482226 DOI: 10.1007/s11030-022-10579-2] [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: 09/02/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
DNA damage response (DDR) and autophagy are concerned with maintaining cellular homeostasis and dysregulation of these two pathways lead to pathologic conditions including tumorigenesis. Autophagy is activated as a protective mechanism during DDR which is indicative of their functional cooperativity but the molecular mechanism leading to the convergence of these two pathways during genotoxic stress remains elusive. In this study, through in silico analysis, we have shown an interaction between the Mediator of DNA damage checkpoint 1 (MDC1), an important DDR-associated protein, and Beclin-1, an autophagy inducer. MDC1 is an adaptor or scaffold protein known to regulate DDR, apoptosis, and cell cycle progression. While, Beclin-1 is involved in autophagosome nucleation and exhibits affinity for binding to Fork-head-associated domain (FHA) containing proteins. The FHA domain is commonly conserved in DDR-related proteins including MDC1. Through molecular docking, we have predicted the modeled complex between the MDC1 FHA domain and the Beclin-1 Coiled coil domain (CCD). The docking complex was modeled using ClusPro2.0, based on the crystal structure for the dimerized MDC1 FHA domain and Beclin-1 CCD. The complex stability and binding affinities were assessed using a Ramachandran plot, MD simulation, MM/GBSA, and PRODIGY webserver. Finally, the hot-spot residues at the interface were determined using computational alanine scanning by the DrugScorePPI webserver. Our analysis unveils significant interaction between MDC1 and Beclin-1, involving hydrogen bonds, non-bonded contacts, and salt bridges and indicates MDC1 possibly recruits Beclin-1 to the DSBs, as a consequence of which Beclin-1 is able to modulate DDR.
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Affiliation(s)
- Kavya Pandya
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India
| | - Neeru Singh
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India.
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Xu B, Zeng F, Deng J, Yao L, Liu S, Hou H, Huang Y, Zhu H, Wu S, Li Q, Zhan W, Qiu H, Wang H, Li Y, Yang X, Cao Z, Zhang Y, Zhou H. A homologous and molecular dual-targeted biomimetic nanocarrier for EGFR-related non-small cell lung cancer therapy. Bioact Mater 2023; 27:337-347. [PMID: 37122898 PMCID: PMC10140750 DOI: 10.1016/j.bioactmat.2023.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
The abnormal activation of epidermal growth factor receptor (EGFR) drives the development of non-small cell lung cancer (NSCLC). The EGFR-targeting tyrosine kinase inhibitor osimertinib is frequently used to clinically treat NSCLC and exhibits marked efficacy in patients with NSCLC who have an EGFR mutation. However, free osimertinib administration exhibits an inadequate response in vivo, with only ∼3% patients demonstrating a complete clinical response. Consequently, we designed a biomimetic nanoparticle (CMNP@Osi) comprising a polymeric nanoparticle core and tumor cell-derived membrane-coated shell that combines membrane-mediated homologous and molecular targeting for targeted drug delivery, thereby supporting a dual-target strategy for enhancing osimertinib efficacy. After intravenous injection, CMNP@Osi accumulates at tumor sites and displays enhanced uptake into cancer cells based on homologous targeting. Osimertinib is subsequently released into the cytoplasm, where it suppresses the phosphorylation of upstream EGFR and the downstream AKT signaling pathway and inhibits the proliferation of NSCLC cells. Thus, this dual-targeting strategy using a biomimetic nanocarrier can enhance molecular-targeted drug delivery and improve clinical efficacy.
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Affiliation(s)
- Bin Xu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Fanjun Zeng
- Department of General Practice, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
| | - Jialong Deng
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Lintong Yao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- Shantou University Medical College, Shantou, 515063, PR China
| | - Shengbo Liu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China
| | - Hengliang Hou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Yucheng Huang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- School of Medicine, South China University of Technology, Guangzhou, 510006, PR China
| | - Hongyuan Zhu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
| | - Shaowei Wu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China
| | - Qiaxuan Li
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- Shantou University Medical College, Shantou, 515063, PR China
| | - Weijie Zhan
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China
| | - Hongrui Qiu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
| | - Huili Wang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
| | - Yundong Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China
| | - Xianzhu Yang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Ziyang Cao
- Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510006, PR China
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
- Corresponding author. Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510006, PR China.
| | - Yu Zhang
- Department of Orthopedics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- Corresponding author.
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China
- Shantou University Medical College, Shantou, 515063, PR China
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
- School of Medicine, South China University of Technology, Guangzhou, 510006, PR China
- Corresponding author. The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China.
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Li Z, Zhang W, Jiao D, Tian C, Xu K, Zhu H, Han X. All-in-one properties of an anticancer-covered airway stent for the prevention of malignant central airway obstruction. APL Bioeng 2023; 7:036116. [PMID: 37719298 PMCID: PMC10503995 DOI: 10.1063/5.0157341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023] Open
Abstract
Malignant central airway obstruction (MCAO) resulting from tumor metastasis and compression severely impairs respiration, posing life-threatening risks. To address this, we employed a synergistic modification strategy, combining cisplatin (CIS) and silver nanoparticles (AgNPs). Polycaprolactone (PCL) served as a drug carrier, enabling the preparation of a functional CIS@AgNPs@PCL fiber membrane-covered airway stent via electrospinning. This approach aimed to enhance the patency rate of MCAO. Characterization via ATR-FTIR, scanning electron microscope-energy-dispersive spectroscopy, and transmission electron microscope confirmed successful immobilization of CIS and AgNPs onto the stent surface. CIS@AgNPs@PCL substantially suppressed non-small cell lung cancer cells (A549), causing DNA damage, ultrastructural disruption, and over 50% apoptosis in 48 h. It also displayed potent antibacterial activity against Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans biofilms. A mouse subcutaneous tumor recurrence model assessed anti-cancer efficacy. CIS@AgNPs@PCL fiber-covered stents significantly inhibited lung cancer tissue and enhanced anti-cancer effects by up-regulating caspase-3 and Bax, while down-regulating Bcl-2. This study's functional airway stent provides a proof-of-concept for an integrated anti-cancer and antibacterial strategy. It promptly restores the lumen, inhibits biofilm formation, prevents tumor progression, and improves postoperative MCAO patency.
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Affiliation(s)
| | - Wenguang Zhang
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Dechao Jiao
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Chuan Tian
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Kaihao Xu
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Haidong Zhu
- Center of Interventional Radiology and Vascular Surgery, Department of Radiology, Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Xinwei Han
- Department of Interventional Radiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
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Ganzinelli M, Guffanti F, Ianza A, Sobhani N, Crovella S, Zanconati F, Bottin C, Confalonieri M, Fumagalli S, Guglielmi A, Generali D, Damia G. Epithelioid Mesothelioma Patients with Very Long Survival Display Defects in DNA Repair. Cancers (Basel) 2023; 15:4309. [PMID: 37686585 PMCID: PMC10486625 DOI: 10.3390/cancers15174309] [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: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
AIM DNA repair has an important role in malignant pleural mesothelioma (MPM) tumorigenesis and progression. Prognostic/predictive biomarkers for better management of MPM patients are needed. In the present manuscript, we analyzed the expression of more than 700 genes in a cohort of MPM patients to possibly find biomarkers correlated with survival. METHODS A total of 54 MPM patients, all with epithelioid histology, whose survival follow-up and formalin-fixed paraffin-embedded tumors were available, were included in the study. Gene expression profiles were evaluated using a Nanostring platform analyzing 760 genes involved in different cellular pathways. The percentages of proliferating tumor cells positive for RAD51 and BRCA1 foci were evaluated using an immunofluorescence assay, as a readout of homologous recombination repair status. RESULTS Patient median survival time was 16.9 months, and based on this value, they were classified as long and short survivors (LS/SS) with, respectively, an overall survival ≥ and <16.9 months as well as very long and very short survivors (VLS/VSS) with an overall survival ≥ than 33.8 and < than 8.45 months. A down-regulation in the DNA damage/repair expression score was observed in LS and VLS as compared to SS and VSS. These findings were validated by the lower number of both RAD51 and BRCA1-positive tumor cells in VLS as compared to VSS. CONCLUSIONS The down-regulation of DNA repair signature in VLS was functionally validated by a lower % of RAD51 and BRCA1-positive tumor cells. If these data can be corroborated in a prospective trial, an easy, cost-effective test could be routinely used to better manage treatment in MPM patients.
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Affiliation(s)
- Monica Ganzinelli
- Unit of Thoracic Oncology, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Federica Guffanti
- Laboratory of Preclinical Gynecological Oncology, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Anna Ianza
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Navid Sobhani
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Sergio Crovella
- IRCCS Burlo Garofolo, Via dell’Istria 65/1, 34137 Trieste, Italy;
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Cristina Bottin
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Marco Confalonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34139 Trieste, Italy; (N.S.); (F.Z.); (C.B.); (M.C.)
| | - Stefano Fumagalli
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Alessandra Guglielmi
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Daniele Generali
- Oncology Department, University Health Organization Giuliano Isontina, ASUGI, Piazza Ospitale 1, 34129 Trieste, Italy; (A.I.); (A.G.); (D.G.)
| | - Giovanna Damia
- Laboratory of Preclinical Gynecological Oncology, Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
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Bruserud Ø, Reikvam H. Casein Kinase 2 (CK2): A Possible Therapeutic Target in Acute Myeloid Leukemia. Cancers (Basel) 2023; 15:3711. [PMID: 37509370 PMCID: PMC10378128 DOI: 10.3390/cancers15143711] [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: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
The protein kinase CK2 (also known as casein kinase 2) is one of the main contributors to the human phosphoproteome. It is regarded as a possible therapeutic strategy in several malignant diseases, including acute myeloid leukemia (AML), which is an aggressive bone marrow malignancy. CK2 is an important regulator of intracellular signaling in AML cells, especially PI3K-Akt, Jak-Stat, NFκB, Wnt, and DNA repair signaling. High CK2 levels in AML cells at the first time of diagnosis are associated with decreased survival (i.e., increased risk of chemoresistant leukemia relapse) for patients receiving intensive and potentially curative antileukemic therapy. However, it is not known whether these high CK2 levels can be used as an independent prognostic biomarker because this has not been investigated in multivariate analyses. Several CK2 inhibitors have been developed, but CX-4945/silmitasertib is best characterized. This drug has antiproliferative and proapoptotic effects in primary human AML cells. The preliminary results from studies of silmitasertib in the treatment of other malignancies suggest that gastrointestinal and bone marrow toxicities are relatively common. However, clinical AML studies are not available. Taken together, the available experimental and clinical evidence suggests that the possible use of CK2 inhibition in the treatment of AML should be further investigated.
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Affiliation(s)
- Øystein Bruserud
- Institute for Clinical Science, Faculty of Medicine, University of Bergen, 5021 Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Håkon Reikvam
- Institute for Clinical Science, Faculty of Medicine, University of Bergen, 5021 Bergen, Norway
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
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Maudsley S, Schrauwen C, Harputluoğlu İ, Walter D, Leysen H, McDonald P. GPR19 Coordinates Multiple Molecular Aspects of Stress Responses Associated with the Aging Process. Int J Mol Sci 2023; 24:ijms24108499. [PMID: 37239845 DOI: 10.3390/ijms24108499] [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: 02/21/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 05/28/2023] Open
Abstract
G protein-coupled receptors (GPCRs) play a significant role in controlling biological paradigms such as aging and aging-related disease. We have previously identified receptor signaling systems that are specifically associated with controlling molecular pathologies associated with the aging process. Here, we have identified a pseudo-orphan GPCR, G protein-coupled receptor 19 (GPR19), that is sensitive to many molecular aspects of the aging process. Through an in-depth molecular investigation process that involved proteomic, molecular biological, and advanced informatic experimentation, this study found that the functionality of GPR19 is specifically linked to sensory, protective, and remedial signaling systems associated with aging-related pathology. This study suggests that the activity of this receptor may play a role in mitigating the effects of aging-related pathology by promoting protective and remedial signaling systems. GPR19 expression variation demonstrates variability in the molecular activity in this larger process. At low expression levels in HEK293 cells, GPR19 expression regulates signaling paradigms linked with stress responses and metabolic responses to these. At higher expression levels, GPR19 expression co-regulates systems involved in sensing and repairing DNA damage, while at the highest levels of GPR19 expression, a functional link to processes of cellular senescence is seen. In this manner, GPR19 may function as a coordinator of aging-associated metabolic dysfunction, stress response, DNA integrity management, and eventual senescence.
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Affiliation(s)
- Stuart Maudsley
- Receptor Biology Lab, University of Antwerp, 2610 Antwerpen, Belgium
| | - Claudia Schrauwen
- Receptor Biology Lab, University of Antwerp, 2610 Antwerpen, Belgium
| | - İrem Harputluoğlu
- Receptor Biology Lab, University of Antwerp, 2610 Antwerpen, Belgium
| | - Deborah Walter
- Receptor Biology Lab, University of Antwerp, 2610 Antwerpen, Belgium
| | - Hanne Leysen
- Receptor Biology Lab, University of Antwerp, 2610 Antwerpen, Belgium
| | - Patricia McDonald
- Moffitt Cancer Center, Department of Metabolism & Physiology, 12902 Magnolia Drive, Tampa, FL 33612, USA
- Lexicon Pharmaceuticals Inc. Research & Development, 2445 Technology Forest, The Woodlands, TX 77381, USA
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10
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Thomas R, Wiley CA, Droste EL, Robertson J, Inman BA, Breen M. Whole exome sequencing analysis of canine urothelial carcinomas without BRAF V595E mutation: Short in-frame deletions in BRAF and MAP2K1 suggest alternative mechanisms for MAPK pathway disruption. PLoS Genet 2023; 19:e1010575. [PMID: 37079639 PMCID: PMC10153751 DOI: 10.1371/journal.pgen.1010575] [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: 08/08/2022] [Revised: 05/02/2023] [Accepted: 12/16/2022] [Indexed: 04/21/2023] Open
Abstract
Molecular profiling studies have shown that 85% of canine urothelial carcinomas (UC) harbor an activating BRAF V595E mutation, which is orthologous to the V600E variant found in several human cancer subtypes. In dogs, this mutation provides both a powerful diagnostic marker and a potential therapeutic target; however, due to their relative infrequency, the remaining 15% of cases remain understudied at the molecular level. We performed whole exome sequencing analysis of 28 canine urine sediments exhibiting the characteristic DNA copy number signatures of canine UC, in which the BRAF V595E mutation was undetected (UDV595E specimens). Among these we identified 13 specimens (46%) harboring short in-frame deletions within either BRAF exon 12 (7/28 cases) or MAP2K1 exons 2 or 3 (6/28 cases). Orthologous variants occur in several human cancer subtypes and confer structural changes to the protein product that are predictive of response to different classes of small molecule MAPK pathway inhibitors. DNA damage response and repair genes, and chromatin modifiers were also recurrently mutated in UDV595E specimens, as were genes that are positive predictors of immunotherapy response in human cancers. Our findings suggest that short in-frame deletions within BRAF exon 12 and MAP2K1 exons 2 and 3 in UDV595E cases are alternative MAPK-pathway activating events that may have significant therapeutic implications for selecting first-line treatment for canine UC. We developed a simple, cost-effective capillary electrophoresis genotyping assay for detection of these deletions in parallel with the BRAF V595E mutation. The identification of these deletion events in dogs offers a compelling cross-species platform in which to study the relationship between somatic alteration, protein conformation, and therapeutic sensitivity.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Claire A. Wiley
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Emma L. Droste
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - James Robertson
- Office of Research (Biostatistics), College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Brant A. Inman
- Department of Surgery, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, United States of America
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11
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Deacetylation induced nuclear condensation of HP1γ promotes multiple myeloma drug resistance. Nat Commun 2023; 14:1290. [PMID: 36894562 PMCID: PMC9998874 DOI: 10.1038/s41467-023-37013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
Acquired chemoresistance to proteasome inhibitors is a major obstacle in managing multiple myeloma but key regulators and underlying mechanisms still remain to be explored. We find that high level of HP1γ is associated with low acetylation modification in the bortezomib-resistant myeloma cells using SILAC-based acetyl-proteomics assay, and higher HP1γ level is positively correlated with poorer outcomes in the clinic. Mechanistically, elevated HDAC1 in the bortezomib-resistant myeloma cells deacetylates HP1γ at lysine 5 and consequently alleviates the ubiquitin-mediated protein degradation, as well as the aberrant DNA repair capacity. HP1γ interacts with the MDC1 to induce DNA repair, and simultaneously the deacetylation modification and the interaction with MDC1 enhance the nuclear condensation of HP1γ protein and the chromatin accessibility of its target genes governing sensitivity to proteasome inhibitors, such as CD40, FOS and JUN. Thus, targeting HP1γ stability by using HDAC1 inhibitor re-sensitizes bortezomib-resistant myeloma cells to proteasome inhibitors treatment in vitro and in vivo. Our findings elucidate a previously unrecognized role of HP1γ in inducing drug resistance to proteasome inhibitors of myeloma cells and suggest that targeting HP1γ may be efficacious for overcoming drug resistance in refractory or relapsed multiple myeloma patients.
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12
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MDC1 maintains active elongation complexes of RNA polymerase II. Cell Rep 2023; 42:111979. [PMID: 36640322 DOI: 10.1016/j.celrep.2022.111979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 10/04/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The role of MDC1 in the DNA damage response has been extensively studied; however, its impact on other cellular processes is not well understood. Here, we describe the role of MDC1 in transcription as a regulator of RNA polymerase II (RNAPII). Depletion of MDC1 causes a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein-encoding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to changes in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.
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Mohapatra S, Winkle M, Ton AN, Nguyen D, Calin GA. The Role of Non-Coding RNAs in Chromosomal Instability in Cancer. J Pharmacol Exp Ther 2023; 384:10-19. [PMID: 36167417 PMCID: PMC9827503 DOI: 10.1124/jpet.122.001357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/22/2022] [Accepted: 08/17/2022] [Indexed: 01/12/2023] Open
Abstract
Chromosomal instability (CIN) is characterized by an increased frequency of changes in chromosome structure or number and is regarded as a hallmark of cancer. CIN plays a prevalent role in tumorigenesis and cancer progression by assisting the cancer cells' phenotypic adaptation to stress, which have been tightly linked to therapy resistance and metastasis. Both CIN-inducing and CIN-repressing agents are being clinically tested for the treatment of cancer to increase CIN levels to unsustainable levels leading to cell death or to decrease CIN levels to limit the development of drug resistance, respectively. Non-coding RNAs (ncRNAs) including microRNAs and long ncRNAs (lncRNAs) have been fundamentally implicated in CIN. The miR-22, miR-26a, miR-28, and miR-186 target important checkpoint proteins involved in mediating chromosomal stability and their expression modulation has been directly related to CIN occurrence. lncRNAs derived from telomeric, centrosomal, and enhancer regions play an important role in mediating genome stability, while specific lncRNA transcripts including genomic instability inducing RNA called Ginir, P53-responsive lncRNA termed as GUARDIN, colon cancer-associated transcript 2, PCAT2, and ncRNA activated by DNA damage called NORAD have been shown to act within CIN-associated pathways. In this review, we discuss how these ncRNAs either maintain or disrupt the stability of chromosomes and how these mechanisms could be exploited for novel therapeutic approaches targeting CIN in cancer patients. SIGNIFICANCE STATEMENT: Chromosomal instability increases tumor heterogeneity and thereby assists the phenotypic adaptation of cancer cells, causing therapy resistance and metastasis. Several microRNAs and long non-coding RNAs that have been causally linked to chromosomal instability could represent novel therapeutic targets. Understanding the role of non-coding RNAs in regulating different genes involved in driving chromosomal instability will give insights into how non-coding RNAs can be utilized toward modifying chemotherapeutic regimens in different cancers.
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Affiliation(s)
- Swati Mohapatra
- Department of Translational Molecular Pathology (S.M., M.W., A.N.T., G.A.C.), UT Health Graduate School of Biomedical Sciences (S.M.), Program in Molecular Genetic Technology, School of Health Professions (A.N.T.), and Center for RNA Interference and Non-Coding RNAs (G.A.C.), The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts (D.N.)
| | - Melanie Winkle
- Department of Translational Molecular Pathology (S.M., M.W., A.N.T., G.A.C.), UT Health Graduate School of Biomedical Sciences (S.M.), Program in Molecular Genetic Technology, School of Health Professions (A.N.T.), and Center for RNA Interference and Non-Coding RNAs (G.A.C.), The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts (D.N.)
| | - Anh N Ton
- Department of Translational Molecular Pathology (S.M., M.W., A.N.T., G.A.C.), UT Health Graduate School of Biomedical Sciences (S.M.), Program in Molecular Genetic Technology, School of Health Professions (A.N.T.), and Center for RNA Interference and Non-Coding RNAs (G.A.C.), The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts (D.N.)
| | - Dien Nguyen
- Department of Translational Molecular Pathology (S.M., M.W., A.N.T., G.A.C.), UT Health Graduate School of Biomedical Sciences (S.M.), Program in Molecular Genetic Technology, School of Health Professions (A.N.T.), and Center for RNA Interference and Non-Coding RNAs (G.A.C.), The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts (D.N.)
| | - George A Calin
- Department of Translational Molecular Pathology (S.M., M.W., A.N.T., G.A.C.), UT Health Graduate School of Biomedical Sciences (S.M.), Program in Molecular Genetic Technology, School of Health Professions (A.N.T.), and Center for RNA Interference and Non-Coding RNAs (G.A.C.), The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts (D.N.)
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14
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Liu Y, Han J, Kong T, Xiao N, Mei Q, Liu J. DriverMP enables improved identification of cancer driver genes. Gigascience 2022; 12:giad106. [PMID: 38091511 PMCID: PMC10716827 DOI: 10.1093/gigascience/giad106] [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: 07/19/2023] [Revised: 10/30/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cancer is widely regarded as a complex disease primarily driven by genetic mutations. A critical concern and significant obstacle lies in discerning driver genes amid an extensive array of passenger genes. FINDINGS We present a new method termed DriverMP for effectively prioritizing altered genes on a cancer-type level by considering mutated gene pairs. It is designed to first apply nonsilent somatic mutation data, protein‒protein interaction network data, and differential gene expression data to prioritize mutated gene pairs, and then individual mutated genes are prioritized based on prioritized mutated gene pairs. Application of this method in 10 cancer datasets from The Cancer Genome Atlas demonstrated its great improvements over all the compared state-of-the-art methods in identifying known driver genes. Then, a comprehensive analysis demonstrated the reliability of the novel driver genes that are strongly supported by clinical experiments, disease enrichment, or biological pathway analysis. CONCLUSIONS The new method, DriverMP, which is able to identify driver genes by effectively integrating the advantages of multiple kinds of cancer data, is available at https://github.com/LiuYangyangSDU/DriverMP. In addition, we have developed a novel driver gene database for 10 cancer types and an online service that can be freely accessed without registration for users. The DriverMP method, the database of novel drivers, and the user-friendly online server are expected to contribute to new diagnostic and therapeutic opportunities for cancers.
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Affiliation(s)
- Yangyang Liu
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai 264209, China
| | - Jiyun Han
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai 264209, China
| | - Tongxin Kong
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai 264209, China
| | - Nannan Xiao
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai 264209, China
| | - Qinglin Mei
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Juntao Liu
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai 264209, China
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15
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Melone V, Salvati A, Palumbo D, Giurato G, Nassa G, Rizzo F, Palo L, Giordano A, Incoronato M, Vitale M, Mian C, Di Biase I, Cristiano S, Narciso V, Cantile M, Di Mauro A, Tatangelo F, Tafuto S, Modica R, Pivonello C, Salvatore M, Colao A, Weisz A, Tarallo R. Identification of functional pathways and molecular signatures in neuroendocrine neoplasms by multi-omics analysis. J Transl Med 2022; 20:306. [PMID: 35794609 PMCID: PMC9258165 DOI: 10.1186/s12967-022-03511-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Neuroendocrine neoplasms (NENs) represent a heterogeneous class of rare tumors with increasing incidence. They are characterized by the ability to secrete peptide hormones and biogenic amines but other reliable biomarkers are lacking, making diagnosis and identification of the primary site very challenging. While in some NENs, such as the pancreatic ones, next generation sequencing technologies allowed the identification of new molecular hallmarks, our knowledge of the molecular profile of NENs from other anatomical sites is still poor. METHODS Starting from the concept that NENs from different organs may be clinically and genetically correlated, we applied a multi-omics approach by combining multigene panel testing, CGH-array, transcriptome and miRNome profiling and computational analyses, with the aim to highlight common molecular and functional signatures of gastroenteropancreatic (GEP)-NENs and medullary thyroid carcinomas (MTCs) that could aid diagnosis, prognosis and therapy. RESULTS By comparing genomic and transcriptional profiles, ATM-dependent signaling emerged among the most significant pathways at multiple levels, involving gene variations and miRNA-mediated regulation, thus representing a novel putative druggable pathway in these cancer types. Moreover, a set of circulating miRNAs was also selected as possible diagnostic/prognostic biomarkers useful for clinical management of NENs. CONCLUSIONS These findings depict a complex molecular and functional landscape of NENs, shedding light on novel therapeutic targets and disease biomarkers to be exploited.
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Affiliation(s)
- Viola Melone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Luigi Palo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Alessandro Giordano
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | | | - Mario Vitale
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Caterina Mian
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Immacolata Di Biase
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Stefano Cristiano
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Viviana Narciso
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Annabella Di Mauro
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Fabiana Tatangelo
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Salvatore Tafuto
- Sarcomas and Rare Tumors Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Roberta Modica
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
| | - Claudia Pivonello
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
| | - Marco Salvatore
- IRCCS Synlab SDN s.p.a, Via Gianturco 113, 80143, Naples, Italy
| | - Annamaria Colao
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
- UNESCO Chair for Health Education and Sustainable Development, Federico II University, Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy.
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy.
- Genome Research Center for Health, 84081, Baronissi, SA, Italy.
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy.
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy.
- Genome Research Center for Health, 84081, Baronissi, SA, Italy.
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Functional defects of cancer-associated MDC1 mutations in DNA damage repair. DNA Repair (Amst) 2022; 114:103330. [PMID: 35378404 DOI: 10.1016/j.dnarep.2022.103330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022]
Abstract
Mediator of DNA damage checkpoint protein 1 (MDC1) serves as a docking platform to promote the localization of various DNA damage response (DDR) components to DNA double-strand break (DSB) sites. MDC1 is vital in controlling proper DDR and maintaining genomic stability. In cancers, genomic instability results from mutations in DNA repair genes and drives cancer development. The mutations of MDC1 in human cancers have not been systematically examined and little is known about the molecular phenotypes caused by these genetic changes. Here, we summarized cancer-associated mutations of MDC1 including insertion/deletion mutations as well as missense mutations in key functional domains of MDC1 from ICGC, TCGA and COSMIC databases. We analyzed 711 somatic mutations of MDC1 across 26 types of human cancers and examined the functional defects of these cancer-associated mutations of MDC1 in the context of DNA damage repair. 6 truncation mutations and 7 missense mutations of MDC1 were chosen for further study. 6 truncation mutations which abolish MDC1-γH2AX interaction abrogate its biological functions in DNA damage repair. 2 missense mutations in FHA domain impaired ATM (ataxia telangiectasia mutated) phosphorylation. 5 missense mutations in BRCT domain also abolished its interaction with γH2AX, resulting in defects in foci formation of MDC1, 53BP1 and BRCA1 as well as defects in G2/M checkpoints. We further used structural modeling to analyze the potential molecular mechanism by which the 7 missense mutations cause the DNA damage repair defects. Taken together, our results reveal these cancer-associated MDC1 mutations can result in functional defects in DNA damage response and may serve as biomarkers for cancer diagnostics in future.
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17
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Sex disparities in DNA damage response pathways: Novel determinants in cancer formation and therapy. iScience 2022; 25:103875. [PMID: 35243237 PMCID: PMC8858993 DOI: 10.1016/j.isci.2022.103875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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18
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Ueno S, Sudo T, Hirasawa A. ATM: Functions of ATM Kinase and Its Relevance to Hereditary Tumors. Int J Mol Sci 2022; 23:523. [PMID: 35008949 PMCID: PMC8745051 DOI: 10.3390/ijms23010523] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Ataxia-telangiectasia mutated (ATM) functions as a key initiator and coordinator of DNA damage and cellular stress responses. ATM signaling pathways contain many downstream targets that regulate multiple important cellular processes, including DNA damage repair, apoptosis, cell cycle arrest, oxidative sensing, and proliferation. Over the past few decades, associations between germline ATM pathogenic variants and cancer risk have been reported, particularly for breast and pancreatic cancers. In addition, given that ATM plays a critical role in repairing double-strand breaks, inhibiting other DNA repair pathways could be a synthetic lethal approach. Based on this rationale, several DNA damage response inhibitors are currently being tested in ATM-deficient cancers. In this review, we discuss the current knowledge related to the structure of the ATM gene, function of ATM kinase, clinical significance of ATM germline pathogenic variants in patients with hereditary cancers, and ongoing efforts to target ATM for the benefit of cancer patients.
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Affiliation(s)
- Sayaka Ueno
- Section of Translational Research, Hyogo Cancer Center, 13-70 Kita-Oji-cho, Akashi-shi 673-8558, Japan;
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
| | - Tamotsu Sudo
- Section of Translational Research, Hyogo Cancer Center, 13-70 Kita-Oji-cho, Akashi-shi 673-8558, Japan;
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
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19
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Li Y, Gao W, Cai X, Jin A, Shen J, Zhang Y, Chen Y, Hu B, Zeng T, Yu X, Zheng Y, Wang Y. Exploring Somatic Alteration Associating With Aggressive Behaviors of Papillary Thyroid Carcinomas by Targeted Sequencing. Front Oncol 2021; 11:722814. [PMID: 34692499 PMCID: PMC8529196 DOI: 10.3389/fonc.2021.722814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022] Open
Abstract
Wisely differentiating high-risk papillary thyroid carcinoma (PTC) patients from low-risk PTC patients preoperatively is necessary when comes to making a personalized treatment plan. It is not easy to stratify the risk of patients according to sonography or lab results before surgery. This study aims to seek out potential mutation gene markers that may be helpful in stratifying the risk of PTC. A custom panel of 439 PTC relevant and classic tumor metabolic pathway relevant genes was designed. Targeted capture sequencing was performed on 35 pairs of samples from 35 PTC tumors and 35 para-tumor thyroid tissues obtained during surgery. Variant calling and detection of cancer gene mutations were identified by bio-information analysis. Ingenuity Pathway Analysis (IPA) was performed to do functional enrichment analysis of high-frequency mutant genes. Immunohistochemistry (IHC) was performed on 6 PTC patients to explore the expression of protein associated with interested genes. Event-free survival (EFS) was calculated to determine which genes might affect the prognosis of patients. We have identified 32 high-frequency mutant genes in PTC including BRAF. RBL2 was found to be significantly correlated to event-free survival, FOXO1, MUC6, PCDHB9, NOTCH1, FIZ1, and RTN1 were significantly associated with EFS, while BRAF mutant was not correlated to any of the prognosis indicators. Our findings in this study might open more choices when designing thyroid gene panels used in FNA samples to diagnose PTC and predict the potentially aggressive behavior of PTC.
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Affiliation(s)
- Yi Li
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China
| | - Wei Gao
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China
| | - Xiaojun Cai
- Shanghai Institute of Ultrasound in Medicine, Shanghai, China
| | - Anqi Jin
- Department of Ultrasound Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jian Shen
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China
| | - Yichun Zhang
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China
| | - Yutong Chen
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China
| | - Bing Hu
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China.,Shanghai Institute of Ultrasound in Medicine, Shanghai, China
| | - Tao Zeng
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xiangtian Yu
- Clinical Research Center, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yuanyi Zheng
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China.,Shanghai Institute of Ultrasound in Medicine, Shanghai, China
| | - Yan Wang
- Department of Ultrasound in Medicine, Shanghai Jiao Tong University Affiliated Shanghai Sixth People's Hospital, Shanghai, China.,Shanghai Institute of Ultrasound in Medicine, Shanghai, China
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20
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Schmitt M, Sinnberg T, Bratl K, Zittlau K, Garbe C, Macek B, Nalpas NC. Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. Mol Cell Proteomics 2021; 20:100163. [PMID: 34673281 PMCID: PMC8603206 DOI: 10.1016/j.mcpro.2021.100163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/04/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Analysis of nucleotide variants is a cornerstone of cancer medicine. Although only 2% of the genomic sequence is protein coding, mutations occurring in these regions have the potential to influence protein structure or modification status and may have severe impact on disease aetiology. Proteogenomics enables the analysis of sample-specific nonsynonymous nucleotide variants with regard to their effect at the proteome and phosphoproteome levels. Here, we developed a proof-of-concept proteogenomics workflow and applied it to the malignant melanoma cell line A375. Initially, we studied the resistance to serine/threonine-protein kinase B-raf (BRAF) inhibitor (BRAFi) vemurafenib in A375 cells. This allowed identification of several oncogenic nonsynonymous nucleotide variants, including a gain-of-function variant on aurora kinase A (AURKA) at F31I. We also detected significant changes in abundance among (phospho)proteins, which led to reactivation of the MAPK signaling pathway in BRAFi-resistant A375 cells. Upon reconstruction of the multiomic integrated signaling networks, we predicted drug therapies with the potential to disrupt BRAFi resistance mechanism in A375 cells. Notably, we showed that AURKA inhibition is effective and specific against BRAFi-resistant A375 cells. Subsequently, we investigated amino acid variants that interfere with protein posttranslational modification (PTM) status and potentially influence A375 cell signaling irrespective of BRAFi resistance. Mass spectrometry (MS) measurements confirmed variant-driven PTM changes in 12 proteins. Among them was the runt-related transcription factor 1 (RUNX1) displaying a variant on a known phosphorylation site S(Ph)276L. We confirmed the loss of phosphorylation site by MS and demonstrated the impact of this variant on RUNX1 interactome.
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Affiliation(s)
- Marisa Schmitt
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias Sinnberg
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Katrin Bratl
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Katharina Zittlau
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Claus Garbe
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Boris Macek
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany.
| | - Nicolas C Nalpas
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany.
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21
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Sottnik JL, Bordeaux EK, Mehrotra S, Ferrara SE, Goodspeed AE, Costello JC, Sikora MJ. Mediator of DNA Damage Checkpoint 1 (MDC1) Is a Novel Estrogen Receptor Coregulator in Invasive Lobular Carcinoma of the Breast. Mol Cancer Res 2021; 19:1270-1282. [PMID: 33947745 PMCID: PMC8349796 DOI: 10.1158/1541-7786.mcr-21-0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/01/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
Invasive lobular carcinoma (ILC) is the most common special histologic subtype of breast cancer, and nearly all ILC tumors express estrogen receptor alpha (ER). However, clinical and laboratory data suggest ILC are strongly estrogen-driven but not equally antiestrogen-sensitive. We hypothesized ILC-specific ER coregulators mediate ER functions and antiestrogen resistance in ILC, and profiled ER-associated proteins by mass spectrometry. Three ER+ ILC cell lines (MDA MB 134VI, SUM44PE, and BCK4) were compared with ER+ invasive ductal carcinoma (IDC) line data, and we examined whether siRNA of identified proteins suppressed ER-driven proliferation in ILC cells. This identified mediator of DNA damage checkpoint 1 (MDC1), a tumor suppressor in DNA damage response (DDR), as a novel ER coregulator in ILC. We confirmed ER:MDC1 interaction was specific to ILC versus IDC cells, and found MDC1 knockdown suppressed ILC cell proliferation and tamoxifen resistance. Using RNA-sequencing, we found in ILC cells MDC1 knockdown broadly dysregulates the ER transcriptome, with ER:MDC1 target genes enriched for promoter hormone response elements. Importantly, our data are inconsistent with MDC1 tumor suppressor functions in DDR, but suggest a novel oncogenic role for MDC1 as an ER coregulator. Supporting this, in breast tumor tissue microarrays, MDC1 protein was frequently low or absent in IDC, but MDC1 loss was rare in ER+ ILC. ER:MDC1 interaction and MDC1 coregulator functions may underlie ER function in ILC and serve as targets to overcome antiestrogen resistance in ILC. IMPLICATIONS: MDC1 has novel ER coregulator activity in ILC, which may underlie ILC-specific ER functions, estrogen response, and antiestrogen resistance.
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Affiliation(s)
- Joseph L Sottnik
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Evelyn K Bordeaux
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sanjana Mehrotra
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sarah E Ferrara
- Biostatistics and Bioinformatics Shared Resource, University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Andrew E Goodspeed
- Biostatistics and Bioinformatics Shared Resource, University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - James C Costello
- Biostatistics and Bioinformatics Shared Resource, University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Matthew J Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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22
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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