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Li M, Cai Y, Zhang M, Deng S, Wang L. NNBGWO-BRCA marker: Neural Network and binary grey wolf optimization based Breast cancer biomarker discovery framework using multi-omics dataset. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 254:108291. [PMID: 38909399 DOI: 10.1016/j.cmpb.2024.108291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/09/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND AND OBJECTIVE Breast cancer is a multifaceted condition characterized by diverse features and a substantial mortality rate, underscoring the imperative for timely detection and intervention. The utilization of multi-omics data has gained significant traction in recent years to identify biomarkers and classify subtypes in breast cancer. This kind of research idea from part to whole will also be an inevitable trend in future life science research. Deep learning can integrate and analyze multi-omics data to predict cancer subtypes, which can further drive targeted therapies. However, there are few articles leveraging the nature of deep learning for feature selection. Therefore, this paper proposes a Neural Network and Binary grey Wolf Optimization based BReast CAncer bioMarker (NNBGWO-BRCAMarker) discovery framework using multi-omics data to obtain a series of biomarkers for precise classification of breast cancer subtypes. METHODS NNBGWO-BRCAMarker consists of two phases: in the first phase, relevant genes are selected using the weights obtained from a trained feedforward neural network; in the second phase, the binary grey wolf optimization algorithm is leveraged to further screen the selected genes, resulting in a set of potential breast cancer biomarkers. RESULTS The SVM classifier with RBF kernel achieved a classification accuracy of 0.9242 ± 0.03 when trained using the 80 biomarkers identified by NNBGWO-BRCAMarker, as evidenced by the experimental results. We conducted a comprehensive gene set analysis, prognostic analysis, and druggability analysis, unveiling 25 druggable genes, 16 enriched pathways strongly linked to specific subtypes of breast cancer, and 8 genes linked to prognostic outcomes. CONCLUSIONS The proposed framework successfully identified 80 biomarkers from the multi-omics data, enabling accurate classification of breast cancer subtypes. This discovery may offer novel insights for clinicians to pursue in further studies.
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Affiliation(s)
- Min Li
- School of Information Engineering, Nanchang Institute of Technology, No. 289 Tianxiang Road, Nanchang Jiangxi, PR China.
| | - Yuheng Cai
- School of Information Engineering, Nanchang Institute of Technology, No. 289 Tianxiang Road, Nanchang Jiangxi, PR China
| | - Mingzhuang Zhang
- School of Information Engineering, Nanchang Institute of Technology, No. 289 Tianxiang Road, Nanchang Jiangxi, PR China
| | - Shaobo Deng
- School of Information Engineering, Nanchang Institute of Technology, No. 289 Tianxiang Road, Nanchang Jiangxi, PR China
| | - Lei Wang
- School of Information Engineering, Nanchang Institute of Technology, No. 289 Tianxiang Road, Nanchang Jiangxi, PR China
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Liu Y, Yang H, Fu X, Zhong L, Xu P, Fang F, Liu Y, Li Q, Yan Y, Wei S, Wang J, Zhang C. BRCA2, PALB2, RECQL4 Germline Pathogenic Variants, and Somatic TP53 Mutation in Triple Metachronous Malignancies: A Case Report and Literature Review. Int Med Case Rep J 2024; 17:23-29. [PMID: 38223534 PMCID: PMC10788051 DOI: 10.2147/imcrj.s440132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024] Open
Abstract
Background Multiple primary cancer (MPC) refers to the presence of more than one cancer in an individual. Triple primary malignancies are uncommon. Case We report the case of a 50-year-old postmenopausal woman in our gynecology department, diagnosed with endometrial cancer, ovarian cancer, and unilateral breast cancer. She carried germline mutations in BRCA2, PALB2, and RECQL4, along with a somatic pathogenic variant in TP53. Endometrial cancer patients harboring germline pathogenic variants in BRCA2 exhibit a heightened risk of ovarian and breast cancer. BRCA2 is known to play a role in the development of ovarian and breast cancer, while PALB2 is identified as a gene associated with breast cancer susceptibility. RECQL4 has been linked to breast cancer, cervical cancer, and other tumors. Conclusion Genetic testing may be imperative for identifying MPC in endometrial cancer patients. For individuals with BRCA2 and other gene pathogenic variants, routine examination and monitoring of the endometrium, ovaries, breasts, and other sites prone to polygenic cancer are recommended.
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Affiliation(s)
- Yang Liu
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Hui Yang
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Xueshu Fu
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Luting Zhong
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Ping Xu
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Fang Fang
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Ying Liu
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Qing Li
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Ya’nan Yan
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Shanchuang Wei
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Junqing Wang
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
| | - Chunhua Zhang
- Department of Gynaecology, Affiliated Hospital of YangZhou University Huai ‘an Maternal and Child Health Care Center, Huai’an, Jiangsu, People’s Republic of China
- Department of Gynaecology, The Huai’an Maternity and Child Clinical College of Xuzhou Medical University, Huai’an, Jiangsu, People’s Republic of China
- Department of Integrated Traditional Chinese & Western Clinical Medicine, Macau University of Science and Technology, Macau, People’s Republic of China
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Amin M, Mahmoodi-Khaledi E, Narrei S, Zeinalian M. A Novel Germline Pathogenic Variant of RECQL4 Gene in an Iranian Pedigree with Familial Squamous Cell Carcinoma: A Brief Report. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:420-424. [PMID: 37456212 PMCID: PMC10349162 DOI: 10.30476/ijms.2022.94539.2587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/19/2022] [Accepted: 07/18/2022] [Indexed: 07/18/2023]
Abstract
Squamous cell carcinoma (SCC) is the most common human solid tumor and the leading cause of cancer death. SCC of the breast is a very rare type of cancer that has not been well researched. Early identification of the genetic factors involved can lead to early diagnosis and targeted treatment. The present study was conducted in 2018 at Isfahan University of Medical Sciences (Isfahan, Iran). The proband was a 66-year-old woman with SCC of the breast and a positive family history of cancer. Blood DNA samples were used for whole-exome sequencing to identify germline pathogenic variants. Variant annotation and prioritization were done on variant call format files using bioinformatics software tools. The screened variants were confirmed using the Sanger sequencing method. Co-segregation analysis was performed on the blood DNA samples of the first- and second-degree relatives of the proband to assess the presence of the mutation. A novel germline pathogenic variant was identified in the RECQL4 gene of the family. RECQL4 is a known protein in DNA repair and replication. Considering its effect on other types of SCC, it may play an important role in SCC initiation and progression in the breast.
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Affiliation(s)
- Mina Amin
- Department of Cell and Molecular Biology, School of Chemistry, University of Kashan, Kashan, Iran
| | - Elaheh Mahmoodi-Khaledi
- Department of Cell and Molecular Biology, School of Chemistry, University of Kashan, Kashan, Iran
| | - Sina Narrei
- Ala Cancer Prevention and Control Center, Isfahan, Iran
| | - Mehrdad Zeinalian
- Ala Cancer Prevention and Control Center, Isfahan, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Ahmed F, Khan AA, Ansari HR, Haque A. A Systems Biology and LASSO-Based Approach to Decipher the Transcriptome-Interactome Signature for Predicting Non-Small Cell Lung Cancer. BIOLOGY 2022; 11:biology11121752. [PMID: 36552262 PMCID: PMC9774707 DOI: 10.3390/biology11121752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
The lack of precise molecular signatures limits the early diagnosis of non-small cell lung cancer (NSCLC). The present study used gene expression data and interaction networks to develop a highly accurate model with the least absolute shrinkage and selection operator (LASSO) for predicting NSCLC. The differentially expressed genes (DEGs) were identified in NSCLC compared with normal tissues using TCGA and GTEx data. A biological network was constructed using DEGs, and the top 20 upregulated and 20 downregulated hub genes were identified. These hub genes were used to identify signature genes with penalized logistic regression using the LASSO to predict NSCLC. Our model’s development involved the following steps: (i) the dataset was divided into 80% for training (TR) and 20% for testing (TD1); (ii) a LASSO logistic regression analysis was performed on the TR with 10-fold cross-validation and identified a combination of 17 genes as NSCLC predictors, which were used further for development of the LASSO model. The model’s performance was assessed on the TD1 dataset and achieved an accuracy and an area under the curve of the receiver operating characteristics (AUC-ROC) of 0.986 and 0.998, respectively. Furthermore, the performance of the LASSO model was evaluated using three independent NSCLC test datasets (GSE18842, GSE27262, GSE19804) and achieved high accuracy, with an AUC-ROC of >0.99, >0.99, and 0.95, respectively. Based on this study, a web application called NSCLCpred was developed to predict NSCLC.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, P.O. Box 80327, Jeddah 21589, Saudi Arabia
- Correspondence:
| | - Abdul Arif Khan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hifzur Rahman Ansari
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, P.O. Box 9515, Jeddah 21423, Saudi Arabia
| | - Absarul Haque
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
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Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer. PLoS Genet 2022; 18:e1010122. [PMID: 36126066 PMCID: PMC9488787 DOI: 10.1371/journal.pgen.1010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Human RECQL4 is a member of the RecQ family of DNA helicases and functions during DNA replication and repair. RECQL4 mutations are associated with developmental defects and cancer. Although RECQL4 mutations lead to disease, RECQL4 overexpression is also observed in cancer, including breast and prostate. Thus, tight regulation of RECQL4 protein levels is crucial for genome stability. Because mammalian RECQL4 is essential, how cells regulate RECQL4 protein levels is largely unknown. Utilizing budding yeast, we investigated the RECQL4 homolog, HRQ1, during DNA crosslink repair. We find that Hrq1 functions in the error-free template switching pathway to mediate DNA intrastrand crosslink repair. Although Hrq1 mediates repair of cisplatin-induced lesions, it is paradoxically degraded by the proteasome following cisplatin treatment. By identifying the targeted lysine residues, we show that preventing Hrq1 degradation results in increased recombination and mutagenesis. Like yeast, human RECQL4 is similarly degraded upon exposure to crosslinking agents. Furthermore, over-expression of RECQL4 results in increased RAD51 foci, which is dependent on its helicase activity. Using bioinformatic analysis, we observe that RECQL4 overexpression correlates with increased recombination and mutations. Overall, our study uncovers a role for Hrq1/RECQL4 in DNA intrastrand crosslink repair and provides further insight how misregulation of RECQL4 can promote genomic instability, a cancer hallmark. RECQL4 is a DNA helicase and functions during DNA replication and repair. While loss-of-function RECQL4 mutations are found in diseases characterized by developmental defects and cancer, such as Rothmund-Thomson syndrome, over-expression of RECQL4 is also observed in cancer, such as breast cancer. Therefore, RECQL4 protein expression must be tightly regulated. Here we used the budding yeast homolog of RECQL4, Hrq1, and discovered that overexpression of Hrq1 protein levels result in increased recombination and mutations, both cancer hallmarks. We find that Hrq1 functions to mediate repair of a specific type of DNA damage, intrastrand crosslinks, which occur when DNA nucleotides on the same strand are chemically linked together. These findings are also conserved in humans suggesting a common mechanism between yeast Hrq1 and human RECQL4. Overall, our study identifies a conserved role for RECQL4 in DNA intrastrand crosslink repair and provides insights into how its misregulation could promote cancer development.
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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Thakkar MK, Lee J, Meyer S, Chang VY. RecQ Helicase Somatic Alterations in Cancer. Front Mol Biosci 2022; 9:887758. [PMID: 35782872 PMCID: PMC9240438 DOI: 10.3389/fmolb.2022.887758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Named the “caretakers” of the genome, RecQ helicases function in several pathways to maintain genomic stability and repair DNA. This highly conserved family of enzymes consist of five different proteins in humans: RECQL1, BLM, WRN, RECQL4, and RECQL5. Biallelic germline mutations in BLM, WRN, and RECQL4 have been linked to rare cancer-predisposing syndromes. Emerging research has also implicated somatic alterations in RecQ helicases in a variety of cancers, including hematological malignancies, breast cancer, osteosarcoma, amongst others. These alterations in RecQ helicases, particularly overexpression, may lead to increased resistance of cancer cells to conventional chemotherapy. Downregulation of these proteins may allow for increased sensitivity to chemotherapy, and, therefore, may be important therapeutic targets. Here we provide a comprehensive review of our current understanding of the role of RecQ DNA helicases in cancer and discuss the potential therapeutic opportunities in targeting these helicases.
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Affiliation(s)
- Megha K. Thakkar
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jamie Lee
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stefan Meyer
- Division of Cancer Studies, University of Manchester, Manchester, United Kingdom
- Department of Pediatric Hematology Oncology, Royal Manchester Children’s Hospital and Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Vivian Y. Chang
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
- Childrens Discovery and Innovation Institute, UCLA, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, United States
- *Correspondence: Vivian Y. Chang,
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Maity J, Horibata S, Zurcher G, Lee JM. Targeting of RecQ Helicases as a Novel Therapeutic Strategy for Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14051219. [PMID: 35267530 PMCID: PMC8909030 DOI: 10.3390/cancers14051219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
RecQ helicases are essential for DNA replication, recombination, DNA damage repair, and other nucleic acid metabolic pathways required for normal cell growth, survival, and genome stability. More recently, RecQ helicases have been shown to be important for replication fork stabilization, one of the major mechanisms of PARP inhibitor resistance. Cancer cells often have upregulated helicases and depend on these enzymes to repair rapid growth-promoted DNA lesions. Several studies are now evaluating the use of RecQ helicases as potential biomarkers of breast and gynecologic cancers. Furthermore, RecQ helicases have attracted interest as possible targets for cancer treatment. In this review, we discuss the characteristics of RecQ helicases and their interacting partners that may be utilized for effective treatment strategies (as cancers depend on helicases for survival). We also discuss how targeting helicase in combination with DNA repair inhibitors (i.e., PARP and ATR inhibitors) can be used as novel approaches for cancer treatment to increase sensitivity to current treatment to prevent rise of treatment resistance.
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Affiliation(s)
- Jyotirindra Maity
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
| | - Sachi Horibata
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (S.H.); (J.M.L.)
| | - Grant Zurcher
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
- Correspondence: (S.H.); (J.M.L.)
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Yang M, Lu H, Liu J, Wu S, Kim P, Zhou X. lncRNAfunc: a knowledgebase of lncRNA function in human cancer. Nucleic Acids Res 2022; 50:D1295-D1306. [PMID: 34791419 PMCID: PMC8728133 DOI: 10.1093/nar/gkab1035] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 02/05/2023] Open
Abstract
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3'-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
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Affiliation(s)
- Mengyuan Yang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Huifen Lu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- College of Electronic and Information Engineering, Tongji University, Shanghai, Shanghai 201804, China
| | - Sijia Wu
- School of Life Sciences and Technology, Xidian University, Xi'an 710126, China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Xu X, Chang CW, Li M, Liu C, Liu Y. Molecular Mechanisms of the RECQ4 Pathogenic Mutations. Front Mol Biosci 2021; 8:791194. [PMID: 34869606 PMCID: PMC8637615 DOI: 10.3389/fmolb.2021.791194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022] Open
Abstract
The human RECQ4 gene encodes an ATP-dependent DNA helicase that contains a conserved superfamily II helicase domain located at the center of the polypeptide. RECQ4 is one of the five RECQ homologs in human cells, and its helicase domain is flanked by the unique amino and carboxyl termini with sequences distinct from other members of the RECQ helicases. Since the identification of the RECQ4 gene in 1998, multiple RECQ4 mutations have been linked to the pathogenesis of three clinical diseases, which are Rothmund-Thomson syndrome, Baller-Gerold syndrome, and RAPADILINO. Patients with these diseases show various developmental abnormalities. In addition, a subset of RECQ4 mutations are associated with high cancer risks, especially for osteosarcoma and/or lymphoma at early ages. The discovery of clinically relevant RECQ4 mutations leads to intriguing questions: how is the RECQ4 helicase responsible for preventing multiple clinical syndromes? What are the mechanisms by which the RECQ4 disease mutations cause tissue abnormalities and drive cancer formation? Furthermore, RECQ4 is highly overexpressed in many cancer types, raising the question whether RECQ4 acts not only as a tumor suppressor but also an oncogene that can be a potential new therapeutic target. Defining the molecular dysfunctions of different RECQ4 disease mutations is imperative to improving our understanding of the complexity of RECQ4 clinical phenotypes and the dynamic roles of RECQ4 in cancer development and prevention. We will review recent progress in examining the molecular and biochemical properties of the different domains of the RECQ4 protein. We will shed light on how the dynamic roles of RECQ4 in human cells may contribute to the complexity of RECQ4 clinical phenotypes.
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Affiliation(s)
- Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Chao Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
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Luong TT, Bernstein KA. Role and Regulation of the RECQL4 Family during Genomic Integrity Maintenance. Genes (Basel) 2021; 12:1919. [PMID: 34946868 PMCID: PMC8701316 DOI: 10.3390/genes12121919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 12/14/2022] Open
Abstract
RECQL4 is a member of the evolutionarily conserved RecQ family of 3' to 5' DNA helicases. RECQL4 is critical for maintaining genomic stability through its functions in DNA repair, recombination, and replication. Unlike many DNA repair proteins, RECQL4 has unique functions in many of the central DNA repair pathways such as replication, telomere, double-strand break repair, base excision repair, mitochondrial maintenance, nucleotide excision repair, and crosslink repair. Consistent with these diverse roles, mutations in RECQL4 are associated with three distinct genetic diseases, which are characterized by developmental defects and/or cancer predisposition. In this review, we provide an overview of the roles and regulation of RECQL4 during maintenance of genome homeostasis.
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Affiliation(s)
| | - Kara A. Bernstein
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA;
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12
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Ye Y, Yu F, Li Z, Xie Y, Yu X. RNA binding protein serine/arginine splicing factor 1 promotes the proliferation, migration and invasion of hepatocellular carcinoma by interacting with RecQ protein-like 4 mRNA. Bioengineered 2021; 12:6144-6154. [PMID: 34486474 PMCID: PMC8806490 DOI: 10.1080/21655979.2021.1972785] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abnormally high expression of RecQ protein-like 4 (RECQL4) has been observed in many cancers, including hepatocellular carcinoma (HCC). We aimed to explore the effects of RECQL4 on HCC progression and the possible mechanisms. RECQL4 expression in HCC tissues and its correlation with the prognosis of HCC patients were analyzed using GEPIA2 and UALCAN databases. After detecting RECQL4 levels in several human HC cell lines, RECQL4 was silenced by siRNA transfection. Cell viability, migration and invasion were tested with CCK-8, wound healing and transwell assays. The levels of epithelial–mesenchymal transition (EMT) proteins were evaluated by western blotting. The ENCORI database was adopted for the analysis of the correlation between RECQL4 and serine/arginine splicing factor 1 (SRSF1) in HCC tissues. RNA immunoprecipitation and actinomycin D addition assay were employed to evaluate the combination of these two genes. SRSF1 was overexpressed to assess the biological function of HCC cells with RECQL4 silencing. Results suggested that RECQL4 was overexpressed in HCC tissues and cell lines, which was related to poor prognosis of HCC patients. RECQL4 loss-of-function repressed the proliferation, migration, invasion and EMT of HCC cells. RECQL4 was positively correlated with SRSF1 in HCC tissues. Moreover, SRSF1 was confirmed as an RNA binding protein of RECQL4. Further experiments found that SRSF1 knockdown reduced the stability of RECQL4 mRNA. Rescue assays indicated that SRSF1 overexpression crippled the braking effects of RECQL4 knockdown on the progression of HCC cells. Collectively, SRSF1 can bind to RECQL4 mRNA and enhance its stability, thereby promoting the progression of HCC.
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Affiliation(s)
- Ying Ye
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Feng Yu
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Zhao Li
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Yaping Xie
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Xiaohong Yu
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
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13
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Zhou F, Wang L, Jin K, Wu Y. RecQ-like helicase 4 (RECQL4) exacerbates resistance to oxaliplatin in colon adenocarcinoma via activation of the PI3K/AKT signaling pathway. Bioengineered 2021; 12:5859-5869. [PMID: 34477047 PMCID: PMC8806715 DOI: 10.1080/21655979.2021.1964156] [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] [Indexed: 01/12/2023] Open
Abstract
Oxaliplatin (OXA) resistance is a great challenge for colon adenocarcinoma (COAD) chemotherapy. The promoting role of RecQ-Like Helicase 4 (RECQL4) in chemoresistance to platinum-based drugs has been identified, whereas the effect and specific mechanism of RECQL4 in regulating OXA resistance within COAD have not been explicated yet. In this work, RECQL4 mRNA expression was detected by RT-qPCR. RECQL4, phosphorylated PI3K (p-PI3K), PI3K, phosphorylated AKT (p-AKT), and AKT protein expression were measured by western blotting. CCK-8, flow cytometry, wound healing, and transwell assays were utilized to analyze OXA resistance, cell proliferation, apoptosis, cell cycle, migration and invasion. Herein, we found RECQL4 was upregulated in COAD, especially in OXA-resistant COAD tissues and cells. RECQL4 overexpression facilitated proliferation and metastasis of OXA-resistant COAD cells; on the contrary, RECQL4 knockdown attenuated proliferative and metastatic capabilities in OXA-resistant COAD cells. Moreover, RECQL4 promoted OXA resistance in OXA-resistant COAD cells via activating the P13 K/AKT signaling. To sum up, the results suggest that RECQL4 depletion may be a crucial mechanism to reverse OXA resistance in COAD via inhibition of the P13 K/AKT pathway in vitro, thereby providing a novel target for overcoming OXA resistance in COAD.
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Affiliation(s)
- Fei Zhou
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, China
| | - Leiming Wang
- Department of General Surgery, The Affiliated Shuyang Hospital of Xuzhou Medical University, China
| | - Kangpeng Jin
- Department of Colorectal Surgery, Jiangsu Provincial People's Hospital, China
| | - Yang Wu
- Department of Colorectal Surgery, Jiangsu Provincial People's Hospital, China
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14
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Balajee AS. Human RecQL4 as a Novel Molecular Target for Cancer Therapy. Cytogenet Genome Res 2021; 161:305-327. [PMID: 34474412 DOI: 10.1159/000516568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/24/2021] [Indexed: 11/19/2022] Open
Abstract
Human RecQ helicases play diverse roles in the maintenance of genomic stability. Inactivating mutations in 3 of the 5 human RecQ helicases are responsible for the pathogenesis of Werner syndrome (WS), Bloom syndrome (BS), Rothmund-Thomson syndrome (RTS), RAPADILINO, and Baller-Gerold syndrome (BGS). WS, BS, and RTS patients are at increased risk for developing many age-associated diseases including cancer. Mutations in RecQL1 and RecQL5 have not yet been associated with any human diseases so far. In terms of disease outcome, RecQL4 deserves special attention because mutations in RecQL4 result in 3 autosomal recessive syndromes (RTS type II, RAPADILINO, and BGS). RecQL4, like other human RecQ helicases, has been demonstrated to play a crucial role in the maintenance of genomic stability through participation in diverse DNA metabolic activities. Increased incidence of osteosarcoma in RecQL4-mutated RTS patients and elevated expression of RecQL4 in sporadic cancers including osteosarcoma suggest that loss or gain of RecQL4 expression is linked with cancer susceptibility. In this review, current and future perspectives are discussed on the potential use of RecQL4 as a novel cancer therapeutic target.
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Affiliation(s)
- Adayabalam S Balajee
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
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15
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Chen B, Ma Y, Bi J, Wang W, He A, Su G, Zhao Z, Shi J, Zhang L. Regulation Network of Colorectal-Cancer-Specific Enhancers in the Progression of Colorectal Cancer. Int J Mol Sci 2021; 22:ijms22158337. [PMID: 34361106 PMCID: PMC8348541 DOI: 10.3390/ijms22158337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/31/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022] Open
Abstract
Enhancers regulate multiple genes via higher-order chromatin structures, and they further affect cancer progression. Epigenetic changes in cancer cells activate several cancer-specific enhancers that are silenced in normal cells. These cancer-specific enhancers are potential therapeutic targets of cancer. However, the functions and regulation networks of colorectal-cancer-specific enhancers are still unknown. In this study, we profile colorectal-cancer-specific enhancers and reveal their regulation network through the analysis of HiChIP data that were derived from a colorectal cancer cell line and Hi-C and RNA-seq data that were derived from tissue samples by in silico analysis and in vitro experiments. Enhancer-promoter loops in colorectal cancer cells containing colorectal-cancer-specific enhancers are involved in more than 50% of the topological associated domains (TADs) changed in colorectal cancer cells compared to normal colon cells. In addition, colorectal-cancer-specific enhancers interact with 152 genes that are significantly and highly expressed in colorectal cancer cells. These colorectal-cancer-specific enhancer target genes include ITGB4, RECQL4, MSLN, and GDF15. We propose that the regulation network of colorectal-cancer-specific enhancers plays an important role in the progression of colorectal cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lei Zhang
- Correspondence: ; Tel./Fax: +86-(22)-23503617
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16
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Li S, Wu H, Huang X, Jian Y, Kong L, Xu H, Ouyang Y, Chen X, Wu G, Yu L, Wang X. BOP1 confers chemoresistance of triple-negative breast cancer by promoting CBP-mediated β-catenin acetylation. J Pathol 2021; 254:265-278. [PMID: 33797754 DOI: 10.1002/path.5676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/03/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Chemoresistance is a major obstacle to the treatment of triple-negative breast cancer (TNBC), which has a poor prognosis. Increasing evidence has demonstrated the essential role of cancer stem cells (CSCs) in the process of TNBC chemoresistance. However, the underlying mechanism remains unclear. In the present study, we report that block of proliferation 1 (BOP1) serves as a key regulator of chemoresistance in TNBC. BOP1 expression was significantly upregulated in chemoresistant TNBC tissues, and high expression of BOP1 correlated with shorter overall survival and relapse-free survival in patients with TNBC. BOP1 overexpression promoted, while BOP1 downregulation inhibited the drug resistance and CSC-like phenotype of TNBC cells in vitro and in vivo. Moreover, BOP1 activated Wnt/β-catenin signaling by increasing the recruitment of cyclic AMP response element-binding protein (CBP) to β-catenin, enhancing CBP-mediated acetylation of β-catenin, and increasing the transcription of downstream stemness-related genes CD133 and ALDH1A1. Notably, treating with the β-catenin/CBP inhibitor PRI-724 induced an enhancement of chemotherapeutic response of paclitaxel in BOP1-overexpressing TNBC cells. These findings indicate that BOP1 is involved in chemoresistance development and might serve as a prognostic marker and therapeutic target in TNBC. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Siqi Li
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Haoming Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | | | - Yunting Jian
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Lingzhi Kong
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Hongyi Xu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Ouyang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Xiangfu Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Geyan Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Liang Yu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Xi Wang
- Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
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17
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Zeng B, Huang P, Du P, Sun X, Huang X, Fang X, Li L. Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer. Front Oncol 2021; 11:637431. [PMID: 33889545 PMCID: PMC8056176 DOI: 10.3389/fonc.2021.637431] [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: 12/03/2020] [Accepted: 02/10/2021] [Indexed: 01/12/2023] Open
Abstract
Esophageal squamous cell cancer (ESCC) is the eighth most common cancer around the world. Several reports have focused on somatic mutations and common germline mutations in ESCC. However, the contributions of pathogenic germline alterations in cancer susceptibility genes (CSGs), highly frequently mutated CSGs, and pathogenically mutated CSG-related pathways in ESCC remain unclear. We obtained data on 571 ESCC cases from public databases and East Asian from the 1000 Genomes Project database and the China Metabolic Analytics Project database to characterize pathogenic mutations. We detected 157 mutations in 75 CSGs, accounting for 25.0% (143/571) of ESCC cases. Six genes had more than five mutations: TP53 (n = 15 mutations), GJB2 (n = 8), BRCA2 (n = 6), RECQL4 (n = 6), MUTYH (n = 6), and PMS2 (n = 5). Our results identified significant differences in pathogenic germline mutations of TP53, BRCA2, and RECQL4 between the ESCC and control cohorts. Moreover, we identified 84 double-hit events (16 germline/somatic double-hit events and 68 somatic/somatic double-hit events) occurring in 18 tumor suppressor genes from 83 patients. Patients who had ESCC with germline/somatic double-hit events were diagnosed at younger ages than patients with the somatic/somatic double-hit events, though the correlation was not significant. Fanconi anemia was the most enriched pathway of pathogenically mutated CSGs, and it appeared to be a primary pathway for ESCC predisposition. The results of this study identified the underlying roles that pathogenic germline mutations in CSGs play in ESCC pathogenesis, increased our awareness about the genetic basis of ESCC, and provided suggestions for using highly mutated CSGs and double-hit features in the early discovery, prevention, and genetic counseling of ESCC.
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Affiliation(s)
- Bing Zeng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Peina Du
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Xiaodong Fang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Lin Li
- BGI-Shenzhen, Shenzhen, China
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18
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Du X, Zhang C, Yin C, Wang W, Yan X, Xie D, Zheng X, Zheng Q, Li M, Song Z. High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. Front Oncol 2021; 11:633899. [PMID: 33828983 PMCID: PMC8019910 DOI: 10.3389/fonc.2021.633899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Molecular mechanisms underlying the tumorigenesis of a highly malignant cancer, cholangiocarcinoma (CCA), are still obscure. In our study, the CCA expression profile data were acquired from The Cancer Genome Atlas (TCGA) database, and differentially expressed genes (DEGs) in the TCGA-Cholangiocarcinoma (TCGA-CHOL) data set were utilized to construct a co-expression network via weighted gene co-expression network analysis (WGCNA). The blue gene module associated with the histopathologic grade of CCA was screened. Then, five candidate hub genes were screened by combining the co-expression network with protein–protein interaction (PPI) network. After progression and survival analyses, bloom syndrome helicase (BLM) was ultimately identified as a real hub gene. Moreover, the receiver operating characteristic (ROC) curve analysis suggested that BLM had a favorable diagnostic and predictive recurrence value for CCA. The gene set enrichment analysis (GSEA) results for a single hub gene revealed the importance of cell cycle-related pathways in the CCA progression and prognosis. Furthermore, we detected the BLM expression in vitro, and the results demonstrated that the expression level of BLM was much higher in the CCA tissues and cells relative to adjacent non-tumor samples and normal bile duct epithelial cells. Additionally, after further silencing the BLM expression by small interfering RNA (siRNA), the proliferation and migration ability of CCA cells were all inhibited, and the cell cycle was arrested. Altogether, a real hub gene (BLM) and cell cycle-related pathways were identified in the present study, and the gene BLM may be involved in the CCA progression and could act as a reliable biomarker for potential diagnosis and prognostic evaluation.
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Affiliation(s)
- Xiaolong Du
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Zhang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuanzheng Yin
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueke Yan
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dawei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichuan Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qichang Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Li
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zifang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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19
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Lyu G, Su P, Hao X, Chen S, Ren S, Zhao Z, Gong Y, Liu Q, Shao C. RECQL4 regulates DNA damage response and redox homeostasis in esophageal cancer. Cancer Biol Med 2021; 18:120-138. [PMID: 33628589 PMCID: PMC7877169 DOI: 10.20892/j.issn.2095-3941.2020.0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Objective: RECQL4 (a member of the RECQ helicase family) upregulation has been reported to be associated with tumor progression in several malignancies. However, whether RECQL4 sustains esophageal squamous cell carcinoma (ESCC) has not been elucidated. In this study, we determined the functional role for RECQL4 in ESCC progression. Methods: RECQL4 expression in clinical samples of ESCC was examined by immunohistochemistry. Cell proliferation, cellular senescence, the epithelial-mesenchymal transition (EMT), DNA damage, and reactive oxygen species in ESCC cell lines with RECQL4 depletion or overexpression were analyzed. The levels of proteins involved in the DNA damage response (DDR), cell cycle progression, survival, and the EMT were determined by Western blot analyses. Results: RECQL4 was highly expressed in tumor tissues when compared to adjacent non-tumor tissues in ESCC (P < 0.001) and positively correlated with poor differentiation (P = 0.011), enhanced invasion (P = 0.033), and metastasis (P = 0.048). RECQL4 was positively associated with proliferation and migration in ESCC cells. Depletion of RECQL4 also inhibited growth of tumor xenografts in vivo. RECQL4 depletion induced G0/G1 phase arrest and cellular senescence. Importantly, the levels of DNA damage and reactive oxygen species were increased when RECQL4 was depleted. DDR, as measured by the activation of ATM, ATR, CHK1, and CHK2, was impaired. RECQL4 was also shown to promote the activation of AKT, ERK, and NF-kB in ESCC cells. Conclusions: The results indicated that RECQL4 was highly expressed in ESCC and played critical roles in the regulation of DDR, redox homeostasis, and cell survival.
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Affiliation(s)
- Guosheng Lyu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiaohe Hao
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Shiming Chen
- Department of Pathology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Shuai Ren
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Zixiao Zhao
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Yaoqin Gong
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Qiao Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Changshun Shao
- State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, Suzhou 215123, China
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20
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Aberrantly Expressed RECQL4 Helicase Supports Proliferation and Drug Resistance of Human Glioma Cells and Glioma Stem Cells. Cancers (Basel) 2020; 12:cancers12102919. [PMID: 33050631 PMCID: PMC7650617 DOI: 10.3390/cancers12102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Human RecQ helicases participate in DNA replication, repair and transcription. Due to important roles in many cellular processes, deregulation of these helicases in cancer could be tumour promoting. We found upregulated RECQL4 expression in highly malignant brain tumours (glioblastomas) associated with poor survival of patients. While RECQL4 depletion in human glioma cells with genetic tools slightly impaired cell viability and DNA replication, it induced gross changes in gene expression and increased sensitivity of glioma cells and glioma stem cells to chemotherapeutics. Therefore, targeting RECQL4 in deadly brain tumours could be a new strategy to improve eradication of tumour cells by chemotherapeutics. Abstract Anti-tumour therapies eliminate proliferating tumour cells by induction of DNA damage, but genomic aberrations or transcriptional deregulation may limit responses to therapy. Glioblastoma (GBM) is a malignant brain tumour, which recurs inevitably due to chemo- and radio-resistance. Human RecQ helicases participate in DNA repair, responses to DNA damage and replication stress. We explored if a helicase RECQL4 contributes to gliomagenesis and responses to chemotherapy. We found upregulated RECQL4 expression in GBMs associated with poor survival of GBM patients. Increased levels of nuclear and cytosolic RECQL4 proteins were detected in GBMs on tissue arrays and in six glioma cell lines. RECQL4 was detected both in cytoplasm and mitochondria by Western blotting and immunofluorescence. RECQL4 depletion in glioma cells with siRNAs and CRISPR/Cas9 did not affect basal cell viability, slightly impaired DNA replication, but induced profound transcriptomic changes and increased chemosensitivity of glioma cells. Sphere cultures originated from RECQL4-depleted cells had reduced sphere forming capacity, stronger responded to temozolomide upregulating cell cycle inhibitors and pro-apoptotic proteins. RECQL4 deficiency affected mitochondrial network and reduced mitochondrial membrane polarization in LN18 glioblastoma cells. We demonstrate that targeting RECQL4 overexpressed in glioblastoma could be a new strategy to sensitize glioma cells to chemotherapeutics.
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21
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Guo L, Li Y, Zhao C, Peng J, Song K, Chen L, Zhang P, Ma H, Yuan C, Yan S, Fang Y, Kong B. RECQL4, Negatively Regulated by miR-10a-5p, Facilitates Cell Proliferation and Invasion via MAFB in Ovarian Cancer. Front Oncol 2020; 10:524128. [PMID: 33014878 PMCID: PMC7500455 DOI: 10.3389/fonc.2020.524128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
The high frequency of somatic copy number alterations, as opposed to point mutations, is considered a unique feature of ovarian cancer. Amplification-dependent overexpression of RecQ protein-like 4 (RECQL4), which participates in DNA replication and repair, mediates the development of various cancers, but its pathobiological and clinical roles are poorly understood. Here, using bioinformatics analysis, RECQL4 amplification was found to occur in 27% of ovarian cancer samples in the TCGA cohort. RECQL4 was found to be upregulated and associated with a poor prognosis based on the immunohistochemistry staining of ovarian cancer. Functionally, RECQL4 overexpression increased proliferation and invasion of ovarian cancer cells. RECQL4 silencing had the opposite effects. In addition, RECQL4 knockdown enhanced the sensitivity of ovarian cancer cells to cisplatin and PARP inhibitor (PARPi). Further mechanistic investigations revealed that MAFB was a downstream target of RECQL4. The oncogenic effect of RECQL4 was attenuated after MAFB knockdown. Moreover, RECQL4 overexpression was negatively regulated by the tumor suppressor miR-10a-5p. Collectively, these findings indicate that genomic amplification and low expression of miR-10a-5p contribute to RECQL4 overexpression in ovarian cancer. This is the first study to reveal the oncogenic functions and clinical significance of RECQL4 in ovarian cancer.
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Affiliation(s)
- Li Guo
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Yingwei Li
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chen Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Long Chen
- Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Ping Zhang
- Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Hanlin Ma
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yan Fang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Next-generation sequencing identifies recurrent copy number variations in invasive breast carcinomas from Ghana. Mod Pathol 2020; 33:1537-1545. [PMID: 32152520 PMCID: PMC7390688 DOI: 10.1038/s41379-020-0515-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 01/31/2023]
Abstract
African and African-American (AA) women have higher incidence of triple-negative breast cancers (TNBC) with high histological grade and aggressive clinical behavior, but the reasons are not fully understood. We recently found that the oncogenic protein EZH2 is overexpressed in Ghanaian breast cancer patients, with 16% of the tumors expressing cytoplasmic EZH2. Understanding the molecular underpinnings of these aggressive tumors may lead to the identification of potential targetable oncogenic drivers. We characterized the copy number variations of 11 Ghanaian breast tumor patients by targeted multiplexed PCR-based DNA next-generation sequencing (NGS) over 130 cancer-relevant genes. While the DNA quality was not optimal for mutation analysis, 90% of the tumors had frequent recurrent copy number alterations (CNAs) of 17 genes: SDHC, RECQL4, TFE3, BCL11A, BCL2L1, PDGFRA, DEK, SMUG1, AKT3, SMARCA4, VHL, KLF6, CCNE1, G6PD, FGF3, ABL1, and CCND1, with the top oncogenic functions being mitotic G1-G1/S-phase regulation, gene transcription, apoptosis, and PI3K/AKT pathway. The most common recurrent high-level CNAs were gains of RECQL4 and SDHC, in 50% and 60% of cases, respectively. Network analyses revealed a significant predicted interaction among 12 of the 17 (70.6%) genes with high-level CNAs (p = 5.7E-07), which was highly correlated with EZH2 expression (r = 0.4-0.75). By immunohistochemistry, RECQL4 and SDHC proteins were upregulated in 53 of 86 (61.6%) and 48 of 86 (56%) of Ghanaian invasive carcinoma tissue samples. In conclusion, our data show that invasive carcinomas from Ghana exhibit recurrent CNAs in 17 genes, with functions in oncogenic pathways, including PI3K/AKT and G1-G1/S regulation, which may have implications for the biology and treatment of invasive carcinomas in African and AA women.
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Werner Syndrome Protein Expression in Breast Cancer. Clin Breast Cancer 2020; 21:57-73.e7. [PMID: 32919863 DOI: 10.1016/j.clbc.2020.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Werner protein (WRN) plays an important role in DNA repair, replication, transcription, and consequently genomic stability via its DNA-helicase and exonuclease activity. Loss of function of WRN is associated with Werner syndrome (WS), which is characterized by premature aging and cancer predisposition. Malignancies that are commonly linked to WS are thyroid carcinoma, melanoma, breast cancer, meningioma, and soft tissue and bone sarcomas. Currently, the clinicopathologic significance of WRN in breast cancer is largely unknown. PATIENTS AND METHODS We investigated the clinicopathologic and prognostic significance of WRN protein expression in a cohort of clinically annotated series of sporadic (n = 1650) and BRCA-mutated (n = 75) invasive breast cancers. We correlated WRN protein expression to clinicopathologic characteristics, DNA repair protein expression, and survival outcomes. RESULTS There is strong evidence of association between low nuclear and cytoplasmic WRN co-expression and low levels of KU70/KU80, DNA-PK, DNA Pol-B, CKD18, cytoplasmic RECQL4, and nuclear BLM protein expression (adjusted P-values < .05). Tumors with low nuclear or cytoplasmic WRN expression have worse overall breast cancer-specific survival (BCSS) (adjusted P-values < .05). In topoisomerase I overexpressed tumors, low WRN nuclear expression was associated with poor BCSS (P-value < .05). In BRCA-mutated tumors, low WRN cytoplasmic expression conferred shortest BCSS (P < .05). CONCLUSIONS Low WRN protein expression is associated with poor BCSS in patients with breast cancer. This can be used to optimize the risk stratification for personalized treatment.
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Miller DB, Piccolo SR. Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review. Front Genet 2020; 11:493. [PMID: 32508881 PMCID: PMC7249936 DOI: 10.3389/fgene.2020.00493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
A compound heterozygous (CH) variant is a type of germline variant that occurs when each parent donates one alternate allele and these alleles are located at different loci within the same gene. Pathogenic germline variants have been identified for some pediatric cancer types but in most studies, CH variants are overlooked. Thus, the prevalence of pathogenic CH variants in most pediatric cancer types is unknown. We identified 26 studies (published between 1999 and 2019) that identified a CH variant in at least one pediatric cancer patient. These studies encompass 21 cancer types and have collectively identified 25 different genes in which a CH variant occurred. However, the sequencing methods used and the number of patients and genes evaluated in each study were highly variable across the studies. In addition, methods for assessing pathogenicity of CH variants varied widely and were often not reported. In this review, we discuss technologies and methods for identifying CH variants, provide an overview of studies that have identified CH variants in pediatric cancer patients, provide insights into future directions in the field, and give a summary of publicly available pediatric cancer sequencing data. Although considerable insights have been gained over the last 20 years, much has yet to be learned about the involvement of CH variants in pediatric cancers. In future studies, larger sample sizes, more pediatric cancer types, and better pathogenicity assessment and filtering methods will be needed to move this field forward.
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Affiliation(s)
- Dustin B Miller
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States
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Lu L, Jin W, Wang LL. RECQ DNA Helicases and Osteosarcoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:37-54. [PMID: 32767233 DOI: 10.1007/978-3-030-43085-6_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RECQ family of DNA helicases is a conserved group of enzymes that plays an important role in maintaining genomic stability. Humans possess five RECQ helicase genes, and mutations in three of them - BLM, WRN, and RECQL4 - are associated with the genetic disorders Bloom syndrome, Werner syndrome, and Rothmund-Thomson syndrome (RTS), respectively. These syndromes share overlapping clinical features, and importantly they are all associated with an increased risk of cancer. Patients with RTS have the highest specific risk of developing osteosarcoma compared to all other cancer predisposition syndromes; therefore, RTS serves as a relevant model to study the pathogenesis and molecular genetics of osteosarcoma. The "tumor suppressor" function of the RECQ helicases continues to be an area of active investigation. This chapter will focus primarily on the known cellular functions of RECQL4 and how these may relate to tumorigenesis, as well as ongoing efforts to understand RECQL4's functions in vivo using animal models. Understanding the RECQ pathways will provide insight into avenues for novel cancer therapies in the future.
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Affiliation(s)
- Linchao Lu
- Department of Pediatrics, Section of Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Weidong Jin
- Department of Pediatrics, Section of Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lisa L Wang
- Department of Pediatrics, Section of Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Alshabi AM, Shaikh IA, Vastrad C. Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. Biomolecules 2019; 9:biom9070282. [PMID: 31311202 PMCID: PMC6681318 DOI: 10.3390/biom9070282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
: Breast cancer (BRCA) remains the leading cause of cancer morbidity and mortality worldwide. In the present study, we identified novel biomarkers expressed during estradiol and tamoxifen treatment of BRCA. The microarray dataset of E-MTAB-4975 from Array Express database was downloaded, and the differential expressed genes (DEGs) between estradiol-treated BRCA sample and tamoxifen-treated BRCA sample were identified by limma package. The pathway and gene ontology (GO) enrichment analysis, construction of protein-protein interaction (PPI) network, module analysis, construction of target genes-miRNA interaction network and target genes-transcription factor (TF) interaction network were performed using bioinformatics tools. The expression, prognostic values, and mutation of hub genes were validated by SurvExpress database, cBioPortal, and human protein atlas (HPA) database. A total of 856 genes (421 up-regulated genes and 435 down-regulated genes) were identified in T47D (overexpressing Split Ends (SPEN) + estradiol) samples compared to T47D (overexpressing Split Ends (SPEN) + tamoxifen) samples. Pathway and GO enrichment analysis revealed that the DEGs were mainly enriched in response to lysine degradation II (pipecolate pathway), cholesterol biosynthesis pathway, cell cycle pathway, and response to cytokine pathway. DEGs (MCM2, TCF4, OLR1, HSPA5, MAP1LC3B, SQSTM1, NEU1, HIST1H1B, RAD51, RFC3, MCM10, ISG15, TNFRSF10B, GBP2, IGFBP5, SOD2, DHF and MT1H) , which were significantly up- and down-regulated in estradiol and tamoxifen-treated BRCA samples, were selected as hub genes according to the results of protein-protein interaction (PPI) network, module analysis, target genes-miRNA interaction network and target genes-TF interaction network analysis. The SurvExpress database, cBioPortal, and Human Protein Atlas (HPA) database further confirmed that patients with higher expression levels of these hub genes experienced a shorter overall survival. A comprehensive bioinformatics analysis was performed, and potential therapeutic applications of estradiol and tamoxifen were predicted in BRCA samples. The data may unravel the future molecular mechanisms of BRCA.
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Affiliation(s)
- Ali Mohamed Alshabi
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, 66237, Saudi Arabia
| | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, Najran, 66237, Saudi Arabia
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, ChanabasavaNilaya, Bharthinagar, Dharwad 580001, Karnataka, India.
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Zhu X, Chen H, Yang Y, Xu C, Zhou J, Zhou J, Chen Y. Distinct prognosis of mRNA expression of the five RecQ DNA-helicase family members - RECQL, BLM, WRN, RECQL4, and RECQL5 - in patients with breast cancer. Cancer Manag Res 2018; 10:6649-6668. [PMID: 30584360 PMCID: PMC6287649 DOI: 10.2147/cmar.s185769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Five RecQ helicase family members have a role in maintaining genome stability. However, their prognostic roles in breast cancer remain unknown. We aimed to investigate the prognostic values of the RecQ family and clinical outcomes in breast cancer. Methods We used the Kaplan-Meier Plotter database (http://kmplot.com/analysis) to analyze prognostic values of RecQ-family mRNA expression in all breast cancers and in different intrinsic subtypes and clinicopathological characteristics. Protein-expression levels of WRN and RECQL4 were confirmed by immunohistochemistry (IHC) in breast cancer tissues. Results Increased expression of RECQL mRNA was significantly associated with reduced relapse-free survival (RFS) and postprogression survival (PPS) in all breast cancers, and improved overall survival (OS) in patients with basal-like breast cancer and in mutant-p53-type breast cancer patients. Increased expression of BLM mRNA was correlated with reduced distant metastasis-free survival (DMFS) in all patients. Increased expression of WRN mRNA was associated with improved OS and RFS in breast cancer patients. Increased expression of RECQL4 mRNA was associated with reduced OS, DMFS, and RFS in all breast cancers, and with reduced OS in patients with luminal A, HER2-positive, ER-positive, and PR-positive breast cancer. Increased expression of RECQL5 mRNA was associated with improved RFS in all patients, and with improved OS in patients with lymph-node-negative breast cancer, but with reduced OS in patients with HER2-positive breast cancer. IHC staining confirmed that high expression of WRN was correlated with increased OS and high expression of RECQL4 associated with reduced OS at protein levels. Conclusion mRNA-expression levels of RecQ members were significantly correlated with prognosis in breast cancer patients. These preliminary findings require further study to determine whether RecQ-targeting reagents might be developed for clinical application in breast cancer.
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Affiliation(s)
- Xuan Zhu
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China, .,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China,
| | - Huihui Chen
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China,
| | - Yi Yang
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China, .,Department of Breast Surgery, Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, People's Republic of China
| | - Chunjing Xu
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China, .,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China,
| | - Jun Zhou
- Department of Breast Surgery, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaojiao Zhou
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China, .,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China,
| | - Yiding Chen
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China, .,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China,
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Chen H, Yuan K, Wang X, Wang H, Wu Q, Wu X, Peng J. Overexpression of RECQL4 is associated with poor prognosis in patients with gastric cancer. Oncol Lett 2018; 16:5419-5425. [PMID: 30250613 DOI: 10.3892/ol.2018.9318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 07/30/2018] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to investigate the expression, clinical association, and prognosis of RecQ protein-like 4 (RECQL4) protein in human gastric cancers (GCs). The expression levels and prognostic value of RECQL4 were initially predicted by using bioinformatics. GC specimens and matched normal gastric tissues were evaluated by immunohistochemistry (IHC), and patient clinicopathological parameters and survival times were analyzed. Multivariate Cox analysis was used to determine the prognostic role of RECQL4 expression. The Oncomine database predicted that RECQL4 mRNA expression levels were significantly increased in GCs as compared with those in normal gastric tissues (P<0.05) and that patients with increased RECQL4 mRNA expression levels had significantly lower overall survival (OS) (P<0.001). The results of IHC showed that the positive rate of RECQL4 in the GC samples was significantly higher than that in the normal gastric mucosa specimens (P<0.05). RECQL4 expression was positively associated with depth of invasion and TNM (P<0.05). High RECQL4 expression in GC samples was significantly associated with poor OS (P=0.024). Positive RECQL4 expression, depth of invasion, lymphatic invasion, and TNM staging were independent factors for predicting worse OS rates by using multivariate analysis. Compared with expression levels in normal gastric tissues, RECQL4 was significantly overexpressed in GC samples, and increased RECQL4 expression was an independent predictor of poor prognosis in GC patients.
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Affiliation(s)
- Honglei Chen
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Kaitao Yuan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong 510080, P.R. China
| | - Xinyou Wang
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Huashe Wang
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Qiuning Wu
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xiaobin Wu
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Junsheng Peng
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
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Emerging functional markers for cancer stem cell-based therapies: Understanding signaling networks for targeting metastasis. Semin Cancer Biol 2018; 53:90-109. [PMID: 29966677 DOI: 10.1016/j.semcancer.2018.06.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
Metastasis is one of the most challenging issues in cancer patient management, and effective therapies to specifically target disease progression are missing, emphasizing the urgent need for developing novel anti-metastatic therapeutics. Cancer stem cells (CSCs) gained fast attention as a minor population of highly malignant cells within liquid and solid tumors that are responsible for tumor onset, self-renewal, resistance to radio- and chemotherapies, and evasion of immune surveillance accelerating recurrence and metastasis. Recent progress in the identification of their phenotypic and molecular characteristics and interactions with the tumor microenvironment provides great potential for the development of CSC-based targeted therapies and radical improvement in metastasis prevention and cancer patient prognosis. Here, we report on newly uncovered signaling mechanisms controlling CSC's aggressiveness and treatment resistance, and CSC-specific agents and molecular therapeutics, some of which are currently under investigation in clinical trials, gearing towards decisive functional CSC intrinsic or surface markers. One special research focus rests upon subverted regulatory pathways such as insulin-like growth factor 1 receptor signaling and its interactors in metastasis-initiating cell populations directly related to the gain of stem cell- and EMT-associated properties, as well as key components of the E2F transcription factor network regulating metastatic progression, microenvironmental changes, and chemoresistance. In addition, the study provides insight into systems biology tools to establish complex molecular relationships behind the emergence of aggressive phenotypes from high-throughput data that rely on network-based analysis and their use to investigate immune escape mechanisms or predict clinical outcome-relevant CSC receptor signaling signatures. We further propose that customized vector technologies could drastically enhance systemic drug delivery to target sites, and summarize recent progress and remaining challenges. This review integrates available knowledge on CSC biology, computational modeling approaches, molecular targeting strategies, and delivery techniques to envision future clinical therapies designed to conquer metastasis-initiating cells.
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30
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Mo D, Zhao Y, Balajee AS. Human RecQL4 helicase plays multifaceted roles in the genomic stability of normal and cancer cells. Cancer Lett 2017; 413:1-10. [PMID: 29080750 DOI: 10.1016/j.canlet.2017.10.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 02/06/2023]
Abstract
Human RecQ helicases that share homology with E. coli RecQ helicase play critical roles in diverse biological activities such as DNA replication, transcription, recombination and repair. Mutations in three of the five human RecQ helicases (RecQ1, WRN, BLM, RecQL4 and RecQ5) result in autosomal recessive syndromes characterized by accelerated aging symptoms and cancer incidence. Mutational inactivation of Werner (WRN) and Bloom (BLM) genes results in Werner syndrome (WS) and Bloom syndrome (BS) respectively. However, mutations in RecQL4 result in three human disorders: (I) Rothmund-Thomson syndrome (RTS), (II) RAPADILINO and (III) Baller-Gerold syndrome (BGS). Cells from WS, BS and RTS are characterized by a unique chromosomal anomaly indicating that each of the RecQ helicases performs specialized function(s) in a non-redundant manner. Elucidating the biological functions of RecQ helicases will enable us to understand not only the aging process but also to determine the cause for age-associated human diseases. Recent biochemical and molecular studies have given new insights into the multifaceted roles of RecQL4 that range from genomic stability to carcinogenesis and beyond. This review summarizes some of the existing and emerging knowledge on diverse biological functions of RecQL4 and its significance as a potential molecular target for cancer therapy.
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Affiliation(s)
- Dongliang Mo
- Chinese Academy of Science, Beijing Institute of Genomics, Beijing CN 100029, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongliang Zhao
- Chinese Academy of Science, Beijing Institute of Genomics, Beijing CN 100029, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Adayabalam S Balajee
- Radiation Emergency Assistance Center and Training Site, Oak Ridge Associated Universities, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA.
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31
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Pützer BM, Solanki M, Herchenröder O. Advances in cancer stem cell targeting: How to strike the evil at its root. Adv Drug Deliv Rev 2017; 120:89-107. [PMID: 28736304 DOI: 10.1016/j.addr.2017.07.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/10/2017] [Accepted: 07/16/2017] [Indexed: 12/18/2022]
Abstract
Cancer progression to metastatic stages is still unmanageable and the promise of effective anti-metastatic therapy remains largely unmet, emphasizing the need to develop novel therapeutics. The special focus here is on cancer stem cells (CSC) as the seed of tumor initiation, epithelial-mesenchymal transition, chemoresistance and, as a consequence, drivers of metastatic dissemination. We report on targeted therapies gearing towards the CSC's internal and membrane-anchored markers using agents such as antibody derivatives, nucleic therapeutics, small molecules and genetic payloads. Another emphasis lies on novel proceedings envisaged to deliver current and prospective therapies to the target sites using newest viral and non-viral vector technologies. In this review, we summarize recent progress and remaining challenges in therapeutic strategies to combat CSC.
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Affiliation(s)
- Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Biomedical Research Center (BMFZ), Rostock University Medical School, Germany.
| | - Manish Solanki
- Institute of Experimental Gene Therapy and Cancer Research, Biomedical Research Center (BMFZ), Rostock University Medical School, Germany
| | - Ottmar Herchenröder
- Institute of Experimental Gene Therapy and Cancer Research, Biomedical Research Center (BMFZ), Rostock University Medical School, Germany
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Abstract
Tumor syndromes, including bone neoplasias, are genetic predisposing conditions characterized by the development of a pattern of malignancies within a family at an early age of onset. Occurrence of bilateral, multifocal, or metachronous neoplasias and specific histopathologic findings suggest a genetic predisposition syndrome. Additional clinical features not related to the neoplasia can be a hallmark of specific genetic syndromes. Mostly, those diseases have an autosomal dominant pattern of inheritance with variable percentage of penetrance. Some syndromic disorders with an increased tumor risk may show an autosomal recessive transmission or are related to somatic mosaicism. Many genetic tumor syndromes are known. This update is specifically focused on syndromes predisposing to osteosarcoma and chondrosarcoma.
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Affiliation(s)
- Maria Gnoli
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopedic Institute, Via Pupilli 1, Bologna 40136, Italy.
| | - Francesca Ponti
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopedic Institute, Via Pupilli 1, Bologna 40136, Italy
| | - Luca Sangiorgi
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopedic Institute, Via Pupilli 1, Bologna 40136, Italy
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Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. Sci Rep 2017; 7:641. [PMID: 28377632 PMCID: PMC5428069 DOI: 10.1038/s41598-017-00219-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/14/2017] [Indexed: 02/03/2023] Open
Abstract
Identification of driver genes contributes to the understanding of cancer etiology and is imperative for the development of individualized therapies. Gene amplification is a major event in oncogenesis. Driver genes with tumor-specific amplification-dependent overexpression can be therapeutic targets. In this study, we aimed to identify amplification-dependent driver genes in 1,454 solid tumors, across more than 15 cancer types, by integrative analysis of gene expression and copy number. Amplification-dependent overexpression of 64 known driver oncogenes were found in 587 tumors (40%); genes frequently observed were MYC (25%) and MET (18%) in colorectal cancer; SKP2 (21%) in lung squamous cell carcinoma; HIST1H3B (19%) and MYCN (13%) in liver cancer; KIT (57%) in gastrointestinal stromal tumors; and FOXL2 (12%) in squamous cell carcinoma across tissues. Genomic aberrations in 138 known cancer driver genes and 491 established fusion genes were found in 1,127 tumors (78%). Further analyses of 820 cancer-related genes revealed 16 as potential driver genes, with amplification-dependent overexpression restricted to the remaining 22% of samples (327 tumors) initially undetermined genetic drivers. Among them, AXL, which encodes a receptor tyrosine kinase, was recurrently overexpressed and amplified in sarcomas. Our studies of amplification-dependent overexpression identified potential drug targets in individual tumors.
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Green AR, Aleskandarany MA, Ali R, Hodgson EG, Atabani S, De Souza K, Rakha EA, Ellis IO, Madhusudan S. Clinical Impact of Tumor DNA Repair Expression and T-cell Infiltration in Breast Cancers. Cancer Immunol Res 2017; 5:292-299. [PMID: 28254786 DOI: 10.1158/2326-6066.cir-16-0195] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/22/2016] [Accepted: 02/20/2017] [Indexed: 11/16/2022]
Abstract
Impaired DNA repair drives mutagenicity, which increases neoantigen load and immunogenicity. We investigated the expression of proteins involved in the DNA damage response (ATM, Chk2), double-strand break repair (BRCA1, BLM, WRN, RECQL4, RECQL5, TOPO2A, DNA-PKcs, Ku70/Ku80), nucleotide excision repair (ERCC1), base excision repair (XRCC1, pol β, FEN1, PARP1), and immune responses (CD8, PD-1, PD-L1, FOXP3) in 1,269 breast cancers and validated our findings in an independent estrogen receptor-negative (ER-) cohort (n = 279). Patients with tumors that expressed low XRCC1, low ATM, and low BRCA1 were not only associated with high numbers of CD8+ tumor-infiltrating lymphocytes, but were also linked to higher grades, high proliferation indexes, presence of dedifferentiated cells, ER- cells, and poor survival (all P ≤ 0.01). PD-1+ or PD-L1+ breast cancers with low XRCC1 were also linked to an aggressive phenotype that was high grade, had high proliferation indexes, contained dedifferentiated cells and ER- (all with P values ≤ 0.01), and poor survival (P = 0.00021 and P = 0.00022, for PD-1+ and PD-L1+ cancers, respectively) including in an independent ER- validation cohort (P = 0.007 and P = 0.047, respectively). We conclude that the interplay between DNA repair, CD8, PD-L1, and PD-1 can promote aggressive tumor phenotypes. XRCC1-directed personalization of immune checkpoint inhibitor therapy may be feasible and warrants further investigation in breast cancer. Cancer Immunol Res; 5(4); 292-9. ©2017 AACR.
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Affiliation(s)
- Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Mohammed A Aleskandarany
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Reem Ali
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Eleanor Grace Hodgson
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Suha Atabani
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Karen De Souza
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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Kim YC, Soliman AS, Cui J, Ramadan M, Hablas A, Abouelhoda M, Hussien N, Ahmed O, Zekri ARN, Seifeldin IA, Wang SM. Unique Features of Germline Variation in Five Egyptian Familial Breast Cancer Families Revealed by Exome Sequencing. PLoS One 2017; 12:e0167581. [PMID: 28076423 PMCID: PMC5226826 DOI: 10.1371/journal.pone.0167581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/16/2016] [Indexed: 12/31/2022] Open
Abstract
Genetic predisposition increases the risk of familial breast cancer. Recent studies indicate that genetic predisposition for familial breast cancer can be ethnic-specific. However, current knowledge of genetic predisposition for the disease is predominantly derived from Western populations. Using this existing information as the sole reference to judge the predisposition in non-Western populations is not adequate and can potentially lead to misdiagnosis. Efforts are required to collect genetic predisposition from non-Western populations. The Egyptian population has high genetic variations in reflecting its divergent ethnic origins, and incident rate of familial breast cancer in Egypt is also higher than the rate in many other populations. Using whole exome sequencing, we investigated genetic predisposition in five Egyptian familial breast cancer families. No pathogenic variants in BRCA1, BRCA2 and other classical breast cancer-predisposition genes were present in these five families. Comparison of the genetic variants with those in Caucasian familial breast cancer showed that variants in the Egyptian families were more variable and heterogeneous than the variants in Caucasian families. Multiple damaging variants in genes of different functional categories were identified either in a single family or shared between families. Our study demonstrates that genetic predisposition in Egyptian breast cancer families may differ from those in other disease populations, and supports a comprehensive screening of local disease families to determine the genetic predisposition in Egyptian familial breast cancer.
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Affiliation(s)
- Yeong C. Kim
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amr S. Soliman
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail: (ASS); (SMW)
| | - Jian Cui
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mohamed Ramadan
- Gharbiah Cancer Society, Gharbiah Population-based Registry, Tanta, Egypt
| | - Ahmed Hablas
- Gharbiah Cancer Society, Gharbiah Population-based Registry, Tanta, Egypt
| | | | - Nehal Hussien
- Egypt National Cancer Institute, Cairo University, Giza, Egypt
| | - Ola Ahmed
- Egypt National Cancer Institute, Cairo University, Giza, Egypt
| | | | | | - San Ming Wang
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail: (ASS); (SMW)
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36
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Mojumdar A, De March M, Marino F, Onesti S. The Human RecQ4 Helicase Contains a Functional RecQ C-terminal Region (RQC) That Is Essential for Activity. J Biol Chem 2016; 292:4176-4184. [PMID: 27998982 DOI: 10.1074/jbc.m116.767954] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/18/2016] [Indexed: 11/06/2022] Open
Abstract
RecQ helicases are essential in the maintenance of genome stability. Five paralogues (RecQ1, Bloom, Werner, RecQ4, and RecQ5) are found in human cells, with distinct but overlapping roles. Mutations in human RecQ4 give rise to three distinct genetic disorders (Rothmund-Thomson, RAPADILINO, and Baller-Gerold syndromes), characterized by genetic instability, growth deficiency, and predisposition to cancer. Previous studies suggested that RecQ4 was unique because it did not seem to contain a RecQ C-terminal region (RQC) found in the other RecQ paralogues; such a region consists of a zinc domain and a winged helix domain and plays an important role in enzyme activity. However, our recent bioinformatic analysis identified in RecQ4 a putative RQC. To experimentally confirm this hypothesis, we report the purification and characterization of the catalytic core of human RecQ4. Inductively coupled plasma-atomic emission spectrometry detected the unusual presence of two zinc clusters within the zinc domain, consistent with the bioinformatic prediction. Analysis of site-directed mutants, targeting key RQC residues (putative zinc ligands and the aromatic residue predicted to be at the tip of the winged helix β-hairpin), showed a decrease in DNA binding, unwinding, and annealing, as expected for a functional RQC domain. Low resolution structural information obtained by small angle X-ray scattering data suggests that RecQ4 interacts with DNA in a manner similar to RecQ1, whereas the winged helix domain may assume alternative conformations, as seen in the bacterial enzymes. These combined results experimentally confirm the presence of a functional RQC domain in human RecQ4.
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Affiliation(s)
- Aditya Mojumdar
- From the Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy and.,the Dipartimento di Scienze della Vita, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Matteo De March
- From the Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy and
| | - Francesca Marino
- From the Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy and
| | - Silvia Onesti
- From the Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy and
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Arora A, Parvathaneni S, Aleskandarany MA, Agarwal D, Ali R, Abdel-Fatah T, Green AR, Ball GR, Rakha EA, Ellis IO, Sharma S, Madhusudan S. Clinicopathological and Functional Significance of RECQL1 Helicase in Sporadic Breast Cancers. Mol Cancer Ther 2016; 16:239-250. [PMID: 27837030 DOI: 10.1158/1535-7163.mct-16-0290] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/14/2016] [Accepted: 11/01/2016] [Indexed: 01/16/2023]
Abstract
RECQL1, a key member of the RecQ family of DNA helicases, is required for DNA replication and DNA repair. Two recent studies have shown that germline RECQL1 mutations are associated with increased breast cancer susceptibility. Whether altered RECQL1 expression has clinicopathologic significance in sporadic breast cancers is unknown. We evaluated RECQL1 at the transcriptomic level (METABRIC cohort, n = 1,977) and at the protein level [cohort 1, n = 897; cohort 2, n = 252; cohort 3 (BRCA germline deficient), n = 74]. In RECQL1-depleted breast cancer cells, we investigated anthracycline sensitivity. High RECQL1 mRNA was associated with intClust.3 (P = 0.026), which is characterized by low genomic instability. On the other hand, low RECQL1 mRNA was linked to intClust.8 [luminal A estrogen receptor-positive (ER+) subgroup; P = 0.0455] and intClust.9 (luminal B ER+ subgroup; P = 0.0346) molecular phenotypes. Low RECQL1 expression was associated with shorter breast cancer-specific survival (P = 0.001). At the protein level, low nuclear RECQL1 level was associated with larger tumor size, lymph node positivity, high tumor grade, high mitotic index, pleomorphism, dedifferentiation, ER negativity, and HER-2 overexpression (P < 0.05). In ER+ tumors that received endocrine therapy, low RECQL1 was associated with poor survival (P = 0.008). However, in ER- tumors that received anthracycline-based chemotherapy, high RECQL1 was associated with poor survival (P = 0.048). In RECQL1-depleted breast cancer cell lines, we confirmed doxorubicin sensitivity, which was associated with DNA double-strand breaks accumulation, S-phase cell-cycle arrest, and apoptosis. We conclude that RECQL1 has prognostic and predictive significance in breast cancers. Mol Cancer Ther; 16(1); 239-50. ©2016 AACR.
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Affiliation(s)
- Arvind Arora
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC
| | - Mohammed A Aleskandarany
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham, United Kingdom
| | - Reem Ali
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Tarek Abdel-Fatah
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Graham R Ball
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham, United Kingdom
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC.
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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38
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Mo D, Fang H, Niu K, Liu J, Wu M, Li S, Zhu T, Aleskandarany MA, Arora A, Lobo DN, Madhusudan S, Balajee AS, Chi Z, Zhao Y. Human Helicase RECQL4 Drives Cisplatin Resistance in Gastric Cancer by Activating an AKT-YB1-MDR1 Signaling Pathway. Cancer Res 2016; 76:3057-66. [PMID: 27013200 DOI: 10.1158/0008-5472.can-15-2361] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/14/2016] [Indexed: 11/16/2022]
Abstract
Elevation of the DNA-unwinding helicase RECQL4, which participates in various DNA repair pathways, has been suggested to contribute to the pathogenicity of various human cancers, including gastric cancer. In this study, we addressed the prognostic and chemotherapeutic significance of RECQL4 in human gastric cancer, which has yet to be determined. We observed significant increases in RECQL4 mRNA or protein in >70% of three independent sets of human gastric cancer specimens examined, relative to normal gastric tissues. Strikingly, high RECQL4 expression in primary tumors correlated well with poor survival and gastric cancer lines with high RECQL4 expression displayed increased resistance to cisplatin treatment. Mechanistic investigations revealed a novel role for RECQL4 in transcriptional regulation of the multidrug resistance gene MDR1, through a physical interaction with the transcription factor YB1. Notably, ectopic expression of RECQL4 in cisplatin-sensitive gastric cancer cells with low endogenous RECQL4 was sufficient to render them resistant to cisplatin, in a manner associated with YB1 elevation and MDR1 activation. Conversely, RECQL4 silencing in cisplatin-resistant gastric cancer cells with high endogenous RECQL4 suppressed YB1 phosphorylation, reduced MDR1 expression, and resensitized cells to cisplatin. In establishing RECQL4 as a critical mediator of cisplatin resistance in gastric cancer cells, our findings provide a therapeutic rationale to target RECQL4 or the downstream AKT-YB1-MDR1 axis to improve gastric cancer treatment. Cancer Res; 76(10); 3057-66. ©2016 AACR.
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Affiliation(s)
- Dongliang Mo
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. University of Chinese Academy of Sciences, Beijing, China
| | - Hongbo Fang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Kaifeng Niu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. University of Chinese Academy of Sciences, Beijing, China
| | - Jing Liu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. University of Chinese Academy of Sciences, Beijing, China
| | - Meng Wu
- Biological Institute, Hebei Academy of Sciences, Shijiazhuang, China
| | - Shiyou Li
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Tienian Zhu
- Department of Medical Oncology, Bethune International Peace Hospital, Shijiazhuang, China
| | - Mohammed A Aleskandarany
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, City Hospital Campus, Nottingham, United Kingdom
| | - Arvind Arora
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, City Hospital Campus, Nottingham, United Kingdom
| | - Dileep N Lobo
- Gastrointestinal Surgery, National Institute for Health Research Nottingham Digestive Diseases Centre, Biomedical Research Unit, Nottingham University Hospitals and University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, City Hospital Campus, Nottingham, United Kingdom
| | - Adayabalam S Balajee
- REAC/TS, Oak Ridge Associated Universities, Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Zhenfen Chi
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
| | - Yongliang Zhao
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
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