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Li Y, Zhou C, Wang G, Xin H, Xiao Y, Qin C. Identification and validation of the role of ZNF281 in 5-fluorouracil chemotherapy of gastric cancer. J Cancer Res Clin Oncol 2024; 150:307. [PMID: 38880820 PMCID: PMC11180638 DOI: 10.1007/s00432-024-05838-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND The early diagnosis of gastric cancer (GC) and overcoming chemotherapy resistance is challenging. The aberrant expression of zinc finger protein 281 (ZNF281) and the over-activation of the Wnt/β-catenin pathway are oncogenic factors and confer tumor chemoresistance. ZNF281 modulates the Wnt/β-catenin pathway to influence malignant tumor behavior. However, the role of ZNF281 in GC chemotherapy and the relationship with the Wnt/β-catenin pathway have not been elucidated by researchers. METHODS We explored differences in ZNF281 expression in Pan-cancer and normal tissues, the effect of its expression on prognosis of patients treated with 5-fluorouracil (5-FU). Cox regression was utilized to determine whether ZNF281 is an independent prognostic factor. Enrichment analysis was performed to explore the mechanism underlying ZNF281's role in 5-FU treatment. We assessed the relationship between ZNF281 and the tumour microenvironment (TME) and combined bulk-RNA and single-cell RNA data to analyse the relationship between ZNF281 and immune infiltration. In vitro experiments verified the effects of ZNF281 knockdown on proliferation, invasion, migration, apoptosis, DNA damage of GC cells with 5-FU treated and the Wnt/β-catenin pathway proteins. RESULTS ZNF281 was highly expressed in seven cancers and correlates with the prognosis. It is an independent prognostic factor in 5-FU treatment. ZNF281 correlates with TME score, CD8T cell abundance. ZNF281 is primarily associated with DNA repair and the Wnt/β-catenin pathway. ZNF281 knockdown enhanced the effect of 5-FU on phenotypes of GC cells. CONCLUSION We identified and verified ZNF281 as one of the potential influencing factors of 5-FU treatment in GC and may be associated with the Wnt/β-catenin pathway. Low ZNF281 may contribute to improved 5-FU sensitivity in GC patients.
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Affiliation(s)
- Yifan Li
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China
| | - Chengying Zhou
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China
| | - Guoxu Wang
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China
| | - Huiru Xin
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China
| | - Yafei Xiao
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China
| | - Changjiang Qin
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan Province, China.
- Key Laboratory of Inflammatory Diseases and Immunoregulation, Henan Provincial Health Commission, Kaifeng, China.
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Hatakeyama K, Muramatsu K, Nagashima T, Ichida H, Kawanishi Y, Fukumura R, Ohshima K, Shimoda Y, Ohnami S, Ohnami S, Maruyama K, Naruoka A, Kenmotsu H, Urakami K, Akiyama Y, Sugino T, Yamaguchi K. Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer with low tumor content. Sci Rep 2024; 14:13699. [PMID: 38871991 DOI: 10.1038/s41598-024-64541-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
The detection of copy number variations (CNVs) and somatic mutations in cancer is important for the selection of specific drugs for patients with cancer. In cancers with sporadic tumor cells, low tumor content prevents the accurate detection of somatic alterations using targeted sequencing. To efficiently identify CNVs, we performed tumor cell enrichment using tissue suspensions of formalin-fixed paraffin-embedded (FFPE) tissue sections with low tumor cell content. Tumor-enriched and residual fractions were separated from FFPE tissue suspensions of intestinal and diffuse-type gastric cancers containing sporadic tumor cells, and targeted sequencing was performed on 225 cancer-related genes. Sequencing of a targeted panel of cancer-related genes using tumor-enriched fractions increased the number of detectable CNVs and the copy number of amplified genes. Furthermore, CNV analysis using the normal cell-enriched residual fraction as a reference for CNV scoring allowed targeted sequencing to detect CNV characteristics of diffuse-type gastric cancer with low tumor content. Our approach improves the CNV detection rate in targeted sequencing with tumor enrichment and the accuracy of CNV detection in archival samples without paired blood.
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Affiliation(s)
- Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Koji Muramatsu
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Hiroyuki Ichida
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuichi Kawanishi
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ryutaro Fukumura
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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3
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Kalli M, Poskus MD, Stylianopoulos T, Zervantonakis IK. Beyond matrix stiffness: targeting force-induced cancer drug resistance. Trends Cancer 2023; 9:937-954. [PMID: 37558577 PMCID: PMC10592424 DOI: 10.1016/j.trecan.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
During tumor progression, mechanical abnormalities in the tumor microenvironment (TME) trigger signaling pathways in cells that activate cellular programs, resulting in tumor growth and drug resistance. In this review, we describe mechanisms of action for anti-cancer therapies and mechanotransduction programs that regulate cellular processes, including cell proliferation, apoptosis, survival and phenotype switching. We discuss how the therapeutic response is impacted by the three main mechanical TME abnormalities: high extracellular matrix (ECM) composition and stiffness; interstitial fluid pressure (IFP); and elevated mechanical forces. We also review drugs that normalize these abnormalities or block mechanosensors and mechanotransduction pathways. Finally, we discuss current challenges and perspectives for the development of new strategies targeting mechanically induced drug resistance in the clinic.
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Affiliation(s)
- Maria Kalli
- Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
| | - Matthew D Poskus
- Department of Bioengineering and Hillman Cancer Center, University of Pittsburgh, PA, USA
| | - Triantafyllos Stylianopoulos
- Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus.
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4
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Fenech MF, Bull CF, Van Klinken BJW. Protective Effects of Micronutrient Supplements, Phytochemicals and Phytochemical-Rich Beverages and Foods Against DNA Damage in Humans: A Systematic Review of Randomized Controlled Trials and Prospective Studies. Adv Nutr 2023; 14:1337-1358. [PMID: 37573943 PMCID: PMC10721466 DOI: 10.1016/j.advnut.2023.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023] Open
Abstract
Accumulation of deoxyribonucleic acid (DNA) damage diminishes cellular health, increases risk of developmental and degenerative diseases, and accelerates aging. Optimizing nutrient intake can minimize accrual of DNA damage. The objectives of this review are to: 1) assemble and systematically analyze high-level evidence for the effect of supplementation with micronutrients and phytochemicals on baseline levels of DNA damage in humans, and 2) use this knowledge to identify which of these essential micronutrients or nonessential phytochemicals promote DNA integrity in vivo in humans. We conducted systematic literature searches of the PubMed database to identify interventional, prospective, cross-sectional, or in vitro studies that explored the association between nutrients and established biomarkers of DNA damage associated with developmental and degenerative disease risk. Biomarkers included lymphocyte chromosome aberrations, lymphocyte and buccal cell micronuclei, DNA methylation, lymphocyte/leukocyte DNA strand breaks, DNA oxidation, telomere length, telomerase activity, and mitochondrial DNA mutations. Only randomized, controlled interventions and uncontrolled longitudinal intervention studies conducted in humans were selected for evaluation and data extraction. These studies were ranked for the quality of their study design. In all, 96 of the 124 articles identified reported studies that achieved a quality assessment score ≥ 5 (from a maximum score of 7) and were included in the final review. Based on these studies, nutrients associated with protective effects included vitamin A and its precursor β-carotene, vitamins C, E, B1, B12, folate, minerals selenium and zinc, and phytochemicals such as curcumin (with piperine), lycopene, and proanthocyanidins. These findings highlight the importance of nutrients involved in (i) DNA metabolism and repair (folate, vitamin B12, and zinc) and (ii) prevention of oxidative stress and inflammation (vitamins A, C, E, lycopene, curcumin, proanthocyanidins, selenium, and zinc). Supplementation with certain micronutrients and their combinations may reduce DNA damage and promote cellular health by improving the maintenance of genome integrity.
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Affiliation(s)
- Michael F Fenech
- Molecular Diagnostics Solutions, CSIRO Health & Biosecurity, Adelaide, South Australia, Australia; Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, South Australia, Australia; Genome Health Foundation, North Brighton, South Australia, Australia.
| | - Caroline F Bull
- Molecular Diagnostics Solutions, CSIRO Health & Biosecurity, Adelaide, South Australia, Australia; School of Molecular and Biomedical Sciences, University of Adelaide, North Terrace, Adelaide, South Australia, Australia.
| | - B Jan-Willem Van Klinken
- GSK Consumer Healthcare (now named Haleon), Warren, New Jersey, USA; Brightseed, San Francisco, CA, United States.
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5
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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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Otahalova B, Volkova Z, Soukupova J, Kleiblova P, Janatova M, Vocka M, Macurek L, Kleibl Z. Importance of Germline and Somatic Alterations in Human MRE11, RAD50, and NBN Genes Coding for MRN Complex. Int J Mol Sci 2023; 24:ijms24065612. [PMID: 36982687 PMCID: PMC10051278 DOI: 10.3390/ijms24065612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The MRE11, RAD50, and NBN genes encode for the nuclear MRN protein complex, which senses the DNA double strand breaks and initiates the DNA repair. The MRN complex also participates in the activation of ATM kinase, which coordinates DNA repair with the p53-dependent cell cycle checkpoint arrest. Carriers of homozygous germline pathogenic variants in the MRN complex genes or compound heterozygotes develop phenotypically distinct rare autosomal recessive syndromes characterized by chromosomal instability and neurological symptoms. Heterozygous germline alterations in the MRN complex genes have been associated with a poorly-specified predisposition to various cancer types. Somatic alterations in the MRN complex genes may represent valuable predictive and prognostic biomarkers in cancer patients. MRN complex genes have been targeted in several next-generation sequencing panels for cancer and neurological disorders, but interpretation of the identified alterations is challenging due to the complexity of MRN complex function in the DNA damage response. In this review, we outline the structural characteristics of the MRE11, RAD50 and NBN proteins, the assembly and functions of the MRN complex from the perspective of clinical interpretation of germline and somatic alterations in the MRE11, RAD50 and NBN genes.
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Affiliation(s)
- Barbora Otahalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University in Prague, 12800 Prague, Czech Republic
| | - Zuzana Volkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine and General University Hospital in Prague, 12853 Prague, Czech Republic
- Correspondence: ; Tel.: +420-22496-4287
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7
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DNA Damage and Its Role in Cancer Therapeutics. Int J Mol Sci 2023; 24:ijms24054741. [PMID: 36902170 PMCID: PMC10003233 DOI: 10.3390/ijms24054741] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
DNA damage is a double-edged sword in cancer cells. On the one hand, DNA damage exacerbates gene mutation frequency and cancer risk. Mutations in key DNA repair genes, such as breast cancer 1 (BRCA1) and/or breast cancer 2 (BRCA2), induce genomic instability and promote tumorigenesis. On the other hand, the induction of DNA damage using chemical reagents or radiation kills cancer cells effectively. Cancer-burdening mutations in key DNA repair-related genes imply relatively high sensitivity to chemotherapy or radiotherapy because of reduced DNA repair efficiency. Therefore, designing specific inhibitors targeting key enzymes in the DNA repair pathway is an effective way to induce synthetic lethality with chemotherapy or radiotherapy in cancer therapeutics. This study reviews the general pathways involved in DNA repair in cancer cells and the potential proteins that could be targeted for cancer therapeutics.
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8
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Yi Q, Feng J, Liao Y, Sun W. Circular RNAs in chemotherapy resistance of lung cancer and their potential therapeutic application. IUBMB Life 2023; 75:225-237. [PMID: 35594011 DOI: 10.1002/iub.2624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Lung cancer is one of the high malignancy-related incidence and mortality worldwide, accounting for about 13% of total cancer diagnoses. Currently, the use of anti-cancer agents is still the main therapeutic method for lung cancer. However, cancer cells will gradually show resistance to these drugs with the progress of treatment. And the molecular mechanisms underlying chemotherapy agents resistance remain unclear. circRNAs are newly identified noncoding RNAs molecules with covalently closed circular structures. Previous studies have shown that circRNAs are associated with tumorigenesis and progression of various cancers, including lung cancer. Recently, growing reports have suggested that circRNAs could contribute to drug resistance of lung cancer cell through different mechanisms. Therefore, in this review, we summarized the functions and underlying mechanisms of circRNAs in regulating chemoresistance of lung cancer and discussed their potential applications for diagnosis, prognosis, and treatment of lung cancer.
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Affiliation(s)
- Qian Yi
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yi Liao
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Weichao Sun
- The Central Laboratory, Shenzhen Second People's Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, Guangdong, China.,Department of Orthopedics, Shenzhen Second People's Hospital (First Affiliated Hospital of Shenzhen University), Shenzhen, Guangdong, China
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Ding K, He Y, Wei J, Fu S, Wang J, Chen Z, Zhang H, Qu Y, Liang K, Gong X, Qiu L, Chen D, Xiao B, Du H. A score of DNA damage repair pathway with the predictive ability for chemotherapy and immunotherapy is strongly associated with immune signaling pathway in pan-cancer. Front Immunol 2022; 13:943090. [PMID: 36081518 PMCID: PMC9445361 DOI: 10.3389/fimmu.2022.943090] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
DNA damage repair (DDR) is critical in maintaining normal cellular function and genome integrity and is associated with cancer risk, progression, and therapeutic response. However, there is still a lack of a thorough understanding of the effects of DDR genes’ expression level in cancer progression and therapeutic resistance. Therefore, we defined a tumor-related DDR score (TR-DDR score), utilizing the expression levels of 20 genes, to quantify the tumor signature of DNA damage repair pathways in tumors and explore the possible function and mechanism for the score among different cancers. The TR-DDR score has remarkably predictive power for tumor tissues. It is a more accurate indicator for the response of chemotherapy or immunotherapy combined with the tumor-infiltrating lymphocyte (TIL) and G2M checkpoint score than the pre-existing predictors (CD8 or PD-L1). This study points out that the TR-DDR score generally has positive correlations with patients of advanced-stage, genome-instability, and cell proliferation signature, while negative correlations with inflammatory response, apoptosis, and p53 pathway signature. In the context of tumor immune response, the TR-DDR score strongly positively correlates with the number of T cells (CD4+ activated memory cells, CD8+ cells, T regs, Tfh) and macrophages M1 polarization. In addition, by difference analysis and correlation analysis, COL2A1, MAGEA4, FCRL4, and ZIC1 are screened out as the potential modulating factors for the TR-DDR score. In summary, we light on a new biomarker for DNA damage repair pathways and explore its possible mechanism to guide therapeutic strategies and drug response prediction.
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Affiliation(s)
- Ke Ding
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Youhua He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jinfen Wei
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuying Fu
- College of Life Science, Zhaoqing University, Zhaoqing, China
| | - Jiajian Wang
- Clinical Laboratory Department of Longgang District People’s Hospital of Shenzhen & The Second Affiliated Hospital of the Chinese University of Hong Kong, Shenzhen, China
| | - Zixi Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Haibo Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yimo Qu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Keying Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaocheng Gong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Li Qiu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Dong Chen
- Fangrui Institute of Innovative Drugs, South China University of Technology, Guangzhou, China
| | - Botao Xiao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Botao Xiao, ; Hongli Du,
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Botao Xiao, ; Hongli Du,
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10
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Improving the Management of Endometrial Cancer Patients through the Use of Liquid Biopsy Analyses: A Case Report. Int J Mol Sci 2022; 23:ijms23158539. [PMID: 35955673 PMCID: PMC9369153 DOI: 10.3390/ijms23158539] [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: 06/28/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 12/10/2022] Open
Abstract
Endometrial cancer (EC) is the 4th most common neoplasm of the female genital tract, with 15–20% of patients being of high risk of recurrence which leads to a significant decrease in patient survival. Current therapeutic options for patients with EC are poor, being the combined therapy of carboplatin and paclitaxel the standard of care, with limited efficacy. Therefore, new therapeutic options and better monitoring tools are needed to improve the management of the disease. In the current case report, we showcase the value of liquid biopsy analyses in a microsatellite instability EC patient with initially good prognosis that however underwent rapid progression disease within 6 months post-surgery; through the study of plasma cfDNA/ctDNA dynamics to assess the tumour evolution during treatment, as well as the study of the uterine aspirate as a valuable sample that captures the intra-tumour heterogeneity that allows a comprehensive genomic profiling of the disease to identify potential therapeutic options. Furthermore, preclinical models were generated at the time of tumour progression to assess the efficacy of the identified targeted therapies.
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11
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Epithelial-Mesenchymal Transition-Mediated Tumor Therapeutic Resistance. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154750. [PMID: 35897925 PMCID: PMC9331826 DOI: 10.3390/molecules27154750] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 12/17/2022]
Abstract
Cancer is one of the world’s most burdensome diseases, with increasing prevalence and a high mortality rate threat. Tumor recurrence and metastasis due to treatment resistance are two of the primary reasons that cancers have been so difficult to treat. The epithelial–mesenchymal transition (EMT) is essential for tumor drug resistance. EMT causes tumor cells to produce mesenchymal stem cells and quickly adapt to various injuries, showing a treatment-resistant phenotype. In addition, multiple signaling pathways and regulatory mechanisms are involved in the EMT, resulting in resistance to treatment and hard eradication of the tumors. The purpose of this study is to review the link between EMT, therapeutic resistance, and the molecular process, and to offer a theoretical framework for EMT-based tumor-sensitization therapy.
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12
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Li Q, Zhang P, Hu H, Huang H, Pan D, Mao G, Hu B. The DDR-related gene signature with cell cycle checkpoint function predicts prognosis, immune activity, and chemoradiotherapy response in lung adenocarcinoma. Respir Res 2022; 23:190. [PMID: 35840978 PMCID: PMC9288070 DOI: 10.1186/s12931-022-02110-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/09/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND As a DNA surveillance mechanism, cell cycle checkpoint has recently been discovered to be closely associated with lung adenocarcinoma (LUAD) prognosis. It is also an essential link in the process of DNA damage repair (DDR) that confers resistance to radiotherapy. Whether genes that have both functions play a more crucial role in LUAD prognosis remains unclear. METHODS In this study, DDR-related genes with cell cycle checkpoint function (DCGs) were selected to investigate their effects on the prognosis of LUAD. The TCGA-LUAD cohort and two GEO external validation cohorts (GSE31210 and GSE42171) were performed to construct a prognosis model based on the least absolute shrinkage and selection operator (LASSO) regression. Patients were divided into high-risk and low-risk groups based on the model. Subsequently, the multivariate COX regression was used to construct a prognostic nomogram. The ssGSEA, CIBERSORT algorithm, TIMER tool, CMap database, and IC50 of chemotherapeutic agents were used to analyze immune activity and responsiveness to chemoradiotherapy. RESULTS 4 DCGs were selected as prognostic signatures, and patients in the high-risk group had a lower overall survival (OS). The lower infiltration levels of immune cells and the higher expression levels of immune checkpoints appeared in the high-risk group. The damage repair pathways were upregulated, and chemotherapeutic agent sensitivity was poor in the high-risk group. CONCLUSIONS The 4-DCGs signature prognosis model we constructed could predict the survival rate, immune activity, and chemoradiotherapy responsiveness of LUAD patients.
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Affiliation(s)
- Quan Li
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Pan Zhang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Huixiao Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hang Huang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Dong Pan
- Department of Dermatology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Guangyun Mao
- Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China. .,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China. .,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.
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13
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Saburi A, Kahrizi MS, Naghsh N, Etemadi H, İlhan A, Adili A, Ghoreishizadeh S, Tamjidifar R, Akbari M, Ercan G. A comprehensive survey into the role of microRNAs in ovarian cancer chemoresistance; an updated overview. J Ovarian Res 2022; 15:81. [PMID: 35799305 PMCID: PMC9264529 DOI: 10.1186/s13048-022-01012-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Ovarian cancer (OC), a frequent malignant tumor that affects women, is one of the leading causes of cancer-related death in this group of individuals. For the treatment of ovarian cancer, systemic chemotherapy with platinum-based drugs or taxanes is the first-line option. However, drug resistance developed over time during chemotherapy medications worsens the situation. Since uncertainty exists for the mechanism of chemotherapy resistance in ovarian cancer, there is a need to investigate and overcome this problem. miRNAs are engaged in various signaling pathways that contribute to the chemotherapeutic resistance of ovarian cancer. In the current study, we have tried to shed light on the mechanisms by which microRNAs contribute to the drug resistance of ovarian cancer and the use of some microRNAs to combat this chemoresistance, leading to the worse outcome of ovarian cancer patients treated with systemic chemotherapeutics.
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Affiliation(s)
- Ahmad Saburi
- Department of Biology, Faculty of Basic Sciences, Gonbad Kavous University, Gonbad Kavous, Iran
| | | | - Navid Naghsh
- Department of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hasti Etemadi
- Department of Biotechnology, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth University, Pune, India
| | - Ahmet İlhan
- Department of Medical Biochemistry, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Ali Adili
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South Florida, Tampa, Florida USA
- Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Rozita Tamjidifar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, 35100 Turkey
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gülinnaz Ercan
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, 35100 Turkey
- Department of Stem Cell, Institute of Health Sciences, Ege University, Izmir, 35100 Turkey
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14
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Zhao Y, Wang Y, Yang D, Suh K, Zhang M. A Computational Framework to Characterize the Cancer Drug Induced Effect on Aging Using Transcriptomic Data. Front Pharmacol 2022; 13:906429. [PMID: 35847024 PMCID: PMC9277350 DOI: 10.3389/fphar.2022.906429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Cancer treatments such as chemotherapies may change or accelerate aging trajectories in cancer patients. Emerging evidence has shown that “omics” data can be used to study molecular changes of the aging process. Here, we integrated the drug-induced and normal aging transcriptomic data to computationally characterize the potential cancer drug-induced aging process in patients. Our analyses demonstrated that the aging-associated gene expression in the GTEx dataset can recapitulate the well-established aging hallmarks. We next characterized the drug-induced transcriptomic changes of 28 FDA approved cancer drugs in brain, kidney, muscle, and adipose tissues. Further drug-aging interaction analysis identified 34 potential drug regulated aging events. Those events include aging accelerating effects of vandetanib (Caprelsa®) and dasatinib (Sprycel®) in brain and muscle, respectively. Our result also demonstrated aging protective effect of vorinostat (Zolinza®), everolimus (Afinitor®), and bosutinib (Bosulif®) in brain.
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Affiliation(s)
- Yueshan Zhao
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kangho Suh
- Department of Pharmacy and Therapeutics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Min Zhang,
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15
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Functional regulations between genetic alteration-driven genes and drug target genes acting as prognostic biomarkers in breast cancer. Sci Rep 2022; 12:10641. [PMID: 35739271 PMCID: PMC9226112 DOI: 10.1038/s41598-022-13835-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
Differences in genetic molecular features including mutation, copy number alterations and DNA methylation, can explain interindividual variability in response to anti-cancer drugs in cancer patients. However, identifying genetic alteration-driven genes and characterizing their functional mechanisms in different cancer types are still major challenges for cancer studies. Here, we systematically identified functional regulations between genetic alteration-driven genes and drug target genes and their potential prognostic roles in breast cancer. We identified two mutation and copy number-driven gene pairs (PARP1-ACSL1 and PARP1-SRD5A3), three DNA methylation-driven gene pairs (PRLR-CDKN1C, PRLR-PODXL2 and PRLR-SRD5A3), six gene pairs between mutation-driven genes and drug target genes (SLC19A1-SLC47A2, SLC19A1-SRD5A3, AKR1C3-SLC19A1, ABCB1-SRD5A3, NR3C2-SRD5A3 and AKR1C3-SRD5A3), and four copy number-driven gene pairs (ADIPOR2-SRD5A3, CASP12-SRD5A3, SLC39A11-SRD5A3 and GALNT2-SRD5A3) that all served as prognostic biomarkers of breast cancer. In particular, RARP1 was found to be upregulated by simultaneous copy number amplification and gene mutation. Copy number deletion and downregulated expression of ACSL1 and upregulation of SRD5A3 both were observed in breast cancers. Moreover, copy number deletion of ACSL1 was associated with increased resistance to PARP inhibitors. PARP1-ACSL1 pair significantly correlated with poor overall survival in breast cancer owing to the suppression of the MAPK, mTOR and NF-kB signaling pathways, which induces apoptosis, autophagy and prevents inflammatory processes. Loss of SRD5A3 expression was also associated with increased sensitivity to PARP inhibitors. The PARP1-SRD5A3 pair significantly correlated with poor overall survival in breast cancer through regulating androgen receptors to induce cell proliferation. These results demonstrate that genetic alteration-driven gene pairs might serve as potential biomarkers for the prognosis of breast cancer and facilitate the identification of combination therapeutic targets for breast cancers.
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16
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Chen Y, Huang M, Zhu J, Xu L, Cheng W, Lu X, Yan F. Identification of a DNA Damage Response and Repair-Related Gene-Pair Signature for Prognosis Stratification Analysis in Hepatocellular Carcinoma. Front Pharmacol 2022; 13:857060. [PMID: 35496321 PMCID: PMC9038539 DOI: 10.3389/fphar.2022.857060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Nowadays, although the cause of hepatocellular carcinoma (HCC) mortality and recurrence remains at a high level, the 5-year survival rate is still very low. The DNA damage response and repair (DDR) pathway may affect HCC patients’ survival by influencing tumor development and therapeutic response. It is necessary to identify a prognostic DDR-related gene signature to predict the outcome of patients. Methods: Level 3 mRNA expression and clinical information were extracted from the TCGA website. The GSE14520 datasets, ICGC-LIRI datasets, and a Chinese HCC cohort were served as validation sets. Univariate Cox regression analysis and LASSO-penalized Cox regression analysis were performed to construct the DDR-related gene pair (DRGP) signature. Kaplan–Meier survival curves and time-dependent receiver operating characteristic (ROC) analysis curves were calculated to determine the predictive ability of this prognostic model. Then, a prognostic nomogram was established to help clinical management. We investigated the difference in biological processes between HRisk and LRisk by conducting several enrichment analyses. The TIDE algorithm and R package “pRRophetic” were applied to estimate the immunotherapeutic and chemotherapeutic response. Results: We constructed the prognostic signature based on 23 DDR-related gene pairs. The patients in the training datasets were divided into HRisk and LRisk groups at median cut-off. The HRisk group had significantly poorer OS than the LRisk group, and the signature was an independent prognostic indicator in HCC. Furthermore, a nomogram of the riskscore combined with TNM stage was constructed and detected by the calibration curve and decision curve. The LRisk group was associated with higher expression of HBV oncoproteins and metabolism pathways, while DDR-relevant pathways and cell cycle process were enriched in the HRisk group. Moreover, patients in the LRisk group may be more beneficial from immunotherapy. We also found that TP53 gene was more frequently mutated in the HRisk group. As for chemotherapeutic drugs commonly used in HCC, the HRisk group was highly sensitive to 5-fluorouracil, while the LRisk group presented with a significantly higher response to gefitinib and gemcitabine. Conclusion: Overall, we developed a novel DDR-related gene pair signature and nomogram to assist in predicting survival outcomes and clinical treatment of HCC patients. It also helps understand the underlying mechanisms of different DDR patterns in HCC.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mengjia Huang
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Junkai Zhu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Li Xu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenxuan Cheng
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaofan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangrong Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
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17
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Jangili P, Kong N, Kim JH, Zhou J, Liu H, Zhang X, Tao W, Kim JS. DNA-Damage-Response-Targeting Mitochondria-Activated Multifunctional Prodrug Strategy for Self-Defensive Tumor Therapy. Angew Chem Int Ed Engl 2022; 61:e202117075. [PMID: 35133703 DOI: 10.1002/anie.202117075] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 12/14/2022]
Abstract
We report a novel multifunctional construct, M1, designed explicitly to target the DNA damage response in cancer cells. M1 contains both a floxuridine (FUDR) and protein phosphatase 2A (PP2A) inhibitor combined with a GSH-sensitive linker. Further conjugation of the triphenylphosphonium moiety allows M1 to undergo specific activation in the mitochondria, where mitochondria-mediated apoptosis is observed. Moreover, M1 has enormous effects on genomic DNA ascribed to FUDR's primary function of impeding DNA/RNA synthesis combined with diminishing PP2A-activated DNA repair pathways. Importantly, mechanistic studies highlight the PP2A obtrusion in FUDR/5-fluorouracil (5-FU) therapy and underscore the importance of its inhibition to harbor therapeutic potential. HCT116 cell xenograft-bearing mice that have a low response rate to 5-FU show a prominent effect with M1, emphasizing the importance of DNA damage response targeting strategies using tumor-specific microenvironment-activatable systems.
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Affiliation(s)
| | - Na Kong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, 311121, China.,Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ji Hyeon Kim
- Department of Chemistry, Korea University, Seoul, 02841, Korea
| | - Jun Zhou
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Haijun Liu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xingcai Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02134, USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul, 02841, Korea
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18
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Jangili P, Kong N, Kim JH, Zhou J, Liu H, Zhang X, Tao W, Kim JS. DNA‐Damage‐Response‐Targeting Mitochondria‐Activated Multifunctional Prodrug Strategy for Self‐Defensive Tumor Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Na Kong
- Liangzhu Laboratory Zhejiang University Medical Center Hangzhou Zhejiang 311121 China
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School Boston MA 02115 USA
| | - Ji Hyeon Kim
- Department of Chemistry Korea University Seoul 02841 Korea
| | - Jun Zhou
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School Boston MA 02115 USA
| | - Haijun Liu
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School Boston MA 02115 USA
| | - Xingcai Zhang
- School of Engineering and Applied Sciences Harvard University Cambridge MA 02134 USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School Boston MA 02115 USA
| | - Jong Seung Kim
- Department of Chemistry Korea University Seoul 02841 Korea
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19
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The oncogenic role of treacle ribosome biogenesis factor 1 ( TCOF1) in human tumors: a pan-cancer analysis. Aging (Albany NY) 2022; 14:943-960. [PMID: 35093935 PMCID: PMC8833134 DOI: 10.18632/aging.203852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022]
Abstract
Treacle ribosome biogenesis factor 1 (TCOF1) plays a crucial role in multiple processes, including ribosome biogenesis, DNA damage response (DDR), mitotic regulation, and telomere integrity. However, its role in cancers remains unclear. We aimed to visualize the expression, prognostic, and mutational landscapes of TCOF1 across cancers and to explore its association with immune infiltration. In this work, we integrated information from TCGA and GEO to explore the differential expression and prognostic value of TCOF1. Then, the mutational profiles of TCOF1 in cancers were investigated. We further determined the correlation between TCOF1 and immune cell infiltration levels. Additionally, we determined correlations among certain immune checkpoints, microsatellite instability, tumor mutational burden (TMB), and TCOF1. Potential pathways of TCOF1 in tumorigenesis were analyzed as well. In general, tumor tissue had a higher expression level of TCOF1 than normal tissue. The prognostic value of TCOF1 was multifaceted, depending on type of cancer. TCOF1 was correlated with tumor purity, CD8+ T cells, CD4+ T cells, B cells, neutrophils, macrophages, and dendritic cells (DCs) in 6, 14, 16, 12, 20, 13, and 17 cancer types, respectively. TCOF1 might act on ATPase activity, microtubule binding, tubulin binding, and catalytic activity (on DNA), and participate in tumorigenesis through “cell cycle” and “cellular-senescence” pathways. TCOF1 could affect pan-cancer prognosis and was correlated with immune cell infiltration. “Cell cycle” and “cellular-senescence” pathways were involved in the functional mechanisms of TCOF1, a finding that awaits further experimental validation.
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20
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Bermúdez-Guzmán L. Pan-cancer analysis of non-oncogene addiction to DNA repair. Sci Rep 2021; 11:23264. [PMID: 34853396 PMCID: PMC8636604 DOI: 10.1038/s41598-021-02773-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer cells usually depend on the aberrant function of one or few driver genes to initiate and promote their malignancy, an attribute known as oncogene addiction. However, cancer cells might become dependent on the normal cellular functions of certain genes that are not oncogenes but ensure cell survival (non-oncogene addiction). The downregulation or silencing of DNA repair genes and the consequent genetic and epigenetic instability is key to promote malignancy, but the activation of the DNA-damage response (DDR) has been shown to become a type of non-oncogene addiction that critically supports tumour survival. In the present study, a systematic evaluation of DNA repair addiction at the pan-cancer level was performed using data derived from The Cancer Dependency Map and The Cancer Genome Atlas (TCGA). From 241 DDR genes, 59 were identified as commonly essential in cancer cell lines. However, large differences were observed in terms of dependency scores in 423 cell lines and transcriptomic alterations across 18 cancer types. Among these 59 commonly essential genes, 14 genes were exclusively associated with better overall patient survival and 19 with worse overall survival. Notably, a specific molecular signature among the latter, characterized by DDR genes like UBE2T, RFC4, POLQ, BRIP1, and H2AFX showing the weakest dependency scores, but significant upregulation was strongly associated with worse survival. The present study supports the existence and importance of non-oncogenic addiction to DNA repair in cancer and may facilitate the identification of prognostic biomarkers and therapeutic opportunities.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Robotic Radiosurgery Center, International Cancer Center, San José, Costa Rica. .,Section of Genetics and Biotechnology, School of Biology, University of Costa Rica, San Pedro, San José, Costa Rica.
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21
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Li G, Gong J, Cao S, Wu Z, Cheng D, Zhu J, Huang X, Tang J, Yuan Y, Cai W, Zhang H. The Non-Coding RNAs Inducing Drug Resistance in Ovarian Cancer: A New Perspective for Understanding Drug Resistance. Front Oncol 2021; 11:742149. [PMID: 34660304 PMCID: PMC8514763 DOI: 10.3389/fonc.2021.742149] [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: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Ovarian cancer, a common malignant tumor, is one of the primary causes of cancer-related deaths in women. Systemic chemotherapy with platinum-based compounds or taxanes is the first-line treatment for ovarian cancer. However, resistance to these chemotherapeutic drugs worsens the prognosis. The underlying mechanism of chemotherapeutic resistance in ovarian cancer remains unclear. Non-coding RNAs, including long non-coding RNAs, microRNAs, and circular RNAs, have been implicated in the development of drug resistance. Abnormally expressed non-coding RNAs can promote ovarian cancer resistance by inducing apoptosis inhibition, protective autophagy, abnormal tumor cell proliferation, epithelial-mesenchymal transition, abnormal glycolysis, drug efflux, and cancer cell stemness. This review summarizes the role of non-coding RNAs in the development of chemotherapeutic resistance in ovarian cancer, including their mechanisms, targets, and potential signaling pathways. This will facilitate the development of novel chemotherapeutic agents that can target these non-coding RNAs and improve ovarian cancer treatment.
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Affiliation(s)
- Gaofeng Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Jun Gong
- Department of Abdominal and Pelvic Medical Oncology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, China
| | - Shulong Cao
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Zhaoyang Wu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Dong Cheng
- Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Zhu
- Hubei Enshi College, Enshi, China
| | - Xuqun Huang
- Department of Thoracic Medical Oncology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, China
| | - Jingyi Tang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Yuning Yuan
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Wenqi Cai
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Haiyuan Zhang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
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22
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Therapeutic Potential of PARP Inhibitors in the Treatment of Gastrointestinal Cancers. Biomedicines 2021; 9:biomedicines9081024. [PMID: 34440228 PMCID: PMC8392860 DOI: 10.3390/biomedicines9081024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/20/2022] Open
Abstract
Gastrointestinal (GI) malignancies are a major global health burden, with high mortality rates. The identification of novel therapeutic strategies is crucial to improve treatment and survival of patients. The poly (ADP-ribose) polymerase (PARP) enzymes involved in the DNA damage response (DDR) play major roles in the development, progression and treatment response of cancer, with PARP inhibitors (PARPi) currently used in the clinic for breast, ovarian, fallopian, primary peritoneal, pancreatic and prostate cancers with deficiencies in homologous recombination (HR) DNA repair. This article examines the current evidence for the role of the DDR PARP enzymes (PARP1, 2, 3 and 4) in the development, progression and treatment response of GI cancers. Furthermore, we discuss the role of HR status as a predictive biomarker of PARPi efficacy in GI cancer patients and examine the pre-clinical and clinical evidence for PARPi and cytotoxic therapy combination strategies in GI cancer. We also include an analysis of the genomic and transcriptomic landscape of the DDR PARP genes and key HR genes (BRCA1, BRCA2, ATM, RAD51, MRE11, PALB2) in GI patient tumours (n = 1744) using publicly available datasets to identify patients that may benefit from PARPi therapeutic approaches.
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23
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Singh J, Arora M, Kumari S, Verma D, Palanichamy JK, Qamar I, Chauhan SS, Chopra A. Molecular associations and clinical significance of core NHEJ pathway genes in renal clear cell carcinoma. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Barger CJ, Chee L, Albahrani M, Munoz-Trujillo C, Boghean L, Branick C, Odunsi K, Drapkin R, Zou L, Karpf AR. Co-regulation and function of FOXM1/ RHNO1 bidirectional genes in cancer. eLife 2021; 10:e55070. [PMID: 33890574 PMCID: PMC8104967 DOI: 10.7554/elife.55070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co-expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers.
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MESH Headings
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/metabolism
- Carboplatin/pharmacology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Checkpoint Kinase 1/genetics
- Checkpoint Kinase 1/metabolism
- Databases, Genetic
- Drug Resistance, Neoplasm
- Female
- Forkhead Box Protein M1/genetics
- Forkhead Box Protein M1/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Neoplasms, Cystic, Mucinous, and Serous/drug therapy
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/metabolism
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Promoter Regions, Genetic
- Recombinational DNA Repair
- Signal Transduction
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Affiliation(s)
- Carter J Barger
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Linda Chee
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Mustafa Albahrani
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Catalina Munoz-Trujillo
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Lidia Boghean
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Connor Branick
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
| | - Kunle Odunsi
- Departments of Gynecologic Oncology, Immunology, and Center for Immunotherapy, Roswell Park Comprehensive Cancer CenterBuffaloUnited States
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical SchoolCharlestownUnited States
| | - Adam R Karpf
- Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical CenterOmahaUnited States
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25
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de Almeida LC, Calil FA, Machado-Neto JA, Costa-Lotufo LV. DNA damaging agents and DNA repair: From carcinogenesis to cancer therapy. Cancer Genet 2021; 252-253:6-24. [DOI: 10.1016/j.cancergen.2020.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 02/09/2023]
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Chilimoniuk J, Gosiewska A, Słowik J, Weiss R, Deckert PM, Rödiger S, Burdukiewicz M. countfitteR: efficient selection of count distributions to assess DNA damage. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:528. [PMID: 33987226 DOI: 10.21037/atm-20-6363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background DNA double-strand breaks can be counted as discrete foci by imaging techniques. In personalized medicine and pharmacology, the analysis of counting data is relevant for numerous applications, e.g., for cancer and aging research and the evaluation of drug efficacy. By default, it is assumed to follow the Poisson distribution. This assumption, however, may lead to biased results and faulty conclusions in datasets with excess zero values (zero-inflation), a variance larger than the mean (overdispersion), or both. In such cases, the assumption of a Poisson distribution would skew the estimation of mean and variance, and other models like the negative binomial (NB), zero-inflated Poisson or zero-inflated NB distributions should be employed. The model chosen has an influence on the parameter estimation (mean value and confidence interval). Yet the choice of the suitable distribution model is not trivial. Methods To support, simplify and objectify this process, we have developed the countfitteR software as an R package. We used a Bayesian approach for distribution model selection and the shiny web application framework for interactive data analysis. Results We show the application of our software based on examples of DNA double-strand break count data from phenotypic imaging by multiplex fluorescence microscopy. In analyzing numerous datasets of molecular pharmacological markers (phosphorylated histone H2AX and p53 binding protein), countfitteR demonstrated an equal or superior statistical performance compared to the usually employed two-step procedure, with an overall power of up to 98%. In addition, it still gave information in cases with no result at all from the two-step procedure. In our data sample we found that the NB distribution was the most frequent, with the Poisson distribution taking second place. Conclusions countfitteR can perform an automated distribution model selection and thus support the data analysis and lead to objective statistically verifiable estimated values. Originally designed for the analysis of foci in biomedical image data, countfitteR can be used in a variety of areas where non-Poisson distributed counting data is prevalent.
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Affiliation(s)
- Jarosław Chilimoniuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.,Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Alicja Gosiewska
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Jadwiga Słowik
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Romano Weiss
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - P Markus Deckert
- Faculty of Medicine and Psychology, Brandenburg Medical School Theodor Fontane, and Faculty of Health Sciences Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Stefan Rödiger
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.,Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.,Medical University of Białystok, Białystok, Poland
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27
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The Role of TCOF1 Gene in Health and Disease: Beyond Treacher Collins Syndrome. Int J Mol Sci 2021; 22:ijms22052482. [PMID: 33804586 PMCID: PMC7957619 DOI: 10.3390/ijms22052482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/23/2022] Open
Abstract
The nucleoli are membrane-less nuclear substructures that govern ribosome biogenesis and participate in multiple other cellular processes such as cell cycle progression, stress sensing, and DNA damage response. The proper functioning of these organelles is ensured by specific proteins that maintain nucleolar structure and mediate key nucleolar activities. Among all nucleolar proteins, treacle encoded by TCOF1 gene emerges as one of the most crucial regulators of cellular processes. TCOF1 was initially discovered as a gene involved in the Treacher Collins syndrome, a rare genetic disorder characterized by severe craniofacial deformations. Later studies revealed that treacle regulates ribosome biogenesis, mitosis, proliferation, DNA damage response, and apoptosis. Importantly, several reports indicate that treacle is also involved in cancer development, progression, and response to therapies, and may contribute to other pathologies such as Hirschsprung disease. In this manuscript, we comprehensively review the structure, function, and the regulation of TCOF1/treacle in physiological and pathological processes.
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28
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Risdon EN, Chau CH, Price DK, Sartor O, Figg WD. PARP Inhibitors and Prostate Cancer: To Infinity and Beyond BRCA. Oncologist 2021; 26:e115-e129. [PMID: 32790034 PMCID: PMC7794174 DOI: 10.1634/theoncologist.2020-0697] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
The U.S. Food and Drug Administration recently approved two poly-adenosine diphosphate-ribose polymerase (PARP) inhibitors, olaparib and rucaparib, for treatment of biomarker-positive metastatic castrate resistant prostate cancer. The benefits of PARP inhibition have been well characterized in patients who have BRCA1 and BRCA2 mutations in several forms of cancer. BRCA1 and BRCA2 occupy key roles in DNA damage repair, which is comprised of several different pathways with numerous participants. Patients with mutations in other key genes within the DNA damage repair pathway may also respond to treatment with PARP inhibitors, and identification of these alterations could significantly increase the percentage of patients that may benefit from PARP inhibition. This review focuses on the potential for synthetically lethal interactions between PARP inhibitors and non-BRCA DNA damage repair genes. IMPLICATIONS FOR PRACTICE: The treatment potential of PARP inhibition has been well characterized in patients with BRCA1 and BRCA2 mutations, but there is compelling evidence for expanding the use of PARP inhibitors to mutations of other non-BRCA DNA damage repair (DDR) genes. This could increase the percentage of patients that may benefit from treatment with PARP inhibitors alone or in combination with other therapies. Understanding the significance of PARP inhibitor-sensitizing alterations in other common non-BRCA DDR genes will help guide clinical decisions to provide targeted treatment options to a wider population of patients.
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Affiliation(s)
- Emily N. Risdon
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Cindy H. Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Douglas K. Price
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | | | - William D. Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
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Xiao J, Jin X, Zhang C, Zou H, Chang Z, Han N, Li X, Zhang Y, Li Y. Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma. Am J Cancer Res 2021; 11:3060-3073. [PMID: 33537074 PMCID: PMC7847679 DOI: 10.7150/thno.54150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Enhancers are emerging regulatory regions controlling gene expression in diverse cancer types. However, the functions of enhancer regulatory circuit perturbations driven by copy number variations (CNVs) in malignant glioma are unclear. Therefore, we aimed to investigate the comprehensive enhancer regulatory perturbation and identify potential biomarkers in glioma. Results: We performed a meta-analysis of the enhancer centered regulatory circuit perturbations in 683 gliomas by integrating CNVs, gene expression, and transcription factors (TFs) binding. We found widespread CNVs of enhancers during glioma progression, and CNVs were associated with the perturbations of enhancer activities. In particular, the degree of perturbations for amplified enhancers was much greater accompanied by the glioma malignant progression. In addition, CNVs and enhancers cooperatively regulated the expressions of cancer-related genes. Genome-wide TF binding profiles revealed that enhancers were pervasively regulated by TFs. A network-based analysis of TF-enhancer-gene regulatory circuits revealed a core TF-gene module (58 interactions including seven genes and 14 TFs) that was associated survival of patients with glioma (p < 0.001). Finally, we validated this prognosis-associated TF-gene regulatory module in an independent cohort. In summary, our analyses provided new molecular insights for enhancer-centered transcriptional perturbation in glioma therapy. Conclusion: Integrative analysis revealed enhancer regulatory perturbations in glioma and also identified a network module that was associated with patient survival, thereby providing novel insights into enhancer-centered cancer therapy.
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30
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Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Int J Mol Sci 2020; 21:ijms21239226. [PMID: 33287345 PMCID: PMC7730500 DOI: 10.3390/ijms21239226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is the second leading cause of death with tens of millions of people diagnosed with cancer every year around the world. Most radio- and chemotherapies aim to eliminate cancer cells, notably by causing severe damage to the DNA. However, efficient repair of such damage represents a common mechanism of resistance to initially effective cytotoxic agents. Thus, development of new generation anticancer drugs that target DNA repair pathways, and more particularly the base excision repair (BER) pathway that is responsible for removal of damaged bases, is of growing interest. The BER pathway is initiated by a set of enzymes known as DNA glycosylases. Unlike several downstream BER enzymes, DNA glycosylases have so far received little attention and the development of specific inhibitors of these enzymes has been lagging. Yet, dysregulation of DNA glycosylases is also known to play a central role in numerous cancers and at different stages of the disease, and thus inhibiting DNA glycosylases is now considered a valid strategy to eliminate cancer cells. This review provides a detailed overview of the activities of DNA glycosylases in normal and cancer cells, their modes of regulation, and their potential as anticancer drug targets.
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31
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Rangel-Pozzo A, Liu S, Wajnberg G, Wang X, Ouellette RJ, Hicks GG, Drachenberg D, Mai S. Genomic Analysis of Localized High-Risk Prostate Cancer Circulating Tumor Cells at the Single-Cell Level. Cells 2020; 9:cells9081863. [PMID: 32784507 PMCID: PMC7466090 DOI: 10.3390/cells9081863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Accurate risk classification of men with localized high-risk prostate cancer directly affects treatment management decisions and patient outcomes. A wide range of risk assessments and classifications are available. However, each one has significant limitations to distinguish between indolent and aggressive prostate cancers. Circulating tumor cells (CTCs) may provide an alternate additional source, beyond tissue biopsies, to enable individual patient-specific clinical assessment, simply because CTCs can reveal both tumor-derived and germline-specific genetic information more precisely than that gained from a single diagnostic biopsy. In this study, we combined a filtration-based CTC isolation technology with prostate cancer CTC immunophenotyping to identify prostate cancer CTCs. Next, we performed 3-D telomere profiling prior to laser microdissection and single-cell whole-exome sequencing (WES) of 21 CTCs and 4 lymphocytes derived from 10 localized high-risk prostate cancer patient samples. Localized high-risk prostate cancer patient CTCs present a high number of telomere signals with lower signal intensities (short telomeres). To capture the genetic diversity/heterogeneity of high-risk prostate cancer CTCs, we carried out whole-exome sequencing. We identified 202,241 single nucleotide variants (SNVs) and 137,407 insertion-deletions (indels), where less than 10% of these genetic variations were within coding regions. The genetic variation (SNVs + indels) and copy number alteration (CNAs) profiles were highly heterogeneous and intra-patient CTC variation was observed. The pathway enrichment analysis showed the presence of genetic variation in nine telomere maintenance pathways (patients 3, 5, 6, and 7), including an important gene for telomere maintenance called telomeric repeat-binding factor 2 (TRF2). Using the PharmGKB database, we identified nine genetic variations associated with response to docetaxel. A total of 48 SNVs can affect drug response for 24 known cancer drugs. Gene Set Enrichment Analysis (GSEA) (patients 1, 3, 6, and 8) identified the presence of CNAs in 11 different pathways, including the DNA damage repair (DDR) pathway. In conclusion, single-cell approaches (WES and 3-D telomere profiling) showed to be useful in unmasking CTC heterogeneity. DDR pathway mutations have been well-established as a target pathway for cancer therapy. However, the frequent CNA amplifications found in localized high-risk patients may play critical roles in the therapeutic resistance in prostate cancer.
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Affiliation(s)
- Aline Rangel-Pozzo
- Cell Biology, Research Institute of Hematology and Oncology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3C 2B1, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
| | - Songyan Liu
- Department of Biochemistry and Medical Genetics, Research Institute of Hematology and Oncology, University of Manitoba, Winnipeg, MB R3C 2B1, Canada; (S.L.); (G.G.H.)
| | - Gabriel Wajnberg
- Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, NB E1C 8X3, Canada; (G.W.); (R.J.O.)
| | - Xuemei Wang
- Cell Biology, Research Institute of Hematology and Oncology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3C 2B1, Canada;
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, NB E1C 8X3, Canada; (G.W.); (R.J.O.)
| | - Geoffrey G. Hicks
- Department of Biochemistry and Medical Genetics, Research Institute of Hematology and Oncology, University of Manitoba, Winnipeg, MB R3C 2B1, Canada; (S.L.); (G.G.H.)
| | - Darrel Drachenberg
- Manitoba Prostate Center, Cancer Care Manitoba, Section of Urology, Department of Surgery, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Sabine Mai
- Cell Biology, Research Institute of Hematology and Oncology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3C 2B1, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
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32
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Li K, Peng S, Li Z, Lai Y, Wang Q, Tao Y, Wu W, Zhou Q, Gao Z, Chen J, Li H, Cai W, Guo Z, Huang H. Topoisomerase II-binding protein 1 promotes the progression of prostate cancer via ATR-CHK1 signaling pathway. Aging (Albany NY) 2020; 12:9948-9958. [PMID: 32459662 PMCID: PMC7288942 DOI: 10.18632/aging.103260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/18/2020] [Indexed: 12/24/2022]
Abstract
DNA damage response (DDR) plays an important role in the progression of cancers, including prostate cancer (PCa). Topoisomerase II-binding protein 1 (TopBP1) is an essential promotor of ATR-mediated DDR. Herein, we investigated the association between TopBP1 and PCa and determined its effect on the progression of PCa. The expression and clinical features of TopBP1 were analyzed using large-scale cohort of tissue microarray analyses and The Cancer Genome Atlas database, which indicated that TopBP1 was positively correlated with high Gleason Score, advanced clinical and pathological stages, the metastasis status. Multivariate analysis revealed that the upregulation of TopBP1 was an independent predictor for a worse biochemical recurrence-free survival (BCR-free survival). Furthermore, we discovered that downregulation of TopBP1 significantly suppressed the growth and migration ability of PCa lines by loss-of-function assays in vitro. Further mechanistic investigations clarified that TopBP1 promoted proliferation and migration by activating ATR-Chk1 signaling pathway.
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Affiliation(s)
- Kaiwen Li
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shirong Peng
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zean Li
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yiming Lai
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiong Wang
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yiran Tao
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wanhua Wu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qianghua Zhou
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ze Gao
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Junxiu Chen
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Wenli Cai
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhenghui Guo
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hai Huang
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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