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Nakagawa S, Yamaguchi K, Takane K, Tabata S, Ikenoue T, Furukawa Y. Wnt/β-catenin signaling regulates amino acid metabolism through the suppression of CEBPA and FOXA1 in liver cancer cells. Commun Biol 2024; 7:510. [PMID: 38684876 PMCID: PMC11058205 DOI: 10.1038/s42003-024-06202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Deregulation of the Wnt/β-catenin pathway is associated with the development of human cancer including colorectal and liver cancer. Although we previously showed that histidine ammonia lyase (HAL) was transcriptionally reduced by the β-catenin/TCF complex in liver cancer cells, the mechanism(s) of its down-regulation by the complex remain to be clarified. In this study, we search for the transcription factor(s) regulating HAL, and identify CEBPA and FOXA1, two factors whose expression is suppressed by the knockdown of β-catenin or TCF7L2. In addition, RNA-seq analysis coupled with genome-wide mapping of CEBPA- and FOXA1-binding regions reveals that these two factors also increase the expression of arginase 1 (ARG1) that catalyzes the hydrolysis of arginine. Metabolome analysis discloses that activated Wnt signaling augments intracellular concentrations of histidine and arginine, and that the signal also increases the level of lactic acid suggesting the induction of the Warburg effect in liver cancer cells. Further analysis reveals that the levels of metabolites of the urea cycle and genes coding its related enzymes are also modulated by the Wnt signaling. These findings shed light on the altered cellular metabolism in the liver by the Wnt/β-catenin pathway through the suppression of liver-enriched transcription factors including CEBPA and FOXA1.
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Affiliation(s)
- Saya Nakagawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
| | - Kiyoko Takane
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Sho Tabata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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Chowdhury B, Garg S, Ni W, Sattler M, Sanchez D, Meng C, Akatsu T, Stone R, Forrester W, Harrington E, Buhrlage SJ, Griffin JD, Weisberg E. Synergy between BRD9- and IKZF3-Targeting as a Therapeutic Strategy for Multiple Myeloma. Cancers (Basel) 2024; 16:1319. [PMID: 38610997 PMCID: PMC11010819 DOI: 10.3390/cancers16071319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Progress in the treatment of multiple myeloma (MM) has resulted in improvement in the survival rate. However, there is still a need for more efficacious and tolerated therapies. We and others have shown that bromodomain-containing protein 9 (BRD9), a member of the non-canonical SWI/SNF chromatin remodeling complex, plays a role in MM cell survival, and targeting BRD9 selectively blocks MM cell proliferation and synergizes with IMiDs. We found that synergy in vitro is associated with the downregulation of MYC and Ikaros proteins, including IKZF3, and overexpression of IKZF3 or MYC could partially reverse synergy. RNA-seq analysis revealed synergy to be associated with the suppression of pathways associated with MYC and E2F target genes and pathways, including cell cycle, cell division, and DNA replication. Stimulated pathways included cell adhesion and immune and inflammatory response. Importantly, combining IMiD treatment and BRD9 targeting, which leads to the downregulation of MYC protein and upregulation of CRBN protein, was able to override IMiD resistance of cells exposed to iberdomide in long-term culture. Taken together, our results support the notion that combination therapy based on agents targeting BRD9 and IKZF3, two established dependencies in MM, represents a promising novel therapeutic strategy for MM and IMiD-resistant disease.
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Affiliation(s)
- Basudev Chowdhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Swati Garg
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Ni
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Dana Sanchez
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
| | - Chengcheng Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
| | - Taisei Akatsu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
| | - Richard Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Sara J. Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
| | - James D. Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; (B.C.); (S.G.); (W.N.); (M.S.); (D.S.); (T.A.); (R.S.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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3
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Wang J, Gilani SF, Noor N, Ahmed MR, Munazir M, Zubair A, Sultan R, Abdel-Maksoud MA, Saleh IA, Zomot N, Kodous AS, Ibrahim SS, El-Tayeb MA, Aufy M, Zaky MY, Hassan SS, Hameed Y. Decoding the DSCC1 gene as a pan-cancer biomarker in human cancers via comprehensive multi-omics analyses. Am J Transl Res 2024; 16:738-754. [PMID: 38586115 PMCID: PMC10994803 DOI: 10.62347/yorr3755] [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: 09/20/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVES While dysregulation of DSCC1 (DNA Replication And Sister Chromatid Cohesion 1) has been established in breast cancer and colorectal cancer, its associations with other tumors remain unclear. Therefore, this study was launched to explore the role of DSCC1 in pan-cancer. METHODOLOGY In this study, we investigate the biological functions of DSCC1 across 33 solid tumors, elucidating its role in promoting oncogenesis and progression in various cancers through comprehensive analysis of multi-omics data. RESULTS We conducted a comprehensive analysis of DSCC1 expression using RNA-seq data from TCGA and GTEx databases across 30 cancer types. Striking variations were observed, with significant overexpression of DSCC1 identified in numerous cancers. Elevated DSCC1 level was strongly associated with poorer prognosis, shorter survival, and advanced tumor stages in kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), as indicated by Kaplan-Meier curves and GEPIA2 analysis. Further investigation into the molecular mechanisms revealed reduced DNA methylation in the DSCC1 promoter region in KIRP, LIHC, and LUAD, supporting enhanced RNA transcription. Protein expression analysis via the Human Protein Atlas (HPA) corroborated mRNA expression findings, showcasing elevated DSCC1 protein in KIRP, LIHC, and LUAD tissues. Mutational analysis using cBioPortal revealed alterations in 0.4% of KIRP, 17% of LIHC, and 5% of LUAD samples, predominantly characterized by amplification. Immune cell infiltration analysis demonstrated robust positive correlations between DSCC1 expression and CD8+ T cells, CD4+ T cells, and B cells, influencing the tumor microenvironment. STRING and gene enrichment analyses unveiled DSCC1's involvement in critical pathways, emphasizing its multifaceted impact. Notably, drug sensitivity analysis highlighted a significant correlation between DSCC1 mRNA expression and responses to 78 anticancer treatments, suggesting its potential as a predictive biomarker and therapeutic target for KIRP, LIHC, and LUAD. Finally, immunohistochemistry staining of clinical samples validated computational results, confirming elevated DSCC1 protein expression. CONCLUSION Overall, this study provides comprehensive insights into the pivotal role of DSCC1 in KIRP, LIHC, and LUAD initiation, progression, and therapeutic responsiveness, laying the foundation for further investigations and personalized treatment strategies.
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Affiliation(s)
- Jingru Wang
- Mengcheng County Hospital of Chinese MedicineChina
- Bozhou Second Chinese Medicine HospitalChina
| | | | - Nazia Noor
- Department of Pathology, Continental Medical CollegeLahore, Pakistan
| | | | - Mehmooda Munazir
- Department of Botany, Government College Women UniversitySialkot, Pakistan
| | - Ayesha Zubair
- Department of Biochemistry, CMH Lahore Medical College and Institute of DentistryLahore 54000, Punjab, Pakistan
| | - Rizwana Sultan
- Department of Pathology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal SciencesBahawalpur 63100, Punjab, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Naser Zomot
- Faculty of Science, Zarqa UniversityZarqa 13110, Jordan
| | - Ahmad S Kodous
- Department of Molecular Oncology, Cancer Institute (WIA)38, Sardar Patel Road, P.O. Box 600036, Chennai, Tamilnadu, India
- Department of Radiation Biology, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA)P.O. Box 13759, Cairo, Egypt
| | - Shebl Salah Ibrahim
- Department of Biochemistry, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed A El-Tayeb
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohammed Aufy
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of ViennaVienna 1090, Austria
| | - Mohamed Y Zaky
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburgh, PA 15213, USA
| | - Syed Sairum Hassan
- Department of Medicine, Bilawal Medical College, Liaquat University of Medical and Health Sciences (LUMHS)Jamshoro 76090, Sindh, Pakistan
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Punjab, Pakistan
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Nanamiya T, Takane K, Yamaguchi K, Okawara Y, Arakawa M, Saku A, Ikenoue T, Fujiyuki T, Yoneda M, Kai C, Furukawa Y. Expression of PVRL4, a molecular target for cancer treatment, is transcriptionally regulated by FOS. Oncol Rep 2024; 51:17. [PMID: 38063270 PMCID: PMC10739986 DOI: 10.3892/or.2023.8676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/04/2023] [Indexed: 12/18/2023] Open
Abstract
PVRL4 (or nectin‑4) is a promising therapeutic target since its upregulated expression is found in a wide range of human cancer types. Enfortumab vedotin, an antibody‑drug conjugate targeting PVRL4, is clinically used for the treatment of urothelial bladder cancer. In addition, rMV‑SLAMblind, a genetically engineered oncolytic measles virus, can infect cancer cells and induce apoptosis through interaction with PVRL4. Although PVRL4 transcript levels are elevated in breast, lung and ovarian cancer, the mechanisms of its upregulation have not yet been uncovered. To clarify the regulatory mechanisms of elevated PVRL4 expression in breast cancer cells, Assay for Transposase‑Accessible Chromatin‑sequencing and chromatin immunoprecipitation‑sequencing (ChIP‑seq) data were used to search for its regulatory regions. Using breast cancer cells, an enhancer region was ultimately identified. Additional analyses, including ChIP and reporter assays, demonstrated that FOS interacted with the PVRL4 enhancer region, and that alterations of the FOS‑binding motifs in the enhancer region decreased reporter activity. Consistent with these data, exogenous expression of FOS enhanced the reporter activity and PVRL4 expression in breast cancer cells. Furthermore, RNA‑seq analysis using breast cancer cells treated with PVRL4 small interfering RNA revealed its possible involvement in the cytokine response and immune system. These data suggested that FOS was involved, at least partly, in the regulation of PVRL4 expression in breast cancer cells, and that elevated PVRL4 expression may regulate the response of cancer cells to cytokines and the immune system.
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Affiliation(s)
- Tomoyuki Nanamiya
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kiyoko Takane
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yuya Okawara
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mariko Arakawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Akari Saku
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tomoko Fujiyuki
- Division of Virus Engineering, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Misako Yoneda
- Division of Virological Medicine, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Chieko Kai
- Division of Infectious Disease Control Science, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Hou S, Zhang J, Chi X, Li X, Zhang Q, Kang C, Shan H. Roles of DSCC1 and GINS1 in gastric cancer. Medicine (Baltimore) 2023; 102:e35681. [PMID: 37904396 PMCID: PMC10615490 DOI: 10.1097/md.0000000000035681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Gastric carcinoma is a common malignant tumor originating from gastric mucosal epithelium. However, role of DS-cell cycle-dependent protein 1 (DSCC1) and GINS1 in gastric carcinoma remains unclear. The gastric carcinoma datasets GSE79973 and GSE118916 were downloaded from gene expression omnibus. Multiple datasets were merged and batched. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis was performed. Functional enrichment analysis, gene set enrichment analysis and immune infiltration analysis were performed. Construction and analysis of protein-protein interaction Network. Survival analysis and comparative toxicogenomics database were performed. A heat map of gene expression was drawn. Target Scan screen miRNAs regulating DEGs. Two thousand forty-four DEGs were identified. According to gene ontology analysis, in biological process, they were mainly enriched in cell migration, transforming growth factor β receptor signaling pathway, angiogenesis, and steroid metabolism process. In cellular component, they were mainly enriched in extracellular vesicles, basement membrane, endoplasmic reticulum lumen, and extracellular space. In molecular function, they focused on extracellular matrix structural components, protein binding, platelet-derived growth factor binding, and catalytic activity. In Kyoto encyclopedia of genes and genomes, they were mainly enriched in protein digestion and absorption, metabolic pathways, fatty acid degradation, Glycerophospholipid metabolism, ether lipid metabolism. Gene set enrichment analysis showed that DEGs were mainly enriched in transforming growth factor β receptor signaling pathway, steroid metabolism process, basement membrane, endoplasmic reticulum lumen, structural components of extracellular matrix, platelet-derived growth factor binding, Glycerophospholipid metabolism, ether lipid metabolism. The results of immune infiltration analysis showed that expression of T cell CD4 memory resting was lower in the samples of gastric cancer. The core genes (TRIP13, CHEK1, DSCC1, GINS1) are protective factors, their expression shows a downward trend with increase of risk score. Comparative toxicogenomics database analysis showed that TRIP13, CHEK1, DSCC1, GINS1 were related to gastric tumors, gastric diseases, tumors, inflammation, and necrosis. DSCC1 and GINS1 are highly expressed in gastric cancer. Higher expression levels of DSCC1 and GINS1, worse the prognosis.
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Affiliation(s)
- Shiyang Hou
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Jie Zhang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Xiaoqian Chi
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Xiaowei Li
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Qijun Zhang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Chunbo Kang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Haifeng Shan
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
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Lin X, Liu YH, Zhang HQ, Wu LW, Li Q, Deng J, Zhang Q, Yang Y, Zhang C, Li YL, Hu J. DSCC1 interacts with HSP90AB1 and promotes the progression of lung adenocarcinoma via regulating ER stress. Cancer Cell Int 2023; 23:208. [PMID: 37742009 PMCID: PMC10518103 DOI: 10.1186/s12935-023-03047-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023] Open
Abstract
Lung cancer is a leading cause of cancer-related deaths, and the most common type is lung adenocarcinoma (LUAD). LUAD is frequently diagnosed in people who never smoked, patients are always diagnosed at advanced inoperable stages, and the prognosis is ultimately poor. Thus, there is an urgent need for the development of novel targeted therapeutics to suppress LUAD progression. In this study, we demonstrated that the expression of DNA replication and sister chromatid cohesion 1 (DSCC1) was higher in LUAD samples than normal tissues, and the overexpression of DSCC1 or its coexpressed genes were highly correlated with poor outcomes of LUAD patients, highlighting DSCC1 might be involved in LUAD progression. Furthermore, the expression of DSCC1 was positively correlated with multiple genetic mutations which drive cancer development, including TP53, TTN, CSMD, and etc. More importantly, DSCC1 could promote the cell proliferation, stemness, EMT, and metastatic potential of LUAD cells. In addition, DSCC1 interacted with HSP90AB1 and promoted the progression of LUAD via regulating ER stress. Meanwhile, DSCC1 expression negatively correlated with immune cell infiltration in lung cancer, and DSCC1 positively regulated the expression of PD-L1 in LUAD cells. Collectively, this study revealed that DSCC1 is a novel therapeutic target to treat LUAD and a biomarker for predicting the efficiency of PD-1/PD-L1 blockade treatment.
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Affiliation(s)
- Xu Lin
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Ye-Han Liu
- School of Medicine, Hangzhou City University, No.51 Huzhou Street, Hangzhou, Zhejiang, 310015, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huan-Qi Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lin-Wen Wu
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Qi Li
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Jun Deng
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Qingyi Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yuhong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chong Zhang
- School of Medicine, Hangzhou City University, No.51 Huzhou Street, Hangzhou, Zhejiang, 310015, China.
| | - Yang-Ling Li
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
- Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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7
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Wang X, Wu Y, Liu J, Xu X, Sheng Z, Liu W, Chen M, Ma Y, Zhao D, Li D, Zheng X. Identification of target and pathway of aspirin combined with Lipitor treatment in prostate cancer through integrated bioinformatics analysis. Toxicol Appl Pharmacol 2022; 452:116169. [PMID: 35926565 DOI: 10.1016/j.taap.2022.116169] [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: 02/17/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Our previous studies have confirmed that aspirin combined with Lipitor inhibited the development of prostate cancer (PCa), but the mechanisms need to be comprehensively expounded. The study aims to screen out the hub genes of combination therapy and to explore their association with the pathogenesis and prognosis of PCa. METHODS Gene expressions were quantified by RNA sequencing (RNA-seq). Altered biological function, pathways of differentially expressed genes (DEGs), protein-protein interaction network, the filtering of hub genes, gene co-expression and the pathogenesis and prognosis were revealed by bioinformatics analysis. The correlation between hub gene expression and patient survival was validated by Kaplan-Meier. The effects of silent DNA replication and sister chromatid cohesion 1 (siDSCC1) combined with Lipitor and aspirin on DSCC1 expression, viability, invasion and migration of PCa cells were detected by qRT-PCR, Wound healing and transwell assays. RESULTS 157 overlapped DEGs involved in FoxO, PI3K-Akt and p53 signaling pathways were identified. Ten hub genes (NEIL3, CDC7, DSCC1, CDC25C, PRIM1, MCM10, FBXO5, DTL, SERPINE1, EXO1) were verified to be correlated with the pathology and prognosis of PCa. DSCC1 silencing not only inhibited the viability, migration and invasion of PCa cells, but also strengthened the suppressing effects of Lipitor and aspirin alone or in combination on PCa cells. CONCLUSION The enrichment pathways and targets of Lipitor combined with aspirin in PCa are discovered, and DSCC1 silencing can potentiate the effect of Lipitor combined with aspirin in the treatment of PCa.
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Affiliation(s)
- Xiao Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Yi Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Junlei Liu
- Allan H. Conney Laboratory for Anticancer Research, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Xuetao Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Zhaojun Sheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Wenfeng Liu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Min Chen
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Yanyan Ma
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Denggao Zhao
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Dongli Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen City 529020, China
| | - Xi Zheng
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Ruters University, Piscataway NJ08854, USA.
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8
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Horie C, Zhu C, Yamaguchi K, Nakagawa S, Isobe Y, Takane K, Ikenoue T, Ohta Y, Tanaka Y, Aikou S, Tsurita G, Ahiko Y, Shida D, Furukawa Y. Motile sperm domain containing 1 is upregulated by the Wnt/β‑catenin signaling pathway in colorectal cancer. Oncol Lett 2022; 24:282. [DOI: 10.3892/ol.2022.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chiaki Horie
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Chi Zhu
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Saya Nakagawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Yumiko Isobe
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Kiyoko Takane
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Yasunori Ohta
- Department of Pathology, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Yukihisa Tanaka
- Department of Pathology, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Susumu Aikou
- Department of Surgery, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Giichiro Tsurita
- Department of Surgery, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Yuka Ahiko
- Department of Surgery, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Dai Shida
- Department of Surgery, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Yoichi Furukawa
- Department of Surgery, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo 108‑8639, Japan
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9
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Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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10
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Lin DL, Wang LL, Zhao P, Ran WW, Wang W, Zhang LX, Han M, Bao H, Liu K, Wu X, Shao Y, Xing XM. Gastrointestinal Goblet Cell Adenocarcinomas Harbor Distinctive Clinicopathological, Immune, and Genomic Landscape. Front Oncol 2021; 11:758643. [PMID: 34804955 PMCID: PMC8603204 DOI: 10.3389/fonc.2021.758643] [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: 08/14/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Goblet cell adenocarcinoma (GCA) is a rare amphicrine tumor and difficult to diagnose. GCA is traditionally found in the appendix, but extra-appendiceal GCA may be underestimated. Intestinal adenocarcinoma with signet ring cell component is also very rare, and some signet ring cell carcinomas are well cohesive, having some similar morphological features to GCAs. It is necessary to differentiate GCA from intestinal adenocarcinomas with cohesive signet ring cell component (IACSRCC). The goal of this study is to find occurrence of extra-appendiceal GCA and characterize the histological, immunohistochemical, transcriptional, and immune landscape of GCA. We collected 12 cases of GCAs and 10 IACSRCCs and reviewed the clinicopathologic characters of these cases. Immunohistochemical stains were performed with synaptophysin, chromogranin A, CD56, somatostatin receptor (SSTR) 2, and Ki-67. Whole transcriptome RNA-sequencing was performed, and data were used to analyze differential gene expression and predict immune cell infiltration levels in GCA and IACSRCC. RNA-sequencing data for colorectal adenocarcinoma were gathered from TCGA data portal. Of the 12 patients with GCA, there were 4 women and 8 men. There were three appendiceal cases and nine extra-appendiceal cases. GCAs were immunohistochemically different from IACSRCC. GCA also had different levels of B-cell and CD8+ T-cell infiltration compared to both colorectal adenocarcinoma and cohesive IACSRCCs. Differential gene expression analysis showed distinct gene expression patterns in GCA compared to colorectal adenocarcinoma, with a number of cancer-related differentially expressed genes, including upregulation of TMEM14A, GOLT1A, DSCC1, and HSD17B8, and downregulation of KCNQ1OT1 and MXRA5. GCA also had several differentially expressed genes compared to IACSRCCs, including upregulation of PRSS21, EPPIN, RPRM, TNFRSF12A, and BZRAP1, and downregulation of HIST1H2BE, TCN1, AC069363.1, RP11-538I12.2, and REG4. In summary, the number of extra-appendiceal GCA was underestimated in Chinese patients. GCA can be seen as a distinct morphological, immunohistochemical, transcriptomic, and immunological entity. The classic low-grade component of GCA and the immunoreactivity for neuroendocrine markers are the key points to diagnosing GCA.
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Affiliation(s)
- Dong-Liang Lin
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Li-Li Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Peng Zhao
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wen-Wen Ran
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wei Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Long-Xiao Zhang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ming Han
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Kaihua Liu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiao-Ming Xing
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
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11
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Chang S, Zhu Y, Xi Y, Gao F, Lu J, Dong L, Ma C, Li H. High DSCC1 Level Predicts Poor Prognosis of Lung Adenocarcinoma. Int J Gen Med 2021; 14:6961-6974. [PMID: 34707388 PMCID: PMC8542575 DOI: 10.2147/ijgm.s329482] [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: 08/20/2021] [Indexed: 12/04/2022] Open
Abstract
Purpose To evaluate the role of DSCC1 in LUAD. Patients and Methods Based on TCGA and GTEx, the Wilcoxon rank-sum test was used to compare the expression differences of DSCC1 between the normal samples of GTEx combined TCGA and the unpaired tumor samples of TCGA, and to compare DSCC1 expression values between tumor tissues and paired normal LUAD tissues in the TCGA cohort. Kruskal–Wallis rank-sum test, Wilcoxon rank-sum test, and logistics regression were used to compare the relationship between the expression of DSCC1 and the clinicopathological parameters. The biological function of DSCC1 was annotated by GSEA and ssGSEA, while Kaplan–Meier and Cox regression analysis were used to evaluate the prognostic value of DSCC1. Furthermore, the time-dependent ROC curve was used to analyze the diagnostic efficacy of DSCC1 in LUAD. Results We downloaded the RNA-Seq data of 513 LUAD cases. The expression of DSCC1 was significantly correlated with T stage (OR = 1.04(1.02–1.07), P = 0.002), pathological stage (OR=1.03 (1.01–1.05), P = 0.008) and TP53 status (OR=1.10 (1.07–1.14), P < 0.001). The high expression of DSCC1 was significantly correlated with DSS (HR=1.56 (1.07–2.26), P = 0.021) and OS (HR=1.53 (1.14–2.05), P = 0.004). Moreover, ROC curve analysis (AUC=0.845, CI (0.820-0.870)) indicated DSCC1 as a potential diagnostic molecule for LUAD. In the group with high DSCC1 expression phenotype, down-regulation of EGFR signal, reduction of IL-6 deprivation, cell cycle, and p53 signal pathway were significantly abundant. Spearman correlation analysis showed that the expression of DSCC1 was positively correlated with the infiltration of Th2 cells, T Helper cells. Conclusion Our results suggest that DSCC1 may be an important biomarker for the treatment of LUAD.
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Affiliation(s)
- Sisi Chang
- Department of Oncology, Henan Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan Province, People's Republic of China
| | - Yahui Zhu
- Department of Oncology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan Province, People's Republic of China
| | - Yutan Xi
- Department of Oncology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan Province, People's Republic of China
| | - Fuyan Gao
- Department of Oncology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan Province, People's Republic of China
| | - Juanjuan Lu
- Department of Oncology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan Province, People's Republic of China
| | - Liang Dong
- Department of Oncology, Henan Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan Province, People's Republic of China
| | - Chunzheng Ma
- Department of Oncology, Henan Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan Province, People's Republic of China
| | - Honglin Li
- Department of Oncology, Henan Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan Province, People's Republic of China
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12
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Jin G, Wang W, Cheng P, Tian Y, Zhang L, Niu H. DNA replication and sister chromatid cohesion 1 promotes breast carcinoma progression by modulating the Wnt/β-catenin signaling and p53 protein. J Biosci 2020. [DOI: 10.1007/s12038-020-00100-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Grabarczyk DB. Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex. Nucleic Acids Res 2020; 48:6996-7004. [PMID: 32469068 PMCID: PMC7337906 DOI: 10.1093/nar/gkaa456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/13/2022] Open
Abstract
The Tof1-Csm3 fork protection complex has a central role in the replisome-it promotes the progression of DNA replication forks and protects them when they stall, while also enabling cohesion establishment and checkpoint responses. Here, I present the crystal structure of the Tof1-Csm3 complex from Chaetomium thermophilum at 3.1 Å resolution. The structure reveals that both proteins together form an extended alpha helical repeat structure, which suggests a mechanical or scaffolding role for the complex. Expanding on this idea, I characterize a DNA interacting region and a cancer-associated Mrc1 binding site. This study provides the molecular basis for understanding the functions of the Tof1-Csm3 complex, its human orthologue the Timeless-Tipin complex and additionally the Drosophila circadian rhythm protein Timeless.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg, Germany
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14
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Wu MJ, Gao YL, Liu JX, Zheng CH, Wang J. Integrative Hypergraph Regularization Principal Component Analysis for Sample Clustering and Co-Expression Genes Network Analysis on Multi-Omics Data. IEEE J Biomed Health Inform 2020; 24:1823-1834. [DOI: 10.1109/jbhi.2019.2948456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Kim JT, Cho HJ, Park SY, Oh BM, Hwang YS, Baek KE, Lee YH, Kim HC, Lee HG. DNA Replication and Sister Chromatid Cohesion 1 (DSCC1) of the Replication Factor Complex CTF18-RFC is Critical for Colon Cancer Cell Growth. J Cancer 2019; 10:6142-6153. [PMID: 31762824 PMCID: PMC6856584 DOI: 10.7150/jca.32339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 08/26/2019] [Indexed: 01/01/2023] Open
Abstract
DNA replication and sister chromatid cohesion 1 (DSCC1) combines with chromosome transmission-fidelity protein 18 (CTF18) to form a CTF18-DSCC1-CTF8 (CTF18-1-8) module, which in combination with CTF18-replication factor C (RFC) acts as a proliferating cell nuclear antigen (PCNA) loader during DNA replication-associated processes. It was found that DSCC1 was overexpressed in tumor tissues from patients with colon cancer and that the survival probability of patients with colon cancer was lower when the expression of cytosolic DSCC1 was higher in tumor regions (P=0.047). By using DSCC1- or CTF18-knockdown cell lines (HCT116-shDSCC1 or HCT116-shCTF18, respectively), it was confirmed that DSCC1-knockdown inhibits cell proliferation and invasion, but that CTF18-knockdown does not. Tumors in mice xenografted with shDSCC1 cells were significantly smaller compared with those in mice in the mock group or those xenografted with shCTF18 cells. The shDSCC1 cells were highly sensitive to γ-irradiation and other DNA replication inhibitory treatments, resulting in low cell viability. The present results suggested that DSCC1 is the most important component in the CTF18-1-8 module for CTF18-RFC and is highly relevant to the growth and metastasis of colon cancer cells, and, therefore, it may be a potential therapeutic target for colon cancer treatment.
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Affiliation(s)
- Jong-Tae Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Hee Jun Cho
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Sang Yoon Park
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Byung Moo Oh
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Yo Sep Hwang
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kyoung Eun Baek
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Young-Ha Lee
- Department of Infection Biology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, Republic of Korea
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16
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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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17
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Xie XW, Wang XY, Liao WJ, Fei R, Cong X, Chen Q, Wei L, Chen HS, Wang Y. Effect of Upregulated DNA Replication and Sister Chromatid Cohesion 1 Expression on Proliferation and Prognosis in Hepatocellular Carcinoma. Chin Med J (Engl) 2018; 131:2827-2835. [PMID: 30511685 PMCID: PMC6278189 DOI: 10.4103/0366-6999.246076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: DNA replication and sister chromatid cohesion 1 (DSCC1) (also called DCC1) is a component of an alternative replication factor C complex that loads proliferating cell nuclear antigen onto DNA during S phase of the cell cycle. It is located at 8q24 and frequently amplified in hepatocellular carcinoma (HCC). However, the role of DSCC1 in the carcinogenesis and progress of HCC has not been fully investigated. Here, we aimed to assert the importance of DSCC1 in the HCC. Methods: In this study, copy number variation data and RNA sequencing data were used to calculate the DNA copy number and mRNA expression of DSCC1 in HCC. Quantitative polymerase chain reaction, Western blotting, and immunohistochemistry analysis were used to determine the mRNA and protein level of DSCC1 in HCC. The Kaplan–Meier analysis and univariate and multivariate Cox regression analysis were used to assess the association of DSCC1 with the overall survival (OS) of HCC patients. Moreover, lentiviral shRNA was used to knockdown DSCC1, and then, colony-forming assay, cell cycle assay, and cell proliferation assay were performed to evaluate the impact of DSCC1 silencing on HCC cell lines. Results: We found that DSCC1 was amplified and highly expressed in HCC tumor tissues than in nontumor tissues. We then found that the overexpression of both mRNA and protein of DSCC1 was linked to the bad prognosis of HCC patients. Astonishingly, the protein level of DSCC1 was an independent prognostic factor for OS (hazard ratio, 1.79; 95% confidence interval, 1.17–2.74; P = 0.007). Furthermore, the clonogenic capacity of DSCC1-amplified HCC cell lines (MHCC-97H, MHCC-97L, and Hep3B) was significantly inhibited by transduction of a lentiviral shRNA that targets DSCC1. We also showed that knockdown of DSCC1 induced G0–G1 cell cycle arrest (increased from 60% to more than 80%) and greatly inhibited the proliferation of HCC cell lines. Conclusion: These results suggest that DSCC1 is a putative HCC driver gene that promotes proliferation and is associated with poor prognosis in HCC.
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Affiliation(s)
- Xing-Wang Xie
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xue-Yan Wang
- Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Peking University People's Hospital, Beijing 100044, China
| | - Wei-Jia Liao
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Ran Fei
- Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Peking University People's Hospital, Beijing 100044, China
| | - Xu Cong
- Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Peking University People's Hospital, Beijing 100044, China
| | - Qian Chen
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Lai Wei
- Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Peking University People's Hospital, Beijing 100044, China
| | - Hong-Song Chen
- Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Peking University People's Hospital, Beijing 100044, China
| | - Yu Wang
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
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18
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Xu W, Rao Q, An Y, Li M, Zhang Z. Identification of biomarkers for Barcelona Clinic Liver Cancer staging and overall survival of patients with hepatocellular carcinoma. PLoS One 2018; 13:e0202763. [PMID: 30138346 PMCID: PMC6107203 DOI: 10.1371/journal.pone.0202763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of the current study was to identify biomarkers that correlate with the Barcelona Clinic Liver Cancer (BCLC) staging system and prognosis of patients with hepatocellular carcinoma (HCC). We downloaded 4 gene expression datasets from the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo), and screened for genes that were differentially expressed between HCC and normal liver tissues, using significance analysis of the microarray algorithm. We used a weighted gene co-expression network analysis (WGCNA) to identify hub genes that correlate with BCLC staging, functional enrichment analysis to associate hub genes with their functions, protein-protein interaction network analysis to identify interactions among hub genes, UALCAN analysis to assess gene expression levels based on tumour stage, and survival analyses to clarify the effects of hub genes on patients’ overall survival (OS). We identified 50 relevant hub genes using WGCNA; among them, 13 genes (including TIGD5, C8ORF33, NUDCD1, INSB8, and STIP1) correlated with OS and BCLC staging. Significantly enriched gene ontology biological process terms included RNA processing, non-coding RNA processing and phosphodiester bond hydrolysis, and 6 genes were found to interact with 10 or more hub genes. We identified several candidate biomarkers that correlate with BCLC staging and OS of HCC. These genes might be used for prognostic assessment and selection of HCC patients for surgery, especially those with intermediate or advanced disease.
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Affiliation(s)
- Wei Xu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, P.R. China
| | - Quan Rao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, P.R. China
| | - Yongbo An
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, P.R. China
| | - Mengyi Li
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, P.R. China
| | - Zhongtao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, National Clinical Research Center for Digestive Diseases, Beijing, P.R. China
- * E-mail:
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19
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Grabarczyk DB, Silkenat S, Kisker C. Structural Basis for the Recruitment of Ctf18-RFC to the Replisome. Structure 2017; 26:137-144.e3. [PMID: 29225079 DOI: 10.1016/j.str.2017.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/20/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022]
Abstract
Ctf18-RFC is an alternative PCNA loader which plays important but poorly understood roles in multiple DNA replication-associated processes. To fulfill its specialist roles, the Ctf18-RFC clamp loader contains a unique module in which the Dcc1-Ctf8 complex is bound to the C terminus of Ctf18 (the Ctf18-1-8 module). Here, we report the structural and functional characterization of the heterotetrameric complex formed between Ctf18-1-8 and a 63 kDa fragment of DNA polymerase ɛ. Our data reveal that Ctf18-1-8 binds stably to the polymerase and far from its other functional sites, suggesting that Ctf18-RFC could be associated with Pol ɛ throughout normal replication as the leading strand clamp loader. We also show that Pol ɛ and double-stranded DNA compete to bind the same winged-helix domain on Dcc1, with Pol ɛ being the preferred binding partner, thus suggesting that there are two alternative pathways to recruit Ctf18-RFC to sites of replication.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
| | - Sabrina Silkenat
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
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20
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Baur B, Bozdag S. ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. Genomics 2017; 109:233-240. [PMID: 28438487 DOI: 10.1016/j.ygeno.2017.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/19/2017] [Accepted: 04/20/2017] [Indexed: 12/12/2022]
Abstract
Copy number amplifications and deletions that are recurrent in cancer samples harbor genes that confer a fitness advantage to cancer tumor proliferation and survival. One important challenge in computational biology is to separate the causal (i.e., driver) genes from passenger genes in large, aberrated regions. Many previous studies focus on the genes within the aberration (i.e., cis genes), but do not utilize the genes that are outside of the aberrated region and dysregulated as a result of the aberration (i.e., trans genes). We propose a computational pipeline, called ProcessDriver, that prioritizes candidate drivers by relating cis genes to dysregulated trans genes and biological processes. ProcessDriver is based on the assumption that a driver cis gene should be closely associated with the dysregulated trans genes and biological processes, as opposed to previous studies that assume a driver cis gene should be the most correlated gene to the copy number of an aberrated region. We applied our method on breast, bladder and ovarian cancer data from the Cancer Genome Atlas database. Our results included previously known driver genes and cancer genes, as well as potentially novel driver genes. Additionally, many genes in the final set of drivers were linked to new tumor events after initial treatment using survival analysis. Our results highlight the importance of selecting driver genes based on their widespread downstream effects in trans.
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Affiliation(s)
- Brittany Baur
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA
| | - Serdar Bozdag
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA.
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Oncolytic Activity of a Recombinant Measles Virus, Blind to Signaling Lymphocyte Activation Molecule, Against Colorectal Cancer Cells. Sci Rep 2016; 6:24572. [PMID: 27090874 PMCID: PMC4835780 DOI: 10.1038/srep24572] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/31/2016] [Indexed: 12/13/2022] Open
Abstract
Oncolytic virotherapy is a distinctive antitumor therapy based on the cancer-cell-specific infectivity and killing activity of viruses, which exert a considerable antitumor effect with only a few treatments. Because colorectal cancer cells often acquire resistance to the molecular-targeted therapies and alternative treatments are called for, in this study, we evaluated the oncolytic activity against colorectal cancer cells of a recombinant measles virus (rMV-SLAMblind), which is blind to signaling lymphocytic activation molecule (SLAM) and infects target cells via nectin-4/poliovirus receptor-related 4 protein. We examined 10 cell lines including 8 cell lines that were resistant to epidermal-growth-factor-receptor (EGFR) targeted therapy. rMV-SLAMblind infected and lysed the nectin-4-positive cell lines dependently on nectin-4 expression, in spite of mutation in EGFR cascade. Tumour progression in xenograft models was also abrogated by the virus, and the infection of cancer cells in vivo by the virus was demonstrated with both flow cytometry and a histological analysis. Therefore, rMV-SLAMblind is considered a novel therapeutic agent for colorectal cancers, including those resistant to molecular-targeted therapies.
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