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Liu X, Hu J, Zheng J. SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. Bioinformatics 2024; 40:btae016. [PMID: 38244572 PMCID: PMC10868331 DOI: 10.1093/bioinformatics/btae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
SUMMARY Synthetic lethality (SL) refers to a type of genetic interaction in which the simultaneous inactivation of two genes leads to cell death, while the inactivation of a single gene does not affect cell viability. It significantly expands the range of potential therapeutic targets for anti-cancer treatments. SL interactions are primarily identified through experimental screening and computational prediction. Although various computational methods have been proposed, they tend to ignore providing evidence to support their predictions of SL. Besides, they are rarely user-friendly for biologists who likely have limited programming skills. Moreover, the genetic context specificity of SL interactions is often not taken into consideration. Here, we introduce a web server called SL-Miner, which is designed to mine the evidence of SL relationships between a primary gene and a few candidate SL partner genes in a specific type of cancer, and to prioritize these candidate genes by integrating various types of evidence. For intuitive data visualization, SL-Miner provides a range of charts (e.g. volcano plot and box plot) to help users get insights from the data. AVAILABILITY AND IMPLEMENTATION SL-Miner is available at https://slminer.sist.shanghaitech.edu.cn.
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Affiliation(s)
- Xin Liu
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jieni Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Zheng
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai 201210, China
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Wang Y, Yan X, Qu X, Mao J, Wang J, Yang M, Tao M. Topoisomerase IIβ binding protein 1 serves as a novel prognostic biomarker for stage II-III colorectal cancer patients. Pathol Res Pract 2023; 241:154287. [PMID: 36586311 DOI: 10.1016/j.prp.2022.154287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is a commonly diagnosed human malignancy worldwide. Accumulating evidence has suggested DNA repair related proteins widely participate in CRC initiation and development. TOPBP1 is recently identified as a novel regulator for DNA repair, however, its biological role in CRC remains unknown. METHODS Firstly, the bioinformatics analysis was utilized to investigate the expression and clinical significance of TOPBP1 in CRC patients. Then, a retrospective study enrolling 129 stage II/III CRC patients was performed for validation. The CCK-8, colony formation, transwell assay and xenograft model were used to clarify the biological impact of TOPBP1 on CRC cells. Finally, transcriptome sequencing was performed to investigate the potential oncogenic mechanisms regulated by TOPBP1 in CRC development. RESULTS The expression of TOPBP1 was significantly higher in CRC tissues than that in normal tissues. High TOPBP1 expression was an independent unfavorable prognostic factor for overall and disease-free survival in II/III CRC patients. Knockdown of TOPBP1 not only significantly inhibited the proliferation, colony formation, invasion, migration and epithelial-mesenchymal transition (EMT) molecular phenotype of CRC cells, while the opposite was for TOPBP1 expression. Moreover, knockdown of TOPBP1 slowed down the growth speed of xenografts. The transcriptome sequencing identified MAP3K3 as a downstream gene of TOPBP1 and MAP3K3 knockdown inhibited the EMT molecular phenotype in CRC cells. Finally, the rescue assay indicated MAP3K3 overexpression counteracted the inhibitory effect of TOPBP1 knockdown on the proliferation, colony formation, invasion, migration and EMT phenotype of CRC cells. CONCLUSION TOPBP1 promotes the malignant progression of CRC through MAP3K3 induced EMT. TOPBP1 is a promising clinical biomarker or therapeutical target for CRC patients.
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Affiliation(s)
- Ying Wang
- Department of Oncology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Xuebing Yan
- Department of Oncology, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xiao Qu
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jingxian Mao
- Department of Oncology, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Jiaxin Wang
- Department of Oncology, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Mengxue Yang
- Department of Oncology, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Min Tao
- Department of Oncology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China.
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TOPBP1 regulates resistance of gastric cancer to oxaliplatin by promoting transcription of PARP1. DNA Repair (Amst) 2022; 111:103278. [DOI: 10.1016/j.dnarep.2022.103278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022]
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Wenmaekers S, Viergever BJ, Kumar G, Kranenburg O, Black PC, Daugaard M, Meijer RP. A Potential Role for HUWE1 in Modulating Cisplatin Sensitivity. Cells 2021; 10:cells10051262. [PMID: 34065298 PMCID: PMC8160634 DOI: 10.3390/cells10051262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cisplatin is a widely used antineoplastic agent, whose efficacy is limited by primary and acquired therapeutic resistance. Recently, a bladder cancer genome-wide CRISPR/Cas9 knock-out screen correlated cisplatin sensitivity to multiple genetic biomarkers. Among the screen’s top hits was the HECT domain-containing ubiquitin E3 ligase (HUWE1). In this review, HUWE1 is postulated as a therapeutic response modulator, affecting the collision between platinum-DNA adducts and the replication fork, the primary cytotoxic action of platins. HUWE1 can alter the cytotoxic response to platins by targeting essential components of the DNA damage response including BRCA1, p53, and Mcl-1. Deficiency of HUWE1 could lead to enhanced DNA damage repair and a dysfunctional apoptotic apparatus, thereby inducing resistance to platins. Future research on the relationship between HUWE1 and platins could generate new mechanistic insights into therapy resistance. Ultimately, HUWE1 might serve as a clinical biomarker to tailor cancer treatment strategies, thereby improving cancer care and patient outcomes.
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Affiliation(s)
- Stijn Wenmaekers
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Bastiaan J. Viergever
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Gunjan Kumar
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Onno Kranenburg
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
| | - Peter C. Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
- Correspondence: (M.D.); (R.P.M.)
| | - Richard P. Meijer
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
- Correspondence: (M.D.); (R.P.M.)
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Pan C, Duan H, Wu Y, Zhu C, Yi C, Duan Y, Lu D, Guo C, Wu D, Wang Y, Fu X, Xu J, Chen Y, Luo M, Tian W, Pan T, Xu W, Zhang S, Huang J. Inhibition of DNA‑PK by gefitinib causes synergism between gefitinib and cisplatin in NSCLC. Int J Oncol 2020; 57:939-955. [PMID: 32945394 PMCID: PMC7473755 DOI: 10.3892/ijo.2020.5103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 05/04/2020] [Indexed: 01/14/2023] Open
Abstract
Lung cancer has the highest incidence and mortality rates among the malignant tumor types worldwide. Platinum‑based chemotherapy is the main treatment for advanced non‑small‑cell lung cancer (NSCLC), and epidermal growth factor receptor‑tyrosine kinase inhibitors (EGFR‑TKIs) have greatly improved the survival of patients with EGFR‑sensitive mutations. However, there is no standard therapy for treating patients who are EGFR‑TKI resistant. Combining EGFR‑TKIs and platinum‑based chemotherapy is the most popular strategy in the clinical practice. However, the synergistic mechanism between EGFR‑TKIs and platinum remains unknown. Therefore, the aim of the present study was to determine the synergistic mechanism of gefitinib (an EGFR‑TKI) and cisplatin (a main platinum‑based drug). MTT assay, apoptosis analysis, tumorsphere formation and an orthotropic xenograft mouse model were used to examine the combination effects of gefitinib and cisplatin on NSCLC. Co‑immunoprecipitation and immunofluorescence were used to identify the underlying mechanism. It was found that gefitinib could selectively inhibit EGFR from entering the nucleus, decrease DNA‑PK activity and enhance the cytotoxicity of cisplatin on NSCLC. Collectively, the results suggested that inhibition of DNA‑dependent protein kinase by gefitinib may be due to the synergistic mechanism between gefitinib and cisplatin. Thus, the present study provides a novel insight into potential biomarkers for the selection of combination therapy of gefitinib and cisplatin.
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Affiliation(s)
- Chi Pan
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Huijie Duan
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yinan Wu
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Chunpeng Zhu
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Chenghao Yi
- Department of Breast Surgery, The Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yin Duan
- Department of Breast Surgery, The Zhejiang Provincial Hospital of Traditional Chinese Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Demin Lu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Cheng Guo
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Deqi Wu
- Department of Gastrointestinal Thyroid and Breast Surgery, The Shulan (Hangzhou) Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yanyan Wang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Xianhua Fu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jing Xu
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yiding Chen
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Meng Luo
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Wei Tian
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Tao Pan
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Wenhong Xu
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Suzhan Zhang
- Cancer Institute (National Ministry of Education Key Laboratory of Cancer Prevention and Intervention), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jianjin Huang
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
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Ying J, Zhou D, Gu T, Huang J, Liu H. Pretreatment albumin/fibrinogen ratio as a promising predictor for the survival of advanced non small-cell lung cancer patients undergoing first-line platinum-based chemotherapy. BMC Cancer 2019; 19:288. [PMID: 30925910 PMCID: PMC6441182 DOI: 10.1186/s12885-019-5490-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND This study aimed to identify potential predictive factors for the survival of advanced non small-cell lung cancer (NSCLC) patients undergoing first-line platinum-based chemotherapy. METHODS A total of 270 advanced NSCLC patients who underwent first-line platinum-based chemotherapy from June, 2011 to June, 2015 were enrolled. A receiver operating characteristic (ROC) curve analysis was used to evaluate the predictive value of the albumin-to-fibrinogen ratio (AFR) for overall survival (OS). The predictive factors for survival were evaluated by univariate and multivariate analyses via the Cox proportional hazards regression model. The OS and progression free survival (PFS) results were determined via the Kaplan-Meier method using the log-rank analysis. RESULTS Based on the results of the ROC curve analysis, 8.02 was accepted as the cut-off AFR value for OS. The metastasis stage (M0 vs M1a/b, HR: 1.73, 95% CI: 1.15-2.59, P = 0.020) and AFR (≤8.02 vs > 8.02, HR: 1.80, 95% CI: 1.09-2.78, P = 0.025) were two independent risk factors for PFS by multivariate Cox regression analysis. The AFR (≤8.02 vs > 8.02, HR: 1.79, 95% CI: 1.11-2.59, P = 0.029) was a significant predictive factor for OS in advanced NSCLC patients. The PFS (P = 0.008) and OS (P = 0.003) in the high AFR group were significantly improved compared with those in the low AFR group via the Kaplan-Meier method using the log-rank analysis. CONCLUSIONS The AFR could be a potential effective predictive factor for the survival in advanced NSCLC patients undergoing first-line platinum-based chemotherapy.
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Affiliation(s)
- Jun Ying
- Department of Respiratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, NO. 41, Xibei Street, Ningbo, 315000, Zhejiang Province, China
| | - Danfei Zhou
- Department of Respiratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, NO. 41, Xibei Street, Ningbo, 315000, Zhejiang Province, China
| | - Tongjie Gu
- Department of Respiratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, NO. 41, Xibei Street, Ningbo, 315000, Zhejiang Province, China
| | - Jianda Huang
- Department of Respiratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, NO. 41, Xibei Street, Ningbo, 315000, Zhejiang Province, China
| | - Haijian Liu
- Department of Respiratory, Hwa Mei Hospital, University of Chinese Academy of Sciences, NO. 41, Xibei Street, Ningbo, 315000, Zhejiang Province, China.
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Comparative sequence analysis of patient-matched primary colorectal cancer, metastatic, and recurrent metastatic tumors after adjuvant FOLFOX chemotherapy. BMC Cancer 2019; 19:255. [PMID: 30898102 PMCID: PMC6429751 DOI: 10.1186/s12885-019-5479-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Background In the era of genome-guided personalized cancer treatment, we must understand chemotherapy-induced genomic changes in tumors. This study evaluated whether adjuvant FOLFOX chemotherapy modifies the mutational profile of recurrent colorectal cancer (CRC). Methods Whole exome sequencing was performed on samples from primary CRC tumors, untreated metastatic tumors, and recurrent tumors following adjuvant FOLFOX chemotherapy. The samples were resected from four patients. Results The number of mutations or the mutation spectrum in individual patients was nearly identical. Copy number variants persisted regardless of FOLFOX therapy administration. The genomic signature of oxaliplatin exposure (G > T/C > A, T > A/A > T) was not enriched after FOLFOX chemotherapy. Overlapping single nucleotide variants (SNVs) and indels remained in 26–65% of the patient-matched tumor samples. One patient harbored an AKT1 E17K mutation in the recurrent tumor, whereas PIK3CA E542K and E88Q mutations were detected in the primary and untreated metastatic tumor samples. Genes related to intracellular Ca2+ homeostasis were enriched among the genes uniquely mutated after FOLFOX chemotherapy. Conclusions We found that the mutation rates, mutation spectrum, and copy number variants were nearly identical regardless of the administration of FOLFOX therapy in the four CRC cases. The mutational discordance between the patient-matched tumor samples is likely caused by tumor heterogeneity and chemotherapy-induced clonal selection. These findings might be useful as pilot data for larger studies to clarify the changes in the mutational landscape induced by adjuvant FOLFOX chemotherapy. Electronic supplementary material The online version of this article (10.1186/s12885-019-5479-6) contains supplementary material, which is available to authorized users.
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Calcein-acetoxymethy ester enhances the antitumor effects of doxorubicin in nonsmall cell lung cancer by regulating the TopBP1/p53RR pathway. Anticancer Drugs 2017. [PMID: 28628491 DOI: 10.1097/cad.0000000000000527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Calcein acetoxymethyl ester (calcein-AM) treatment has been reported to exert antitumor effects in certain cancer cells; however, the detailed mechanism of action of calcein-AM in cancers remains unclear, especially in nonsmall cell lung cancer (NSCLC). This study focused on the function and mechanism of action of calcein-AM in NSCLC. We used cell viability assays, western blotting, and EdU proliferation assay combined with calcein-AM treatment or siRNA interference to investigate the role of topoisomerase IIβ binding protein 1 (TopBP1) and p53 in NSCLC chemotherapy. We found that calcein-AM has antitumor effects in lung cancer and enhances the antitumor effects of doxorubicin in NSCLC. Furthermore, we found that TopBP1, which we previously showed was involved in doxorubicin resistance through upregulation of aberrant p53, was involved in calcein-AM-mediated increased doxorubicin sensitivity. Doxorubicin upregulated the expression of aberrant p53. Calcein-AM repressed the expression of TopBP1, which resulted in reduced expression of aberrant p53 and disrupted the antiapoptotic activity mediated by the TopBP1/mutp53 pathway in NSCLC. Together, our findings show that calcein-AM, the cell-permeable derivative of calcein, exerts significant antitumor effects in NSCLC, and can enhance the antitumor effect of doxorubicin by regulating the TopBP1/mutp53 pathway. These findings provide novel insight into lung cancer treatment.
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