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Dou Y, Ren Y, Zhao X, Jin J, Xiong S, Luo L, Xu X, Yang X, Yu J, Guo L, Liang T. CSSLdb: Discovery of cancer-specific synthetic lethal interactions based on machine learning and statistic inference. Comput Biol Med 2024; 170:108066. [PMID: 38310806 DOI: 10.1016/j.compbiomed.2024.108066] [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: 11/04/2023] [Revised: 12/22/2023] [Accepted: 01/27/2024] [Indexed: 02/06/2024]
Abstract
Synthetic lethality (SL) occurs when the inactivation of two genes results in cell death while the inactivation of either gene alone is non-lethal. SL-based therapy has become a promising anti-cancer treatment option with the increasing researches and applications in clinical practice, while the specific therapeutic opportunities for various cancers have not yet been comprehensively investigated. Herein, we described a computational approach based on machine learning and statistical inference to discover the cancer-specific synthetic lethal interactions. First, Random Forest and One-Class SVM were used to perform cancer unbiased prediction of synthetic lethality. Then, two strategies, including mutual exclusivity and differential expression, were used to screen cancer-specific synthetic lethal interactions, resulting in 14,582 SL gene pairs in 33 cancer types. Finally, we developed a freely available database of CSSLdb (Cancer Specific Synthetic Lethality Database, http://www.tmliang.cn/CSSL/) to present cancer-specific synthetic lethal genetic interactions, which would enrich the relevant research and contribute to underlying therapy strategies based on synthetic lethality.
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Affiliation(s)
- Yuyang Dou
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Yujie Ren
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Xinmiao Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Shizheng Xiong
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xinru Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xueni Yang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China.
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Ma XY, Zhao JF, Ruan Y, Zhang WM, Zhang LQ, Cai ZD, Xu HQ. ML216-Induced BLM Helicase Inhibition Sensitizes PCa Cells to the DNA-Crosslinking Agent Cisplatin. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248790. [PMID: 36557923 PMCID: PMC9788632 DOI: 10.3390/molecules27248790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Using standard DNA-damaging medicines with DNA repair inhibitors is a promising anticancer tool to achieve better therapeutic responses and reduce therapy-related side effects. Cell viability assay, neutral comet assay, western blotting (WB), and cell cycle and apoptosis analysis were used to determine the synergistic effect and mechanism of ML216, a Bloom syndrome protein (BLM) helicase inhibitor, and cisplatin (CDDP), a DNA-crosslinking agent, in PCa cells. Based on the online database research, our findings revealed that BLM was substantially expressed in PCa, which is associated with a bad prognosis for PCa patients. The combination of ML216 and CDDP improved the antiproliferative properties of three PCa cell lines. As indicated by the increased production of γH2AX and caspase-3 cleavage, ML216 significantly reduced the DNA damage-induced high expression of BLM, making PC3 more susceptible to apoptosis and DNA damage caused by CDDP. Furthermore, the combination of ML216 and CDDP increased p-Chk1 and p-Chk2 expression. The DNA damage may have triggered the ATR-Chk1 and ATM-Chk2 pathways simultaneously. Our results demonstrated that ML216 and CDDP combination therapy exhibited synergistic effects, and combination chemotherapy could be a novel anticancer tactic.
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Affiliation(s)
- Xiao-Yan Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Institute of Technology, College of Food and Pharmaceutical Engineering, Guiyang 550003, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jia-Fu Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang-Ming Zhang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Guiyang 550014, China
| | - Lun-Qing Zhang
- Guizhou Institute of Technology, College of Food and Pharmaceutical Engineering, Guiyang 550003, China
| | - Zheng-Dong Cai
- Guizhou Institute of Technology, College of Food and Pharmaceutical Engineering, Guiyang 550003, China
| | - Hou-Qiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence: ; Tel.: +86-13765056884
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Zhang R, Liu Z, Chang X, Gao Y, Han H, Liu X, Cai H, Fu Q, Liu L, Yin K. Clinical significance of chromosomal integrity in gastric cancers. Int J Biol Markers 2022; 37:296-305. [PMID: 35722719 DOI: 10.1177/03936155221106217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND A whole-exome or targeted cancer genes panel by next-generation sequencing has been used widely in assisting individualized treatment decisions. Currently, multiple algorithms are developed to estimate DNA copy numbers based on sequencing data, which makes a comprehensive global glance at chromosomal integrity possible. We aim to classify gastric cancers based on chromosomal integrity to guide personalized therapy. METHODS We investigated copy number variations (CNV) across the entire genome of 124 gastric carcinomas via exome or targeted sequencing. Chromosomal integrity was classified as chromosomal stability (CS), chromosomal instability (CIN) and intermediate state (CIN/CS) based on CNV results. Chromosomal integrity was correlated to molecular features and clinical characteristics. RESULTS According the states of chromosomal integrity, gastric carcinomas can be stratified into two cohorts: CS and CIN. Our results showed a significant relationship between CIN status and TP53 mutation, but not RB1, phosphatase and tensin homolog (PTEN), or other reported DNA damage repair genes. The mutation frequency of the TP53 gene had great relevance. Our study initially revealed clinical significance of chromosomal integrity that CIN patients were prone to HER2-positive and mucinous adenocarcinoma, while CS patients were a diffuse subtype and poorly differentiated but had longer overall survival. CONCLUSIONS We classified gastric carcinomas into two states of chromosomal integrity with clinical implications. The dichotomy is applicable to clinical transformation. We proposed that classifying gastric cancers based on chromosomal integrity would enable us to achieve personalized therapy for patients and may be beneficial to patient stratification in future clinical trials.
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Affiliation(s)
- Rukui Zhang
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Zhaorui Liu
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xusheng Chang
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yuan Gao
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Huan Han
- Department of Pathology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaona Liu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Hui Cai
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Qiqing Fu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China
| | - Lei Liu
- Institutes of Biomedical Sciences, 262117Fudan University, Shanghai, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kai Yin
- Department of Gastrointestinal Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, China
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Mfarej MG, Skibbens RV. DNA damage induces Yap5-dependent transcription of ECO1/CTF7 in Saccharomyces cerevisiae. PLoS One 2020; 15:e0242968. [PMID: 33373396 PMCID: PMC7771704 DOI: 10.1371/journal.pone.0242968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast Eco1 (ESCO2 in humans) acetyltransferase converts chromatin-bound cohesins to a DNA tethering state, thereby establishing sister chromatid cohesion. Eco1 establishes cohesion during DNA replication, after which Eco1 is targeted for degradation by SCF E3 ubiquitin ligase. SCF E3 ligase, and sequential phosphorylations that promote Eco1 ubiquitination and degradation, remain active throughout the M phase. In this way, Eco1 protein levels are high during S phase, but remain low throughout the remaining cell cycle. In response to DNA damage during M phase, however, Eco1 activity increases-providing for a new wave of cohesion establishment (termed Damage-Induced Cohesion, or DIC) which is critical for efficient DNA repair. To date, little evidence exists as to the mechanism through which Eco1 activity increases during M phase in response to DNA damage. Possibilities include that either the kinases or E3 ligase, that target Eco1 for degradation, are inhibited in response to DNA damage. Our results reveal instead that the degradation machinery remains fully active during M phase, despite the presence of DNA damage. In testing alternate models through which Eco1 activity increases in response to DNA damage, the results reveal that DNA damage induces new transcription of ECO1 and at a rate that exceeds the rate of Eco1 turnover, providing for rapid accumulation of Eco1 protein. We further show that DNA damage induction of ECO1 transcription is in part regulated by Yap5-a stress-induced transcription factor. Given the role for mutated ESCO2 (homolog of ECO1) in human birth defects, this study highlights the complex nature through which mutation of ESCO2, and defects in ESCO2 regulation, may promote developmental abnormalities and contribute to various diseases including cancer.
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Affiliation(s)
- Michael G. Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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Gallegos JE, Adames NR, Rogers MF, Kraikivski P, Ibele A, Nurzynski-Loth K, Kudlow E, Murali TM, Tyson JJ, Peccoud J. Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants. NPJ Syst Biol Appl 2020; 6:11. [PMID: 32376972 PMCID: PMC7203125 DOI: 10.1038/s41540-020-0134-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/06/2020] [Indexed: 11/09/2022] Open
Abstract
Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of the regulatory networks controlling the division of eukaryotic cells. These models capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing the functions of small numbers of genes, and large-scale genetic interaction screens that provide a systems-level perspective on the cell division process. The former is insufficient to capture the interconnectivity of the genetic control network, while the latter is fraught with irreproducibility issues. Here, we describe a hybrid approach in which the 630 genetic interactions between 36 cell-cycle genes are quantitatively estimated by high-throughput phenotyping with an unprecedented number of biological replicates. Using this approach, we identify a subset of high-confidence genetic interactions, which we use to refine a previously published mathematical model of the cell cycle. We also present a quantitative dataset of the growth rate of these mutants under six different media conditions in order to inform future cell cycle models.
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Affiliation(s)
- Jenna E Gallegos
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA
| | - Neil R Adames
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA.,New Culture, Inc., San Francisco, CA, USA
| | | | - Pavel Kraikivski
- Virginia Tech, Academy of Integrated Sciences, Blacksburg, VA, USA
| | - Aubrey Ibele
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA
| | - Kevin Nurzynski-Loth
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA
| | - Eric Kudlow
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA
| | - T M Murali
- Virginia Tech, Computer Science, Blacksburg, VA, USA
| | - John J Tyson
- Virginia Tech, Biological Sciences, Blacksburg, VA, USA
| | - Jean Peccoud
- Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA. .,GenoFAB, Inc., Fort Collins, CO, USA.
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Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms. J Microbiol 2019; 58:81-91. [DOI: 10.1007/s12275-020-9520-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
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