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Wen W, Zhang WL, Tan R, Zhong TT, Zhang MR, Fang XS. Progress in deciphering the role of p53 in diffuse large B-cell lymphoma: mechanisms and therapeutic targets. Am J Cancer Res 2024; 14:3280-3293. [PMID: 39113862 PMCID: PMC11301306 DOI: 10.62347/lhio8294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/30/2024] [Indexed: 08/10/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma subtype, accounting for 30%-40% of non-Hodgkin lymphoma in adults. The mechanisms underlying DLBCL occurrence are extremely complex, and involve the B-cell receptor (BCR) and Toll-like receptor (TLR) signaling pathways, as well as genetic abnormalities and other factors. With the development of high-throughput sequencing, an increasing number of abnormal genes have been identified in DLBCL. Among them, the tumor protein p53 (TP53/p53) gene is important in DLBCL occurrence. Patients with DLBCL carrying TP53 gene abnormalities generally have poor prognosis and studies of p53 have potential to provide a better basis for their treatment. Normally, p53 is maintained at low levels through its interaction with murine double minute 2 (MDM2), and prevents tumorigenesis by mediating cell cycle arrest, apoptosis, and repair of damaged cells, among other processes. Therefore, the prognosis of patients with DLBCL harboring TP53 gene abnormalities (mutations, deletions, etc.) is poor, and targeting p53 for tumor therapy has become a research hotspot, following developments in molecular biology technologies. Current treatments targeting p53 mainly act by restoring the function or promoting degradation of mutant p53, and enhancing wild-type p53 protein stability and activity. Based on the current status of p53 research, exploration of existing therapeutic methods to improve the prognosis of patients with DLBCL with TP53 abnormalities is warranted.
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Affiliation(s)
- Wen Wen
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
| | - Wen-Lu Zhang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
| | - Ran Tan
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
| | - Tan-Tan Zhong
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
| | - Mei-Rui Zhang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
| | - Xiao-Sheng Fang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021, Shandong, China
- Shandong First Medical UniversityJinan 250024, Shandong, China
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Caputa DA, Blankenship QP, Smith ZD, Huebner MM, Vetter ZA, Parks RW, Armendariz Lobera S, Leddin EM, Taylor CA, Parish CA, Miller BR. Computational drug discovery of an inhibitor of APOBEC3B as a treatment for epithelial cancers. J Biomol Struct Dyn 2023:1-14. [PMID: 38109103 DOI: 10.1080/07391102.2023.2293269] [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: 03/09/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Cancer is one of the leading causes of death in the U.S., and tumorous cancers such as cervical, lung, breast, and ovarian cancers are the most common types. APOBEC3B is a nonessential cytidine deaminase found in humans and theorized to defend against viral infection. However, overexpression of APOBEC3B is linked to cancer in humans, which makes APOBEC3B a potential cancer treatment target through competitive inhibition for several tumorous cancers. Computational studies can help reveal a small molecule inhibitor using high-throughput virtual screening of millions of candidates with relatively little cost. This study aims to narrow the field of potential APOBEC3B inhibition candidates for future in vitro assays and provide an effective scaffold for drug design studies. Another goal of this project is to provide critical amino acid targets in the active site for future drug design studies. This study simulated 7.8 million drug candidates using high-throughput virtual screening and further processed the top scoring 241 molecules from AutoDock Vina, DOCK 6, and de novo design. Using virtual screening, de novo design, and molecular dynamics simulations, a competitive inhibitor candidate was discovered with an average binding free energy score of -46.03 kcal/mol, more than 10 kcal/mol better than the substrate control (dCMP). These results indicate that this molecule (or a structural derivative) may be an effective inhibitor of APOBEC3B and prevent host genome mutagenesis resulting from protein overexpression. Another important finding is the confirmation of essential amino acid targets, such as Tyr250 and Gln213 within the active site of APOBEC3B. Therefore, study used novel computational methods to provide a theoretical scaffold for future drug design studies that may prove useful as a treatment for epithelial cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dominic A Caputa
- Physics Department, Truman State University, Kirksville, MO, USA
| | | | - Zachary D Smith
- Chemistry Department, Truman State University, Kirksville, MO, USA
- Biology Department, Truman State University, Kirksville, MO, USA
| | - Molly M Huebner
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Zoe A Vetter
- Physics Department, Truman State University, Kirksville, MO, USA
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Richard W Parks
- Chemistry Department, Truman State University, Kirksville, MO, USA
- Biology Department, Truman State University, Kirksville, MO, USA
| | | | - Emmett M Leddin
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Cooper A Taylor
- Department of Chemistry, University of Richmond, Richmond, VA, USA
| | - Carol A Parish
- Department of Chemistry, University of Richmond, Richmond, VA, USA
| | - Bill R Miller
- Chemistry Department, Truman State University, Kirksville, MO, USA
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Zong C, Zhang Z, Gao L, He J, Wang Y, Li Q, Liu X, Yang J, Chen D, Huang R, Zheng G, Jin X, Wei W, Jia R, Shen J. APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors. Cell Death Dis 2023; 14:348. [PMID: 37270643 DOI: 10.1038/s41419-023-05867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023]
Abstract
The cytidine deaminase, Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B, herein termed A3B), is a critical mutation driver that induces genomic instability in cancer by catalyzing cytosine-to-thymine (C-to-T) conversion and promoting replication stress (RS). However, the detailed function of A3B in RS is not fully determined and it is not known whether the mechanism of A3B action can be exploited for cancer therapy. Here, we conducted an immunoprecipitation-mass spectrometry (IP-MS) study and identified A3B to be a novel binding component of R-loops, which are RNA:DNA hybrid structures. Mechanistically, overexpression of A3B exacerbated RS by promoting R-loop formation and altering the distribution of R-loops in the genome. This was rescued by the R-loop gatekeeper, Ribonuclease H1 (RNASEH1, herein termed RNH1). In addition, a high level of A3B conferred sensitivity to ATR/Chk1 inhibitors (ATRi/Chk1i) in melanoma cells, which was dependent on R-loop status. Together, our results provide novel insights into the mechanistic link between A3B and R-loops in the promotion of RS in cancer. This will inform the development of markers to predict the response of patients to ATRi/Chk1i.
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Affiliation(s)
- Chunyan Zong
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Li Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiran Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoting Liu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Di Chen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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