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Dai L, Yu P, Fan H, Xia W, Zhao Y, Zhang P, Zhang JZH, Zhang H, Chen Y. Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification. Int J Mol Sci 2024; 25:7982. [PMID: 39063224 PMCID: PMC11277333 DOI: 10.3390/ijms25147982] [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: 06/07/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA-PKcs is a crucial protein target involved in DNA repair and response pathways, with its abnormal activity closely associated with the occurrence and progression of various cancers. In this study, we employed a deep learning-based screening and molecular dynamics (MD) simulation-based pipeline, identifying eight candidates for DNA-PKcs targets. Subsequent experiments revealed the effective inhibition of DNA-PKcs-mediated cell proliferation by three small molecules (5025-0002, M769-1095, and V008-1080). These molecules exhibited anticancer activity with IC50 (inhibitory concentration at 50%) values of 152.6 μM, 30.71 μM, and 74.84 μM, respectively. Notably, V008-1080 enhanced homology-directed repair (HDR) mediated by CRISPR/Cas9 while inhibiting non-homologous end joining (NHEJ) efficiency. Further investigations into the structure-activity relationships unveiled the binding sites and critical interactions between these small molecules and DNA-PKcs. This is the first application of DeepBindGCN_RG in a real drug screening task, and the successful discovery of a novel DNA-PKcs inhibitor demonstrates its efficiency as a core component in the screening pipeline. Moreover, this study provides important insights for exploring novel anticancer therapeutics and advancing the development of gene editing techniques by targeting DNA-PKcs.
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Affiliation(s)
- Liujiang Dai
- Department of Physiology, Guangxi University of Chinese Medicine, Nanning 530200, China
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-Based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pengfei Yu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Wei Xia
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yaopeng Zhao
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Pengfei Zhang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - John Z. H. Zhang
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Haiping Zhang
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Yang K, Zhu T, Yin J, Zhang Q, Li J, Fan H, Han G, Xu W, Liu N, Lv X. The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis. J Genet Genomics 2024; 51:594-607. [PMID: 38403115 DOI: 10.1016/j.jgg.2024.02.003] [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: 10/23/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The post-transcriptional regulation of mRNA is a crucial component of gene expression. The disruption of this process has detrimental effects on the normal development and gives rise to various diseases. Searching for novel post-transcriptional regulators and exploring their roles are essential for understanding development and disease. Through a multimodal analysis of red blood cell trait genome-wide association studies (GWAS) and transcriptomes of erythropoiesis, we identify FAM46C, a non-canonical RNA poly(A) polymerase, as a necessary factor for proper red blood cell development. FAM46C is highly expressed in the late stages of the erythroid lineage, and its developmental upregulation is controlled by an erythroid-specific enhancer. We demonstrate that FAM46C stabilizes mRNA and regulates erythroid differentiation in a polymerase activity-dependent manner. Furthermore, we identify transcripts of lysosome and mitochondria components as highly confident in vivo targets of FAM46C, which aligns with the need of maturing red blood cells for substantial clearance of organelles and maintenance of cellular redox homeostasis. In conclusion, our study unveils a unique role of FAM46C in positively regulating lysosome and mitochondria components, thereby promoting erythropoiesis.
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Affiliation(s)
- Ke Yang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China; The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
| | - Tianqi Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jiaying Yin
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Qiaoli Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jing Li
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hong Fan
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Gaijing Han
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Weiyin Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Nan Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China.
| | - Xiang Lv
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
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Lai G, De Grossi F, Catusi I, Pesce E, Manfrini N. Dissecting the Puzzling Roles of FAM46C: A Multifaceted Pan-Cancer Tumour Suppressor with Increasing Clinical Relevance. Cancers (Basel) 2024; 16:1706. [PMID: 38730656 PMCID: PMC11083040 DOI: 10.3390/cancers16091706] [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: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
FAM46C is a well-established tumour suppressor with a role that is not completely defined or universally accepted. Although FAM46C expression is down-modulated in several tumours, significant mutations in the FAM46C gene are only found in multiple myeloma (MM). Consequently, its tumour suppressor activity has primarily been studied in the MM context. However, emerging evidence suggests that FAM46C is involved also in other cancer types, namely colorectal, prostate and gastric cancer and squamous cell and hepatocellular carcinoma, where FAM46C expression was found to be significantly reduced in tumoural versus non-tumoural tissues and where FAM46C was shown to possess anti-proliferative properties. Accordingly, FAM46C was recently proposed to function as a pan-cancer prognostic marker, bringing FAM46C under the spotlight and attracting growing interest from the scientific community in the pathways modulated by FAM46C and in its mechanistic activity. Here, we will provide the first comprehensive review regarding FAM46C by covering (1) the intracellular pathways regulated by FAM46C, namely the MAPK/ERK, PI3K/AKT, β-catenin and TGF-β/SMAD pathways; (2) the models regarding its mode of action, specifically the poly(A) polymerase, intracellular trafficking modulator and inhibitor of centriole duplication models, focusing on connections and interdependencies; (3) the regulation of FAM46C expression in different environments by interferons, IL-4, TLR engagement or transcriptional modulators; and, lastly, (4) how FAM46C expression levels associate with increased/decreased tumour cell sensitivity to anticancer agents, such as bortezomib, dexamethasone, lenalidomide, pomalidomide, doxorubicin, melphalan, SK1-I, docetaxel and norcantharidin.
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Affiliation(s)
- Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federica De Grossi
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Ilaria Catusi
- SC Clinical Pathology, SS Medical Genetics Laboratory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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Han J, Lv X, Zhang Y, Wang J, Fan D, Dong S. Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits. Anal Chem 2023; 95:16725-16732. [PMID: 37906527 DOI: 10.1021/acs.analchem.3c03793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Intelligent Wearable Engineering Research Center of Qingdao, Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. SCIENCE ADVANCES 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Hanamura I. Multiple myeloma with high-risk cytogenetics and its treatment approach. Int J Hematol 2022; 115:762-777. [PMID: 35534749 PMCID: PMC9160142 DOI: 10.1007/s12185-022-03353-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
Despite substantial advances in anti-myeloma treatments, early recurrence and death remain an issue in certain subpopulations. Cytogenetic abnormalities (CAs) are the most widely accepted predictors for poor prognosis in multiple myeloma (MM), such as t(4;14), t(14;16), t(14;20), gain/amp(1q21), del(1p), and del(17p). Co-existing high-risk CAs (HRCAs) tend to be associated with an even worse prognosis. Achievement of sustained minimal residual disease (MRD)-negativity has recently emerged as a surrogate for longer survival, regardless of cytogenetic risk. Information from newer clinical trials suggests that extended intensified treatment can help achieve MRD-negativity in patients with HRCAs, which may lead to improved outcomes. Therapy should be considered to include a 3- or 4-drug induction regimen (PI/IMiD/Dex or PI/IMiD/Dex/anti-CD38 antibody), auto-transplantation, and consolidation/maintenance with lenalidomide ± a PI. Results from ongoing clinical trials for enriched high-risk populations will reveal the precise efficacy of the investigated regimens. Genetic abnormalities of MM cells are intrinsic critical factors determining tumor characteristics, which reflect the natural course and drug sensitivity of the disease. This paper reviews the clinicopathological features of genomic abnormalities related to adverse prognosis, focusing on HRCAs that are the most relevant in clinical practice, and outline current optimal therapeutic approaches for newly diagnosed MM with HRCAs.
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Affiliation(s)
- Ichiro Hanamura
- Division of Hematology, Department of Internal Medicine, Aichi Medical University, 1 Karimata, Yazako, Nagakute, Aichi, 480-1195, Japan.
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Cancer Commun (Lond) 2021; 41:615-630. [PMID: 34048638 PMCID: PMC8286142 DOI: 10.1002/cac2.12163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Multiple myeloma (MM) is a hematologic malignancy characterized by the accumulation of aberrant plasma cells within the bone marrow. The high frequent mutation of family with sequence similarity 46, member C (FAM46C) is closely related with the occurrence and progression of MM. Recently, FAM46C has been identified as a non‐canonical poly(A) polymerase (PAP) that functions as a tumor suppressor in MM. This study aimed to elucidate the structural features of this novel non‐canonical PAP and how MM‐related mutations affect the structural and biochemical properties of FAM46C, eventually advancing our understandings towards FAM46C mutation‐related MM occurrence. Methods We purified and crystallized a mammalian FAM46C construct, and solved its structure. Next, we characterized the property of FAM46C as a PAP through a combination of structural analysis, site‐directed mutagenesis and biochemical assays, and by comparison with its homolog FAM46B. Finally, we structurally analyzed MM‐related FAM46C mutations and tested the enzymatic activity of corresponding mutants. Results We determined the crystal structure of a mammalian FAM46C protein at 2.35 Å, and confirmed that FAM46C preferentially consumed adenosine triphosphate (ATP) and extended A‐rich RNA substrates. FAM46C showed a weaker PAP activity than its homolog FAM46B, and this difference was largely dependent on the residue variance at particular sites. Of them, residues at positions 77, 290, and 298 of mouse FAM46C were most important for the divergence in enzymatic activity. Among the MM‐associated FAM46C mutants, those residing at the catalytic site (D90G and D90H) or putative RNA‐binding site (I155L, S156F, D182Y, F184L, Y247V, and M270V) showed abolished or compromised PAP activity of FAM46C, while N72A and S248A did not severely affect the PAP activity. FAM46C mutants D90G, D90H, I155L, S156F, F184L, Y247V, and M270V had significantly lower inhibitory effect on apoptosis of RPMI‐8226 cells as compared to wild‐type FAM46C. Conclusions FAM46C is a prokaryotic‐like PAP with preference for A‐rich RNA substrates, and showed distinct enzymatic efficiency with its homolog FAM46B. The MM‐related missense mutations of FAM46C lead to various structural and biochemical outcomes to the protein.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shi-Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yu-Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510530, P. R. China
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