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Hu LZ, Douglass E, Turunen M, Pampou S, Grunn A, Realubit R, Antolin AA, Wang ALE, Li H, Subramaniam P, Mundi PS, Karan C, Alvarez M, Califano A. Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.08.561457. [PMID: 37873470 PMCID: PMC10592689 DOI: 10.1101/2023.10.08.561457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The Mechanism of Action (MoA) of a drug is generally represented as a small, non-tissue-specific repertoire of high-affinity binding targets. Yet, drug activity and polypharmacology are increasingly associated with a broad range of off-target and tissue-specific effector proteins. To address this challenge, we have leveraged a microfluidics-based Plate-Seq technology to survey drug perturbational profiles representing >700 FDA-approved and experimental oncology drugs, in cell lines selected as high-fidelity models of 23 aggressive tumor subtypes. Built on this dataset, we implemented an efficient computational framework to define a tissue-specific protein activity landscape of these drugs and reported almost 50 million differential protein activities derived from drug perturbations vs. vehicle controls. These analyses revealed thousands of highly reproducible and novel, drug-mediated modulation of tissue-specific targets, leading to generation of a proteome-wide drug functional network, characterization of MoA-related drug clusters and off-target effects, dramatical expansion of druggable human proteome, and identification and experimental validation of novel, tissue-specific inhibitors of undruggable oncoproteins, most never reported before. The drug perturbation profile resource described here represents the first, large-scale, whole-genome-wide, RNA-Seq based dataset assembled to date, with the proposed framework, which is easily extended to elucidating the MoA of novel small-molecule libraries, facilitates mechanistic exploration of drug functions, supports systematic and quantitative approaches to precision oncology, and serves as a rich data foundation for drug discovery.
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Wu Y, Li B, Yu X, Liu Y, Chui R, Sun K, Geng D, Ma L. Histone deacetylase 6 as a novel promising target to treat cardiovascular disease. CANCER INNOVATION 2024; 3:e114. [PMID: 38947757 PMCID: PMC11212282 DOI: 10.1002/cai2.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 07/02/2024]
Abstract
Histone deacetylase 6 (HDAC6) belongs to a class of epigenetic targets that have been found to be a key protein in the association between tumors and cardiovascular disease. Recent studies have focused on the crucial role of HDAC6 in regulating cardiovascular diseases such as atherosclerosis, myocardial infarction, myocardial hypertrophy, myocardial fibrosis, hypertension, pulmonary hypertension, and arrhythmia. Here, we review the association between HDAC6 and cardiovascular disease, the research progress of HDAC6 inhibitors in the treatment of cardiovascular disease, and discuss the feasibility of combining HDAC6 inhibitors with other therapeutic agents to treat cardiovascular disease.
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Affiliation(s)
- Ya‐Xi Wu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Bing‐Qian Li
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Xiao‐Qian Yu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Yu‐Lin Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Rui‐Hao Chui
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Kai Sun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
| | - Dian‐Guang Geng
- Key Laboratory of Cardio‐Cerebrovascular Drugs'China Meheco Topfond Pharmaceutical Co.ZhumadianHenanChina
| | - Li‐Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical ScienceZhengzhou UniversityZhengzhouHenanChina
- Key Laboratory of Cardio‐Cerebrovascular Drugs'China Meheco Topfond Pharmaceutical Co.ZhumadianHenanChina
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3
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Zhou L, Yu CW. Epigenetic modulations in triple-negative breast cancer: Therapeutic implications for tumor microenvironment. Pharmacol Res 2024; 204:107205. [PMID: 38719195 DOI: 10.1016/j.phrs.2024.107205] [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: 02/24/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype lacking estrogen receptors, progesterone receptors and lacks HER2 overexpression. This absence of critical molecular targets poses significant challenges for conventional therapies. Immunotherapy, remarkably immune checkpoint blockade, offers promise for TNBC treatment, but its efficacy remains limited. Epigenetic dysregulation, including altered DNA methylation, histone modifications, and imbalances in regulators such as BET proteins, plays a crucial role in TNBC development and resistance to treatment. Hypermethylation of tumor suppressor gene promoters and the imbalance of histone methyltransferases such as EZH2 and histone deacetylases (HDACs) profoundly influence tumor cell proliferation, survival, and metastasis. In addition, epigenetic alterations critically shape the tumor microenvironment (TME), including immune cell composition, cytokine signaling, and immune checkpoint expression, ultimately contributing to immune evasion. Targeting these epigenetic mechanisms with specific inhibitors such as EZH2 and HDAC inhibitors in combination with immunotherapy represents a compelling strategy to remodel the TME, potentially overcoming immune evasion and enhancing therapeutic outcomes in TNBC. This review aims to comprehensively elucidate the current understanding of epigenetic modulation in TNBC, its influence on the TME, and the potential of combining epigenetic therapies with immunotherapy to overcome the challenges posed by this aggressive breast cancer subtype.
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Affiliation(s)
- Linlin Zhou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chen-Wei Yu
- Department of Statistics and Information Science, Fu Jen Catholic University, New Taipei City, Taiwan.
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4
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Fernández EC, Tomassoni L, Zhang X, Wang J, Obradovic A, Laise P, Griffin AT, Vlahos L, Minns HE, Morales DV, Simmons C, Gallitto M, Wei HJ, Martins TJ, Becker PS, Crawford JR, Tzaridis T, Wechsler-Reya RJ, Garvin J, Gartrell RD, Szalontay L, Zacharoulis S, Wu CC, Zhang Z, Califano A, Pavisic J. Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585370. [PMID: 38559080 PMCID: PMC10979998 DOI: 10.1101/2024.03.17.585370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis-whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations-including avapritinib, larotrectinib, and ruxolitinib-produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.
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Yue K, Sun S, Liu E, Liu J, Hou B, Qi K, Chou CJ, Jiang Y, Li X. HDAC/NAMPT dual inhibitors overcome initial drug-resistance in p53-null leukemia cells. Eur J Med Chem 2024; 266:116127. [PMID: 38224650 DOI: 10.1016/j.ejmech.2024.116127] [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: 11/05/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024]
Abstract
The occurrence of cancer is closely related to metabolism and epigenetics. Histone deacetylases (HDACs) play a crucial role in the regulation of gene expression as epigenetic regulators, while nicotinamide phosphoribosyltransferase (NAMPT) is significantly involved in maintaining cellular metabolism. In this study, we rationally designed a series of novel HDAC/NAMPT dual inhibitors based on the structural similarity between HDAC and NAMPT inhibitors. The representative compounds 39a and 39h exhibit significant selective inhibitory activity on HDAC1-3 with IC50 values of 0.71-25.1 nM, while displaying modest activity against NAMPT. Compound 39h did not exhibit inhibitory activity against 370 kinases, demonstrating its target specificity. These two compounds exhibit potent anti-proliferative activity in multiple leukemia cell lines with low nanomolar IC50s. It is worth noticing that the dual inhibitors 39a and 39h overcome the primary resistance of HDAC or NAMPT single target inhibitor in p53-null AML cell lines, with the induction of apoptosis-related cell death. NMN recovers the cell death induced by HDAC/NAMPT dual inhibitors, which indicates the lethal effects are caused by the inhibition of NAD biosynthesis pathway as well as HDAC. This research provides an effective strategy to overcome the limitations of HDAC inhibitors in treating p53-null leukemia.
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Affiliation(s)
- Kairui Yue
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - Simin Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - Enqiang Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - Jinyu Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - Baogeng Hou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - Kangjing Qi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China
| | - C James Chou
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, 29425, United States; Neuroene Therapeutics, JLABS at the Children's National Research and Innovation Campus, 7144 13th PL NW, Washington, DC, 20012-2358, United States.
| | - Yuqi Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China; Center for Targeted Protein Degradation and Drug Discovery, Ocean University of China, Qingdao, Shandong, 266003, China.
| | - Xiaoyang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266071, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China; Center for Targeted Protein Degradation and Drug Discovery, Ocean University of China, Qingdao, Shandong, 266003, China.
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6
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Chen G, Bao B, Cheng Y, Tian M, Song J, Zheng L, Tong Q. Acetyl-CoA metabolism as a therapeutic target for cancer. Biomed Pharmacother 2023; 168:115741. [PMID: 37864899 DOI: 10.1016/j.biopha.2023.115741] [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: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023] Open
Abstract
Acetyl-coenzyme A (acetyl-CoA), an essential metabolite, not only takes part in numerous intracellular metabolic processes, powers the tricarboxylic acid cycle, serves as a key hub for the biosynthesis of fatty acids and isoprenoids, but also serves as a signaling substrate for acetylation reactions in post-translational modification of proteins, which is crucial for the epigenetic inheritance of cells. Acetyl-CoA links lipid metabolism with histone acetylation to create a more intricate regulatory system that affects the growth, aggressiveness, and drug resistance of malignancies such as glioblastoma, breast cancer, and hepatocellular carcinoma. These fascinating advances in the knowledge of acetyl-CoA metabolism during carcinogenesis and normal physiology have raised interest regarding its modulation in malignancies. In this review, we provide an overview of the regulation and cancer relevance of main metabolic pathways in which acetyl-CoA participates. We also summarize the role of acetyl-CoA in the metabolic reprogramming and stress regulation of cancer cells, as well as medical application of inhibitors targeting its dysregulation in therapeutic intervention of cancers.
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Affiliation(s)
- Guo Chen
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Banghe Bao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Yang Cheng
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Minxiu Tian
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Jiyu Song
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
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7
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Zhuang A, Gu X, Ge T, Wang S, Ge S, Chai P, Jia R, Fan X. Targeting histone deacetylase suppresses tumor growth through eliciting METTL14-modified m 6 A RNA methylation in ocular melanoma. Cancer Commun (Lond) 2023; 43:1185-1206. [PMID: 37466203 PMCID: PMC10631484 DOI: 10.1002/cac2.12471] [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: 11/13/2022] [Revised: 03/31/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Diversified histone deacetylation inhibitors (HDACis) have demonstrated encouraging outcomes in multiple malignancies. N6-methyladenine (m6 A) is the most prevalent messenger RNA modification that plays an essential role in the regulation of tumorigenesis. Howbeit, an in-depth understanding of the crosstalk between histone acetylation and m6 A RNA modifications remains enigmatic. This study aimed to explore the role of histone acetylation and m6 A modifications in the regulation of tumorigenesis of ocular melanoma. METHODS Histone modification inhibitor screening was used to explore the effects of HDACis on ocular melanoma cells. Dot blot assay was used to detect the global m6 A RNA modification level. Multi-omics assays, including RNA-sequencing, cleavage under targets and tagmentation, single-cell sequencing, methylated RNA immunoprecipitation-sequencing (meRIP-seq), and m6 A individual nucleotide resolution cross-linking and immunoprecipitation-sequencing (miCLIP-seq), were performed to reveal the mechanisms of HDACis on methyltransferase-like 14 (METTL14) and FAT tumor suppressor homolog 4 (FAT4) in ocular melanoma. Quantitative real-time polymerase chain reaction (qPCR), western blotting, and immunofluorescent staining were applied to detect the expression of METTL14 and FAT4 in ocular melanoma cells and tissues. Cell models and orthotopic xenograft models were established to determine the roles of METTL14 and FAT4 in the growth of ocular melanoma. RNA-binding protein immunoprecipitation-qPCR, meRIP-seq, miCLIP-seq, and RNA stability assay were adopted to investigate the mechanism by which m6 A levels of FAT4 were affected. RESULTS First, we found that ocular melanoma cells presented vulnerability towards HDACis. HDACis triggered the elevation of m6 A RNA modification in ocular melanoma. Further studies revealed that METTL14 served as a downstream candidate for HDACis. METTL14 was silenced by the hypo-histone acetylation status, whereas HDACi restored the normal histone acetylation level of METTL14, thereby inducing its expression. Subsequently, METTL14 served as a tumor suppressor by promoting the expression of FAT4, a tumor suppressor, in a m6 A-YTH N6-methyladenosine RNA-binding protein 1-dependent manner. Taken together, we found that HDACi restored the histone acetylation level of METTL14 and subsequently elicited METTL14-mediated m6 A modification in tumorigenesis. CONCLUSIONS These results demonstrate that HDACis exert anti-cancer effects by orchestrating m6 A modification, which unveiling a "histone-RNA crosstalk" of the HDAC/METTL14/FAT4 epigenetic cascade in ocular melanoma.
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Affiliation(s)
- Ai Zhuang
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Xiang Gu
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Tongxin Ge
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Shaoyun Wang
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Shengfang Ge
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Peiwei Chai
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Renbing Jia
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
| | - Xianqun Fan
- Department of OphthalmologyShanghai Ninth People's HospitalShanghai JiaoTong University School of MedicineShanghaiP. R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular OncologyShanghaiP. R. China
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8
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Hu S, Xia K, Huang X, Zhao Y, Zhang Q, Huang D, Xu W, Chen Z, Wang C, Zhang Z. Multifunctional CaCO 3@Cur@QTX125@HA nanoparticles for effectively inhibiting growth of colorectal cancer cells. J Nanobiotechnology 2023; 21:353. [PMID: 37773145 PMCID: PMC10543835 DOI: 10.1186/s12951-023-02104-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer-related deaths in humans, and effective treatments are still needed in clinical practice. Despite significant developments in anticancer drugs and inhibitors, their poor stability, water solubility, and cellular membrane permeability limit their therapeutic efficacy. To address these issues, multifunctional CaCO3 nanoparticles loaded with Curcumin (Cur) and protein deacetylase (HDAC) inhibitor QTX125, and coated with hyaluronic acid (HA) (CaCO3@Cur@QTX125@HA), were prepared through a one-step gas diffusion strategy. Dynamic light scattering (DLS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) showed that CaCO3@Cur@QTX125@HA nanoparticles have uniform spherical morphology and elemental distribution, with diameters around 450 nm and a Zeta potential of - 8.11 mV. The controlled release of Cur from the nanoparticles was observed over time periods of 48 h. Cellular uptake showed that CaCO3@Cur@QTX125@HA nanoparticles were efficiently taken up by cancer cells and significantly inhibited their growth. Importantly, CaCO3@Cur@QTX125@HA nanoparticles showed specific inhibitory effects on CRC cell growth. Encouragingly, CaCO3@Cur@QTX125@HA nanoparticles successfully internalized into CRC patient-derived organoid (PDO) models and induced apoptosis of tumor cells. The multifunctional CaCO3@Cur@QTX125@HA nanoparticles hold promise for the treatment of CRC.
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Affiliation(s)
- Shengyun Hu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Kunkun Xia
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiaobei Huang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ye Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Qingqing Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Dongdong Huang
- Pooling Medical Research Institutes of 100Biotech, Beijing, 100006, China
| | - Weiyi Xu
- Department of Dermatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Zhengju Chen
- Pooling Medical Research Institutes of 100Biotech, Beijing, 100006, China.
| | - Chenfei Wang
- Department of Dermatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Zhiyong Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Harding R, Franzoni I, Mann MK, Szewczyk MM, Mirabi B, Ferreira de Freitas R, Owens DDG, Ackloo S, Scheremetjew A, Juarez-Ornelas KA, Sanichar R, Baker RJ, Dank C, Brown PJ, Barsyte-Lovejoy D, Santhakumar V, Schapira M, Lautens M, Arrowsmith CH. Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J Med Chem 2023; 66:10273-10288. [PMID: 37499118 PMCID: PMC10424181 DOI: 10.1021/acs.jmedchem.3c00314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 07/29/2023]
Abstract
Histone deacetylase 6 (HDAC6) inhibition is an attractive strategy for treating numerous cancers, and HDAC6 catalytic inhibitors are currently in clinical trials. The HDAC6 zinc-finger ubiquitin-binding domain (UBD) binds free C-terminal diglycine motifs of unanchored ubiquitin polymer chains and protein aggregates, playing an important role in autophagy and aggresome assembly. However, targeting this domain with small molecule antagonists remains an underdeveloped avenue of HDAC6-focused drug discovery. We report SGC-UBD253 (25), a chemical probe potently targeting HDAC6-UBD in vitro with selectivity over nine other UBDs, except for weak USP16 binding. In cells, 25 is an effective antagonist of HDAC6-UBD at 1 μM, with marked proteome-wide selectivity. We identified SGC-UBD253N (32), a methylated derivative of 25 that is 300-fold less active, serving as a negative control. Together, 25 and 32 could enable further exploration of the biological function of the HDAC6-UBD and investigation of the therapeutic potential of targeting this domain.
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Affiliation(s)
- Rachel
J. Harding
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ivan Franzoni
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Valence
Discovery Inc., 6666
Rue St-Urbain, Suite 200, Montreal, Quebec H2S 3H1, Canada
| | - Mandeep K. Mann
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Magdalena M. Szewczyk
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bijan Mirabi
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Dominic D. G. Owens
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Suzanne Ackloo
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alexej Scheremetjew
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kevin A. Juarez-Ornelas
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Randy Sanichar
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rachel J. Baker
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Christian Dank
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mark Lautens
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Cheryl H. Arrowsmith
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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10
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Khetmalis YM, Fathima A, Schweipert M, Debarnot C, Bandaru NVMR, Murugesan S, Jamma T, Meyer-Almes FJ, Sekhar KVGC. Design, Synthesis, and Biological Evaluation of Novel Quinazolin-4(3H)-One-Based Histone Deacetylase 6 (HDAC6) Inhibitors for Anticancer Activity. Int J Mol Sci 2023; 24:11044. [PMID: 37446224 DOI: 10.3390/ijms241311044] [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: 05/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
A series of novel quinazoline-4-(3H)-one derivatives were designed and synthesized as histone deacetylase 6 (HDAC6) inhibitors based on novel quinazoline-4-(3H)-one as the cap group and benzhydroxamic acid as the linker and metal-binding group. A total of 19 novel quinazoline-4-(3H)-one analogues (5a-5s) were obtained. The structures of the target compounds were characterized using 1H-NMR, 13C-NMR, LC-MS, and elemental analyses. Characterized compounds were screened for inhibition against HDAC8 class I, HDAC4 class IIa, and HDAC6 class IIb. Among the compounds tested, 5b proved to be the most potent and selective inhibitor of HDAC6 with an IC50 value 150 nM. Some of these compounds showed potent antiproliferative activity in several tumor cell lines (HCT116, MCF7, and B16). Amongst all the compounds tested for their anticancer effect against cancer cell lines, 5c emerged to be most active against the MCF-7 line with an IC50 of 13.7 μM; it exhibited cell-cycle arrest in the G2 phase, as well as promoted apoptosis. Additionally, we noted a significant reduction in the colony-forming capability of cancer cells in the presence of 5c. At the intracellular level, selective inhibition of HDAC6 was enumerated by monitoring the acetylation of α-tubulin with a limited effect on acetyl-H3. Importantly, the obtained results suggested a potent effect of 5c at sub-micromolar concentrations as compared to the other molecules as HDAC6 inhibitors in vitro.
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Affiliation(s)
- Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad 500078, Telangana, India
| | - Ashna Fathima
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad 500078, Telangana, India
| | - Markus Schweipert
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Cécile Debarnot
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | | | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science Pilani, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Trinath Jamma
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad 500078, Telangana, India
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
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11
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Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [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: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
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Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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12
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Mundi PS, Dela Cruz FS, Grunn A, Diolaiti D, Mauguen A, Rainey AR, Guillan K, Siddiquee A, You D, Realubit R, Karan C, Ortiz MV, Douglass EF, Accordino M, Mistretta S, Brogan F, Bruce JN, Caescu CI, Carvajal RD, Crew KD, Decastro G, Heaney M, Henick BS, Hershman DL, Hou JY, Iwamoto FM, Jurcic JG, Kiran RP, Kluger MD, Kreisl T, Lamanna N, Lassman AB, Lim EA, Manji GA, McKhann GM, McKiernan JM, Neugut AI, Olive KP, Rosenblat T, Schwartz GK, Shu CA, Sisti MB, Tergas A, Vattakalam RM, Welch M, Wenske S, Wright JD, Hibshoosh H, Kalinsky K, Aburi M, Sims PA, Alvarez MJ, Kung AL, Califano A. A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies. Cancer Discov 2023; 13:1386-1407. [PMID: 37061969 PMCID: PMC10239356 DOI: 10.1158/2159-8290.cd-22-1020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/14/2023] [Accepted: 03/14/2023] [Indexed: 04/17/2023]
Abstract
Predicting in vivo response to antineoplastics remains an elusive challenge. We performed a first-of-kind evaluation of two transcriptome-based precision cancer medicine methodologies to predict tumor sensitivity to a comprehensive repertoire of clinically relevant oncology drugs, whose mechanism of action we experimentally assessed in cognate cell lines. We enrolled patients with histologically distinct, poor-prognosis malignancies who had progressed on multiple therapies, and developed low-passage, patient-derived xenograft models that were used to validate 35 patient-specific drug predictions. Both OncoTarget, which identifies high-affinity inhibitors of individual master regulator (MR) proteins, and OncoTreat, which identifies drugs that invert the transcriptional activity of hyperconnected MR modules, produced highly significant 30-day disease control rates (68% and 91%, respectively). Moreover, of 18 OncoTreat-predicted drugs, 15 induced the predicted MR-module activity inversion in vivo. Predicted drugs significantly outperformed antineoplastic drugs selected as unpredicted controls, suggesting these methods may substantively complement existing precision cancer medicine approaches, as also illustrated by a case study. SIGNIFICANCE Complementary precision cancer medicine paradigms are needed to broaden the clinical benefit realized through genetic profiling and immunotherapy. In this first-in-class application, we introduce two transcriptome-based tumor-agnostic systems biology tools to predict drug response in vivo. OncoTarget and OncoTreat are scalable for the design of basket and umbrella clinical trials. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Prabhjot S. Mundi
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Adina Grunn
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Daniel Diolaiti
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Allison R. Rainey
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Kristina Guillan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Armaan Siddiquee
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Ronald Realubit
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Eugene F. Douglass
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Melissa Accordino
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Suzanne Mistretta
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Frances Brogan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Jeffrey N. Bruce
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurological Surgery, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
| | - Cristina I. Caescu
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Richard D. Carvajal
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Katherine D Crew
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Guarionex Decastro
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Urology, Columbia University Irving Medical Center, 160 Fort Washington Ave, New York, NY USA 10032
| | - Mark Heaney
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Brian S Henick
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Dawn L Hershman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th St. NY, NY 10032
| | - June Y. Hou
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Fabio M. Iwamoto
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurology, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
| | - Joseph G. Jurcic
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Ravi P. Kiran
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Surgery, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Michael D Kluger
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Surgery, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Teri Kreisl
- Novartis Five Cambridge, MA 02142, United States
| | - Nicole Lamanna
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Andrew B. Lassman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurology, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
| | - Emerson A. Lim
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Gulam A. Manji
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Guy M McKhann
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurological Surgery, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
| | - James M. McKiernan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Urology, Columbia University Irving Medical Center, 160 Fort Washington Ave, New York, NY USA 10032
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th St. NY, NY 10032
| | - Kenneth P. Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Todd Rosenblat
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Gary K. Schwartz
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Catherine A Shu
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Michael B. Sisti
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurological Surgery, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
- Department of Otolaryngology Head and Neck Surgery, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
- Department of Radiation Oncology, Columbia University Irving Medical Center, 161 Fort Washington Avenue, New York, NY 10032, United States
| | - Ana Tergas
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Reena M Vattakalam
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Mary Welch
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Neurology, Columbia University Irving Medical Center, 710 W 168th Street, New York, NY USA 10032
| | - Sven Wenske
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Urology, Columbia University Irving Medical Center, 160 Fort Washington Ave, New York, NY USA 10032
| | - Jason D. Wright
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
| | - Hanina Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
| | - Kevin Kalinsky
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Winship Cancer Institute of Emory University and Department of Hematology and Medical Oncology, Emory University School of Medicine, 1365-C Clifton Road NE, Atlanta, GA 30322, United States
| | - Mahalaxmi Aburi
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, 701 W 168th Street, New York, NY USA 10032
| | - Mariano J. Alvarez
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- DarwinHealth Inc. New York
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY USA 10065
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave, New York, NY USA 10032
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY USA 10032
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, 701 W 168th Street, New York, NY USA 10032
- Department of Biomedical Informatics, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY USA 10032
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13
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Médard G, Sheltzer JM. Ricolinostat is not a highly selective HDAC6 inhibitor. NATURE CANCER 2023; 4:807-808. [PMID: 37322365 DOI: 10.1038/s43018-023-00582-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Guillaume Médard
- Proteomics Core Facility, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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14
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Silva J, Yu J, Kalinsky K. Reply to: Ricolinostat is not a highly selective HDAC6 inhibitor. NATURE CANCER 2023; 4:809-811. [PMID: 37322366 DOI: 10.1038/s43018-023-00583-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Jose Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA.
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kevin Kalinsky
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
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15
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Dong X, Ding L, Thrasher A, Wang X, Liu J, Pan Q, Rash J, Dhungana Y, Yang X, Risch I, Li Y, Yan L, Rusch M, McLeod C, Yan KK, Peng J, Chi H, Zhang J, Yu J. NetBID2 provides comprehensive hidden driver analysis. Nat Commun 2023; 14:2581. [PMID: 37142594 PMCID: PMC10160099 DOI: 10.1038/s41467-023-38335-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
Many signaling and other genes known as "hidden" drivers may not be genetically or epigenetically altered or differentially expressed at the mRNA or protein levels, but, rather, drive a phenotype such as tumorigenesis via post-translational modification or other mechanisms. However, conventional approaches based on genomics or differential expression are limited in exposing such hidden drivers. Here, we present a comprehensive algorithm and toolkit NetBID2 (data-driven network-based Bayesian inference of drivers, version 2), which reverse-engineers context-specific interactomes and integrates network activity inferred from large-scale multi-omics data, empowering the identification of hidden drivers that could not be detected by traditional analyses. NetBID2 has substantially re-engineered the previous prototype version by providing versatile data visualization and sophisticated statistical analyses, which strongly facilitate researchers for result interpretation through end-to-end multi-omics data analysis. We demonstrate the power of NetBID2 using three hidden driver examples. We deploy NetBID2 Viewer, Runner, and Cloud apps with 145 context-specific gene regulatory and signaling networks across normal tissues and paediatric and adult cancers to facilitate end-to-end analysis, real-time interactive visualization and cloud-based data sharing. NetBID2 is freely available at https://jyyulab.github.io/NetBID .
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Affiliation(s)
- Xinran Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, 201102, P.R. China
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Andrew Thrasher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xinge Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jordan Rash
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yogesh Dhungana
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xu Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Isabel Risch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, Centre for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Lei Yan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Clay McLeod
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Centre for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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16
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Sun N, Yang K, Yan W, Yao M, Yu C, Duan W, Gu X, Guo D, Jiang H, Xie C, Cheng J. Design and Synthesis of Triazole-Containing HDAC Inhibitors That Induce Antitumor Effects and Immune Response. J Med Chem 2023; 66:4802-4826. [PMID: 36934335 DOI: 10.1021/acs.jmedchem.2c01985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
Abstract
Histone deacetylase (HDAC) is an epigenetic antitumor drug target, but most existing HDAC inhibitors show limited antitumor activity and their use is often accompanied by serious adverse effects. To overcome these problems, we designed and synthesized a series of triazole-containing compounds as novel HDAC inhibitors. Among them, compound 19h exhibited potent and selective inhibition of HDAC1, with good antiproliferative activity in vitro and an excellent pharmacokinetic profile. Compound 19h significantly inhibited the growth of human tumor xenografts in nude mice and murine tumor growth in immune-competent mice bearing MC38 colon cancer. In the MC38 model, 19h increased the ratio of splenic CD4+ T effector cells and promoted complete tumor regression in 5/6 animals when combined with the mPD-1 antibody. These results suggested that selective class I HDAC inhibitors exert direct tumor growth inhibition and indirect immune cell-mediated antitumor effects and are synergistic with immune checkpoint inhibitors.
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Affiliation(s)
- Nan Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Kexin Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenzhong Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Mingyue Yao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China
| | - Chengcheng Yu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Wenwen Duan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Xiaoke Gu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Chengying Xie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Hey J, Llamazares Prada M, Plass C. HDAC6 score: to treat or not to treat? NATURE CANCER 2023; 4:156-158. [PMID: 36585451 DOI: 10.1038/s43018-022-00494-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Maria Llamazares Prada
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany. .,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany.
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