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Ding W, Xiao Q, Yue Y, Chen S, She X, Pan B, Zhou L, Yin Y, Li Y, Wang S, Xu M. Deciphering alternative splicing events and their therapeutic implications in colorectal Cancer. Cell Signal 2024; 118:111134. [PMID: 38484942 DOI: 10.1016/j.cellsig.2024.111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors with complex molecular regulatory mechanisms. Alternative splicing (AS), a fundamental regulatory process of gene expression, plays an important role in the occurrence and development of CRC. This study analyzed AS Percent Spliced In (PSI) values from 49 pairs of CRC and normal samples in the TCGA SpliceSeq database. Using Lasso and SVM, AS features that can differentiate colorectal cancer from normal were screened. Univariate COX regression analysis identified prognosis-related AS events. A risk model was constructed and validated using machine learning, Kaplan-Meier analysis, and Decision Curve Analysis. The regulatory effect of protein arginine methyltransferase 5 (PRMT5) on poly(RC) binding protein 1 (PCBP1) was verified by immunoprecipitation experiments, and the effect of PCBP1 on the AS of Obscurin (OBSCN) was verified by PCR. Five AS events, including HNF4A.59461.AP and HNF4A.59462.AP, were identified, which can distinguish CRC from normal tissue. A machine learning model using 21 key AS events accurately predicted CRC prognosis. High-risk patients had significantly shorter survival times. PRMT5 was found to regulate PCBP1 function and then influence OBSCN AS, which may drive CRC progression. The study concluded that some AS events is significantly different in CRC and normal tissues, and some of these AS events are related to the prognosis of CRC. In addition, PRMT family-driven arginine modifications play an important role in CRC-specific AS events.
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Affiliation(s)
- Wenbo Ding
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianni Xiao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yanzhe Yue
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shuyu Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiangjian She
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Linpeng Zhou
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yujuan Yin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Youyue Li
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China.; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China..
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China..
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Ma X, Mandausch FJ, Wu Y, Sahoo VK, Ma W, Leoni G, Hostiuc M, Wintgens JP, Qiu J, Kannaiyan N, Rossner MJ, Wehr MC. Comprehensive split TEV based protein-protein interaction screening reveals TAOK2 as a key modulator of Hippo signalling to limit growth. Cell Signal 2024; 113:110917. [PMID: 37813295 DOI: 10.1016/j.cellsig.2023.110917] [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: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
The conserved Hippo signalling pathway plays a crucial role in tumour formation by limiting tissue growth and proliferation. At the core of this pathway are tumour suppressor kinases STK3/4 and LATS1/2, which limit the activity of the oncogene YAP1, the primary downstream effector. Here, we employed a split TEV-based protein-protein interaction screen to assess the physical interactions among 28 key Hippo pathway components and potential upstream modulators. This screen led us to the discovery of TAOK2 as pivotal modulator of Hippo signalling, as it binds to the pathway's core kinases, STK3/4 and LATS1/2, and leads to their phosphorylation. Specifically, our findings revealed that TAOK2 binds to and phosphorylates LATS1, resulting in the reduction of YAP1 phosphorylation and subsequent transcription of oncogenes. Consequently, this decrease led to a decrease in cell proliferation and migration. Interestingly, a correlation was observed between reduced TAOK2 expression and decreased patient survival time in certain types of human cancers, including lung and kidney cancer as well as glioma. Moreover, in cellular models corresponding to these cancer types the downregulation of TAOK2 by CRISPR inhibition led to reduced phosphorylation of LATS1 and increased proliferation rates, supporting TAOK2's role as tumour suppressor gene. By contrast, overexpression of TAOK2 in these cellular models lead to increased phospho-LATS1 but reduced cell proliferation. As TAOK2 is a druggable kinase, targeting TAOK2 could serve as an attractive pharmacological approach to modulate cell growth and potentially offer strategies for combating cancer.
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Affiliation(s)
- Xiao Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Fiona J Mandausch
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Wenbo Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Giovanna Leoni
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Madalina Hostiuc
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jan P Wintgens
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jiajun Qiu
- Department of Otolaryngology Head & Neck Surgery, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | | | - Moritz J Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany; Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University of Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
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3
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Colaco V, Goswami N, Goel VK, Srivastava SK, Lalrohlua P, Senthil Kumar N, Borah P, Baruah R, Varma AK. In silico and structure-based evaluation of deleterious mutations identified in human Chk1, Chk2, and Wee1 protein kinase. J Cell Biochem 2024; 125:89-99. [PMID: 38047473 DOI: 10.1002/jcb.30508] [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: 05/31/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Checkpoint kinases Chk1, Chk2, Wee1 are playing a key role in DNA damage response and genomic integrity. Cancer-associated mutations identified in human Chk1, Chk2, and Wee1 were retrieved to understand the function associated with the mutation and also alterations in the folding pattern. Therefore, an attempt has been made to identify deleterious effect of variants using in silico and structure-based approach. Variants of uncertain significance for Chk1, Chk2, and Wee1 were retrieved from different databases and four prediction servers were employed to predict pathogenicity of mutations. Further, Interpro, I-Mutant 3.0, Consurf, TM-align, and have (y)our protein explained were used for comprehensive study of the deleterious effects of variants. The sequences of Chk1, Chk2, and Wee1 were analyzed using Clustal Omega, and the three-dimensional structures of the proteins were aligned using TM-align. The molecular dynamics simulations were performed to explore the differences in folding pattern between Chk1, Chk2, Wee1 wild-type, and mutant protein and also to evaluate the structural integrity. Thirty-six variants in Chk1, 250 Variants in Chk2, and 29 in Wee1 were categorized as pathogenic using in silico prediction tools. Furthermore, 25 mutations in Chk1, 189 in Chk2, and 14 in Wee1 were highly conserved, possessing deleterious effect and also influencing the protein structure and function. These identified mutations may provide underlying genetic intricacies to serve as potential targets for therapeutic inventions and clinical management.
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Affiliation(s)
- Venessa Colaco
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, India
| | - Nabajyoti Goswami
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, India
| | - Vijay Kumar Goel
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | | | - Probodh Borah
- College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, India
| | - Reshita Baruah
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, India
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
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4
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Wei X, Pan C, Zhang X, Zhang W. Total network controllability analysis discovers explainable drugs for Covid-19 treatment. Biol Direct 2023; 18:55. [PMID: 37670359 PMCID: PMC10478273 DOI: 10.1186/s13062-023-00410-9] [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: 07/07/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND The active pursuit of network medicine for drug repurposing, particularly for combating Covid-19, has stimulated interest in the concept of structural controllability in cellular networks. We sought to extend this theory, focusing on the defense rather than control of the cell against viral infections. Accordingly, we extended structural controllability to total structural controllability and introduced the concept of control hubs. Perturbing any control hub may render the cell uncontrollable by exogenous stimuli like viral infections, so control hubs are ideal drug targets. RESULTS We developed an efficient algorithm to identify all control hubs, applying it to a largest homogeneous network of human protein interactions, including interactions between human and SARS-CoV-2 proteins. Our method recognized 65 druggable control hubs with enriched antiviral functions. Utilizing these hubs, we categorized potential drugs into four groups: antiviral and anti-inflammatory agents, drugs acting on the central nervous system, dietary supplements, and compounds enhancing immunity. An exemplification of our approach's effectiveness, Fostamatinib, a drug initially developed for chronic immune thrombocytopenia, is now in clinical trials for treating Covid-19. Preclinical trial data demonstrated that Fostamatinib could reduce mortality rates, ICU stay length, and disease severity in Covid-19 patients. CONCLUSIONS Our findings confirm the efficacy of our novel strategy that leverages control hubs as drug targets. This approach provides insights into the molecular mechanisms of potential therapeutics for Covid-19, making it a valuable tool for interpretable drug discovery. Our new approach is general and applicable to repurposing drugs for other diseases.
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Affiliation(s)
- Xinru Wei
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, 210001, China
| | - Chunyu Pan
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Xizhe Zhang
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, 210001, China.
| | - Weixiong Zhang
- Department of Health Technology and Informatics, Department of Computing, The Hong Kong Polytechnic University, Hong Kong, China.
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5
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Wei X, Pan C, Zhang X, Zhang W. Total network controllability analysis discovers explainable drugs for Covid-19 treatment. RESEARCH SQUARE 2023:rs.3.rs-3147521. [PMID: 37503262 PMCID: PMC10371104 DOI: 10.21203/rs.3.rs-3147521/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background The active pursuit of network medicine for drug repurposing, particularly for combating Covid-19, has stimulated interest in the concept of structural control capability in cellular networks. We sought to extend this theory, focusing on the defense rather than control of the cell against viral infections. Accordingly, we extended structural controllability to total structural controllability and introduced the concept of control hubs. Perturbing any control hub may render the cell uncontrollable by exogenous stimuli like viral infections, so control hubs are ideal drug targets. Results We developed an efficient algorithm to identify all control hubs, applying it to the largest homogeneous network of human protein interactions, including interactions between human and SARS-CoV-2 proteins. Our method recognized 65 druggable control hubs with enriched antiviral functions. Utilizing these hubs, we categorized potential drugs into four groups: antiviral and anti-inflammatory agents, drugs acting on the central nervous system, dietary supplements, and compounds enhancing immunity. An exemplification of our approach's effectiveness, Fostamatinib, a drug initially developed for chronic immune thrombocytopenia, is now in clinical trials for treating Covid-19. Preclinical trial data demonstrated that Fostamatinib could reduce mortality rates, ICU stay length, and disease severity in Covid-19 patients. Conclusions Our findings confirm the efficacy of our novel strategy that leverages control hubs as drug targets. This approach provides insights into the molecular mechanisms of potential therapeutics for Covid-19, making it a valuable tool for interpretable drug discovery.
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Affiliation(s)
- Xinru Wei
- The Affiliated Brain Hospital of Nanjing Medical University
| | | | - Xizhe Zhang
- The Affiliated Brain Hospital of Nanjing Medical University
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6
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Yoder MD, Van Osten S, Weber GF. Gene expression analysis of the Tao kinase family of Ste20p-like map kinase kinase kinases during early embryonic development in Xenopus laevis. Gene Expr Patterns 2023; 48:119318. [PMID: 37011704 PMCID: PMC10453956 DOI: 10.1016/j.gep.2023.119318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/15/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Development of the vertebrate embryo requires strict coordination of a highly complex series of signaling cascades, that drive cell proliferation, differentiation, migration, and the general morphogenetic program. Members of the Map kinase signaling pathway are repeatedly required throughout development to activate the downstream effectors, ERK, p38, and JNK. Regulation of these pathways occurs at many levels in the signaling cascade, with the Map3Ks playing an essential role in target selection. The thousand and one amino acid kinases (Taoks) are Map3Ks that have been shown to activate both p38 and JNK and are linked to neurodevelopment in both invertebrate and vertebrate organisms. In vertebrates, there are three Taok paralogs (Taok1, Taok2, and Taok3) which have not yet been ascribed a role in early development. Here we describe the spatiotemporal expression of Taok1, Taok2, and Taok3 in the model organism Xenopus laevis. The X. laevis Tao kinases share roughly 80% identity to each other, with the bulk of the conservation in the kinase domain. Taok1 and Taok3 are highly expressed in pre-gastrula and gastrula stage embryos, with initial expression localized to the animal pole and later expression in the ectoderm and mesoderm. All three Taoks are expressed in the neural and tailbud stages, with overlapping expression in the neural tube, notochord, and many anterior structures (including branchial arches, brain, otic vesicles, and eye). The expression patterns described here provide evidence that the Tao kinases may play a central role in early development, in addition to their function during neural development, and establish a framework to better understand the developmental roles of Tao kinase signaling.
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Affiliation(s)
- Michael D Yoder
- Department of Biology, University of Central Arkansas, Conway, AR, 72035, USA.
| | - Steven Van Osten
- Sciences Division, Brandywine Campus, The Pennsylvania State University, Media, PA, 19063, USA.
| | - Gregory F Weber
- Department of Biology, University of Indianapolis, Indianapolis, IN, 46227, USA.
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Huang G, Cierpicki T, Grembecka J. 2-Aminobenzothiazoles in anticancer drug design and discovery. Bioorg Chem 2023; 135:106477. [PMID: 36989736 DOI: 10.1016/j.bioorg.2023.106477] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/26/2023] [Accepted: 03/10/2023] [Indexed: 03/22/2023]
Abstract
Cancer is one of the major causes of mortality and morbidity worldwide. Substantial research efforts have been made to develop new chemical entities with improved anticancer efficacy. 2-Aminobenzothiazole is an important class of heterocycles containing one sulfur and two nitrogen atoms, which is associated with a broad spectrum of medical and pharmacological activities, including antitumor, antibacterial, antimalarial, anti-inflammatory, and antiviral activities. In recent years, an extraordinary collection of potent and low-toxicity 2-aminobenzothiazole compounds have been discovered as new anticancer agents. Herein, we provide a comprehensive review of this class of compounds based on their activities against tumor-related proteins, including tyrosine kinases (CSF1R, EGFR, VEGFR-2, FAK, and MET), serine/threonine kinases (Aurora, CDK, CK, RAF, and DYRK2), PI3K kinase, BCL-XL, HSP90, mutant p53 protein, DNA topoisomerase, HDAC, NSD1, LSD1, FTO, mPGES-1, SCD, hCA IX/XII, and CXCR. In addition, the anticancer potentials of 2-aminobenzothiazole-derived chelators and metal complexes are also described here. Moreover, the design strategies, mechanism of actions, structure-activity relationships (SAR) and more advanced stages of pre-clinical development of 2-aminobenzothiazoles as new anticancer agents are extensively reviewed in this article. Finally, the examples that 2-aminobenzothiazoles showcase an advantage over other heterocyclic systems are also highlighted.
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Affiliation(s)
- Guang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
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Song M, Pang L, Zhang M, Qu Y, Laster KV, Dong Z. Cdc2-like kinases: structure, biological function, and therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:148. [PMID: 37029108 PMCID: PMC10082069 DOI: 10.1038/s41392-023-01409-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
The CLKs (Cdc2-like kinases) belong to the dual-specificity protein kinase family and play crucial roles in regulating transcript splicing via the phosphorylation of SR proteins (SRSF1-12), catalyzing spliceosome molecular machinery, and modulating the activities or expression of non-splicing proteins. The dysregulation of these processes is linked with various diseases, including neurodegenerative diseases, Duchenne muscular dystrophy, inflammatory diseases, viral replication, and cancer. Thus, CLKs have been considered as potential therapeutic targets, and significant efforts have been exerted to discover potent CLKs inhibitors. In particular, clinical trials aiming to assess the activities of the small molecules Lorecivivint on knee Osteoarthritis patients, and Cirtuvivint and Silmitasertib in different advanced tumors have been investigated for therapeutic usage. In this review, we comprehensively documented the structure and biological functions of CLKs in various human diseases and summarized the significance of related inhibitors in therapeutics. Our discussion highlights the most recent CLKs research, paving the way for the clinical treatment of various human diseases.
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Affiliation(s)
- Mengqiu Song
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Luping Pang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Mengmeng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingzi Qu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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9
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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NEK6 Regulates Redox Balance and DNA Damage Response in DU-145 Prostate Cancer Cells. Cells 2023; 12:cells12020256. [PMID: 36672191 PMCID: PMC9856815 DOI: 10.3390/cells12020256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 01/10/2023] Open
Abstract
NEK6 is a central kinase in developing castration-resistant prostate cancer (CRPC). However, the pathways regulated by NEK6 in CRPC are still unclear. Cancer cells have high reactive oxygen species (ROS) levels and easily adapt to this circumstance and avoid cell death by increasing antioxidant defenses. We knocked out the NEK6 gene and evaluated the redox state and DNA damage response in DU-145 cells. The knockout of NEK6 decreases the clonogenic capacity, proliferation, cell viability, and mitochondrial activity. Targeting the NEK6 gene increases the level of intracellular ROS; decreases the expression of antioxidant defenses (SOD1, SOD2, and PRDX3); increases JNK phosphorylation, a stress-responsive kinase; and increases DNA damage markers (p-ATM and γH2AX). The exogenous overexpression of NEK6 also increases the expression of these same antioxidant defenses and decreases γH2AX. The depletion of NEK6 also induces cell death by apoptosis and reduces the antiapoptotic Bcl-2 protein. NEK6-lacking cells have more sensitivity to cisplatin. Additionally, NEK6 regulates the nuclear localization of NF-κB2, suggesting NEK6 may regulate NF-κB2 activity. Therefore, NEK6 alters the redox balance, regulates the expression of antioxidant proteins and DNA damage, and its absence induces the death of DU-145 cells. NEK6 inhibition may be a new strategy for CRPC therapy.
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11
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Wu W, Yu S, Yu X. Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188842. [PMID: 36460141 DOI: 10.1016/j.bbcan.2022.188842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12), a transcription-related cyclin dependent kinase (CDK), plays a momentous part in multitudinous biological functions, such as replication, transcription initiation to elongation and termination, precursor mRNA (pre-mRNA) splicing, intron polyadenylation (IPA), and translation. CDK12 can act as a tumour suppressor or oncogene in disparate cellular environments, and its dysregulation likely provokes tumorigenesis. A comprehensive understanding of CDK12 will tremendously facilitate the exploitation of novel tactics for the treatment and precaution of cancer. Currently, CDK12 inhibitors are nonspecific and nonselective, which profoundly hinders the pharmacological target validation and drug exploitation process. Herein, we summarize the newly comprehension of the biological functions of CDK12 with a focus on recently emerged advancements of CDK12-associated therapeutic approaches in cancers.
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Affiliation(s)
- Wence Wu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiying Yu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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12
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Saha S, Pradhan N, B N, Mahadevappa R, Minocha S, Kumar S. Cancer plasticity: Investigating the causes for this agility. Semin Cancer Biol 2023; 88:138-156. [PMID: 36584960 DOI: 10.1016/j.semcancer.2022.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Cancer is not a hard-wired phenomenon but an evolutionary disease. From the onset of carcinogenesis, cancer cells continuously adapt and evolve to satiate their ever-growing proliferation demands. This results in the formation of multiple subtypes of cancer cells with different phenotypes, cellular compositions, and consequently displaying varying degrees of tumorigenic identity and function. This phenomenon is referred to as cancer plasticity, during which the cancer cells exist in a plethora of cellular states having distinct phenotypes. With the advent of modern technologies equipped with enhanced resolution and depth, for example, single-cell RNA-sequencing and advanced computational tools, unbiased cancer profiling at a single-cell resolution are leading the way in understanding cancer cell rewiring both spatially and temporally. In this review, the processes and mechanisms that give rise to cancer plasticity include both intrinsic genetic factors such as epigenetic changes, differential expression due to changes in DNA, RNA, or protein content within the cancer cell, as well as extrinsic environmental factors such as tissue perfusion, extracellular milieu are detailed and their influence on key cancer plasticity hallmarks such as epithelial-mesenchymal transition (EMT) and cancer cell stemness (CSCs) are discussed. Due to therapy evasion and drug resistance, tumor heterogeneity caused by cancer plasticity has major therapeutic ramifications. Hence, it is crucial to comprehend all the cellular and molecular mechanisms that control cellular plasticity. How this process evades therapy, and the therapeutic avenue of targeting cancer plasticity must be diligently investigated.
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Affiliation(s)
- Shubhraneel Saha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Nikita Pradhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Neha B
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ravikiran Mahadevappa
- Department of Biotechnology, School of Science, Gandhi Institute of Technology and Management, Deemed to be University, Bengaluru, Karnataka 562163, India
| | - Shilpi Minocha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Saran Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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13
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Cicek M, Unsal V, Emre A, Doganer A. Investigation of the Effects of Apigenin, a Possible Therapeutic Agent, on Cytotoxic and SWH Pathway in Colorectal Cancer (HT29) Cells. Adv Pharm Bull 2023; 13:188-195. [PMID: 36721804 PMCID: PMC9871274 DOI: 10.34172/apb.2023.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 02/03/2023] Open
Abstract
Purpose: Colorectal cancer (CRC) is one of the most common and fatal malignancies in humans, still leading to serious morbidity and mortality. We here aimed to investigate the effects of flavonoid apigenin, which is considered to have anti-tumoral activity on CRC with high epidemiological prevalence, on cell proliferation and cell survivals, and the positive and negative dose-dependent effects of genetic or mutational alterations in SWH pathway components on HT29 CRC cell lines. Methods: Human colon cancer cell lines HT-29 were commercially available. In each flask, 5 groups were formed, each of which consists of 5,000 cells for different dose groups and the cells were plated. After a 24 and 48 h incubation period, cytotoxicity values were measured by MTT assay and gene expression was assessed by real-time polymerase chain reaction (PCR) analysis method. Results: Application of 12.5 and 25 nM of apigenin significantly increased cell death in HT29 cell lines. LATS1, STK3 and TP53 gene expression decreased in the same dose groups compared to control and other groups. Conclusion: It has been concluded that TP53 gene is strongly correlated with LATS1 and STK3 genes among the SWH pathway factors in the progression of CRC and could be used as an important marker for early detection of malignant transmission. In addition, it may be effective in CRC cases especially when 25 nM of apigenin applies for therapeutic purpose.
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Affiliation(s)
- Mustafa Cicek
- Department of Medical Biology, Faculty of Medicine, Kahramanmaras Sutcu Imam University, Kahramanmaraş, Turkey
| | - Velid Unsal
- Department of Nutrition and Dietetics, Faculty of Health Science, Mardin Artuklu University, 47200, Mardin, Turkey.,Corresponding Author: Velid Unsal, Tel: (0482) 2134002,
| | - Arif Emre
- Department of Surgery, Kahramanmaras Sutcu Imam University Faculty of Medicine, 46100, Kahramanmaras, Turkey
| | - Adem Doganer
- Department of Biostatistics and Medical Informatics, Kahramanmaras Sutcu Imam University Faculty of Medicine, 46100, Kahramanmaras, Turkey
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Integrated single-cell transcriptome analysis of CD34 + enriched leukemic stem cells revealed intra- and inter-patient transcriptional heterogeneity in pediatric acute myeloid leukemia. Ann Hematol 2023; 102:73-87. [PMID: 36527458 DOI: 10.1007/s00277-022-05021-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
To gain insights into the idiosyncrasies of CD34 + enriched leukemic stem cells, we investigated the nature and extent of transcriptional heterogeneity by single-cell sequencing in pediatric AML. Whole transcriptome analysis of 28,029 AML single cells was performed using the nanowell cartridge-based barcoding technology. Integrated transcriptional analysis identified unique leukemic stem cell clusters of each patient and intra-patient heterogeneity was revealed by multiple LSC-enriched clusters differing in their cell cycle processes and BCL2 expression. All LSC-enriched clusters exhibited gene expression profile of dormancy and self-renewal. Upregulation of genes involved in non-coding RNA processing and ribonucleoprotein assembly were observed in LSC-enriched clusters relative to HSC. The genes involved in regulation of apoptotic processes, response to cytokine stimulus, and negative regulation of transcription were upregulated in LSC-enriched clusters as compared to the blasts. Validation of top altered genes in LSC-enriched clusters confirmed upregulation of TCF7L2, JUP, ARHGAP25, LPAR6, and PRDX1 genes, and serine/threonine kinases (STK24, STK26). Upregulation of LPAR6 showed trend towards MRD positive status (Odds ratio = 0.126; 95% CI = 0.0144-1.10; p = 0.067) and increased expression of STK26 significantly correlated with higher RFS (HR = 0.231; 95% CI = 0.0506-1.052; p = 0.04). Our findings addressed the inter- and intra-patient diversity within AML LSC and potential signaling and chemoresistance-associated targets that warrant investigation in larger cohort that may guide precision medicine in the near future.
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15
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Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [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: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
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Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
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16
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TAOK1 Promotes Proliferation and Invasion of Non-Small-Cell Lung Cancer Cells by Inhibition of WWC1. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3157448. [PMID: 36158126 PMCID: PMC9499761 DOI: 10.1155/2022/3157448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022]
Abstract
Background For patients with advanced non-small-cell lung cancer (NSCLC), targeted therapy significantly improves the therapeutic effect of NSCLC patients. With the development of molecular targeted therapy, more and more NSCLC-related genes have been found. Thousand and one amino-acid kinase 1 (TAOK1) has been identified as a potential target for drug research in various cancers. The main objective of this study was to explore the expression and function of TAOK1 in NSCLC. Methods Western blotting was employed to assess TAOK1 expression in NSCLC cell lines. The effects of TAOK1 on biological behaviors, including proliferation, invasion, and apoptosis of NSCLC cells, were assessed. The relationship between TAOK1 and WW and C2 domain containing 1 (WWC1) was assessed by Co-IP assay. The subcutaneous injection of tumor cells in nude mice was used to verify it in vivo. Results As expected, TAOK1 was increased in NSCLC cell lines. Following TAOK1 knockdown, NSCLC cells exhibited a significant decrease in the invasion and increased apoptosis in vitro. Instead, the TAOK1 elevation showed the opposite results. The Co-IP assay identified that TAOK1 specifically interacted with WWC1. Knockdown of WWC1 overturned TAOK1 silencing-mediated malignant phenotype of NSCLC cells. Additionally, subcutaneous tumorigenesis assays in nude mice confirmed that TAOK1 knockdown markedly restrained the proliferation capacity of NSCLC cells in vivo. Conclusion Surprisingly, TAOK1 overexpression in NSCLC promotes tumor cell growth and invasion, which is associated with downregulation of its downstream protein WWC1, and this result might provide a robust research basis to inquire about the precise therapeutic targets for NSCLC.
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17
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Chilà R, Chiappa M, Guffanti F, Panini N, Conconi D, Rinaldi A, Cascione L, Bertoni F, Fratelli M, Damia G. Stable CDK12 Knock-Out Ovarian Cancer Cells Do Not Show Increased Sensitivity to Cisplatin and PARP Inhibitor Treatment. Front Oncol 2022; 12:903536. [PMID: 35912188 PMCID: PMC9328802 DOI: 10.3389/fonc.2022.903536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a serine/threonine kinase involved in the regulation of RNA polymerase II and in the transcription of a subset of genes involved in the DNA damage response. CDK12 is one of the most mutated genes in ovarian carcinoma. These mutations result in loss-of-function and can predict the responses to PARP1/2 inhibitor and platinum. To investigate the role of CDK12 in ovarian cancer, CRISPR/Cas9 technology was used to generate a stable CDK12 knockout (KO) clone in A2780 ovarian carcinoma cells. This is the first report on a CDK12 null cell line. The clone had slower cell growth and was less clonogenic than parental cells. These data were confirmed in vivo, where CDK12 KO transplanted cells had a much longer time lag and slightly slower growth rate than CDK12-expressing cells. The slower growth was associated with a higher basal level of apoptosis, but there were no differences in the basal level of autophagy and senescence. While cell cycle distribution was similar in parental and knockout cells, there was a doubling in DNA content, with an almost double modal number of chromosomes in the CDK12 KO clone which, however did not display any increase in γH2AX, a marker of DNA damage. We found partial down-regulation of the expression of DNA repair genes at the mRNA level and, among the down-regulated genes, an enrichment in the G2/M checkpoint genes. Although the biological features of CDK12 KO cells are compatible with the function of CDK12, contrary to some reports, we could not find any difference in the sensitivity to cisplatin and olaparib between wild-type and CDK12 KO cells.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Michela Chiappa
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Guffanti
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Nicolò Panini
- Laboratory of Cancer Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Maddalena Fratelli
- Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- *Correspondence: Giovanna Damia,
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18
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Wang J, Chen S, Liu M, Zhang M, Jia X. NEK7: a new target for the treatment of multiple tumors and chronic inflammatory diseases. Inflammopharmacology 2022; 30:1179-1187. [PMID: 35829941 DOI: 10.1007/s10787-022-01026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/20/2022] [Indexed: 11/05/2022]
Abstract
NIMA-related kinase 7 (NEK7) is a serine/threonine kinase, which is the smallest one in mammalian NEK family. At present, many studies have reported that NEK7 has a physiological role in regulating the cell cycle and promoting the mitotic process of cells. In recent years, an increasing number of studies have proposed that NEK7 is involved in the activation of the NLRP3 inflammasome. Under normal conditions, NEK7 is in a low activity state, while under pathological conditions, NEK7 is abnormally expressed and therefore plays a key role in the progression of multiple tumors and chronic inflammatory diseases. This review will concentrate on the mechanism of NEK7 participates in the process of mitosis and regulates the activation of NLRP3 inflammasome, the aberrant expression of NEK7 in a variety of tumors and chronic inflammatory diseases, and some potential inhibitors, which may provide some new ideas for the treatment of diverse tumors and chronic inflammatory diseases associated with NEK7.
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Affiliation(s)
- Jin Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, People's Republic of China
| | - Simeng Chen
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, People's Republic of China
| | - Min Liu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China.,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, People's Republic of China
| | - Min Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, People's Republic of China
| | - Xiaoyi Jia
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, People's Republic of China. .,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, People's Republic of China. .,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, People's Republic of China.
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19
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Exploring the roles of the Cdc2-like kinases in cancers. Bioorg Med Chem 2022; 70:116914. [PMID: 35872347 DOI: 10.1016/j.bmc.2022.116914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022]
Abstract
The Cdc2-like kinases (CLKs 1-4) are involved in regulating the alternative splicing of a variety of genes. Their activity contributes to important cellular processes such as proliferation, differentiation, apoptosis, migration, and cell cycle regulation. Abnormal expression of CLKs can lead to cancers; therefore, pharmacological inhibition of CLKs may be a useful therapeutic strategy. This review summarises what is known about the roles of each of the CLKs in cancerous cells, as well as the effects of relevant small molecule CLK inhibitors.
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20
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Filippone MG, Gaglio D, Bonfanti R, Tucci FA, Ceccacci E, Pennisi R, Bonanomi M, Jodice G, Tillhon M, Montani F, Bertalot G, Freddi S, Vecchi M, Taglialatela A, Romanenghi M, Romeo F, Bianco N, Munzone E, Sanguedolce F, Vago G, Viale G, Di Fiore PP, Minucci S, Alberghina L, Colleoni M, Veronesi P, Tosoni D, Pece S. CDK12 promotes tumorigenesis but induces vulnerability to therapies inhibiting folate one-carbon metabolism in breast cancer. Nat Commun 2022; 13:2642. [PMID: 35550508 PMCID: PMC9098894 DOI: 10.1038/s41467-022-30375-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) overexpression is implicated in breast cancer, but whether it has a primary or only a cooperative tumorigenic role is unclear. Here, we show that transgenic CDK12 overexpression in the mouse mammary gland per se is sufficient to drive the emergence of multiple and multifocal tumors, while, in cooperation with known oncogenes, it promotes earlier tumor onset and metastasis. Integrative transcriptomic, metabolomic and functional data reveal that hyperactivation of the serine-glycine-one-carbon network is a metabolic hallmark inherent to CDK12-induced tumorigenesis. Consistently, in retrospective patient cohort studies and in patient-derived xenografts, CDK12-overexpressing breast tumors show positive response to methotrexate-based chemotherapy targeting CDK12-induced metabolic alterations, while being intrinsically refractory to other types of chemotherapy. In a retrospective analysis of hormone receptor-negative and lymph node-positive breast cancer patients randomized in an adjuvant phase III trial to 1-year low-dose metronomic methotrexate-based chemotherapy or no maintenance chemotherapy, a high CDK12 status predicts a dramatic reduction in distant metastasis rate in the chemotherapy-treated vs. not-treated arm. Thus, by coupling tumor progression with metabolic reprogramming, CDK12 creates an actionable vulnerability for breast cancer therapy and might represent a suitable companion biomarker for targeted antimetabolite therapies in human breast cancers. Finding biomarkers for targeted therapy is a promising approach to treat cancer. Here, the authors show that in breast cancer preclinical models and patients, CDK12 promotes tumourigenesis but induces selective vulnerability to therapies that target folate one-carbon metabolism.
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Affiliation(s)
- M G Filippone
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - D Gaglio
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR) Segrate, Milan, Italy.,ISBE.IT/Centre of Systems Biology, Piazza della Scienza 4, 20126, Milan, Italy
| | - R Bonfanti
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - F A Tucci
- School of Pathology, University of Milan, Milan, Italy
| | - E Ceccacci
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - R Pennisi
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - M Bonanomi
- ISBE.IT/Centre of Systems Biology, Piazza della Scienza 4, 20126, Milan, Italy
| | - G Jodice
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - M Tillhon
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - F Montani
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - G Bertalot
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - S Freddi
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - M Vecchi
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.,IFOM, The FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
| | - A Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - M Romanenghi
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - F Romeo
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - N Bianco
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - E Munzone
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - F Sanguedolce
- Department of Pathology, University of Foggia, Foggia, Italy
| | - G Vago
- School of Pathology, University of Milan, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy
| | - G Viale
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy
| | - P P Di Fiore
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy
| | - S Minucci
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy
| | - L Alberghina
- ISBE.IT/Centre of Systems Biology, Piazza della Scienza 4, 20126, Milan, Italy.,Department of Biotechnology and Biosciences, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - M Colleoni
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - P Veronesi
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy
| | - D Tosoni
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.
| | - S Pece
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy. .,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20142, Milano, Italy.
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21
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He YW, Walsh CM. Editorial: Editor’s Pick 2021: Highlights in Cell Death and Survival. Front Cell Dev Biol 2022; 10:887688. [PMID: 35615699 PMCID: PMC9125200 DOI: 10.3389/fcell.2022.887688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- You-Wen He
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: You-Wen He, ; Craig M. Walsh,
| | - Craig M. Walsh
- Department of Molecular Biology and Biochemistry, Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
- *Correspondence: You-Wen He, ; Craig M. Walsh,
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22
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Kim CL, Lim SB, Kim K, Jeong HS, Mo JS. Phosphorylation analysis of the Hippo-YAP pathway using Phos-tag. J Proteomics 2022; 261:104582. [DOI: 10.1016/j.jprot.2022.104582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
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23
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Wang XJ, Li S, Fang J, Yan ZJ, Luo GC. LncRNA FAM13A-AS1 Promotes Renal Carcinoma Tumorigenesis Through Sponging miR-141-3p to Upregulate NEK6 Expression. Front Mol Biosci 2022; 9:738711. [PMID: 35402517 PMCID: PMC8984162 DOI: 10.3389/fmolb.2022.738711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs are a diverse catalog of RNAs that have been implicated in various aspects of tumorigenesis. Emerging evidence indicates that they play crucial roles in tumor growth, disease progression, and drug resistance. However, the clinical significance of lncRNAs in tumor behavior prediction and disease prognosis as well as the underlying mechanism in renal cell carcinoma (RCC) remains elusive. By analyzing the gene expression profiles of 539 RCC patients from the TCGA cohort and 40 RCC patients from an independent cohort, we identified FAM13A-AS1, a poorly studied lncRNA, upregulated in RCC patients. Knockdown experiments revealed that FAM13A-AS1 promotes cell proliferation, migration, and invasion by interacting with miR-141-3p. FAM13A-AS1 regulates the expression of NEK6 by decoying miR-141-3p. In addition, there was a strong positive correlation between the expression of FAM13A-AS1 and NEK6 in RCC patients. In summary, our results demonstrate the oncogenic role of FAM13A-AS1 in RCC and suggest that it promotes tumorigenesis by upregulating the expression of NEK6 by competitively binding to miR-141-3p.
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Affiliation(s)
- Xin Jun Wang
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Si Li
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Jiang Fang
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Zhi Jian Yan
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Guang Cheng Luo
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
- *Correspondence: Guang Cheng Luo,
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24
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Yan Z, Da Q, Li Z, Lin Q, Yi J, Su Y, Yu G, Ren Q, Liu X, Lin Z, Qu J, Yin W, Liu J. Inhibition of NEK7 Suppressed Hepatocellular Carcinoma Progression by Mediating Cancer Cell Pyroptosis. Front Oncol 2022; 12:812655. [PMID: 35223495 PMCID: PMC8866693 DOI: 10.3389/fonc.2022.812655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/07/2022] [Indexed: 02/05/2023] Open
Abstract
NIMA-related kinase 7 (NEK7) is a serine/threonine kinase involved in cell cycle progression via mitotic spindle formation and cytokinesis. It has been related to multiple cancers, including breast cancer, hepatocellular cancer, lung cancer, and colorectal cancer. Moreover, NEK7 regulated the NLRP3 inflammasome to activate Caspase-1, resulting in cell pyroptosis. In the present study, we investigated whether NEK7 is involved in cell pyroptosis of hepatocellular carcinoma (HCC). Interestingly, we found that NEK7 was significantly related to expression of pyroptosis marker GSDMD in HCC. We found that NEK7 expression was significantly correlated with GSDMD expression in bioinformatics analysis, and NEK7 expression was significantly co-expressed with GSDMD in our HCC specimens. Cell viability, migration, and invasion capacity of HCC cell lines were inhibited, and the tumor growth in the xenograft mouse model was also suppressed following knockdown of NEK7 expression. Mechanistic studies revealed that knockdown of NEK7 in HCC cells significantly upregulated the expression of pyroptosis markers such as NLRP3, Caspase-1, and GSDMD. Coculture of HCC cells stimulated hepatic stellate cell activation by increasing p-ERK1/2 and α-SMA. Knockdown of NEK7 impaired the stimulation of HCC cells. Therefore, downregulation of NEK7 inhibited cancer–stromal interaction by triggering cancer cell pyroptosis. Taken together, this study highlights the functional role of NEK7-regulated pyroptosis in tumor progression and cancer–stromal interaction of HCC, suggesting NEK7 as a potential target for a new therapeutic strategy of HCC treatment.
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Affiliation(s)
- Zilong Yan
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qingen Da
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Zhangfu Li
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qirui Lin
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jing Yi
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yanze Su
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guanyin Yu
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qingqi Ren
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xu Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zewei Lin
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianhua Qu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weihua Yin
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jikui Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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25
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Shi X, Zhou Q, Huang B, Xia S, Jiang Y, Fang S, Lin J. Prognostic and immune-related value of STK17B in skin cutaneous melanoma. PLoS One 2022; 17:e0263311. [PMID: 35171924 PMCID: PMC8849620 DOI: 10.1371/journal.pone.0263311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/16/2022] [Indexed: 11/26/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is a common cancer of which mortality is increasing continuously. Our study conducted a series of analyses on the clinical significance of Serine/threonine kinase 17B (STK17B) in SKCM to provide a new biomarker for diagnosis and treatment. The RNA-sequence data were obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases. The data of 468 SKCM patients were divided into STK17B high- and low-expression groups and analyzed by Bioconductor package to identify the differential expressed genes. The R package of "clusterProfiler" was used for Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene-Set Enrichment Analysis analyses. A protein-protein interaction network and immune infiltration landscape were respectively constructed via STRING database and ssGSEA. STK17B had lower expression in SKCM than normal tissues. Besides, STK17B expression was significantly related to some clinicopathological characteristics in SKCM patients including T stage, Breslow depth, radiation therapy, melanoma Clark level, and pathologic stage. The Kaplan-Meier curve analyses revealed that the low expression of STK17B was correlated with poor overall survival and disease-specific survival. We constructed nomograms to predict the 1-, 3-, and 5-year survival of SKCM patients. The function enrichment analyses showed STK17B-related differential expressed genes were enriched in cellular differentiation and immune-related progress. STK17B expression level were positively correlated with infiltrating level of immune cells. In this study, we found that STK17B, which played an important role in immune infiltration, could be a new biomarker for diagnosis and prognosis in SKCM patients.
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Affiliation(s)
- Xueying Shi
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Qi Zhou
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Bingqian Huang
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Shilin Xia
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yuankuan Jiang
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Shifeng Fang
- Department of Ophthalmology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jingrong Lin
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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26
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Wang X, Huang R, Lu Z, Wang Z, Chen X, Huang D. Exosomes from M1‐polarized macrophages promote apoptosis in lung adenocarcinoma via the miR‐181a‐5p/ETS1/STK16 axis. Cancer Sci 2022; 113:986-1001. [PMID: 35092121 PMCID: PMC8898733 DOI: 10.1111/cas.15268] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
Serine/threonine kinase 16 (STK16) is crucial in on regulating tumor cell proliferation, apoptosis, and prognosis. Activated M1 macrophages regulate lung adenocarcinoma (LUAD) growth by releasing exosomes. This study aims to investigate the role of STK16 and then focus on the possible mechanisms through which exosomes derived from M1 macrophages play their roles in LUAD cells by targeting STK16. Clinical LUAD samples were used to evaluate the expression of STK16 and its association with prognosis. Exosomes were isolated from M0 and M1 macrophages by ultracentrifugation and were then identified by electron microscopy and western blotting. In vitro gain‐ and loss‐of‐function experiments with LUAD cells were performed to elucidate the functions of miR‐181a‐5p, ETS1, and STK16, and mouse xenograft models were used to verify the function of STK16 in vivo. Western blotting, quantitative real‐time PCR, CCK‐8 assay, cell apoptosis, immunohistochemistry staining, luciferase assay, ChIP assay, and bioinformatics analysis were performed to reveal the underlying mechanisms. High expression of STK16 was observed in LUAD tissues and cells, and higher expression of STK16 was associated with worse prognosis. Silencing STK16 expression inhibited cell proliferation and promoted apoptosis via the AKT1 pathway. Exosomes from M1 macrophages inhibited viability and promoted apoptosis by inhibiting STK16. Moreover, miR‐181a‐5p is the functional molecule in M1 macrophage‐derived exosomes and plays a vital role in inhibiting cell proliferation and promoting apoptosis by targeting ETS1 and STK16. Hence, exosomes derived from M1 macrophages were capable of inhibiting viability and promoting apoptosis in LUAD via the miR‐181a‐5p/ETS1/STK16 axis.
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Affiliation(s)
- Xuan Wang
- Department of Thoracic Surgery Huashan Hospital Fudan University 12 Urumqi Road (M) Shanghai 200040 China
| | - Renhong Huang
- Department of General Surgery Comprehensive Breast Health Center Ruijin Hospital Shanghai Jiao Tong University School of Medicine 197 Ruijin Second Road Shanghai 200025 China
| | - Zhouyi Lu
- Department of Thoracic Surgery Huashan Hospital Fudan University 12 Urumqi Road (M) Shanghai 200040 China
| | - Zheng Wang
- Department of General Surgery Comprehensive Breast Health Center Ruijin Hospital Shanghai Jiao Tong University School of Medicine 197 Ruijin Second Road Shanghai 200025 China
| | - Xiaofeng Chen
- Department of Thoracic Surgery Huashan Hospital Fudan University 12 Urumqi Road (M) Shanghai 200040 China
| | - Dayu Huang
- Department of Thoracic Surgery Huashan Hospital Fudan University 12 Urumqi Road (M) Shanghai 200040 China
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27
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Joladarashi D, Zhu Y, Willman M, Nash K, Cimini M, Thandavarayan RA, Youker KA, Song X, Ren D, Li J, Kishore R, Krishnamurthy P, Wang L. STK35 Gene Therapy Attenuates Endothelial Dysfunction and Improves Cardiac Function in Diabetes. Front Cardiovasc Med 2022; 8:798091. [PMID: 35097018 PMCID: PMC8792894 DOI: 10.3389/fcvm.2021.798091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022] Open
Abstract
Diabetic cardiomyopathy (DCM) is characterized by microvascular pathology and interstitial fibrosis that leads to progressive heart failure. The mechanisms underlying DCM pathogenesis remain obscure, and no effective treatments for the disease have been available. In the present study, we observed that STK35, a novel kinase, is decreased in the diabetic human heart. High glucose treatment, mimicking hyperglycemia in diabetes, downregulated STK35 expression in mouse cardiac endothelial cells (MCEC). Knockdown of STK35 attenuated MCEC proliferation, migration, and tube formation, whereas STK35 overexpression restored the high glucose-suppressed MCEC migration and tube formation. Angiogenesis gene PCR array analysis revealed that HG downregulated the expression of several angiogenic genes, and this suppression was fully restored by STK35 overexpression. Intravenous injection of AAV9-STK35 viral particles successfully overexpressed STK35 in diabetic mouse hearts, leading to increased vascular density, suppression of fibrosis in the heart, and amelioration of left ventricular function. Altogether, our results suggest that hyperglycemia downregulates endothelial STK35 expression, leading to microvascular dysfunction in diabetic hearts, representing a novel mechanism underlying DCM pathogenesis. Our study also emerges STK35 is a novel gene therapeutic target for preventing and treating DCM.
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Affiliation(s)
- Darukeshwara Joladarashi
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Yanan Zhu
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
| | - Matthew Willman
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
| | - Kevin Nash
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
| | - Maria Cimini
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | | | - Keith A. Youker
- Houston Methodist DeBakey Heart & Vascular Center, Houston, TX, United States
| | - Xuehong Song
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
| | - Di Ren
- Department of Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Ji Li
- Department of Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
- Prasanna Krishnamurthy
| | - Lianchun Wang
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, Bryd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States
- *Correspondence: Lianchun Wang
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28
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Synthesis, functional proteomics and biological evaluation of new 5-pyrazolyl ureas as potential anti-angiogenic compounds. Eur J Med Chem 2021; 226:113872. [PMID: 34600191 DOI: 10.1016/j.ejmech.2021.113872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/09/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022]
Abstract
Based on biological results of previous synthesized pyrazolyl ureas able to interfere with angiogenesis process, we planned and synthesized the new benzyl-urea derivatives 2-4; some of them showed an interesting anti-proliferative profile and particularly 4e potently inhibited HUVEC proliferation. To shed light on the mechanism of action of 4e, its interactome has been deeply inspected to identify the most prominent protein partners, mainly taking into account kinome and phosphatome, through drug affinity responsive target stability experiments, followed by targeted limited proteolysis analysis. From these studies, PP1γ emerged as the most reliable 4e potential target in HUVEC. Molecular docking simulations on PP1γ were carried out to predict 4e binding mode. To assess its potential anti-angiogenic effect, 4e was tested in vitro to verify interference on kinase and phosphate activities. Overall, our results evidenced for 4e an interesting anti-angiogenic action, probably due to its action at intracellular level on PP1γ signalling pathways.
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29
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Anuraga G, Wang WJ, Phan NN, An Ton NT, Ta HDK, Berenice Prayugo F, Minh Xuan DT, Ku SC, Wu YF, Andriani V, Athoillah M, Lee KH, Wang CY. Potential Prognostic Biomarkers of NIMA (Never in Mitosis, Gene A)-Related Kinase (NEK) Family Members in Breast Cancer. J Pers Med 2021; 11:1089. [PMID: 34834441 PMCID: PMC8625415 DOI: 10.3390/jpm11111089] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer remains the most common malignant cancer in women, with a staggering incidence of two million cases annually worldwide; therefore, it is crucial to explore novel biomarkers to assess the diagnosis and prognosis of breast cancer patients. NIMA-related kinase (NEK) protein kinase contains 11 family members named NEK1-NEK11, which were discovered from Aspergillus Nidulans; however, the role of NEK family genes for tumor development remains unclear and requires additional study. In the present study, we investigate the prognosis relationships of NEK family genes for breast cancer development, as well as the gene expression signature via the bioinformatics approach. The results of several integrative analyses revealed that most of the NEK family genes are overexpressed in breast cancer. Among these family genes, NEK2/6/8 overexpression had poor prognostic significance in distant metastasis-free survival (DMFS) in breast cancer patients. Meanwhile, NEK2/6 had the highest level of DNA methylation, and the functional enrichment analysis from MetaCore and Gene Set Enrichment Analysis (GSEA) suggested that NEK2 was associated with the cell cycle, G2M checkpoint, DNA repair, E2F, MYC, MTORC1, and interferon-related signaling. Moreover, Tumor Immune Estimation Resource (TIMER) results showed that the transcriptional levels of NEK2 were positively correlated with immune infiltration of B cells and CD4+ T Cell. Collectively, the current study indicated that NEK family genes, especially NEK2 which is involved in immune infiltration, and may serve as prognosis biomarkers for breast cancer progression.
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Affiliation(s)
- Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Wei-Jan Wang
- Research Center for Cancer Biology, Department of Biological Science and Technology, China Medical University, Taichung 40604, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Nu Thuy An Ton
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Yung-Fu Wu
- Department of Medical Research, Tri-Service General Hospital, School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
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30
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Liang Y, Qian C, Xie Y, Huang X, Chen J, Ren Y, Fu Z, Li Y, Zeng T, Yang F, Zhou J, Li W, Yin Y, Wang C. JWA suppresses proliferation in trastuzumab-resistant breast cancer by downregulating CDK12. Cell Death Discov 2021; 7:306. [PMID: 34686673 PMCID: PMC8536718 DOI: 10.1038/s41420-021-00693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer worldwide. JWA is a microtubule-associated protein that has been identified as a tumor suppressor, and its downregulation in tumors is an independent adverse prognostic factor. The objective of this study was to explore the expression, regulation, and mechanism of JWA in trastuzumab-resistant breast cancers. In this study, we found that JWA expression was lower in trastuzumab-resistant breast cancers than that in trastuzumab-sensitive breast cancers. Furthermore, it was confirmed that overexpression of JWA inhibited proliferation and promoted apoptosis in trastuzumab-resistant breast cancers both in vitro and in vivo. In addition, the low expression of JWA in trastuzumab-resistant breast cancers is associated with a poor prognosis. Combining RNA-sequence datasets and next-generation sequencing, it was found that JWA negatively regulated CDK12, and was involved in the G1-to-S transition of the cell cycle. It has been reported that CDK12 drives breast cancer initiation and induces trastuzumab resistance. Taken together, high expression of JWA could inhibit the growth of trastuzumab-resistant breast cancer, and JWA is a potential predictive marker for trastuzumab resistance. In addition, targeted therapy with JWA may be a novel therapeutic strategy to improve the survival rate of trastuzumab-resistant breast cancer.
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Affiliation(s)
- Yan Liang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chao Qian
- Department of General Surgery, Sir Run Run Hospital, Nanjing, China
| | - Yinghong Xie
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junjie Chen
- Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Yanlin Ren
- Nantong Center for Disease Control and Prevention, Nantong, China
| | - Ziyi Fu
- Laboratory of Breast Disease Department, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongfei Li
- Department of General Surgery, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Tianyu Zeng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology & Toxicology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Changqing Wang
- School of Health Policy and Management, Nanjing Medical University, Nanjing, China.
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31
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Mendoza FA, Jimenez SA. Serine-Threonine Kinase inhibition as antifibrotic therapy: TGF-β and ROCK inhibitors. Rheumatology (Oxford) 2021; 61:1354-1365. [PMID: 34664623 DOI: 10.1093/rheumatology/keab762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/18/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Serine-threonine kinases mediate the phosphorylation of intracellular protein targets, transferring a phosphorus group from an ATP molecule to the specific amino acid residues within the target proteins. Serine-threonine kinases regulate multiple key cellular functions. From this large group of kinases, transforming growth factor beta (TGF-β) through the serine-threonine activity of its receptors and Rho kinase (ROCK) play an important role in the development and maintenance of fibrosis in various human diseases, including systemic sclerosis. In recent years, multiple drugs targeting and inhibiting these kinases, have been developed, opening the possibility of becoming potential antifibrotic agents of clinical value for treating fibrotic diseases. This review analyzes the contribution of TGF- β and ROCK-mediated serine-threonine kinase molecular pathways to the development and maintenance of pathological fibrosis and the potential clinical use of their inhibition.
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Affiliation(s)
- Fabian A Mendoza
- Division of Rheumatology, Department of Medicine. Thomas Jefferson University. Philadelphia, PA, USA 19107.,Jefferson Institute of Molecular Medicine and Scleroderma Center. Thomas Jefferson University. Philadelphia, PA, USA 19107
| | - Sergio A Jimenez
- Jefferson Institute of Molecular Medicine and Scleroderma Center. Thomas Jefferson University. Philadelphia, PA, USA 19107
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Najar MA, Aravind A, Dagamajalu S, Sidransky D, Ashktorab H, Smoot DT, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Hyperactivation of MEK/ERK pathway by Ca 2+ /calmodulin-dependent protein kinase kinase 2 promotes cellular proliferation by activating cyclin-dependent kinases and minichromosome maintenance protein in gastric cancer cells. Mol Carcinog 2021; 60:769-783. [PMID: 34437731 DOI: 10.1002/mc.23343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023]
Abstract
Although CAMKK2 is overexpressed in several cancers, its role and relevant downstream signaling pathways in gastric cancer (GC) are poorly understood. Treatment of AGS GC cells with a CAMKK2 inhibitor, STO-609, resulted in decreased cell proliferation, cell migration, invasion, colony-forming ability, and G1/S-phase arrest. Quantitative phosphoproteomics in AGS cells with the CAMKK2 inhibitor led to the identification of 9603 unique phosphosites mapping to 3120 proteins. We observed decreased phosphorylation of 1101 phosphopeptides (1.5-fold) corresponding to 752 proteins upon CAMKK2 inhibition. Bioinformatics analysis of hypo-phosphorylated proteins revealed enrichment of MAPK1/MAPK3 signaling. Kinase enrichment analysis of hypo-phosphorylated proteins using the X2K Web tool identified ERK1, cyclin-dependant kinase 1 (CDK1), and CDK2 as downstream substrates of CAMKK2. Moreover, inhibition of CAMKK2 and MEK1 resulted in decreased phosphorylation of ERK1, CDK1, MCM2, and MCM3. Immunofluorescence results were in concordance with our mass spectroscopy data and Western blot analysis results. Taken together, our data reveal the essential role of CAMKK2 in the pathobiology of GC through the activation of the MEK/ERK1 signaling cascade.
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Affiliation(s)
- Mohd A Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, District of Columbia, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant K Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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Sharma PK, Kalia I, Kaushik V, Brünnert D, Quadiri A, Kashif M, Chahar KR, Agrawal A, Singh AP, Goyal P. STK35L1 regulates host cell cycle-related genes and is essential for Plasmodium infection during the liver stage of malaria. Exp Cell Res 2021; 406:112764. [PMID: 34358525 DOI: 10.1016/j.yexcr.2021.112764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 11/28/2022]
Abstract
Protein kinases of both the parasite and the host are crucial in parasite invasion and survival and might act as drug targets against drug-resistant malaria. STK35L1 was among the top five hits in kinome-wide screening, suggesting its role in malaria's liver stage. However, the role of host STK35L1 in malaria remains elusive. In this study, we found that STK35L1 was highly upregulated during the infection of Plasmodium berghei (P. berghei) in HepG2 cells and mice liver, and knockdown of STK35L1 remarkably suppressed the sporozoites' infection in HepG2 cells. We showed that STAT3 is upregulated and phosphorylated during P. berghei sporozoites' infection, and STAT3 activation is required for both the upregulation of STK35L1 and STAT3. Furthermore, we found that ten cell cycle genes were upregulated in the sporozoite-infected hepatocytes. Knockdown of STK35L1 inhibited the basal expression of these genes except CDKN3 and GTSE1 in HepG2 cells. Thus, we identified STK35L1 as a host kinase that plays an obligatory role in malaria's liver stage and propose that it may serve as a potential drug target against drug-resistant malaria.
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Affiliation(s)
- Phulwanti Kumari Sharma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan, 305 817, India
| | - Inderjeet Kalia
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibha Kaushik
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan, 305 817, India
| | - Daniela Brünnert
- Experimental Tumor Immunology, Department of Obstetrics and Gynecology, University of Würzburg Medical School, Würzburg, Germany
| | - Afshana Quadiri
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohammad Kashif
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kirti Raj Chahar
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan, 305 817, India
| | - Akhil Agrawal
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan, 305 817, India
| | - Agam Prasad Singh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Pankaj Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan, 305 817, India.
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Yan Z, Qu J, Li Z, Yi J, Su Y, Lin Q, Yu G, Lin Z, Yin W, Lu F, Liu J. NEK7 Promotes Pancreatic Cancer Progression And Its Expression Is Correlated With Poor Prognosis. Front Oncol 2021; 11:705797. [PMID: 34295827 PMCID: PMC8290842 DOI: 10.3389/fonc.2021.705797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022] Open
Abstract
The prognosis for pancreatic ductal adenocarcinoma (PDAC) patients is still dismal. Elucidation of associated genomic alteration may provide effective therapeutic strategies for PDAC treatment. NIMA-related protein kinase 7 is widely expressed in various tumors, including breast cancer, colorectal cancer and lung cancer, and promotes the proliferation of liver cancer cells in vitro and in vivo. We investigated the protein expression level of NEK7 in tumor tissues and adjacent normal tissues using immunohistochemistry of 90 patients with PADC. Meanwhile, the RNA expression level of NEK7 was examined using database-based bioinformatic analysis. Correlation and significance of NEK7 expression with patient clinicopathological features and prognosis were examined. Cell proliferation, cell adhesion, migration and invasion capabilities were measured following downregulation of NEK7 expression. 3D tumor organoids of pancreatic cancer were established and splenic xenografted into nude mice, then liver metastatic ability of NEK7 was evaluated in following 4 weeks. We observed NEK7 expression was upregulated in tumor tissues compared to normal tissues at both RNA and protein levels using bioinformatic analysis and immunohistochemistry analysis in PDAC. NEK7 expression was undetectable in normal pancreatic ducts; NEK7 was overexpressed in primary tumor of PDAC; NEK7 expression was highly correlated with advanced T stage, poorly differentiated histological grade invasive ductal carcinoma, and lymphatic invasion. Meanwhile, patients with higher NEK7 expression accompanied by worse survival outcome. Moreover, NEK7 promoted migration, invasion, adhesion, proliferation and liver metastatic ability of pancreatic cancer cells. Taken together, our data indicate that NEK7 promotes pancreatic cancer progression and it may be a potential marker for PDAC prognosis.
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Affiliation(s)
- Zilong Yan
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianhua Qu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhangfu Li
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jing Yi
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yanze Su
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qirui Lin
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guangyin Yu
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zewei Lin
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weihua Yin
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jikui Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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35
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Roosan MR, Mambetsariev I, Pharaon R, Fricke J, Baroz AR, Chao J, Chen C, Nasser MW, Chirravuri-Venkata R, Jain M, Smith L, Yost SE, Reckamp KL, Pillai R, Arvanitis L, Afkhami M, Wang EW, Chung V, Cristea M, Fakih M, Koczywas M, Massarelli E, Mortimer J, Yuan Y, Batra SK, Pal S, Salgia R. Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients. Cancers (Basel) 2021; 13:2776. [PMID: 34204917 PMCID: PMC8199748 DOI: 10.3390/cancers13112776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
Metastasis continues to be the primary cause of all cancer-related deaths despite the recent advancements in cancer treatments. To evaluate the role of mutations in overall survival (OS) and treatment outcomes, we analyzed 957 metastatic patients with seven major cancer types who had available molecular testing results with a FoundationOne CDx® panel. The most prevalent genes with somatic mutations were TP53, KRAS, APC, and LRP1B. In this analysis, these genes had mutation frequencies higher than in publicly available datasets. We identified that the somatic mutations were seven mutually exclusive gene pairs and an additional fifty-two co-occurring gene pairs. Mutations in the mutually exclusive gene pair APC and CDKN2A showed an opposite effect on the overall survival. However, patients with CDKN2A mutations showed significantly shorter OS (HR: 1.72, 95% CI: 1.34-2.21, p < 0.001) after adjusting for cancer type, age at diagnosis, and sex. Five-year post metastatic diagnosis survival analysis showed a significant improvement in OS (median survival 28 and 43 months in pre-2015 and post-2015 metastatic diagnosis, respectively, p = 0.00021) based on the year of metastatic diagnosis. Although the use of targeted therapies after metastatic diagnosis prolonged OS, the benefit was not statistically significant. However, longer five-year progression-free survival (PFS) was significantly associated with targeted therapy use (median 10.9 months (CI: 9.7-11.9 months) compared to 9.1 months (CI: 8.1-10.1 months) for non-targeted therapy, respectively, p = 0.0029). Our results provide a clinically relevant overview of the complex molecular landscape and survival mechanisms in metastatic solid cancers.
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Affiliation(s)
- Moom R. Roosan
- School of Pharmacy, Chapman University, Irvine, CA 92618, USA;
| | - Isa Mambetsariev
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Rebecca Pharaon
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Jeremy Fricke
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Angel R. Baroz
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Joseph Chao
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Chen Chen
- Applied AI and Data Science, City of Hope, Duarte, CA 91010, USA;
| | - Mohd W. Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Ramakanth Chirravuri-Venkata
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Lynette Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Susan E. Yost
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Karen L. Reckamp
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
- Cedars-Sinai Medical Center, Department of Medicine, Division of Medical Oncology, Los Angeles, CA 90048, USA
| | - Raju Pillai
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Michelle Afkhami
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Edward W. Wang
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Vincent Chung
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Mihaela Cristea
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Marwan Fakih
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Marianna Koczywas
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Erminia Massarelli
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Joanne Mortimer
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Yuan Yuan
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Sumanta Pal
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
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Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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37
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Southekal S, Mishra NK, Guda C. Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers. Cancers (Basel) 2021; 13:cancers13061189. [PMID: 33801837 PMCID: PMC8001681 DOI: 10.3390/cancers13061189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Kinases are a group of intracellular signaling molecules that play critical roles in various biological processes. Even though kinases comprise one of the most well-known therapeutic targets, many have been understudied and therefore warrant further investigation. DNA methylation is one of the key epigenetic regulators that modulate gene expression. In this study, the human kinome's DNA methylation and gene expression patterns were analyzed using the level-3 TCGA data for 32 cancers. Unsupervised clustering based on kinome data revealed the grouping of cancers based on their organ level and tissue type. We further observed significant differences in overall kinase methylation levels (hyper- and hypomethylation) between the tumor and adjacent normal samples from the same tissue. Methylation expression quantitative trait loci (meQTL) analysis using kinase gene expression with the corresponding methylated probes revealed a highly significant and mostly negative association (~92%) within 1.5 kb from the transcription start site (TSS). Several understudied (dark) kinases (PKMYT1, PNCK, BRSK2, ERN2, STK31, STK32A, and MAPK4) were also identified with a significant role in patient survival. This study leverages results from multi-omics data to identify potential kinase markers of prognostic and diagnostic importance and further our understanding of kinases in cancer.
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Affiliation(s)
| | | | - Chittibabu Guda
- Correspondence: (N.K.M.); (C.G.); Tel.: +1-402-559-5954 (C.G.)
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38
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ElHady AK, El-Gamil DS, Chen PJ, Hwang TL, Abadi AH, Abdel-Halim M, Engel M. 5-Methoxybenzothiophene-2-Carboxamides as Inhibitors of Clk1/4: Optimization of Selectivity and Cellular Potency. Molecules 2021; 26:molecules26041001. [PMID: 33668683 PMCID: PMC7918793 DOI: 10.3390/molecules26041001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/04/2023] Open
Abstract
Clks have been shown by recent studies to be promising targets for cancer therapy, as they are considered key regulators in the process of pre-mRNA splicing, which in turn affects every aspect of tumor biology. In particular, Clk1 and -4 are overexpressed in several human tumors. Most of the potent Clk1 inhibitors reported in the literature are non-selective, mainly showing off-target activity towards Clk2, Dyrk1A and Dyrk1B. Herein, we present new 5-methoxybenzothiophene-2-carboxamide derivatives with unprecedented selectivity. In particular, the introduction of a 3,5-difluoro benzyl extension to the methylated amide led to the discovery of compound 10b (cell-free IC50 = 12.7 nM), which was four times more selective for Clk1 over Clk2 than the previously published flagship compound 1b. Moreover, 10b showed an improved growth inhibitory activity with T24 cells (GI50 = 0.43 µM). Furthermore, a new binding model in the ATP pocket of Clk1 was developed based on the structure-activity relationships derived from new rigidified analogues.
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Affiliation(s)
- Ahmed K. ElHady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11865, Egypt
| | - Dalia S. El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Po-Jen Chen
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (P.-J.C.); (T.-L.H.)
- Department of Cosmetic Science, Providence University, Taichung 433, Taiwan
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (P.-J.C.); (T.-L.H.)
- Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City 243, Taiwan
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-302-70312; Fax: +49-681-302-70308
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Aydin E, Faehling S, Saleh M, Llaó Cid L, Seiffert M, Roessner PM. Phosphoinositide 3-Kinase Signaling in the Tumor Microenvironment: What Do We Need to Consider When Treating Chronic Lymphocytic Leukemia With PI3K Inhibitors? Front Immunol 2021; 11:595818. [PMID: 33552053 PMCID: PMC7857022 DOI: 10.3389/fimmu.2020.595818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
Phosphoinositide 3-kinases (PI3Ks) and their downstream proteins constitute a signaling pathway that is involved in both normal cell growth and malignant transformation of cells. Under physiological conditions, PI3K signaling regulates various cellular functions such as apoptosis, survival, proliferation, and growth, depending on the extracellular signals. A deterioration of these extracellular signals caused by mutational damage in oncogenes or growth factor receptors may result in hyperactivation of this signaling cascade, which is recognized as a hallmark of cancer. Although higher activation of PI3K pathway is common in many types of cancer, it has been therapeutically targeted for the first time in chronic lymphocytic leukemia (CLL), demonstrating its significance in B-cell receptor (BCR) signaling and malignant B-cell expansion. The biological activity of the PI3K pathway is not only limited to cancer cells but is also crucial for many components of the tumor microenvironment, as PI3K signaling regulates cytokine responses, and ensures the development and function of immune cells. Therefore, the success or failure of the PI3K inhibition is strongly related to microenvironmental stimuli. In this review, we outline the impacts of PI3K inhibition on the tumor microenvironment with a specific focus on CLL. Acknowledging the effects of PI3K inhibitor-based therapies on the tumor microenvironment in CLL can serve as a rationale for improved drug development, explain treatment-associated adverse events, and suggest novel combinatory treatment strategies in CLL.
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Affiliation(s)
- Ebru Aydin
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Faehling
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Mariam Saleh
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Molecular Medicine, Ulm University, Ulm, Germany
| | - Laura Llaó Cid
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Bioscience, University of Heidelberg, Heidelberg, Germany
| | - Martina Seiffert
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp M Roessner
- Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Murugesan S, Murugesan J, Palaniappan S, Palaniappan S, Murugan T, Siddiqui SS, Loganathan S. Tyrosine Kinase Inhibitors (TKIs) in Lung Cancer Treatment: A Comprehensive Analysis. Curr Cancer Drug Targets 2021; 21:55-69. [PMID: 33038912 DOI: 10.2174/1568009620666201009130008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is the leading type of cancer worldwide today. Kinases play a crucial role in mediating the signaling pathways, and it directs to control several necessary cellular processes. Conversely, the deregulation of tyrosine kinases leads to oncogenic conversion, uncontrolled cell proliferation and tumorigenesis. Tyrosine kinases are largely deregulated in lung cancer and specifically in non-small cell lung cancer (NSCLC). Therefore, the inhibition of pathogenic kinases is a breakthrough development in cancer research, treatment and care, which clinically improve the quality of life. In the last decades, various single or combination inhibitors are approved by U.S Food and Drug Administration (FDA) and commercially available in clinics, and currently, several preclinical studies are ongoing and examining the kinase inhibitors. However, many gaps remain in understanding the mechanisms of kinase inhibitors and their selectivity. In this analysis, we focus on a class of receptor and non-receptor tyrosine kinase inhibitors and their novel role in lung cancer.
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Affiliation(s)
- Sivakumar Murugesan
- Department of Environmental Science, Periyar University, Salem-636011, Tamil Nadu, India
| | - Jayakumar Murugesan
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar- 608002, Tamilnadu, India
| | - Seedevi Palaniappan
- Department of Environmental Science, Periyar University, Salem-636011, Tamil Nadu, India
| | - Sivasankar Palaniappan
- Department of Environmental Science, Periyar University, Salem-636011, Tamil Nadu, India
| | - Tamilselvi Murugan
- Department of Zoology, Government Arts College (Autonomous), Coimbatore-641018, Tamil Nadu, India
| | - Shahid S Siddiqui
- Department of Medicine, University of Chicago, Chicago, IL-60637, United States
| | - Sivakumar Loganathan
- Department of Environmental Science, Periyar University, Salem-636011, Tamil Nadu, India
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Batai K, Trejo MJ, Chen Y, Kohler LN, Lance P, Ellis NA, Cornelis MC, Chow HHS, Hsu CH, Jacobs ET. Genome-Wide Association Study of Response to Selenium Supplementation and Circulating Selenium Concentrations in Adults of European Descent. J Nutr 2020; 151:293-302. [PMID: 33382417 PMCID: PMC7849979 DOI: 10.1093/jn/nxaa355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Selenium (Se) is a trace element that has been linked to many health conditions. Genome-wide association studies (GWAS) have identified variants for blood and toenail Se levels, but no GWAS has been conducted to date on responses to Se supplementation. OBJECTIVES A GWAS was performed to identify the single nucleotide polymorphisms (SNPs) associated with changes in Se concentrations after 1 year of supplementation. A GWAS of basal plasma Se concentrations at study entry was conducted to evaluate whether SNPs for Se responses overlap with SNPs for basal Se levels. METHODS A total of 428 participants aged 40-80 years of European descent from the Selenium and Celecoxib Trial (Sel/Cel Trial) who received daily supplementation with 200 µg of selenized yeast were included for the GWAS of responses to supplementation. Plasma Se concentrations were measured from blood samples collected at the time of recruitment and after 1 year of supplementation. Linear regression analyses were performed to assess the relationship between each SNP and changes in Se concentrations. We further examined whether the identified SNPs overlapped with those related to basal Se concentrations. RESULTS No SNP was significantly associated with changes in Se concentration at a genome-wide significance level. However, rs56856693, located upstream of the NEK6, was nominally associated with changes in Se concentrations after supplementation (P = 4.41 × 10-7), as were 2 additional SNPs, rs11960388 and rs6887869, located in the dimethylglycine dehydrogenase (DMGDH)/betaine-homocysteine S-methyltransferase (BHMT) region (P = 0.01). Alleles of 2 SNPs in the DMGDH/BHMT region associated with greater increases in Se concentrations after supplementation were also strongly associated with higher basal Se concentrations (P = 8.67 × 10-8). CONCLUSIONS This first GWAS of responses to Se supplementation in participants of European descent from the Sel/Cel Trial suggests that SNPs in the NEK6 and DMGDH/BHMT regions influence responses to supplementation.
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Affiliation(s)
- Ken Batai
- Address correspondence to KB (E-mail: )
| | - Mario J Trejo
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - Yuliang Chen
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - Lindsay N Kohler
- Department of Health Promotion Science, University of Arizona, Tucson, AZ, USA
| | - Peter Lance
- University of Arizona Cancer Center, Tucson, AZ, USA,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Nathan A Ellis
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - H-H Sherry Chow
- University of Arizona Cancer Center, Tucson, AZ, USA,Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Chiu-Hsieh Hsu
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - Elizabeth T Jacobs
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA,University of Arizona Cancer Center, Tucson, AZ, USA
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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ShcD Binds DOCK4, Promotes Ameboid Motility and Metastasis Dissemination, Predicting Poor Prognosis in Melanoma. Cancers (Basel) 2020; 12:cancers12113366. [PMID: 33202906 PMCID: PMC7696252 DOI: 10.3390/cancers12113366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Metastasis formation and dissemination is a complex process that relies on several steps. Even though highly inefficient, metastasis spreading is the primary cause of cancer morbidity and mortality in patients. The aim of our study was to investigate the molecular pathways leading to metastases making use of human-in-mouse melanoma models of patient-derived xenografts. We demonstrate that the modulation of the expression of an adaptor protein of the Shc family, ShcD, can change the phenotype and the invasive properties of melanoma cells when highly expressed. We also show that ShcD binds DOCK4 and confines it into the cytoplasm, blocking the Rac1 signaling pathways, thus leading to metastasis development. Moreover, our results indicate that melanoma cells are more sensitive to therapeutic treatments when the ShcD molecular pathway is inactivated, suggesting that new therapeutic strategies can be designed in melanomas. Abstract Metastases are the primary cause of cancer-related deaths. The underlying molecular and biological mechanisms remain, however, elusive, thus preventing the design of specific therapies. In melanomas, the metastatic process is influenced by the acquisition of metastasis-associated mutational and epigenetic traits and the activation of metastatic-specific signaling pathways in the primary melanoma. In the current study, we investigated the role of an adaptor protein of the Shc family (ShcD) in the acquisition of metastatic properties by melanoma cells, exploiting our cohort of patient-derived xenografts (PDXs). We provide evidence that the depletion of ShcD expression increases a spread cell shape and the capability of melanoma cells to attach to the extracellular matrix while its overexpression switches their morphology from elongated to rounded on 3D matrices, enhances cells’ invasive phenotype, as observed on collagen gel, and favors metastasis formation in vivo. ShcD overexpression sustains amoeboid movement in melanoma cells, by suppressing the Rac1 signaling pathway through the confinement of DOCK4 in the cytoplasm. Inactivation of the ShcD signaling pathway makes melanoma cells more sensitive to therapeutic treatments. Consistently, ShcD expression predicts poor outcome in a cohort of 183 primary melanoma patients.
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Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One 2020; 15:e0242030. [PMID: 33156866 PMCID: PMC7647101 DOI: 10.1371/journal.pone.0242030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/23/2020] [Indexed: 11/18/2022] Open
Abstract
Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
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Affiliation(s)
- Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Regeneration NEXT, Duke University School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Haibo Liu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Niraj K. Nirala
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alexey Stukalov
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Usha Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael R. Green
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Singh R, Bhardwaj VK, Sharma J, Das P, Purohit R. Discovery and in silico evaluation of aminoarylbenzosuberene molecules as novel checkpoint kinase 1 inhibitor determinants. Genomics 2020; 113:707-715. [PMID: 33065246 DOI: 10.1016/j.ygeno.2020.10.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 10/01/2020] [Indexed: 01/12/2023]
Abstract
Checkpoint kinase 1 (CHK1) is an essential kinase with a critical function in cell cycle arrest. Several potent inhibitors targeting CHK1 have been published, but most of them have failed in clinical trials. Acknowledging the emerging consequence of CHK1 inhibitors in medication of cancer, there is a demand for widening the chemical range of CHK1 inhibitors. In this research, we considered a set of in-house plant based semi-synthetic aminoarylbenzosuberene molecules as potential CHK1 inhibitors. Based on a combined computational research that consolidates molecular docking and binding free energy computations we recognized the crucial determinants for their receptor binding. The drug likeness of these molecules were also scrutinized based on their toxicity and bioavailibilty profile. The computational strategy indicates that the Bch10 could be regarded as a potential CHK1 inhibitor in comparison with top five co-crystallize molecules. Bch10 signifies a promising outlet for the development of potent inhibitors for CHK1.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India.
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The Diverse Roles of TAO Kinases in Health and Diseases. Int J Mol Sci 2020; 21:ijms21207463. [PMID: 33050415 PMCID: PMC7589832 DOI: 10.3390/ijms21207463] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Thousand and one kinases (TAOKs) are members of the MAP kinase kinase kinase (MAP3K) family. Three members of this subfamily, TAOK1, 2, and 3, have been identified in mammals. It has been shown that TAOK1, 2 and 3 regulate the p38 MAPK and Hippo signaling pathways, while TAOK 1 and 2 modulate the SAPK/JNK cascade. Furthermore, TAOKs are involved in additional interactions with other cellular proteins and all of these pathways modulate vital physiological and pathophysiological responses in cells and tissues. Dysregulation of TAOK-related pathways is implicated in the development of diseases including inflammatory and immune disorders, cancer and drug resistance, and autism and Alzheimer’s diseases. This review collates current knowledge concerning the roles of TAOKs in protein–protein interaction, signal transduction, physiological regulation, and pathogenesis and summarizes the recent development of TAOK-specific inhibitors that have the potential to ameliorate TAOKs’ effects in pathological situations.
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Yang H, Zhu J, Wang G, Liu H, Zhou Y, Qian J. STK35 Is Ubiquitinated by NEDD4L and Promotes Glycolysis and Inhibits Apoptosis Through Regulating the AKT Signaling Pathway, Influencing Chemoresistance of Colorectal Cancer. Front Cell Dev Biol 2020; 8:582695. [PMID: 33117809 PMCID: PMC7578231 DOI: 10.3389/fcell.2020.582695] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The development of colorectal cancer (CRC) is often sporadic, but its etiology is multifactorial. Chemoresistance of CRC leads to tumor recurrence and poor prognosis in patients. The phosphorylation of protein kinase B (AKT) can activate metabolic reprogramming toward cellular glycolysis. Serine/threonine kinase 35 (STK35) regulates the cell cycle and is frequently associated with cancer progression, whereas little is known about its specific roles in CRC. In the current study, bioinformatics analyses were performed to investigate the relationship between STK35 and CRC prognosis. STK35 knockdown and overexpressing CRC cells were established to examine its functions in CRC. Fluorouracil (5-FU) was utilized to evaluate the effect of STK35 on CRC chemoresistance. Moreover, co-immunoprecipitation was performed to explore the ubiquitination of STK35. STK35 was highly expressed in CRC, and its protein expression was negatively correlated with the survival of CRC patients. Furthermore, STK35 overexpression could promote glycolysis, suppress apoptosis, upregulate p-AKT, and counteract the antitumor functions of 5-FU and neural precursor cell expressed developmentally downregulated gene 4-like (NEDD4L) in CRC cells. NEDD4L was associated with and could ubiquitinate STK35. STK35 could be a prognostic biomarker for CRC prognosis and has promotive effects on CRC cellular activities, partially through the AKT pathway. Moreover, STK35 also interferes with the chemosensitivity of CRC.
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Affiliation(s)
- Haojun Yang
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jie Zhu
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Guangyao Wang
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Hanyang Liu
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yan Zhou
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jun Qian
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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Christodoulou CC, Zachariou M, Tomazou M, Karatzas E, Demetriou CA, Zamba-Papanicolaou E, Spyrou GM. Investigating the Transition of Pre-Symptomatic to Symptomatic Huntington's Disease Status Based on Omics Data. Int J Mol Sci 2020; 21:ijms21197414. [PMID: 33049985 PMCID: PMC7582902 DOI: 10.3390/ijms21197414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Huntington’s disease is a rare neurodegenerative disease caused by a cytosine–adenine–guanine (CAG) trinucleotide expansion in the Huntingtin (HTT) gene. Although Huntington’s disease (HD) is well studied, the pathophysiological mechanisms, genes and metabolites involved in HD remain poorly understood. Systems bioinformatics can reveal synergistic relationships among different omics levels and enables the integration of biological data. It allows for the overall understanding of biological mechanisms, pathways, genes and metabolites involved in HD. The purpose of this study was to identify the differentially expressed genes (DEGs), pathways and metabolites as well as observe how these biological terms differ between the pre-symptomatic and symptomatic HD stages. A publicly available dataset from the Gene Expression Omnibus (GEO) was analyzed to obtain the DEGs for each HD stage, and gene co-expression networks were obtained for each HD stage. Network rewiring, highlights the nodes that change most their connectivity with their neighbors and infers their possible implication in the transition between different states. The CACNA1I gene was the mostly highly rewired node among pre-symptomatic and symptomatic HD network. Furthermore, we identified AF198444 to be common between the rewired genes and DEGs of symptomatic HD. CNTN6, DEK, LTN1, MST4, ZFYVE16, CEP135, DCAKD, MAP4K3, NUPL1 and RBM15 between the DEGs of pre-symptomatic and DEGs of symptomatic HD and CACNA1I, DNAJB14, EPS8L3, HSDL2, SNRPD3, SOX12, ACLY, ATF2, BAG5, ERBB4, FOCAD, GRAMD1C, LIN7C, MIR22, MTHFR, NABP1, NRG2, OTC, PRAMEF12, SLC30A10, STAG2 and Y16709 between the rewired genes and DEGs of pre-symptomatic HD. The proteins encoded by these genes are involved in various biological pathways such as phosphatidylinositol-4,5-bisphosphate 3-kinase activity, cAMP response element-binding protein binding, protein tyrosine kinase activity, voltage-gated calcium channel activity, ubiquitin protein ligase activity, adenosine triphosphate (ATP) binding, and protein serine/threonine kinase. Additionally, prominent molecular pathways for each HD stage were then obtained, and metabolites related to each pathway for both disease stages were identified. The transforming growth factor beta (TGF-β) signaling (pre-symptomatic and symptomatic stages of the disease), calcium (Ca2+) signaling (pre-symptomatic), dopaminergic synapse pathway (symptomatic HD patients) and Hippo signaling (pre-symptomatic) pathways were identified. The in silico metabolites we identified include Ca2+, inositol 1,4,5-trisphosphate, sphingosine 1-phosphate, dopamine, homovanillate and L-tyrosine. The genes, pathways and metabolites identified for each HD stage can provide a better understanding of the mechanisms that become altered in each disease stage. Our results can guide the development of therapies that may target the altered genes and metabolites of the perturbed pathways, leading to an improvement in clinical symptoms and hopefully a delay in the age of onset.
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Affiliation(s)
- Christiana C. Christodoulou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Neurology Clinic D; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus;
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Marios Tomazou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Evangelos Karatzas
- Department of Informatics and Telecommunications, University of Athens, 157 72 Athens, Greece;
| | - Christiana A. Demetriou
- Department of Primary Care and Population Health, University of Nicosia, 2417 Nicosia, Cyprus;
| | - Eleni Zamba-Papanicolaou
- Neurology Clinic D; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus;
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - George M. Spyrou
- Bioinformatics Department; Cyprus Institute of Neurology and Genetics; Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus; (C.C.C.); (M.Z.); (M.T.)
- Cyprus School of Molecular Medicine of the Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
- Correspondence:
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AL-Eitan LN, ababa’h DM, Aman HA. The Associations of Common Genetic Susceptibility Variants with Breast Cancer in Jordanian Arabs: A Case-Control Study. Asian Pac J Cancer Prev 2020; 21:3045-3054. [PMID: 33112566 PMCID: PMC7798142 DOI: 10.31557/apjcp.2020.21.10.3045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE In Jordan, breast cancer (BC) affects a substantial proportion of Jordanian women, highlighting the need for studies to be carried out regarding the genetic component of the disease. The aim of the present study was to investigate the interaction between BC risk and prognosis and polymorphisms in genes (ATM, CASP8, FGFR2, FN1, IGF1, LSP1, MAP3K, MMP7, and RHOC) that were chosen for this study previously reported as having a role in the disease. MATERIALS AND METHODS Blood samples were collected from 242 BC patients and 231 disease-free volunteers recruited from the Jordanian population. DNA was extracted from blood and each sample was sent to the Australian Genome Research Facility for genotyping. RESULTS The rs1219648 SNP of the FGFR2 gene was the only investigated variant to show any direct association with BC in Jordanian women (p-value = 0.04). However, the CASP8rs6760993 SNP was found to be significantly associated with BC (p-value = 0.04) when using the dominant model. Other gene polymorphisms showed varying levels of association between some investigated SNPs and different BC risk and prognostic factors. CONCLUSION Despite reports to the contrary in other populations, most of the investigated genes and their respective SNPs did not show any significant association with BC in Jordanian women. Our results underline the need for independent BC research to be carried out in the Jordanian population to decipher the genetic basis of the disease. .
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Affiliation(s)
- Laith N AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Doaa M ababa’h
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Hatem A Aman
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
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Babbitt GA, Lynch ML, McCoy M, Fokoue EP, Hudson AO. Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition. J Biomol Struct Dyn 2020; 40:468-483. [DOI: 10.1080/07391102.2020.1815578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Miranda L. Lynch
- Hauptmann-Woodward Medical Research Institute, Buffalo, New York, USA
| | - Matthew McCoy
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Ernest P. Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
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