1
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Tang N, Li Y, Tang J, Chen J, Chen L, Dang L. ACOT7 positively regulated by CREB1 promotes the progression of cutaneous melanoma. Acta Histochem 2024; 126:152186. [PMID: 39142244 DOI: 10.1016/j.acthis.2024.152186] [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: 02/09/2024] [Revised: 06/24/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024]
Abstract
Cutaneous melanoma (cM) is a prevalent invasive cancer resulting from the malignant transformation of melanocytes. At present, the primary treatment for melanoma is surgical resection, which is not appropriate for patients with metastasis. Therefore, it is necessary to identify effective therapeutic targets for the early diagnosis and treatment of metastatic melanoma. Acyl-CoA thioesterase 7 (ACOT7) has been reported to be involved in the progression of multiple cancer, while its role in melanoma has not been extensively researched. Through gain-of-function and loss-of-function experiments, ACOT7 was identified as a tumor promoter that facilitates the progression of melanoma cells. Cell proliferation was promoted by overexpressing ACOT7 in M14 cells, and was suppressed by silencing ACOT7 in MeWo cells. Knockdown of ACOT7 induced cell cycle arrest by increasing the expressions of cyclin dependent kinase inhibitor 1B (P27) and cyclin dependent kinase inhibitor 1 A (P21), while simultaneously reducing proliferating cell nuclear antigen (PCNA) expression. Upregulation of ACOT7 promoted the cell cycle of melanoma cells. Additionally, apoptosis was induced by the absence of ACOT7 through activating caspase-3 and poly (ADP-ribose) polymerase (PARP). The metastatic and invasive capacity of melanoma cells was significantly enhanced by the overexpression of ACOT7 and inhibited by the downregulation of ACOT7. Moreover, the cAMP responsive element binding protein 1 (CREB1) positively regulates ACOT7 expression by binding to its promoter region. A decrease of cell proliferation, migration and invasion, as well as an increase of cell apoptosis induced by silencing CREB1 were obviously reversed by ACOT7. In summary, ACOT7 transcriptionally activated by CREB1 elevates the progression of cM.
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Affiliation(s)
- Ni Tang
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China
| | - Yunhui Li
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China
| | - Junchi Tang
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China
| | - Juexin Chen
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China
| | - Lili Chen
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China
| | - Lin Dang
- Department of Dermatology, Longgang Central Hospital, Shenzhen, China.
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2
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [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: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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3
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Ramesh H, Bhuyan AK. The food and pharmaceutical additive benzoic acid induces amyloid fibrillation of an intrinsically disordered protein. Biophys Chem 2024; 306:107172. [PMID: 38183957 DOI: 10.1016/j.bpc.2024.107172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
Benzoic acid (BA) is a microbe-inhibiting flavoring agent used extensively as an additive in foods, pharmaceuticals, and hygiene and cosmetic products. The level of BA in foodstuffs prescribed by world bodies and governmental agencies is assumed to be safe so as to prevent adverse health effects. The safety level of BA is however controversial, and whether different conditions of its use would be generally regarded as safe (GRAS) has been rarely determined. In the quest of how food additives affect the structure and conformation of proteins, this study evaluates the interaction of BA with an intrinsically disordered protein (IDP) at pH 4.2 that matches the pH conditions applicable for the commercial use of benzoate preservatives, and examines its structural transformation by NMR, fluorescence, and high-resolution microscopy. The interaction with BA transforms the protein to a denatured aggregated mesophase that undergoes reconfiguration to yield rigid amyloid fibrils. Significantly, fibrils are observed even with 0.1 mM BA while the recommended level of its use as a preservative is in the 0.4-8 mM range. The discussion refrains from safety comments with no projection of the BA level that could be GRAS.
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Affiliation(s)
- Halavath Ramesh
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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4
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Ye S, Wang S, Chan R, Cao L, Wang H. Identification of short protein-destabilizing sequences in Arabidopsis cyclin-dependent kinase inhibitors, ICKs. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:772-788. [PMID: 37862584 DOI: 10.1093/jxb/erad411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Plants have a family of cyclin-dependent kinase (CDK) inhibitors called interactors/inhibitors of CDK (ICKs) or Kip-related proteins (KRPs). ICK proteins have important functions in cell proliferation, endoreduplication, plant growth, and reproductive development, and their functions depend on the protein levels. However, understanding of how ICK protein levels are regulated is very limited. We fused Arabidopsis ICK sequences to green fluorescent protein (GFP) and determined their effects on the fusion proteins in plants, yeast, and Escherichia coli. The N-terminal regions of ICKs drastically reduced GFP fusion protein levels in Arabidopsis plants. A number of short sequences of 10-20 residues were found to decrease GFP fusion protein levels when fused at the N-terminus or C-terminus. Three of the four short sequences from ICK3 showed a similar function in yeast. Intriguingly, three short sequences from ICK1 and ICK3 caused the degradation of the fusion proteins in E. coli. In addition, computational analyses showed that ICK proteins were mostly disordered and unstructured except for the conserved C-terminal region, suggesting that ICKs are intrinsically disordered proteins. This study has identified a number of short protein-destabilizing sequences, and evidence suggests that some of them may cause protein degradation through structural disorder and instability.
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Affiliation(s)
- Shengjian Ye
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ron Chan
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ling Cao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
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5
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Saikia B, Baruah A. Recent advances in de novo computational design and redesign of intrinsically disordered proteins and intrinsically disordered protein regions. Arch Biochem Biophys 2024; 752:109857. [PMID: 38097100 DOI: 10.1016/j.abb.2023.109857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
In the early 2000s, the concept of "unstructured biology" has emerged to be an important field in protein science by generating various new research directions. Many novel strategies and methods have been developed that are focused on effectively identifying/predicting intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs), identifying their potential functions, disorder based drug design etc. Due to the range of functions of IDPs/IDPRs and their involvement in various debilitating diseases they are of contemporary interest to the scientific community. Recent researches are focused on designing/redesigning specific IDPs/IDPRs de novo. These de novo design/redesigns of IDPs/IDPRs are carried out by altering compositional biases and specific sequence patterning parameters. The main focus of these researches is to influence specific molecular functions, phase behavior, cellular phenotypes etc. In this review, we first provide the differences of natively folded and natively unfolded or IDPs with respect to their potential energy landscapes. Here, we provide current understandings on the different computational design strategies and methods that have been utilized in de novo design and redesigns of IDPs and IDPRs. Finally, we conclude the review by discussing the challenges that have been faced during the computational design/design attempts of IDPs/IDPRs.
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Affiliation(s)
- Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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6
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Saito A, Omura I, Imaizumi K. CREB3L1/OASIS: cell cycle regulator and tumor suppressor. FEBS J 2024. [PMID: 38215153 DOI: 10.1111/febs.17052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/09/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
Cell cycle checkpoints detect DNA errors, eventually arresting the cell cycle to promote DNA repair. Failure of such cell cycle arrest causes aberrant cell proliferation, promoting the pathogenesis of multiple diseases, including cancer. Endoplasmic reticulum (ER) stress transducers activate the unfolded protein response, which not only deals with unfolded proteins in ER lumen but also orchestrates diverse physiological phenomena such as cell differentiation and lipid metabolism. Among ER stress transducers, cyclic AMP-responsive element-binding protein 3-like protein 1 (CREB3L1) [also known as old astrocyte specifically induced substance (OASIS)] is an ER-resident transmembrane transcription factor. This molecule is cleaved by regulated intramembrane proteolysis, followed by activation as a transcription factor. OASIS is preferentially expressed in specific cells, including astrocytes and osteoblasts, to regulate their differentiation. In accordance with its name, OASIS was originally identified as being upregulated in long-term-cultured astrocytes undergoing cell cycle arrest because of replicative stress. In the context of cell cycle regulation, previously unknown physiological roles of OASIS have been discovered. OASIS is activated as a transcription factor in response to DNA damage to induce p21-mediated cell cycle arrest. Although p21 is directly induced by the master regulator of the cell cycle, p53, no crosstalk occurs between p21 induction by OASIS or p53. Here, we summarize previously unknown cell cycle regulation by ER-resident transcription factor OASIS, particularly focusing on commonalities and differences in cell cycle arrest between OASIS and p53. This review also mentions tumorigenesis caused by OASIS dysfunctions, and OASIS's potential as a tumor suppressor and therapeutic target.
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Affiliation(s)
- Atsushi Saito
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Issei Omura
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, Japan
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7
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He H, Jamal M, Zeng X, Lei Y, Xiao D, Wei Z, Zhang C, Zhang X, Pan S, Ding Q, Tan H, Xie S, Zhang Q. Matrin-3 acts as a potential biomarker and promotes hepatocellular carcinoma progression by interacting with cell cycle-regulating genes. Cell Cycle 2024; 23:15-35. [PMID: 38252499 PMCID: PMC11005806 DOI: 10.1080/15384101.2024.2305535] [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: 01/15/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. The oncogenic role of Matrin-3 (MATR3), an a nuclear matrix protein, in HCC remains largely unknown. Here, we document the biological function of MATR3 in HCC based on integrated bioinformatics analysis and functional studies. According to the TCGA database, MATR3 expression was found to be positively correlated with clinicopathological characteristics in HCC. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve displayed the diagnostic and prognostic potentials of MATR3 in HCC patients, respectively. Pathway enrichment analysis represented the enrichment of MATR3 in various molecular pathways, including the regulation of the cell cycle. Functional assays in HCC cell lines showed reduced proliferation of cells with stable silencing of MATR3. At the same time, the suppressive effects of MATR3 depletion on HCC development were verified by xenograft tumor experiments. Moreover, MATR3 repression also resulted in cell cycle arrest by modulating the expression of cell cycle-associated genes. In addition, the interaction of MATR3 with cell cycle-regulating factors in HCC cells was further corroborated with co-immunoprecipitation and mass spectrometry (Co-IP/MS). Furthermore, CIBERSORT and TIMER analyses showed an association between MATR3 and immune infiltration in HCC. In general, this study highlights the novel oncogenic function of MATR3 in HCC, which could comprehensively address how aberrant changes in the cell cycle promote HCC development. MATR3 might serve as a prognostic predictor and therapeutic target for HCC patients.
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Affiliation(s)
- Hengjing He
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Muhammad Jamal
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xingruo Zeng
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yufei Lei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Di Xiao
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zimeng Wei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chengjie Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shan Pan
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Qianshan Ding
- School of Medicine, Northwest University, Xian, China
| | - Haiyan Tan
- Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Songping Xie
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiuping Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China
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8
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Weston WA, Barr AR. A cell cycle centric view of tumour dormancy. Br J Cancer 2023; 129:1535-1545. [PMID: 37608096 PMCID: PMC10645753 DOI: 10.1038/s41416-023-02401-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023] Open
Abstract
Tumour dormancy and recurrent metastatic cancer remain the greatest clinical challenge for cancer patients. Dormant tumour cells can evade treatment and detection, while retaining proliferative potential, often for years, before relapsing to tumour outgrowth. Cellular quiescence is one mechanism that promotes and maintains tumour dormancy due to its central role in reducing proliferation, elevating cyto-protective mechanisms, and retaining proliferative potential. Quiescence/proliferation decisions are dictated by intrinsic and extrinsic signals, which regulate the activity of cyclin-dependent kinases (CDKs) to modulate cell cycle gene expression. By clarifying the pathways regulating CDK activity and the signals which activate them, we can better understand how cancer cells enter, maintain, and escape from quiescence throughout the progression of dormancy and metastatic disease. Here we review how CDK activity is regulated to modulate cellular quiescence in the context of tumour dormancy and highlight the therapeutic challenges and opportunities it presents.
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Affiliation(s)
- William A Weston
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Alexis R Barr
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Imperial College London, Du Cane Rd, London, W12 0NN, UK.
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9
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Nussinov R, Liu Y, Zhang W, Jang H. Protein conformational ensembles in function: roles and mechanisms. RSC Chem Biol 2023; 4:850-864. [PMID: 37920394 PMCID: PMC10619138 DOI: 10.1039/d3cb00114h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/02/2023] [Indexed: 11/04/2023] Open
Abstract
The sequence-structure-function paradigm has dominated twentieth century molecular biology. The paradigm tacitly stipulated that for each sequence there exists a single, well-organized protein structure. Yet, to sustain cell life, function requires (i) that there be more than a single structure, (ii) that there be switching between the structures, and (iii) that the structures be incompletely organized. These fundamental tenets called for an updated sequence-conformational ensemble-function paradigm. The powerful energy landscape idea, which is the foundation of modernized molecular biology, imported the conformational ensemble framework from physics and chemistry. This framework embraces the recognition that proteins are dynamic and are always interconverting between conformational states with varying energies. The more stable the conformation the more populated it is. The changes in the populations of the states are required for cell life. As an example, in vivo, under physiological conditions, wild type kinases commonly populate their more stable "closed", inactive, conformations. However, there are minor populations of the "open", ligand-free states. Upon their stabilization, e.g., by high affinity interactions or mutations, their ensembles shift to occupy the active states. Here we discuss the role of conformational propensities in function. We provide multiple examples of diverse systems, including protein kinases, lipid kinases, and Ras GTPases, discuss diverse conformational mechanisms, and provide a broad outlook on protein ensembles in the cell. We propose that the number of molecules in the active state (inactive for repressors), determine protein function, and that the dynamic, relative conformational propensities, rather than the rigid structures, are the hallmark of cell life.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978 Israel
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
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10
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Füzesi-Levi MG, Ben-Nissan G, Listov D, Fridmann Sirkis Y, Hayouka Z, Fleishman S, Sharon M. The C-terminal tail of CSNAP attenuates the CSN complex. Life Sci Alliance 2023; 6:e202201634. [PMID: 37460146 PMCID: PMC10355216 DOI: 10.26508/lsa.202201634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Protein degradation is one of the essential mechanisms that enables reshaping of the proteome landscape in response to various stimuli. The largest E3 ubiquitin ligase family that targets proteins to degradation by catalyzing ubiquitination is the cullin-RING ligases (CRLs). Many of the proteins that are regulated by CRLs are central to tumorigenesis and tumor progression, and dysregulation of the CRL family is frequently associated with cancer. The CRL family comprises ∼300 complexes, all of which are regulated by the COP9 signalosome complex (CSN). Therefore, CSN is considered an attractive target for therapeutic intervention. Research efforts for targeted CSN inhibition have been directed towards inhibition of the complex enzymatic subunit, CSN5. Here, we have taken a fresh approach focusing on CSNAP, the smallest CSN subunit. Our results show that the C-terminal region of CSNAP is tightly packed within the CSN complex, in a groove formed by CSN3 and CSN8. We show that a 16 amino acid C-terminal peptide, derived from this CSN-interacting region, can displace the endogenous CSNAP subunit from the complex. This, in turn, leads to a CSNAP null phenotype that attenuates CSN activity and consequently CRLs function. Overall, our findings emphasize the potential of a CSNAP-based peptide for CSN inhibition as a new therapeutic avenue.
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Affiliation(s)
- Maria G Füzesi-Levi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sarel Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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11
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Li Z, Duan Y, Yan S, Zhang Y, Wu Y. The miR-302/367 cluster: Aging, inflammation, and cancer. Cell Biochem Funct 2023; 41:752-766. [PMID: 37555645 DOI: 10.1002/cbf.3836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs that occupy a significant role in biological processes as important regulators of intracellular homeostasis. First, we will discuss the biological genesis and functions of the miR-302/367 cluster, including miR-302a, miR-302b, miR-302c, miR-302d, and miR-367, as well as their roles in physiologically healthy tissues. The second section of this study reviews the progress of the miR-302/367 cluster in the treatment of cancer, inflammation, and diseases associated with aging. This cluster's aberrant expression in cells and/or tissues exhibits similar or different effects in various diseases through molecular mechanisms such as proliferation, apoptosis, cycling, drug resistance, and invasion. This article also discusses the upstream and downstream regulatory networks of miR-302/367 clusters and their related mechanisms. Particularly because studies on the upstream regulatory molecules of miR-302/367 clusters, which include age-related macular degeneration, myocardial infarction, and cancer, have become more prevalent in recent years. MiR-302/367 cluster can be an important therapeutic target and the use of miRNAs in combination with other molecular markers may improve diagnostic or therapeutic capabilities, providing unique insights and a more dynamic view of various diseases. It is noted that miRNAs can be an important bio-diagnostic target and offer a promising method for illness diagnosis, prevention, and treatment.
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Affiliation(s)
- Zhou Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yan Duan
- Department of Stomatology, Shanxi Provincial People's Hospital, Taiyuan, Shanxi Province, China
| | - Shaofu Yan
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yao Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yunxia Wu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
- Department of Stomatology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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12
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Han M, Guo Y, Li Y, Zeng Q, Zhu W, Jiang J. SMURF2 facilitates ubiquitin-mediated degradation of ID2 to attenuate lung cancer cell proliferation. Int J Biol Sci 2023; 19:3324-3340. [PMID: 37497010 PMCID: PMC10367561 DOI: 10.7150/ijbs.80979] [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: 11/18/2022] [Accepted: 06/10/2023] [Indexed: 07/28/2023] Open
Abstract
SMAD-specific E3 ubiquitin protein ligase 2 (SMURF2) functions as either a tumor promoter or tumor suppressor in several tumors. However, the detailed effect of SMURF2 on non-small cell lung cancer has not been fully understood. In this study, SMURF2 expression and its diagnostic value were analyzed. Co-Immunoprecipitation (Co-IP), proximity ligation assay (PLA), chromatin immunoprecipitation (ChIP) and nude mice tumor-bearing model were applied to further clarify the role of SMURF2 in lung cancer. SMURF2 expression was reduced in the tumor tissues of patients with NSCLC and high SMURF2 expression was significantly correlated with favorable outcomes. Furthermore, the overexpression of SMURF2 significantly inhibited lung cancer cell progression. Mechanistically, SMURF2 interacted with inhibitor of DNA binding 2 (ID2), subsequently promoting the poly-ubiquitination and degradation of ID2 through the ubiquitin-proteasome pathway. Downregulated ID2 in lung cells dissociates endogenous transcription factor E2A, a positive regulator of the cyclin-dependent kinase inhibitor p21, and finally induces G1/S arrest in lung cancer cells. This study revealed that the manipulation of ID2 via SMURF2 may control tumor progression and contribute to the development of novel targeted antitumor drugs.
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Affiliation(s)
| | | | | | | | | | - Jianli Jiang
- ✉ Corresponding author: Jianli Jiang, National Translational Science Center for Molecular Medicine and Department of Cell Biology, Fourth Military Medical University, Xi'an 710032, China.
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13
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Yu S, Zhao H, Qin X, Li X, Guo J, Li W. Giardia duodenalis-induced G0/G1 intestinal epithelial cell cycle arrest and apoptosis involve activation of endoplasmic reticulum stress in vitro. Front Immunol 2023; 14:1127552. [PMID: 37006313 PMCID: PMC10050679 DOI: 10.3389/fimmu.2023.1127552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
Giardia duodenalis is a zoonotic intestinal protozoan parasite that may cause host diarrhea and chronic gastroenteritis, resulting in great economic losses annually and representing a significant public health burden across the world. However, thus far, our knowledge on the pathogenesis of Giardia and the related host cell responses is still extensively limited. The aim of this study is to assess the role of endoplasmic reticulum (ER) stress in regulating G0/G1 cell cycle arrest and apoptosis during in vitro infection of intestinal epithelial cells (IECs) with Giardia. The results showed that the mRNA levels of ER chaperone proteins and ER-associated degradation genes were increased and the expression levels of the main unfolded protein response (UPR)-related proteins (GRP78, p-PERK, ATF4, CHOP, p-IRE1, XBP1s and ATF6) were increased upon Giardia exposure. In addition, cell cycle arrest was determined to be induced by UPR signaling pathways (IRE1, PERK and ATF6) through upregulation of p21 and p27 levels and promotion of E2F1-RB complex formation. Upregulation of p21 and p27 expression was shown to be related to Ufd1-Skp2 signaling. Therefore, the cell cycle arrest was induced by ER stress when infected with Giardia. Furthermore, the apoptosis of the host cell was also assessed after exposure to Giardia. The results indicated that apoptosis would be promoted by UPR signaling (PERK and ATF6), but would be suppressed by the hyperphosphorylation of AKT and hypophosphorylation of JNK that were modulated by IRE1 pathway. Taken together, both of the cell cycle arrest and apoptosis of IECs induced by Giardia exposure involved the activation of the UPR signaling. The findings of this study will deepen our understanding of the pathogenesis of Giardia and the associated regulatory network.
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Affiliation(s)
| | | | | | | | | | - Wei Li
- *Correspondence: Wei Li, ; Jiaying Guo,
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14
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Tsoi PS, Quan MD, Ferreon JC, Ferreon ACM. Aggregation of Disordered Proteins Associated with Neurodegeneration. Int J Mol Sci 2023; 24:3380. [PMID: 36834792 PMCID: PMC9966039 DOI: 10.3390/ijms24043380] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration, disrupts cellular functions and leads to neuronal death. Mutations, posttranslational modifications, and truncations are common molecular underpinnings in the formation of aberrant protein conformations that seed aggregation. The major proteins involved in neurodegeneration include amyloid beta (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, and TAR DNA-binding protein (TDP-43) in amyotrophic lateral sclerosis (ALS). These proteins are described as intrinsically disordered and possess enhanced ability to partition into biomolecular condensates. In this review, we discuss the role of protein misfolding and aggregation in neurodegenerative diseases, specifically highlighting implications of changes to the primary/secondary (mutations, posttranslational modifications, and truncations) and the quaternary/supramolecular (oligomerization and condensation) structural landscapes for the four aforementioned proteins. Understanding these aggregation mechanisms provides insights into neurodegenerative diseases and their common underlying molecular pathology.
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Affiliation(s)
| | | | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Taylor A, Gu Y, Chang ML, Yang W, Francisco S, Rowan S, Bejarano E, Pruitt S, Zhu L, Weiss G, Brennan L, Kantorow M, Whitcomb EA. Repurposing a Cyclin-Dependent Kinase 1 (CDK1) Mitotic Regulatory Network to Complete Terminal Differentiation in Lens Fiber Cells. Invest Ophthalmol Vis Sci 2023; 64:6. [PMID: 36734965 PMCID: PMC9907369 DOI: 10.1167/iovs.64.2.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/22/2022] [Indexed: 02/04/2023] Open
Abstract
Purpose During lens fiber cell differentiation, organelles are removed in an ordered manner to ensure lens clarity. A critical step in this process is removal of the cell nucleus, but the mechanisms by which this occurs are unclear. In this study, we investigate the role of a cyclin-dependent kinase 1 (CDK1) regulatory loop in controlling lens fiber cell denucleation (LFCD). Methods We examined lens differentiation histologically in two different vertebrate models. An embryonic chick lens culture system was used to test the role of CDK1, cell division cycle 25 (CDC25), WEE1, and PP2A in LFCD. Additionally, we used three mouse models that express high levels of the CDK inhibitor p27 to test whether increased p27 levels affect LFCD. Results Using chick lens organ cultures, small-molecule inhibitors of CDK1 and CDC25 inhibit LFCD, while inhibiting the CDK1 inhibitory kinase WEE1 potentiates LFCD. Additionally, treatment with an inhibitor of PP2A, which indirectly inhibits CDK1 activity, also increased LFCD. Three different mouse models that express increased levels of p27 through different mechanisms show impaired LFCD. Conclusions Here we define a conserved nonmitotic role for CDK1 and its upstream regulators in controlling LFCD. We find that CDK1 functionally interacts with WEE1, a nuclear kinase that inhibits CDK1 activity, and CDC25 activating phosphatases in cells where CDK1 activity must be exquisitely regulated to allow for LFCD. We also provide genetic evidence in multiple in vivo models that p27, a CDK1 inhibitor, inhibits lens growth and LFCD.
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Affiliation(s)
- Allen Taylor
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
- Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, United States
| | - Yumei Gu
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Min-Lee Chang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Wenxin Yang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Sarah Francisco
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Sheldon Rowan
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
- Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, United States
| | - Eloy Bejarano
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
| | - Steven Pruitt
- Roswell Park Cancer Institute, Buffalo, New York, United States
| | - Liang Zhu
- Albert Einstein College of Medicine, New York City, New York, United States
| | - Grant Weiss
- Department of Neuroscience Tufts University School of Medicine, Boston, Massachusetts, United States
| | - Lisa Brennan
- Florida Atlantic University, Boca Raton, Florida, United States
| | - Marc Kantorow
- Florida Atlantic University, Boca Raton, Florida, United States
| | - Elizabeth A. Whitcomb
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States
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16
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Xie L, Zhang J, Yan H, Cai Y, Xu L. β-elemene induced apoptosis and senescence of triple-negative breast cancer cells through IGF1/IGF1R pathway. Tissue Cell 2022; 79:101914. [DOI: 10.1016/j.tice.2022.101914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/24/2022] [Accepted: 08/30/2022] [Indexed: 10/14/2022]
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17
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Chemical Composition, Antitumor Properties, and Mechanism of the Essential Oil from Plagiomnium acutum T. Kop. Int J Mol Sci 2022; 23:ijms232314790. [PMID: 36499119 PMCID: PMC9738176 DOI: 10.3390/ijms232314790] [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: 10/09/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Plagiomnium acutum T. Kop. (P. acutum) has been used as a traditional Chinese medicine for thousands of years to treat cancer but lacks evidence. The objective of this work was to reveal the chemical composition of P. acutum essential oil (PEO) and explore its potential antitumor activity and molecular mechanism. PEO was prepared by the simultaneous distillation-extraction method and characterized by gas chromatography/mass spectroscopy. CCK8 assay, flow cytometry, western blot, and immunofluorescence techniques were used to analyze the effects and mechanism of PEO against cancer cells. A total of 74 constituents of PEO were identified, with diterpenes (26.5%), sesquiterpenes (23.89%), and alcohols (21.81%) being the major constituents. Two terpenoids, selina-6-en-4-ol and dolabella-3,7-dien-18-ol, were detected in PEO for the first time. PEO showed significant cell growth inhibitory activity on HepG2 and A549 cells by blocking the G1 phase and inducing apoptosis, which may be attributed to its upregulation of p21Cip1 and p27Kip1 proteins and interference with mitochondrial membrane potential effect. Dolabella-3,7-dien-18-ol accounts for 25.5% of PEO and is one of the main active components of PEO, with IC50 values in HepG2 and A549 cells of (25.820 ± 0.216) µg/mL and (23.597 ± 1.207) μg/mL, respectively. These results confirmed the antitumor medicinal value of P. acutum and showed great application potential in the pharmaceutical industry.
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18
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Selvaraj C, Pravin MA, Alhoqail WA, Nayarisseri A, Singh SK. Intrinsically disordered proteins in viral pathogenesis and infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:221-242. [PMID: 36088077 DOI: 10.1016/bs.apcsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Disordered proteins serve a crucial part in many biological processes that go beyond the capabilities of ordered proteins. A large number of virus-encoded proteins have extremely condensed proteomes and genomes, which results in highly disordered proteins. The presence of these IDPs allows them to rapidly adapt to changes in their biological environment and play a significant role in viral replication and down-regulation of host defense mechanisms. Since viruses undergo rapid evolution and have a high rate of mutation and accumulation in their proteome, IDPs' insights into viruses are critical for understanding how viruses hijack cells and cause disease. There are many conformational changes that IDPs can adopt in order to interact with different protein partners and thus stabilize the particular fold and withstand high mutation rates. This chapter explains the molecular mechanism behind viral IDPs, as well as the significance of recent research in the field of IDPs, with the goal of gaining a deeper comprehension of the essential roles and functions played by viral proteins.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Wardah A Alhoqail
- Department of Biology, College of Education, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Anuraj Nayarisseri
- In Silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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19
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Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Panoramic Perspective on Human Phosphosites. J Proteome Res 2022; 21:1894-1915. [PMID: 35793420 DOI: 10.1021/acs.jproteome.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the information in these large-scale phospho-proteomics data sets, as contained in Scop3P, to analyze and characterize proteome-wide protein phosphorylation sites (P-sites). First, we set out to differentiate correctly observed P-sites from false-positive sites using five complementary site properties. We then describe the context of these P-sites in terms of the protein structure, solvent accessibility, structural transitions and disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P-sites. Moreover, we assess the structural dynamics of P-sites in their phosphorylated and unphosphorylated states. As a result, we show how large-scale reprocessing of available proteomics experiments can enable a more reliable view on proteome-wide P-sites. Furthermore, adding the structural context of proteins around P-sites helps uncover possible conformational switches upon phosphorylation. Moreover, by placing sites in different biophysical contexts, we show the differential preference in protein dynamics at phosphorylated sites when compared to the nonphosphorylated counterparts.
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Affiliation(s)
- Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | | | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
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20
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Lu AX, Lu AX, Pritišanac I, Zarin T, Forman-Kay JD, Moses AM. Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. PLoS Comput Biol 2022; 18:e1010238. [PMID: 35767567 PMCID: PMC9275697 DOI: 10.1371/journal.pcbi.1010238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 07/12/2022] [Accepted: 05/23/2022] [Indexed: 02/07/2023] Open
Abstract
A major challenge to the characterization of intrinsically disordered regions (IDRs), which are widespread in the proteome, but relatively poorly understood, is the identification of molecular features that mediate functions of these regions, such as short motifs, amino acid repeats and physicochemical properties. Here, we introduce a proteome-scale feature discovery approach for IDRs. Our approach, which we call "reverse homology", exploits the principle that important functional features are conserved over evolution. We use this as a contrastive learning signal for deep learning: given a set of homologous IDRs, the neural network has to correctly choose a held-out homolog from another set of IDRs sampled randomly from the proteome. We pair reverse homology with a simple architecture and standard interpretation techniques, and show that the network learns conserved features of IDRs that can be interpreted as motifs, repeats, or bulk features like charge or amino acid propensities. We also show that our model can be used to produce visualizations of what residues and regions are most important to IDR function, generating hypotheses for uncharacterized IDRs. Our results suggest that feature discovery using unsupervised neural networks is a promising avenue to gain systematic insight into poorly understood protein sequences.
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Affiliation(s)
- Alex X. Lu
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Amy X. Lu
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
| | - Taraneh Zarin
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Julie D. Forman-Kay
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Alan M. Moses
- Department of Computer Science, University of Toronto, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
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21
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Alhashem Z, Feldner-Busztin D, Revell C, Alvarez-Garcillan Portillo M, Camargo-Sosa K, Richardson J, Rocha M, Gauert A, Corbeaux T, Milanetto M, Argenton F, Tiso N, Kelsh RN, Prince VE, Bentley K, Linker C. Notch controls the cell cycle to define leader versus follower identities during collective cell migration. eLife 2022; 11:e73550. [PMID: 35438077 PMCID: PMC9129880 DOI: 10.7554/elife.73550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Coordination of cell proliferation and migration is fundamental for life, and its dysregulation has catastrophic consequences, such as cancer. How cell cycle progression affects migration, and vice versa, remains largely unknown. We address these questions by combining in silico modelling and in vivo experimentation in the zebrafish trunk neural crest (TNC). TNC migrate collectively, forming chains with a leader cell directing the movement of trailing followers. We show that the acquisition of migratory identity is autonomously controlled by Notch signalling in TNC. High Notch activity defines leaders, while low Notch determines followers. Moreover, cell cycle progression is required for TNC migration and is regulated by Notch. Cells with low Notch activity stay longer in G1 and become followers, while leaders with high Notch activity quickly undergo G1/S transition and remain in S-phase longer. In conclusion, TNC migratory identities are defined through the interaction of Notch signalling and cell cycle progression.
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Affiliation(s)
- Zain Alhashem
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, King's College LondonLondonUnited Kingdom
| | | | - Christopher Revell
- Cellular Adaptive Behaviour Lab, Francis Crick InstituteLondonUnited Kingdom
| | | | - Karen Camargo-Sosa
- Department of Biology & Biochemistry, University of BathBathUnited Kingdom
| | - Joanna Richardson
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, King's College LondonLondonUnited Kingdom
| | - Manuel Rocha
- Committee on Development, Regeneration and Stem Cell Biology, The University of ChicagoChicagoUnited States
| | - Anton Gauert
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, King's College LondonLondonUnited Kingdom
| | - Tatianna Corbeaux
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, King's College LondonLondonUnited Kingdom
| | | | | | - Natascia Tiso
- Department of Biology, University of PadovaPadovaItaly
| | - Robert N Kelsh
- Department of Biology & Biochemistry, University of BathBathUnited Kingdom
| | - Victoria E Prince
- Committee on Development, Regeneration and Stem Cell Biology, The University of ChicagoChicagoUnited States
- Department of Organismal Biology and Anatomy, The University of ChicagoChicagoUnited States
| | - Katie Bentley
- Cellular Adaptive Behaviour Lab, Francis Crick InstituteLondonUnited Kingdom
- Department of Informatics, King's College LondonLondonUnited Kingdom
| | - Claudia Linker
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, King's College LondonLondonUnited Kingdom
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22
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
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23
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Hanselmann RG, Welter C. Origin of Cancer: Cell work is the Key to Understanding Cancer Initiation and Progression. Front Cell Dev Biol 2022; 10:787995. [PMID: 35300431 PMCID: PMC8921603 DOI: 10.3389/fcell.2022.787995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
The cell is the smallest unit of life. It is a structure that maintains order through self-organization, characterized by a high level of dynamism, which in turn is characterized by work. For this work to take place, a continuous high flow of energy is necessary. However, a focused view of the physical relationship between energy and work is inadequate for describing complex biological/medical mechanisms or systems. In this review, we try to make a connection between the fundamental laws of physics and the mechanisms and functions of biology, which are characterized by self-organization. Many different physical work processes (work) in human cells are called cell work and can be grouped into five forms: synthetic, mechanical, electrical, concentration, and heat generation cell work. In addition to the flow of energy, these cell functions are based on fundamental processes of self-organization that we summarize with the term Entirety of molecular interaction (EoMI). This illustrates that cell work is caused by numerous molecular reactions, flow equilibrium, and mechanisms. Their number and interactions are so complex that they elude our perception in their entirety. To be able to describe cell functions in a biological/medical context, the parameters influencing cell work should be summarized in overarching influencing variables. These are “biological” energy, information, matter, and cell mechanics (EMIM). This makes it possible to describe and characterize the cell work involved in cell systems (e.g., respiratory chain, signal transmission, cell structure, or inheritance processes) and to demonstrate changes. If cell work and the different influencing parameters (EMIM influencing variables) are taken as the central property of the cell, specific gene mutations cannot be regarded as the sole cause for the initiation and progression of cancer. This reductionistic monocausal view does not do justice to the dynamic and highly complex system of a cell. Therefore, we postulate that each of the EMIM influencing variables described above is capable of changing the cell work and thus the order of a cell in such a way that it can develop into a cancer cell.
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24
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Naullage PM, Haghighatlari M, Namini A, Teixeira JMC, Li J, Zhang O, Gradinaru CC, Forman-Kay JD, Head-Gordon T. Protein Dynamics to Define and Refine Disordered Protein Ensembles. J Phys Chem B 2022; 126:1885-1894. [PMID: 35213160 PMCID: PMC10122607 DOI: 10.1021/acs.jpcb.1c10925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse R2 relaxation rates and Lipari-Szabo order parameters (S2 values). We illustrate our approach using the unfolded state of the drkN SH3 domain to show that the dynamical ensembles give better agreement than a static ensemble for a wide range of experimental validation data including NMR chemical shifts, J-couplings, nuclear Overhauser effects, paramagnetic relaxation enhancements, residual dipolar couplings, hydrodynamic radii, single-molecule fluorescence Förster resonance energy transfer, and small-angle X-ray scattering.
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Affiliation(s)
- Pavithra M Naullage
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Mojtaba Haghighatlari
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ashley Namini
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - João M C Teixeira
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Jie Li
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Oufan Zhang
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Claudiu C Gradinaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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CRL4Cdt2 Ubiquitin Ligase, A Genome Caretaker Controlled by Cdt2 Binding to PCNA and DNA. Genes (Basel) 2022; 13:genes13020266. [PMID: 35205311 PMCID: PMC8871960 DOI: 10.3390/genes13020266] [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: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin ligase CRL4Cdt2 plays a vital role in preserving genomic integrity by regulating essential proteins during S phase and after DNA damage. Deregulation of CRL4Cdt2 during the cell cycle can cause DNA re-replication, which correlates with malignant transformation and tumor growth. CRL4Cdt2 regulates a broad spectrum of cell cycle substrates for ubiquitination and proteolysis, including Cdc10-dependent transcript 1 or Chromatin licensing and DNA replication factor 1 (Cdt1), histone H4K20 mono-methyltransferase (Set8) and cyclin-dependent kinase inhibitor 1 (p21), which regulate DNA replication. However, the mechanism it operates via its substrate receptor, Cdc10-dependent transcript 2 (Cdt2), is not fully understood. This review describes the essential features of the N-terminal and C-terminal parts of Cdt2 that regulate CRL4 ubiquitination activity, including the substrate recognition domain, intrinsically disordered region (IDR), phosphorylation sites, the PCNA-interacting protein-box (PIP) box motif and the DNA binding domain. Drugs targeting these specific domains of Cdt2 could have potential for the treatment of cancer.
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reda R, Al-Karmalawy AA, Alotaibi M, saleh M. Quinoxaline Derivatives as a Promising Scaffold for Breast Cancer Treatment. NEW J CHEM 2022. [DOI: 10.1039/d2nj00050d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
According to Global Cancer Statistics 2021, female breast cancer has exceeded lung cancer as the most frequently diagnosed cancer. As a result of this widespread breast cancer, it was necessary...
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Protein conformational dynamics and phenotypic switching. Biophys Rev 2021; 13:1127-1138. [PMID: 35059032 PMCID: PMC8724335 DOI: 10.1007/s12551-021-00858-x] [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: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure but exist as conformational ensembles. Because of their structural plasticity, they can interact with multiple partners. The protein interactions between IDPs and their partners form scale-free protein interaction networks (PINs) that facilitate information flow in the cell. Because of their plasticity, IDPs typically occupy hub positions in cellular PINs. Furthermore, their conformational dynamics and propensity for post-translational modifications contribute to "conformational" noise which is distinct from the well-recognized transcriptional noise. Therefore, upregulation of IDPs in response to a specific input, such as stress, contributes to increased noise and, hence, an increase in stochastic, "promiscuous" interactions. These interactions lead to activation of latent pathways or can induce "rewiring" of the PIN to yield an optimal output underscoring the critical role of IDPs in regulating information flow. We have used PAGE4, a highly intrinsically disordered stress-response protein as a paradigm. Employing a variety of experimental and computational techniques, we have elucidated the role of PAGE4 in phenotypic switching of prostate cancer cells at a systems level. These cumulative studies over the past decade provide a conceptual framework to better understand how IDP conformational dynamics and conformational noise might facilitate cellular decision-making.
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Fatafta H, Kav B, Bundschuh BF, Loschwitz J, Strodel B. Disorder-to-order transition of the amyloid-β peptide upon lipid binding. Biophys Chem 2021; 280:106700. [PMID: 34784548 DOI: 10.1016/j.bpc.2021.106700] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
There is mounting evidence that Alzheimer's disease progression and severity are linked to neuronal membrane damage caused by aggregates of the amyloid-β (Aβ) peptide. However, the detailed mechanism behind the membrane damage is not well understood yet. Recently, the lipid-chaperone hypothesis has been put forward, based on which the formation of complexes between Aβ and free lipids enables an easy insertion of Aβ into membranes. In order to test this hypothesis, we performed numerous all-atom molecular dynamics simulations. We studied the complex formation between individual lipids, considering both POPC and DPPC, and Aβ and examined whether the resulting complexes would be able to insert into lipid membranes. Complex formation at a one-to-one ratio was readily observed, yet with minimal effects on Aβ's characteristics. Most importantly, the peptide remains largely disordered in 1:1 complexes, and the complex does not insert into the membrane; instead, it is adsorbed to the membrane surface. The results change considerably once Aβ forms a complex with a POPC cluster composed of three lipid molecules. The hydrophobic interactions between Aβ and the lipid tails cause the peptide to fold into either a helical or a β-sheet structure. These observations provide atomic insight into the disorder-to-order transition that is needed for membrane insertion or amyloid aggregation to proceed.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Bastian F Bundschuh
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany.
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation. J Biol Chem 2021; 297:101075. [PMID: 34391778 PMCID: PMC8405934 DOI: 10.1016/j.jbc.2021.101075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
SETD2 is an important methyltransferase that methylates crucial substrates such as histone H3, tubulin, and STAT1 and also physically interacts with transcription and splicing regulators such as Pol II and various hnRNPs. Of note, SETD2 has a functionally uncharacterized extended N-terminal region, the removal of which leads to its stabilization. How this region regulates SETD2 half-life is unclear. Here we show that SETD2 consists of multiple long disordered regions across its length that cumulatively destabilize the protein by facilitating its proteasomal degradation. SETD2 disordered regions can reduce the half-life of the yeast homolog Set2 in mammalian cells as well as in yeast, demonstrating the importance of intrinsic structural features in regulating protein half-life. In addition to the shortened half-life, by performing fluorescence recovery after photobleaching assay we found that SETD2 forms liquid droplets in vivo, another property associated with proteins that contain disordered regions. The phase-separation behavior of SETD2 is exacerbated upon the removal of its N-terminal segment and results in activator-independent histone H3K36 methylation. Our findings reveal that disordered region-facilitated proteolysis is an important mechanism governing SETD2 function.
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Xu J, Wu KJ, Jia QJ, Ding XF. Roles of miRNA and lncRNA in triple-negative breast cancer. J Zhejiang Univ Sci B 2021; 21:673-689. [PMID: 32893525 PMCID: PMC7519626 DOI: 10.1631/jzus.b1900709] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is currently the most malignant subtype of breast cancer without effective targeted therapies, which makes its pathogenesis an important target for research. A growing number of studies have shown that non-coding RNA (ncRNA), including microRNA (miRNA) and long non-coding RNA (lncRNA), plays a significant role in tumorigenesis. This review summarizes the roles of miRNA and lncRNA in the progression, diagnosis, and neoadjuvant chemotherapy of TNBC. Aberrantly expressed miRNA and lncRNA are listed according to their roles. Further, it describes the multiple mechanisms that lncRNA shows for regulating gene expression in the nucleus and cytoplasm, and more importantly, describes lncRNA-regulated TNBC progression through complete combining with miRNA at the post-transcriptional level. Focusing on miRNA and lncRNA associated with TNBC can provide new insights for early diagnosis and treatment-they can be targeted in the future as a novel anticancer target of TNBC.
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Mohamed MF, Wood SJ, Roy R, Reiser J, Kuzel TM, Shafikhani SH. Pseudomonas aeruginosa ExoT induces G1 cell cycle arrest in melanoma cells. Cell Microbiol 2021; 23:e13339. [PMID: 33821556 PMCID: PMC8277761 DOI: 10.1111/cmi.13339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022]
Abstract
Recently, we demonstrated that Pseudomonas aeruginosa Exotoxin T (ExoT) employs two distinct mechanisms to induce potent apoptotic cytotoxicity in a variety of cancer cell lines. We further demonstrated that it can significantly reduce tumour growth in an animal model for melanoma. During these studies, we observed that melanoma cells that were transfected with ExoT failed to undergo mitosis, regardless of whether they eventually succumbed to ExoT-induced apoptosis or survived in ExoT's presence. In this report, we sought to investigate ExoT's antiproliferative activity in melanoma. We delivered ExoT into B16 melanoma cells by bacteria (to show necessity) and by transfection (to show sufficiency). Our data indicate that ExoT exerts a potent antiproliferative function in melanoma cells. We show that ExoT causes cell cycle arrest in G1 interphase in melanoma cells by dampening the G1/S checkpoint proteins. Our data demonstrate that both domains of ExoT; (the ADP-ribosyltransferase (ADPRT) domain and the GTPase activating protein (GAP) domain); contribute to ExoT-induced G1 cell cycle arrest in melanoma. Finally, we show that the ADPRT-induced G1 cell cycle arrest in melanoma cells likely involves the Crk adaptor protein. Our data reveal a novel virulence function for ExoT and further highlight the therapeutic potential of ExoT against cancer.
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Affiliation(s)
- Mohamed F. Mohamed
- Department of Medicine/ Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, Chicago, IL, USA
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Beni-Suef University, Egypt
| | - Stephen J. Wood
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Ruchi Roy
- Department of Medicine/ Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Jochen Reiser
- Department of Medicine/ Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Timothy M. Kuzel
- Department of Medicine/ Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Sasha H. Shafikhani
- Department of Medicine/ Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, Chicago, IL, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
- Cancer Center, Rush University Medical Center, Chicago, IL, USA
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Shupp AB, Neupane M, Agostini LC, Ning G, Brody JR, Bussard KM. Stromal-Derived Extracellular Vesicles Suppress Proliferation of Bone Metastatic Cancer Cells Mediated By ERK2. Mol Cancer Res 2021; 19:1763-1777. [PMID: 34021072 DOI: 10.1158/1541-7786.mcr-20-0981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/01/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Bone is a common site of cancer metastasis, including cancers such as breast, prostate, and multiple myeloma. Disseminated tumor cells (DTC) shed from a primary tumor may travel to bone and can survive undetected for years before proliferating to form overt metastatic lesions. This period of time can be defined as metastatic latency. Once in the metastatic microenvironment, DTCs engage in intercellular communication with surrounding stromal cells, which can influence cancer cell survival, proliferation, and ultimately disease progression. The role of the surrounding tumor microenvironment in regulating DTC fate is becoming increasingly recognized. We have previously shown that in the bone microenvironment, osteoblasts are "educated" by interactions with breast cancer cells, and these "educated" osteoblasts (EO) produce soluble factors that regulate cancer cell proliferation. In this study, we provide evidence indicating that EOs produce small extracellular vesicles (sEV) that suppress breast cancer proliferation, in part through regulation of ERK1/2 signaling. In addition, using EdU-incorporation assays and propidium iodide staining we demonstrate that exposure to EO-derived sEVs decreases breast cancer cell entry to S-phase of cell cycle. We also have evidence that particular microRNAs, including miR-148a-3p, are enriched in EO-derived sEVs, and that miR-148a-3p is capable of regulating breast cancer proliferation. IMPLICATIONS: These findings underscore the importance of sEV-mediated communication in the earlier stages of cancer progression, and suggest that EO-derived sEVs may be one mechanism by which the bone microenvironment suppresses breast cancer cell proliferation.
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Affiliation(s)
- Alison B Shupp
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Manish Neupane
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Lebaron C Agostini
- Department of Surgery, The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gang Ning
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Jonathan R Brody
- Department of Surgery, Brenden Colson Center for Pancreatic Care, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Department of Cell, Brenden Colson Center for Pancreatic Care, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Karen M Bussard
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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Werle SD, Schwab JD, Tatura M, Kirchhoff S, Szekely R, Diels R, Ikonomi N, Sipos B, Sperveslage J, Gress TM, Buchholz M, Kestler HA. Unraveling the Molecular Tumor-Promoting Regulation of Cofilin-1 in Pancreatic Cancer. Cancers (Basel) 2021; 13:725. [PMID: 33578795 PMCID: PMC7916621 DOI: 10.3390/cancers13040725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/26/2021] [Accepted: 02/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cofilin-1 (CFL1) overexpression in pancreatic cancer correlates with high invasiveness and shorter survival. Besides a well-documented role in actin remodeling, additional cellular functions of CFL1 remain poorly understood. Here, we unraveled molecular tumor-promoting functions of CFL1 in pancreatic cancer. For this purpose, we first show that a knockdown of CFL1 results in reduced growth and proliferation rates in vitro and in vivo, while apoptosis is not induced. By mechanistic modeling we were able to predict the underlying regulation. Model simulations indicate that an imbalance in actin remodeling induces overexpression and activation of CFL1 by acting on transcription factor 7-like 2 (TCF7L2) and aurora kinase A (AURKA). Moreover, we could predict that CFL1 impacts proliferation and apoptosis via the signal transducer and activator of transcription 3 (STAT3). These initial model-based regulations could be substantiated by studying protein levels in pancreatic cancer cell lines and human datasets. Finally, we identified the surface protein CD44 as a promising therapeutic target for pancreatic cancer patients with high CFL1 expression.
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Affiliation(s)
- Silke D. Werle
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany; (S.D.W.); (J.D.S.); (R.S.); (N.I.)
| | - Julian D. Schwab
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany; (S.D.W.); (J.D.S.); (R.S.); (N.I.)
| | - Marina Tatura
- Department of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, 35043 Marburg, Germany; (M.T.); (S.K.); (R.D.); (T.M.G.); (M.B.)
| | - Sandra Kirchhoff
- Department of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, 35043 Marburg, Germany; (M.T.); (S.K.); (R.D.); (T.M.G.); (M.B.)
| | - Robin Szekely
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany; (S.D.W.); (J.D.S.); (R.S.); (N.I.)
| | - Ramona Diels
- Department of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, 35043 Marburg, Germany; (M.T.); (S.K.); (R.D.); (T.M.G.); (M.B.)
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany; (S.D.W.); (J.D.S.); (R.S.); (N.I.)
| | - Bence Sipos
- Institute of Pathology, University of Tübingen, 72076 Tübingen, Germany; (B.S.); (J.S.)
| | - Jan Sperveslage
- Institute of Pathology, University of Tübingen, 72076 Tübingen, Germany; (B.S.); (J.S.)
| | - Thomas M. Gress
- Department of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, 35043 Marburg, Germany; (M.T.); (S.K.); (R.D.); (T.M.G.); (M.B.)
| | - Malte Buchholz
- Department of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, 35043 Marburg, Germany; (M.T.); (S.K.); (R.D.); (T.M.G.); (M.B.)
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany; (S.D.W.); (J.D.S.); (R.S.); (N.I.)
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Hu J, Wang R, Liu Y, Zhou J, Shen K, Dai Y. Baicalein Represses Cervical Cancer Cell Growth, Cell Cycle Progression and Promotes Apoptosis via Blocking AKT/mTOR Pathway by the Regulation of circHIAT1/miR-19a-3p Axis. Onco Targets Ther 2021; 14:905-916. [PMID: 33603395 PMCID: PMC7881781 DOI: 10.2147/ott.s282790] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background Baicalein has a significant anti-cancerous function in the treatment of cervical cancer (CC). Its functional mechanism regarding circular RNA (circRNA) hippocampus abundant transcript 1 (circHIAT1) and microRNA-19a-3p (miR-19a-3p) was explored in this research. Methods CC cell viability and colony formation were determined using Cell Counting Kit-8 (CCK-8) and colony formation assay. Cell cycle progression and apoptosis were analyzed via flow cytometry. Protein markers of cell cycle, apoptosis and protein kinase B/mammalian target of rapamycin (AKT/mTOR) pathway were detected by Western blot. CircHIAT1 and miR-19a-3p levels were assayed through the quantitative real-time polymerase chain reaction (qRT-PCR). The interaction between circHIAT1 and miR-19a-3p was validated by dual-luciferase reporter and RNA pull-down assays. In vivo experiment was performed by xenograft model. Results CC cell growth and cell cycle progression were repressed while apoptosis was enhanced by baicalein. MiR-19a-3p was downregulated in baicalein-treated CC cells and miR-19a-3p overexpression lightened the baicalein-induced CC progression inhibition. Moreover, circHIAT1 was found to be a sponge of miR-19a-3p in CC cells. Baicalein-induced cell growth inhibition, cell cycle arrest and apoptosis promotion were neutralized by knockdown of circHIAT1 via targeting miR-19a-3p. Baicalein acted on the circHIAT1/miR-19a-3p to inactivate AKT/mTOR pathway. Baicalein also reduced CC tumor growth in vivo via regulating the levels of circHIAT1 and miR-19a-3p. Conclusion These findings demonstrated that the inhibitory function of baicalein in CC progression was dependent on the repression of AKT/mTOR pathway by upregulating circHIAT1 to sponge miR-19a-3p, showing a specific mechanism for baicalein in CC.
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Affiliation(s)
- Jiaojiao Hu
- Department of Oncology, Suizhou Hospital, Hubei University of Medicine, Suizhou, People's Republic of China
| | - Runkun Wang
- Department of Oncology, The First People's Hospital of Guangshui, Guangshui, People's Republic of China
| | - Yi Liu
- Department of Traditional Chinese Medicine, Suizhou Hospital, Hubei University of Medicine, Suizhou, People's Republic of China
| | - Jianbo Zhou
- Department of General Surgery, Suizhou Hospital, Hubei University of Medicine, Suizhou, People's Republic of China
| | - Ka Shen
- Department of General Surgery, Suizhou Hospital, Hubei University of Medicine, Suizhou, People's Republic of China
| | - Yun Dai
- Department of Oncology, Suizhou Hospital, Hubei University of Medicine, Suizhou, People's Republic of China
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Bencivenga D, Stampone E, Aulitto A, Tramontano A, Barone C, Negri A, Roberti D, Perrotta S, Della Ragione F, Borriello A. A cancer-associated CDKN1B mutation induces p27 phosphorylation on a novel residue: a new mechanism for tumor suppressor loss-of-function. Mol Oncol 2021; 15:915-941. [PMID: 33316141 PMCID: PMC8024736 DOI: 10.1002/1878-0261.12881] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/16/2020] [Accepted: 12/11/2020] [Indexed: 01/12/2023] Open
Abstract
CDKN1B haploinsufficiency promotes the development of several human cancers. The gene encodes p27Kip1, a protein playing pivotal roles in the control of growth, differentiation, cytoskeleton dynamics, and cytokinesis. CDKN1B haploinsufficiency has been associated with chromosomal or gene aberrations. However, very few data exist on the mechanisms by which CDKN1B missense mutations facilitate carcinogenesis. Here, we report a functional study on a cancer‐associated germinal p27Kip1 variant, namely glycine9‐>arginine‐p27Kip1 (G9R‐p27Kip1) identified in a parathyroid adenoma. We unexpectedly found that G9R‐p27Kip1 lacks the major tumor suppressor activities of p27Kip1 including its antiproliferative and pro‐apoptotic functions. In addition, G9R‐p27Kip1 transfection in cell lines induces the formation of more numerous and larger spheres when compared to wild‐type p27Kip1‐transfected cells. We demonstrated that the mutation creates a consensus sequence for basophilic kinases causing a massive phosphorylation of G9R‐p27Kip1 on S12, a residue normally never found modified in p27Kip1. The novel S12 phosphorylation appears responsible for the loss of function of G9R‐p27Kip1 since S12AG9R‐p27Kip1 recovers most of the p27Kip1 tumor suppressor activities. In addition, the expression of the phosphomimetic S12D‐p27Kip1 recapitulates G9R‐p27Kip1 properties. Mechanistically, S12 phosphorylation enhances the nuclear localization of the mutant protein and also reduces its cyclin‐dependent kinase (CDK)2/CDK1 inhibition activity. To our knowledge, this is the first reported case of quantitative phosphorylation of a p27Kip1 variant on a physiologically unmodified residue associated with the loss of several tumor suppressor activities. In addition, our findings demonstrate that haploinsufficiency might be due to unpredictable post‐translational modifications due to generation of novel consensus sequences by cancer‐associated missense mutations.
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Affiliation(s)
- Debora Bencivenga
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Emanuela Stampone
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Arianna Aulitto
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Annunziata Tramontano
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Clementina Barone
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aide Negri
- Department of Medicine and Surgery, University of Parma, Italy
| | - Domenico Roberti
- Department of Woman, Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Silverio Perrotta
- Department of Woman, Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Fulvio Della Ragione
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Adriana Borriello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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Metformin mediated microRNA-7 upregulation inhibits growth, migration, and invasion of non-small cell lung cancer A549 cells. Anticancer Drugs 2021; 31:345-352. [PMID: 31789625 PMCID: PMC7077962 DOI: 10.1097/cad.0000000000000875] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Metformin, a medication widely used in the treatment of type 2 diabetes mellitus, has a possible antitumor effect in type 2 diabetes mellitus patients. MicroRNA-7 is a significant microRNA in non-small cell lung cancer. Metformin has an inhibitory effect on lung cancer and regulates the expression of certain microRNAs, but there is no report connecting metformin with microRNA-7 in lung cancer. Thus, we used qPCR to measure microRNA-7 expression in A549 non-small cell lung cancer cells treated with metformin. We used CCK8, cell scratch, and Transwell assays to test the growth, migration, and invasion of A549 cells. Western blotting was used to measure the expression level of relevant proteins in A549 cells. We found that microRNA-7 was dramatically upregulated by metformin via AMPK in a dose- and time-dependent manner. Both metformin and microRNA-7 mimic reduced A549 cell growth, migration, and invasion. Metformin downregulated the levels of p-NF-κB p65, p-Erk1/2, p-AKT, and p-mTOR proteins. The treatment with the microRNA-7 mimic had the same result. The decrease of these proteins caused the inhibition of A549 cell growth, migration, and invasion. Our discovery revealed that metformin, via increasing the expression of microRNA-7 mediated by AMPK, regulates the AKT/mTOR, MAPK/Erk, and NF-κB signaling pathways, thereby suppressing A549 cell growth, migration, and invasion.
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Vázquez-Martínez JA, Gómez-Lim MA, Morales-Ríos E, Gonzalez-y-Merchand JA, Ortiz-Navarrete V. Short Disordered Epitope of CRTAM Ig-Like V Domain as a Potential Target for Blocking Antibodies. Int J Mol Sci 2020; 21:ijms21228798. [PMID: 33233764 PMCID: PMC7699905 DOI: 10.3390/ijms21228798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Class-I Restricted T Cell-Associated Molecule (CRTAM) is a protein that is expressed after T cell activation. The interaction of CRTAM with its ligand, nectin-like 2 (Necl2), is required for the efficient production of IL-17, IL-22, and IFNγ by murine CD4 T cells, and it plays a role in optimal CD8 T and NK cell cytotoxicity. CRTAM promotes the pro-inflammatory cytokine profile; therefore, it may take part in the immunopathology of autoimmune diseases such as diabetes type 1 or colitis. Thus, antibodies that block the interaction between CRTAM and Necl2 would be useful for controlling the production of these inflammatory cytokines. In this work, using bioinformatics predictions, we identified three short disordered epitopes (sDE1-3) that are located in the Ig-like domains of murine CRTAM and are conserved in mammalian species. We performed a structural analysis by molecular dynamics simulations of sDE1 (QHPALKSSKY, Ig-like V), sDE2 (QRNGEKSVVK, Ig-like C1), and sDE3 (CSTERSKKPPPQI, Ig-like C1). sDE1, which is located within a loop of the contact interface of the heterotypic interaction with Nectl2, undergoes an order–disorder transition. On the contrary, even though sDE2 and sDE3 are flexible and also located within loops, they do not undergo order–disorder transitions. We evaluated the immunogenicity of sDE1 and sDE3 through the expression of these epitopes in chimeric L1 virus-like particles. We confirmed that sDE1 induces polyclonal antibodies that recognize the native folding of CRTAM expressed in activated murine CD4 T cells. In contrast, sDE3 induces polyclonal antibodies that recognize the recombinant protein hCRTAM-Fc, but not the native CRTAM. Thus, in this study, an exposed disordered epitope in the Ig-like V domain of CRTAM was identified as a potential site for therapeutic antibodies.
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Affiliation(s)
- Julio Angel Vázquez-Martínez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de Mexico, Mexico; (J.A.V.-M.); (J.A.G.-y.-M.)
- Departamento de Biomedicina Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico
- Departamento de Ingeniería Genética, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821 Irapuato, Guanajuato, Mexico;
| | - Miguel Angel Gómez-Lim
- Departamento de Ingeniería Genética, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821 Irapuato, Guanajuato, Mexico;
| | - Edgar Morales-Ríos
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico;
| | - Jorge Alberto Gonzalez-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de Mexico, Mexico; (J.A.V.-M.); (J.A.G.-y.-M.)
| | - Vianney Ortiz-Navarrete
- Departamento de Biomedicina Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico
- Correspondence:
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Creff J, Besson A. Functional Versatility of the CDK Inhibitor p57 Kip2. Front Cell Dev Biol 2020; 8:584590. [PMID: 33117811 PMCID: PMC7575724 DOI: 10.3389/fcell.2020.584590] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/17/2020] [Indexed: 12/19/2022] Open
Abstract
The cyclin/CDK inhibitor p57Kip2 belongs to the Cip/Kip family, with p21Cip1 and p27Kip1, and is the least studied member of the family. Unlike the other family members, p57Kip2 has a unique role during embryogenesis and is the only CDK inhibitor required for embryonic development. p57Kip2 is encoded by the imprinted gene CDKN1C, which is the gene most frequently silenced or mutated in the genetic disorder Beckwith-Wiedemann syndrome (BWS), characterized by multiple developmental anomalies. Although initially identified as a cell cycle inhibitor based on its homology to other Cip/Kip family proteins, multiple novel functions have been ascribed to p57Kip2 in recent years that participate in the control of various cellular processes, including apoptosis, migration and transcription. Here, we will review our current knowledge on p57Kip2 structure, regulation, and its diverse functions during development and homeostasis, as well as its potential implication in the development of various pathologies, including cancer.
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Affiliation(s)
- Justine Creff
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Centre de Biologie Intégrative, Université de Toulouse, Toulouse, France
| | - Arnaud Besson
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Centre de Biologie Intégrative, Université de Toulouse, Toulouse, France
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Viswanathan G, Chung LY, Srinivas UK. Heterogeneous Differentiation of Highly Proliferative Embryonal Carcinoma PCC4 Cells Induced by Curcumin: An In Vitro Study. Nutr Cancer 2020; 73:1780-1791. [PMID: 32875900 DOI: 10.1080/01635581.2020.1811883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Curcumin, the yellow pigment derived from turmeric rhizomes, exhibits antioxidant, anti-inflammatory, antimicrobial, and anticancer properties. We have previously reported in a study that curcumin could induce differentiation in embryonal carcinoma cell (EC). EC cells are the primary constituents of teratocarcinoma tumors, and hence differentiating them to a non-proliferative cell type may be useful in anticancer therapies. Here, we conducted a detailed study using various molecular approaches to characterize this differentiation at the cellular and molecular levels. The cells were treated with 20 µM curcumin, which was the optimal concentration to produce the highest amount of differentiated cells. Changes in protein and RNA expression, membrane dynamics, and migration of these cells after treatment with curcumin were then studied in a time-dependent manner. The differentiated cells were morphologically distinct from the precursor cells, and gene expression profiles were altered in curcumin-treated cells. Curcumin promoted cell motility and cell adhesion. Curcumin also induced changes in membrane fluidity and the lateral mobility of lipids in the plasma membrane. The findings of this study suggest that curcumin might have therapeutic potential in differentiation therapy for the treatment of teratocarcinomas or germ cell tumors (GCTs) such as testicular and ovarian GCTs.
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Affiliation(s)
- Geetha Viswanathan
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Lip Yong Chung
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Usha K Srinivas
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
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Chapman FM, Sparham C, Hastie C, Sanders DJ, van Egmond R, Chapman KE, Doak SH, Scott AD, Jenkins GJS. Comparison of passive-dosed and solvent spiked exposures of pro-carcinogen, benzo[a]pyrene, to human lymphoblastoid cell line, MCL-5. Toxicol In Vitro 2020; 67:104905. [PMID: 32497684 DOI: 10.1016/j.tiv.2020.104905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/26/2020] [Accepted: 05/28/2020] [Indexed: 11/17/2022]
Abstract
Genotoxicity testing methods in vitro provide a means to predict the DNA damaging effects of chemicals on human cells. This is hindered in the case of hydrophobic test compounds, however, which will partition to in vitro components such as plastic-ware and medium proteins, in preference to the aqueous phase of the exposure medium. This affects the freely available test chemical concentration, and as this freely dissolved aqueous concentration is that bioavailable to cells, it is important to define and maintain this exposure. Passive dosing promises to have an advantage over traditional 'solvent spiking' exposure methods and involves the establishment and maintenance of known chemical concentrations in the in vitro medium, and therefore aqueous phase. Passive dosing was applied in a novel format to expose the MCL-5 human lymphoblastoid cell line to the pro-carcinogen, benzo[a]pyrene (B[a]P) and was compared to solvent (dimethyl sulphoxide) spiked B[a]P exposures over 48 h. Passive dosing induced greater changes, at lower concentrations, to micronucleus frequency, p21 mRNA expression, cell cycle abnormalities, and cell and nuclear morphology. This was attributed to a maintained, definable, free chemical concentration using passive dosing and the presence or absence of solvent, and highlights the influence of exposure choice on genotoxic outcomes.
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Affiliation(s)
- Fiona M Chapman
- In Vitro Toxicology Group, Institute of Life Science 1, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK.
| | - Chris Sparham
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Colin Hastie
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - David J Sanders
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Roger van Egmond
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Katherine E Chapman
- In Vitro Toxicology Group, Institute of Life Science 1, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
| | - Shareen H Doak
- In Vitro Toxicology Group, Institute of Life Science 1, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
| | - Andrew D Scott
- Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Gareth J S Jenkins
- In Vitro Toxicology Group, Institute of Life Science 1, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
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Mani S, Balasubramanian B, Balasubramani R, Chang SW, Ponnusamy P, Esmail GA, Arasu MV, Al-Dhabi NA, Duraipandiyan V. Synthesis and characterization of proanthocyanidin-chitosan nanoparticles: An assessment on human colorectal carcinoma HT-29 cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 210:111966. [PMID: 32711334 DOI: 10.1016/j.jphotobiol.2020.111966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 07/06/2020] [Accepted: 07/15/2020] [Indexed: 12/09/2022]
Abstract
Cancer nanotheranostic materials are helpful in monitoring drug delivery and efficacy against tumor cells. Current chemotherapeutic may have adverse side effects and this necessity to discover the new modern therapeutic nano-drugs. In the present study, we designed the new targeted and degradable polymer of bio-active chitosan nanoparticles with proanthocyanidin (PAC-CSNPs) and evaluated its apoptotic effects against human colorectal carcinoma cells (HT-29). The functional groups were characterized by Fourier-transform infrared spectroscopy and transmission electron microscope. Further, their dispersion of spherical form nanoparticle with an average size of 73.43 nm used for drug delivery system. The PAC-CSNPs were targeted to inhibit the cyclin-dependent kinases and prevent cell cycle/cell division in cancer cells. At high concentrations of PAC (25 μg/mL) exposure, cell viability of HT-29 cells was greater than 80%. However, at low concentrations of PAC-CSNPs (6.25 μg/mL) exposure, HT-29 cell mortality was high, which may be due to the efficient drug release by CSNPs. The percentage of reactive oxygen species (ROS) levels were 12 ± 2.52% (control), 39 ± 4.32% (PAC), and 85.06 ± 3.54% (PAC-CSNPs). The over production of ROS by PAC-CSNPs can prompt DNA damage, cell death and apoptosis in HT-29 cells. The in vivo toxicity of synthesized PAC-CSNPs was tested against zebra fish observed at dose-time-dependent intervals. In conclusion, the PAC-CSNPs enhanced HT-29 cell death and shows promise as a novel future nano-therapy for cancer.
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Affiliation(s)
- Suganya Mani
- Department of Biotechnology, K. S. Rangasamy College of Technology, Tiruchengode 637 215, Tamil Nadu, India
| | | | - Ravindran Balasubramani
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do 16227, South Korea
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do 16227, South Korea
| | - Ponmurugan Ponnusamy
- Department of Botany, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India.
| | - Galal Ali Esmail
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Veeramuthu Duraipandiyan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Entomology Research Institute, Loyola College, Chennai 600034, Tamilnadu, India
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Kiani BH, Kayani WK, Khayam AU, Dilshad E, Ismail H, Mirza B. Artemisinin and its derivatives: a promising cancer therapy. Mol Biol Rep 2020; 47:6321-6336. [PMID: 32710388 DOI: 10.1007/s11033-020-05669-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022]
Abstract
The world is experiencing a cancer epidemic and an increase in the prevalence of the disease. Cancer remains a major killer, accounting for more than half a million deaths annually. There is a wide range of natural products that have the potential to treat this disease. One of these products is artemisinin; a natural product from Artemisia plant. The Nobel Prize for Medicine was awarded in 2015 for the discovery of artemisinin in recognition of the drug's efficacy. Artemisinin produces highly reactive free radicals by the breakdown of two oxygen atoms that kill cancerous cells. These cells sequester iron and accumulate as much as 1000 times in comparison with normal cells. Generally, chemotherapy is toxic to both cancerous cells and normal cells, while no significant cytotoxicity from artemisinin to normal cells has been found in more than 4000 case studies, which makes it far different than conventional chemotherapy. The pleiotropic response of artemisinin in cancer cells is responsible for growth inhibition by multiple ways including inhibition of angiogenesis, apoptosis, cell cycle arrest, disruption of cell migration, and modulation of nuclear receptor responsiveness. It is very encouraging that artemisinin and its derivatives are anticipated to be a novel class of broad-spectrum antitumor agents based on efficacy and safety. This review aims to highlight these achievements and propose potential strategies to develop artemisinin and its derivatives as a new class of cancer therapeutic agents.
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Affiliation(s)
- Bushra Hafeez Kiani
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, 44000, Pakistan.
| | - Waqas Khan Kayani
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Växtskyddsvägen 1, 23053, Alnarp, Sweden
| | - Asma Umer Khayam
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Hammad Ismail
- Department of Biochemistry and Molecular Biology, University of Gujrat, Gujrat, 50700, Pakistan
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
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Sala D, Cosentino U, Ranaudo A, Greco C, Moro G. Dynamical Behavior and Conformational Selection Mechanism of the Intrinsically Disordered Sic1 Kinase-Inhibitor Domain. Life (Basel) 2020; 10:life10070110. [PMID: 32664566 PMCID: PMC7399826 DOI: 10.3390/life10070110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 01/04/2023] Open
Abstract
Intrinsically Disordered Peptides and Proteins (IDPs) in solution can span a broad range of conformations that often are hard to characterize by both experimental and computational methods. However, obtaining a significant representation of the conformational space is important to understand mechanisms underlying protein functions such as partner recognition. In this work, we investigated the behavior of the Sic1 Kinase-Inhibitor Domain (KID) in solution by Molecular Dynamics (MD) simulations. Our results point out that application of common descriptors of molecular shape such as Solvent Accessible Surface (SAS) area can lead to misleading outcomes. Instead, more appropriate molecular descriptors can be used to define 3D structures. In particular, we exploited Weighted Holistic Invariant Molecular (WHIM) descriptors to get a coarse-grained but accurate definition of the variegated Sic1 KID conformational ensemble. We found that Sic1 is able to form a variable amount of folded structures even in absence of partners. Among them, there were some conformations very close to the structure that Sic1 is supposed to assume in the binding with its physiological complexes. Therefore, our results support the hypothesis that this protein relies on the conformational selection mechanism to recognize the correct molecular partners.
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Affiliation(s)
- Davide Sala
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy;
| | - Ugo Cosentino
- Dipartimento di Scienze dell’Ambiente e della Terra, Università di Milano-Bicocca, P.zza della Scienza 1, 20126 Milano, Italy; (U.C.); (A.R.)
| | - Anna Ranaudo
- Dipartimento di Scienze dell’Ambiente e della Terra, Università di Milano-Bicocca, P.zza della Scienza 1, 20126 Milano, Italy; (U.C.); (A.R.)
| | - Claudio Greco
- Dipartimento di Scienze dell’Ambiente e della Terra, Università di Milano-Bicocca, P.zza della Scienza 1, 20126 Milano, Italy; (U.C.); (A.R.)
- Correspondence: (C.G.); (G.M.)
| | - Giorgio Moro
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy;
- Correspondence: (C.G.); (G.M.)
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Wolfarth AA, Liu X, Darby TM, Boyer DJ, Spizman JB, Owens JA, Chandrasekharan B, Naudin CR, Hanley KZ, Robinson BS, Ortlund EA, Jones RM, Neish AS. Proline-Rich Acidic Protein 1 (PRAP1) Protects the Gastrointestinal Epithelium From Irradiation-Induced Apoptosis. Cell Mol Gastroenterol Hepatol 2020; 10:713-727. [PMID: 32629119 PMCID: PMC7498829 DOI: 10.1016/j.jcmgh.2020.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS The intestinal epithelium must be resilient to physiochemical stress to uphold the physiological barrier separating the systemic compartment from the microbial and antigenic components of the gut lumen. Identifying proteins that mediate protection and enhancing their expression is therefore a clear approach to promote intestinal health. We previously reported that oral ingestion of the probiotic Lactobacillus rhamnosus GG not only induced the expression of several recognized cytoprotective factors in the murine colon, but also many genes with no previously described function, including the gene encoding proline-rich acidic protein 1 (PRAP1). PRAP1 is a highly expressed protein in the epithelium of the gastrointestinal tract and we sought to define its function in this tissue. METHODS Purified preparations of recombinant PRAP1 were analyzed biochemically and PRAP1 antisera were used to visualize localization in tissues. Prap1-/- mice were characterized at baseline and challenged with total body irradiation, then enteroids were generated to recapitulate the irradiation challenge ex vivo. RESULTS PRAP1 is a 17-kilodalton intrinsically disordered protein with no recognizable sequence homology. PRAP1 expression levels were high in the epithelia of the small intestine. Although Prap1-/- mice presented only mild phenotypes at baseline, they were highly susceptible to intestinal injury upon challenge. After irradiation, the Prap1-/- mice showed accelerated death with a significant increase in apoptosis and p21 expression in the small intestinal epithelium. CONCLUSIONS PRAP1 is an intrinsically disordered protein highly expressed by the gastrointestinal epithelium and functions at exposed surfaces to protect the barrier from oxidative insult.
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Affiliation(s)
- Alexandra A Wolfarth
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Trevor M Darby
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Darra J Boyer
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jocelyn B Spizman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Joshua A Owens
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Bindu Chandrasekharan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Crystal R Naudin
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Krisztina Z Hanley
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Brian S Robinson
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Rheinallt M Jones
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Emory Microbiome Research Center, Emory University School of Medicine, Atlanta, Georgia
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Emory Microbiome Research Center, Emory University School of Medicine, Atlanta, Georgia.
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Pennycook BR, Barr AR. Restriction point regulation at the crossroads between quiescence and cell proliferation. FEBS Lett 2020; 594:2046-2060. [PMID: 32564372 DOI: 10.1002/1873-3468.13867] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 02/11/2024]
Abstract
The coordination of cell proliferation with reversible cell cycle exit into quiescence is crucial for the development of multicellular organisms and for tissue homeostasis in the adult. The decision between quiescence and proliferation occurs at the restriction point, which is widely thought to be located in the G1 phase of the cell cycle, when cells integrate accumulated extracellular and intracellular signals to drive this binary cellular decision. On the molecular level, decision-making is exerted through the activation of cyclin-dependent kinases (CDKs). CDKs phosphorylate the retinoblastoma (Rb) transcriptional repressor to regulate the expression of cell cycle genes. Recently, the classical view of restriction point regulation has been challenged. Here, we review the latest findings on the activation of CDKs, Rb phosphorylation and the nature and position of the restriction point within the cell cycle.
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Affiliation(s)
- Betheney R Pennycook
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alexis R Barr
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
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The emerging molecular mechanism of m 6A modulators in tumorigenesis and cancer progression. Biomed Pharmacother 2020; 127:110098. [PMID: 32299028 DOI: 10.1016/j.biopha.2020.110098] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification; m6A modifications are installed by methyltransferases, removed by demethylases and recognized by reader proteins. M6A plays crucial roles in a variety of biological processes by regulating target RNA translation, splicing, nuclear export, and decay. Since the establishment of methylated RNA immunoprecipitation-sequencing methodology, over three hundred articles about m6A modulators, including "writers", "erasers" and "readers", have been reported in the last four years. In addition, an increasing number of molecular mechanisms underlying m6A RNA methylation in human cancers have been comprehensively clarified. The recently emerged molecular mechanisms of m6A modulators in cancer cell proliferation, cell cycle progression, migration and invasion, apoptosis, and autophagy remain to be summarized. Hence, this review specifically summarizes these recent advances in the understanding of m6A molecular mechanisms in tumorigenesis and cancer progression. In addition, we discuss the prospect of using an m6A methylation modulator as a new diagnostic biomarker and therapeutic target for human cancers.
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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Tang M, Dai W, Wu H, Xu X, Jiang B, Wei Y, Qian H, Han L. Transcriptome analysis of tongue cancer based on high‑throughput sequencing. Oncol Rep 2020; 43:2004-2016. [PMID: 32236620 PMCID: PMC7160550 DOI: 10.3892/or.2020.7560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
Tongue cancer is one of the most common types of cancer, but its molecular etiology and pathogenesis remain unclear. The aim of the present study was to elucidate the pathogenesis of tongue cancer and investigate novel potential diagnostic and therapeutic targets. Four matched pairs of tongue cancer and paracancerous tissues were collected for RNA sequencing (RNA-Seq), and the differentially expressed genes were analyzed. The RNA-Seq data of tongue cancer tissues were further analyzed using bioinformatics and reverse transcription-quantitative PCR analysis. The sequenced reads were quantified and qualified in accordance with the analysis demands. The transcriptomes of the tongue cancer tissues and paired paracancerous tissues were analyzed, and 1,700 upregulated and 2,249 downregulated genes were identified. Gene Ontology analysis uncovered a significant enrichment in the terms associated with extracellular matrix (ECM) organization, cell adhesion and collagen catabolic processes. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that these differentially expressed genes were mainly enriched in the focal adhesion pathway, ECM-receptor interaction pathway, phosphoinositide 3-kinase (PI3K)-Akt pathway, and cell adhesion molecules. Comprehensive analyses of the gene tree and pathway network revealed that the majority of cell cycle genes were upregulated, while the majority of the genes associated with intracellular response, cell adhesion and cell differentiation were downregulated. The ECM-receptor interaction, focal adhesion kinase (FAK) and PI3K-Akt pathways were closely associated with one another and held key positions in differential signaling pathways. The ECM-receptor, FAK and PI3K-Akt signaling pathways were found to synergistically promote tongue cancer occurrence and progression, and may serve as potential diagnostic and therapeutic targets for this type of cancer.
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Affiliation(s)
- Mingming Tang
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Wencheng Dai
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Hao Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xinjiang Xu
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Bin Jiang
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Yingze Wei
- Department of Clinical Pathology, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Hongyan Qian
- Key Laboratory of Cancer Research Center Nantong, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Liang Han
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
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