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Li Y, Qi X, Wang Q, He Y, Li Z, Cen X, Wei L. Comprehensive analysis of key host gene-microbe networks in the cecum tissues of the obese rabbits induced by a high-fat diet. Front Cell Infect Microbiol 2024; 14:1407051. [PMID: 38947127 PMCID: PMC11211605 DOI: 10.3389/fcimb.2024.1407051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
The Cecum is a key site for cellulose digestion in nutrient metabolism of intestine, but its mechanisms of microbial and gene interactions has not been fully elucidated during pathogenesis of obesity. Therefore, the cecum tissues of the New Zealand rabbits and their contents between the high-fat diet-induced group (Ob) and control group (Co) were collected and analyzed using multi-omics. The metagenomic analysis indicated that the relative abundances of Corallococcus_sp._CAG:1435 and Flavobacteriales bacterium species were significantly lower, while those of Akkermansia glycaniphila, Clostridium_sp._CAG:793, Mycoplasma_sp._CAG:776, Mycoplasma_sp._CAG:472, Clostridium_sp._CAG:609, Akkermansia_sp._KLE1605, Clostridium_sp._CAG:508, and Firmicutes_bacterium_CAG:460 species were significantly higher in the Ob as compared to those in Co. Transcriptomic sequencing results showed that the differentially upregulated genes were mainly enriched in pathways, including calcium signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway, while the differentially downregulated genes were mainly enriched in pathways of NF-kappaB signaling pathway and T cell receptor signaling pathway. The comparative analysis of metabolites showed that the glycine, serine, and threonine metabolism and cysteine and methionine metabolism were the important metabolic pathways between the two groups. The combined analysis showed that CAMK1, IGFBP6, and IGFBP4 genes were highly correlated with Clostridium_sp._CAG:793, and Akkermansia_glycaniphila species. Thus, the preliminary study elucidated the microbial and gene interactions in cecum of obese rabbit and provided a basis for further studies in intestinal intervention for human obesity.
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Affiliation(s)
- Yanhong Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhupeng Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xi Cen
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
| | - Limin Wei
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
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Wang C, Li X, Yi W, Kang J, Nuermaimaiti N, Guan Y. Differential expression of microRNAs in serum exosomes of obese and non-obese mice and analysis of their function. Gene 2024; 927:148604. [PMID: 38838872 DOI: 10.1016/j.gene.2024.148604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
OBJECTIVE To extract exosomes from obese and non-obese mice, screen specifically expressed microRNAs by high-throughput sequencing and explore their roles. METHODS An animal obesity model was constructed, and the successful construction of the obesity model was verified by HE staining, Western Blot and RT-qPCR. In addition, exosomes were extracted and verified by Western Blot. High-throughput sequencing was performed on the extracted serum exosomes to screen for differentially expressed microRNAs. fluorescence quantitative RT-PCR (RT-qPCR) was used to validate the differentially expressed miRNAs and explore their functions. RESULTS 8 microRNAs were up-regulated and 11 microRNAs were down-regulated. mmu-miR-674-5p and X_28316 were significantly down-regulated and had the greatest impact on protein pathways. 8_13258 was significantly up-regulated and affected multiple protein pathways. GO enrichment analysis suggested that the differentially expressed microRNAs were mainly involved in the cleavage of microtubule activity, transferase activity/transferase pentameric acid. GO enrichment analysis suggested that differentially expressed microRNAs were mainly involved in the processes of cleavage microtubule activity, transferase activity/transfer pentamer, and threonine phosphatase/threonine kinase activity.KEGG pathway enrichment analysis showed that differentially expressed microRNAs were mainly involved in the processes of regulating the phosphorylation of TP53 activity, the G2/M DNA damage checkpoint, and the processing of the ends of DNA double-strand breaks. Protein interaction networks were enriched for Stat3, Fgr, Camk2b, Rac1, Asb6, and Ankfy1. Suggesting that they may be mediated by differential genes to participate in the process of insulin resistance. qRT-PCR results showed that the expression trend of mmu-miR-674-5p was consistent with the sequencing results. It suggests that it may be able to participate in the regulation of insulin resistance as a target gene. CONCLUSION microRNAs were differentially expressed in serum exosomes of obese and non-obese mice and might be involved in the specific regulation of insulin resistance. mmu-miR-674-5p was differentially expressed significantly and the validation trend was consistent with it, suggesting that it might be able to participate in the regulation of insulin resistance as a target gene.
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Affiliation(s)
- Changzan Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China
| | - Xianghui Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China
| | - Wenying Yi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China
| | - Jiawei Kang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China
| | - Nuerbiye Nuermaimaiti
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China.
| | - Yaqun Guan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, 830017 Urumqi, Xinjiang, China.
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Acharya M, Singh N, Gupta G, Tambuwala MM, Aljabali AAA, Chellappan DK, Dua K, Goyal R. Vitamin D, Calbindin, and calcium signaling: Unraveling the Alzheimer's connection. Cell Signal 2024; 116:111043. [PMID: 38211841 DOI: 10.1016/j.cellsig.2024.111043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
Calcium is a ubiquitous second messenger that is indispensable in regulating neurotransmission and memory formation. A precise intracellular calcium level is achieved through the concerted action of calcium channels, and calcium exerts its effect by binding to an array of calcium-binding proteins, including calmodulin (CAM), calcium-calmodulin complex-dependent protein kinase-II (CAMK-II), calbindin (CAL), and calcineurin (CAN). Calbindin orchestrates a plethora of signaling events that regulate synaptic transmission and depolarizing signals. Vitamin D, an endogenous fat-soluble metabolite, is synthesized in the skin upon exposure to ultraviolet B radiation. It modulates calcium signaling by increasing the expression of the calcium-sensing receptor (CaSR), stimulating phospholipase C activity, and regulating the expression of calcium channels such as TRPV6. Vitamin D also modulates the activity of calcium-binding proteins, including CAM and calbindin, and increases their expression. Calbindin, a high-affinity calcium-binding protein, is involved in calcium buffering and transport in neurons. It has been shown to inhibit apoptosis and caspase-3 activity stimulated by presenilin 1 and 2 in AD. Whereas CAM, another calcium-binding protein, is implicated in regulating neurotransmitter release and memory formation by phosphorylating CAN, CAMK-II, and other calcium-regulated proteins. CAMK-II and CAN regulate actin-induced spine shape changes, which are further modulated by CAM. Low levels of both calbindin and vitamin D are attributed to the pathology of Alzheimer's disease. Further research on vitamin D via calbindin-CAMK-II signaling may provide newer insights, revealing novel therapeutic targets and strategies for treatment.
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Affiliation(s)
- Manish Acharya
- Department of Neuropharmacology, School of Pharmaceutical Sciences, Shoolini University, Himachal Pradesh, India
| | - Nicky Singh
- Department of Neuropharmacology, School of Pharmaceutical Sciences, Shoolini University, Himachal Pradesh, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Jaipur 302017, India
| | - Murtaza M Tambuwala
- Lincoln Medical School, Universities of Nottingham and Lincoln College of Science, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Yarmouk University, Irbid 21163, Jordan.
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia.
| | - Rohit Goyal
- Department of Neuropharmacology, School of Pharmaceutical Sciences, Shoolini University, Himachal Pradesh, India.
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Lecluze E, Lettre G. Association Analyses of Predicted Loss-of-Function Variants Prioritized 15 Genes as Blood Pressure Regulators. Can J Cardiol 2023; 39:1888-1897. [PMID: 37451613 DOI: 10.1016/j.cjca.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Hypertension, clinically defined by elevated blood pressure (BP), is an important cause of mortality and morbidity worldwide. Many risk factors for hypertension are known, including a positive family history, which suggests that genetics contribute to interindividual BP variation. Genome-wide association studies (GWAS) have identified > 1000 loci associated with BP, yet the identity of the genes responsible for these associations remains largely unknown. METHODS To pinpoint genes that causally affect variation of BP in humans, we analyzed predicted loss-of-function (pLoF) variants in the UK Biobank whole-exome sequencing dataset (n = 454,709 participants, 6% non-European ancestry). We analyzed genetic associations between systolic or diastolic BP (SBP/DBP) and single pLoF variants (additive and recessive genetic models) as well as with the burden of very rare pLoF variants (minor allele frequency [MAF] < 0.01%). RESULTS Single pLoF variants in 10 genes were associated with BP (ANKDD1B, ENPEP, PNCK, BTN3A2, C1orf145 [OBSCN-AS1], CASP9, DBH, KIAA1161 [MYORG], OR4X1, and TMC3). We also found a burden of rare pLoF variants in 5 additional genes associated with BP (TTN, NOS3, FES, SMAD6, COL21A1). Except for PNCK, which is located on the X-chromosome, these genes map near variants previously associated with BP by GWAS, validating the study of pLoF variants to prioritize causal genes at GWAS loci. CONCLUSIONS Our study highlights 15 genes that likely modulate BP in humans, including 5 genes that harbour pLoF variants associated with lower BP.
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Affiliation(s)
- Estelle Lecluze
- Montreal Heart Institute, Montréal, Québec, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Québec, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.
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Essegian DJ, Chavez V, Khurshid R, Merchan JR, Schürer SC. AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. PLoS Comput Biol 2023; 19:e1010263. [PMID: 37235579 PMCID: PMC10249896 DOI: 10.1371/journal.pcbi.1010263] [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: 05/31/2022] [Revised: 06/08/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
PNCK, or CAMK1b, is an understudied kinase of the calcium-calmodulin dependent kinase family which recently has been identified as a marker of cancer progression and survival in several large-scale multi-omics studies. The biology of PNCK and its relation to oncogenesis has also begun to be elucidated, with data suggesting various roles in DNA damage response, cell cycle control, apoptosis and HIF-1-alpha related pathways. To further explore PNCK as a clinical target, potent small-molecule molecular probes must be developed. Currently, there are no targeted small molecule inhibitors in pre-clinical or clinical studies for the CAMK family. Additionally, there exists no experimentally derived crystal structure for PNCK. We herein report a three-pronged chemical probe discovery campaign which utilized homology modeling, machine learning, virtual screening and molecular dynamics to identify small molecules with low-micromolar potency against PNCK activity from commercially available compound libraries. We report the discovery of a hit-series for the first targeted effort towards discovering PNCK inhibitors that will serve as the starting point for future medicinal chemistry efforts for hit-to-lead optimization of potent chemical probes.
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Affiliation(s)
- Derek J. Essegian
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Valery Chavez
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rabia Khurshid
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jaime R. Merchan
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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6
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Zhang F, Zhang Z, Li Y, Sun Y, Zhou X, Chen X, Sun S. Integrated Bioinformatics Analysis Identifies Robust Biomarkers and Its Correlation With Immune Microenvironment in Nonalcoholic Fatty Liver Disease. Front Genet 2022; 13:942153. [PMID: 35910194 PMCID: PMC9330026 DOI: 10.3389/fgene.2022.942153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Objective: Nonalcoholic fatty liver disease (NAFLD) is a serious threat to human health worldwide. In this study, the aim is to analyze diagnosis biomarkers in NAFLD and its relationship with the immune microenvironment based on bioinformatics analysis. Methods: We downloaded microarray datasets (GSE48452 and GSE63067) from the Gene Expression Omnibus (GEO) database for screening differentially expressed genes (DEGs). The hub genes were screened by a series of machine learning analyses, such as support vector machine (SVM), least absolute shrinkage and selection operator (LASSO), and weighted gene co-expression network analysis (WGCNA). It is worth mentioning that we used the gene enrichment analysis to explore the driver pathways of NAFLD occurrence. Subsequently, the aforementioned genes were validated by external datasets (GSE66676). Moreover, the CIBERSORT algorithm was used to estimate the proportion of different types of immune cells. Finally, the Spearman analysis was used to verify the relationship between hub genes and immune cells. Results: Hub genes (CAMK1D, CENPV, and TRHDE) were identified. In addition, we found that the pathogenesis of NAFLD is mainly related to nutrient metabolism and the immune system. In correlation analysis, CENPV expression had a strong negative correlation with resting memory CD4 T cells, and TRHDE expression had a strong positive correlation with naive B cells. Conclusion: CAMK1D, CENPV, and TRHDE play regulatory roles in NAFLD. In particular, CENPV and TRHDE may regulate the immune microenvironment by mediating resting memory CD4 T cells and naive B cells, respectively, and thus influence disease progression.
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Affiliation(s)
| | | | | | | | | | | | - Shibo Sun
- *Correspondence: Xiaoning Chen, ; Shibo Sun,
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7
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Puhl AC, Gomes GF, Damasceno S, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Monakhova N, Riabova O, Lane TR, Makarov V, Veras FP, Batah SS, Fabro AT, Oliva G, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Pyronaridine Protects against SARS-CoV-2 Infection in Mouse. ACS Infect Dis 2022; 8:1147-1160. [PMID: 35609344 PMCID: PMC9159503 DOI: 10.1021/acsinfecdis.2c00091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 12/23/2022]
Abstract
There are currently relatively few small-molecule antiviral drugs that are either approved or emergency-approved for use against severe acute respiratory coronavirus 2 (SARS-CoV-2). One of these is remdesivir, which was originally repurposed from its use against Ebola. We evaluated three molecules we had previously identified computationally with antiviral activity against Ebola and Marburg and identified pyronaridine, which inhibited the SARS-CoV-2 replication in A549-ACE2 cells. The in vivo efficacy of pyronaridine has now been assessed in a K18-hACE transgenic mouse model of COVID-19. Pyronaridine treatment demonstrated a statistically significant reduction of viral load in the lungs of SARS-CoV-2-infected mice, reducing lung pathology, which was also associated with significant reduction in the levels of pro-inflammatory cytokines/chemokine and cell infiltration. Pyronaridine inhibited the viral PLpro activity in vitro (IC50 of 1.8 μM) without any effect on Mpro, indicating a possible molecular mechanism involved in its ability to inhibit SARS-CoV-2 replication. We have also generated several pyronaridine analogs to assist in understanding the structure activity relationship for PLpro inhibition. Our results indicate that pyronaridine is a potential therapeutic candidate for COVID-19.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
| | - Giovanni F. Gomes
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Andre S. Godoy
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Gabriela D. Noske
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Aline M. Nakamura
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Victor O. Gawriljuk
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Rafaela S. Fernandes
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Natalia Monakhova
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Olga Riabova
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Thomas R. Lane
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
| | - Vadim Makarov
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Flavio P. Veras
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Sabrina S. Batah
- Department of Pathology and Legal Medicine,
Ribeirão Preto Medical School, University of São
Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São
Paulo, Brazil
| | - Alexandre T. Fabro
- Department of Pathology and Legal Medicine,
Ribeirão Preto Medical School, University of São
Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São
Paulo, Brazil
| | - Glaucius Oliva
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Fernando Q. Cunha
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - José C. Alves-Filho
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Thiago M. Cunha
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
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Grant P, Kumar J, Kar S, Overduin M. Effects of Specific Inhibitors for CaMK1D on a Primary Neuron Model for Alzheimer's Disease. Molecules 2021; 26:7669. [PMID: 34946752 PMCID: PMC8707680 DOI: 10.3390/molecules26247669] [Citation(s) in RCA: 3] [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: 11/16/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide. Despite extensive research and targeting of the main molecular components of the disease, beta-amyloid (Aβ) and tau, there are currently no treatments that alter the progression of the disease. Here, we examine the effects of two specific kinase inhibitors for calcium/calmodulin-dependent protein kinase type 1D (CaMK1D) on Aβ-mediated toxicity, using mouse primary cortical neurons. Tau hyperphosphorylation and cell death were used as AD indicators. These specific inhibitors were found to prevent Aβ induced tau hyperphosphorylation in culture, but were not able to protect cells from Aβ induced toxicity. While inhibitors were able to alter AD pathology in cell culture, they were insufficient to prevent cell death. With further research and development, these inhibitors could contribute to a multi-drug strategy to combat AD.
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Affiliation(s)
- Paige Grant
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
| | - Satyabrata Kar
- Centre for Prions and Protein Folding Diseases, Department of Medicine (Neurology), University of Alberta, Edmonton, AB T6G 2MB, Canada;
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
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Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases. Int J Mol Sci 2021; 22:ijms22084187. [PMID: 33919522 PMCID: PMC8073710 DOI: 10.3390/ijms22084187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Man-Chun Wong
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan;
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 81148, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
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10
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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11
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Tong MHG, Jeeves M, Rajesh S, Ludwig C, Lenoir M, Kumar J, McClelland DM, Berditchevski F, Hubbard JA, Kenyon C, Butterworth S, Knapp S, Overduin M. Backbone resonance assignments of the catalytic and regulatory domains of Ca 2+/calmodulin-dependent protein kinase 1D. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:221-225. [PMID: 32535836 PMCID: PMC7462902 DOI: 10.1007/s12104-020-09950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The CaMK subfamily of Ser/Thr kinases are regulated by calmodulin interactions with their C-terminal regions. They are exemplified by Ca2+/calmodulin dependent protein kinase 1δ which is known as CaMK1D, CaMKIδ or CKLiK. CaMK1D mediates intracellular signalling downstream of Ca2+ influx and thereby exhibits amplifications of Ca2+signals and polymorphisms that have been implicated in breast cancer and diabetes. Here we report the backbone 1H, 13C, 15N assignments of the 38 kDa human CaMK1D protein in its free state, including both the canonical bi-lobed kinase fold as well as the autoinhibitory and calmodulin binding domains.
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Affiliation(s)
- Michael H G Tong
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sundaresan Rajesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marc Lenoir
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Darren M McClelland
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julia A Hubbard
- Computational, Analytical and Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Colin Kenyon
- Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town, 7505, South Africa
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Stefan Knapp
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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