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Zhang Q, Chen Y, Teng Z, Lin Z, Liu H. CDK11 facilitates centromeric transcription to maintain centromeric cohesion during mitosis. Mol Biol Cell 2024; 35:ar18. [PMID: 38019613 PMCID: PMC10881149 DOI: 10.1091/mbc.e23-08-0303] [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: 08/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Actively-transcribing RNA polymerase (RNAP)II is remained on centromeres to maintain centromeric cohesion during mitosis, although it is largely released from chromosome arms. This pool of RNAPII plays an important role in centromere functions. However, the mechanism of RNAPII retention on mitotic centromeres is poorly understood. We here demonstrate that Cyclin-dependent kinase (Cdk)11 is involved in RNAPII regulation on mitotic centromeres. Consistently, we show that Cdk11 knockdown induces centromeric cohesion defects and decreases Bub1 on kinetochores, but the centromeric cohesion defects are partially attributed to Bub1. Furthermore, Cdk11 knockdown and the expression of its kinase-dead version significantly reduce both RNAPII and elongating RNAPII (pSer2) levels on centromeres and decrease centromeric transcription. Importantly, the overexpression of centromeric α-satellite RNAs fully rescues Cdk11-knockdown defects. These results suggest that the maintenance of centromeric cohesion requires Cdk11-facilitated centromeric transcription. Mechanistically, Cdk11 localizes on centromeres where it binds and phosphorylates RNAPII to promote transcription. Remarkably, mitosis-specific degradation of G2/M Cdk11-p58 recapitulates Cdk11-knockdown defects. Altogether, our findings establish Cdk11 as an important regulator of centromeric transcription and as part of the mechanism for retaining RNAPII on centromeres during mitosis.
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Affiliation(s)
- Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Teng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA 70112
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2
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Sudhakaran M, Navarrete TG, Mejía-Guerra K, Mukundi E, Eubank TD, Grotewold E, Arango D, Doseff AI. Transcriptome reprogramming through alternative splicing triggered by apigenin drives cell death in triple-negative breast cancer. Cell Death Dis 2023; 14:824. [PMID: 38092740 PMCID: PMC10719380 DOI: 10.1038/s41419-023-06342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized by its aggressiveness and resistance to cancer-specific transcriptome alterations. Alternative splicing (AS) is a major contributor to the diversification of cancer-specific transcriptomes. The TNBC transcriptome landscape is characterized by aberrantly spliced isoforms that promote tumor growth and resistance, underscoring the need to identify approaches that reprogram AS circuitry towards transcriptomes, favoring a delay in tumorigenesis or responsiveness to therapy. We have previously shown that flavonoid apigenin is associated with splicing factors, including heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2). Here, we showed that apigenin reprograms TNBC-associated AS transcriptome-wide. The AS events affected by apigenin were statistically enriched in hnRNPA2 substrates. Comparative transcriptomic analyses of human TNBC tumors and non-tumor tissues showed that apigenin can switch cancer-associated alternative spliced isoforms (ASI) to those found in non-tumor tissues. Apigenin preferentially affects the splicing of anti-apoptotic and proliferation factors, which are uniquely observed in cancer cells, but not in non-tumor cells. Apigenin switches cancer-associated aberrant ASI in vivo in TNBC xenograft mice by diminishing proliferation and increasing pro-apoptotic ASI. In accordance with these findings, apigenin increased apoptosis and reduced tumor proliferation, thereby halting TNBC growth in vivo. Our results revealed that apigenin reprograms transcriptome-wide TNBC-specific AS, thereby inducing apoptosis and hindering tumor growth. These findings underscore the impactful effects of nutraceuticals in altering cancer transcriptomes, offering new options to influence outcomes in TNBC treatments.
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Affiliation(s)
- Meenakshi Sudhakaran
- Molecular, Cellular, and Integrative Physiology Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Eric Mukundi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Timothy D Eubank
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Daniel Arango
- Department of Pharmacology and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Andrea I Doseff
- Department of Physiology and Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
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3
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Wang C, Xu L, Du C, Yun H, Wang K, Liu H, Ye M, Fan J, Zhou Y, Cheng H. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. EMBO J 2023; 42:e114051. [PMID: 38059508 PMCID: PMC10711644 DOI: 10.15252/embj.2023114051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/08/2023] Open
Abstract
CDK11 is an emerging druggable target for cancer therapy due to its prevalent roles in phosphorylating critical transcription and splicing factors and in facilitating cell cycle progression in cancer cells. Like other cyclin-dependent kinases, CDK11 requires its cognate cyclin, cyclin L1 or cyclin L2, for activation. However, little is known about how CDK11 activities might be modulated by other regulators. In this study, we show that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, the latter of which is a poorly characterized factor. Acute degradation of SAP30BP mirrors that of CDK11 in causing widespread and strong defects in pre-mRNA splicing. Furthermore, we demonstrate that SAP30BP facilitates CDK11 kinase activities in vitro and in vivo, through ensuring the stabilities and the assembly of cyclins L1/L2 with CDK11. Together, these findings uncover SAP30BP as a critical CDK11 activator that regulates global pre-mRNA splicing.
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Affiliation(s)
- Changshou Wang
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Lin Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hao Yun
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Hui Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Jing Fan
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hong Cheng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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Kasprzak A. Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques. Cancers (Basel) 2023; 15:4570. [PMID: 37760539 PMCID: PMC10526446 DOI: 10.3390/cancers15184570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common and severe malignancies worldwide. Recent advances in diagnostic methods allow for more accurate identification and detection of several molecular biomarkers associated with this cancer. Nonetheless, non-invasive and effective prognostic and predictive testing in CRC patients remains challenging. Classical prognostic genetic markers comprise mutations in several genes (e.g., APC, KRAS/BRAF, TGF-β, and TP53). Furthermore, CIN and MSI serve as chromosomal markers, while epigenetic markers include CIMP and many other candidates such as SERP, p14, p16, LINE-1, and RASSF1A. The number of proliferation-related long non-coding RNAs (e.g., SNHG1, SNHG6, MALAT-1, CRNDE) and microRNAs (e.g., miR-20a, miR-21, miR-143, miR-145, miR-181a/b) that could serve as potential CRC markers has also steadily increased in recent years. Among the immunohistochemical (IHC) proliferative markers, the prognostic value regarding the patients' overall survival (OS) or disease-free survival (DFS) has been confirmed for thymidylate synthase (TS), cyclin B1, cyclin D1, proliferating cell nuclear antigen (PCNA), and Ki-67. In most cases, the overexpression of these markers in tissues was related to worse OS and DFS. However, slowly proliferating cells should also be considered in CRC therapy (especially radiotherapy) as they could represent a reservoir from which cells are recruited to replenish the rapidly proliferating population in response to cell-damaging factors. Considering the above, the aim of this article is to review the most common proliferative markers assessed using various methods including IHC and selected molecular biology techniques (e.g., qRT-PCR, in situ hybridization, RNA/DNA sequencing, next-generation sequencing) as prognostic and predictive markers in CRC.
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Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland
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7
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Li Y, Mo N, Yang D, Lin Q, Huang W, Wang R. Predictive value of DNA methylation in the efficacy of chemotherapy for gastric cancer. Front Oncol 2023; 13:1238310. [PMID: 37771430 PMCID: PMC10523571 DOI: 10.3389/fonc.2023.1238310] [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: 06/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Background Gastric cancer (GC) is one of the most common causes of cancer-related death. Drug resistance in chemotherapy often occurs in patients with GC, leading to tumor recurrence and poor survival. DNA methylation is closely related to the development of cancer. Methods To investigate the role of DNA methylation in chemotherapy resistance in GC patients, we conducted a comprehensive analysis using DNA methylation data and survival information obtained from The Cancer Genome Atlas. Univariate Cox analysis was performed to screen for differential DNA methylation of chemotherapy response in patients who did and did not receive chemotherapy. Multivariate Cox analysis was then performed to identify the independent prognostic genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to explore the biological function of the signature genes. Results Patients receiving adjuvant chemotherapy for GC survived longer. 308 differentially methylated genes were demonstrated to be associated with prognosis. Six genes were optimally chosed for establisehing the risk model, including C6orf222, CCNL1, CREBZF, GCKR, TFCP2, and VIPR2. It was constructed based on the DNA methylation levels of these six genes: risk score = 0.47123374*C6orf222 + 9.53554803*CCNL1 + 10.40234138* CREBZF + 0.07611856* GCKR + 18.87661557*TFCP2 - 0.46396254* VIPR2. According to the risk score, patients receiving chemotherapy were divided into high- and low-risk groups, and the prognosis of the two groups was compared. The high-risk group had a shorter survival; however, this association was not present in patients without chemotherapy. The accuracy and predictive efficacy of the risk score in predicting the 1-, 3-, and 5-year survival of patients was evaluated with the receiver operating characteristic curve. In patients receiving chemotherapy, the area under the curve of the risk score for 1-, 3-, and 5-year survival was 0.841, 0.72, and 0.734, respectively. In patients who did not receive chemotherapy, the area under the curve was 0.406, 0.585, and 0.585, respectively. A nomogram model was constructed based on the risk score and clinical indicators. The model showed good consistency in the predicted probabilities and actual probabilities. Gene Ontology functional enrichment of these candidate methylated genes showed the following molecular functions: RNA binding, protein binding, mRNA binding, and nucleic acid binding; that they were mediated mainly through the following cell components: nuclear speck, nucleoplasm, nucleus, catalytic step 2 spliceosome, and the transcription factor AP-1 complex; and that they were involved in the following biological processes: mRNA processing, mRNA splicing, and RNA polymerase II promoter transcription. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment results revealed that the signaling pathways mainly enriched were transcriptional misregulation in cancer, spliceosome, and the IL-17 signaling pathway. Conclusion Our work identifies a six DNA methylated expression signature as a promising biomarker of chemo-resistance in GC, which provides new insights into the development of new strategies to overcome chemo-resistance in GC.
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Affiliation(s)
- Ye Li
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ning Mo
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Dong Yang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Oncology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - QiuLu Lin
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - WenFeng Huang
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Rensheng Wang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Wang W, Liu W, Wang B. Identification of CDK gene family and functional analysis of CqCDK15 under drought and salt stress in quinoa. BMC Genomics 2023; 24:461. [PMID: 37592203 PMCID: PMC10433607 DOI: 10.1186/s12864-023-09570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
as one of the oldest cultivated crops in the world, quinoa has been widely valued for its rich nutritional value and green health. In this study, 22 CDK genes (CqCDK01-CqCDK22) were identified from quinoa genome using bioinformatics method. The number of amino acids was 173-811, the molecular weight was 19,554.89 Da-91,375.70 Da, and the isoelectric point was 4.57-9.77. The phylogenetic tree divided 21 CqCDK genes into six subfamilies, the gene structure showed that 12 (54.5%) CqCDK genes (CqCDK03, CqCDK04, CqCDK05, CqCDK06, CqCDK07, CqCDK11, CqCDK14, CqCDK16, CqCDK18, CqCDK19, CqCDK20 and CqCDK21) had UTR regions at 5' and 3' ends. Each CDK protein had different motifs (3-9 motifs), but the genes with the same motifs were located in the same branch. Promoter analysis revealed 41 cis-regulatory elements related to plant hormones, abiotic stresses, tissue-specific expression and photoresponse. The results of real-time fluorescence quantitative analysis showed that the expression level of some CDK genes was higher under drought and salt stress, which indicated that CDK genes could help plants to resist adverse environmental effects. Subcellular localization showed that CqCDK15 gene was localized to the nucleus and cytoplasm, and transgenic plants overexpressing CqCDK15 gene showed higher drought and salt tolerance compared to the controls. Therefore, CDK genes are closely related to quinoa stress resistance. In this study, the main functions of quinoa CDK gene family and its expression level in different tissues and organs were analyzed in detail, which provided some theoretical support for quinoa stress-resistant breeding. Meanwhile, this study has important implications for further understanding the function of the CDK gene family in quinoa and our understanding of the CDK family in vascular plant.
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Affiliation(s)
- Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of life science and technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wenyu Liu
- Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Baoqiang Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of life science and technology, Gansu Agricultural University, Lanzhou, 730070, China.
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Gong R, Gao X, Liu Y, Shen Y, Jiang Z, Wang X, Zagidullin N, Ma W, Wang N, Cai B. Cyclin L1 controls cardiomyocyte proliferation and heart repair after injury. Signal Transduct Target Ther 2023; 8:243. [PMID: 37339953 DOI: 10.1038/s41392-023-01444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/19/2023] [Accepted: 04/14/2023] [Indexed: 06/22/2023] Open
Affiliation(s)
- Rui Gong
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Xinlu Gao
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Yu Liu
- Department of Laboratory Medicine at The Fourth Affiliated Hospital, Harbin Medical University, 150086, Harbin, China
| | - Yifu Shen
- Department of Laboratory Medicine at The Fourth Affiliated Hospital, Harbin Medical University, 150086, Harbin, China
| | - Zuke Jiang
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Xiuxiu Wang
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Naufal Zagidullin
- Department of Internal Diseases, Bashkir State Medical University, Ufa, 450008, Russia
| | - Wenya Ma
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Ning Wang
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China
| | - Benzhi Cai
- Department of Pharmacy at The Second Affiliated Hospital, and Department of Pharmacology at College of Pharmacy (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, 150081, Harbin, China.
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Sharma VK, Campbell K, Yang X, Dale R, Loh YP. Characterization of serotonin-5-HTR1E signaling pathways and its role in cell survival. FASEB J 2023; 37:e22925. [PMID: 37078547 PMCID: PMC10259216 DOI: 10.1096/fj.202300128r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
5-Hydroxytryptamine receptor 1E (5-HTR1E) is reported to activate cyclic AMP (cAMP) and extracellular-signal related kinases (ERK) pathways via its ligands and binding partners, but the detailed mechanism underlying the serotonin-induced 5-HTR1E signaling is still not known. In the present study, we determined the cellular regulators of ERK and cAMP signaling pathways in response to serotonin-induced 5-HTR1E activation in 5-HTR1E overexpressing HEK293 cells. We found that Pertussis Toxin (PTX) treatment completely reversed the effect of serotonin-5-HTR1E mediated signaling on cAMP and ERK pathways, confirming the involvement of a Gαi-linked cascade. We also observed that Gβγ and Gq were not associated with 5-HTR1E activation, while blocking protein kinase A (PKA) inhibited ERK signaling only, and had no effect on cAMP. Additionally, serotonin-stimulated ERK1/2 phosphorylation was similar in 5-HTR1E overexpressing, β-arrestin-deficient HEK293 cells and is solely dependent on G protein signaling. siRNA mediated gene knockdown studies in SH-SY5Y cells revealed that the inhibition of 5-HTR1E reduced the expression of cMyc, Cyclin D1, Cyclin E and BCL2 genes which are related to cell cycle regulation and survival. MTT assays showed that 5-HTR1E knockdown in SHSY-5Y and U118 cells inhibited cell survival significantly. In addition to the signaling mechanism, we also performed RNA-seq analysis in 5-HTR1E overexpressing HEK293 cells and found that 5-HTR1E can regulate the expression of Receptor activity modifying protein 1 (RAMP1), Nuclear receptor 1 (NR4A1) and other Cyclin genes. These findings indicate that serotonin interaction with 5-HTR1E receptor simultaneously activates cAMP and ERK pathway in HEK293 cells and its expression is important for cell survival.
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Affiliation(s)
- Vinay Kumar Sharma
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiersten Campbell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuyu Yang
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Y. Peng Loh
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Blazek D. Therapeutic potential of CDK11 in cancer. Clin Transl Med 2023; 13:e1201. [PMID: 36855776 PMCID: PMC9975460 DOI: 10.1002/ctm2.1201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/23/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
Human cyclin-dependent kinases (CDKs) direct the progression of the cell cycle and transcription. They are deregulated in tumours, and despite their involvement in the regulation of basic cellular processes, many CDKs are promising targets for cancer therapy. CDK11 is an essential gene for the growth of many malignancies; however, its primary cellular function has been obscure, and the mode-of-action of OTS964, the first CDK11 inhibitor and antiproliferative compound, has been unknown. A recent study has shown that OTS964 prevents spliceosome activation, revealing a key role of CDK11 in the regulation of pre-mRNA splicing. In light of these findings, we discuss the therapeutic potential of CDK11 in cancer.
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Affiliation(s)
- Dalibor Blazek
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
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12
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Zhou K, Xiao J, Wang H, Ni B, Huang J, Long X. Estradiol regulates oxidative stress and angiogenesis of myocardial microvascular endothelial cells via the CDK1/CDK2 pathway. Heliyon 2023; 9:e14305. [PMID: 36942258 PMCID: PMC10023923 DOI: 10.1016/j.heliyon.2023.e14305] [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: 09/01/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Cardiovascular diseases remain the leading cause of death, morbidity, and disability. Recently, it has been reported that gonadal hormones such as estradiol can act on membrane receptors and activate intracellular signaling mechanisms, thereby altering cellular function. This study aims to explore the function and molecular mechanism of estradiol on cardiac microvascular endothelial cells (CMVECs). Estradiol had low toxicity to CMVECs. Hypoxia/reoxygenation (H/R) stimulation inhibited the proliferation and migration of CMVECs, while estradiol significantly promoted proliferation and migration. Estradiol inhibited il-1, IL6, and TNF-α secretion levels after H/R stimulation. Meanwhile, estradiol inhibits oxidative stress and promotes angiogenesis. Further, estradiol upregulated the gene and protein levels of cyclin-dependent kinases 1 (CDK1) and CDK2 after H/R stimulation. When knocking down CDK1 and CDK2 of CMVECs, estradiol did not affect the protein expression of Cyclin E1 and Cyclin D1. Meanwhile, the regulatory effect of estradiol on oxidative stress, angiogenesis, and inflammatory response was significantly weakened or even disappeared. In conclusion, estradiol mediates oxidative stress and angiogenesis of myocardial microvascular endothelial cells by regulating the CDK/cyclin signaling pathway.
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Affiliation(s)
- Ke Zhou
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Jun Xiao
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
- Corresponding author.
| | - Hao Wang
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Bing Ni
- Institute of Immunology of Army Medical University, Chongqing, 400014, China
| | - Jietao Huang
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Xueyuan Long
- Vasculocardiology Department, Chongqing University Central Hospital, Chongqing, 400014, China
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13
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Hope I, Endicott JA, Watt JE. Emerging approaches to CDK inhibitor development, a structural perspective. RSC Chem Biol 2023; 4:146-164. [PMID: 36794018 PMCID: PMC9906319 DOI: 10.1039/d2cb00201a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of the cyclin-dependent kinase family is frequently noted in a number of diseases identifying them as potential targets for drug development. However, current CDK inhibitors lack specificity owing to the high sequence and structural conservation of the ATP binding cleft across family members, highlighting the necessity of finding novel modes of CDK inhibition. The wealth of structural information regarding CDK assemblies and inhibitor complexes derived from X-ray crystallographic studies has been recently complemented through the use of cryo-electron microscopy. These recent advances have provided insights into the functional roles and regulatory mechanisms of CDKs and their interaction partners. This review explores the conformational malleability of the CDK subunit, the importance of SLiM recognition sites in CDK complexes, the progress made in chemically induced CDK degradation and how these studies can contribute to CDK inhibitor design. Additionally, fragment-based drug discovery can be utilised to identify small molecules that bind to allosteric sites on the CDK surface employing interactions which mimic those of native protein-protein interactions. These recent structural advances in CDK inhibitor mechanisms and in chemical probes which do not occupy the orthosteric ATP binding site can provide important insights for targeted CDK therapies.
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Affiliation(s)
- Ian Hope
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jessica E Watt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
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14
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D'costa M, Bothe A, Das S, Udhaya Kumar S, Gnanasambandan R, George Priya Doss C. CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:125-177. [PMID: 37061330 DOI: 10.1016/bs.apcsb.2022.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
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Affiliation(s)
- Maria D'costa
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Anusha Bothe
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Gnanasambandan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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15
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O'Brien S, Kelso S, Steinhart Z, Orlicky S, Mis M, Kim Y, Lin S, Sicheri F, Angers S. SCF FBXW7 regulates G2-M progression through control of CCNL1 ubiquitination. EMBO Rep 2022; 23:e55044. [PMID: 36278408 PMCID: PMC9724663 DOI: 10.15252/embr.202255044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
FBXW7, which encodes a substrate-specific receptor of an SCF E3 ligase complex, is a frequently mutated human tumor suppressor gene known to regulate the post-translational stability of various proteins involved in cellular proliferation. Here, using genome-wide CRISPR screens, we report a novel synthetic lethal genetic interaction between FBXW7 and CCNL1 and describe CCNL1 as a new substrate of the SCF-FBXW7 E3 ligase. Further analysis showed that the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle since defective CCNL1 accumulation, resulting from FBXW7 mutation, leads to shorter mitotic time. Cells harboring FBXW7 loss-of-function mutations are hypersensitive to treatment with a CDK11 inhibitor, highlighting a genetic vulnerability that could be leveraged for cancer treatment.
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Affiliation(s)
- Siobhan O'Brien
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
| | - Susan Kelso
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Zachary Steinhart
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
- Present address:
Gladstone InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Stephen Orlicky
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Monika Mis
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
- Present address:
GenentechSouth San FranciscoCAUSA
| | - Yunhye Kim
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
| | - Sichun Lin
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
| | - Frank Sicheri
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Stephane Angers
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
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16
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Plasmodium falciparum CRK5 Is Critical for Male Gametogenesis and Infection of the Mosquito. mBio 2022; 13:e0222722. [PMID: 36154191 PMCID: PMC9600428 DOI: 10.1128/mbio.02227-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) and cyclins are critical cell cycle regulators in eukaryotes. In this study, we functionally characterized a CDK-related kinase (CRK5) of the human malaria parasite Plasmodium falciparum. P. falciparum CRK5 (PfCRK5) was expressed in asexual blood stages and sexual gametocyte stages, but showed male gametocyte- specific expression. In contrast to previous findings, we showed that gene deletion Pfcrk5− parasites grew normally as asexual stages and underwent normal gametocytogenesis to stage V gametocytes. However, Pfcrk5− parasites showed a severe defect in male gametogenesis, which was evident by a significant reduction in the emergence of male gametes (exflagellation). This defect caused a severe reduction of parasite transmission to the mosquito. Genetic crosses performed using sex-specific sterile transgenic parasites revealed that Pfcrk5− parasites suffered a defect in male fertility but female gametes were fertile. Taken together, these results demonstrate that PfCRK5 is a critical sexual stage kinase which regulates male gametogenesis and transmission to the mosquito.
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17
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Trembley JH, Kren BT, Afzal M, Scaria GA, Klein MA, Ahmed K. Protein kinase CK2 – diverse roles in cancer cell biology and therapeutic promise. Mol Cell Biochem 2022; 478:899-926. [PMID: 36114992 PMCID: PMC9483426 DOI: 10.1007/s11010-022-04558-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022]
Abstract
The association of protein kinase CK2 (formerly casein kinase II or 2) with cell growth and proliferation in cells was apparent at early stages of its investigation. A cancer-specific role for CK2 remained unclear until it was determined that CK2 was also a potent suppressor of cell death (apoptosis); the latter characteristic differentiated its function in normal versus malignant cells because dysregulation of both cell growth and cell death is a universal feature of cancer cells. Over time, it became evident that CK2 exerts its influence on a diverse range of cell functions in normal as well as in transformed cells. As such, CK2 and its substrates are localized in various compartments of the cell. The dysregulation of CK2 is documented in a wide range of malignancies; notably, by increased CK2 protein and activity levels with relatively moderate change in its RNA abundance. High levels of CK2 are associated with poor prognosis in multiple cancer types, and CK2 is a target for active research and testing for cancer therapy. Aspects of CK2 cellular roles and targeting in cancer are discussed in the present review, with focus on nuclear and mitochondrial functions and prostate, breast and head and neck malignancies.
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Affiliation(s)
- Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA.
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Betsy T Kren
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
| | - Muhammad Afzal
- Department of Biochemistry, Riphah International University, Islamabad, Pakistan
| | - George A Scaria
- Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
| | - Mark A Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Khalil Ahmed
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA.
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Urology, University of Minnesota, Minneapolis, MN, 55455, USA.
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18
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Li Z, Ishida R, Liu Y, Wang J, Li Y, Gao Y, Jiang J, Che J, Sheltzer JM, Robers MB, Zhang T, Westover KD, Nabet B, Gray NS. Synthesis and Structure-Activity relationships of cyclin-dependent kinase 11 inhibitors based on a diaminothiazole scaffold. Eur J Med Chem 2022; 238:114433. [PMID: 35597007 PMCID: PMC9477540 DOI: 10.1016/j.ejmech.2022.114433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022]
Abstract
Cyclin-dependent kinases (CDK) are attractive targets for drug discovery due to their wide range of cellular functions. CDK11 is an understudied CDK with roles in transcription and splicing, cell cycle regulation, neuronal function, and apoptosis. In this study, we describe a medicinal chemistry campaign to identify a CDK11 inhibitor. Employing a promising but nonselective CDK11-targeting scaffold (JWD-047), extensive structure-guided medicinal chemistry modifications led to the identification of ZNL-05-044. A combination of biochemical evaluations and NanoBRET cellular assays for target engagement guided the SAR towards a 2,4-diaminothiazoles CDK11 probe with significantly improved kinome-wide selectivity over JWD-047. CDK11 inhibition with ZNL-05-044 leads to G2/M cell cycle arrest, consistent with prior work evaluating OTS964, and impacts CDK11-dependent mRNA splicing in cells. Together, ZNL-05-044 serves as a tool compound for further optimization and interrogation of the consequences of CDK11 inhibition.
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Affiliation(s)
- Zhengnian Li
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Ryosuke Ishida
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Yan Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yina Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yang Gao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | - Tinghu Zhang
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Kenneth D Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nathanael S Gray
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA.
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19
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Peng S, Guo D, Guo Y, Zhao H, Mei J, Han Y, Guan R, Wang T, Song T, Sun K, Liu Y, Mao T, Chang H, Xue J, Cai Y, Chen D, Wang S. CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 is an RNA-binding protein controlling plant immunity via an RNA processing complex. THE PLANT CELL 2022; 34:1724-1744. [PMID: 35137215 PMCID: PMC9048907 DOI: 10.1093/plcell/koac037] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/27/2022] [Indexed: 06/01/2023]
Abstract
Plant innate immunity is capable of combating diverse and ever evolving pathogens. The plasticity of innate immunity could be boosted by RNA processing. Arabidopsis thaliana CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 (CPR5), a key negative immune regulator, is a component of the nuclear pore complex. Here we further identified CPR5 as a component of RNA processing complexes. Through genetic screening, we found that RNA splicing activator NineTeen Complex and RNA polyadenylation factor CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, coordinately function downstream of CPR5 to activate plant immunity. CPR5 and these two regulators form a complex that is localized in nuclear speckles, an RNA processing organelle. Intriguingly, we found that CPR5 is an RNA-binding protein belonging to the Transformer 2 (Tra2) subfamily of the serine/arginine-rich family. The RNA recognition motif of CPR5 protein binds the Tra2-targeted RNA sequence in vitro and is functionally replaceable by those of Tra2 subfamily proteins. In planta, it binds RNAs of CPR5-regulated alternatively spliced genes (ASGs) identified by RNA-seq. ARGONAUTE 1 (AGO1) is one of the ASGs and, consistent with this, the ago1 mutant suppresses the cpr5 phenotype. These findings reveal that CPR5 is an RNA-binding protein linking RNA processing with plant immunity.
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Affiliation(s)
| | | | | | - Heyu Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jun Mei
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yakun Han
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Rui Guan
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tianhua Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Teng Song
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Keke Sun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yunhan Liu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ting Mao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Huan Chang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingshi Xue
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Hubei, Wuhan 430075, China
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20
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Zhang L, Ye B, Lin Y, Li YD, Wang JQ, Chen Z, Ping FF, Chen ZS. Ribociclib Inhibits P-gp-Mediated Multidrug Resistance in Human Epidermoid Carcinoma Cells. Front Pharmacol 2022; 13:867128. [PMID: 35450042 PMCID: PMC9016416 DOI: 10.3389/fphar.2022.867128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
The efficacy of cancer chemotherapy can be attenuated or abrogated by multidrug resistance (MDR) in cancer cells. In this study, we determined the effect of the CDK4/6 inhibitor, ribociclib (or LEE011), on P-glycoprotein (P-gp)-mediated MDR in the human epidermoid carcinoma MDR cell line, KB-C2, which is widely used for studying P-gp-mediated MDR in cancers. The incubation of KB-C2 cells with ribociclib (3–9 µM) increased the efficacy of colchicine, a substrate for P-gp. The cell expression of P-gp was down-regulated at both translation and transcription levels. Furthermore, ribociclib produced a 3.5-fold increase in the basal activity of P-gp ATPase, and the concentration required to increase basal activity by 50% (EC50) was 0.04 μM. Docking studies indicated that ribociclib interacted with the drug-substrate binding site of P-gp. The short-term and long-term intracellular accumulation of doxorubicin greatly increased in the KB-C2 cells co-cultured with ribociclib, indicating ribociclib inhibited the drug efflux activity of P-gp. The results of our study indicate that LEE011 may be a potential agent for combined therapy of the cancers with P-gp mediated MDR.
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Affiliation(s)
- Lei Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Biwei Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunfeng Lin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Dong Li
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng-Feng Ping
- Department of Reproductive Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
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21
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Zhang L, Li Y, Hu C, Chen Y, Chen Z, Chen ZS, Zhang JY, Fang S. CDK6-PI3K signaling axis is an efficient target for attenuating ABCB1/P-gp mediated multi-drug resistance (MDR) in cancer cells. Mol Cancer 2022; 21:103. [PMID: 35459184 PMCID: PMC9027122 DOI: 10.1186/s12943-022-01524-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Multidrug resistance (MDR) mediated by ATP binding cassette subfamily B member 1 (ABCB1/P-gp) is a major cause of cancer chemotherapy failure, but the regulation mechanisms are largely unknown. METHODS Based on single gene knockout, we studied the regulation of CDK6-PI3K axis on ABCB1-mediated MDR in human cancer cells. CRISPR/Cas9 technique was performed in KB-C2 cells to knockout cdk6 or cdk4 gene. Western blot, RT-PCR and transcriptome analysis were performed to investigate target gene deletion and expression of critical signaling factors. The effect of cdk4 or cdk6 deficiency on cell apoptosis and the cell cycle was analyzed using flow cytometry. In vivo studies were performed to study the sensitivity of KB-C2 tumors to doxorubicin, tumor growth and metastasis. RESULTS Deficiency of cdk6 led to remarkable downregulation of ABCB1 expression and reversal of ABCB1-mediated MDR. Transcriptomic analysis revealed that CDK6 knockout regulated a series of signaling factors, among them, PI3K 110α and 110β, KRAS and MAPK10 were downregulated, and FOS-promoting cell autophagy and CXCL1-regulating multiple factors were upregulated. Notably, PI3K 110α/110β deficiency in-return downregulated CDK6 and the CDK6-PI3K axis synergizes in regulating ABCB1 expression, which strengthened the regulation of ABCB1 over single regulation by either CDK6 or PI3K 110α/110β. High frequency of alternative splicing (AS) of premature ABCB1 mRNA induced by CDK6, CDK4 or PI3K 110α/110β level change was confirmed to alter the ABCB1 level, among them 10 common skipped exon (SE) events were found. In vivo experiments demonstrated that loss of cdk6 remarkably increased the sensitivity of KB-C2 tumors to doxorubicin by increasing drug accumulation of the tumors, resulting in remarkable inhibition of tumor growth and metastasis, as well as KB-C2 survival in the nude mice. CONCLUSIONS CDK6-PI3K as a new target signaling axis to reverse ABCB1-mediated MDR is reported for the first time in cancers. Pathways leading to inhibition of cancer cell proliferation were revealed to be accompanied by CDK6 deficiency.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China. .,College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yidong Li
- College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA
| | - Chaohua Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yangmin Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, New York, 11439, USA
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Shuo Fang
- The department of clinical oncology, Guangdong Provincial Key Laboratory of Digestive Cancer Research, Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
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22
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Taniguchi-Ponciano K, Portocarrero-Ortiz LA, Guinto G, Moreno-Jimenez S, Gomez-Apo E, Chavez-Macias L, Peña-Martínez E, Silva-Román G, Vela-Patiño S, Ordoñez-García J, Andonegui-Elguera S, Ferreira-Hermosillo A, Ramirez-Renteria C, Espinosa-Cardenas E, Sosa E, Espinosa-de-Los-Monteros AL, Salame-Khouri L, Perez C, Lopez-Felix B, Vargas-Ortega G, Gonzalez-Virla B, Lisbona-Buzali M, Marrero-Rodríguez D, Mercado M. The kinome, cyclins and cyclin-dependent kinases of pituitary adenomas, a look into the gene expression profile among tumors from different lineages. BMC Med Genomics 2022; 15:52. [PMID: 35260162 PMCID: PMC8905767 DOI: 10.1186/s12920-022-01206-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Background Pituitary adenomas (PA) are the second most common intracranial tumors and are classified according to hormone they produce, and the transcription factors they express. The majority of PA occur sporadically, and their molecular pathogenesis is incompletely understood. Methods Here we performed transcriptome and proteome analysis of tumors derived from POU1F1 (GH-, TSH-, and PRL-tumors, N = 16), NR5A1 (gonadotropes and null cells adenomas, n = 17) and TBX19 (ACTH-tumors, n = 6) lineages as well as from silent ACTH-tumors (n = 3) to determine expression of kinases, cyclins, CDKs and CDK inhibitors. Results The expression profiles of genes encoding kinases were distinctive for each of the three PA lineage: NR5A1-derived tumors showed upregulation of ETNK2 and PIK3C2G and alterations in MAPK, ErbB and RAS signaling, POU1F1-derived adenomas showed upregulation of PIP5K1B and NEK10 and alterations in phosphatidylinositol, insulin and phospholipase D signaling pathways and TBX19-derived adenomas showed upregulation of MERTK and STK17B and alterations in VEGFA-VEGFR, EGF-EGFR and Insulin signaling pathways. In contrast, the expression of the different genes encoding cyclins, CDK and CDK inhibitors among NR5A1-, POU1F1- and TBX19-adenomas showed only subtle differences. CDK9 and CDK18 were upregulated in NR5A1-adenomas, whereas CDK4 and CDK7 were upregulated in POUF1-adenomas. Conclusions The kinome of PA clusters these lesions into three distinct groups according to the transcription factor that drives their terminal differentiation. And these complexes could be harnessed as molecular therapy targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01206-y.
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Affiliation(s)
- Keiko Taniguchi-Ponciano
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | | | | | - Sergio Moreno-Jimenez
- Instituto Nacional de Neurología Y Neurocirugía "Manuel Velasco Suarez", Mexico, Mexico.,Centro Neurológico, Centro Medico ABC, Mexico, Mexico
| | - Erick Gomez-Apo
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México Dr. Eduardo Liceaga, Mexico, Mexico
| | - Laura Chavez-Macias
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México Dr. Eduardo Liceaga, Mexico, Mexico.,Facultad de Medicina, Universidad Nacional Autonoma de México, Mexico, Mexico
| | - Eduardo Peña-Martínez
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Gloria Silva-Román
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Sandra Vela-Patiño
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Jesús Ordoñez-García
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Sergio Andonegui-Elguera
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Aldo Ferreira-Hermosillo
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico.,Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Claudia Ramirez-Renteria
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico.,Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Etual Espinosa-Cardenas
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Ernesto Sosa
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Ana Laura Espinosa-de-Los-Monteros
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Latife Salame-Khouri
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Carolina Perez
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Blas Lopez-Felix
- Servicio de Neurocirugia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Guadalupe Vargas-Ortega
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Baldomero Gonzalez-Virla
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Marcos Lisbona-Buzali
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico
| | - Daniel Marrero-Rodríguez
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico.
| | - Moisés Mercado
- CONACyT-Unidad de Investigación Médica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, D.F. 06720, Mexico, Mexico.
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23
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Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022; 50:283-295. [PMID: 35166324 DOI: 10.1042/bst20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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24
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Z-Guggulsterone alleviates renal fibrosis by mitigating G2/M cycle arrest through Klotho/p53 signaling. Chem Biol Interact 2022; 354:109846. [DOI: 10.1016/j.cbi.2022.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/19/2022]
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25
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Naro C, Bielli P, Sette C. Oncogenic dysregulation of pre-mRNA processing by protein kinases: challenges and therapeutic opportunities. FEBS J 2021; 288:6250-6272. [PMID: 34092037 PMCID: PMC8596628 DOI: 10.1111/febs.16057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/13/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing and polyadenylation represent two major steps in pre-mRNA-processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes contributes to oncogenic programmes involved in the onset, progression and evolution of human cancers, which often result in the acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA-processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA-processing mechanisms is played by three main families of protein kinases: serine arginine protein kinase (SRPK), CDC-like kinase (CLK) and cyclin-dependent kinase (CDK). These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells, and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.
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Affiliation(s)
- Chiara Naro
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Pamela Bielli
- Department of Biomedicine and PreventionUniversity of Rome Tor VergataItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| | - Claudio Sette
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Santa LuciaIRCCSRomeItaly
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26
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Parrish PCR, Thomas JD, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH. Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome. Cell Rep 2021; 36:109597. [PMID: 34469736 PMCID: PMC8534300 DOI: 10.1016/j.celrep.2021.109597] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/26/2023] Open
Abstract
CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single-gene knockout phenotypes can be masked by redundancy among related genes. Paralogs constitute two-thirds of the human protein-coding genome, so existing methods are likely inadequate for assaying a large portion of gene function. Here, we develop paired guide RNAs for paralog genetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single- and double-knockout approach targeting more than 2,000 human paralogs. We apply pgPEN to two cell types and discover that 12% of human paralogs exhibit synthetic lethality in at least one context. We recover known synthetic lethal paralogs MEK1/MEK2, important drug targets CDK4/CDK6, and other synthetic lethal pairs including CCNL1/CCNL2. Additionally, we identify ten tumor suppressor paralog pairs whose compound loss promotes cell proliferation. These findings nominate drug targets and suggest that paralog genetic interactions could shape the landscape of positive and negative selection in cancer.
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Affiliation(s)
- Phoebe C R Parrish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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27
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Ottesen EW, Luo D, Singh NN, Singh RN. High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. Int J Mol Sci 2021; 22:ijms22168378. [PMID: 34445083 PMCID: PMC8395096 DOI: 10.3390/ijms22168378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/17/2022] Open
Abstract
Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.
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28
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Koliopoulos MG, Alfieri C. Cell cycle regulation by complex nanomachines. FEBS J 2021; 289:5100-5120. [PMID: 34143558 DOI: 10.1111/febs.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The cell cycle is the essential biological process where one cell replicates its genome and segregates the resulting two copies into the daughter cells during mitosis. Several aspects of this process have fascinated humans since the nineteenth century. Today, the cell cycle is exhaustively investigated because of its profound connections with human diseases and cancer. At the heart of the molecular network controlling the cell cycle, we find the cyclin-dependent kinases (CDKs) acting as an oscillator to impose an orderly and highly regulated progression through the different cell cycle phases. This oscillator integrates both internal and external signals via a multitude of signalling pathways involving posttranslational modifications including phosphorylation, protein ubiquitination and mechanisms of transcriptional regulation. These tasks are specifically performed by multi-subunit complexes, which are intensively studied both biochemically and structurally with the aim to unveil mechanistic insights into their molecular function. The scope of this review is to summarise the structural biology of the cell cycle machinery, with specific focus on the core cell cycle machinery involving the CDK-cyclin oscillator. We highlight the contribution of cryo-electron microscopy, which has started to revolutionise our understanding of the molecular function and dynamics of the key players of the cell cycle.
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Affiliation(s)
- Marios G Koliopoulos
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
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29
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Etman AM, Abdel Mageed SS, Ali MA, El Hassab MAEM. Cyclin-Dependent Kinase as a Novel Therapeutic Target: An Endless Story. CURRENT CHEMICAL BIOLOGY 2021; 15:139-162. [DOI: 10.2174/2212796814999201123194016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 09/02/2023]
Abstract
Cyclin-Dependent Kinases (CDKs) are a family of enzymes that, along with their Cyclin
partners, play a crucial role in cell cycle regulation at many biological functions such as proliferation,
differentiation, DNA repair, and apoptosis. Thus, they are tightly regulated by a number of inhibitory
and activating enzymes. Deregulation of these kinases’ activity either by amplification,
overexpression or mutation of CDKs or Cyclins leads to uncontrolled proliferation of cancer cells.
Hyperactivity of these kinases has been reported in a wide variety of human cancers. Hence, CDKs
have been established as one of the most attractive pharmacological targets in the development of
promising anticancer drugs. The elucidated structural features and the well-characterized molecular
mechanisms of CDKs have been the guide in designing inhibitors to these kinases. Yet, they remain
a challenging therapeutic class as they share conserved structure similarity in their active site.
Several inhibitors have been discovered from natural sources or identified through high throughput
screening and rational drug design approaches. Most of these inhibitors target the ATP binding
pocket, therefore, they suffer from a number of limitations. Here, a growing number of ATP noncompetitive
peptides and small molecules has been reported.
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Affiliation(s)
- Ahmed Mohamed Etman
- Department of Pharmacology, Faculty of Pharmacy, Tanta University, Tanta, 31111,Egypt
| | - Sherif Sabry Abdel Mageed
- Department of Pharmacology, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
| | - Mohamed Ahmed Ali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
| | - Mahmoud Abd El Monem El Hassab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
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30
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Cheng J, Nie D, Li B, Gui S, Li C, Zhang Y, Zhao P. CircNFIX promotes progression of pituitary adenoma via CCNB1 by sponging miR-34a -5p. Mol Cell Endocrinol 2021; 525:111140. [PMID: 33359304 DOI: 10.1016/j.mce.2020.111140] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Previous studies have shown that CCNB1 affects the invasiveness of pituitary adenomas, and it is of great significance to find the upstream mechanism of regulating CCNB1.In this study, we explored a significantly overexpressed circRNA in invasive pituitary adenomas. Based on bioinformatics analysis and mechanism experiments, we determined that circNFIX (has-circ_0005660) affects cell invasion, migration and proliferation in pituitary adenomas by sponging miR-34a-5p through CCNB1. In pituitary adenoma tissues, the expression of circNFIX and CCNB1 was upregulated, while miR-34a-5p expression was downregulated. The silencing of circNFIX or overexpression of miR-34a-5p inhibited cell invasion, migration and proliferation. Inhibition of miR-34a-5p expression reversed the inhibitory effect of circNFIX silencing on the progression of pituitary adenoma. In conclusion, CircNFIX affects cell invasion, migration, and proliferation in pituitary adenomas by sponging miR-34a-5p through CCNB1. Therefore, circNFIX is expected to serve as a potential target for the treatment of pituitary adenomas.
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Affiliation(s)
- Jianhua Cheng
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Ding Nie
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Bin Li
- Department of Cell and Biology, Beijing Neurosurgical Institute, Beijing, 100070, China
| | - SongBai Gui
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - ChuZhong Li
- Department of Cell and Biology, Beijing Neurosurgical Institute, Beijing, 100070, China
| | - YaZhuo Zhang
- Department of Cell and Biology, Beijing Neurosurgical Institute, Beijing, 100070, China
| | - Peng Zhao
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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31
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Zhang C, Zhang X, Gong Y, Li T, Yang L, Xu W, Dong L. Role of the lncRNA-mRNA network in atherosclerosis using ox-low-density lipoprotein-induced macrophage-derived foam cells. Mol Omics 2020; 16:543-553. [PMID: 32915179 DOI: 10.1039/d0mo00077a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Atherosclerosis (AS) is the leading cause of coronary heart disease, cerebral infarction, peripheral vascular disease, and other cardiovascular diseases, making it a major risk factor for high morbidity and mortality. Although long non-coding RNAs (lncRNAs) have been reported to play a role in AS, the specific effects of lncRNAs on AS remain largely unknown. Thus the purpose of this study was to explore the roles of mRNAs and lncRNAs in atherosclerosis via an ox-low-density lipoprotein induced macrophage-derived foam cell model. Microarray analysis identified a total of 50 688 mRNAs and 1514 lncRNAs, including 51 lncRNAs and 1730 mRNAs that were significantly dysregulated in the model group (p-adjust < 0.05 and |log 2FC| > 2). The results of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses demonstrated that the dysregulated genes were associated with cell proliferation, cell apoptosis, and inflammatory responses. An lncRNA-mRNA co-expression network was created to further analyze the key regulatory genes. The lncRNAs Brip1os, Gm16586, AU020206, 9430034N14Rik, 2510016D11Rik, LNC_000709, Gm15472, Gm20703, and Dubr were identified as potential biomarkers in macrophage-derived foam cells. Based on 9 lncRNAs and 13 mRNAs, key genes influencing the degree of cell proliferation and cell apoptosis and the subsequent development of AS were identified. Q-PCR verified the key dysregulated genes. Thus, our results suggest potential therapeutic targets for AS and provide avenues for further research on AS pathogenesis.
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Affiliation(s)
- Caijuan Zhang
- School of Life Science, Beijing University of Chinese Medicine, Northeast Corner of Intersection of Sunshine South Street and Baiyang East Road, Fang-Shan District, Beijing, 102488, China.
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