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Luo Y, Li Y, Ge P, Zhang K, Liu H, Jiang N. QKI-Regulated Alternative Splicing Events in Cervical Cancer: Pivotal Mechanism and Potential Therapeutic Strategy. DNA Cell Biol 2021; 40:1261-1277. [PMID: 34551268 DOI: 10.1089/dna.2021.0069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
QKI is a vital regulator in RNA splicing and maturation, but its role in cervical cancer (CC) is little known. In this study, we found that QKI is decreased in human CC, and overexpression of QKI inhibits HeLa cell proliferation and promotes the apoptosis of cancer cells. We identified hundreds of endogenous QKI-regulated alternative splicing events (ASEs) and differentially expressed genes (DEGs) in QKI-overexpressed HeLa cells by RNA-seq and selectively validated their expression by quantitative reverse-transcription polymerase chain reaction. The gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that QKI-regulated ASEs and DEGs were closely related to cancer, apoptosis, and transcriptional regulatory functions. In short, QKI may affect the occurrence and development of CC by regulating gene expression through AS.
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Affiliation(s)
- Yalan Luo
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Yuyuan Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Peng Ge
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Kaina Zhang
- Department of Gynecology and Obstetrics, Central Hospital of Zhuanghe City, Zhuanghe, China
| | - Huanhuan Liu
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Nan Jiang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital, Dalian Medical University, Dalian, China
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The Structural Biology of Bcl-x L. Int J Mol Sci 2019; 20:ijms20092234. [PMID: 31067648 PMCID: PMC6540150 DOI: 10.3390/ijms20092234] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/12/2023] Open
Abstract
Interactions between the pro-survival and pro-apoptotic members of the Bcl-2 family of proteins dictate whether a cell lives or dies. Much of our knowledge of the molecular details of these interactions has come from biochemical and structural studies on the pro-survival protein Bcl-xL. The first high-resolution structure of any Bcl-2 family member was of Bcl-xL, which revealed the conserved topology amongst all family members. Subsequent structures of Bcl-xL complexes with pro-apoptotic ligands demonstrated the general features of all pro-survival:pro-apoptotic complexes. Structural studies involving Bcl-xL were also the basis for the discovery of the first small-molecule pro-survival protein inhibitors, leading ultimately to the development of a new class of drugs now successfully used for cancer treatment in the clinic. This article will review our current knowledge of the structural biology of Bcl-xL and how this has impacted our understanding of the molecular details of the intrinsic apoptotic pathway.
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Ivanov SM, Cawley A, Huber RG, Bond PJ, Warwicker J. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PLoS One 2017; 12:e0185928. [PMID: 29016650 PMCID: PMC5634604 DOI: 10.1371/journal.pone.0185928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/21/2017] [Indexed: 12/05/2022] Open
Abstract
An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.
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Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Andrew Cawley
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- * E-mail:
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Abstract
High-resolution protein structures determined by X-ray crystallography or NMR have proven invaluable for deciphering the molecular mechanisms underlying the function of a vast range of proteins. Here, we describe methods to generate complexes of proteins belonging to the Bcl-2 family of proteins with either biological ligands or small molecule antagonists.
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Affiliation(s)
- Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Physical Sciences 4, Room 205, Kingsbury Drive, Bundoora, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.
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Sarkar S, Jain S, Rai V, Sahoo DK, Raha S, Suklabaidya S, Senapati S, Rangnekar VM, Maiti IB, Dey N. Plant-derived SAC domain of PAR-4 (Prostate Apoptosis Response 4) exhibits growth inhibitory effects in prostate cancer cells. FRONTIERS IN PLANT SCIENCE 2015; 6:822. [PMID: 26500666 PMCID: PMC4595782 DOI: 10.3389/fpls.2015.00822] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/22/2015] [Indexed: 05/10/2023]
Abstract
The gene Par-4 (Prostate Apoptosis Response 4) was originally identified in prostate cancer cells undergoing apoptosis and its product Par-4 showed cancer specific pro-apoptotic activity. Particularly, the SAC domain of Par-4 (SAC-Par-4) selectively kills cancer cells leaving normal cells unaffected. The therapeutic significance of bioactive SAC-Par-4 is enormous in cancer biology; however, its large scale production is still a matter of concern. Here we report the production of SAC-Par-4-GFP fusion protein coupled to translational enhancer sequence (5' AMV) and apoplast signal peptide (aTP) in transgenic Nicotiana tabacum cv. Samsun NN plants under the control of a unique recombinant promoter M24. Transgene integration was confirmed by genomic DNA PCR, Southern and Northern blotting, Real-time PCR, and Nuclear run-on assays. Results of Western blot analysis and ELISA confirmed expression of recombinant SAC-Par-4-GFP protein and it was as high as 0.15% of total soluble protein. In addition, we found that targeting of plant recombinant SAC-Par-4-GFP to the apoplast and endoplasmic reticulum (ER) was essential for the stability of plant recombinant protein in comparison to the bacterial derived SAC-Par-4. Deglycosylation analysis demonstrated that ER-targeted SAC-Par-4-GFP-SEKDEL undergoes O-linked glycosylation unlike apoplast-targeted SAC-Par-4-GFP. Furthermore, various in vitro studies like mammalian cells proliferation assay (MTT), apoptosis induction assays, and NF-κB suppression suggested the cytotoxic and apoptotic properties of plant-derived SAC-Par-4-GFP against multiple prostate cancer cell lines. Additionally, pre-treatment of MAT-LyLu prostate cancer cells with purified SAC-Par-4-GFP significantly delayed the onset of tumor in a syngeneic rat prostate cancer model. Taken altogether, we proclaim that plant made SAC-Par-4 may become a useful alternate therapy for effectively alleviating cancer in the new era.
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Affiliation(s)
- Shayan Sarkar
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Sumeet Jain
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
- Manipal UniversityManipal, India
| | - Vineeta Rai
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Dipak K. Sahoo
- Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, LexingtonKY, USA
- Department of Agronomy, Iowa State University, AmesIA, USA
| | - Sumita Raha
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, ChicagoIL, USA
| | - Sujit Suklabaidya
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Shantibhusan Senapati
- Department of Translational Research and Technology Development, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
| | - Vivek M. Rangnekar
- Department of Radiation Medicine, Markey Cancer Center, University of Kentucky, LexingtonKY, USA
| | - Indu B. Maiti
- Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, LexingtonKY, USA
- *Correspondence: Nrisingha Dey, Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of India, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha-751 023, India, ; Indu B. Maiti, Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA,
| | - Nrisingha Dey
- Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of IndiaBhubaneswar, India
- *Correspondence: Nrisingha Dey, Department of Gene Function and Regulation, Institute of Life Sciences, Department of Biotechnology, Government of India, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha-751 023, India, ; Indu B. Maiti, Kentucky Tobacco Research & Development Center, Plant Genetic Engineering Research and Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA,
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