1
|
Fatoki TH, Chukwuejim S, Udenigwe CC, Aluko RE. In Silico Exploration of Metabolically Active Peptides as Potential Therapeutic Agents against Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:ijms24065828. [PMID: 36982902 PMCID: PMC10058213 DOI: 10.3390/ijms24065828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is regarded as a fatal neurodegenerative disease that is featured by progressive damage of the upper and lower motor neurons. To date, over 45 genes have been found to be connected with ALS pathology. The aim of this work was to computationally identify unique sets of protein hydrolysate peptides that could serve as therapeutic agents against ALS. Computational methods which include target prediction, protein-protein interaction, and peptide-protein molecular docking were used. The results showed that the network of critical ALS-associated genes consists of ATG16L2, SCFD1, VAC15, VEGFA, KEAP1, KIF5A, FIG4, TUBA4A, SIGMAR1, SETX, ANXA11, HNRNPL, NEK1, C9orf72, VCP, RPSA, ATP5B, and SOD1 together with predicted kinases such as AKT1, CDK4, DNAPK, MAPK14, and ERK2 in addition to transcription factors such as MYC, RELA, ZMIZ1, EGR1, TRIM28, and FOXA2. The identified molecular targets of the peptides that support multi-metabolic components in ALS pathogenesis include cyclooxygenase-2, angiotensin I-converting enzyme, dipeptidyl peptidase IV, X-linked inhibitor of apoptosis protein 3, and endothelin receptor ET-A. Overall, the results showed that AGL, APL, AVK, IIW, PVI, and VAY peptides are promising candidates for further study. Future work would be needed to validate the therapeutic properties of these hydrolysate peptides by in vitro and in vivo approaches.
Collapse
Affiliation(s)
| | - Stanley Chukwuejim
- Department of Biochemistry, Federal University Oye-Ekiti, PMB 373, Oye 371104, Nigeria
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Chibuike C Udenigwe
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Richardson Centre for Food Technology and Research, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
2
|
Post WM, Widomska J, Grens H, Coenen MJH, Martens FMJ, Janssen DAW, IntHout J, Poelmans G, Oosterwijk E, Kluivers KB. Molecular Processes in Stress Urinary Incontinence: A Systematic Review of Human and Animal Studies. Int J Mol Sci 2022; 23:ijms23063401. [PMID: 35328824 PMCID: PMC8949972 DOI: 10.3390/ijms23063401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Stress urinary incontinence (SUI) is a common and burdensome condition. Because of the large knowledge gap around the molecular processes involved in its pathophysiology, the aim of this review was to provide a systematic overview of genetic variants, gene and protein expression changes related to SUI in human and animal studies. On 5 January 2021, a systematic search was performed in Pubmed, Embase, Web of Science, and the Cochrane library. The screening process and quality assessment were performed in duplicate, using predefined inclusion criteria and different quality assessment tools for human and animal studies respectively. The extracted data were grouped in themes per outcome measure, according to their functions in cellular processes, and synthesized in a narrative review. Finally, 107 studies were included, of which 35 used animal models (rats and mice). Resulting from the most examined processes, the evidence suggests that SUI is associated with altered extracellular matrix metabolism, estrogen receptors, oxidative stress, apoptosis, inflammation, neurodegenerative processes, and muscle cell differentiation and contractility. Due to heterogeneity in the studies (e.g., in examined tissues), the precise contribution of the associated genes and proteins in relation to SUI pathophysiology remained unclear. Future research should focus on possible contributors to these alterations.
Collapse
Affiliation(s)
- Wilke M. Post
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (W.M.P.); (H.G.)
| | - Joanna Widomska
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.W.); (G.P.)
| | - Hilde Grens
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (W.M.P.); (H.G.)
| | - Marieke J. H. Coenen
- Radboud Institute of Health Sciences, Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Frank M. J. Martens
- Department of Urology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (F.M.J.M.); (D.A.W.J.); (E.O.)
| | - Dick A. W. Janssen
- Department of Urology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (F.M.J.M.); (D.A.W.J.); (E.O.)
| | - Joanna IntHout
- Department of Health Evidence, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.W.); (G.P.)
| | - Egbert Oosterwijk
- Department of Urology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (F.M.J.M.); (D.A.W.J.); (E.O.)
| | - Kirsten B. Kluivers
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (W.M.P.); (H.G.)
- Correspondence:
| |
Collapse
|
3
|
Chen H, Wang T, Huang S, Zeng P. New novel non-MHC genes were identified for cervical cancer with an integrative analysis approach of transcriptome-wide association study. J Cancer 2021; 12:840-848. [PMID: 33403041 PMCID: PMC7778537 DOI: 10.7150/jca.47918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/18/2020] [Indexed: 12/28/2022] Open
Abstract
Although genome-wide association studies (GWAS) have successfully identified multiple genetic variants associated with cervical cancer, the functional role of those variants is not well understood. To bridge such gap, we integrated the largest cervical cancer GWAS (N = 9,347) with gene expression measured in six human tissues to perform a multi-tissue transcriptome-wide association study (TWAS). We identified a total of 20 associated genes in the European population, especially four novel non-MHC genes (i.e. WDR19, RP11-384K6.2, RP11-384K6.6 and ITSN1). Further, we attempted to validate our results in another independent cervical cancer GWAS from the East Asian population (N = 3,314) and re-discovered four genes including WDR19, HLA-DOB, MICB and OR2B8P. In our subsequent co-expression analysis, we discovered SLAMF7 and LTA were co-expressed in TCGA tumor samples and showed both WDR19 and ITSN1 were enriched in "plasma membrane". Using the protein-protein interaction analysis we observed strong interactions between the proteins produced by genes that are associated with cervical cancer. Overall, our study identified multiple candidate genes, especially four non-MHC genes, which may be causally associated with the risk of cervical cancer. However, further investigations with larger sample size are warranted to validate our findings in diverse populations.
Collapse
Affiliation(s)
- Haimiao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Shuiping Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
- Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
- Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| |
Collapse
|
4
|
Trněný O, Vlk D, Macková E, Matoušková M, Řepková J, Nedělník J, Hofbauer J, Vejražka K, Jakešová H, Jansa J, Piálek L, Knotová D. Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover ( Trifolium pratense L.). Int J Mol Sci 2019; 20:ijms20215470. [PMID: 31684086 PMCID: PMC6862357 DOI: 10.3390/ijms20215470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
Plant–rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study’s main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural 15N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover.
Collapse
Affiliation(s)
- Oldřich Trněný
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic.
| | - David Vlk
- Department of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic.
| | - Eliška Macková
- Department of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic.
| | | | - Jana Řepková
- Department of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic.
| | - Jan Nedělník
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic.
| | - Jan Hofbauer
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic.
| | - Karel Vejražka
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic.
| | - Hana Jakešová
- Red Clover and Grass Breeding, 724 47 Hladké Životice, Czech Republic.
| | - Jan Jansa
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic.
| | - Lubomír Piálek
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic.
| | - Daniela Knotová
- Research Institute for Fodder Crops, Ltd., 664 41 Troubsko, Czech Republic.
| |
Collapse
|
5
|
Zamborsky R, Kokavec M, Harsanyi S, Attia D, Danisovic L. Developmental Dysplasia of Hip: Perspectives in Genetic Screening. Med Sci (Basel) 2019; 7:medsci7040059. [PMID: 30979092 PMCID: PMC6524033 DOI: 10.3390/medsci7040059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/16/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
Development dysplasia of the hip (DDH) is a complex developmental disorder despite being a relatively common condition mainly caused by incompatibility of the femoral head and the abnormal joint socket. Development dysplasia of the hip describes a wide spectrum of disorders ranging from minor acetabular dysplasia to irreducible dislocation of the hip. Modern medicine still suffers from lack of information about screening and precise genetic examination. Genome wide linkage and association studies have brought significant progress to DDH diagnosis. Association studies managed to identify many candidate (susceptible) genes, such as PAPPA2, COL2A1, HOXD9, GDF-5, and TGFB1, which play a considerable role in the pathogenesis of DDH. Early detection of DDH has a big chance to help in preventing further disability and improve the psychological health and quality of life in those children. This emphasizes the importance to establish a universal screening program along with the genetic counseling.
Collapse
Affiliation(s)
- Radoslav Zamborsky
- Department of Orthopaedics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40 Bratislava, Slovakia.
| | - Milan Kokavec
- Department of Orthopaedics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40 Bratislava, Slovakia.
| | - Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia.
| | - Doaa Attia
- Department of Internal Medicine, Faculty of Medicine, Alexandria University, Chamblion St., Azarita, 21131 Alexandria, Egypt.
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia.
| |
Collapse
|
6
|
El-Sabrout K, Aggag SA. Associations between single nucleotide polymorphisms in multiple candidate genes and body weight in rabbits. Vet World 2017; 10:136-139. [PMID: 28246458 PMCID: PMC5301173 DOI: 10.14202/vetworld.2017.136-139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022] Open
Abstract
Aim: In this study, we examined parts of six growth genes (growth hormone [GH], melanocortin 4 receptor [MC4R], growth hormone receptor [GHR], phosphorglycerate mutase [PGAM], myostatin [MSTN], and fibroblast growth factor [FGF]) as specific primers for two rabbit lines (V-line, Alexandria) using nucleotide sequence analysis, to investigate association between detecting single nucleotide polymorphism (SNP) of these genes and body weight (BW) at market. Materials and Methods: Each line kits were grouped into high and low weight rabbits to identify DNA markers useful for association studies with high BW. DNA from blood samples of each group was extracted to amplify the six growth genes. SNP technique was used to study the associate polymorphism in the six growth genes and marketing BW (at 63 days) in the two rabbit lines. The purified polymerase chain reaction products were sequenced in those had the highest and lowest BW in each line. Results: Alignment of sequence data from each group revealed the following SNPs: At nucleotide 23 (A-C) and nucleotide 35 (T-G) in MC4R gene (sense mutation) of Alexandria and V-line high BW. Furthermore, we detected the following SNPs variation between the two lines: A SNP (T-C) at nucleotide 27 was identified by MC4R gene (sense mutation) and another one (A-C) at nucleotide 14 was identified by GHR gene (nonsense mutation) of Alexandria line. The results of individual BW at market (63 days) indicated that Alexandria rabbits had significantly higher BW compared with V-line rabbits. MC4R polymorphism showed significant association with high BW in rabbits. Conclusion: The results of polymorphism demonstrate the possibility to detect an association between BW in rabbits and the efficiency of the used primers to predict through the genetic specificity using the SNP of MC4R.
Collapse
Affiliation(s)
- Karim El-Sabrout
- Department of Poultry Production, Faculty of Agriculture, Aflaton St., El-Shatby, P.O. Box 21545, University of Alexandria, Alexandria, Egypt
| | - Sarah A Aggag
- Department of Genetics, Faculty of Agriculture, Aflaton St., El-Shatby, P.O. Box 21545, University of Alexandria, Alexandria, Egypt
| |
Collapse
|