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Densi A, Iyer RS, Bhat PJ. Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0384722. [PMID: 36840598 PMCID: PMC10100761 DOI: 10.1128/spectrum.03847-22] [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: 09/21/2022] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
Ammonium transporters are present in all three domains of life. They have undergone extensive horizontal gene transfer (HGT), gene duplication, and functional diversification and therefore offer an excellent paradigm to study protein evolution. We attempted to complement a mep1Δmep2Δmep3Δ strain of Saccharomyces cerevisiae (triple-deletion strain), which otherwise cannot grow on ammonium as a sole nitrogen source at concentrations of <3 mM, with amtA of Dictyostelium discoideum, an orthologue of S. cerevisiae MEP2. We observed that amtA did not complement the triple-deletion strain of S. cerevisiae for growth on low-ammonium medium. We isolated two mutant derivatives of amtA (amtA M1 and amtA M2) from a PCR-generated mutant plasmid library that complemented the triple-deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions, which are necessary for its functionality. amtA M2 bears two nonsynonymous substitutions and one synonymous substitution, all of which are necessary for functionality. Interestingly, AmtA M1 transports ammonium but does not confer methylamine toxicity, while AmtA M2 transports ammonium and confers methylamine toxicity, demonstrating functional diversification. Preliminary biochemical analyses indicated that the mutants differ in their conformations as well as their mechanisms of ammonium transport. These intriguing results clearly point out that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions in isolation. The above-described observations have significant implications for various facets of biological processes and are discussed in detail. IMPORTANCE Functional diversification following gene duplication is one of the major driving forces of protein evolution. While the role of nonsynonymous substitutions in the functional diversification of proteins is well recognized, knowledge of the role of synonymous substitutions in protein evolution is in its infancy. Using functional complementation, we isolated two functional alleles of the D. discoideum ammonium transporter gene (amtA), which otherwise does not function in S. cerevisiae as an ammonium transporters. One of them is an ammonium transporter, while the other is an ammonium transporter that also confers methylammonium (ammonium analogue) toxicity, suggesting functional diversification. Surprisingly, both alleles require a combination of synonymous and nonsynonymous substitutions for their functionality. These results bring out a hitherto-unknown pathway of protein evolution and pave the way for not only understanding protein evolution but also interpreting single nucleotide polymorphisms (SNPs).
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Affiliation(s)
- Asha Densi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Revathi S. Iyer
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Paike Jayadeva Bhat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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102
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Wang Z, Wang C, Zhang Y, Liu S, Cheng Y, Wang S, Xia P, Hao L. Porcine IGF-1R synonymous mutations in the extracellular domain affect proliferation and differentiation of skeletal muscle cells. Gene 2023; 854:147098. [PMID: 36496177 DOI: 10.1016/j.gene.2022.147098] [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: 03/16/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Miniature pigs are considered ideal organ donors for xenotransplantation in humans, but the mechanism underlying their dwarfism remains to be elucidated. IGF-1R is a crucial factor in body size formation in mammals, including skeletal muscle formation and development. The extracellular domain (ECD) binds to the ligand, a phenomenon that results in the activation of downstream pathways. METHODS In this study, the coding sequences of two IGF-1R ECD haplotypes of the large Landrace (LP) pig and the small Bama Xiang (BM) pig were cloned into pcDNA3.1 vectors to generate pcDNA3.1-LP and pcDNA3.1-BM. The two recombinant vectors were then transfected into skeletal muscle cells. RESULTS IGF-1R transcript was found to be expressed at higher levels in the pcDNA3.1-LP group than in the pcDNA3.1-BM group. The IGF-1R ECD from LP promoted cell proliferation and CyclinD1 expression, and promoted the phosphorylation of protein kinase B (to yield p-AKT). Moreover, the IGF-1R ECD from LP increased cell differentiation and the expression of myogenic determination factor (MyoD). CONCLUSION Our data indicated that the IGF-1R ECD haplotypes between pig breeds with different body sizes affect IGF-1R expression, in turn affecting the proliferation and differentiation of skeletal muscle cells by activating downstream signalling pathways.
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Affiliation(s)
- Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Ying Zhang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
| | - Yunyun Cheng
- Ministry of Health Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun, Jilin 130061, China
| | - Siyao Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
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103
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Lee SHT, Kim JY, Kim P, Dong Z, Su CY, Ahn EH. Changes of Mutations and Copy-Number and Enhanced Cell Migration during Breast Tumorigenesis. Adv Biol (Weinh) 2023; 7:e2200072. [PMID: 36449747 PMCID: PMC10836759 DOI: 10.1002/adbi.202200072] [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: 03/16/2022] [Revised: 11/14/2022] [Indexed: 12/02/2022]
Abstract
Although cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost in in vitro cell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
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Affiliation(s)
- Seung Hyuk T. Lee
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Joon Yup Kim
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Peter Kim
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, USA
| | - Zhipeng Dong
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Chia-Yi Su
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Eun Hyun Ahn
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
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104
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Shan J, Megarbane A, Chouchane A, Karthik D, Temanni R, Romero AR, Hua H, Pan C, Chen X, Subramanian M, Saad C, Mbarek H, Mehawej C, Chouery E, Abuaqel SW, Dömling A, Remadi S, Yaghi C, Li P, Chouchane L. Genetic predisposition to porto-sinusoidal vascular disorder: A functional genomic-based, multigenerational family study. Hepatology 2023; 77:501-511. [PMID: 35989577 PMCID: PMC9869943 DOI: 10.1002/hep.32735] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS Porto-sinusoidal vascular disorder (PSVD) is a group of liver vascular diseases featuring lesions encompassing the portal venules and sinusoids unaccompanied by cirrhosis, irrespective of the presence/absence of portal hypertension. It can occur secondary to coagulation disorders or insult by toxic agents. However, the cause of PSVD remains unknown in most cases. Hereditary cases of PSVD are exceptionally rare, but they are of particular interest and may unveil genetic alterations and molecular mechanisms associated with the disease. APPROACH AND RESULTS We performed genome sequencing of four patients and two healthy individuals of a large multigenerational Lebanese family with PSVD and identified a heterozygous deleterious variant (c.547C>T, p.R183W) of FCH and double SH3 domains 1 ( FCHSD1 ), an uncharacterized gene, in patients. This variant segregated with the disease, and its pattern of inheritance was suggestive of autosomal dominant with variable expressivity. RNA structural modelling of human FCHSD1 suggests that the C-to-T substitution at position 547, corresponding to FCHSD1R183W , may increase both messenger RNA (mRNA) and protein stability and its interaction with MTOR-associated protein, LST8 homolog, a key protein of the mechanistic target of rapamycin (mTOR pathway). These predictions were substantiated by biochemical analyses, which showed that FCHSD1R183W induced high FCHSD1 mRNA stability, overexpression of FCHSD1 protein, and an increase in mTORC1 activation. This human FCHSD1 variant was introduced into mice through CRISPR/Cas9 genome editing. Nine out of the 15 mice carrying the human FCHSD1R183W variant mimicked the phenotype of human PSVD, including splenomegaly and enlarged portal vein. CONCLUSIONS Aberrant FCHSD1 structure and function leads to mTOR pathway overactivation and may cause PSVD.
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Affiliation(s)
- Jingxuan Shan
- Genetic Intelligence Laboratory , Weill Cornell Medicine-Qatar , Qatar Foundation , Doha , Qatar.,Department of Genetic Medicine , Weill Cornell Medicine , New York , New York , USA
| | - André Megarbane
- Department of Human Genetics , Gilbert and Rose-Marie Chagoury School of Medicine , Lebanese American University , Beirut , Lebanon.,Institut Jérôme Lejeune , CRB BioJeL , Paris , France
| | - Aziz Chouchane
- Faculta di Medicina e Chirurgia , Universita Cattolica del Sacro Cuero , Rome , Italy.,Institute of Pathology , University of Bern , Bern , Switzerland
| | - Deepak Karthik
- Genetic Intelligence Laboratory , Weill Cornell Medicine-Qatar , Qatar Foundation , Doha , Qatar
| | | | - Atilio Reyes Romero
- Drug Design Group, Department of Pharmacy , University of Groningen , Groningen , Netherlands
| | - Huiying Hua
- Department of Pediatrics , Ruijin Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Chun Pan
- Department of Pediatrics , Ruijin Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Xixi Chen
- Department of Pediatrics , Ruijin Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Murugan Subramanian
- Genetic Intelligence Laboratory , Weill Cornell Medicine-Qatar , Qatar Foundation , Doha , Qatar
| | - Chadi Saad
- Genome Programme , Qatar Foundation Research, Development and Innovation , Qatar Foundation , Doha , Qatar
| | - Hamdi Mbarek
- Genome Programme , Qatar Foundation Research, Development and Innovation , Qatar Foundation , Doha , Qatar
| | - Cybel Mehawej
- Department of Human Genetics , Gilbert and Rose-Marie Chagoury School of Medicine , Lebanese American University , Beirut , Lebanon
| | - Eliane Chouery
- Department of Human Genetics , Gilbert and Rose-Marie Chagoury School of Medicine , Lebanese American University , Beirut , Lebanon
| | - Sirin W Abuaqel
- Genetic Intelligence Laboratory , Weill Cornell Medicine-Qatar , Qatar Foundation , Doha , Qatar
| | - Alexander Dömling
- Drug Design Group, Department of Pharmacy , University of Groningen , Groningen , Netherlands
| | | | - Cesar Yaghi
- Department of Gastroenterology , Hotel-Dieu de France Hospital , Faculty of Medicine, Saint Joseph University of Beirut , Beirut , Lebanon
| | - Pu Li
- Department of Pediatrics , Ruijin Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Lotfi Chouchane
- Genetic Intelligence Laboratory , Weill Cornell Medicine-Qatar , Qatar Foundation , Doha , Qatar.,Department of Genetic Medicine , Weill Cornell Medicine , New York , New York , USA.,Department of Microbiology and Immunology , Weill Cornell Medicine , New York , New York , USA
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105
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Implementing computational methods in tandem with synonymous gene recoding for therapeutic development. Trends Pharmacol Sci 2023; 44:73-84. [PMID: 36307252 DOI: 10.1016/j.tips.2022.09.008] [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: 06/21/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
Abstract
Synonymous gene recoding, the substitution of synonymous variants into the genetic sequence, has been used to overcome many production limitations in therapeutic development. However, the safety and efficacy of recoded therapeutics can be difficult to evaluate because synonymous codon substitutions can result in subtle, yet impactful changes in protein features and require sensitive methods for detection. Given that computational approaches have made significant leaps in recent years, we propose that machine-learning (ML) tools may be leveraged to assess gene-recoded therapeutics and foresee an opportunity to adapt codon contexts to enhance some powerful existing tools. Here, we examine how synonymous gene recoding has been used to address challenges in therapeutic development, explain the biological mechanisms underlying its effects, and explore the application of computational platforms to improve the surveillance of functional variants in therapeutic design.
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106
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Moreira-Ramos S, Arias L, Flores R, Katz A, Levicán G, Orellana O. Synonymous mutations in the phosphoglycerate kinase 1 gene induce an altered response to protein misfolding in Schizosaccharomyces pombe. Front Microbiol 2023; 13:1074741. [PMID: 36713198 PMCID: PMC9875302 DOI: 10.3389/fmicb.2022.1074741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Background Proteostasis refers to the processes that regulate the biogenesis, folding, trafficking, and degradation of proteins. Any alteration in these processes can lead to cell malfunction. Protein synthesis, a key proteostatic process, is highly-regulated at multiple levels to ensure adequate adaptation to environmental and physiological challenges such as different stressors, proteotoxic conditions and aging, among other factors. Because alterations in protein translation can lead to protein misfolding, examining how protein translation is regulated may also help to elucidate in part how proteostasis is controlled. Codon usage bias has been implicated in the fine-tuning of translation rate, as more-frequent codons might be read faster than their less-frequent counterparts. Thus, alterations in codon usage due to synonymous mutations may alter translation kinetics and thereby affect the folding of the nascent polypeptide, without altering its primary structure. To date, it has been difficult to predict the effect of synonymous mutations on protein folding and cellular fitness due to a scarcity of relevant data. Thus, the purpose of this work was to assess the effect of synonymous mutations in discrete regions of the gene that encodes the highly-expressed enzyme 3-phosphoglycerate kinase 1 (pgk1) in the fission yeast Schizosaccharomyces pombe. Results By means of systematic replacement of synonymous codons along pgk1, we found slightly-altered protein folding and activity in a region-specific manner. However, alterations in protein aggregation, heat stress as well as changes in proteasome activity occurred independently of the mutated region. Concomitantly, reduced mRNA levels of the chaperones Hsp9 and Hsp16 were observed. Conclusion Taken together, these data suggest that codon usage bias of the gene encoding this highly-expressed protein is an important regulator of protein function and proteostasis.
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Affiliation(s)
- Sandra Moreira-Ramos
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Loreto Arias
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rodrigo Flores
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Assaf Katz
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile,*Correspondence: Omar Orellana,
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107
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Guo X, Li T, Lu D, Yamada T, Li X, Bao S, Liu J, Borjigin G, Cang M, Tong B. Effects of the Expressions and Variants of the CAST Gene on the Fatty Acid Composition of the Longissimus Thoracis Muscle of Grazing Sonid Sheep. Animals (Basel) 2023; 13:ani13020195. [PMID: 36670735 PMCID: PMC9855194 DOI: 10.3390/ani13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Fatty acid (FA) composition has an important impact on the nutrition and flavor of meat, and on consumer health, and is receiving more attention in the sheep industry. This study aimed to evaluate the relationship between the expression levels of the CAST gene and the FA composition in the longissimus thoracis (LL) muscle, to identify novel variants of CAST, and to perform association analysis with the FA composition in grazing Sonid lambs. The correlation results showed that high expression levels of CAST are correlated with better FA compositions and classes in LL. For association studies, the results showed that c.1210C>T and c.1437G>A in LD-M, and c.2097C>T mutations are associated with some compositions and classes of FA in the LL of grazing Sonid sheep. Two missense c.646G>C (G216R) and c.1210C>T (R404C) mutations were predicted to influence the Calpain_inhib domains of CAST. Thus, the correlation results and associated mutations are expected to be genetic selection markers for the FA composition and meat quality of grazing Sonid lamb muscle and provide new insights into sheep meat quality traits influenced by the ovine CAST gene.
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Affiliation(s)
- Xin Guo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Terigele Li
- Inner Mongolia Agriculture Animal Husbandry Fishery and Biology Experiment Research Centre, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Datong Lu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Jiasen Liu
- Institute of Animal Science, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Ming Cang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (M.C.); (B.T.)
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (M.C.); (B.T.)
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108
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Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata. Commun Biol 2023; 6:5. [PMID: 36596992 PMCID: PMC9810668 DOI: 10.1038/s42003-022-04407-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
The roles of synonymous mutations for adapting to stressful thermal environments are of fundamental biological and ecological interests but poorly understood. To study whether synonymous mutations influence thermal adaptation at specific microhabitats, a genome-wide genotype-phenotype association analysis is carried out in the black mussels Mytilisepta virgata. A synonymous mutation of Ubiquitin-specific Peptidase 15 (MvUSP15) is significantly associated with the physiological upper thermal limit. The individuals carrying GG genotype (the G-type) at the mutant locus possess significantly lower heat tolerance compared to the individuals carrying GA and AA genotypes (the A-type). When heated to sublethal temperature, the G-type exhibit higher inter-individual variations in MvUSP15 expression, especially for the mussels on the sun-exposed microhabitats. Taken together, a synonymous mutation in MvUSP15 can affect the gene expression profile and interact with microhabitat heterogeneity to influence thermal resistance. This integrative study sheds light on the ecological importance of adaptive synonymous mutations as an underappreciated genetic buffer against heat stress and emphasizes the importance of integrative studies at a microhabitat scale for evaluating and predicting the impacts of climate change.
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109
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The potential of RNA-based therapy for kidney diseases. Pediatr Nephrol 2023; 38:327-344. [PMID: 35507149 PMCID: PMC9066145 DOI: 10.1007/s00467-021-05352-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023]
Abstract
Inherited kidney diseases (IKDs) are a large group of disorders affecting different nephron segments, many of which progress towards kidney failure due to the absence of curative therapies. With the current advances in genetic testing, the understanding of the molecular basis and pathophysiology of these disorders is increasing and reveals new potential therapeutic targets. RNA has revolutionized the world of molecular therapy and RNA-based therapeutics have started to emerge in the kidney field. To apply these therapies for inherited kidney disorders, several aspects require attention. First, the mRNA must be combined with a delivery vehicle that protects the oligonucleotides from degradation in the blood stream. Several types of delivery vehicles have been investigated, including lipid-based, peptide-based, and polymer-based ones. Currently, lipid nanoparticles are the most frequently used formulation for systemic siRNA and mRNA delivery. Second, while the glomerulus and tubules can be reached by charge- and/or size-selectivity, delivery vehicles can also be equipped with antibodies, antibody fragments, targeting peptides, carbohydrates or small molecules to actively target receptors on the proximal tubule epithelial cells, podocytes, mesangial cells or the glomerular endothelium. Furthermore, local injection strategies can circumvent the sequestration of RNA formulations in the liver and physical triggers can also enhance kidney-specific uptake. In this review, we provide an overview of current and potential future RNA-based therapies and targeting strategies that are in development for kidney diseases, with particular interest in inherited kidney disorders.
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110
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Zabolotskii AI, Kozlovskiy SV, Katrukha AG. The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2023; 88:S176-S191. [PMID: 37069120 DOI: 10.1134/s0006297923140109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Recombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time, achieving higher protein expression levels and correct protein folding still remains the key problem, since optimization of nutrient media, growth conditions, and methods for induction of protein synthesis do not always lead to the desired result. Often, low protein expression is determined by the sequences of the expressed genes and their regulatory regions. The genetic code is degenerated; 18 out of 20 amino acids are encoded by more than one codon. Choosing between synonymous codons in the coding sequence can significantly affect the level of protein expression and protein folding due to the influence of the gene nucleotide composition on the probability of formation of secondary mRNA structures that affect the ribosome binding at the translation initiation phase, as well as the ribosome movement along the mRNA during elongation, which, in turn, influences the mRNA degradation and the folding of the nascent protein. The nucleotide composition of the mRNA untranslated regions, in particular the promoter and Shine-Dalgarno sequences, also affects the efficiency of mRNA transcription, translation, and degradation. In this review, we describe the genetic principles that determine the efficiency of protein production in Escherichia coli.
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Affiliation(s)
- Artur I Zabolotskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Alexey G Katrukha
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Jiang Z, Wu Z, Liu R, Du Q, Fu X, Li M, Kuang Y, Lin S, Wu J, Xie W, Shi G, Peng Y, Zheng F. Effect of polymorphisms in drug metabolism and transportation on plasma concentration of atorvastatin and its metabolites in patients with chronic kidney disease. Front Pharmacol 2023; 14:1102810. [PMID: 36923356 PMCID: PMC10010391 DOI: 10.3389/fphar.2023.1102810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
Dyslipidemia due to renal insufficiency is a common complication in patients with chronic kidney diseases (CKD), and a major risk factor for the development of cardiovascular events. Atorvastatin (AT) is mainly used in the treatment of dyslipidemia in patients with CKD. However, response to the atorvastatin varies inter-individually in clinical applications. We examined the association between polymorphisms in genes involved in drug metabolism and transport, and plasma concentrations of atorvastatin and its metabolites (2-hydroxy atorvastatin (2-AT), 2-hydroxy atorvastatin lactone (2-ATL), 4-hydroxy atorvastatin (4-AT), 4-hydroxy atorvastatin lactone (4-ATL), atorvastatin lactone (ATL)) in kidney diseases patients. Genotypes were determined using TaqMan real time PCR in 212 CKD patients, treated with 20 mg of atorvastatin daily for 6 weeks. The steady state plasma concentrations of atorvastatin and its metabolites were quantified using ultraperformance liquid chromatography in combination with triple quadrupole mass spectrometry (UPLC-MS/MS). Univariate and multivariate analyses showed the variant in ABCC4 (rs3742106) was associated with decreased concentrations of AT and its metabolites (2-AT+2-ATL: β = -0.162, p = 0.028 in the dominant model; AT+2-AT+4-AT: β = -0.212, p = 0.028 in the genotype model), while patients carrying the variant allele ABCC4-rs868853 (β = 0.177, p = 0.011) or NR1I2-rs6785049 (β = 0.123, p = 0.044) had higher concentrations of 2-AT+2-ATL in plasma compared with homozygous wildtype carriers. Luciferase activity was enhanced in HepG2 cells harboring a construct expressing the rs3742106-T allele or the rs868853-G allele (p < 0.05 for each) compared with a construct expressing the rs3742106G or the rs868853-A allele. These findings suggest that two functional polymorphisms in the ABCC4 gene may affect transcriptional activity, thereby directly or indirectly affecting release of AT and its metabolites from hepatocytes into the circulation.
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Affiliation(s)
- Zebin Jiang
- Clinical Pharmacology Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zemin Wu
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Ruixue Liu
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Qin Du
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xian Fu
- Clinical Pharmacology Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Min Li
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Yongjun Kuang
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Shen Lin
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Jiaxuan Wu
- Department of Anesthesiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Weiji Xie
- Department of Nephrology, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Ganggang Shi
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Yanqiang Peng
- Department of Nephrology, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Fuchun Zheng, ; Yanqiang Peng,
| | - Fuchun Zheng
- Clinical Pharmacology Laboratory, First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Pharmacology, Shantou University Medical College, Shantou, China
- *Correspondence: Fuchun Zheng, ; Yanqiang Peng,
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Wang C, Yang Y, Liu Y, Zhang Y, Song J, Wang H, Li G, Wang X, Gong S, Chen S, He D. Molecular characterization, expression pattern and genetic variant of insulin-like growth factor 2 mRNA-binding protein 3 gene in goose ( Anser cygnoides). JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2022.2116441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Cui Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Yi Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Yuting Zhang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, People’s Republic of China
| | - Jiawei Song
- Xiangshan Animal Husbandry and Veterinary General Station, Ningbo, People’s Republic of China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Guangquan Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Xianze Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Shaoming Gong
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Shufang Chen
- NingBo Academy of Agricultural Sciences, Ningbo, People’s Republic of China
| | - Daqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, People’s Republic of China
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113
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Apparent Absence of Selective Pressure on Pneumocystis jirovecii Organisms in Patients with Prior Methotrexate Exposure. Antimicrob Agents Chemother 2022; 66:e0099022. [PMID: 36317930 PMCID: PMC9765006 DOI: 10.1128/aac.00990-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pneumocystis jirovecii infections occur in patients treated with methotrexate (MTX) because of immunosuppressive effects of this highly potent dihydrofolate reductase (DHFR) inhibitor. Conversely, MTX may act as an anti-P. jirovecii drug and consequently may exert a selective pressure on this fungus. In this context, we compared the sequences of the dhfr gene of P. jirovecii isolates obtained from two groups of patients with P. jirovecii infections. The first group, with systemic diseases or malignancies, had prior exposure to MTX (21 patients), whereas the second group (22 patients), the control group, did not. Three single nucleotide polymorphisms (SNPs) were observed at positions 278, 312, and 381. The first one was located in the intronic region and the two others were synonymous. Based on these SNPs, three P. jirovecii dhfr alleles, named A, B, and C, were specified. Allele A was the most frequent, as it was observed in 18 patients (85.7%) and in 16 patients (72.7%) of the first and second groups, respectively. No significant difference in P. jirovecii dhfr gene diversity in the two patient groups was observed. In conclusion, these original results suggest that MTX does not exert an overt selective pressure on P. jirovecii organisms.
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114
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Some New Aspects of Genetic Variability in Patients with Cutaneous T-Cell Lymphoma. Genes (Basel) 2022; 13:genes13122401. [PMID: 36553668 PMCID: PMC9778129 DOI: 10.3390/genes13122401] [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: 11/10/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
AIM Cutaneous T-cell lymphoma (CTCL) is a group of T-cell malignancies that develop in the skin. Though studied intensively, the etiology and pathogenesis of CTCL remain elusive. This study evaluated the survival of CTCL patients in the 1st Department of Dermatovenereology of St. Anne's University Hospital Brno. It included analysis of 19 polymorphic gene variants based on their expected involvement in CTCL severity. MATERIAL AND METHODS 75 patients with CTCL, evaluated and treated at the 1st Department of Dermatovenereology of St. Anne´s University Hospital Brno, Faculty of Medicine, Masaryk University, were recruited for the study over the last 28 years (44 men and 31 women, average age 58 years, range 20-82 years). All patients were genotyped for 19 chosen gene polymorphisms by the conventional PCR method with restriction analysis. A multivariate Cox regression model was calculated to reveal genetic polymorphisms and other risk factors for survival. RESULTS The model identified MDR Ex21 2677 (rs2032582) as a significant genetic factor influencing the survival of the patients, with the T-allele playing a protective role. A multivariate stepwise Cox regression model confirmed the following as significant independent risk factors for overall survival: increased age at admission, clinical staging of the tumor, and male sex. CONCLUSION We showed that the TT genotype at position 2677 of the MDR1 gene exhibited statistically significant longer survival in CTCL patients. As such, the TT genotype of MDR1 confers a significant advantage for the CTCL patients who respond to treatment.
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115
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Mahadevan S. Silence of the mutations. J Biosci 2022. [DOI: 10.1007/s12038-022-00320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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116
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Expression and Polymorphisms of SMAD1, SMAD2 and SMAD3 Genes and Their Association with Litter Size in Tibetan Sheep ( Ovis aries). Genes (Basel) 2022; 13:genes13122307. [PMID: 36553573 PMCID: PMC9777977 DOI: 10.3390/genes13122307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
SMAD1, SMAD2, and SMAD3 are important transcription factors downstream of the TGF-β/SMAD signaling pathway that mediates several physiological processes. In the current study, we used cloning sequencing, RT-qPCR, bioinformatics methods and iMLDR technology to clone the coding region of Tibetan sheep genes, analyze the protein structure and detect the tissue expression characteristics of Tibetan sheep genes, and detect the polymorphisms of 433 Tibetan sheep and analyze their correlation with litter size. The results showed that the ORFs of the SMAD1, SMAD2 and SMAD3 genes were 1398 bp, 1404 bp and 1278 bp, respectively, and encoded 465, 467 and 425 amino acids, respectively. The SMAD1, SMAD2, and SMAD3 proteins were all unstable hydrophilic mixed proteins. SMAD1, SMAD2 and SMAD3 were widely expressed in Tibetan sheep tissues, and all were highly expressed in the uterus, spleen, ovary and lung tissues. Litter sizes of the genotype CC in the SMAD1 gene g.10729C>T locus were significantly higher than that of CT (p < 0.05). In the SMAD3 gene g.21447C>T locus, the genotype TT individuals showed a higher litter size than the CC and CT genotype individuals (p < 0.05). These results preliminarily demonstrated that SMAD1, SMAD2 and SMAD3 were the major candidate genes that affected litter size traits in Tibetan sheep and could be used as a molecular genetic marker for early auxiliary selection for improving reproductive traits during sheep breeding.
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Association between Synonymous SNPs of SOX10 and Plumage Color and Reproductive Traits of Ducks. Animals (Basel) 2022; 12:ani12233345. [PMID: 36496864 PMCID: PMC9736065 DOI: 10.3390/ani12233345] [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: 08/11/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
Mutations in the SOX10 gene affect the plumage color of chickens and pigeons. The mutation also causes abnormal pigmentation of the skin and hair color, as well as postnatal growth retardation and reproduction problems in humans and mice. In this study, we investigated the association between the SOX10 gene and plumage color and reproductive traits of ducks using SNPs. We found six novel SNPs from 11 identified SNP sites using direct sequencing for PCR products from three different mixed DNA pools. We found two coding SNPs to be associated with the plumage color of ducks (ZJU1.0 Chr1. g.54065419C>T and g.54070844C>T), and found three coding SNPs associated with the reproductive traits of ducks (g.54065419C>T, g.54070844C>T, and g.54070904C>T), which were age at sexual maturity, body weight at sexual maturity, and the Haugh unit for egg quality traits and egg production in different productive periods. These results also indicated that the T alleles of the three SNPs of the coding region of SOX10 contribute to lower reproductive traits.
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Liu L, Cheng M, Guo H, Guan Q, You J, Dou H. Multidimensional Quantitative Measurement of Cancer Chemoresistance through Differential ZIF-8 Nanoparticle Cellular Retention. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51798-51807. [PMID: 36367515 DOI: 10.1021/acsami.2c17692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chemoresistance of cancer cells is conventionally quantified by half-maximal inhibitory concentration (IC50) or multidrug resistance gene 1 (MDR1) values, but these metrics can only reflect the overall drug resistance level of a cancer cell line. Meanwhile, the multidimensional evaluation of both the heterogeneity in a cell line and the drug resistance degree of each cell still presents a daunting challenge. We report here that the cellular heterogeneity, cellular cross contamination, and the proportion of chemoresistant cancer cells can be visualized via flow cytometry through the differential cellular retention of fluorescent ZIF-8 nanoparticles. In addition, we show that the degree of drug resistance exhibited by each cell subpopulation can be quantified by differing fluorescence of the drug-resistant and drug-sensitive cells in the corresponding flow cytometry profile, and the quantified metric S is highly consistent with the MDR1 expression results. Importantly, this novel strategy is applicable to various cancer cell lines, thus demonstrating a universal diagnosis platform for multidimensional, quantitative, and highly efficient diagnosis of cancer chemoresistance.
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Affiliation(s)
- Lingshan Liu
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Meng Cheng
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
| | - Heze Guo
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Qixiao Guan
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Jiayi You
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
| | - Hongjing Dou
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
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Yang J, Mao Z, Wang X, Zhuang J, Gong S, Gao Z, Xu G, Yang N, Sun C. Identification of crucial genes and metabolites regulating the eggshell brownness in chicken. BMC Genomics 2022; 23:761. [PMID: 36411402 PMCID: PMC9677642 DOI: 10.1186/s12864-022-08987-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Protoporphyrin IX (Pp IX) is the primary pigment for brown eggshells. However, the regulatory mechanisms directing Pp IX synthesis, transport, and genetic regulation during eggshell calcification in chickens remain obscure. In this study, we investigated the mechanism of brown eggshell formation at different times following oviposition, using White Leghorn hens (WS group), Rhode Island Red light brown eggshell line hens (LBS group) and Rhode Island Red dark brown eggshell line hens (DBS group). RESULTS At 4, 16 and 22 h following oviposition, Pp IX concentrations in LBS and DBS groups were significantly higher in shell glands than in liver (P < 0.05). Pp IX concentrations in shell glands of LBS and DBS groups at 16 and 22 h following oviposition were significantly higher than WS group (P < 0.05). In comparative transcriptome analysis, δ-aminolevulinate synthase 1 (ALAS1), solute carrier family 25 member 38 (SLC25A38), ATP binding cassette subfamily G member 2 (ABCG2) and feline leukemia virus subgroup C cellular receptor 1 (FLVCR1), which were associated with Pp IX synthesis, were identified as differentially expressed genes (DEGs). RT-qPCR results showed that the expression level of ALAS1 in shell glands was significantly higher in DBS group than in WS group at 16 and 22 h following oviposition (P < 0.05). In addition, four single nucleotide polymorphisms (SNPs) in ALAS1 gene that were significantly associated with eggshell brownness were identified. By identifying the differential metabolites in LBS and DBS groups, we found 11-hydroxy-E4-neuroprostane in shell glands and 15-dehydro-prostaglandin E1(1-) and prostaglandin G2 2-glyceryl ester in uterine fluid were related to eggshell pigment secretion. CONCLUSIONS In this study, the regulatory mechanisms of eggshell brownness were studied comprehensively by different eggshell color and time following oviposition. Results show that Pp IX is synthesized de novo and stored in shell gland, and ALAS1 is a key gene regulating Pp IX synthesis in the shell gland. We found three transporters in Pp IX pathway and three metabolites in shell glands and uterine fluid that may influence eggshell browning.
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Affiliation(s)
- Jing Yang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Zhiqiong Mao
- Beinongda Technology Co,.Ltd, Beijing, 100083 China
| | - Xiqiong Wang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Jingjie Zhuang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Sijia Gong
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Zhouyang Gao
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Guiyun Xu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Ning Yang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Congjiao Sun
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
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Saleem T, Maqbool H, Sheikh N, Tayyeb A, Mukhtar M, Ashfaq A. GABRG2 C588T Polymorphism Is Associated with Idiopathic Generalized Epilepsy but Not with Antiepileptic Drug Resistance in Pakistani Cohort. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3460792. [PMID: 36425336 PMCID: PMC9681559 DOI: 10.1155/2022/3460792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 10/19/2022] [Accepted: 10/29/2022] [Indexed: 08/30/2023]
Abstract
Idiopathic generalized epilepsy (IGE) is the most prevalent type of epilepsy with genetic origin. Mutations in ion channel genes have been identified as a common cause of IGE. Several studies have reported various epilepsy risk variants of GABRG2 (gamma-aminobutyric acid type A receptor subunit gamma2 subunit) gene in different ethnic groups, but the results are inconsistent. The purpose of this case-control research is to determine if GABRG2 polymorphisms contribute to IGE susceptibility and antiepileptic drug resistance in Pakistani population. For this purpose, we genotyped exon2, exon5 (C540T and C588T), exon7 (T813C), exon8 (K289M), and exon9 of GABRG2 gene by restriction fragment length polymorphism and Sanger's sequencing in 87 drug-responsive idiopathic generalized epilepsy patients, 55 drug-resistant epilepsy patients, and 83 healthy controls. Restriction fragment length polymorphism (RFLP) and sequencing results indicated only C588T polymorphism in the studied subjects. The comparison of genotypic and allelic frequencies showed significant differences between IGE patients and control groups (P = 0.008 and odds ratio = 4.2) and nonsignificant association of C588T polymorphism in antiseizure medication-resistant patients (P = 0.9). Our findings showed that C588T polymorphism of GABRG2 is a risk variant for IGE in Pakistani population. Further studies are required to validate the results.
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Affiliation(s)
- Tayyaba Saleem
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Hafsa Maqbool
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Nadeem Sheikh
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Asima Tayyeb
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Maryam Mukhtar
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Aqsa Ashfaq
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore, Pakistan
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:msac187. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
- Soumyanetra Chandra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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Tian Y, Deng Z, Yang P. mRNA vaccines: A novel weapon to control infectious diseases. Front Microbiol 2022; 13:1008684. [PMID: 36267192 PMCID: PMC9576954 DOI: 10.3389/fmicb.2022.1008684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/06/2022] [Indexed: 12/01/2022] Open
Abstract
Infectious diseases have always threatened human life, but with the development of vaccines, effective strategies for preventing and controlling these diseases have become available. The global outbreak of COVID-19 ushered in the advent of mRNA vaccine technologies, which quickly led to the introduction of mRNA vaccines effective against SARS-CoV-2. The success of this approach has stimulated research into the use of mRNA vaccines in the fight against other emerging as well as remerging infectious diseases. This review examines the constructive strategies and delivery systems used in mRNA vaccines and provides an overview of current clinical trials of those vaccines in the prevention of infectious diseases. The underlying mechanisms of mRNA vaccines are also discussed, including the double-edged sword of the innate immune response. Finally, the challenges but also the potential of mRNA vaccines are considered.
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Affiliation(s)
- Yuying Tian
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Inner Mongolia Medical University, Hohhot, China
| | - Zhuoya Deng
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Penghui Yang
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Inner Mongolia Medical University, Hohhot, China
- *Correspondence: Penghui Yang,
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Alhamoudi KM, Alghamdi B, Alswailem M, Nasir A, Aljomaiah A, Al-Hindi H, Alzahrani AS. A Unique Mechanism of a Novel Synonymous PHEX Variant Causing X-Linked Hypophosphatemia. J Clin Endocrinol Metab 2022; 107:2883-2891. [PMID: 35896147 DOI: 10.1210/clinem/dgac435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Synonymous mutations are usually nonpathogenic. OBJECTIVE We report here a family with X-linked hypophosphatemia (XLH) due to a novel synonymous PHEX variant with a unique mechanism. METHODS We studied a 4-member family (a mother, a son, and 2 daughters), all affected with XLH. Genomic DNA was extracted from peripheral leucocytes. Whole exome sequencing (WES) was used to identify the underlying genetic variant in the proband (the son). Sanger sequencing was used to confirm this variant in the proband and his family members. RT-PCR and sequencing of the cDNA revealed the effect of this variant on the PHEX structure and function. RESULTS A synonymous variant in the PHEX gene (c.1701A>C) was identified in all affected members. This variant changes the first nucleotide of exon 17 from adenine to cytosine. Using RT-PCR, this variant was shown to interfere with splicing of exons 16 with 17 resulting in a single shorter PHEX transcript in the proband compared to normal control. Sanger sequencing of the cDNA revealed a complete skipping of exon 17 and direct splicing of exons 16 and 18. This led to a frameshift and an introduction of a new stop codon in the next codon (codon 568), which ultimately led to truncation and loss of the final 183 amino acids of PHEX. CONCLUSION This novel variant shows how a synonymous exonic mutation may induce a complex series of changes in the transcription and translation of the gene and causes a disease, a mechanism that is not commonly recognized.
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Affiliation(s)
- Kheloud M Alhamoudi
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Balgees Alghamdi
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Meshael Alswailem
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
| | - Abdul Nasir
- Department of Molecular science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Abeer Aljomaiah
- Department of Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
| | - Ali S Alzahrani
- Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, MBC#03, PO BOX 3354, Riyadh, 11211, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital & Research Centre, P.O Box 3354, Riyadh 11211, Saudi Arabia
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Cosemans C, Wang C, Alfano R, Martens DS, Sleurs H, Dockx Y, Vanbrabant K, Janssen BG, Vanpoucke C, Lefebvre W, Smeets K, Nawrot TS, Plusquin M. In utero particulate matter exposure in association with newborn mitochondrial ND4L 10550A>G heteroplasmy and its role in overweight during early childhood. Environ Health 2022; 21:88. [PMID: 36117180 PMCID: PMC9484069 DOI: 10.1186/s12940-022-00899-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/01/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Mitochondria play an important role in the energy metabolism and are susceptible to environmental pollution. Prenatal air pollution exposure has been linked with childhood obesity. Placental mtDNA mutations have been associated with prenatal particulate matter exposure and MT-ND4L10550A>G heteroplasmy has been associated with BMI in adults. Therefore, we hypothesized that in utero PM2.5 exposure is associated with cord blood MT-ND4L10550A>G heteroplasmy and early life growth. In addition, the role of cord blood MT-ND4L10550A>G heteroplasmy in overweight during early childhood is investigated. METHODS This study included 386 mother-newborn pairs. Outdoor PM2.5 concentrations were determined at the maternal residential address. Cord blood MT-ND4L10550A>G heteroplasmy was determined using Droplet Digital PCR. Associations were explored using logistic regression models and distributed lag linear models. Mediation analysis was performed to quantify the effects of prenatal PM2.5 exposure on childhood overweight mediated by cord blood MT-ND4L10550A>G heteroplasmy. RESULTS Prenatal PM2.5 exposure was positively associated with childhood overweight during the whole pregnancy (OR = 2.33; 95% CI: 1.20 to 4.51; p = 0.01), which was mainly driven by the second trimester. In addition, prenatal PM2.5 exposure was associated with cord blood MT-ND4L10550A>G heteroplasmy from gestational week 9 - 13. The largest effect was observed in week 10, where a 5 µg/m3 increment in PM2.5 was linked with cord blood MT-ND4L10550A>G heteroplasmy (OR = 0.93; 95% CI: 0.87 to 0.99). Cord blood MT-ND4L10550A>G heteroplasmy was also linked with childhood overweight (OR = 3.04; 95% CI: 1.15 to 7.50; p = 0.02). The effect of prenatal PM2.5 exposure on childhood overweight was mainly direct (total effect OR = 1.18; 95% CI: 0.99 to 1.36; natural direct effect OR = 1.20; 95% CI: 1.01 to 1.36)) and was not mediated by cord blood MT-ND4L10550A>G heteroplasmy. CONCLUSIONS Cord blood MT-ND4L10550A>G heteroplasmy was linked with childhood overweight. In addition, in utero exposure to PM2.5 during the first trimester of pregnancy was associated with cord blood MT-ND4L10550A>G heteroplasmy in newborns. Our analysis did not reveal any mediation of cord blood MT-ND4L10550A>G heteroplasmy in the association between PM2.5 exposure and childhood overweight.
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Affiliation(s)
- Charlotte Cosemans
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Hanne Sleurs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Yinthe Dockx
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Kenneth Vanbrabant
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Wouter Lefebvre
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Karen Smeets
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- School of Public Health, Occupational & Environmental Medicine, Leuven University, Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
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Huang KY, Kan SL, Shen TT, Gong P, Feng YY, Du H, Zhao YP, Wan T, Wang XQ, Ran JH. A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms. Int J Mol Sci 2022; 23:ijms231810844. [PMID: 36142757 PMCID: PMC9505161 DOI: 10.3390/ijms231810844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022] Open
Abstract
Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.
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Affiliation(s)
- Kai-Yuan Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Pin Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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Tu T, Song Z, Liu X, Wang S, He X, Xi H, Wang J, Yan T, Chen H, Zhang Z, Lv X, Lv J, Huang XF, Zhao J, Lin CP, Gao C, Zhang J, Gu F. A precise and efficient adenine base editor. Mol Ther 2022; 30:2933-2941. [PMID: 35821638 PMCID: PMC9481987 DOI: 10.1016/j.ymthe.2022.07.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/26/2022] [Accepted: 07/09/2022] [Indexed: 11/22/2022] Open
Abstract
Adenine base editors (ABEs) are novel genome-editing tools, and their activity has been greatly enhanced by eight additional mutations, thus named ABE8e. However, elevated catalytic activity was concomitant with frequent generation of bystander mutations. This bystander effect precludes its safe applications required in human gene therapy. To develop next-generation ABEs that are both catalytically efficient and positionally precise, we performed combinatorial engineering of NG-ABE8e. We identify a novel variant (NG-ABE9e), which harbors nine mutations. NG-ABE9e exhibits robust and precise base-editing activity in human cells, with more than 7-fold bystander editing reduction at some sites, compared with NG-ABE8e. To demonstrate its practical utility, we used NG-ABE9e to correct the frequent T17M mutation in Rhodopsin for autosomal dominant retinitis pigmentosa. It reduces bystander editing by ∼4-fold while maintaining comparable efficiency. NG-ABE9e possesses substantially higher activity than NG-ABEmax and significantly lower bystander editing than NG-ABE8e in rice. Therefore, this study provides a versatile and improved adenine base editor for genome editing.
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Affiliation(s)
- Tianxiang Tu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zongming Song
- Henan Eye Hospital, Henan Eye Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou, Henan, China
| | - Xiaoyu Liu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shengxing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxue He
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haitao Xi
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiahua Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tong Yan
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haoran Chen
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhenwu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiujuan Lv
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jineng Lv
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiu-Feng Huang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junzhao Zhao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Zhang H, Lianto P, Li W, Xu M, Moore JB, Thorne JL. Associations between liver X receptor polymorphisms and blood lipids: A systematic review and meta-analysis. Steroids 2022; 185:109057. [PMID: 35679909 DOI: 10.1016/j.steroids.2022.109057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/07/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022]
Abstract
Genetic susceptibility to dyslipidaemia remains incompletely understood. The liver X receptors (LXRs), members of the nuclear receptor superfamily of ligand dependent transcription factors, are homeostatic regulators of lipid metabolism. Multiple single nucleotide polymorphisms (SNPs)have been identified previously in the coding and regulatory regions of the LXRs. The aim of this systematic review and meta-analysis was to summarise associations between SNPs of LXRs (α and β isoforms) with blood lipid and lipoprotein traits. Five databases (PubMed, Ovid Embase, Scopus, Web of Science, and the Cochrane Library) were systematically searched for population-based studies that assessed associations between one or more blood lipid/lipoprotein traits and LXR SNPs. Of seventeen articles included in the qualitative synthesis, ten were eligible for meta-analysis. Nine LXRα SNPs and five LXRβ SNPs were identified, and the three most studied LXRα SNPs were quantitatively summarised. Carriers of the minor allele A of LXRα rs12221497 (-115G>A) had higher triglyceride levels than GG homozygotes (0.13 mmol/L; 95%CI: [0.03, 0.23], P = 0.01). Heterozygote carriers of LXRα rs2279238 (297C/T) had higher total cholesterol levels (0.12 mmol/L; (95%CI: [0.01, 0.23], P = 0.04) than either CC or TT homozygotes. For LXRα rs11039155 (-6G>A), no significant differences in blood levels of either triglyceride (P = 0.39) or HDL-C (P = 0.98) were detected between genotypes in meta-analyses. In addition, there were no strong associations for other SNPs of LXRα and LXRβ. This study provides the evidence of an association between LXRα, but not LXRβ, SNPs and blood-lipid traits. Systematic review registration: PROSPERO No. CRD42021246158.
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Affiliation(s)
- Huifeng Zhang
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK; Clinical Nutrition Department, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Priscilia Lianto
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Weiming Li
- Clinical Nutrition Department, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Mengfan Xu
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - J Bernadette Moore
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - James L Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK.
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128
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Zhao LP, Lybrand TP, Gilbert P, Madeleine M, Payne TH, Cohen S, Geraghty DE, Jerome KR, Corey L. Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States. JAMA Netw Open 2022; 5:e2230293. [PMID: 36069983 PMCID: PMC9453543 DOI: 10.1001/jamanetworkopen.2022.30293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/21/2022] [Indexed: 12/01/2022] Open
Abstract
Importance With timely collection of SARS-CoV-2 viral genome sequences, it is important to apply efficient data analytics to detect emerging variants at the earliest time. Objective To evaluate the application of a statistical learning strategy (SLS) to improve early detection of novel SARS-CoV-2 variants using viral sequence data from global surveillance. Design, Setting, and Participants This case series applied an SLS to viral genomic sequence data collected from 63 686 individuals in Africa and 531 827 individuals in the United States with SARS-CoV-2. Data were collected from January 1, 2020, to December 28, 2021. Main Outcomes and Measures The outcome was an indicator of Omicron variant derived from viral sequences. Centering on a temporally collected outcome, the SLS used the generalized additive model to estimate locally averaged Omicron caseload percentages (OCPs) over time to characterize Omicron expansion and to estimate when OCP exceeded 10%, 25%, 50%, and 75% of the caseload. Additionally, an unsupervised learning technique was applied to visualize Omicron expansions, and temporal and spatial distributions of Omicron cases were investigated. Results In total, there were 2698 cases of Omicron in Africa and 12 141 in the United States. The SLS found that Omicron was detectable in South Africa as early as December 31, 2020. With 10% OCP as a threshold, it may have been possible to declare Omicron a variant of concern as early as November 4, 2021, in South Africa. In the United States, the application of SLS suggested that the first case was detectable on November 21, 2021. Conclusions and Relevance The application of SLS demonstrates how the Omicron variant may have emerged and expanded in Africa and the United States. Earlier detection could help the global effort in disease prevention and control. To optimize early detection, efficient data analytics, such as SLS, could assist in the rapid identification of new variants as soon as they emerge, with or without lineages designated, using viral sequence data from global surveillance.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Terry P. Lybrand
- Quintepa Computing LLC, Nashville, Tennessee
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Peter Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Margaret Madeleine
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine, Seattle
| | - Seth Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Medicine, University of Washington School of Medicine, Seattle
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Medicine, University of Washington School of Medicine, Seattle
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Ma Z, Wang W, Zhang D, Zhang Y, Zhao Y, Li X, Zhao L, Lin C, Wang J, Zhou B, Cheng J, Xu D, Li W, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Zhang X. Ovine RAP1GAP and rBAT gene polymorphisms and their association with tail fat deposition in Hu sheep. Front Vet Sci 2022; 9:974513. [PMID: 36090178 PMCID: PMC9453205 DOI: 10.3389/fvets.2022.974513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Excessive fat deposition in the tail of sheep will affect its feed efficiency, which will increase the feeding cost. The purpose of this study was to identify the single nucleotide polymorphisms (SNPs) of RAP1GAP and rBAT genes by PCR amplification and Sanger sequencing, the SNPs were genotyped by KASP genotyping assays to evaluate their association with tail fat deposition traits. The results showed that two intronic mutations of g.13561 G > A and g.1460 T > C were found in RAP1GAP and rBAT, respectively. There were three genotypes of GG, AG, AA and CC, CT and TT at these two loci, respectively. Association analysis showed that g.13561 G > A of RAP1GAP was associated with tail width, tail fat weight and relative tail fat weight (P < 0.05). The g.1460 T > C of rBAT was associated with tail width and tail fat weight (P < 0.05). Different combinations of genotypes also differed significantly with tail fat deposition traits. In the tail fat tissue, the expression levels of RAP1GAP gene was significantly higher in small-tailed sheep than in big-tailed sheep, and the expression levels of rBAT gene was significantly higher in big-tailed sheep than in small-tailed sheep. In the liver, the expression levels of RAP1GAP and rBAT gene was significantly higher at 6 months than at 0 and 3 months. In conclusion, RAP1GAP and rBAT polymorphisms can be used as a candidate molecular marker to reduce tail fat deposition in sheep.
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Affiliation(s)
- Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaoxue Zhang
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Affiliation(s)
- Ryan C Hunt
- From the Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Chava Kimchi-Sarfaty
- From the Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
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NLRP3 Susceptible Gene Polymorphisms in Patients with Primary Gouty Arthritis and Hyperuricemia. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1427607. [PMID: 36051474 PMCID: PMC9427315 DOI: 10.1155/2022/1427607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/30/2022] [Indexed: 12/02/2022]
Abstract
Polymorphisms have been identified to predispose to primary gouty arthritis (GA) and hyperuricemia (HUA). Here, we accessed the five polymorphisms of rs10754558, rs35829419, rs3738448, rs3806268, and rs7525979 in NLRP3 on GA and HUA susceptibility. We collected 1198 samples (314 GA, 377 HUA, and 507 controls) for this case-control study. Our data detected that the rs3806268 (GA vs. AA: OR = 0.65, p = 0.012) was significantly associated with the susceptibility to GA. The rs3738448 (TT vs. GG: OR = 2.05, p = 0.024) and rs7525979 (TT vs. CC: OR = 1.96, p = 0.037) were significantly associated with the susceptibility to HUA. The rs3806268 AG genotype presented decreased risk of GA among the hypertension (OR = 0.54, p = 0.0093), smoking (OR = 0.59, p = 0.018), and no obesity (OR = 0.60, p = 0.0097) subjects compared to the GG genotype group. The rs3738448 TT genotype demonstrated increased risk of HUA among the hypertension (OR = 4.10, p = 0.0056) and no drinking population (OR = 3.56, p = 0.016) compared to the GG genotype group. The rs7525979 TT genotype demonstrated increased risk of HUA among the hypertension (OR = 4.01, p = 0.0064) and no drinking population (OR = 3.24, p = 0.034) compared to the CC genotype group. Furthermore, a significant haplotype effect of rs10754558/C-rs35829419/C-rs3738448/G-rs3806268/A-rs7525979/C was found (OR = 1.60, p = 0.0046) compared with GCGAC haplotype. Bioinformatics analyses indicated that rs3738448, rs3806268, and rs7525979 might influence the gene regulation, while the T-allele of rs3738448 increased the stability of NLRP3-mRNA. Collectively, our case-control study confirms NLRP3 polymorphisms might participate in regulating immune and inflammation responses in GA and HUA.
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A Study of Combined Genotype Effects of SHCBP1 on Wool Quality Traits in Chinese Merino. Biochem Genet 2022; 61:551-564. [PMID: 35986828 DOI: 10.1007/s10528-022-10268-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
SHCBP1 (Shc SH2-domain binding protein 1) is a member of the Src and collagen homolog (Shc) protein family and is closely associated with multiple signaling pathways that play important roles during hair follicle induction, morphogenesis, and cycling. The purpose of this study was to investigate SHCBP1 gene expression, polymorphisms, and the association between SHCBP1 and wool quality traits in Chinese Merino sheep. The SHCBP1 gene was shown, by qPCR, to be ubiquitously expressed in sheep tissues and differentially expressed in the adult skin of Chinese Merino and Suffolk sheep. Four SNPs (termed SHCBP1SNPs 1-4) were identified by Sanger sequencing and were located in exon 2, intron 9, intron 12, and exon 13 of the sheep SHCBP1 gene, respectively. SHCBP1SNPs 3 and 4 (rs411176240 and rs160910635) were significantly associated with wool crimp (P < 0.05). The combined polymorphism (SHCBP1SNP3-SHCBP1SNP4) was significantly associated with wool crimp (P < 0.05). Bioinformatics analysis showed that the SNPs associated with wool crimp (SHCBP1SNPs 3 and 4) might affect the pre-mRNA splicing by creating binding sites for serine-arginine-rich proteins and that SHCBP1SNP4 might alter the SHCBP1 mRNA and protein secondary structure. Our results suggest that SHCBP1 influences wool crimp and SHCBP1SNPs 3 and 4 might be useful markers for marker-assisted selection and sheep breeding.
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When a Synonymous Variant Is Nonsynonymous. Genes (Basel) 2022; 13:genes13081485. [PMID: 36011397 PMCID: PMC9408308 DOI: 10.3390/genes13081485] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022] Open
Abstract
Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences.
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Saaid A, Monticelli M, Ricci AA, Orlando G, Botta C, Zeppa P, Bianconi A, Osella-Abate S, Bruno F, Pellerino A, Rudà R, Cassoni P, Garbossa D, Cofano F, Bertero L. Prognostic Analysis of the IDH1 G105G (rs11554137) SNP in IDH-Wildtype Glioblastoma. Genes (Basel) 2022; 13:genes13081439. [PMID: 36011350 PMCID: PMC9408597 DOI: 10.3390/genes13081439] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The G105G SNP (rs11554137) in the IDH1 gene is observed in about 10–15% of patients with a diffuse glioma. Data regarding its impact on gliomas are poor and partially conflicting, possibly due to the evolving classification of CNS tumors. The aim of this study was to investigate the G105G SNP prognostic significance in a homogenous cohort of IDH-wildtype glioblastomas, in agreement with the 2021 WHO classification. The study analyzed 211 patients by collecting several clinico-pathological and molecular characteristics, including the age, lesion localization, number of involved lobes, type of surgical treatment, disease outcome and MGMT promoter methylation status. PFS and DSS curves were plotted according to the Kaplan–Meier method and statistical analyses were performed using parametric and non-parametric tests. A total of 32 patients out of 211 (15.2%) were found to be G105G SNP carriers. No significant impact of the IDH1 G105G SNP on patients’ outcomes was observed in terms of PFS and DSS, while MGMT promoter methylation and gross total resection resulted as key prognostic factors in our cohort as expected. No prognostic impact of the IDH1 G105G SNP was detected in this strict cohort of IDH-wildtype glioblastomas. Analysis of larger cohorts is warranted to address the sample size limitations.
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Affiliation(s)
- Ayoub Saaid
- Neurosurgery Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Matteo Monticelli
- Neurosurgery Unit, Department of Neuroscience and Rehabilitation, University of Ferrara, 44100 Ferrara, Italy
| | - Alessia Andrea Ricci
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Giulia Orlando
- Pathology Unit, Department of Oncology, University of Turin, 10126 Turin, Italy
| | - Cristina Botta
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Pietro Zeppa
- Neurosurgery Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Andrea Bianconi
- Neurosurgery Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Simona Osella-Abate
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Francesco Bruno
- Neuro-Oncology Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Alessia Pellerino
- Neuro-Oncology Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Roberta Rudà
- Neuro-Oncology Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
- Department of Neurology, Castelfranco and Treviso Hospitals, 31100 Treviso, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diego Garbossa
- Neurosurgery Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Fabio Cofano
- Neurosurgery Unit, Department of Neuroscience “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
- Correspondence:
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135
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Sychev D, Ostroumova O, Cherniaeva M, Shakhgildian N, Mirzaev K, Abdullaev S, Denisenko N, Sozaeva Z, Kachanova A, Gorbatenkova S, Shastina V. The Influence of ABCB1 (rs1045642 and rs4148738) Gene Polymorphisms on Rivaroxaban Pharmacokinetics in Patients Aged 80 Years and Older with Nonvalvular Atrial Fibrillation. High Blood Press Cardiovasc Prev 2022; 29:469-480. [PMID: 35960493 DOI: 10.1007/s40292-022-00536-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/18/2022] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION ABCB1 gene polymorphisms are associated with rivaroxaban distribution changes and adverse reactions but the data are controversial. AIM To evaluate the influence of ABCB1 (rs1045642 and rs4148738) gene polymorphisms on rivaroxaban pharmacokinetics in patients aged 80 years and older with nonvalvular atrial fibrillation (NAF). METHODS 128 patients aged 80 years and older (median [Me] age 87.5 [83.0-90.0] years) with NAF were included. We performed ABCB1 (rs1045642 and rs4148738) genotyping, measured the trough steady-state plasma concentration (Cmin,ss) of rivaroxaban and prothrombin time (PT) and analyzed prior medical records for clinically relevant non-major bleeding (CRNMB). RESULTS CC genotype carriers had no differences in Cmin,ss (p > 0.05) compared with the CT and TT rs1045642 and rs4148738 genotypes carriers. CC genotype carriers had no differences in PT (p > 0.05) compared with the CT rs1045642 and rs4148738 and TT rs4148738 genotypes carriers. In the TT genotype PT levels were higher than in the CC rs1045642 genotype: Me 14.2 [13.0-16.1] sec vs 13.3 [12.4-14.5] sec (p = 0.049). Incidence of CRNMB was higher in patients with the TT genotype compared with the CC rs1045642 (29.3% vs 4.5%, p = 0.021) and rs4148738 (39.3% vs 8.1%, p = 0.008) and the CT genotype rs4148738 (39.3% vs 14.3%, p = 0.002). CONCLUSION ABCB1 (rs1045642 and rs4148738) polymorphisms didn't influence rivaroxaban pharmacokinetics in patients aged 80 years and older with NAF. TT carriers developed CRNMB more frequently compared with the CC rs1045642 and the CC and CT rs4148738 genotypes. The haplotype TT-TT haplotype was associated with a higher frequency of CRNMB.
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Affiliation(s)
- Dmitry Sychev
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation
| | - Olga Ostroumova
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Department of Therapy and Polymorbid Pathology, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation
| | - Marina Cherniaeva
- Department of Internal and Preventive Medicine, Central State Medical Academy of the Presidential Administration of the Russian Federation, Marshal Timoshenko Street, 19, Building 1A, Moscow, 121359, Russian Federation. .,State Budgetary Institution of Health "Hospital for War Veterans No. 2" of the Department of Health of Moscow, Volgogradskiy Prospekt, 168, Moscow, 109472, Russian Federation.
| | - Nataliia Shakhgildian
- Lomonosov Moscow State University Medical Research and Educational Center, 27\10, Lomonosovskiy Prospekt, Moscow, 119991, Russian Federation
| | - Karin Mirzaev
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Research Center for Medical Genetics, 1 Moskvorechye st., Moscow, 115522, Russian Federation.,Department of Personalized Medicine, Research Institute of Molecular and Personalized Medicine, Russian Medical Academy of Continuous Professional Education, 7/2 2nd Bokinskiy Drive, Moscow, 125284, Russian Federation
| | - Sherzod Abdullaev
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Department of Molecular Medicine, Research Institute of Molecular and Personalized Medicine, Russian Medical Academy of Continuous Professional Education, 7/2 2nd Bokinskiy Drive, Moscow, 125284, Russian Federation
| | - Natalia Denisenko
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Department of Personalized Medicine, Research Institute of Molecular and Personalized Medicine, Russian Medical Academy of Continuous Professional Education, 7/2 2nd Bokinskiy Drive, Moscow, 125284, Russian Federation
| | - Zhannet Sozaeva
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Department of Personalized Medicine, Research Institute of Molecular and Personalized Medicine, Russian Medical Academy of Continuous Professional Education, 7/2 2nd Bokinskiy Drive, Moscow, 125284, Russian Federation
| | - Anastasia Kachanova
- Department of Clinical Pharmacology and Therapy, Russian Medical Academy of Continuous Professional Education, 2/1 Barrikadnaya St., Moscow, 123242, Russian Federation.,Department of Molecular Medicine, Research Institute of Molecular and Personalized Medicine, Russian Medical Academy of Continuous Professional Education, 7/2 2nd Bokinskiy Drive, Moscow, 125284, Russian Federation
| | - Svetlana Gorbatenkova
- State Budgetary Institution of Health "Hospital for War Veterans No. 2" of the Department of Health of Moscow, Volgogradskiy Prospekt, 168, Moscow, 109472, Russian Federation
| | - Vera Shastina
- State Budgetary Institution of Health "Hospital for War Veterans No. 2" of the Department of Health of Moscow, Volgogradskiy Prospekt, 168, Moscow, 109472, Russian Federation
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Knops N, Ramazani Y, De Loor H, Goldschmeding R, Nguyen TQ, van den Heuvel LP, Levtchenko E, Kuypers DJ. Tacrolimus induces a pro-fibrotic response in donor-derived human proximal tubule cells dependent on common variants of the CYP3A5 and ABCB1 genes. Nephrol Dial Transplant 2022; 38:599-609. [PMID: 35945682 PMCID: PMC9976759 DOI: 10.1093/ndt/gfac237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Common genetic variants of the enzymes and efflux pump involved in tacrolimus disposition have been associated with calcineurin inhibitor nephrotoxicity, but their importance is unclear because of the multifactorial background of renal fibrosis. This study explores the pro-fibrotic response of tacrolimus exposure in relation to the differential capacity for tacrolimus metabolism in proximal tubule cells (PTCs) with a variable (pharmaco)genetic background. METHODS PTCs were obtained from protocol allograft biopsies with different combinations of CYP3A5 and ABCB1 variants and were incubated with tacrolimus within the concentration range found in vivo. Gene and protein expression, CYP3A5 and P-glycoprotein function, and tacrolimus metabolites were measured in PTC. Connective tissue growth factor (CTGF) expression was assessed in protocol biopsies of kidney allograft recipients. RESULTS PTCs produce CTGF in response to escalating tacrolimus exposure, which is approximately 2-fold higher in cells with the CYP3A5*1 and ABCB1 TT combination in vitro. Increasing tacrolimus exposure results in relative higher generation of the main tacrolimus metabolite {13-O-desmethyl tacrolimus [M1]} in cells with this same genetic background. Protocol biopsies show a larger increase in in vivo CTGF tissue expression over time in TT vs. CC/CT but was not affected by the CYP3A5 genotype. CONCLUSIONS Tacrolimus exposure induces a pro-fibrotic response in a PTC model in function of the donor pharmacogenetic background associated with tacrolimus metabolism. This finding provides a mechanistic insight into the nephrotoxicity associated with tacrolimus treatment and offers opportunities for a tailored immunosuppressive treatment.
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Affiliation(s)
| | | | - Henriëtte De Loor
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Roel Goldschmeding
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tri Q Nguyen
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lambert P van den Heuvel
- Laboratory of Pediatric Nephrology, Department of Growth and Regeneration, University of Leuven, Leuven, Belgium,Translational Metabolic Laboratory and Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Levtchenko
- Department of Pediatric Nephrology and Solid Organ Transplantation, UZ Leuven, University Hospitals Leuven, Leuven, Belgium,Laboratory of Pediatric Nephrology, Department of Growth and Regeneration, University of Leuven, Leuven, Belgium
| | - Dirk J Kuypers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
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137
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Bharath G, Vishnuprabu DP, Preethi L, Nagappan AS, Dhianeshwaran Isravanya RT, Bhaskar LV, Swaminathan N, Munirajan AK. SLCO1B1 and ABCB1 variants synergistically influence the atorvastatin treatment response in South Indian coronary artery disease patients. Pharmacogenomics 2022; 23:683-694. [PMID: 35968761 DOI: 10.2217/pgs-2022-0044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Introduction: Atorvastatin exhibits wide interindividual variability in treatment response, limiting the drug efficacy in coronary artery disease patients. Aim: To study the effect of genetic variants involved in atorvastatin transport/metabolism and correlate their lipid-lowering efficacy. Materials & methods: Genotyping was performed using 5'-hydrolysis probe method (n = 412), and the study evaluated the treatment response in 86 patients. Results: Significant reduction in total cholesterol and low-density lipoprotein cholesterol (LDL-C) were observed in SLCO1B1-rs4149056, rs4363657 and ABCB1-rs1045642 genotypes. The combined genotypes of ABCB1 and SLCO1B1 showed a strong synergistic effect in reducing the total cholesterol and LDL-C. Diabetes and smoking were observed to influence the LDL-C reduction. Conclusion: The genetic variants of SLCO1B1 and ABCB1 predict the lipid-lowering efficacy of atorvastatin, and this may be useful in genotype-guided statin therapy for coronary artery disease patients.
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Affiliation(s)
- Govindaswamy Bharath
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Durairaj Pandian Vishnuprabu
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
- Center for Vascular and Inflammatory Disease, University of Maryland Baltimore, School of Medicine, Baltimore, MD 21201, USA
| | - Loganathan Preethi
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
- Department of Health Research Multi-Disciplinary Research Unit, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Arumugam Suriyam Nagappan
- Department of Health Research Multi-Disciplinary Research Unit, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | | | - Lakkakula Vks Bhaskar
- Department of Life Sciences, Guru Ghasidas University, Bilaspur, Chhattisgarh, 495009, India
| | - Nagarajan Swaminathan
- Institute of Cardiology, Madras Medical College and Rajiv Gandhi Government General Hospital, Chennai, Tamil Nadu, 600003, India
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
- Department of Health Research Multi-Disciplinary Research Unit, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
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138
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Sun G, Zhang H, Yao H, Dai W, Lin Z, Dong Y. Characteristics of glutathione peroxidase gene and its responses to ammonia-N stress in razor clam Sinonovacula constricta. Comp Biochem Physiol B Biochem Mol Biol 2022; 261:110752. [PMID: 35513263 DOI: 10.1016/j.cbpb.2022.110752] [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: 01/30/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
Glutathione peroxidase (GPX) is a crucial enzyme in the antioxidant defense system. However, the previous studies on the structure and functions of mollusk GPX genes are still very limited. Here, we investigated the GPX gene from Sinonovacula constricta (Sc-GPX), and its expression profiles, protein localization, gene function and association with ammonia tolerance. The full length of sequence of Sc-GPX was 1781 bp, containing an open reading frame (ORF) of 588 bp encoding 195 amino acids. Quantitative expression of seven adult tissues showed that Sc-GPX was most abundant in hepatopancreas, followed by gills. Furthermore, the enzyme activity of Sc-GPX in hepatopancreas increased significantly under different ammonia concentrations (100, 140, and 180 mg/L) (P < 0.01). Further, we explored the mRNA expression level, histological structure and histo-cellular localization in gills and hepatopancreas of Sc-GPX under 140 mg/L ammonia stress. The mRNA expression level in gills and hepatopancreas of Sc-GPX increased significantly (P < 0.05) and immunohistochemistry results suggested that the columnar cells of gills filaments and the endothelial cells of hepatopancreas were the major sites for the action of Sc-GPX protein. In addition, we performed western blotting (WB), RNA interference (RNAi) and single nucleotide polymorphisms (SNPs) in the hepatopancreas of Sc-GPX under ammonia stress (140 mg/L). WB results indicated that the protein expression of Sc-GPX increased significantly (P < 0.01) after ammonia challenge. In addition, expression of Sc-GPX mRNA were significantly downregulated at 24 and 48 h after RNAi (P < 0.01). The association analysis between ammonia-tolerance group and control group identified six SNPs in coding sequence (CDS) of Sc-GPX from 449 individuals. Among them, c.162A > C was missense mutation, which lead to the amino acid change from Lys to Asn. These findings revealed that Sc-GPX may play a critical role in clam ammonia detoxification.
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Affiliation(s)
- Gaigai Sun
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Huan Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Hanhan Yao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China.
| | - Wenfang Dai
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, PR China
| | - Zhihua Lin
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, PR China
| | - Yinghui Dong
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, PR China.
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139
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Wang S, Atkinson GRS, Hayes WB. SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment. NPJ Syst Biol Appl 2022; 8:25. [PMID: 35859153 PMCID: PMC9300714 DOI: 10.1038/s41540-022-00232-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/20/2022] [Indexed: 12/31/2022] Open
Abstract
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two protein-protein interaction (PPI) networks should thus expose protein pairs with similar interaction partners allowing, for example, the prediction of common Gene Ontology (GO) terms. Unfortunately, no network alignment algorithm based on topology alone has been able to achieve this aim, though those that include sequence similarity have seen some success. We argue that this failure of topology alone is due to the sparsity and incompleteness of the PPI network data of almost all species, which provides the network topology with a small signal-to-noise ratio that is effectively swamped when sequence information is added to the mix. Here we show that the weak signal can be detected using multiple stochastic samples of "good" topological network alignments, which allows us to observe regions of the two networks that are robustly aligned across multiple samples. The resulting network alignment frequency (NAF) strongly correlates with GO-based Resnik semantic similarity and enables the first successful cross-species predictions of GO terms based on topology-only network alignments. Our best predictions have an AUPR of about 0.4, which is competitive with state-of-the-art algorithms, even when there is no observable sequence similarity and no known homology relationship. While our results provide only a "proof of concept" on existing network data, we hypothesize that predicting GO terms from topology-only network alignments will become increasingly practical as the volume and quality of PPI network data increase.
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Affiliation(s)
- Siyue Wang
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA
| | - Giles R S Atkinson
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA
| | - Wayne B Hayes
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA.
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140
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Nada D, Julien C, Papillon-Cavanagh S, Majewski J, Elbakry M, Elremaly W, Samuels ME, Moreau A. Identification of FAT3 as a new candidate gene for adolescent idiopathic scoliosis. Sci Rep 2022; 12:12298. [PMID: 35853984 PMCID: PMC9296578 DOI: 10.1038/s41598-022-16620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
In an effort to identify rare alleles associated with adolescent idiopathic scoliosis (AIS) whole-exome sequencing was performed on a discovery cohort of 73 unrelated patients and 70 age-and sex matched controls, all of French-Canadian ancestry. A collapsing gene burden test was performed to analyze rare protein-altering variants using case–control statistics. Since no single gene achieved statistical significance, targeted exon sequencing was performed for 24 genes with the smallest p values, in an independent replication cohort of unrelated severely affected females with AIS and sex-matched controls (N = 96 each). An excess of rare, potentially protein-altering variants was noted in one particular gene, FAT3, although it did not achieve statistical significance. Independently, we sequenced the exomes of all members of a rare multiplex family of three affected sisters and unaffected parents. All three sisters were compound heterozygous for two rare protein-altering variants in FAT3. The parents were single heterozygotes for each variant. The two variants in the family were also present in our discovery cohort. A second validation step was done, using another independent replication cohort of 258 unrelated AIS patients having reach their skeletal maturity and 143 healthy controls to genotype nine FAT3 gene variants, including the two variants previously identified in the multiplex family: p.L517S (rs139595720) and p.L4544F (rs187159256). Interestingly, two FAT3 variants, rs139595720 (genotype A/G) and rs80293525 (genotype C/T), were enriched in severe scoliosis cases (4.5% and 2.7% respectively) compared to milder cases (1.4% and 0.7%) and healthy controls (1.6% and 0.8%). Our results implicate FAT3 as a new candidate gene in the etiology of AIS.
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Affiliation(s)
- Dina Nada
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cédric Julien
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Injury Repair Recovery Program, McGill University Health Center Research Institute, Montreal, QC, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mohamed Elbakry
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Wesam Elremaly
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Mark E Samuels
- Sainte-Justine University Hospital Research Center, Montreal, QC, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Alain Moreau
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada. .,Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada.
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141
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Katneni UK, Alexaki A, Hunt RC, Hamasaki-Katagiri N, Hettiarachchi GK, Kames JM, McGill JR, Holcomb DD, Athey JC, Lin B, Parunov LA, Kafri T, Lu Q, Peters R, Ovanesov MV, Freedberg DI, Bar H, Komar AA, Sauna ZE, Kimchi-Sarfaty C. Structural, functional, and immunogenicity implications of F9 gene recoding. Blood Adv 2022; 6:3932-3944. [PMID: 35413099 PMCID: PMC9278298 DOI: 10.1182/bloodadvances.2022007094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
Hemophilia B is a blood clotting disorder caused by deficient activity of coagulation factor IX (FIX). Multiple recombinant FIX proteins are currently approved to treat hemophilia B, and several gene therapy products are currently being developed. Codon optimization is a frequently used technique in the pharmaceutical industry to improve recombinant protein expression by recoding a coding sequence using multiple synonymous codon substitutions. The underlying assumption of this gene recoding is that synonymous substitutions do not alter protein characteristics because the primary sequence of the protein remains unchanged. However, a critical body of evidence shows that synonymous variants can affect cotranslational folding and protein function. Gene recoding could potentially alter the structure, function, and in vivo immunogenicity of recoded therapeutic proteins. Here, we evaluated multiple recoded variants of F9 designed to further explore the effects of codon usage bias on protein properties. The detailed evaluation of these constructs showed altered conformations, and assessment of translation kinetics by ribosome profiling revealed differences in local translation kinetics. Assessment of wild-type and recoded constructs using a major histocompatibility complex (MHC)-associated peptide proteomics assay showed distinct presentation of FIX-derived peptides bound to MHC class II molecules, suggesting that despite identical amino acid sequence, recoded proteins could exhibit different immunogenicity risks. Posttranslational modification analysis indicated that overexpression from gene recoding results in suboptimal posttranslational processing. Overall, our results highlight potential functional and immunogenicity concerns associated with gene-recoded F9 products. These findings have general applicability and implications for other gene-recoded recombinant proteins.
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Affiliation(s)
- Upendra K. Katneni
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Aikaterini Alexaki
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Ryan C. Hunt
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Nobuko Hamasaki-Katagiri
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Gaya K. Hettiarachchi
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Jacob M. Kames
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Joseph R. McGill
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - David D. Holcomb
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - John C. Athey
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Brian Lin
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Leonid A. Parunov
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Mikhail V. Ovanesov
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT; and
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH
| | - Zuben E. Sauna
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
| | - Chava Kimchi-Sarfaty
- Division of Plasma Protein Therapeutics, Hemostasis Branch, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration (FDA), Silver Spring, MD
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Krami AM, Ratib C, Charoute H, Rouba H, Roky R, Barakat A, Nahili H. Association between G2677T/A polymorphism in ABCB1 gene and the risk of drug resistance epilepsy: An updated systematic review and meta-analysis. Epilepsy Res 2022; 185:106977. [PMID: 35853334 DOI: 10.1016/j.eplepsyres.2022.106977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022]
Abstract
PURPOSE Epilepsy is a common serious brain condition characterized by the abnormal electrical activity of neurons. In most cases, epileptic patients respond to antiepileptic drugs. Approximately, one-third of patients prove medically intractable. The ABCB1 gene is a superfamily of ATP-binding cassette (ABC) transporters that encode a drug-transport protein, lead to cells and organs protects and eliminates toxic agents. We performed this meta-analysis to assess the association between G2677T/A in the ABCB1 gene and the risk of drug resistance in epileptic patients. METHODS Two online libraries (PubMed and Scopus) were used to identify studies that report the relationship between G2677T/A polymorphism in the MDR1 gene and the risk of antiepileptic drug resistance. The meta-analysis was performed using Review Manager 5.3 software. The pooled odds ratios and 95 % confidence intervals (CIs) were calculated using a random or fixed effects model according to the heterogeneity between studies. RESULTS A total of 33 eligible studies were included in this meta-analysis which 4192 patients were drug-resistant and 5079 patients were drug-responsive. As a result, a significant association was observed in overall population for the genetic model GG+GA vs AA (OR with 95 % CI = 0,56 [0.34,0.93]; P = 0.02). The subgroup ethnicity analysis showed a significant decrease in the risk of AEDs resistance in the Caucasian population. CONCLUSION In conclusion, our analysis demonstrates that G2677T/A polymorphism in the ABCB1 gene decreases the risk of drug resistance. More studies are needed in the different ethnic groups to clarify the role of polymorphism in AEDs resistance.
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Affiliation(s)
- Al Mehdi Krami
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, 20360, Casablanca, Morocco; Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Health and Biotechnology Research Centre, Hassan II University of Casablanca, Maarif B.P 5366, Casablanca, Morocco
| | - Chorouk Ratib
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, 20360, Casablanca, Morocco; Laboratory of Biotechnology environment and health, Faculty of Science El Jadida, Morocco
| | - Hicham Charoute
- Research unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco.
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
| | - Rachida Roky
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Health and Biotechnology Research Centre, Hassan II University of Casablanca, Maarif B.P 5366, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
| | - Halima Nahili
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
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143
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Zhang H, Chen C, Wu X, Lou C, Liang Q, Wu W, Wang X, Ding Q. Effects of 14 F9 synonymous codon variants on hemophilia B expression: Alteration of splicing along with protein expression. Hum Mutat 2022; 43:928-939. [PMID: 35391506 DOI: 10.1002/humu.24377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023]
Abstract
There is growing evidence that synonymous codon variants (SCVs) can cause disease through the disruption of different processes of protein production. The aim of the study is to investigate whether the 14 SCVs reported in the F9 variant database were the pathogenic causes of hemophilia B. The impacts of SCVs on splicing and protein expression were detected using a combination of in silico prediction, in vitro minigene splicing assay and cell expression detection. The splicing transcripts were identified and quantified by co-amplification fluorescent PCR. The mechanism of splicing was verified by a modified pU1snRNA and pU7snRNA approach. Aberrant splicing patterns were found in eight SCVs. Five of the 8 SCVs produced almost all aberrant splicing isoforms, which were expected to truncate protein, three of them presented a partial defect on both splicing and protein secretion, the overall effects were consistent with the residual Factor IX activity of the affected cases. Neither the pre-messenger RNA (mRNA) splicing process nor the protein function was impaired in the rest six SCVs. In conclusion, our study firstly revealed the pathogenic mechanism of the 14 F9 SCVs and highlighted the importance of performing mRNA splicing analysis and protein expression studies of SCVs in inherited disorders.
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Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Can Lou
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
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144
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Xu H. Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones. Biomolecules 2022; 12:832. [PMID: 35740957 PMCID: PMC9221429 DOI: 10.3390/biom12060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen's hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
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Affiliation(s)
- Huafeng Xu
- Roivant Sciences, New York, NY 10036, USA
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145
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Aziz MA, Islam MS. The role of ABCB1 gene polymorphisms in steroid-resistant nephrotic syndrome: Evidence from a meta-analysis of steroid-receiving patients. J Gene Med 2022; 24:e3436. [PMID: 35697639 DOI: 10.1002/jgm.3436] [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: 09/24/2021] [Revised: 01/08/2022] [Accepted: 05/31/2022] [Indexed: 11/10/2022] Open
Abstract
Previous studies in nephrotic syndrome have shown that three common variants in the ABCB1 gene, including rs1128503, rs2032582, and rs1045642, change the expression and activity of ABCB1, which may be responsible for the drug resistance. However, as a result of the inconclusive outcomes of these studies, we performed a meta-analysis to validate the association between ABCB1 polymorphisms and the susceptibility of steroid-resistant nephrotic syndrome (SRNS). The association was evaluated by calculating the odds ratio (OR) and 95% confidence interval. A total of 12 studies containing 1,463 subjects (514 steroid-resistant and 949 steroid-sensitive) were included. Single nucleotide polymorphism rs1128503 showed a significant association with SRNS (p < 0.05) only in the allele model (OR = 1.40) in Africans. A statistically significant association was found for rs2032582 in codominant 2, dominant, recessive, and allele models (OR = 1.85, 1.52, 1.38, and 1.34, respectively). Subgroup analysis revealed that rs2032582 showed a significant correlation with SRNS in codominant 1, 2, dominant, over-dominant, and allele models in Africans (OR = 3.22, 3.52, 3.29, 1.74, and 1.83, respectively). In the case of rs1045642, codominant 1 (OR = 0.72) and recessive models (OR = 1.34) revealed a significant correlation with SRNS. Again, codominant 1 (OR = 0.58), dominant (OR = 0.69), and over-dominant models (OR = 0.62) showed a protective effect in Asians. Haplotype analysis showed that the TGC haplotype is associated with a 1.83, 1.77, and 2.17 times significant correlation in overall, Asian, and African populations, respectively. By contrast, the CGC haplotype showed a 0.69 and 0.57 times lower association in the overall and African populations, respectively. The CTC haplotype also showed a 1.79 times enhanced susceptibility for SRNS in the overall population. Our study suggests that ABCB1 polymorphisms are associated with SRNS development, especially in Africans and Asians.
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Affiliation(s)
- Md Abdul Aziz
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
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146
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Sileshi T, Mekonen G, Makonnen E, Aklillu E. Effect of Genetic Variations in Drug-Metabolizing Enzymes and Drug Transporters on the Pharmacokinetics of Rifamycins: A Systematic Review. Pharmgenomics Pers Med 2022; 15:561-571. [PMID: 35693129 PMCID: PMC9176238 DOI: 10.2147/pgpm.s363058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
Background Rifamycins are a novel class of antibiotics clinically approved for tuberculosis chemotherapy. They are characterized by high inter-individual variation in pharmacokinetics. This systematic review aims to present the contribution of genetic variations in drug-metabolizing enzymes and transporter proteins to the inter-individual variation of rifamycin pharmacokinetics. Method We followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. The search for relevant studies was done through PubMed, Embase, Web of Science, and Scopus databases. Studies reporting single nucleotide polymorphism in drug transporters and metabolizing enzymes' influence on rifamycin pharmacokinetics were solely included. Two reviewers independently performed data extraction. Results The search identified 117 articles of which 15 fulfilled the eligibility criteria and were included in the final data synthesis. The single nucleotides polymorphism in the drug transporters SLCO1B1 rs4149032, rs2306283, rs11045819, and ABCB1 rs1045642 for rifampicin, drug metabolizing enzyme AADAC rs1803155 for rifapentine and CES2 c.-22263A>G (g.738A>G) for rifampicin partly contributes to the variability of pharmacokinetic parameters in tuberculosis patients. Conclusion The pharmacokinetics of rifamycins is influenced by genetic variation of drug-metabolizing enzymes and transporters. Controlled clinical studies are, however, required to establish these relationships.
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Affiliation(s)
- Tesemma Sileshi
- Department of Pharmacy, Ambo University, Ambo, Ethiopia
- Department of Pharmacology and Clinical Pharmacy, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Eyasu Makonnen
- Department of Pharmacology and Clinical Pharmacy, Addis Ababa University, Addis Ababa, Ethiopia
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Eleni Aklillu
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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147
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Qureischi M, Mohr J, Arellano-Viera E, Knudsen SE, Vohidov F, Garitano-Trojaola A. mRNA-based therapies: Preclinical and clinical applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:1-54. [PMID: 36064262 DOI: 10.1016/bs.ircmb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
At the fundamental level, messenger RNA (mRNA)-based therapeutics involves the delivery of in vitro-transcribed (IVT) mRNA into the cytoplasm of a target cell, where it is translated into the desired protein. IVT mRNA presents various advantages compared to DNA and recombinant protein-based approaches that make it ideal for a broad range of therapeutic applications. IVT mRNA, which is translated in the cytoplasm after transfection into cells, can encode virtually any target protein. Notably, it does not enter the nucleus, which avoids its integration into the genome and the risk of insertional mutagenesis. The large-scale production of IVT mRNA is less complex than production of recombinant proteins, and Good Manufacturing Practice-compliant mRNA production is easily scalable, ideally poising mRNA for not only off-the-shelf, but more personalized treatment approaches. IVT mRNA's safety profile, pharmacokinetics, and pharmacodynamics, including its inherent immunostimulatory capacity, can be optimized for different therapeutic applications by harnessing a wide array of optimized sequence elements, chemical modifications, purification techniques, and delivery methods. The value of IVT mRNA was recently proved during the COVID-19 pandemic when mRNA-based vaccines outperformed the efficacy of established technologies, and millions of doses were rapidly deployed. In this review, we will discuss chemical modifications of IVT mRNA and highlight numerous preclinical and clinical applications including vaccines for cancer and infectious diseases, cancer immunotherapy, protein replacement, gene editing, and cell reprogramming.
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148
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Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O'Brien EP. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. Nat Commun 2022; 13:3081. [PMID: 35654797 PMCID: PMC9163053 DOI: 10.1038/s41467-022-30548-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/05/2022] [Indexed: 01/12/2023] Open
Abstract
Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
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Affiliation(s)
- Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Karthik B Narayan
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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149
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Genetic screening in patients of Meige syndrome and blepharospasm. Neurol Sci 2022; 43:3683-3694. [PMID: 35044558 DOI: 10.1007/s10072-022-05900-8] [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] [Received: 07/25/2021] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Meige syndrome (MS) is cranial dystonia, including bilateral eyelid spasms (blepharospasm; BSP) and involuntary movements of the jaw muscles (oromandibular dystonia; OMD). Up to now, the pathogenic genes of MS and BSP are still unclear. METHODS We performed Sanger sequencing of GNAL, TOR1A, TOR2A, THAP1, and REEP4 exons on 78 patients, including 53 BSP and 25 MS and 96 healthy controls. RESULTS c.845G > C[R282P] of TOR1A, c.629delC[p.Gly210AlafsTer60] of TOR2A, c.1322A > G[N441S] of GNAL, c.446G > A[R149Q], and c.649C > T[R217C] of REEP4 were identified and predicated as deleterious probably damaging variants. Three potential alterations of splicing variants of TOR1A and TOR2A were identified in patients. The frequencies of TOR1A rs1435566780 and THAP1 rs545930392 were higher in patients than in controls. CONCLUSIONS TOR1A rs1435566780 (c.*16G > C(G > A)) and THAP1 rs545930392 (c.192G > A[K64K]) may contribute to the etiology of MS and BSP. Other identified rare mutations predicted as deleterious probably damaging need further confirmation. Larger MS and BSP cohorts and functional studies will need to be performed further to elucidate the association between these genes and the diseases.
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150
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Cope AL, Gilchrist MA. Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach. BMC Genomics 2022; 23:408. [PMID: 35637464 PMCID: PMC9153123 DOI: 10.1186/s12864-022-08635-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Results Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to prevous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Conclusions Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08635-0).
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Affiliation(s)
- Alexander L Cope
- Genome Science and Technology, University of Tennessee, Knoxville, United States.,Current Address: Department of Genetics, Rutgers University, Piscataway, United States
| | - Michael A Gilchrist
- Genome Science and Technology, University of Tennessee, Knoxville, United States. .,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, United States. .,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, United States.
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