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Ellero AA, van den Bout I, Vlok M, Cromarty AD, Hurrell T. Continual proteomic divergence of HepG2 cells as a consequence of long-term spheroid culture. Sci Rep 2021; 11:10917. [PMID: 34035320 PMCID: PMC8149451 DOI: 10.1038/s41598-021-89907-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/28/2021] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional models are considered a powerful tool for improving the concordance between in vitro and in vivo phenotypes. However, the duration of spheroid culture may influence the degree of correlation between these counterparts. When using immortalised cell lines as model systems, the assumption for consistency and reproducibility is often made without adequate characterization or validation. It is therefore essential to define the biology of each spheroid model by investigating proteomic dynamics, which may be altered relative to culture duration. As an example, we assessed the influence of culture duration on the relative proteome abundance of HepG2 cells cultured as spheroids, which are routinely used to model aspects of the liver. Quantitative proteomic profiling of whole cell lysates labelled with tandem-mass tags was conducted using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In excess of 4800 proteins were confidently identified, which were shared across three consecutive time points over 28 days. The HepG2 spheroid proteome was divergent from the monolayer proteome after 14 days in culture and continued to change over the successive culture time points. Proteins representing the recognised core hepatic proteome, cell junction, extracellular matrix, and cell adhesion proteins were found to be continually modulated.
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Affiliation(s)
- Andrea Antonio Ellero
- Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
- Centre for Neuroendocrinology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Iman van den Bout
- Centre for Neuroendocrinology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Physiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Maré Vlok
- Proteomics Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Allan Duncan Cromarty
- Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Tracey Hurrell
- Bioengineering and Integrated Genomics Group, Next Generation Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa.
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Hydroxylation of protein constituents of the human translation system: structural aspects and functional assignments. Future Med Chem 2019; 11:357-369. [PMID: 30802140 DOI: 10.4155/fmc-2018-0317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During the current decade, data on the post-translational hydroxylation of specific amino acid residues of some ribosomal proteins and translation factors in both eukaryotes and eubacteria have accumulated. The reaction is catalyzed by dedicated oxygenases (so-called ribosomal oxygenases), whose action is impaired under hypoxia conditions. The modification occurs at amino acid residues directly involved in the formation of the main functional sites of ribosomes and factors. This review summarizes currently available data on the specific hydroxylation of protein constituents of eukaryotic and eubacterial translation systems with a special emphasis on the human system, as well as on the links between hypoxia impacts on the operation of ribosomal oxygenases, the functioning of the translational apparatus and human health problems.
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Zhao Z, Fan Q, Zhou P, Ye H, Cai L, Lu Y. Association of alpha A-crystallin polymorphisms with susceptibility to nuclear age-related cataract in a Han Chinese population. BMC Ophthalmol 2017; 17:133. [PMID: 28755661 PMCID: PMC5534246 DOI: 10.1186/s12886-017-0529-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/21/2017] [Indexed: 01/01/2023] Open
Abstract
Background Alpha A-crystallin (CRYAA) is considered critical for the maintenance of lens transparency and is related to the pathogenesis of age-related cataracts (ARCs), especially the nuclear subtype. As the 5′ untranslated region (5′ UTR) modulates gene expression, the purpose of current study was to investigate whether single nucleotide polymorphisms (SNPs) in the 5′ UTR of CRYAA were associated with susceptibility to ARC in a Han Chinese population and to clarify the mechanism of this association. Methods SNPs in the 5′ UTR (−1 to −1000) of CRYAA were identified in 243 nuclear ARC patients and 263 controls using polymerase chain reaction and DNA sequencing. Allele and genotype frequencies were calculated and compared between two groups. Haploview 4.2 was used to calculate the linkage disequilibrium index, and the SHEsis analysis platform was used to infer haplotype construction. A dual-luciferase reporter gene assay was used for transcription of CRYAA in the presence of a protective haplotype with individual SNP alteration, Chromatin immunoprecipitation (ChIP) was employed to determine whether SNPs regulated CRYAA expression by altering the binding affinity of transcription factors. Results Three polymorphisms were identified in the 5′ UTR of CRYAA: rs3761381 (P = 0.000357, odds ratio [OR] = 1.837), rs13053109 (P = 0.788, OR = 1.086), and rs7278468 (P = 0.00136, OR = 0.652). The haplotype C-G-T (P = 0.0014, OR = 1.536) increased the risk of nuclear ARC, whereas the haplotype T-G-G (P = 0.00029, OR = 0.535) decreased the risk. The haplotype C-G-T decreased CRYAA transcription through rs7278468, which is located in the binding site of specificity protein 1 (Sp1). Furthermore, the G allele of rs7278468 increased CRYAA transcription by enhancing the binding affinity of Sp1. Conclusions These data indicate that the CRYAA polymorphism is a genetic marker of inter-individual differences in the risk of nuclear ARC. Electronic supplementary material The online version of this article (doi:10.1186/s12886-017-0529-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhennan Zhao
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 Fenyang Road, Shanghai, 200031, People's Republic of China
| | - Qi Fan
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 Fenyang Road, Shanghai, 200031, People's Republic of China
| | - Peng Zhou
- Department of Ophthalmology, Parkway Health Hong Qiao Medical Center, Shanghai, 200336, People's Republic of China
| | - HongFei Ye
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 Fenyang Road, Shanghai, 200031, People's Republic of China
| | - Lei Cai
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 Fenyang Road, Shanghai, 200031, People's Republic of China
| | - Yi Lu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 Fenyang Road, Shanghai, 200031, People's Republic of China.
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Lin Q, Zhou N, Zhang N, Qi Y. Mutational screening of EFNA5 in Chinese age-related cataract patients. Ophthalmic Res 2014; 52:124-9. [PMID: 25300504 DOI: 10.1159/000363139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/18/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM In the past few years, Ephrin-A5 (EFNA5) had been identified to be associated with lens development, but so far no sequence variation in EFNA5 has been reported in humans. Therefore, we conduct this study to investigate the EFNA5 genetic variations in Chinese age-related cataract (ARC) patients. METHODS Sequencing of EFNA5 was performed in 140 sporadic ARC patients and 142 random unrelated healthy subjects. Genomic DNA was extracted from peripheral blood leukocytes. All exons of EFNA5 were sequenced after being amplified by polymerase chain reaction. The functional consequences of the variations were analyzed using PolyPhen2. RESULTS Three single nucleotide polymorphisms in EFNA5, c.668C>T (rs201008479), c.102C>T (rs199980747) and c.-27C>G (rs200187971), were found in the patients, and none of them presented in the normal controls. Using PolyPhen2, c.668C>T in EFNA5 is predicted to be possibly damaging. CONCLUSIONS The genetic variations c.668C>T (rs201008479), c.102C>T (rs199980747) and c.-27C>G (rs200187971) may present an additional genetic risk factor for ARC in the Chinese population. This study shows the first cases of these genetic variations in EFNA5 in human beings.
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Affiliation(s)
- Qinghong Lin
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
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Jia M, Yang B, Li Z, Shen H, Song X, Gu W. Computational analysis of functional single nucleotide polymorphisms associated with the CYP11B2 gene. PLoS One 2014; 9:e104311. [PMID: 25102047 PMCID: PMC4125216 DOI: 10.1371/journal.pone.0104311] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/07/2014] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans and play a major role in the genetics of human phenotype variation and the genetic basis of human complex diseases. Recently, there is considerable interest in understanding the possible role of the CYP11B2 gene with corticosterone methyl oxidase deficiency, primary aldosteronism, and cardio-cerebro-vascular diseases. Hence, the elucidation of the function and molecular dynamic behavior of CYP11B2 mutations is crucial in current genomics. In this study, we investigated the pathogenic effect of 51 nsSNPs and 26 UTR SNPs in the CYP11B2 gene through computational platforms. Using a combination of SIFT, PolyPhen, I-Mutant Suite, and ConSurf server, four nsSNPs (F487V, V129M, T498A, and V403E) were identified to potentially affect the structure, function, and activity of the CYP11B2 protein. Furthermore, molecular dynamics simulation and structure analyses also confirmed the impact of these nsSNPs on the stability and secondary properties of the CYP11B2 protein. Additionally, utilizing the UTRscan, MirSNP, PolymiRTS and miRNASNP, three SNPs in the 3'UTR region were predicted to exhibit a pattern change in the upstream open reading frames (uORF), and eight microRNA binding sites were found to be highly affected due to 3'UTR SNPs. This cataloguing of deleterious SNPs is essential for narrowing down the number of CYP11B2 mutations to be screened in genetic association studies and for a better understanding of the functional and structural aspects of the CYP11B2 protein.
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Affiliation(s)
- Minyue Jia
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Boyun Yang
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongyi Li
- Department of Urology, the Second Affiliated Hospital (Binjiang Branch) Zhejiang University School of Medicine, Hangzhou Binjiang Hospital, Hangzhou, China
| | - Huiling Shen
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxiao Song
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Gu
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
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Lim SH, St Germain E, Tran-Viet KN, Staffieri S, Marino M, Dollfus PH, Nading EB, Crowe S, Gole G, Perdomo-Trujillo Y, Haybittel M, Elder J, Pelletier V, Traboulsi E, Mackey D, Young TL. Sequencing analysis of the ATOH7 gene in individuals with optic nerve hypoplasia. Ophthalmic Genet 2013; 35:1-6. [PMID: 23802135 DOI: 10.3109/13816810.2012.752017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Atonal Homolog 7 (ATOH7) gene has been implicated in association studies with optic nerve head diameter size. Hence, we screened optic nerve hypoplasia (ONH) patient DNA samples from Australia, France, and the United States for sequence variants in theATOH7 gene using Sanger sequencing. METHODS Sanger sequencing of theATOH7 gene was performed on 34 affected individual DNA samples. Sequencing was also carried out in three unaffected family members to confirm segregation of identified single nucleotide variations. RESULTS Seven sequence variations were identified in ATOH7. No disease-causing sequence changes in the ATOH7 gene was discovered in the ONH patient samples. CONCLUSIONS Mutations within the ATOH7 gene are not implicated in the pathogenesis of optic nerve hypoplasia in our patient cohort.
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Affiliation(s)
- Sing-Hui Lim
- The Center for Human Genetics, Duke University Medical Center , Durham, NC , USA
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Hajibemani A, Sharifiyazdi H, Mirzaei A, Rowshan Ghasrodashti A. Characterization of single nucleotide polymorphism in the 5'-untranslated region (5'-UTR) of Lactoferrin gene and its association with reproductive parameters and uterine infection in dairy cattle. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2012; 3:37-43. [PMID: 25653744 PMCID: PMC4312817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/20/2012] [Accepted: 03/15/2012] [Indexed: 11/29/2022]
Abstract
Uterine infection is one of the reproductive diseases that can have disturbing postpartum uterine health in cattle. Therefore, identification of resistant genotypes to uterine infection is important. Lactoferrin (LF) is one of the major antimicrobial compounds in the normal uterine discharges of cows. We hypothesized that allelic diversity in LF gene may contribute to susceptibility or resistance to uterine infection. We investigated the single nucleotide polymorphism genes identified in the 5' untranslated region (5'-UTR, position +32) of the LF gene using Allele-specific PCR method in cows with and without uterine infection. Blood samples were collected from 89 multiparous Holstein dairy cows with a history of uterine infection (n = 51), and cows without disease as the control group (n= 38). The results indicated the presence of different proportion of polymorphisms (G > C) in the 5'-UTR area of cows in the all groups. The results of Allele specific PCR was in complete agreement with sequencing method. Statistical analysis did not show any statistically significant correlation between disease and SNP in 5'-UTR. While, there was a significant difference in the mean of reproductive parameters of cows without polymorphism compare to those of with SNP in 5'-UTR. Cows with +32:CC genotype and +32:GC genotype (cows with SNP in UTR) had lower average of services per conception and days open compared to cows with the +32:GG genotypes. However, no significant difference in the calving to first service was found between these genotypes. Further studies will be required to determine critical SNPs in LF gene and status of the risk of uterine infection and embryo survival in cows.
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Affiliation(s)
- Abolfazl Hajibemani
- PhD Student at Department of Clinical Sciences, Faculty of Veterinary Medicine, Shiraz University, Shiraz, Iran;
| | - Hassan Sharifiyazdi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shiraz University, Shiraz, Iran;
| | - Abdolah Mirzaei
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shiraz University, Shiraz, Iran;
| | - Abbas Rowshan Ghasrodashti
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Kazerun Branch, Kazerun, Iran.
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Zhou Z, Wang B, Hu S, Zhang C, Ma X, Qi Y. Genetic variations in GJA3, GJA8, LIM2, and age-related cataract in the Chinese population: a mutation screening study. Mol Vis 2011; 17:621-6. [PMID: 21386927 PMCID: PMC3049737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/15/2011] [Indexed: 11/11/2022] Open
Abstract
PURPOSE To investigate the role of genetic variations in three known cataract-associated genes, gap junction protein α3 (GJA3), gap junction protein α8 (GJA8), lens intrinsic membrane protein 2 (LIM2), encoding lens fiber cell membrane proteins in the development of age-related cataracts. METHODS One hundred and forty-five sporadic age-related cataract patients and one hundred and fifty-six unrelated random healthy controls participated in this study. Genomic DNA was extracted from peripheral blood leukocytes. All exons of GJA3, GJA8, and LIM2 were sequenced after being amplified by polymerase chain reaction (PCR). The functional consequences of the mutations were analyzed using PolyPhen. RESULTS We found five novel variations in 145 patients and none of them presented in the 156 controls. There are two variations in GJA3 (c.-39C>G, c. 415G>A); one in GJA8 (c. 823G>A), and two in LIM2 (c.57G>A, c.67A>C). PolyPhen predicted that the LIM2 c.67A>C mutation may have potential pathogenicity. CONCLUSIONS The genetic mutation in GJA3, GJA8, and LIM2 may slightly contribute to the development of age-related cataracts. This study showed a potential relationship between lens fiber cell membrane protein genes and the development of age-related cataracts in the Chinese population.
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Affiliation(s)
- Zhou Zhou
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Binbin Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing, China
| | - Shanshan Hu
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunmei Zhang
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xu Ma
- Department of Genetics, National Research Institute for Family Planning, Beijing, China
| | - Yanhua Qi
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Zuercher J, Neidhardt J, Magyar I, Labs S, Moore AT, Tanner FC, Waseem N, Schorderet DF, Munier FL, Bhattacharya S, Berger W, Kloeckener-Gruissem B. Alterations of the 5'untranslated region of SLC16A12 lead to age-related cataract. Invest Ophthalmol Vis Sci 2010; 51:3354-61. [PMID: 20181839 PMCID: PMC2904002 DOI: 10.1167/iovs.10-5193] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/04/2010] [Accepted: 02/09/2010] [Indexed: 11/24/2022] Open
Abstract
PURPOSE. Knowledge of genetic factors predisposing to age-related cataract is very limited. The aim of this study was to identify DNA sequences that either lead to or predispose for this disease. METHODS. The candidate gene SLC16A12, which encodes a solute carrier of the monocarboxylate transporter family, was sequenced in 484 patients with cataract (134 with juvenile cataract, 350 with age-related cataract) and 190 control subjects. Expression studies included luciferase reporter assay and RT-PCR experiments. RESULTS. One patient with age-related cataract showed a novel heterozygous mutation (c.-17A>G) in the 5'untranslated region (5'UTR). This mutation is in cis with the minor G-allele of the single nucleotide polymorphism (SNP) rs3740030 (c.-42T/G), also within the 5'UTR. Using a luciferase reporter assay system, a construct with the patient's haplotype caused a significant upregulation of luciferase activity. In comparison, the SNP G-allele alone promoted less activity, but that amount was still significantly higher than the amount of the common T-allele. Analysis of SLC16A12 transcripts in surrogate tissue demonstrated striking allele-specific differences causing 5'UTR heterogeneity with respect to sequence and quantity. These differences in gene expression were mirrored in an allele-specific predisposition to age-related cataract, as determined in a Swiss population (odds ratio approximately 2.2; confidence intervals, 1.23-4.3). CONCLUSIONS. The monocarboxylate transporter SLC16A12 may contribute to age-related cataract. Sequences within the 5'UTR modulate translational efficiency with pathogenic consequences.
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Affiliation(s)
- Jurian Zuercher
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - John Neidhardt
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Istvan Magyar
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Stephan Labs
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anthony T. Moore
- Moorfields Eye Hospital London, London, United Kingdom
- UCL-Institute of Ophthalmology, London, United Kingdom
| | - Felix C. Tanner
- the Department of Cardiology, Cardiovascular Center, University of Zurich, Zurich, Switzerland
| | | | - Daniel F. Schorderet
- IRO-Institute for Research in Ophthalmology, EPFL-École polytechnique fédérale of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Francis L. Munier
- Jules Gonin Eye Hospital, Faculté de Biologie et Médecine de L'Université de Lausanne, Switzerland; and
| | | | - Wolfgang Berger
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Barbara Kloeckener-Gruissem
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- the Department of Biology, ETH Zurich, Zurich, Switzerland
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Abstract
Protein synthesis is often regulated at the level of initiation of translation, making it a critical step. This regulation occurs by both the cis-regulatory elements, which are located in the 5'- and 3'-UTRs (untranslated regions), and trans-acting factors. A breakdown in this regulation machinery can perturb cellular metabolism, leading to various physiological abnormalities. The highly structured UTRs, along with features such as GC-richness, upstream open reading frames and internal ribosome entry sites, significantly influence the rate of translation of mRNAs. In this review, we discuss how changes in the cis-regulatory sequences of the UTRs, for example, point mutations and truncations, influence expression of specific genes at the level of translation. Such modifications may tilt the physiological balance from healthy to diseased states, resulting in conditions such as hereditary thrombocythaemia, breast cancer, fragile X syndrome, bipolar affective disorder and Alzheimer's disease. This information tends to establish the crucial role of UTRs, perhaps as much as that of coding sequences, in health and disease.
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