201
|
Gao Y, Hao Q, Cang M, Wang J, Yu H, Liu Y, Zhang W, Tong B. Association between novel variants in BMPR1B gene and litter size in Mongolia and Ujimqin sheep breeds. Reprod Domest Anim 2021; 56:1562-1571. [PMID: 34543455 DOI: 10.1111/rda.14020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
Prolificacy is an important trait of animals, specifically for sheep. The Bone morphogenetic protein receptor 1B (BMPR1B) is a major gene affecting the litter size of many sheep breeds. The well-known FecB mutation (Q249R) was associated fully with the hyper prolific phenotype of Booroola Merino. However, the identification of variation in all exonic regions of BMPR1B was rare. In this study, we sequenced all exonic regions of BMPR1B gene of Mongolia sheep breed, and ten novel variants were detected by direct sequencing. Among them, the litter size of the Mongolia ewes with the CC genotype was significantly higher (0.34 additional lambs, p < .05) than those with the TT genotype of the g.29346567C>T single nucleotide polymorphism (SNP). The litter size of the Mongolia ewes with the TT genotype was significantly higher (0.19 additional lambs, p < .05 and .31 additional lambs, p < .01, respectively) than those with the GT and GG genotypes of the c.1470G>T SNP. The silent c.1470G>T mutation is predicted to increase the stability of the mRNA secondary structure through reducing minimum free energy and is predicted to change the mRNA secondary structure of BMPR1B. Our findings may give potentially useful genetic markers for increasing litter size in sheep.
Collapse
Affiliation(s)
- Yuanyuan Gao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Qi Hao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ming Cang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jianguo Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Haiquan Yu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongbin Liu
- Institute of Animal Science, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenguang Zhang
- College of Animal Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| |
Collapse
|
202
|
Lyu X, Yang Q, Zhao F, Liu Y. Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed. Nucleic Acids Res 2021; 49:9404-9423. [PMID: 34417614 PMCID: PMC8450115 DOI: 10.1093/nar/gkab729] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.
Collapse
Affiliation(s)
- Xueliang Lyu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| |
Collapse
|
203
|
Kim SC, Sekhon SS, Shin WR, Ahn G, Cho BK, Ahn JY, Kim YH. Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency. Mol Cell Toxicol 2021; 18:1-8. [PMID: 34567201 PMCID: PMC8450916 DOI: 10.1007/s13273-021-00171-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 01/15/2023]
Abstract
Background mRNA vaccines hold great potential as therapeutic techniques against viral infections due to their efficacy, safety,
and large-scale production. mRNA vaccines offer flexibility in development as any protein can be produced from
mRNA without altering the production or application process. Objective This review highlights the iterative optimization of mRNA vaccine structural elements that impact the type,
specificity, and intensity of immune responses leading to higher translational potency and intracellular stability. Results Modifying the mRNA structural elements particularly the 5′ cap, 5′-and 3′-untranslated regions (UTRs), the coding region, and polyadenylation tail help reduce the excessive mRNA immunogenicity and consistently improve its
intracellular stability and translational efficiency. Conclusion Further studies regarding mRNA-structural elements and their optimization are needed to create new opportunities
for engineering mRNA vaccines.
Collapse
Affiliation(s)
- Sun Chang Kim
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Simranjeet Singh Sekhon
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea
| | - Woo-Ri Shin
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Gna Ahn
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Byung-Kwan Cho
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| |
Collapse
|
204
|
Serra M, Hattinger CM, Pasello M, Casotti C, Fantoni L, Riganti C, Manara MC. Impact of ABC Transporters in Osteosarcoma and Ewing's Sarcoma: Which Are Involved in Chemoresistance and Which Are Not? Cells 2021; 10:cells10092461. [PMID: 34572110 PMCID: PMC8467338 DOI: 10.3390/cells10092461] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter superfamily consists of several proteins with a wide repertoire of functions. Under physiological conditions, ABC transporters are involved in cellular trafficking of hormones, lipids, ions, xenobiotics, and several other molecules, including a broad spectrum of chemical substrates and chemotherapeutic drugs. In cancers, ABC transporters have been intensely studied over the past decades, mostly for their involvement in the multidrug resistance (MDR) phenotype. This review provides an overview of ABC transporters, both related and unrelated to MDR, which have been studied in osteosarcoma and Ewing's sarcoma. Since different backbone drugs used in first-line or rescue chemotherapy for these two rare bone sarcomas are substrates of ABC transporters, this review particularly focused on studies that have provided findings that have been either translated to clinical practice or have indicated new candidate therapeutic targets; however, findings obtained from ABC transporters that were not directly involved in drug resistance were also discussed, in order to provide a more complete overview of the biological impacts of these molecules in osteosarcoma and Ewing's sarcoma. Finally, therapeutic strategies and agents aimed to circumvent ABC-mediated chemoresistance were discussed to provide future perspectives about possible treatment improvements of these neoplasms.
Collapse
Affiliation(s)
- Massimo Serra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
- Correspondence: ; Tel.: +39-051-6366762
| | - Claudia Maria Hattinger
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Michela Pasello
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Chiara Casotti
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Leonardo Fantoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Chiara Riganti
- Department of Oncology, University of Torino, Via Santena 5/bis, 10126 Torino, Italy;
| | - Maria Cristina Manara
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| |
Collapse
|
205
|
Komar AA. A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell. BIOCHEMISTRY (MOSCOW) 2021; 86:976-991. [PMID: 34488574 DOI: 10.1134/s0006297921080083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.
Collapse
Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA. .,Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,DAPCEL, Inc., Cleveland, OH 44106, USA
| |
Collapse
|
206
|
May A, Su F, Dinh B, Ehlen R, Tran C, Adivikolanu H, Shaw PX. Ongoing controversies and recent insights of the ARMS2-HTRA1 locus in age-related macular degeneration. Exp Eye Res 2021; 210:108605. [PMID: 33930395 PMCID: PMC12053538 DOI: 10.1016/j.exer.2021.108605] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 01/17/2023]
Abstract
Age-related macular degeneration (AMD) is the most common cause of central vision loss among elderly populations in industrialized countries. Genome-wide association studies have consistently associated two genomic loci with progression to late-stage AMD: the complement factor H (CFH) locus on chromosome 1q31 and the age-related maculopathy susceptibility 2-HtrA serine peptidase 1 (ARMS2-HTRA1) locus on chromosome 10q26. While the CFH risk variant has been shown to alter complement activity, the ARMS2-HTRA1 risk haplotype remains enigmatic due to high linkage disequilibrium and inconsistent functional findings spanning two genes that are plausibly causative for AMD risk. In this review, we detail the genetic and functional evidence used to support either ARMS2 or HTRA1 as the causal gene for AMD risk, emphasizing both the historical development and the current understanding of the ARMS2-HTRA1 locus in AMD pathogenesis. We conclude by summarizing the evidence in favor of HTRA1 and present our hypothesis whereby HTRA1-derived ECM fragments mediate AMD pathogenesis.
Collapse
Affiliation(s)
- Adam May
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Fei Su
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Brian Dinh
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Rachael Ehlen
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Christina Tran
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Harini Adivikolanu
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Peter X Shaw
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| |
Collapse
|
207
|
Pintó RM, Bosch A. The Codon Usage Code for Cotranslational Folding of Viral Capsids. Genome Biol Evol 2021; 13:evab089. [PMID: 33914886 PMCID: PMC8410136 DOI: 10.1093/gbe/evab089] [Citation(s) in RCA: 4] [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] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
Codon bias is common to all organisms and is the result of mutation, drift, and selection. Selection for the efficiency and accuracy of translation is well recognized as a factor shaping the codon usage. In contrast, fewer studies report the control of the rate of translation as an additional selective pressure influencing the codon usage of an organism. Experimental molecular evolution using RNA virus populations is a powerful tool for the identification of mechanisms underlying the codon bias. Indeed, the role of deoptimized codons on the cotranslational folding has been proven in the capsids of two fecal-orally transmitted picornaviruses, poliovirus, and the hepatitis A virus, emphasizing the role of the frequency of codons in determining the phenotype. However, most studies on virus codon usage rely only on computational analyses, and experimental studies should be encouraged to clearly define the role of selection on codon evolution.
Collapse
Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| |
Collapse
|
208
|
Yamagishi MEB. Is our immune system a powerful vaccine factory? Genet Mol Biol 2021; 44:e20200468. [PMID: 34410292 PMCID: PMC8358740 DOI: 10.1590/1678-4685-gmb-2020-0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/05/2021] [Indexed: 11/21/2022] Open
|
209
|
The influence of acute coronary syndrome on levels of clopidogrel active metabolite and platelet inhibition in patients with and without CYP2C19*2(681 G>A), *3(636 G>A) and ABCB1(C3435C> T) gene polymorphisms. ADVANCES IN INTERVENTIONAL CARDIOLOGY 2021; 17:179-186. [PMID: 34400920 PMCID: PMC8356835 DOI: 10.5114/aic.2021.106894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/20/2021] [Indexed: 12/02/2022] Open
Abstract
Introduction Although ticagrelor and prasugrel remain the standard antiplatelet treatments in acute coronary syndrome (ACS), numerous patients still present with indications for clopidogrel use. Aim We aimed to assess the levels of clopidogrel active metabolite and to evaluate the effect of the drug on platelet inhibition in patients with ACS as compared with those with stable coronary disease. Patients were assessed for the presence of the most common genetic polymorphisms that reduce the absorption (ABCB1) and activation (CYP2C19*2 and CYP2C19*3) of clopidogrel to exclude the effect of genetic variability on drug concentrations and activity. Material and methods This single-center, open-label, prospective study included 199 patients hospitalized due to ST-segment elevation myocardial infarction (STEMI) or non-STEMI (NSTEMI) in Killip class I–III, who underwent percutaneous coronary intervention. The control group included 22 patients with stable coronary artery disease. Results The mean (SD) levels of active clopidogrel were 17.1 (12.3) ng/ml in controls and 16.4 (12.0) ng/ml in the whole study group (p < 0.68). No differences were noted in clopidogrel levels between patients with STEMI and NSTEMI (mean (SD), 17.6 (2.3) ng/ml and 15.1 (11.5) ng/ml; p < 0.45) or between STEMI and NSTEMI groups and controls (p < 0.38 and p < 0.61, respectively). No effect of ABCB1 or CYP2C19 polymorphism was observed in the study subgroups. Conclusions We concluded that ACS does not affect the levels of clopidogrel active metabolite or platelet inhibition in patients in Killip class I-III with or without CYP2C19 or ABCB1 gene polymorphisms.
Collapse
|
210
|
Gutman T, Goren G, Efroni O, Tuller T. Estimating the predictive power of silent mutations on cancer classification and prognosis. NPJ Genom Med 2021; 6:67. [PMID: 34385450 PMCID: PMC8361094 DOI: 10.1038/s41525-021-00229-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years it has been shown that silent mutations, in and out of the coding region, can affect gene expression and may be related to tumorigenesis and cancer cell fitness. However, the predictive ability of these mutations for cancer type diagnosis and prognosis has not been evaluated yet. In the current study, based on the analysis of 9,915 cancer genomes and approximately three million mutations, we provide a comprehensive quantitative evaluation of the predictive power of various types of silent and non-silent mutations over cancer classification and prognosis. The results indicate that silent-mutation models outperform the equivalent null models in classifying all examined cancer types and in estimating the probability of survival 10 years after the initial diagnosis. Additionally, combining both non-silent and silent mutations achieved the best classification results for 68% of the cancer types and the best survival estimation results for up to nine years after the diagnosis. Thus, silent mutations hold considerable predictive power over both cancer classification and prognosis, most likely due to their effect on gene expression. It is highly advised that silent mutations are integrated in cancer research in order to unravel the full genomic landscape of cancer and its ramifications on cancer fitness.
Collapse
Affiliation(s)
- Tal Gutman
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Guy Goren
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Omri Efroni
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel.
| |
Collapse
|
211
|
Chen MK, Zhou JH, Wang P, Ye YL, Liu Y, Zhou JW, Chen ZJ, Yang JK, Liao DY, Liang ZJ, Xie X, Zhou QZ, Xue KY, Guo WB, Xia M, Bao JM, Yang C, Duan HF, Wang HY, Huang ZP, Qin ZK, Liu CD. BMI1 activates P-glycoprotein via transcription repression of miR-3682-3p and enhances chemoresistance of bladder cancer cell. Aging (Albany NY) 2021; 13:18310-18330. [PMID: 34270461 PMCID: PMC8351696 DOI: 10.18632/aging.203277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Chemoresistance is the most significant reason for the failure of cancer treatment following radical cystectomy. The response rate to the first-line chemotherapy of cisplatin and gemcitabine does not exceed 50%. In our previous research, elevated BMI1 (B-cell specific Moloney murine leukemia virus integration region 1) expression in bladder cancer conferred poor survival and was associated with chemoresistance. Herein, via analysis of The Cancer Genome Atlas database and validation of clinical samples, BMI1 was elevated in patients with bladder cancer resistant to cisplatin and gemcitabine, which conferred tumor relapse and progression. Consistently, BMI1 was markedly increased in the established cisplatin- and gemcitabine-resistant T24 cells (T24/DDP&GEM). Functionally, BMI1 overexpression dramatically promoted drug efflux, enhanced viability and decreased apoptosis of bladder cancer cells upon treatment with cisplatin or gemcitabine, whereas BMI1 downregulation reversed this effect. Mechanically, upon interaction with p53, BMI1 was recruited on the promoter of miR-3682-3p gene concomitant with an increase in the mono-ubiquitination of histone H2A lysine 119, leading to transcription repression of miR-3682-3p gene followed by derepression of ABCB1 (ATP binding cassette subfamily B member 1) gene. Moreover, suppression of P-glycoprotein by miR-3682-3p mimics or its inhibitor XR-9576, could significantly reverse chemoresistance of T24/DDP&GEM cells. These results provided a novel insight into a portion of the mechanism underlying BMI1-mediated chemoresistance in bladder cancer.
Collapse
Affiliation(s)
- Ming-Kun Chen
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Jun-Hao Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Peng Wang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Yun-Lin Ye
- Department of Pathology, Cancer Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Yang Liu
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Jia-Wei Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Zi-Jian Chen
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Jian-Kun Yang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - De-Ying Liao
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Zhi-Jian Liang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Xiao Xie
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Qi-Zhao Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Kang-Yi Xue
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Wen-Bin Guo
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Ming Xia
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Ji-Ming Bao
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Cheng Yang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Hai-Feng Duan
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Hong-Yi Wang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Zhi-Peng Huang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Zi-Ke Qin
- Department of Pathology, Cancer Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Cun-Dong Liu
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| |
Collapse
|
212
|
Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
213
|
Ma L, Xiang Q, Zhao N, Hu C, Fang M, Tan Y, Chen S, Wang Z, Liu P, Sun K, Li Y, Wu F, Tian H, Fang M, Zhao X, Wang G, Cui Y. Effects of CYP2D6, CYP3A5, and ABCB1 gene polymorphisms on the pharmacokinetics of two risperidone long-acting injection microsphere formulations. Prog Neuropsychopharmacol Biol Psychiatry 2021; 109:110241. [PMID: 33400943 DOI: 10.1016/j.pnpbp.2020.110241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/11/2020] [Accepted: 12/30/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND LY03004, a novel investigational risperidone long-acting injection (LAI) microsphere formulation, can release risperidone more quickly after injection than Risperdal Consta®. This study aimed to investigate the effects of genetic polymorphisms on the pharmacokinetics of LY03004 compared with those on Risperdal Consta®. METHODS A total of 100 Chinese patients with stable schizophrenia were randomly assigned to the LY03004 or Risperdal Consta® treatment group. Each patient received five biweekly intramuscular injections of 25 mg risperidone long-acting injection microspheres. A total of 34 blood samples before and after injections from Day 1 to Day 113 were collected from each patient, and polymorphic alleles of cytochrome P450 enzymes CYP2D6 (*4, *10, *14), CYP3A5 (*3), and ABCB1 (C1236 > T, G2677T/A, and C3435T) were analyzed using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism. RESULTS The risperidone Cmax,ss, Cmin,ss, AUC0-tau,ss, and the ratio of risperidone to 9-hydroxyrisperidone (9-OH-R) in CYP2D6 intermediate metabolizers (IMs) were significantly different compared with those in normal metabolizers (NMs) in both the LY03004 and Risperdal Consta® groups (P < 0.05). However, 9-OH-R was not significantly different between IMs and NMs (P > 0.05). The AUC0-tau,ss of the active moiety (risperidone plus 9-OH-R) was 6.51 ± 3.34 in NMs and 7.00 ± 1.81 in IMs (P = 0.071) in the LY03004 group and 6.07 ± 2.31 and 7.95 ± 3.42 (P = 0.053) in NMs and IMs, respectively, in the Risperdal Consta® group. In the LY03004 group, the Cmax,ss of risperidone in carriers of the ABCB1-C3435T TT variant was significantly lower than that in CC and CT carriers (TT 7.76 ± 4.23 ng/mL, CT 11.6 ± 8.27 ng/mL, CC 14.3 ± 7.66 ng/ml; P = 0.045), but no significant differences were found in the active moiety. In the Risperdal Consta® group, C3435T TT carriers had significantly lower Cmin,ss of the active moiety (TT 5.09 ± 4.38 ng/mL, CT 11.4 ± 8.42 ng/mL, CC 14.3 ± 6.43 ng/mL; P = 0.007). Furthermore, Cmin,ss of the active moiety was significantly different among all ABCB1-G2677T/A genotypes (P < 0.05). CONCLUSION The pharmacokinetics of risperidone and the ratio of risperidone to 9-OH-R were highly dependent on CYP2D6 activity. However, there was no significant effect in 9-OH-R. A future study involving a larger sample is required to verify whether CYP2D6 IMs have lower risperidone active moiety clearance than CYP2D6 NMs for LAI formulations. In addition, the risperidone active moiety was eliminated faster in ABCB1-G2677T/A and C3435T TT carriers receiving Risperdal Consta®.
Collapse
Affiliation(s)
- Lingyue Ma
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Qian Xiang
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Nan Zhao
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Changqing Hu
- Beijing Anding Hospital of Capital Medical University, Beijing, China
| | - Meng Fang
- Beijing Anding Hospital of Capital Medical University, Beijing, China
| | - Yunlong Tan
- Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University, Beijing, China
| | - Song Chen
- Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University, Beijing, China
| | - Zining Wang
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Pinglan Liu
- Shandong Luye Pharmaceutical Co., Ltd, Yantai, China
| | - Kaoxiang Sun
- Shandong Luye Pharmaceutical Co., Ltd, Yantai, China; School of Pharmacy in Yantai university, Yantai, China
| | - Youxin Li
- Shandong Luye Pharmaceutical Co., Ltd, Yantai, China
| | - Fuxi Wu
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | | | | | - Xia Zhao
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Gang Wang
- Beijing Anding Hospital of Capital Medical University, Beijing, China.
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, Beijing, China.
| |
Collapse
|
214
|
Domnauer M, Zheng F, Li L, Zhang Y, Chang CE, Unruh JR, Conkright-Fincham J, McCroskey S, Florens L, Zhang Y, Seidel C, Fong B, Schilling B, Sharma R, Ramanathan A, Si K, Zhou C. Proteome plasticity in response to persistent environmental change. Mol Cell 2021; 81:3294-3309.e12. [PMID: 34293321 DOI: 10.1016/j.molcel.2021.06.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/28/2021] [Accepted: 06/22/2021] [Indexed: 01/17/2023]
Abstract
Temperature is a variable component of the environment, and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses, resulting in refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find that many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and, importantly, cellular functions. We postulate that, in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.
Collapse
Affiliation(s)
- Matthew Domnauer
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Fan Zheng
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Liying Li
- UCSF, 1550 Fourth St, RH490 San Francisco, CA 94158, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Catherine E Chang
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | | | - Scott McCroskey
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Christopher Seidel
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Benjamin Fong
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Rishi Sharma
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Arvind Ramanathan
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Institute for Stem Cell Science and Regenerative Medicine GKVK, Bengaluru, Karnataka 560065, India
| | - Kausik Si
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chuankai Zhou
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA.
| |
Collapse
|
215
|
First Survey of SNPs in TMEM154, TLR9, MYD88 and CCR5 Genes in Sheep Reared in Italy and Their Association with Resistance to SRLVs Infection. Viruses 2021; 13:v13071290. [PMID: 34372496 PMCID: PMC8310241 DOI: 10.3390/v13071290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/01/2023] Open
Abstract
Maedi-visna virus (MVV) and caprine arthritis encephalitis virus (CAEV), referred to as small ruminant lentiviruses (SRLVs), belong to the genus Lentivirus of the Retroviridae family. SRLVs infect both sheep and goats, causing significant economic losses and animal welfare damage. Recent findings suggest an association between serological status and allelic variants of different genes such as TMEM154, TLR9, MYD88 and CCR5. The aim of this work was to investigate the role of specific polymorphisms of these genes in SRLVs infection in some sheep flocks in Italy. In addition to those already known, novel variants in the TMEM154 (P7H, I74V, I105V) gene were detected in this study. The risk of infection was determined finding an association between the serological status and polymorphisms P7H, E35K, N70I, I74V, I105V of TMEM154, R447Q, A462S and G520R in TLR9 gene, H176H* and K190K* in MYD88 genes, while no statistical association was observed for the 4-bp deletion of the CCR5 gene. Since no vaccines or treatments have been developed, a genetically based approach could be an innovative strategy to prevent and to control SRLVs infection. Our findings are an important starting point in order to define the genetic resistance profile towards SRLVs infection.
Collapse
|
216
|
Fahmi AR. Profile of gyrA gene mutation in clinical isolate of levofloxacin resistant Escherichia coli. J Basic Clin Physiol Pharmacol 2021; 32:751-754. [PMID: 34214316 DOI: 10.1515/jbcpp-2020-0445] [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: 11/28/2020] [Accepted: 03/03/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Escherichia coli is one of the pathogenic bacteria that caused a nosocomial infection. Levofloxacin is one of the fluoroquinolones group antibiotics which is a broad-spectrum antibiotic that works effectively against E. coli. The mutation can happen in the bacteria which caused a resistant effect in the use of antibacterial. This study aimed at identifying mutation in gene gyrA among E. coli that were resistant to levofloxacin. METHODS The susceptibility of E . coli was determined by disk diffusion. PCR and sequencing were performed to identify the mutation in gyrA. RESULTS A total of 10 isolates showed result resistance to levofloxacin and gyrA gene mutation in the amino acid changes. Nucleotide sequence analysis revealed a point mutation in QRDR (quinolone resistance determining region) of gyrA Ser83→Leu, Asp87→Asn. The silent mutation was also found at codon Val85, Arg91, Ser111, Thr123. CONCLUSIONS Mutation in the gyrA gene affect the occurrence of bacterial resistance of E. coli to levofloxacin.
Collapse
|
217
|
Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides. mBio 2021; 12:e0142321. [PMID: 34154407 PMCID: PMC8262916 DOI: 10.1128/mbio.01423-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The catalytic subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) Nsp12 has a unique nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain that transfers nucleoside monophosphates to the Nsp9 protein and the nascent RNA. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites, and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation in bacterial cells) Nsp12 exists in an inactive state in which NiRAN-RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or nucleoside triphosphates (NTPs) partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote the synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN-RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and the design of its inhibitors.
Collapse
|
218
|
Postnikova OA, Uppal S, Huang W, Kane MA, Villasmil R, Rogozin IB, Poliakov E, Redmond TM. The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA. Int J Mol Sci 2021; 22:6490. [PMID: 34204305 PMCID: PMC8235447 DOI: 10.3390/ijms22126490] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
The SARS-CoV-2 Spike glycoprotein (S protein) acquired a unique new 4 amino acid -PRRA- insertion sequence at amino acid residues (aa) 681-684 that forms a new furin cleavage site in S protein as well as several new glycosylation sites. We studied various statistical properties of the -PRRA- insertion at the RNA level (CCUCGGCGGGCA). The nucleotide composition and codon usage of this sequence are different from the rest of the SARS-CoV-2 genome. One of such features is two tandem CGG codons, although the CGG codon is the rarest codon in the SARS-CoV-2 genome. This suggests that the insertion sequence could cause ribosome pausing as the result of these rare codons. Due to population variants, the Nextstrain divergence measure of the CCU codon is extremely large. We cannot exclude that this divergence might affect host immune responses/effectiveness of SARS-CoV-2 vaccines, possibilities awaiting further investigation. Our experimental studies show that the expression level of original RNA sequence "wildtype" spike protein is much lower than for codon-optimized spike protein in all studied cell lines. Interestingly, the original spike sequence produces a higher titer of pseudoviral particles and a higher level of infection. Further mutagenesis experiments suggest that this dual-effect insert, comprised of a combination of overlapping translation pausing and furin sites, has allowed SARS-CoV-2 to infect its new host (human) more readily. This underlines the importance of ribosome pausing to allow efficient regulation of protein expression and also of cotranslational subdomain folding.
Collapse
Affiliation(s)
- Olga A. Postnikova
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.A.P.); (S.U.)
| | - Sheetal Uppal
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.A.P.); (S.U.)
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy Mass Spectrometry Center, University of Maryland, Baltimore, MD 21201, USA; (W.H.); (M.A.K.)
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy Mass Spectrometry Center, University of Maryland, Baltimore, MD 21201, USA; (W.H.); (M.A.K.)
| | - Rafael Villasmil
- Flow Cytometry Core Facility, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.A.P.); (S.U.)
| | - T. Michael Redmond
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.A.P.); (S.U.)
| |
Collapse
|
219
|
Lee HJ, Kim HJ, Lee SJ. Mismatch Intolerance of 5'-Truncated sgRNAs in CRISPR/Cas9 Enables Efficient Microbial Single-Base Genome Editing. Int J Mol Sci 2021; 22:6457. [PMID: 34208669 PMCID: PMC8235755 DOI: 10.3390/ijms22126457] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas9 system has recently emerged as a useful gene-specific editing tool. However, this approach occasionally results in the digestion of both the DNA target and similar DNA sequences due to mismatch tolerance, which remains a significant drawback of current genome editing technologies. However, our study determined that even single-base mismatches between the target DNA and 5'-truncated sgRNAs inhibited target recognition. These results suggest that a 5'-truncated sgRNA/Cas9 complex could be used to negatively select single-base-edited targets in microbial genomes. Moreover, we demonstrated that the 5'-truncated sgRNA method can be used for simple and effective single-base editing, as it enables the modification of individual bases in the DNA target, near and far from the 5' end of truncated sgRNAs. Further, 5'-truncated sgRNAs also allowed for efficient single-base editing when using an engineered Cas9 nuclease with an expanded protospacer adjacent motif (PAM; 5'-NG), which may enable whole-genome single-base editing.
Collapse
Affiliation(s)
| | | | - Sang Jun Lee
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Korea; (H.J.L.); (H.J.K.)
| |
Collapse
|
220
|
Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021; 13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be 'seen' by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.
Collapse
Affiliation(s)
- Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | | | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
221
|
|
222
|
Zhou Y, Lauschke VM. Computational Tools to Assess the Functional Consequences of Rare and Noncoding Pharmacogenetic Variability. Clin Pharmacol Ther 2021; 110:626-636. [PMID: 33998671 DOI: 10.1002/cpt.2289] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Interindividual differences in drug response are a common concern in both drug development and across layers of care. While genetics clearly influences drug response and toxicity of many drugs, a substantial fraction of the heritable pharmacological and toxicological variability remains unexplained by known genetic polymorphisms. In recent years, population-scale sequencing projects have unveiled tens of thousands of coding and noncoding pharmacogenetic variants with unclear functional effects that might explain at least part of this missing heritability. However, translating these personalized variant signatures into drug response predictions and actionable advice remains challenging and constitutes one of the most important frontiers of contemporary pharmacogenomics. Conventional prediction methods are primarily based on evolutionary conservation, which drastically reduces their predictive accuracy when applied to poorly conserved pharmacogenes. Here, we review the current state-of-the-art of computational variant effect predictors across variant classes and critically discuss their utility for pharmacogenomics. Besides missense variants, we discuss recent progress in the evaluation of synonymous, splice, and noncoding variations. Furthermore, we discuss emerging possibilities to assess haplotypes and structural variations. We advocate for the development of algorithms trained on pharmacogenomic instead of pathogenic data sets to improve the predictive accuracy in order to facilitate the utilization of next-generation sequencing data for personalized clinical decision support and precision pharmacogenomics.
Collapse
Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
223
|
Malekian N, Al-Fatlawi A, Berendonk TU, Schroeder M. Mutations in bdcA and valS Correlate with Quinolone Resistance in Wastewater Escherichia coli. Int J Mol Sci 2021; 22:ijms22116063. [PMID: 34199768 PMCID: PMC8200043 DOI: 10.3390/ijms22116063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/16/2022] Open
Abstract
Single mutations can confer resistance to antibiotics. Identifying such mutations can help to develop and improve drugs. Here, we systematically screen for candidate quinolone resistance-conferring mutations. We sequenced highly diverse wastewater E. coli and performed a genome-wide association study (GWAS) to determine associations between over 200,000 mutations and quinolone resistance phenotypes. We uncovered 13 statistically significant mutations including 1 located at the active site of the biofilm dispersal gene bdcA and 6 silent mutations in the aminoacyl-tRNA synthetase valS. The study also recovered the known mutations in the topoisomerases gyrase (gyrA) and topoisomerase IV (parC). In summary, we demonstrate that GWAS effectively and comprehensively identifies resistance mutations without a priori knowledge of targets and mode of action. The results suggest that mutations in the bdcA and valS genes, which are involved in biofilm dispersal and translation, may lead to novel resistance mechanisms.
Collapse
Affiliation(s)
- Negin Malekian
- Biotechnology Center (BIOTEC), Dresden University of Technology, Tatzberg 47-49, 01307 Dresden, Germany; (N.M.); (A.A.-F.)
| | - Ali Al-Fatlawi
- Biotechnology Center (BIOTEC), Dresden University of Technology, Tatzberg 47-49, 01307 Dresden, Germany; (N.M.); (A.A.-F.)
| | - Thomas U. Berendonk
- Institute of Hydrobiology, Dresden University of Technology, 01217 Dresden, Germany;
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Dresden University of Technology, Tatzberg 47-49, 01307 Dresden, Germany; (N.M.); (A.A.-F.)
- Correspondence:
| |
Collapse
|
224
|
Abstract
Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.
Collapse
Affiliation(s)
- Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| |
Collapse
|
225
|
Lee J, Elliott MR, Yamada T, Jung G. Field Assessment of Six Point-Mutations in SDH Subunit Genes Conferring Varying Resistance Levels to SDHIs in Clarireedia spp. PLANT DISEASE 2021; 105:1685-1691. [PMID: 33944573 DOI: 10.1094/pdis-06-20-1344-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dollar spot, caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa F.T. Bennett), is the most economically important turfgrass disease causing considerable damage on golf courses. While cultural practices are available for reducing dollar spot infection, chemical fungicide use is often necessary for maintaining optimal turf quality. Since the release of boscalid in 2003, the succinate dehydrogenase inhibitor (SDHI) class has become an invaluable tool for managing dollar spot. However, resistance to this class has recently been reported in Clarireedia spp. and many other plant pathogenic fungi. After SDHI field failure on four golf courses and one university research plot, a total of six unique SDH mutations conferring differential in vitro sensitivities to SDHIs have been identified in Clarireedia spp. In 2018 and 2019, turf research plots were inoculated with sensitive, non-mutated isolates of Clarireedia spp., as well as resistant isolates harboring each unique identified mutation. Fungicide efficacy trials were conducted on inoculated plots to assess differential sensitivity to five SDHI active ingredients (boscalid, fluxapyroxad, isofetamid, fluopyram, and pydiflumetofen) across mutations under field conditions. Results indicate unique mutations are associated with distinct SDHI field efficacy profiles as shown in in-vitro sensitivity assays. Isolate populations with B subunit mutations (H267Y/R) were more sensitive to fluopyram, whereas isolate populations with C subunit mutations (C-G91R, C-G150R) showed resistance to all SDHIs tested. Mutation-associated differential sensitivity observed under field conditions indicates a need for a nation-wide survey and frequent monitoring of SDHI sensitivity of dollar spot populations on golf courses in the USA. Further, the information gained from this study will be useful in providing sustainable management recommendations for controlling site-specific resistant populations of Clarireedia spp.
Collapse
Affiliation(s)
- Jaemin Lee
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Michaela R Elliott
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 0606-0808, Japan
| | - Geunhwa Jung
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| |
Collapse
|
226
|
Wang Z, Zhou Y, Han Q, Ye X, Chen Y, Sun Y, Liu Y, Zou J, Qi G, Zhou X, Cheng L, Ren B. Synonymous point mutation of gtfB gene caused by therapeutic X-rays exposure reduced the biofilm formation and cariogenic abilities of Streptococcus mutans. Cell Biosci 2021; 11:91. [PMID: 34001238 PMCID: PMC8130306 DOI: 10.1186/s13578-021-00608-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The shift of oral microbiota is a critical factor of radiation caries in head and neck cancer patients after the radiotherapy. However, the direct effects of irradiation on the genome and virulence of cariogenic bacteria are poorly described. Here we investigated the genomic mutations and virulence change of Streptococcus mutans (S. mutans), the major cariogenic bacteria, exposed to the therapeutic doses of X-rays. RESULTS X-ray reduced the survival fraction of S. mutans and impacted its biofilm formation. We isolated a biofilm formation-deficient mutant #858 whose genome only possessed three synonymous mutations (c.2043 T > C, c.2100C > T, c.2109A > G) in gtfB gene. The "silent mutation" of c.2043 T > C in gtfB gene can cause the down-regulation of all of the gtfs genes' expression and decrease the GtfB enzyme secretion without the effect on the growth due to the codon bias. #858 and synonymous point mutation strain gtfB 2043 T>C, similar to the gtfB gene null mutant Δ gtfB, can significantly decrease the extracellular polysaccharide production, biofilm formation and cariogenic capabilities both in vitro and in vivo compared with wild type. CONCLUSION The direct exposure of X-ray radiation can affect the genome and virulence of oral bacteria even at therapeutic doses. The synonymous mutations of genome are negligent factors for gene expression and related protein translation due to the codon usage frequency.
Collapse
Affiliation(s)
- Zheng Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yujie Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qi Han
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China
| | - Xingchen Ye
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China
| | - Yanyan Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yan Sun
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yaqi Liu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jing Zou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Guohai Qi
- Radiotherapy Center, Sichuan Cancer Hospital, Chengdu, 610041, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China. .,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Lei Cheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China. .,Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Biao Ren
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
227
|
Mordstein C, Cano L, Morales AC, Young B, Ho AT, Rice AM, Liss M, Hurst LD, Kudla G. Transcription, mRNA export and immune evasion shape the codon usage of viruses. Genome Biol Evol 2021; 13:6275682. [PMID: 33988683 PMCID: PMC8410142 DOI: 10.1093/gbe/evab106] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
The nucleotide composition, dinucleotide composition, and codon usage of many viruses differs from their hosts. These differences arise because viruses are subject to unique mutation and selection pressures that do not apply to host genomes; however, the molecular mechanisms that underlie these evolutionary forces are unclear. Here, we analysed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation. We find that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses. In an experimental follow-up, we find that the effects of GC content on gene expression depend on whether the genetic material is delivered to the cell as DNA or mRNA, whether it is transcribed by endogenous or exogenous RNA polymerase, and whether transcription takes place in the nucleus or cytoplasm. Our results suggest that viral codon usage cannot be explained by a simple adaptation to the codon usage of the host - instead, it reflects the combination of multiple selective and mutational pressures, including the need for efficient transcription, export, and immune evasion.
Collapse
Affiliation(s)
- Christine Mordstein
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Bethan Young
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Michael Liss
- Thermo Fisher Scientific, GENEART GmbH, Regensburg, Germany
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
228
|
Maciuba K, Rajasekaran N, Chen X, Kaiser CM. Co-translational folding of nascent polypeptides: Multi-layered mechanisms for the efficient biogenesis of functional proteins. Bioessays 2021; 43:e2100042. [PMID: 33987870 PMCID: PMC8262109 DOI: 10.1002/bies.202100042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 11/09/2022]
Abstract
The coupling of protein synthesis and folding is a crucial yet poorly understood aspect of cellular protein folding. Over the past few years, it has become possible to experimentally follow and define protein folding on the ribosome, revealing principles that shape co-translational folding and distinguish it from refolding in solution. Here, we highlight some of these recent findings from biochemical and biophysical studies and their potential significance for cellular protein biogenesis. In particular, we focus on nascent chain interactions with the ribosome, interactions within the nascent protein, modulation of translation elongation rates, and the role of mechanical force that accompanies nascent protein folding. The ability to obtain mechanistic insight in molecular detail has set the stage for exploring the intricate process of nascent protein folding. We believe that the aspects discussed here will be generally important for understanding how protein synthesis and folding are coupled and regulated.
Collapse
Affiliation(s)
- Kevin Maciuba
- CMDB Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christian M Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| |
Collapse
|
229
|
Ilyinsky NS, Nesterov SV, Shestoperova EI, Fonin AV, Uversky VN, Gordeliy VI. On the Role of Normal Aging Processes in the Onset and Pathogenesis of Diseases Associated with the Abnormal Accumulation of Protein Aggregates. BIOCHEMISTRY (MOSCOW) 2021; 86:275-289. [PMID: 33838629 DOI: 10.1134/s0006297921030056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aging is a prime systemic cause of various age-related diseases, in particular, proteinopathies. In fact, most diseases associated with protein misfolding are sporadic, and their incidence increases with aging. This review examines the process of protein aggregate formation, the toxicity of such aggregates, the organization of cellular systems involved in proteostasis, and the impact of protein aggregates on important cellular processes leading to proteinopathies. We also analyze how manifestations of aging (mitochondrial dysfunction, dysfunction of signaling systems, changes in the genome and epigenome) facilitate pathogenesis of various proteinopathies either directly, by increasing the propensity of key proteins for aggregation, or indirectly, through dysregulation of stress responses. Such analysis might help in outlining approaches for treating proteinopathies and extending healthy longevity.
Collapse
Affiliation(s)
- Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Elizaveta I Shestoperova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexander V Fonin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Forschungszentrum Juelich, Juelich, 52428, Germany.,Institut de Biologie Structurale, Grenoble, 38000, France
| |
Collapse
|
230
|
Sun G, Dong Y, Sun C, Yao H, Lin Z. Vital Role of Glutamate Dehydrogenase Gene in Ammonia Detoxification and the Association Between its SNPs and Ammonia Tolerance in Sinonovacula constricta. Front Physiol 2021; 12:664804. [PMID: 34025453 PMCID: PMC8131826 DOI: 10.3389/fphys.2021.664804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence has revealed accumulated ammonia will cause adverse effects on the growth, reproduction, and survival of aquatic animals. As a marine benthic mollusk, the razor clam Sinonovacula constricta shows better growth and survival under high ammonia nitrogen environment. However, little is known about its adaptation mechanisms to high ammonia stress in an integrated mariculture system. In this study, we analyzed the association between the polymorphism of glutamate dehydrogenase gene (GDH), a key gene involved in ammonia nitrogen detoxification, and ammonia tolerance. The results showed that 26 and 22 single-nucleotide polymorphisms (SNPs) of GDH in S. constricta (denoted as Sc-GDH) were identified from two geographical populations, respectively. Among them, two SNPs (c.323T > C and c.620C > T) exhibited a significant and strong association with ammonia tolerance, suggesting that Sc-GDH gene could serve as a potential genetic marker for molecular marker–assisted selection to increase survival rate and production of S. constricta. To observe the histological morphology and explore the histocellular localization of Sc-GDH, by paraffin section and hematoxylin–eosin staining, the gills were divided into gill filament (contains columnar and flattened cells) and gill cilia, whereas hepatopancreas was made up of individual hepatocytes. The results of immunohistochemistry indicated that the columnar cells of gill filaments and the endothelial cells of hepatocytes were the major sites for Sc-GDH secretion. Under ammonia stress (180 mg/L), the expression levels of Sc-GDH were extremely significantly downregulated at 24, 48, 72, and 96 h (P < 0.01) after RNA interference. Thus, we can speculate that Sc-GDH gene may play an important role in the defense process against ammonia stress. Overall, these findings laid a foundation for further research on the adaptive mechanisms to ammonia–nitrogen tolerance for S. constricta.
Collapse
Affiliation(s)
- Gaigai Sun
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Yinghui Dong
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, China.,Key Laboratory of Aquatic Germplasm Resources of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Changsen Sun
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, China
| | - Hanhan Yao
- Key Laboratory of Aquatic Germplasm Resources of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, China.,Key Laboratory of Aquatic Germplasm Resources of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| |
Collapse
|
231
|
Franceschi E, Biase DD, Di Nunno V, Pession A, Tosoni A, Gatto L, Lodi R, Tallini G, Visani M, Bartolini S, Brandes AA. IDH1 105GGT single nucleotide polymorphism improves progression free survival in patients with IDH mutated grade II and III gliomas. Pathol Res Pract 2021; 221:153445. [PMID: 33887545 DOI: 10.1016/j.prp.2021.153445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND A synonymous single nucleotide polymorphism (SNP) is a substitution of a single base that does not modify the primary amino acid sequence but could influence protein function. In patients with brain tumors, the incidence of the silent SNP IDH 1 105GGT (rs11554137) is three times higher than the normal population. METHODS Our aim was to investigate the prognostic role of the IDH 1 105GGT SNP. We selected only patients with diagnosis of IDH grade II or III mutated glioma. Additional inclusion criteria were: complete clinical data and adequate tumor samples for IDH 1 or 2 sequencing. RESULTS 71 patients with grade II and III IDH-mutated glioma have been evaluated. Nine of 71 patients (12.7 %) presented the SNP 105GGT. Patients with SNP 105GGT had a longer Progression Free Survival (PFS - 47.3 months vs Not reached; p = 0.015). The SNP 105GGT (HR 0.240; 95 %CI 0.074-0.784, p = 0.018) was confirmed as an independent prognostic factors in multivariate analysis. CONCLUSIONS Patients with IDH1 or 2 mutated grade II and III glioma presenting the SNP105GGT had longer PFS regardless adjuvant treatment received and extension of primary surgery. A validation is warranted to confirm our preliminary results.
Collapse
Affiliation(s)
| | - Dario De Biase
- Department of Pharmacy and Biotechnology (FaBiT) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | | | - Annalisa Pession
- Department of Pharmacy and Biotechnology (FaBiT) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Alicia Tosoni
- Department of Oncology, AUSL Bologna, Bologna, Italy
| | - Lidia Gatto
- Department of Oncology, AUSL Bologna, Bologna, Italy
| | - Raffaele Lodi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | | | | |
Collapse
|
232
|
Park D, Propper CR, Wang G, Salanga MC. Synonymous single nucleotide polymorphism in arsenic (+3) methyltransferase of the Western mosquitofish (Gambusia affinis) and its gene expression among field populations. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:711-718. [PMID: 33811567 PMCID: PMC8060185 DOI: 10.1007/s10646-021-02376-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 05/05/2023]
Abstract
Naturally occurring arsenic is toxic at extremely low concentrations, yet some species persist even in high arsenic environments. We wanted to test if these species show evidence of evolution associated with arsenic exposure. To do this, we compared allelic variation across 872 coding nucleotides of arsenic (+3) methyltransferase (as3mt) and whole fish as3mt gene expression from three field populations of Gambusia affinis, from water sources containing low (1.9 ppb), medium-low (3.3 ppb), and high (15.7 ppb) levels of arsenic. The high arsenic site exceeds the US EPA's Maximum Contamination Level for drinking water. Medium-low and high populations exhibited homozygosity, and no sequence variation across all animals sampled. Eleven of 24 fish examined (45.8%) in the low arsenic population harbored synonymous single nucleotide polymorphisms (SNPs) in exons 4 and/or 10. SNP presence in the low arsenic population was not associated with differences in as3mt transcript levels compared to fish from the medium-low site, where SNPs were noted; however, as3mt expression in fish from the high arsenic concentration site was significantly lower than the other two sites. Low sequence variation in fish populations from sites with medium-low and high arsenic concentrations suggests greater selective pressure on this allele, while higher variation in the low population suggests a relaxed selection. Our results suggest gene regulation associated with arsenic detoxification may play a more crucial role in influencing responses to arsenic than polymorphic gene sequence. Understanding microevolutionary processes to various contaminants require the evaluation of multiple populations across a wide range of pollution exposures.
Collapse
Affiliation(s)
- Daesik Park
- Division of Science Education, Kangwon National University, Chuncheon, Kangwon, 24341, South Korea
| | - Catherine R Propper
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Guangning Wang
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Matthew C Salanga
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| |
Collapse
|
233
|
Korem N, Duek O, Xu K, Harpaz-Rotem I, Pietrzak RH. Cannabinoid Receptor 1 rs1049353 Variant, Childhood Abuse, and the Heterogeneity of PTSD Symptoms: Results From the National Health and Resilience in Veterans Study. ACTA ACUST UNITED AC 2021; 5:24705470211011075. [PMID: 33997583 PMCID: PMC8107935 DOI: 10.1177/24705470211011075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 11/15/2022]
Abstract
Background Accumulating evidence implicates the endocannabinoid system, including
variants in the cannabinoid-1 receptor gene (CNR1), in the
pathophysiology of posttraumatic stress disorder (PTSD). The synonymous
G1359A variant (rs1049353) in the CNR1 gene has been linked
to PTSD in individuals exposed to childhood abuse. In this study, the
effects of the rs1049353 genotype and childhood abuse on overall PTSD
symptoms, as well as PTSD symptom clusters were examined in order to examine
how this interaction relates to the phenotypic expression of this
disorder. Method Data were analyzed from 1,372 Caucasian U.S. veterans who participated in the
National Health and Resilience in Veterans Study. Multivariable analyses
were conducted to evaluate the association between rs1049353 genotype,
childhood abuse, and their interaction in relation to PTSD symptoms. Results A significant interaction between rs1049353 genotype and childhood abuse was
observed, with A allele carriers with histories of childhood abuse reporting
greater severity of PTSD symptoms, most notably anxious arousal, relative to
G/G homozygotes. Significant main effects of childhood abuse on overall PTSD
symptoms, and re-experiencing, emotional numbing, and dysphoric arousal
symptom clusters, as well as of A allele carrier status on anxious arousal
symptoms were observed. Conclusions Results of this study replicate prior work and suggest that the
rs1049353-by-childhood abuse interaction is particularly associated with the
manifestation of anxious arousal symptoms of PTSD. Taken together, these
findings underscore the importance of considering the phenotypic
heterogeneity of PTSD in gene-environment studies of this multifaceted
disorder.
Collapse
Affiliation(s)
- Nachshon Korem
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Or Duek
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Ke Xu
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Ilan Harpaz-Rotem
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Robert H Pietrzak
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
234
|
Wang B, Svetlov V, Wolf YI, Koonin EV, Nudler E, Artsimovitch I. Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.24.428004. [PMID: 33948598 PMCID: PMC8095223 DOI: 10.1101/2021.01.24.428004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), Nsp12, has a unique NiRAN domain that transfers nucleoside monophosphates to the Nsp9 protein. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation) Nsp12 exists in inactive state in which NiRAN/RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or NTPs partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN/RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically-linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and design of its inhibitors. HIGHLIGHTS Codon-optimization of Nsp12 triggers misfolding and activity lossSlow translation, accessory Nsp7 and Nsp8 subunits, and NTPs rescue Nsp12Non-substrate nucleotides activate RNA chain synthesis, likely via NiRAN domainCrosstalk between two Nsp12 active sites that bind the same ligands.
Collapse
Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
235
|
Ooi BNS, Raechell, Ying AF, Koh YZ, Jin Y, Yee SWL, Lee JHS, Chong SS, Tan JWC, Liu J, Lee CG, Drum CL. Robust Performance of Potentially Functional SNPs in Machine Learning Models for the Prediction of Atorvastatin-Induced Myalgia. Front Pharmacol 2021; 12:605764. [PMID: 33967749 PMCID: PMC8100589 DOI: 10.3389/fphar.2021.605764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Statins can cause muscle symptoms resulting in poor adherence to therapy and increased cardiovascular risk. We hypothesize that combinations of potentially functional SNPs (pfSNPs), rather than individual SNPs, better predict myalgia in patients on atorvastatin. This study assesses the value of potentially functional single nucleotide polymorphisms (pfSNPs) and employs six machine learning algorithms to identify the combination of SNPs that best predict myalgia. Methods: Whole genome sequencing of 183 Chinese, Malay and Indian patients from Singapore was conducted to identify genetic variants associated with atorvastatin induced myalgia. To adjust for confounding factors, demographic and clinical characteristics were also examined for their association with myalgia. The top factor, sex, was then used as a covariate in the whole genome association analyses. Variants that were highly associated with myalgia from this and previous studies were extracted, assessed for potential functionality (pfSNPs) and incorporated into six machine learning models. Predictive performance of a combination of different models and inputs were compared using the average cross validation area under ROC curve (AUC). The minimum combination of SNPs to achieve maximum sensitivity and specificity as determined by AUC, that predict atorvastatin-induced myalgia in most, if not all the six machine learning models was determined. Results: Through whole genome association analyses using sex as a covariate, a larger proportion of pfSNPs compared to non-pf SNPs were found to be highly associated with myalgia. Although none of the individual SNPs achieved genome wide significance in univariate analyses, machine learning models identified a combination of 15 SNPs that predict myalgia with good predictive performance (AUC >0.9). SNPs within genes identified in this study significantly outperformed SNPs within genes previously reported to be associated with myalgia. pfSNPs were found to be more robust in predicting myalgia, outperforming non-pf SNPs in the majority of machine learning models tested. Conclusion: Combinations of pfSNPs that were consistently identified by different machine learning models to have high predictive performance have good potential to be clinically useful for predicting atorvastatin-induced myalgia once validated against an independent cohort of patients.
Collapse
Affiliation(s)
- Brandon N S Ooi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Raechell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | | | - Yong Zher Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Yu Jin
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Sherman W L Yee
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
| | | | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jack W C Tan
- Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore.,Duke-NUS Graduate School, Singapore, Singapore.,Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Chester L Drum
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore.,Translational Laboratory in Genetic Medicine, Singapore, Singapore
| |
Collapse
|
236
|
Li Q, Li J, Yu CP, Chang S, Xie LL, Wang S. Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development. BMC Cancer 2021; 21:388. [PMID: 33836673 PMCID: PMC8033552 DOI: 10.1186/s12885-021-08131-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/30/2021] [Indexed: 01/11/2023] Open
Abstract
Background Synonymous mutations do not change the protein sequences. Automatically, they have been regarded as neutral events and are ignored in the mutation-based cancer studies. However, synonymous mutations will change the codon optimality, resulting in altered translational velocity. Methods We fully utilized the transcriptome and translatome of liver cancer and normal tissue from ten patients. We profiled the mutation spectrum and examined the effect of synonymous mutations on translational velocity. Results Synonymous mutations that increase the codon optimality significantly enhanced the translational velocity, and were enriched in oncogenes. Meanwhile, synonymous mutations decreasing codon optimality slowed down translation, and were enriched in tumor suppressor genes. These synonymous mutations significantly contributed to the translational changes in tumor samples compared to normal samples. Conclusions Synonymous mutations might play a role in liver cancer development by altering codon optimality and translational velocity. Synonymous mutations should no longer be ignored in the genome-wide studies.
Collapse
Affiliation(s)
- Qun Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jian Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chun-Peng Yu
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuai Chang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ling-Ling Xie
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Song Wang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| |
Collapse
|
237
|
Munisamy M, Munisamy S, Kumar JP, Jose A, Thomas L, Baburaj G, Subbiah V. Pharmacogenetics of ATP binding cassette transporter MDR1(1236C>T) gene polymorphism with glioma patients receiving Temozolomide-based chemoradiation therapy in Indian population. THE PHARMACOGENOMICS JOURNAL 2021; 21:262-272. [PMID: 33589792 DOI: 10.1038/s41397-021-00206-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/18/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023]
Abstract
Temozolomide (TMZ), an alkylating agent with a broad-spectrum antitumor activity, ability to cross blood-brain barrier (BBB), shown to be effective against malignant glioma. This study aims to investigate the effect of 1236C>T (rs1128503) single-nucleotide gene polymorphisms of ABCB1 (MDR1) in north-Indian patients diagnosed with glioma undergoing TMZ-based chemoradiotherapy. Genotyping was performed in 100 patients diagnosed with malignant glioma (50 anaplastic astrocytoma (AA) patients and 50 glioblastoma multiforme (GBM) patients) and 150 age and sex-matched controls by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method, followed by sanger sequencing. TMZ plasma levels were analyzed by reverse phase HPLC method. Glioma patient's survival time was analyzed by Kaplan-Meier's curve. Results of MDR1 gene 1236C>T polymorphism showed significant allelic and genotypic frequency association between glioma patients and controls. The plasma TMZ levels between metabolizers group in Grade III and Grade IV were found to be statistically significant (p < 0.05). The mutant genotype (TT) has less survival benefit compared with other genotypes (CT/CC) and the survival difference between AA and GBM was found to be statistically significant (p < 0.05). Though CT and TT polymorphisms have significant association with lower TMZ levels in both Grade III (AA) and IV (GBM) tumors, the survival difference seems to be mainly among patients with Grade III tumors. Our findings suggest that the MDR1 gene polymorphism plays a role in plasma TMZ levels and in survival time of glioma patients and, hence, TMZ therapy in malignant glioma can be predicted by genotyping MDR1 (1236C>T) gene polymorphism.
Collapse
Affiliation(s)
- Murali Munisamy
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India.,Department of Neuro Biochemistry, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Srinivasan Munisamy
- Department of Neuro Biochemistry, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Julka Pramod Kumar
- Department of Radiotherapy, Dr. B.R.A Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Anmi Jose
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gayathri Baburaj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vivekanandhan Subbiah
- Department of Neuro Biochemistry, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
238
|
Genotype-expression interactions for BDNF across human brain regions. BMC Genomics 2021; 22:207. [PMID: 33757426 PMCID: PMC7989003 DOI: 10.1186/s12864-021-07525-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/11/2021] [Indexed: 01/20/2023] Open
Abstract
Background Genetic variations in brain-derived neurotrophic factor (BDNF) are associated with various psychiatric disorders including depression, obsessive-compulsive disorder, substance use disorders, and schizophrenia; altered gene expression triggered by these genetic variants may serve to create these phenotypes. But genotype-expression interactions for this gene have not been well-studied across brain regions relevant for psychiatric disorders. Results At false discovery rate (FDR) of 10% (q < 0.1), a total of 61 SNPs were associated with BDNF expression in cerebellum (n = 209), 55 SNPs in cortex (n = 205), 48 SNPs in nucleus accumbens (n = 202), 47 SNPs in caudate (n = 194), and 58 SNPs in cerebellar hemisphere (n = 175). We identified a set of 30 SNPs in 2 haplotype blocks that were associated with alterations in expression for each of these 5 regions. The first haplotype block included variants associated in the literature with panic disorders (rs16917204), addiction (rs11030104), bipolar disorder (rs16917237/rs2049045), and obsessive-compulsive disorder (rs6265). Likewise, variants in the second haplotype block have been previously associated with disorders such as nicotine addiction, major depressive disorder (rs988748), and epilepsy (rs6484320/rs7103411). Conclusions This work supports the association of variants within BDNF for expression changes in these key brain regions that may contribute to common behavioral phenotypes for disorders of compulsion, impulsivity, and addiction. These SNPs should be further investigated as possible therapeutic and diagnostic targets to aid in management of these and other psychiatric disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07525-1.
Collapse
|
239
|
Niersch J, Vega-Rubín-de-Celis S, Bazarna A, Mergener S, Jendrossek V, Siveke JT, Peña-Llopis S. A BAP1 synonymous mutation results in exon skipping, loss of function and worse patient prognosis. iScience 2021; 24:102173. [PMID: 33681728 PMCID: PMC7918674 DOI: 10.1016/j.isci.2021.102173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/11/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Synonymous mutations are generally disregarded by genomic analyses because they are considered non-pathogenic. We identified and characterized a somatic synonymous mutation in the epigenetic modifier and tumor suppressor BAP1, resulting in exon skipping and complete protein inactivation. This radically altered the prognosis of a clear-cell renal cell carcinoma patient from The Cancer Genome Atlas (TCGA) with a PBRM1 mutation (a predictor biomarker for positive responses to immune checkpoint inhibitors) from good (an estimated overall survival of 117 months) to a very bad prognosis (an estimated overall survival of 31 months), emphasizing the importance of scrutinizing synonymous mutations near acceptor splice sites of cancer genes for accurate precision medicine.
Collapse
Affiliation(s)
- Jennifer Niersch
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Anna Bazarna
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Svenja Mergener
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Samuel Peña-Llopis
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| |
Collapse
|
240
|
Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens. Animals (Basel) 2021; 11:ani11030825. [PMID: 33804055 PMCID: PMC8001891 DOI: 10.3390/ani11030825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/06/2022] Open
Abstract
Simple Summary Mitochondria are commonly known as “the powerhouse of the cell”, influencing the fitness, lifespan and metabolism of eukaryotic organisms. In our study we examined mitochondrial and nuclear genomic diversity in two high yielding strains of laying hens. We tested if the mitochondrial genome affects functional traits such as body weight and phosphorus utilization. We discovered a surprisingly low mitochondrial genetic diversity and an unequal distribution of the haplotypes among both strains, leading to limitations of robust links to phenotypic traits. In contrast, we found similar levels of nuclear genome diversity in both strains. Our study explores the potential influence of the mitochondrial genome on phenotypic traits and thus contributes to a better understanding of the function of this organelle in laying hens. Further, we focus on its usefulness as a genetic marker, which is often underestimated in breeding approaches, given the different inheritance mechanism compared to the nuclear genome. Abstract Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.
Collapse
|
241
|
CYP7A1, NPC1L1, ABCB1, and CD36 Polymorphisms Are Associated with Increased Serum Coenzyme Q 10 after Long-Term Supplementation in Women. Antioxidants (Basel) 2021; 10:antiox10030431. [PMID: 33799730 PMCID: PMC7998724 DOI: 10.3390/antiox10030431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
Coenzyme Q10 (CoQ10), an essential component for energy production that exhibits antioxidant activity, is considered a health-supporting and antiaging supplement. However, intervention-controlled studies have provided variable results on CoQ10 supplementation benefits, which may be attributed to individual CoQ10 bioavailability differences. This study aimed to investigate the relationship between genetic polymorphisms and CoQ10 serum levels after long-term supplementation. CoQ10 levels at baseline and after one year of supplementation (150 mg) were determined, and eight single nucleotide polymorphisms (SNPs) in cholesterol metabolism and CoQ10 absorption, efflux, and cellular uptake related genes were assessed. Rs2032582 (ABCB1) and rs1761667 (CD36) were significantly associated with a higher increase in CoQ10 levels in women. In addition, in women, rs3808607 (CYP7A1) and rs2072183 (NPC1L1) were significantly associated with a higher increase in CoQ10 per total cholesterol levels. Subgroup analyses showed that these four SNPs were useful for classifying high- or low-responder to CoQ10 bioavailability after long-term supplementation among women, but not in men. On the other hand, in men, no SNP was found to be significantly associated with increased serum CoQ10. These results collectively provide novel evidence on the relationship between genetics and CoQ10 bioavailability after long-term supplementation, which may help understand and assess CoQ10 supplementation effects, at least in women.
Collapse
|
242
|
Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
Collapse
Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
243
|
Lee J, Elliott MR, Kim M, Yamada T, Jung G. A Rapid Molecular Detection System for SdhB and SdhC Point Mutations Conferring Differential Succinate Dehydrogenase Inhibitor Resistance in Clarireedia Populations. PLANT DISEASE 2021; 105:660-666. [PMID: 32757732 DOI: 10.1094/pdis-04-20-0724-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dollar spot, caused by the ascomycete fungus Clarireedia (formerly Sclerotinia), is one of the most resource-demanding diseases on amenity turfgrasses in North America. Differential resistance to the succinate dehydrogenase inhibitor (SDHI) fungicide class, conferred by singular point mutations on the SdhB, SdhC, and SdhD subunits of the succinate dehydrogenase enzyme (SDH), has been reported in dollar spot as well as many other plant-pathogenic fungal diseases. Four unique mutations were previously reported from Clarireedia field isolates collected from two different cool-season golf courses in Japan and Rhode Island: an amino acid substitution H267Y and a silent mutation (CTT to CTC) at codon 181 on the SdhB subunit gene, and amino acid substitutions G91R and G150R on the SdhC subunit gene. To properly diagnose and monitor SDHI resistance in the field, a rapid detection system for known mutations is crucial. As part of this study, additional SDHI-resistant Clarireedia isolates were collected from Rutgers University research plots and in vitro sensitivity to four SDHI active ingredients was assessed. SdhB, SdhC, and SdhD subunits of these isolates were sequenced to reveal an additional mutation on the SdhB subunit gene, H267R, not previously observed in Clarireedia. Cleaved amplified polymorphic sequence (CAPS) and derived CAPS molecular markers were developed to detect five mutations conferring SDHI resistance in Clarireedia isolates and validated using samples from two additional golf courses in Connecticut and Wisconsin experiencing SDHI field failure. This PCR-based molecular detection system will be useful for continued monitoring, assessment, and delay of SDHI resistance in the field.
Collapse
Affiliation(s)
- Jaemin Lee
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Michaela R Elliott
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Minsoo Kim
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 0606-0808, Japan
| | - Geunhwa Jung
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, U.S.A
| |
Collapse
|
244
|
Ghaffari T, Mirhosseini Motlagh N, Daraei A, Tafrihi M, Saravi M, Sabour D. Novel SCN5A variants identified in a group of Iranian Brugada syndrome patients. Funct Integr Genomics 2021; 21:331-340. [PMID: 33641026 DOI: 10.1007/s10142-021-00778-9] [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: 06/16/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 10/22/2022]
Abstract
Brugada syndrome (BrS) is a rare hereditary arrhythmia syndrome that increases an individual's risk for sudden cardiac death (SCD) due to ventricular fibrillation. This disorder is regarded as a notable cause of death in individuals aged less than 40 years, responsible for up to 40% of sudden deaths in cases without structural heart disease, and is reported to be an endemic in Asian countries. Mutations in SCN5A are found in approximately 30% of patients with Brugada syndrome. This study aimed to investigate mutations in the SCN5A gene in a group of Iranian Brugada syndrome patients. Nine probands (n = 9, male, mean age = 39) diagnosed with Brugada syndrome were enrolled in this study. Exon 2 to 29 were amplified by PCR and subjected to direct sequencing. Eight in silico prediction tools were used to anticipate the effects of non-synonymous variants. Seven known polymorphisms and 2 previously reported disease-causing mutations, including H558R and G1406R, were found in the studied cases. Twenty novel variants were identified: 15 missense, 2 frameshift, 2 synonymous, and one nonsense variants. In silico tools predicted 11 non-synonymous variants to have damaging effects, whereas frameshift and nonsense variants were considered inherently pathogenic. The novel variants identified in this study, alongside previously reported mutations, are highly likely to be the cause of the Brugada syndrome phenotype observed in the patient group. Further analysis is required to understand the physiological effects caused by these variants.
Collapse
Affiliation(s)
- Taraneh Ghaffari
- Molecular and Cell Biology Research Lab2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, 47416-95447, Iran.,Department of Laboratory Science, Faculty of Paramedicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran.,Dermatology Research Institute, Suite 310, 8500 Blackfoot Trial SE, Calgary, Alberta, T2J 7E1, Canada
| | - Naser Mirhosseini Motlagh
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11 St, Babol, 47138-18983, Iran
| | - Abdolreza Daraei
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran
| | - Majid Tafrihi
- Molecular and Cell Biology Research Lab2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Mehrdad Saravi
- Department of Cardiology, Faculty of Medicine, Rohani Hospital, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran
| | - Davood Sabour
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11 St, Babol, 47138-18983, Iran. .,Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran.
| |
Collapse
|
245
|
Lusvarghi S, Durell SR, Ambudkar SV. Does the ATP-bound EQ mutant reflect the pre- or post-ATP hydrolysis state in the catalytic cycle of human P-glycoprotein (ABCB1)? FEBS Lett 2021; 595:750-762. [PMID: 33547668 DOI: 10.1002/1873-3468.14054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/14/2021] [Accepted: 01/28/2021] [Indexed: 12/15/2022]
Abstract
P-glycoprotein (P-gp, ABCB1) is an ABC transporter associated with the development of multidrug resistance to chemotherapy. During its catalytic cycle, P-gp undergoes significant conformational changes. Recently, atomic structures of some of these conformations have been resolved using cryo-electron microscopy. The ATP hydrolysis-defective mutant of the catalytic glutamate residue of the Walker B motif (E556Q/E1201Q) has been used to determine the structure of the ATP-bound inward-closed conformation of P-gp. Here, we show that this mutant does not appear to undergo the same steps as wild-type P-gp. We discuss conformational differences in the EQ mutant that may lead to a better understanding of the catalytic cycle of P-gp and propose that additional structural studies with wild-type P-gp are required.
Collapse
Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stewart R Durell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
246
|
Li Y, Fan L, Luo R, Yang Z, Yuan M, Zhang J, Gan J. Case Report: De novo Variants of KMT2E Cause O'Donnell-Luria-Rodan Syndrome: Additional Cases and Literature Review. Front Pediatr 2021; 9:641841. [PMID: 33681112 PMCID: PMC7935518 DOI: 10.3389/fped.2021.641841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 12/30/2022] Open
Abstract
Introduction: O'Donnell-Luria-Rodan syndrome was recently identified as an autosomal dominant systemic disorder caused by variants in KMT2E. It is characterized by global developmental delay, some patients also exhibit autism, seizures, hypotonia, and/or feeding difficulties. Methods: Whole-exome sequencing of family trios were performed for two independent children with unexplained recurrent seizures and developmental delay. Both cases were identified as having de novo variants in KMT2E. We also collected and summarized the clinical data and diagnosed them with O'Donnell-Luria-Rodan syndrome. Structural-prediction programs were used to draw the variants' locations. Results: A 186 G>A synonymous variant [NM_182931.3:exon4: c.186G>A (p.Ala62=)] was found in one family, resulting in alternative splicing acid. A 5417 C>T transition variant [NM_182931.3:exon27: c.5417C>T (p.Pro1806Leu)] was found in another family, resulting in 1806 Pro-to-Leu substitution. Both variants were classified as likely pathogenic according to the ACMG (American College of Medical Genetics and Genomics) guidelines and verified by Sanger sequencing. Conclusion: To date, three studies of O'Donnell-Luria-Rodan syndrome have been reported with heterogeneous clinical manifestations. As a newly recognized inherited systemic disorder, O'Donnell-Luria-Rodan syndrome needs to be paid more attention, especially in gene testing.
Collapse
Affiliation(s)
- Yang Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, China
| | - Lijuan Fan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Rong Luo
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | | | - Meng Yuan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, China
| | - Jinxiu Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Gan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, China
| |
Collapse
|
247
|
Population Pharmacokinetic Model of Plasma and Cellular Mycophenolic Acid in Kidney Transplant Patients from the CIMTRE Study. Drugs R D 2021; 20:331-342. [PMID: 33025511 PMCID: PMC7691413 DOI: 10.1007/s40268-020-00319-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background and Objective Mycophenolate mofetil is widely used in kidney transplant recipients. Mycophenolate mofetil is hydrolysed by blood esterases to mycophenolic acid (MPA), the active drug. Although MPA therapeutic drug monitoring has been recommended to optimise the treatment efficacy by the area under the plasma concentration vs time curve, little is known regarding MPA concentrations in peripheral blood mononuclear cells, where MPA inhibits inosine monophosphate dehydrogenase. This study aimed to build a pharmacokinetic model using a population approach to describe MPA total and unbound concentrations in plasma and into peripheral blood mononuclear cells in 78 adult kidney transplant recipients receiving mycophenolate mofetil therapy combined with tacrolimus and prednisone. Methods Total and unbound plasma concentrations and peripheral blood mononuclear cell concentrations were assayed. A three-compartment model, two for plasma MPA and one for peripheral blood mononuclear cell MPA, with a zero-order absorption and a first-order elimination was used to describe the data. Results Mycophenolic acid average concentrations in peripheral blood mononuclear cells were well above half-maximal effective concentration for inosine monophosphate dehydrogenase and no relationship was found with the occurrence of graft rejection. Three covariates affected unbound and intracellular MPA pharmacokinetics: creatinine clearance, which has an effect on unbound MPA clearance, human serum albumin, which influences fraction unbound MPA and the ABCB1 3435 C>T (rs1045642) genetic polymorphism, which has an effect on MPA efflux transport from peripheral blood mononuclear cells. Conclusion This population pharmacokinetic model demonstrated the intracellular accumulation of MPA, the efflux of MPA out of the cells being dependent on P-glycoprotein transporters. Nevertheless, further studies are warranted to investigate the relevance of MPA concentrations in peripheral blood mononuclear cells to dosing regimen optimisation. Electronic supplementary material The online version of this article (10.1007/s40268-020-00319-y) contains supplementary material, which is available to authorized users.
Collapse
|
248
|
A functional polymorphism in the ATP-Binding Cassette B1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients. Pain 2021; 161:619-629. [PMID: 31738228 DOI: 10.1097/j.pain.0000000000001750] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many genetic markers have been associated with variations in treatment response to analgesics, but none have been assessed in the context of combination therapies. In this study, the treatment effects of nortriptyline and morphine were tested for an association with genetic markers relevant to pain pathways. Treatment effects were determined for single and combination therapies. A total of 24 functional single nucleotide polymorphisms were tested within the gene loci of mu-opioid receptor (OPRM1) gene locus, ATP-Binding Cassette B1 Transporter (ABCB1), Cytochrome P450 gene family (CYP2C19 and CYP2D6), catecholamine inactivator Catechol-O-Methyl Transferase (COMT), and serotonin receptor 2A (HTR2A). Genotyping was performed in a population of neuropathic pain patients who previously participated in a clinical trial. For monotherapy, neither nortriptyline nor morphine responses were associated with single nucleotide polymorphisms. However, for nortriptyline + morphine combination therapy, the single nucleotide polymorphism rs1045642 within the drug efflux pump ABCB1 transporter significantly predicted analgesic response. The presence of the C allele accounted for 51% of pain variance in this subgroup in response to combination treatment. The T-allele homozygotes demonstrated only 20% improvement in pain scores, whereas the C-allele homozygotes 88%. There was no significant contribution of rs1045642 to the medication side effects under all treatment conditions. The UK Biobank data set was then used to validate this genetic association. Here, patients receiving similar combination therapy (opioid + tricyclic antidepressant) carrying the C allele of rs1045642 displayed 33% fewer body pain sites than patients without that allele, suggesting better pain control. In all, our results show a robust effect of the rs1045642 polymorphism in response to chronic pain treatment with a nortriptyline + morphine combination.
Collapse
|
249
|
Yang Q, Lyu X, Zhao F, Liu Y. Effects of codon usage on gene expression are promoter context dependent. Nucleic Acids Res 2021; 49:818-831. [PMID: 33410890 PMCID: PMC7826287 DOI: 10.1093/nar/gkaa1253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the significance of codon usage effect on gene expression. Here we show that gene-specific regulation reduces the genome-wide codon usage and mRNA correlations: Constitutively expressed genes exhibit much higher genome-wide correlations than differentially expressed genes from fungi to human cells. Using Drosophila S2 cells as a model system, we showed that the effect of codon usage on mRNA expression level is promoter-dependent. Regions downstream of the core promoters of differentially expressed genes can repress the codon usage effects on mRNA expression. An element in the Hsp70 promoter was identified to be necessary and sufficient for this inhibitory effect. The promoter-dependent codon usage effects on mRNA levels are regulated at the transcriptional level through modulation of histone modifications, nucleosome densities and premature termination. Together, our results demonstrate that promoters play a major role in determining whether codon usage influences gene expression and further establish the transcription-dependent codon usage effects on gene expression.
Collapse
Affiliation(s)
- Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Xueliang Lyu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| |
Collapse
|
250
|
Bruckmueller H, Cascorbi I. ABCB1, ABCG2, ABCC1, ABCC2, and ABCC3 drug transporter polymorphisms and their impact on drug bioavailability: what is our current understanding? Expert Opin Drug Metab Toxicol 2021; 17:369-396. [PMID: 33459081 DOI: 10.1080/17425255.2021.1876661] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Interindividual differences in drug response are a frequent clinical challenge partly due to variation in pharmacokinetics. ATP-binding cassette (ABC) transporters are crucial determinants of drug disposition. They are subject of gene regulation and drug-interaction; however, it is still under debate to which extend genetic variants in these transporters contribute to interindividual variability of a wide range of drugs. AREAS COVERED This review discusses the current literature on the impact of genetic variants in ABCB1, ABCG2 as well as ABCC1, ABCC2, and ABCC3 on pharmacokinetics and drug response. The aim was to evaluate if results from recent studies would increase the evidence for potential clinically relevant pharmacogenetic effects. EXPERT OPINION Although enormous efforts have been made to investigate effects of ABC transporter genotypes on drug pharmacokinetics and response, the majority of studies showed only weak if any associations. Despite few unique results, studies mostly failed to confirm earlier findings or still remained inconsistent. The impact of genetic variants on drug bioavailability is only minor and other factors regulating the transporter expression and function seem to be more critical. In our opinion, the findings on the so far investigated genetic variants in ABC efflux transporters are not suitable as predictive biomarkers.
Collapse
Affiliation(s)
- Henrike Bruckmueller
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| |
Collapse
|