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Liu Z, Bao Y, Wang W, Pan L, Wang H, Lin GN. Emden: A novel method integrating graph and transformer representations for predicting the effect of mutations on clinical drug response. Comput Biol Med 2023; 167:107678. [PMID: 37976823 DOI: 10.1016/j.compbiomed.2023.107678] [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: 09/14/2023] [Revised: 10/22/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Precision medicine based on personalized genomics provides promising strategies to enhance the efficacy of molecular-targeted therapies. However, the clinical effectiveness of drugs has been severely limited due to genetic variations that lead to drug resistance. Predicting the impact of missense mutations on clinical drug response is an essential way to reduce the cost of clinical trials and understand genetic diseases. Here, we present Emden, a novel method integrating graph and transformer representations that predicts the effect of missense mutations on drug response through binary classification with interpretability. Emden utilized protein sequences-based features and drug structures as inputs for rapid prediction, employing competitive representation learning and demonstrating strong generalization capabilities and robustness. Our study showed promising potential for clinical drug guidance and deep insight into computer-assisted precision medicine. Emden is freely available as a web server at https://www.psymukb.net/Emden.
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Affiliation(s)
- Zhe Liu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yihang Bao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weidi Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Liangwei Pan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Han Wang
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun, China.
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China.
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Tcherniakovsky M, de Oliveira E, Martinelli Sonnenfeld M, Arcoverde Cavalcanti Meniconi MM, Franco de Oliveira M, Tcherniakovsky I, Moscovitz T, Wajman M, Camargo Mariano da Silva R, Fernandes CE. Evaluation of Comt2, Comt3, Cyp1b1, and Esr1 gene polymorphisms as risk factor for endometrial polyp. Women Health 2023; 63:818-827. [PMID: 37908103 DOI: 10.1080/03630242.2023.2272206] [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: 02/09/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023]
Abstract
The aim of this study is to evaluate COMT2, COMT3, CYP1B1, and ESR1 gene polymorphisms and occurrence of endometrial polyps. In addition, we intended to evaluate the clinical and epidemiological features of patients with and without the presence of the disease, characterizing the possible risk factors. A cross-sectional study was performed, with a total of 309 women, including 236 in the group of women with endometrial polyp confirmed by hysteroscopy and anatomical pathological examination and 73 in the group of people with diagnostic hysteroscopy without abnormal findings from the macroscopic point of view. Polymorphisms of four genes were studied: COMT2 (rs4680), COMT3 (rs5031015), CYP1B1 (rs1056836), and ESR1 (rs2234693). Polymorphism genotyping was determined using real-time polymerase chain reaction. Considering the results, no differences were identified between the two groups with respect to age, body mass index, diabetes, dyslipidemia, or smoking. The group of women without endometrial polyps showed higher use of hormone therapy than the other group (16.4 percent versus 3.8 percent, p < .001). The COMT2, COMT3, CYP1B1, and ESR1 genes exhibited no significant difference for the occurrence of endometrial polyp between the two groups. The research concluded that no correlation was identified between the genetic polymorphisms evaluated and the presence of endometrial polyps.
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Affiliation(s)
- Marcos Tcherniakovsky
- Head of the Video Endoscopy and Endometriosis Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
| | - Emerson de Oliveira
- Head of the Urogynecology Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
| | - Marina Martinelli Sonnenfeld
- Fellow of the Video Endoscopy and Endometriosis Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
| | | | | | | | - Thomas Moscovitz
- Member of the Video Endoscopy and Endometriosis Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
| | - Milton Wajman
- Member of the Video Endoscopy and Endometriosis Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
| | - Rogers Camargo Mariano da Silva
- Member of the Video Endoscopy and Endometriosis Section of The Gynecology Department, Faculdade de Medicina do ABC, Santo André, Brazil
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Evaluation of COMT Gene rs4680 Polymorphism as a Risk Factor for Endometrial Cancer. Indian J Clin Biochem 2020; 35:63-71. [PMID: 32071497 DOI: 10.1007/s12291-018-0799-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022]
Abstract
Catechol-O-methyletransferase (COMT) enzyme is involved in the inactivation of catecholamine and catechol estrogens. Catechol estrogens have carcinogenic potential and DNA damaging ability. Several studies investigated COMT Val158Met polymorphism as risk factor for endometrial cancer but the results were inconclusive. Hence the objective of present study was to find out exact association between COMT gene Val158Met polymorphism and endometrial cancer by a meta-analysis. Pubmed, Google Scholar, Springer Link and Science Direct databases were searched for case-control articles which investigated COMT Val158Met polymorphism in endometrial cancer cases. All statistical analysis was performed using MetaAnalyst and Mix programs. The results of meta-analysis suggested that there were no association between COMT Val158Met polymorphism and endometrial cancer risk (allele contrast model-ORA vs. G = 0.97, 95% CI = 0.86-1.10, p = 0.67; co-dominant model-ORAG vs. GG = 0.91, 95% CI = 0.77-1.06, p = 0.23; homozygote model-ORAA vs. GG = 1.01, 95% CI = 0.84-1.19, p = 0.29; dominant model-ORAA+AG vs. GG = 0.93, 95% CI = 0.77-1.11, p = 0.43; recessive model-ORAA vs. AG+GG = 1.02, 95% CI = 0.89-1.20, p = 0.62). Publication bias was absent. Subgroup analysis based on source of controls was also performed. In conclusion, results of present meta-analysis showed no association between COMT Val158Met polymorphism and susceptibility to endometrial cancer.
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Júlio-Costa A, Martins AAS, Wood G, de Almeida MP, de Miranda M, Haase VG, Carvalho MRS. Heterosis in COMT Val158Met Polymorphism Contributes to Sex-Differences in Children's Math Anxiety. Front Psychol 2019; 10:1013. [PMID: 31156495 PMCID: PMC6530072 DOI: 10.3389/fpsyg.2019.01013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/16/2019] [Indexed: 01/03/2023] Open
Abstract
Math anxiety (MA) is a phobic reaction to math activities, potentially impairing math achievement. Higher frequency of MA in females is explainable by the interaction between genetic and environmental factors. The molecular-genetic basis of MA has not been investigated. The COMT Val158Met polymorphism, which affects dopamine levels in the prefrontal cortex, has been associated with anxiety manifestations. The valine allele is associated with lower, and the methionine allele with higher, dopamine availability. In the present study, the effects of sex and COMT Val158Met genotypes on MA were investigated: 389 school children aged 7-12 years were assessed for intelligence, numerical estimation, arithmetic achievement and MA and genotyped for COMT Val158Met polymorphism. The Math Anxiety Questionnaire (MAQ) was used to assess the cognitive and affective components of MA. All genotype groups of boys and girls were comparable regarding genotype frequency, age, school grade, numerical estimation, and arithmetic abilities. We compared the results of all possible genetic models: codominance (Val/Val vs. Val/Met vs. Met/Met), heterosis (Val/Met vs. Val/Val plus Met/Met), valine dominance (Val/Val plus Val/Met vs. Met/Met), and methionine dominance (Met/Met plus Val/Met vs. Val/Val). Models were compared using AIC and AIC weights. No significant differences between girls and boys and no effects of the COMT Val158Met polymorphism on numerical estimation and arithmetic achievement were observed. Sex by genotype effects were significant for intelligence and MA. Intelligence scores were higher in Met/Met girls than in girls with at least one valine allele (valine dominance model). The best fitting model for MA was heterosis. In Anxiety Toward Mathematics, heterozygous individuals presented MA levels close to the grand average regardless of sex. Homozygous boys were significantly less and homozygous girls significantly more math anxious. Heterosis has been seldom explored, but in recent years has emerged as the best genetic model for some phenotypes associated with the COMT Val158Met polymorphism. This is the first study to investigate the genetic-molecular basis of MA.
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Affiliation(s)
- Annelise Júlio-Costa
- Departamento de Psicologia, FAFICH, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-graduação em Neurociências, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aline Aparecida Silva Martins
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme Wood
- Instituto Nacional de Ciência e Tecnologia sobre Comportamento, Cognição e Ensino (INCT-ECCE), São Carlos, Brazil
- Department of Neuropsychology, Institute of Psychology, University of Graz, Graz, Austria
| | - Máira Pedroso de Almeida
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marlene de Miranda
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vitor Geraldi Haase
- Departamento de Psicologia, FAFICH, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-graduação em Neurociências, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto Nacional de Ciência e Tecnologia sobre Comportamento, Cognição e Ensino (INCT-ECCE), São Carlos, Brazil
- Programa de Pós-Graduação em Psicologia: Cognição e Comportamento, Departamento de Psicologia, FAFICH, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Saúde da Criança e Adolescente, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Raquel Santos Carvalho
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Sak K. The Val158Met polymorphism in COMT gene and cancer risk: role of endogenous and exogenous catechols. Drug Metab Rev 2016; 49:56-83. [PMID: 27826992 DOI: 10.1080/03602532.2016.1258075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Catechol-O-methyltransferase, COMT, is an important phase II enzyme catalyzing the transfer of a methyl-group from S-adenosylmethionine to a catechol-containing substrate molecule. A genetic variant Val158Met in the COMT gene leads to a several-fold decrease in the enzymatic activity giving rise to the accumulation of potentially carcinogenic endogenous catechol estrogens and their reactive intermediates and increasing thus the risk of tumorigenesis. However, numerous association studies between the COMT genotype and susceptibility to various malignancies have shown inconsistent and controversial findings indicating that additional gene-gene and gene-environment interactions might be crucial in modulating the physiological role of the COMT. In this review article, the important contribution of dietary catechol-containing flavonoids to modification of the relationships between the COMT genotype and cancer risk is discussed. Whereas, the diverse anticancer activities of common phytochemicals, such as green tea polyphenols, quercetin, fisetin or luteolin, can be markedly changed (both decreased or increased) by the COMT-mediated O-methylation of these exogenous substrates, flavonoids can also behave as potent inhibitors of the COMT enzyme slowing detoxification of endogenous catechol estrogens. Such a many-featured functioning of the COMT and its complex regulation by several different genetic and environmental factors, including plant-based food ingredients, emphasizes the necessity to further stratify the association studies between the COMT genotype and tumor risk by consumption of catechol-containing dietary flavonoids. Currently, it can be only speculated that some of the possible associations might be masked by the regular intake of specific food polyphenols, taking effect in certain communities or populations.
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Affiliation(s)
- Katrin Sak
- a Department of Hematology and Oncology , Institute of Clinical Medicine, University of Tartu , Tartu , Estonia
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Pabalan N, Singian E, Tabangay L, Jarjanazi H, Singh N. Associations of the A66G Methionine Synthase Reductase Polymorphism in Colorectal Cancer: A Systematic Review and Meta-Analysis. BIOMARKERS IN CANCER 2015; 7:21-8. [PMID: 26549973 PMCID: PMC4627415 DOI: 10.4137/bic.s25251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022]
Abstract
Inconsistency in the reported associations between the A66G polymorphism in the methionine synthase reductase (MTRR) gene and colorectal cancer (CRC) prompted a meta-analysis, so that we could obtain a more precise estimate. Databases searches of the published literature yielded 20 case–control studies from 17 articles (8,371 cases and 12,574 controls). We calculated pooled odds ratios (ORs) and 95% confidence intervals in three genetic comparisons (A allele, G allele, and A/G genotype). We found no evidence of overall associations between MTRR A66G and CRC risk (OR 0.96–1.05, P = 0.12–0.44). This was materially unchanged when reanalyzed without the Hardy–Weinberg equilibrium (HWE)-deviating studies (OR 0.97–1.06, P = 0.11–0.65). In the A allele comparison, however, outlier treatment generated significant protection (OR 0.91, P = 0.01). Combined removal of the outliers and HWE-deviating studies reflected this summary effect (OR 0.90, P = 0.01) as did the pooled OR from high-quality studies (OR 0.90, P = 0.01). Only the Asian subgroup showed significant (both at P = 0.05) A allele (OR 1.13) and A/G genotype (OR 0.88) associations. In conclusion, post-outlier A allele effects were protective. Our study also suggests ethnic-specific associations with Asian susceptibility and protection in the A allele and A/G genotype comparisons, respectively. Folate status showed no association of this polymorphism with CRC.
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Affiliation(s)
- Noel Pabalan
- Center for Research and Development, Angeles University Foundation, Angeles City, Philippines
| | - Eloisa Singian
- College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Lani Tabangay
- Department of Biological Sciences, Angeles University Foundation, Angeles City, Philippines
| | - Hamdi Jarjanazi
- Environmental Monitoring and Reporting Branch, Ontario Ministry of the Environment and Climate Change, Toronto, ON, Canada
| | - Neetu Singh
- Genotoxicity Laboratory, Toxicology Division, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
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Pinto MP, Medina RA, Owen GI. 2-methoxyestradiol and disorders of female reproductive tissues. Discov Oncol 2014; 5:274-83. [PMID: 24764201 DOI: 10.1007/s12672-014-0181-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022] Open
Abstract
2-Methoxyestradiol (2ME) is an endogenous metabolite of 17β-estradiol. Once thought of as a mere degradation product, 2ME has gained attention as an important component of reproductive physiology and as a therapeutic agent in reproductive pathologies such as preeclampsia, endometriosis, infertility, and cancer. In this review, we discuss the involvement of 2ME in reproductive pathophysiology and summarize its known mechanisms of action: microtubule disruption, inhibition of angiogenesis and stimulation of apoptosis. Currently, the clinical uses of 2ME as a single agent are limited due to its poor water solubility and thus low bioavailability; however, 2ME analogs and derivatives have been recently developed and tested as cancer treatments. Despite some isolated success stories and ongoing research, 2ME derivatives have not yet provided the expected results. The adjuvant use of 2ME derivatives with chemotherapeutic agents is hindered by their intrinsic toxicity confounding the unwanted secondary effects of chemotherapy. However, due to the well-tested tolerance of the body to high doses of native 2ME, it may the combination of native 2ME with conventional treatments that will offer novel clinically relevant regimens for cancer and other reproductive disorders.
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Affiliation(s)
- Mauricio P Pinto
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Bol SM, Booiman T, van Manen D, Bunnik EM, van Sighem AI, Sieberer M, Boeser-Nunnink B, de Wolf F, Schuitemaker H, Portegies P, Kootstra NA, van 't Wout AB. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia. PLoS One 2012; 7:e30990. [PMID: 22347417 PMCID: PMC3274517 DOI: 10.1371/journal.pone.0030990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/29/2011] [Indexed: 11/18/2022] Open
Abstract
Background Infection with HIV-1 may result in severe cognitive and motor impairment, referred to as HIV-1-associated dementia (HAD). While its prevalence has dropped significantly in the era of combination antiretroviral therapy, milder neurocognitive disorders persist with a high prevalence. To identify additional therapeutic targets for treating HIV-associated neurocognitive disorders, several candidate gene polymorphisms have been evaluated, but few have been replicated across multiple studies. Methods We here tested 7 candidate gene polymorphisms for association with HAD in a case-control study consisting of 86 HAD cases and 246 non-HAD AIDS patients as controls. Since infected monocytes and macrophages are thought to play an important role in the infection of the brain, 5 recently identified single nucleotide polymorphisms (SNPs) affecting HIV-1 replication in macrophages in vitro were also tested. Results The CCR5 wt/Δ32 genotype was only associated with HAD in individuals who developed AIDS prior to 1991, in agreement with the observed fading effect of this genotype on viral load set point. A significant difference in genotype distribution among all cases and controls irrespective of year of AIDS diagnosis was found only for a SNP in candidate gene PREP1 (p = 1.2×10−5). Prep1 has recently been identified as a transcription factor preferentially binding the −2,518 G allele in the promoter of the gene encoding MCP-1, a protein with a well established role in the etiology of HAD. Conclusion These results support previous findings suggesting an important role for MCP-1 in the onset of HIV-1-associated neurocognitive disorders.
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Affiliation(s)
- Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Thijs Booiman
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Evelien M. Bunnik
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ard I. van Sighem
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margit Sieberer
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Frank de Wolf
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Portegies
- Department of Neurology at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Neurology at the OLVG Hospital, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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