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Extensive variation in the intelectin gene family in laboratory and wild mouse strains. Sci Rep 2021; 11:15548. [PMID: 34330944 PMCID: PMC8324875 DOI: 10.1038/s41598-021-94679-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/13/2021] [Indexed: 12/30/2022] Open
Abstract
Intelectins are a family of multimeric secreted proteins that bind microbe-specific glycans. Both genetic and functional studies have suggested that intelectins have an important role in innate immunity and are involved in the etiology of various human diseases, including inflammatory bowel disease. Experiments investigating the role of intelectins in human disease using mouse models are limited by the fact that there is not a clear one-to-one relationship between intelectin genes in humans and mice, and that the number of intelectin genes varies between different mouse strains. In this study we show by gene sequence and gene expression analysis that human intelectin-1 (ITLN1) has multiple orthologues in mice, including a functional homologue Itln1; however, human intelectin-2 has no such orthologue or homologue. We confirm that all sub-strains of the C57 mouse strain have a large deletion resulting in retention of only one intelectin gene, Itln1. The majority of laboratory strains have a full complement of six intelectin genes, except CAST, SPRET, SKIVE, MOLF and PANCEVO strains, which are derived from different mouse species/subspecies and encode different complements of intelectin genes. In wild mice, intelectin deletions are polymorphic in Mus musculus castaneus and Mus musculus domesticus. Further sequence analysis shows that Itln3 and Itln5 are polymorphic pseudogenes due to premature truncating mutations, and that mouse Itln1 has undergone recent adaptive evolution. Taken together, our study shows extensive diversity in intelectin genes in both laboratory and wild-mice, suggesting a pattern of birth-and-death evolution. In addition, our data provide a foundation for further experimental investigation of the role of intelectins in disease.
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Algady W, Weyell E, Mateja D, Garcia A, Courtin D, Hollox EJ. Genotyping complex structural variation at the malaria-associated human glycophorin locus using a PCR-based strategy. Ann Hum Genet 2020; 85:7-17. [PMID: 32895931 DOI: 10.1111/ahg.12405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/23/2020] [Accepted: 08/15/2020] [Indexed: 02/06/2023]
Abstract
Structural variation in the human genome can affect risk of disease. An example is a complex structural variant of the human glycophorin gene cluster, called DUP4, which is associated with a clinically significant level of protection against severe malaria. The human glycophorin gene cluster harbours at least 23 distinct structural variants, and accurate genotyping of this complex structural variation remains a challenge. Here, we use a polymerase chain reaction-based strategy to genotype structural variation at the human glycophorin gene cluster, including the alleles responsible for the U- blood group. We validate our approach, based on a triplex paralogue ratio test, on publically available samples from the 1000 Genomes project. We then genotype 574 individuals from a longitudinal birth cohort (Tori-Bossito cohort) using small amounts of DNA at low cost. Our approach readily identifies known deletions and duplications, and can potentially identify novel variants for further analysis. It will allow exploration of genetic variation at the glycophorin locus, and investigation of its relationship with malaria, in large sample sets at minimal cost, using standard molecular biology equipment.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Eleanor Weyell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Daria Mateja
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - André Garcia
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - David Courtin
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Valsesia A, Kulkarni SS, Marquis J, Leone P, Mironova P, Walter O, Hjorth MF, Descombes P, Hager J, Saris WH, Astrup A, Darimont C, O'Callaghan NJ. Salivary α-amylase copy number is not associated with weight trajectories and glycemic improvements following clinical weight loss: results from a 2-phase dietary intervention study. Am J Clin Nutr 2019; 109:1029-1037. [PMID: 30982860 DOI: 10.1093/ajcn/nqy363] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Several studies recently reported contradicting results regarding the link between amylase 1 (AMY1) copy numbers (CNs), obesity, and type 2 diabetes. OBJECTIVE The aim of this study was to assess the impact of AMY1 CN on anthropometrics and glycemic outcomes in obese individuals following a 2-phase dietary weight loss intervention. METHODS Using the paralog ratio test, AMY1 CNs were accurately measured in 761 obese individuals from the DiOGenes study. Subjects first underwent an 8-wk low-calorie diet (LCD, at 800 kcal/d) and then were randomly assigned to a 6-mo weight maintenance dietary (WMD) intervention with arms having different glycemic loads. RESULTS At baseline, a modest association between AMY1 CN and BMI (P = 0.04) was observed. AMY1 CN was not associated with baseline glycemic variables. In addition, AMY1 CN was not associated with anthropometric or glycemic outcomes following either LCD or WMD. Interaction analyses between AMY1 CN and nutrient intake did not reveal any significant association with clinical parameters (at baseline and following LCD or WMD) or when testing gene × WMD interactions during the WMD phase. CONCLUSION In the absence of association with weight trajectories or glycemic improvements, the AMY1 CN cannot be considered as an important biomarker for response to a clinical weight loss and weight maintenance programs in overweight/obese subjects. This trial was registered at www.clinicaltrials.gov as NCT00390637.
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Affiliation(s)
- Armand Valsesia
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Sameer S Kulkarni
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Julien Marquis
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Patricia Leone
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Polina Mironova
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Ondine Walter
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Mads Fill Hjorth
- University of Copenhagen, Department of Nutrition, Exercise and Sports, Faculty of Science, Copenhagen, Denmark
| | - Patrick Descombes
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Jörg Hager
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Wim H Saris
- Department of Human Biology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Arne Astrup
- University of Copenhagen, Department of Nutrition, Exercise and Sports, Faculty of Science, Copenhagen, Denmark
| | - Christian Darimont
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Nathan J O'Callaghan
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.,CSIRO Health & Biosecurity, South Australian Health & Medical Research Institute, Adelaide, Australia
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Firigato I, de Toledo Gonçalves F, De Antonio J, Alberto Curioni O, Rocha Silva M, Jorge Fígaro Gattás G. How many copies of GSTM1 and GSTT1 are associated with head and neck cancer risk? Biomarkers 2018; 24:262-267. [PMID: 30526121 DOI: 10.1080/1354750x.2018.1556337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Purpose: GSTM1 and GSTT1 present a polymorphism that can drive complete gene deletions. The current methodology can powerfully determine GSTM1 and GSTT1 copy number variations (CNVs), which may clarify the real contribution of each gene copies to the cellular detoxification process and tumour risk. However, only analysing the presence/absence of these genes yielded controversial results for several disorders, including cancer. Because head and neck cancer (HNC) is becoming a serious global health problem, this study determined the CNVs of GSTM1 and GSTT1 in an HNC case-control population and investigated the possible association between gene copy numbers and tumour risk. Methods: CNV was evaluated by (Ct) 2-ΔΔCt qPCR methodology in 619 HNC patients and 448 patients with no tumour diagnosis. Results: The genes copy number range was 0-3. The CNV of GSTM1 and GSTT1 frequencies were similar between the cases and control. Thus, none copy of GSTM1 and GSTT1 were associated with HNC risk. Notwithstanding, one copy of both genes had higher frequencies among individuals who carried GSTM1 and GSTT1. Conclusions: One copy number of GSTM1 and GSTT1 presented a higher frequency among carrier genes, but the CNV of GSTM1 and GSTT1 was not associated with HNC risk.
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Affiliation(s)
- Isabela Firigato
- a Departamento de Medicina Legal, Etica Medica, Medicina Social e do Trabalho , Instituto Oscar Freire, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP) , Sao Paulo , Brazil
| | - Fernanda de Toledo Gonçalves
- a Departamento de Medicina Legal, Etica Medica, Medicina Social e do Trabalho , Instituto Oscar Freire, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP) , Sao Paulo , Brazil
| | - Juliana De Antonio
- a Departamento de Medicina Legal, Etica Medica, Medicina Social e do Trabalho , Instituto Oscar Freire, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP) , Sao Paulo , Brazil
| | - Otávio Alberto Curioni
- b Department of Head and Neck Surgery and Otorhinolaryngology , Hospital Heliopolis , Sao Paulo , Brazil
| | - Mariana Rocha Silva
- a Departamento de Medicina Legal, Etica Medica, Medicina Social e do Trabalho , Instituto Oscar Freire, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP) , Sao Paulo , Brazil
| | - Gilka Jorge Fígaro Gattás
- a Departamento de Medicina Legal, Etica Medica, Medicina Social e do Trabalho , Instituto Oscar Freire, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP) , Sao Paulo , Brazil
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Adewoye AB, Shrine N, Odenthal-Hesse L, Welsh S, Malarstig A, Jelinsky S, Kilty I, Tobin MD, Hollox EJ, Wain LV. Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function. Wellcome Open Res 2018; 3:13. [PMID: 29682616 PMCID: PMC5883389 DOI: 10.12688/wellcomeopenres.13902.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 01/21/2023] Open
Abstract
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful. Here we investigate the potential of perturbation of the CCL3L1-CCR5 axis as treatment for respiratory disease. Europeans typically carry between 0 and 5 copies of CCL3L1 and this multi-allelic variation is not detected by widely used genome-wide single nucleotide polymorphism studies. Methods: We directly measured the complex structural variation of CCL3L1 using the Paralogue Ratio Test and imputed (with validation) CCR5del32 genotypes in 5,000 individuals from UK Biobank, selected from the extremes of the lung function distribution, and analysed DNA and RNAseq data for CCL3L1 from the 1000 Genomes Project. Results: We confirmed the gene dosage effect of CCL3L1 copy number on CCL3L1 mRNA expression levels. We found no evidence for association of CCL3L1 copy number or CCR5del32 genotype with lung function. Conclusions: These results suggest that repositioning CCR5 antagonists is unlikely to be successful for the treatment of airflow obstruction.
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Affiliation(s)
- Adeolu B. Adewoye
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Linda Odenthal-Hesse
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | - Scott Jelinsky
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Iain Kilty
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute of Health Research Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK,
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute of Health Research Biomedical Research Centre, University of Leicester, Leicester, UK,
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Complement receptor 1 gene (CR1) intragenic duplication and risk of Alzheimer's disease. Hum Genet 2018; 137:305-314. [PMID: 29675612 PMCID: PMC5937907 DOI: 10.1007/s00439-018-1883-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/13/2018] [Indexed: 11/09/2022]
Abstract
Single nucleotide variants (SNVs) within and surrounding the complement receptor 1 (CR1) gene show some of the strongest genome-wide association signals with late-onset Alzheimer’s disease. Some studies have suggested that this association signal is due to a duplication allele (CR1-B) of a low copy repeat (LCR) within the CR1 gene, which increases the number of complement C3b/C4b-binding sites in the mature receptor. In this study, we develop a triplex paralogue ratio test assay for CR1 LCR copy number allowing large numbers of samples to be typed with a limited amount of DNA. We also develop a CR1-B allele-specific PCR based on the junction generated by an historical non-allelic homologous recombination event between CR1 LCRs. We use these methods to genotype CR1 and measure CR1-B allele frequency in both late-onset and early-onset cases and unaffected controls from the United Kingdom. Our data support an association of late-onset Alzheimer’s disease with the CR1-B allele, and confirm that this allele occurs most frequently on the risk haplotype defined by SNV alleles. Furthermore, regression models incorporating CR1-B genotype provide a better fit to our data compared to incorporating the SNV-defined risk haplotype, supporting the CR1-B allele as the variant underlying the increased risk of late-onset Alzheimer’s disease.
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Adewoye AB, Shrine N, Odenthal-Hesse L, Welsh S, Malarstig A, Jelinsky S, Kilty I, Tobin MD, Hollox EJ, Wain LV. Human CCL3L1 copy number variation, gene expression, and the role of the CCL3L1-CCR5 axis in lung function. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.13902.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful. Here we investigate the potential of perturbation of the CCL3L1-CCR5 axis as treatment for respiratory disease. Europeans typically carry between 0 and 5 copies of CCL3L1 and this multi-allelic variation is not detected by widely used genome-wide single nucleotide polymorphism studies. Methods: We directly measured the complex structural variation of CCL3L1 using the Paralogue Ratio Test and imputed (with validation) CCR5del32 genotypes in 5,000 individuals from UK Biobank, selected from the extremes of the lung function distribution, and analysed DNA and RNAseq data for CCL3L1 from the 1000 Genomes Project. Results: We confirmed the gene dosage effect of CCL3L1 copy number on CCL3L1 mRNA expression levels. We found no evidence for association of CCL3L1 copy number or CCR5del32 genotype with lung function. Conclusions: These results suggest that repositioning CCR5 antagonists is unlikely to be successful for the treatment of airflow obstruction.
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