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De M, Sukla S, Bharatiya S, Keshri S, Roy DG, Roy S, Dutta D, Saha S, Ejazi SA, Ravichandiran V, Ali N, Chatterjee M, Chinnaswamy S. IFN-λ3 is induced by Leishmania donovani and can inhibit parasite growth in cell line models but not in the mouse model, while it shows a significant association with leishmaniasis in humans. Infect Immun 2024; 92:e0050423. [PMID: 38193711 PMCID: PMC10863405 DOI: 10.1128/iai.00504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
The intracellular protozoan parasite Leishmania donovani causes debilitating human diseases that involve visceral and dermal manifestations. Type 3 interferons (IFNs), also referred to as lambda IFNs (IFNL, IFN-L, or IFN-λ), are known to play protective roles against intracellular pathogens at the epithelial surfaces. Herein, we show that L. donovani induces IFN-λ3 in human as well as mouse cell line-derived macrophages. Interestingly, IFN-λ3 treatment significantly decreased parasite load in infected cells, mainly by increasing reactive oxygen species production. Microscopic examination showed that IFN-λ3 inhibited uptake but not replication, while the phagocytic ability of the cells was not affected. This was confirmed by experiments that showed that IFN-λ3 could decrease parasite load only when added to the medium at earlier time points, either during or soon after parasite uptake, but had no effect on parasite load when added at 24 h post-infection, suggesting that an early event during parasite uptake was targeted. Furthermore, the parasites could overcome the inhibitory effect of IFN-λ3, which was added at earlier time points, within 2-3 days post-infection. BALB/c mice treated with IFN-λ3 before infection led to a significant increase in expression of IL-4 and ARG1 post-infection in the spleen and liver, respectively, and to different pathological changes, especially in the liver, but not to changes in parasite load. Treatment with IFN-λ3 during infection did not decrease the parasite load in the spleen either. However, IFN-λ3 was significantly increased in the sera of visceral leishmaniasis patients, and the IFNL genetic variant rs12979860 was significantly associated with susceptibility to leishmaniasis.
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Affiliation(s)
- Manjarika De
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Soumi Sukla
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
- Centre for High Impact Neuroscience and Translational Applications (CHINTA), TCG-Centres for Research and Education in Science and Technology, Kolkata, West Bengal, India
| | - Seema Bharatiya
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sagar Keshri
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Debarati Guha Roy
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sutopa Roy
- Department of Pharmacology, Institute of Post-Graduate Medical Education and Research, Kolkata, India
| | - Debrupa Dutta
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Shriya Saha
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Sarfaraz Ahmad Ejazi
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Fischell Department of Bioengineering, A. James Clark School of Engineering, University of Maryland, College Park, MD, USA
| | - V. Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mitali Chatterjee
- Department of Pharmacology, Institute of Post-Graduate Medical Education and Research, Kolkata, India
| | - Sreedhar Chinnaswamy
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
- Regional Centre for Biotechnology, Faridabad, India
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Eimanzadeh M, Mohebali M, Zarrabi M, Foroushani AR, Kazemi M, Hajjaran H, Zarei Z, Kakooei Z, Akhoundi B. The Association of Human Leucocyte Antigen (HLA) Class I and II Genes with Cutaneous and Visceral Leishmaniasis in Iranian Patients: A Preliminary Case-Control Study. IRANIAN JOURNAL OF PARASITOLOGY 2023; 18:155-164. [PMID: 37583643 PMCID: PMC10423905 DOI: 10.18502/ijpa.v18i2.13181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/19/2023] [Indexed: 08/17/2023]
Abstract
Background Leishmaniasis is currently considered a re-emerging or emerging infection based on the geographic region. The outcome of leishmaniasis vastly depends on Leishmania-host interaction. This preliminary study aimed to show the association of human leukocyte antigen (HLA) class I and II genes with healed and non-healed cutaneous leishmaniasis (CL), and symptomatic and asymptomatic visceral leishmaniasis (VL) compared with control groups in Iran. Methods Ninety-five people, including 31 patients versus 64 individuals in the control group, were enrolled. Among them, 20 patients had confirmed CL based on amastigote observation, 10 had improved CL and 10 non-healed CL. Eleven patients were suffering from confirmed VL based on direct agglutination test (Five asymptomatic and six symptomatic VL cases). Besides, they were residents in an endemic area of VL in the northwest of Iran. To select a control group, it was ensured that they had no history of leishmaniasis. Peripheral blood samples were collected from each patient. After DNA extraction, HLA typing was conducted using polymerase chain reaction - sequence-specific priming (PCR-SSP). Subsequently, data were statistically analyzed by SPSS. Results There was a statistical relationship between the presence of HLA-A26 and CL, healed CL and the existence of the B38 allele, C1 allele and symptomatic VL, as well as B1.4 allele and asymptomatic VL (P<0.05). Conclusion This primary finding indicates that several HLA genes have a potential role in the susceptibility of Iranian people to CL and VL.
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Affiliation(s)
- Mitra Eimanzadeh
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Center for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran
| | | | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Homa Hajjaran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabih Zarei
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Kakooei
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnaz Akhoundi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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3
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Ornellas-Garcia U, Cuervo P, Ribeiro-Gomes FL. Malaria and leishmaniasis: Updates on co-infection. Front Immunol 2023; 14:1122411. [PMID: 36895563 PMCID: PMC9989157 DOI: 10.3389/fimmu.2023.1122411] [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: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Malaria and leishmaniasis are endemic parasitic diseases in tropical and subtropical countries. Although the overlap of these diseases in the same host is frequently described, co-infection remains a neglected issue in the medical and scientific community. The complex relationship of concomitant infections with Plasmodium spp. and Leishmania spp. is highlighted in studies of natural and experimental co-infections, showing how this "dual" infection can exacerbate or suppress an effective immune response to these protozoa. Thus, a Plasmodium infection preceding or following Leishmania infection can impact the clinical course, accurate diagnosis, and management of leishmaniasis, and vice versa. The concept that in nature we are affected by concomitant infections reinforces the need to address the theme and ensure its due importance. In this review we explore and describe the studies available in the literature on Plasmodium spp. and Leishmania spp. co-infection, the scenarios, and the factors that may influence the course of these diseases.
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Affiliation(s)
- Uyla Ornellas-Garcia
- Laboratory of Malaria Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil.,Malaria Research, Diagnosis and Training Center (CPD-Mal) of Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Patricia Cuervo
- Laboratory on Leishmaniasis Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil.,Rio de Janeiro Research Network on Neuroinflammation, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Flávia Lima Ribeiro-Gomes
- Laboratory of Malaria Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil.,Malaria Research, Diagnosis and Training Center (CPD-Mal) of Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
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Lindsø Andersen P, Jemec GB, Erikstrup C, Didriksen M, Dinh KM, Mikkelsen S, Sørensen E, Nielsen KR, Bruun MT, Hjalgrim H, Hansen TF, Sækmose SG, Ostrowski SR, Saunte DML, Pedersen OB. Human leukocyte antigen system associations in Malassezia-related skin diseases. Arch Dermatol Res 2022; 315:895-902. [PMID: 36394635 DOI: 10.1007/s00403-022-02454-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND The human leukocyte antigen system (HLA) is divided into two classes involved in antigen presentation: class I presenting intracellular antigens and class II presenting extracellular antigens. While susceptibility to infections is correlated with the HLA system, data on associations between HLA genotypes and Malassezia-related skin diseases (MRSD) are lacking. Thus, the objective of this study was to investigate associations between HLA alleles and MRSD. MATERIALS AND METHODS Participants in The Danish Blood Donor Study (2010-2018) provided questionnaire data on life style, anthropometric measures, and registry data on filled prescriptions. Genotyping was done using Illumina Infinium Global Screening Array, and HLA alleles were imputed using the HIBAG algorithm. Cases and controls were defined using filled prescriptions on topical ketoconazole 2% as a proxy of MRSD. Logistic regressions assessed associations between HLA alleles and MRSD adjusted for confounders and Bonferroni corrected for multiple tests. RESULTS A total of 9455 participants were considered MRSD cases and 24,144 participants as controls. We identified four risk alleles B*57:01, OR 1.19 (95% CI: 1.09-1.31), C*01:02, OR 1.19 (95% CI: 1.08-1.32), C*06:02, OR 1.14 (95% CI: 1.08-1.22), and DRB1*01:01, OR 1.10 (95% CI: 1.04-1.17), and two protective alleles, DQB1*02:01, OR 0.89 (95% CI: 0.85-0.94), and DRB1*03:01, OR 0.89 (95% CI: 0.85-0.94). CONCLUSION Five novel associations between HLA alleles and MRSD were identified in our cohort, and one previous association was confirmed. Future studies should assess the correlation between Malassezia antigens and antigen-binding properties of the associated HLA alleles.
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Affiliation(s)
- P Lindsø Andersen
- Department of Dermatology, Zealand University Hospital Roskilde, Sygehusvej 5, 4000, Roskilde, Denmark.
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark.
| | - G B Jemec
- Department of Dermatology, Zealand University Hospital Roskilde, Sygehusvej 5, 4000, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - C Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - M Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - K M Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - S Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - E Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - K R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - M T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - H Hjalgrim
- Department of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - T F Hansen
- Department of Neurology, Danish Headache Center, Copenhagen University Hospital, Glostrup, Denmark
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - S G Sækmose
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - S R Ostrowski
- Department of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - D M L Saunte
- Department of Dermatology, Zealand University Hospital Roskilde, Sygehusvej 5, 4000, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - O B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
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Human genetic polymorphism and Leishmaniasis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105203. [PMID: 34990851 DOI: 10.1016/j.meegid.2021.105203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/03/2023]
Abstract
Leishmaniasis is a disease of the subtropical and tropical spheres of the earth and has various clinical manifestations. The different form of leishmaniasis includes cutaneous leishmaniasis, mucocutaneous leishmaniasis, most lethal visceral leishmaniasis and PKDL form. These different forms depend on many factors such as parasite and vector species, geographical, environmental conditions and population ethnicity. Host genetic factors have been widely investigated for their role in developing the disease in various infections. There are several reports on associations or resistance between candidate gene polymorphisms and the risk and outcome of Leishmania infection. Polymorphism in genes involved in both innate and adaptive immune systems, as well as genes of metabolic processes contributes to disease manifestation. The wide availability and advancement of molecular techniques permits to exploration of hereditary factors related to leishmaniasis. Many candidate gene studies were conducted on family-based and population to identify novel biomarkers for understanding disease pathogenesis pathways and possible drug targets. This comprehensive review presents an update on various human genes polymorphism that influence the outcome of different forms of Leishmania infection in endemic regions of the world. Various electronic databases were searched systematically for relevant publications and thoroughly analyzed. Most of the candidate gene studies were found with discrepancies in findings. Genetic and functional studies with adequate power are needed to validate the contribution of host genes in susceptibility or resistance towards Leishmania infection and understanding pathogenesis.
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Onifade M, Roy-Gagnon MH, Parent MÉ, Burkett KM. Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling. BMC Genomics 2022; 23:98. [PMID: 35120458 PMCID: PMC8815214 DOI: 10.1186/s12864-022-08297-y] [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: 12/05/2021] [Accepted: 01/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Mixed models are used to correct for confounding due to population stratification and hidden relatedness in genome-wide association studies. This class of models includes linear mixed models and generalized linear mixed models. Existing mixed model approaches to correct for population substructure have been previously investigated with both continuous and case-control response variables. However, they have not been investigated in the context of extreme phenotype sampling (EPS), where genetic covariates are only collected on samples having extreme response variable values. In this work, we compare the performance of existing binary trait mixed model approaches (GMMAT, LEAP and CARAT) on EPS data. Since linear mixed models are commonly used even with binary traits, we also evaluate the performance of a popular linear mixed model implementation (GEMMA). Results We used simulation studies to estimate the type I error rate and power of all approaches assuming a population with substructure. Our simulation results show that for a common candidate variant, both LEAP and GMMAT control the type I error rate while CARAT’s rate remains inflated. We applied all methods to a real dataset from a Québec, Canada, case-control study that is known to have population substructure. We observe similar type I error control with the analysis on the Québec dataset. For rare variants, the false positive rate remains inflated even after correction with mixed model approaches. For methods that control the type I error rate, the estimated power is comparable. Conclusions The methods compared in this study differ in their type I error control. Therefore, when data are from an EPS study, care should be taken to ensure that the models underlying the methodology are suitable to the sampling strategy and to the minor allele frequency of the candidate SNPs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08297-y).
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Affiliation(s)
- Maryam Onifade
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada
| | | | - Marie-Élise Parent
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Université du Québec, Laval, Canada
| | - Kelly M Burkett
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada.
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Zijlstra EE. Precision Medicine in Control of Visceral Leishmaniasis Caused by L. donovani. Front Cell Infect Microbiol 2021; 11:707619. [PMID: 34858865 PMCID: PMC8630745 DOI: 10.3389/fcimb.2021.707619] [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: 05/10/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
Precision medicine and precision global health in visceral leishmaniasis (VL) have not yet been described and could take into account how all known determinants improve diagnostics and treatment for the individual patient. Precision public health would lead to the right intervention in each VL endemic population for control, based on relevant population-based data, vector exposures, reservoirs, socio-economic factors and other determinants. In anthroponotic VL caused by L. donovani, precision may currently be targeted to the regional level in nosogeographic entities that are defined by the interplay of the circulating parasite, the reservoir and the sand fly vector. From this 5 major priorities arise: diagnosis, treatment, PKDL, asymptomatic infection and transmission. These 5 priorities share the immune responses of infection with L. donovani as an important final common pathway, for which innovative new genomic and non-genomic tools in various disciplines have become available that provide new insights in clinical management and in control. From this, further precision may be defined for groups (e.g. children, women, pregnancy, HIV-VL co-infection), and eventually targeted to the individual level.
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Affiliation(s)
- Eduard E Zijlstra
- Clinical Sciences, Rotterdam Centre for Tropical Medicine, Rotterdam, Netherlands
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8
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Al-Sarraj Y, Al-Dous E, Taha RZ, Ahram D, Alshaban F, Tolfat M, El-Shanti H, Albagha OM. Family-Based Genome-Wide Association Study of Autism Spectrum Disorder in Middle Eastern Families. Genes (Basel) 2021; 12:761. [PMID: 34069769 PMCID: PMC8157263 DOI: 10.3390/genes12050761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disease characterized by abnormalities in language and social communication with substantial clinical heterogeneity. Genetic factors play an important role in ASD with heritability estimated between 70% to 80%. Genome-wide association studies (GWAS) have identified multiple loci associated with ASD. However, most studies were performed on European populations and little is known about the genetic architecture of ASD in Middle Eastern populations. Here, we report the first GWAS of ASD in the Middle eastern population of Qatar. We analyzed 171 families with ASD, using linear mixed models adjusting for relatedness and other confounders. Results showed that common single nucleotide polymorphisms (SNP) in seven loci are associated with ASD (p < 1 × 10-5). Although the identified loci did not reach genome-wide significance, many of the top associated SNPs are located within or near genes that have been implicated in ASD or related neurodevelopmental disorders. These include GORASP2, GABBR2, ANKS6, THSD4, ERCC6L, ARHGEF6, and HDAC8. Additionally, three of the top associated SNPs were significantly associated with gene expression. We also found evidence of association signals in two previously reported ASD-susceptibility loci (rs10099100 and rs4299400). Our results warrant further functional studies and replication to provide further insights into the genetic architecture of ASD.
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Affiliation(s)
- Yasser Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar; (Y.A.-S.); (E.A.-D.)
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
| | - Eman Al-Dous
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar; (Y.A.-S.); (E.A.-D.)
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
| | - Rowaida Z. Taha
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
| | - Dina Ahram
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
- Division of Nephrology, Columbia University Medical Center, New York, NY 10032, USA
| | - Fouad Alshaban
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
| | - Mohammed Tolfat
- The Shafallah Center for Children with Special Needs, Doha 33123, Qatar;
| | - Hatem El-Shanti
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Omar M.E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar; (Y.A.-S.); (E.A.-D.)
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha 34110, Qatar; (R.Z.T.); (D.A.); (F.A.); (H.E.-S.)
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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Dai X, Fu G, Zhao S, Zeng Y. Statistical Learning Methods Applicable to Genome-Wide Association Studies on Unbalanced Case-Control Disease Data. Genes (Basel) 2021; 12:genes12050736. [PMID: 34068248 PMCID: PMC8153154 DOI: 10.3390/genes12050736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
Despite the fact that imbalance between case and control groups is prevalent in genome-wide association studies (GWAS), it is often overlooked. This imbalance is getting more significant and urgent as the rapid growth of biobanks and electronic health records have enabled the collection of thousands of phenotypes from large cohorts, in particular for diseases with low prevalence. The unbalanced binary traits pose serious challenges to traditional statistical methods in terms of both genomic selection and disease prediction. For example, the well-established linear mixed models (LMM) yield inflated type I error rates in the presence of unbalanced case-control ratios. In this article, we review multiple statistical approaches that have been developed to overcome the inaccuracy caused by the unbalanced case-control ratio, with the advantages and limitations of each approach commented. In addition, we also explore the potential for applying several powerful and popular state-of-the-art machine-learning approaches, which have not been applied to the GWAS field yet. This review paves the way for better analysis and understanding of the unbalanced case-control disease data in GWAS.
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de Vrij N, Meysman P, Gielis S, Adriaensen W, Laukens K, Cuypers B. HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires. Vaccines (Basel) 2021; 9:270. [PMID: 33803005 PMCID: PMC8002611 DOI: 10.3390/vaccines9030270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023] Open
Abstract
Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.
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Affiliation(s)
- Nicky de Vrij
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium; (N.d.V.); (P.M.); (S.G.)
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), University of Antwerp, 2020 Antwerp, Belgium
| | - Pieter Meysman
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium; (N.d.V.); (P.M.); (S.G.)
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), University of Antwerp, 2020 Antwerp, Belgium
| | - Sofie Gielis
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium; (N.d.V.); (P.M.); (S.G.)
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), University of Antwerp, 2020 Antwerp, Belgium
| | - Wim Adriaensen
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium; (N.d.V.); (P.M.); (S.G.)
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), University of Antwerp, 2020 Antwerp, Belgium
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium; (N.d.V.); (P.M.); (S.G.)
- Biomedical Informatics Network Antwerpen (Biomina), University of Antwerp, 2020 Antwerp, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
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11
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Blackwell JM, Fakiola M, Singh OP. Genetics, Transcriptomics and Meta-Taxonomics in Visceral Leishmaniasis. Front Cell Infect Microbiol 2020; 10:590888. [PMID: 33324576 PMCID: PMC7723821 DOI: 10.3389/fcimb.2020.590888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Visceral leishmaniasis (VL) caused by parasites of the Leishmania donovani complex can be fatal in susceptible individuals. Understanding the interactions between host and pathogen is one way to obtain leads to develop better drugs and for vaccine development. In recent years multiple omics-based approaches have assisted researchers to gain a more global picture of this interaction in leishmaniasis. Here we review results from studies using three omics-based approaches to study VL caused by L. donovani in India: (i) chip-based analysis of single nucleotide variants in the first genome-wide association study of host genetic risk factors for VL, followed by analysis of epitope binding to HLA DRB1 risk versus protective alleles; (ii) transcriptional profiling demonstrating pathways important in Amphotericin B treated compared to active VL cases, including demonstration that anti-interleukin-10 unleashes a storm of chemokines and cytokines in whole blood responses to soluble leishmania antigen in active cases; and (iii) a meta-taxonomic approach based on sequencing amplicons derived from regions of 16S ribosomal RNA (16S rRNA) and 18S rRNA genes that allowed us to determine composition of both prokaryotic and eukaryotic gut microflora in VL cases compared to endemic controls. Overall, our omics-based approaches demonstrate that global analyses of genetic risk factors, host responses to infection, and the interaction between host, parasite and the microbiome can point to the most critical factors that determine the outcome of infection.
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Affiliation(s)
- Jenefer M. Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | | | - Om Prakash Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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12
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Gedda MR, Singh B, Kumar D, Singh AK, Madhukar P, Upadhyay S, Singh OP, Sundar S. Post kala-azar dermal leishmaniasis: A threat to elimination program. PLoS Negl Trop Dis 2020; 14:e0008221. [PMID: 32614818 PMCID: PMC7332242 DOI: 10.1371/journal.pntd.0008221] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Leishmaniasis remains a public health concern around the world that primarily affects poor folks of the developing world spanning across 98 countries with mortality of 0.2 million to 0.4 million annually. Post kala-azar dermal leishmaniasis (PKDL) is the late skin manifestation of visceral leishmaniasis (VL). It has been reported that about 2.5% to 20% of patients recovered from VL develop PKDL having stilted macular or nodular lesions with parasites. In the Indian subcontinent (ISC), it manifests a few months after recovery from VL, though in Africa it can occur simultaneously with VL or a little later. New cases of PKDL are also observed without prior VL in the ISC. These individuals with PKDL represent an important but largely neglected reservoir of infection that perpetuates anthroponotic Leishmania donovani transmission in the ISC and can jeopardize the VL elimination program as these cases can infect the sand flies and spread the endemic. Therefore, it becomes imperative to eradicate PKDL as a part of the VL elimination program. With the limited treatment options besides little knowledge on PKDL, this review stands out in focusing on different aspects that should be dealt for sustained VL elimination.
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Affiliation(s)
- Mallikarjuna Rao Gedda
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Center for Cellular Engineering, NIH Clinical Center, Bethesda, Maryland, United States of America
| | - Bhawana Singh
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Dhiraj Kumar
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Zoology, Rameshwar College, BRA Bihar University, Muzaffarpur, India
| | - Abhishek Kumar Singh
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Prasoon Madhukar
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Shreya Upadhyay
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Om Prakash Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shyam Sundar
- Infectious Disease Research Laboratory, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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13
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Lewis MD, Paun A, Romano A, Langston H, Langner CA, Moore IN, Bock KW, Francisco AF, Brenchley JM, Sacks DL. Fatal progression of experimental visceral leishmaniasis is associated with intestinal parasitism and secondary infection by commensal bacteria, and is delayed by antibiotic prophylaxis. PLoS Pathog 2020; 16:e1008456. [PMID: 32282850 PMCID: PMC7179947 DOI: 10.1371/journal.ppat.1008456] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/23/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022] Open
Abstract
Leishmania donovani causes visceral leishmaniasis (VL), which is typically fatal without treatment. There is substantial variation between individuals in rates of disease progression, response to treatment and incidence of post-treatment sequelae, specifically post-kala-azar dermal leishmaniasis (PKDL). Nevertheless, the majority of infected people are asymptomatic carriers. Hamsters and mice are commonly used as models of fatal and non-fatal VL, respectively. Host and parasite genetics are likely to be important factors, but in general the reasons for heterogeneous disease presentation in humans and animal models are poorly understood. Host microbiota has become established as a factor in cutaneous forms of leishmaniasis but this has not been studied in VL. We induced intestinal dysbiosis in mice and hamsters by long-term treatment with broad-spectrum antibiotics in their drinking water. There were no significant differences in disease presentation in dysbiotic mice. In contrast, dysbiotic hamsters infected with L. donovani had delayed onset and progression of weight loss. Half of control hamsters had a rapid progression phenotype compared with none of the ABX-treated animals and the nine-month survival rate was significantly improved compared to untreated controls (40% vs. 10%). Antibiotic-treated hamsters also had significantly less severe hepatosplenomegaly, which was accompanied by a distinct cytokine gene expression profile. The protective effect was not explained by differences in parasite loads or haematological profiles. We further found evidence that the gut-liver axis is a key aspect of fatal VL progression in hamsters, including intestinal parasitism, bacterial translocation to the liver, malakoplakia and iron sequestration, none of which occurred in non-progressing murine VL. Diverse bacterial genera were cultured from VL affected livers, of which Rodentibacter was specifically absent from ABX-treated hamsters, indicating this pathobiont may play a role in promoting disease progression. The results provide experimental support for antibiotic prophylaxis against secondary bacterial infections as an adjunct therapy in human VL patients.
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Affiliation(s)
- Michael D. Lewis
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Audrey Romano
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Harry Langston
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Charlotte A. Langner
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Ian N. Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Kevin W. Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Amanda Fortes Francisco
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - David L. Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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Blackwell JM, Fakiola M, Castellucci LC. Human genetics of leishmania infections. Hum Genet 2020; 139:813-819. [PMID: 32055998 PMCID: PMC7272388 DOI: 10.1007/s00439-020-02130-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/02/2020] [Indexed: 01/15/2023]
Abstract
Identifying genetic risk factors for parasitic infections such as the leishmaniases could provide important leads for improved therapies and vaccines. Until recently most genetic studies of human leishmaniasis were underpowered and/or not replicated. Here, we focus on recent genome-wide association studies of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). For VL, analysis across 2287 cases and 2692 controls from three cohorts identified a single major peak of genome-wide significance (Pcombined = 2.76 × 10–17) at HLA-DRB1–HLA-DQA1. HLA-DRB1*1501 and DRB1*1404/DRB1*1301 were the most significant protective versus risk alleles, respectively, with specific residues at amino acid positions 11 and 13 unique to protective alleles. Epitope-binding studies showed higher frequency of basic AAs in DRB1*1404-/*1301-specific epitopes compared to hydrophobic and polar AAs in DRB1*1501-specific epitopes at anchor residues P4 and P6 which interact with residues at DRB1 positions 11 and 13. For CL, genome-wide significance was not achieved in combined analysis of 2066 cases and 2046 controls across 2 cohorts. Rather, multiple top hits at P < 5 × 10–5 were observed, amongst which IFNG-AS1 was of specific interest as a non-coding anti-sense RNA known to influence responses to pathogens by increasing IFN-γ secretion. Association at LAMP3 encoding dendritic cell lysosomal associated membrane protein 3 was also interesting. LAMP3 increases markedly upon activation of dendritic cells, localizing to the MHC Class II compartment immediately prior to translocation of Class II to the cell surface. Together these GWAS results provide firm confirmation for the importance of antigen presentation and the regulation of IFNγ in determining the outcome of Leishmania infections.
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Affiliation(s)
- Jenefer M Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia. .,Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Michaela Fakiola
- INGM-National Institute of Molecular Genetics "Romeo Ed Enrica Invernizzi" Milan, Milan, Italy
| | - Léa C Castellucci
- National Institute of Science and Technology in Tropical Diseases, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
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15
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Santos-Pereira S, Cardoso FO, Calabrese KS, Zaverucha do Valle T. Leishmania amazonensis resistance in murine macrophages: Analysis of possible mechanisms. PLoS One 2019; 14:e0226837. [PMID: 31856207 PMCID: PMC6922422 DOI: 10.1371/journal.pone.0226837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022] Open
Abstract
Leishmaniasis encompass a group of infectious parasitic diseases occurring in 97 endemic countries where over one billion people live in areas at risk of infection. It is in the World Health Organization list of neglected diseases and it is considered a serious public health problem, with more than 20,000 deaths a year and high morbidity. Infection by protozoa from the genus Leishmania can cause several forms of the disease, which may vary from a self-healing ulcer to fatal visceral infection. Leishmania species, as well as host immune response and genetics can modulate the course of the disease. Leishmania sp are obligatory intracellular parasites that have macrophages as their main host cell. Depending on the activation phenotype, these cells may have distinct roles in disease development, acting in parasite control or proliferation. Therefore, the purpose of this work was to analyze Leishmania amazonensis infection in primary macrophage cells obtained from mice with two distinct genetic backgrounds, ie. different susceptibility to the infection; evaluating the cause for that difference. After infection, peritoneal macrophages from the resistant C3H/He strain presented lower parasite load when compared to susceptible BALB/c macrophages. The same was also true when cells received a Th2 stimulus after infection, but the difference was abrogated under Th1 stimulus. Nitric oxide production and arginase activity was different between the strains under Th1 or Th2 stimulus, respectively, but iNOS inhibition was unable to suppress C3H/He resistance. Hydrogen peroxide production was also higher in C3H/He than BALB/c under Th1 stimulus, but it could not account for differences in susceptibility. These results led us to conclude that, although they have an important role in parasite control, neither NO nor H2O2 production can explain C3H/He resistance to infection. Other studies are needed to uncover different mechanisms of resistance/susceptibility to L. amazonensis.
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Affiliation(s)
- Sandy Santos-Pereira
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Flávia O. Cardoso
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Kátia S. Calabrese
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Tânia Zaverucha do Valle
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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16
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Boquett JA, Bisso-Machado R, Zagonel-Oliveira M, Schüler-Faccini L, Fagundes NJR. HLA diversity in Brazil. HLA 2019; 95:3-14. [PMID: 31596032 DOI: 10.1111/tan.13723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/11/2019] [Accepted: 10/04/2019] [Indexed: 01/18/2023]
Abstract
Brazil is the fifth largest country in the world in area and the fifth most populous. The Brazilian voluntary Bone Marrow Donor Registry is the third largest in terms of number of donors in the world, being a valuable source of HLA genetics to characterize the donor population of Brazil as well. The genetic background of the Brazilian population is quite heterogeneous, resulting from 5 centuries of admixture among Native Americans, Europeans and Africans, making the Brazilian population unique in terms of genetic ancestry. The unique characteristics of populations in different Brazilian regions make them an exciting focus for genetic diversity studies. Studies on HLA genetic diversity of Brazilian populations have been conducted since the late 1980s and, in this review, we highlight the main findings from studies carried out in Brazil based on classical HLA. In addition, we calculated the genetic distance from the molecular data of the studies included in this review in order to have a broader view of the HLA diversity in Brazilian populations. We emphasize that characterization of HLA diversity is not only important for transplantation programs, but can shed a light on ancestry, history and other demographic patterns with or without association with autoimmune disease.
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Affiliation(s)
- Juliano A Boquett
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafael Bisso-Machado
- Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcelo Zagonel-Oliveira
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Applied Computing Graduate Program, Advanced Visualization & Geoinformatics Laboratory (VIZLab), Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Lavínia Schüler-Faccini
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Nelson J R Fagundes
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Acosta-Herrera M, Strauss M, Casares-Marfil D, Martín J. Genomic medicine in Chagas disease. Acta Trop 2019; 197:105062. [PMID: 31201776 DOI: 10.1016/j.actatropica.2019.105062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
Genetic approaches have been proposed for improving the understanding of the causes of differential susceptibility to Trypanosoma cruzi infection and Chagas disease outcome. Polymorphisms in genes involved in the immune/inflammatory response are being studied in order to clarify their possible role in the occurrence or severity of the cardiac and/or gastrointestinal complications. However still today, the number of significant associated genes is limited and the pathophysiological mechanisms underlying this condition are unknown. This article review the information currently available from the published scientific literature regarding the genetic variants of molecules of the immune system and other variants that can contribute to the clinical presentation of the disease. Genomic medicine will improve our knowledge about the molecular basis of Chagas disease, will open new avenues for developing biomarkers of disease progression, new therapeutic strategies to suit the requirements of individual patients, and will contribute to the control of one of the infections with the greatest socio-economic impact in the Americas.
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18
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Braliou GG, Kontou PI, Boleti H, Bagos PG. Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis. Parasitol Res 2019; 118:2329-2342. [PMID: 31230160 DOI: 10.1007/s00436-019-06374-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Leishmaniases are cutaneous, mucocutaneous, and visceral diseases affecting humans and domesticated animals mostly in the tropical and subtropical areas of the planet. Host genetics have been widely investigated for their role in developing various infectious diseases. The SLC11A1 gene has been reported to play a role in neutrophil function and is associated with susceptibility to infectious and inflammatory diseases such as tuberculosis or rheumatoid arthritis. In the present meta-analysis, we investigate the genetic association of SLC11A1 polymorphisms with susceptibility to leishmaniasis. Genotypes and other risk-related data were collected from 13 case-control and family-based studies (after literature search). Conventional random-effects meta-analysis was performed using STATA 13. To pool case-control and family-based data, the weighted Stouffer's method was also applied. Eight polymorphisms were investigated: rs2276631, rs3731865, rs3731864, rs17221959, rs201565523, rs2279015, rs17235409, and rs17235416. We found that rs17235409 (D543N) and rs17235416 (1729 + 55del4) are significantly associated with a risk for cutaneous leishmaniasis (CL), whereas rs17221959, rs2279015, and rs17235409 are associated with visceral leishmaniasis (VL). Our results suggest that polymorphisms in SLC11A1 affect susceptibility to CL and VL. These findings open new pathways in understanding macrophage response to Leishmania infection and the genetic factors predisposing to symptomatic CL or VL that can lead to the usage of predictive biomarkers in populations at risk.
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Affiliation(s)
- Georgia G Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece.
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece
| | - Haralabia Boleti
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece.
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19
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Determinants for progression from asymptomatic infection to symptomatic visceral leishmaniasis: A cohort study. PLoS Negl Trop Dis 2019; 13:e0007216. [PMID: 30917114 PMCID: PMC6453476 DOI: 10.1371/journal.pntd.0007216] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 04/08/2019] [Accepted: 02/05/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Asymptomatic Leishmania donovani infections outnumber clinical presentations, however the predictors for development of active disease are not well known. We aimed to identify serological, immunological and genetic markers for progression from L. donovani infection to clinical Visceral Leishmaniasis (VL). METHODS We enrolled all residents >2 years of age in 27 VL endemic villages in Bihar (India). Blood samples collected on filter paper on two occasions 6-12 months apart, were tested for antibodies against L. donovani with rK39-ELISA and DAT. Sero converters, (negative for both tests in the first round but positive on either of the two during the second round) and controls (negative on both tests on both occasions) were followed for three years. At the start of follow-up venous blood was collected for the following tests: DAT, rK39- ELISA, Quantiferon assay, SNP/HLA genotyping and L.donovani specific quantitative PCR. RESULTS Among 1,606 subjects enrolled,17 (8/476 seroconverters and 9/1,130 controls) developed VL (OR 3.1; 95% CI 1.1-8.3). High DAT and rK39 ELISA antibody titers as well as positive qPCR were strongly and significantly associated with progression from seroconversion to VL with odds ratios of 19.1, 30.3 and 20.9 respectively. Most VL cases arose early (median 5 months) during follow-up. CONCLUSION We confirmed the strong association between high DAT and/or rK39 titers and progression to disease among asymptomatic subjects and identified qPCR as an additional predictor. Low predictive values do not warrant prophylactic treatment but as most progressed to VL early during follow-up, careful oberservation of these subjects for at least 6 months is indicated.
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20
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Asymptomatic Leishmania infection in blood donors from the Southern of Spain. Infection 2019; 47:739-747. [PMID: 30888587 DOI: 10.1007/s15010-019-01297-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVES To investigate the proportion of asymptomatic infection among blood donors in a region endemic for Leishmania; and to ascertain epidemiological and genetic factors associated with this condition. METHODS We studied 1260 blood donors in the Province of Granada in the Southern Spain. After obtaining informed consent in each participant, a poll about habits, housing and contact with animals were carried out. Blood samples were obtained for determining antileishmanial antibodies and a PCR assay. HLA typing was performed in a randomly sample among the donors with positive serology. RESULTS We have found that L. infantum antibodies were present in 7.9% of blood donors and DNA in blood was detected in 2.5% of donors. There was no concordance between both determinations, except in one patient. Taking into consideration both techniques, 129 participants were considered to have asymptomatic Leishmania infection. No participant in this study developed clinical leishmaniasis during a follow-up period of 2 years. HLA were typed in 51 donors. Asymptomatic Leishmania infection might be associated with certain HLA antigens. A multivariate analysis was done with the variables obtained through the participants' interview. The contact with livestock (goats, pigs, and sheep), but not dogs, either at home or in the environment, was significantly and independently associated with asymptomatic leishmania infection. CONCLUSIONS Asymptomatic leishmanial infection among blood donors is frequent in the Granada Province, south of Spain. The presence of livestock in this region is related to this infection, perhaps influencing vector density of this disease. Some HLA genes might be associated with asymptomatic leishmanial state.
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21
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Joshi S, Yadav NK, Rawat K, Kumar V, Ali R, Sahasrabuddhe AA, Siddiqi MI, Haq W, Sundar S, Dube A. Immunogenicity and Protective Efficacy of T-Cell Epitopes Derived From Potential Th1 Stimulatory Proteins of Leishmania (Leishmania) donovani. Front Immunol 2019; 10:288. [PMID: 30873164 PMCID: PMC6403406 DOI: 10.3389/fimmu.2019.00288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/04/2019] [Indexed: 11/24/2022] Open
Abstract
Development of a suitable vaccine against visceral leishmaniasis (VL), a fatal parasitic disease, is considered to be vital for maintaining the success of kala-azar control programs. The fact that Leishmania-infected individuals generate life-long immunity offers a viable proposition in this direction. Our prior studies demonstrated that T-helper1 (Th1) type of cellular response was generated by six potential recombinant proteins viz. elongation factor-2 (elF-2), enolase, aldolase, triose phosphate isomerase (TPI), protein disulfide isomerase (PDI) and p45, derived from a soluble antigenic fraction (89.9–97.1 kDa) of Leishmania (Leishmania) donovani promastigote, in treated Leishmania patients and golden hamsters and showed significant prophylactic potential against experimental VL. Moreover, since, it is well-known that our immune system, in general, triggers production of specific protective immunity in response to a small number of amino acids (peptide), this led to the identification of antigenic epitopes of the above-stated proteins utilizing immunoinformatics. Out of thirty-six, three peptides-P-10 (enolase), P-14, and P-15 (TPI) elicited common significant lymphoproliferative as well as Th1-biased cytokine responses both in golden hamsters and human subjects. Further, immunization with these peptides plus BCG offered 75% prophylactic efficacy with boosted cellular immune response in golden hamsters against Leishmania challenge which is indicative of their candidature as potential vaccine candidates.
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Affiliation(s)
- Sumit Joshi
- Parasitology Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Narendra Kumar Yadav
- Parasitology Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Keerti Rawat
- Parasitology Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Vikash Kumar
- Molecular and Structural Biology Division Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Rafat Ali
- Medicinal Process Chemistry Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Amogh Anant Sahasrabuddhe
- Molecular and Structural Biology Division Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Wahajul Haq
- Medicinal Process Chemistry Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Anuradha Dube
- Parasitology Division, Council of Scientific & Industrial Research-Central Drug Research Institute, Lucknow, India
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Mishra A, Sundaravadivel P, Tripathi SK, Jha RK, Badrukhiya J, Basak N, Anerao I, Sharma A, Idowu AE, Mishra A, Pandey S, Kumar U, Singh S, Nizamuddin S, Tupperwar NC, Jha AN, Thangaraj K. Variations in macrophage migration inhibitory factor gene are not associated with visceral leishmaniasis in India. J Infect Public Health 2019; 12:380-387. [PMID: 30611734 DOI: 10.1016/j.jiph.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/24/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The host genetic factors play important role in determining the outcome of visceral leishmaniasis (VL). Macrophage migration inhibitory factor (MIF) is an important host cytokine, which is a key regulator of innate immune system. Genetic variants in MIF gene have been found to be associated with several inflammatory and infectious diseases. Role of MIF is well documented in leishmaniasis diseases, including Indian visceral leishmaniasis, where elevated level of serum MIF has been associated with VL phenotypes. However, there was no genetic study to correlate MIF variants in VL, therefore, we aimed to study the possible association of three reported MIF gene variants -794 CATT, -173G > C and non-coding RNA gene LOC284889 in Indian VL phenotype. METHODS Study subjects comprised of 214 VL patients along with ethnically and demographically matched 220 controls from VL endemic regions of Bihar state in India. RESULTS We found no significant difference between cases and controls in allelic, genotypic and haplotype frequency of the markers analysed [-794 CATT repeats (χ2=0.86; p=0.35; OR=0.85; 95% CI=0.61-1.19); -173 G>C polymorphism (χ2=1.11; p=0.29; OR=0.83; 95% CI=0.59-1.16); and LOC284889 (χ2=0.78; p=0.37; OR=0.86; 95% CI=0.61-1.20)]. CONCLUSION Since we did not find any significant differences between case and control groups, we conclude that sequencing of complete MIF gene and extensive study on innate and adaptive immunity genes may help in identifying genetic variations that are associated with VL susceptibility/resistance among Indians.
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Affiliation(s)
- Anshuman Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Vinoba Bhave Research Institute, Allahabad, India; Institute of Advanced Materials, Linkoping, Sweden
| | | | | | - Rajan Kumar Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Nipa Basak
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research, India
| | - Isha Anerao
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Akshay Sharma
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ajayi Ebenezer Idowu
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Osun State University, Oshogbo, Nigeria
| | | | | | - Umesh Kumar
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sakshi Singh
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Aditya Nath Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Sickle Cell Institute Chhattisgarh, Raipur, India
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Singh B, Fakiola M, Sudarshan M, Oommen J, Singh SS, Sundar S, Blackwell JM. HLA-DR Class II expression on myeloid and lymphoid cells in relation to HLA-DRB1 as a genetic risk factor for visceral leishmaniasis. Immunology 2018; 156:174-186. [PMID: 30403401 DOI: 10.1111/imm.13018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/27/2022] Open
Abstract
Genetic variation at HLA-DRB1 is a risk factor for visceral leishmaniasis (VL) caused by Leishmania donovani. The single nucleotide polymorphism rs9271252 upstream of the DRB1 gene provides a perfect tag for protective versus risk HLA-DRB1 four-digit alleles. In addition to the traditional role of the membrane-distal region of HLA class II molecules in antigen presentation and CD4 T-cell activation, the membrane-proximal region mediates 'non-traditional' multi-functional activation, differentiation, or death signals, including in DR-expressing T cells. To understand how HLA-DR contributes to disease pathogenesis, we examined expression at the protein level in circulating myeloid (CD14+ , CD16+ ) and lymphoid (CD4+ , CD8+ , CD19+ ) cells of VL patients (pre- and post-treatment) compared with endemic healthy controls (EHC). Although DR expression is reduced in circulating myeloid cells in active disease relative to EHC and post-treatment groups, expression is enhanced on CD4+ DR+ and CD8+ DR+ T cells consistent with T-cell activation. Cells of all myeloid and lymphoid populations from active cases were refractory to stimulation of DR expression with interferon-γ (IFN-γ). In contrast, all populations except CD19+ B cells from healthy blood bank controls showed enhanced DR expression following IFN-γ stimulation. The rs9271252 genotype did not impact significantly on IFN-γ-activated DR expression in myeloid, B or CD8+ T cells, but CD4+ T cells from healthy individuals homozygous for the risk allele were particularly refractory to activated DR expression. Further analysis of DR expression on subsets of CD4+ T cells regulating VL disease could uncover additional ways in which pleiotropy at HLA DRB1 contributes to disease pathogenesis.
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Affiliation(s)
- Bhawana Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Michaela Fakiola
- Department of Pathology, The University of Cambridge, Cambridge, UK
| | - Medhavi Sudarshan
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Joyce Oommen
- Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
| | - Siddharth Sankar Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Jenefer M Blackwell
- Department of Pathology, The University of Cambridge, Cambridge, UK.,Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
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Bunn PT, Montes de Oca M, de Labastida Rivera F, Kumar R, Ng SS, Edwards CL, Faleiro RJ, Sheel M, Amante FH, Frame TCM, Muller W, Haque A, Uzonna JE, Hill GR, Engwerda CR. Distinct Roles for CD4+ Foxp3+ Regulatory T Cells and IL-10–Mediated Immunoregulatory Mechanisms during Experimental Visceral Leishmaniasis Caused by Leishmania donovani. THE JOURNAL OF IMMUNOLOGY 2018; 201:3362-3372. [DOI: 10.4049/jimmunol.1701582] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 09/25/2018] [Indexed: 12/19/2022]
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Hsu Y, Auerbach J, Zheng T, Lo SH. Coping with family structure in genome-wide association studies: a comparative evaluation. BMC Proc 2018; 12:42. [PMID: 30263047 PMCID: PMC6156900 DOI: 10.1186/s12919-018-0151-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In this paper, a fully statistical investigation of the control of family structure as random effects is analyzed and discussed, using both the genome-wide association studies (GWAS) data and simulated data. Three modeling strategies are proposed and the analysis results suggest the hybrid use of results from all possible models should be combined in practice.
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26
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Miao R, Huang S, Li C, Ding S, Wang R, Xu K, Yang C, Xu F, Ge H. An HLA class II locus, previously identified by a genome-wide association study, is also associated with susceptibility to pulmonary tuberculosis in a Chinese population. INFECTION GENETICS AND EVOLUTION 2018; 64:164-167. [PMID: 29933081 DOI: 10.1016/j.meegid.2018.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Genome-wide association study (GWAS) in Icelanders identified HLA class II sequence variants on chromosome 6p21 as tuberculosis (TB) susceptibility loci. To evaluate the role of these loci in other populations with different ancestry, we conducted a case-control study in Chinese population. METHODS We genotyped two genetic variants (rs9272461 and rs9271300) on the reported chromosome 6p21 in 739 pulmonary tuberculosis (PTB) cases and 749 healthy controls from Chinese Han population using TaqMan allelic discrimination assay. Logistic regression was applied to evaluate the association between genetic variants and PTB risk and to estimate corresponding odds ratios (ORs) and 95% confidence intervals (95%CIs). RESULTS We found that rs9272461 was significantly associated with the risk of PTB in various genetic models (dominant OR = 0.75, 95%CI: 0.61-0.92; recessive OR = 0.64, 95%CI: 0.46-0.90, and additive OR = 0.78, 95%CI: 0.67-0.90). Moreover, in the stratified analysis in additive model, the association was also significant in the old (age ≥ 48 years) (OR = 0.76, 95%CI: 0.62-0.93; P = .008), men (OR = 0.71, 95%CI: 0.59-0.85; P < .001), and new PTB cases (OR = 0.76, 95%CI: 0.65-0.90; P = .001). The association results were similar between the microbiologically negative (OR = 0.78, 95%CI: 0.64-0.94; P = .008) and positive cases (OR = 0.77, 95%CI: 0.64-0.93; P = .008). We did not observe significant association for rs9271300 neither in the overall analysis (additive model: OR = 0.98, 95%CI: 0.85-1.13; P = .776) nor in the stratified analysis. CONCLUSIONS Our findings indicate that the HLA class II locus also affects the susceptibility to PTB in Chinese population. Further validation studies and function experiments are required to confirm the roles of the discovered variant.
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Affiliation(s)
- Ruifen Miao
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China.
| | - Shuran Huang
- Nanjing Hospital of Chinese Medicine, Nanjing 210001, China
| | - Chen Li
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Songning Ding
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Rong Wang
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Ke Xu
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Chen Yang
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Fei Xu
- Department of Chronic Communicable Disease, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Haibo Ge
- Nanjing Hospital of Chinese Medicine, Nanjing 210001, China.
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Batista LFS, Utsunomiya YT, Silva TBF, Carneiro MM, Paiva JSF, Silva RB, Tomokane TY, Rossi CN, Pacheco AD, Torrecilha RBP, Silveira FT, Marcondes M, Nunes CM, Laurenti MD. Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva. PLoS One 2018; 13:e0197215. [PMID: 29742167 PMCID: PMC5942812 DOI: 10.1371/journal.pone.0197215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/27/2018] [Indexed: 01/22/2023] Open
Abstract
The anti-inflammatory properties of sand fly saliva favor the establishment of the Leishmania infantum infection. In contrast, an antibody response against Lutzomyia longipalpis saliva is often associated with a protective cell-mediated response against canine visceral leishmaniasis. Genetic studies may demonstrate to what extent the ability to secrete anti-saliva antibodies depends on genetic or environmental factors. However, the genetic basis of canine antibody response against sand fly saliva has not been assessed. The aim of this study was to identify chromosomal regions associated with the anti-Lu. longipalpis salivary IgG response in 189 dogs resident in endemic areas in order to provide information for prophylactic strategies. Dogs were classified into five groups based on serological and parasitological diagnosis and clinical evaluation. Anti-salivary gland homogenate (SGH) IgG levels were assessed by Enzyme-Linked Immunosorbent Assay (ELISA). Genomic DNA was isolated from blood samples and genotyped using a SNP chip with 173,662 single nucleotide polymorphism (SNP) markers. The following linear regression model was fitted: IgG level = mean + origin + sex + age + use of a repellent collar, and the residuals were assumed as pseudo-phenotypes for the association test between phenotypes and genotypes (GWA). A component of variance model that takes into account polygenic and sample structure effects (EMMAX) was employed for GWA. Phenotypic findings indicated that anti-SGH IgG levels remained higher in exposed and subclinically infected dogs than in severely diseased dogs even in regression model residuals. Five associated markers were identified on chromosomes 2, 20 and 31. The mapped genes included CD180 (RP105) and MITF related to the rapid activation of B lymphocytes and differentiation into antibody-secreting plasma cells. The findings pointed to chromosomal segments useful for functional confirmation studies and a search for adjuvant molecules of the anti-saliva response.
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Affiliation(s)
- Luís F. S. Batista
- Departamento de Patologia Veterinária, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
- Escola de Saúde, Universidade Salvador, Salvador, Bahia, Brazil
| | - Yuri T. Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Thaís B. F. Silva
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Thaíse Y. Tomokane
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Claudio N. Rossi
- Departmento de Clínica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Acácio D. Pacheco
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Rafaela B. P. Torrecilha
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Fernando T. Silveira
- Deparatmento de Parasitologia, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Mary Marcondes
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Cáris M. Nunes
- Departmento de Saúde Animal e Produção, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Márcia D. Laurenti
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio. Genetics 2018; 208:1397-1408. [PMID: 29429966 PMCID: PMC5887138 DOI: 10.1534/genetics.117.300360] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/25/2018] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0-1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects.
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Affiliation(s)
- Luke R Lloyd-Jones
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
| | - Matthew R Robinson
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
- Department of Computational Biology, University of Lausanne, CH-1015, Switzerland
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane 4072, Australia
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Singh T, Fakiola M, Oommen J, Singh AP, Singh AK, Smith N, Chakravarty J, Sundar S, Blackwell JM. Epitope-Binding Characteristics for Risk versus Protective DRB1 Alleles for Visceral Leishmaniasis. THE JOURNAL OF IMMUNOLOGY 2018; 200:2727-2737. [PMID: 29507109 DOI: 10.4049/jimmunol.1701764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022]
Abstract
HLA-DRB1 is the major genetic risk factor for visceral leishmaniasis (VL). We used SNP2HLA to impute HLA-DRB1 alleles and SNPTEST to carry out association analyses in 889 human cases and 977 controls from India. NetMHCIIpan 2.1 was used to map epitopes and binding affinities across 49 Leishmania vaccine candidates, as well as across peptide epitopes captured from dendritic cells treated with crude Leishmania Ag and identified using mass spectrometry and alignment to amino acid sequences of a reference Leishmania genome. Cytokines were measured in peptide-stimulated whole blood from 26 cured VL cases and eight endemic healthy controls. HLA-DRB1*1501 and DRB1*1404/DRB1*1301 were the most significant protective and risk alleles, respectively, with specific residues at aa positions 11 and 13 unique to protective alleles. We observed greater peptide promiscuity in sequence motifs for 9-mer core epitopes predicted to bind to risk (*1404/*1301) compared with protective (*1501) DRB1 alleles. There was a higher frequency of basic amino acids in DRB1*1404/*1301-specific epitopes compared with hydrophobic and polar amino acids in DRB1*1501-specific epitopes at anchor residues pocket 4 and pocket 6, which interact with residues at DRB1 positions 11 and 13. Cured VL patients made variable, but robust, IFN-γ, TNF, and IL-10 responses to 20-mer peptides based on captured epitopes, with peptides based on DRB1*1501-captured epitopes resulting in a higher proportion (odds ratio 2.23, 95% confidence interval 1.17-4.25, p = 0.017) of patients with IFN-γ/IL-10 ratios > 2-fold compared with peptides based on DRB1*1301-captured epitopes. Our data provide insight into the molecular mechanisms underpinning the association of HLA-DRB1 alleles with risk versus protection in VL in humans.
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Affiliation(s)
- Toolika Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Michaela Fakiola
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Joyce Oommen
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia; and
| | - Akhil Pratap Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Abhishek K Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Noel Smith
- Lonza Biologics PLC, Great Abington, Cambridge CB21 6GS, United Kingdom
| | - Jaya Chakravarty
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Shyam Sundar
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Jenefer M Blackwell
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; .,Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia; and
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Banu SS, Meyer W, Ahmed BN, Kim R, Lee R. Detection of Leishmania donovani in peripheral blood of asymptomatic individuals in contact with patients with visceral leishmaniasis. Trans R Soc Trop Med Hyg 2017; 110:286-93. [PMID: 27198212 DOI: 10.1093/trstmh/trw027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/28/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The majority of individuals infected with Leishmania donovani complex remain asymptomatic. They may act as transmission reservoirs for visceral leishmaniasis (VL). We investigated sero-prevalence of L. donovani complex amongst those closely associated with patients with VL and whether these sero-reactive individuals had Leishmania parasites in their peripheral blood. Other risk factors were also investigated. METHODS A total of 257 individuals in contact with patients with VL were tested for anti-Leishmania antibodies by rK39 immunochromatographic test (rK39 ICT), ELISA using promastigote antigen (p-ELISA) and indirect fluorescent antibody test (IFAT). Buffy coats of rK39 ICT positive individuals were cultured; sero-reactive buffy coats were tested for Leishmania DNA by ITS1 PCR. DNA obtained from culture was sequenced to confirm Leishmania species. Risk factors were evaluated for each sero-positive sample. RESULTS The results showed 29.2% (75/257) prevalence by serological tests: 14.4% (37/257) were positive by rK39 ICT, 25.3% (65/257) by p-ELISA, 18.3% (47/257) by IFAT and 10.9% (28/257) by all three serological methods. Ten percent (3/30) of cultures were positive for Leishmania promastigotes. Only 3% (2/74) sero-reactive buffy coats were positive for DNA; sequence analysis revealed L. donovani species. Significant risk factors were age, working as farmers, domestic animals in household and proximity to animal shelters. CONCLUSIONS Asymptomatic family members of patients with VL can carry live L. donovani in peripheral blood and may act as potential reservoirs. GENBANK ACCESSION NUMBER BankIt1863680 Leishmania KT921417 (DNA sequences of the ribosomal ITS1 region of L. donovani).
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Affiliation(s)
- Sultana S Banu
- Parasitology Department, Centre for Infectious Diseases and Microbiology Laboratory Services (CIDMLS), ICPMR, Westmead Hospital, NSW, Australia Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute, Westmead Institute for Medical Research, NSW, Australia Discipline of Medicine, Sydney Medical School, University of Sydney, NSW, Australia Communicable Disease Control Unit, Directorate General of Health Services, Mohakhali, Dhaka, Bangladesh.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute, Westmead Institute for Medical Research, NSW, Australia Discipline of Medicine, Sydney Medical School, University of Sydney, NSW, Australia
| | - Be-Nazir Ahmed
- Communicable Disease Control Unit, Directorate General of Health Services, Mohakhali, Dhaka, Bangladesh
| | - Rady Kim
- Parasitology Department, Centre for Infectious Diseases and Microbiology Laboratory Services (CIDMLS), ICPMR, Westmead Hospital, NSW, Australia
| | - Rogan Lee
- Parasitology Department, Centre for Infectious Diseases and Microbiology Laboratory Services (CIDMLS), ICPMR, Westmead Hospital, NSW, Australia Discipline of Medicine, Sydney Medical School, University of Sydney, NSW, Australia
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Genome-wide linkage and association study implicates the 10q26 region as a major genetic contributor to primary nonsyndromic vesicoureteric reflux. Sci Rep 2017; 7:14595. [PMID: 29097723 PMCID: PMC5668427 DOI: 10.1038/s41598-017-15062-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/06/2017] [Indexed: 12/29/2022] Open
Abstract
Vesicoureteric reflux (VUR) is the commonest urological anomaly in children. Despite treatment improvements, associated renal lesions – congenital dysplasia, acquired scarring or both – are a common cause of childhood hypertension and renal failure. Primary VUR is familial, with transmission rate and sibling risk both approaching 50%, and appears highly genetically heterogeneous. It is often associated with other developmental anomalies of the urinary tract, emphasising its etiology as a disorder of urogenital tract development. We conducted a genome-wide linkage and association study in three European populations to search for loci predisposing to VUR. Family-based association analysis of 1098 parent-affected-child trios and case/control association analysis of 1147 cases and 3789 controls did not reveal any compelling associations, but parametric linkage analysis of 460 families (1062 affected individuals) under a dominant model identified a single region, on 10q26, that showed strong linkage (HLOD = 4.90; ZLRLOD = 4.39) to VUR. The ~9Mb region contains 69 genes, including some good biological candidates. Resequencing this region in selected individuals did not clearly implicate any gene but FOXI2, FANK1 and GLRX3 remain candidates for further investigation. This, the largest genetic study of VUR to date, highlights the 10q26 region as a major genetic contributor to VUR in European populations.
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Courtenay O, Peters NC, Rogers ME, Bern C. Combining epidemiology with basic biology of sand flies, parasites, and hosts to inform leishmaniasis transmission dynamics and control. PLoS Pathog 2017; 13:e1006571. [PMID: 29049371 PMCID: PMC5648254 DOI: 10.1371/journal.ppat.1006571] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quantitation of the nonlinear heterogeneities in Leishmania parasites, sand fly vectors, and mammalian host relationships provides insights to better understand leishmanial transmission epidemiology towards improving its control. The parasite manipulates the sand fly via production of promastigote secretory gel (PSG), leading to the “blocked sand fly” phenotype, persistent feeding attempts, and feeding on multiple hosts. PSG is injected into the mammalian host with the parasite and promotes the establishment of infection. Animal models demonstrate that sand flies with the highest parasite loads and percent metacyclic promastigotes transmit more parasites with greater frequency, resulting in higher load infections that are more likely to be both symptomatic and efficient reservoirs. The existence of mammalian and sand fly “super-spreaders” provides a biological basis for the spatial and temporal clustering of clinical leishmanial disease. Sand fly blood-feeding behavior will determine the efficacies of indoor residual spraying, topical insecticides, and bed nets. Interventions need to have sufficient coverage to include transmission hot spots, especially in the absence of field tools to assess infectiousness. Interventions that reduce sand fly densities in the absence of elimination could have negative consequences, for example, by interfering with partial immunity conferred by exposure to sand fly saliva. A deeper understanding of both sand fly and host biology and behavior is essential to ensuring effectiveness of vector interventions. We review recent research that sheds light on the quantitative biology of leishmanial transmission between sand flies and mammalian hosts and use these insights to better understand transmission, the observed epidemiology of the disease, and their implications in choice of control strategy. Using animal models, we show how the parasite-induced processes manipulate sand fly blood-feeding behavior and the infectious metacyclic dose to promote host infection and to differentially regulate the onward transmission potential of individual vectors and hosts. The existence of subpopulations of mammalian and sand fly “super-spreaders” provides a biological basis for the spatial and temporal clustering of clinical leishmanial disease. While tools are unavailable to distinguish these individuals in mixed populations, blanket interventions will be necessary to ensure inclusion of transmission hot spots. Interventions that reduce sand fly densities without elimination could interfere with vector—host dynamics and conferred partial immunity to host populations.
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Affiliation(s)
- Orin Courtenay
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Zeeman Institute, University of Warwick, Coventry, United Kingdom
- * E-mail:
| | - Nathan C. Peters
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Matthew E. Rogers
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, School of Medicine, University of California San Francisco, San Francisco, California, United States of America
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de Vasconcelos TCB, Furtado MC, Belo VS, Morgado FN, Figueiredo FB. Canine susceptibility to visceral leishmaniasis: A systematic review upon genetic aspects, considering breed factors and immunological concepts. INFECTION GENETICS AND EVOLUTION 2017; 74:103293. [PMID: 28987807 DOI: 10.1016/j.meegid.2017.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/30/2017] [Accepted: 10/03/2017] [Indexed: 01/01/2023]
Abstract
Dogs have different susceptibility degrees to leishmaniasis; however, genetic research on this theme is scarce, manly on visceral form. The aims of this systematic review were to describe and discuss the existing scientific findings on genetic susceptibility to canine leishmaniasis, as well as to show the gaps of the existing knowledge. Twelve articles were selected, including breed immunological studies, genome wide associations or other gene polymorphism or gene sequencing studies, and transcription approaches. As main results of literature, there was a suggestion of genetic clinical resistance background for Ibizan Hound dogs, and alleles associated with protection or susceptibility to visceral leishmaniasis in Boxer dogs. Genetic markers can explain phenotypic variance in both pro- and anti-inflammatory cytokines and in cellular immune responses, including antigen presentation. Many gene segments are involved in canine visceral leishmaniasis phenotype, with Natural Resistance Associated Macrophage Protein 1 (NRAMP1) as the most studied. This was related to both protection and susceptibility. In comparison with murine and human genetic approaches, lack of knowledge in dogs is notorious, with many possibilities for new studies, revealing a wide field to be assessed on canine leishmaniasis susceptibility research.
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Affiliation(s)
- Tassia Cristina Bello de Vasconcelos
- Centro de Controle de Zoonoses, Vigilância em Saúde, Secretaria Municipal de Saúde, Prefeitura Municipal de Resende, Rua Euridices Paulina de Almeida, 300, Vicentina II, Resende, RJ 27500-000, Brazil.
| | - Marina Carvalho Furtado
- Fiocruz Mata Atlântica, Fundação Oswaldo Cruz, Estrada Rodrigues Caldas, 3400, Taquara, Rio de Janeiro, RJ 22713-375, Brazil
| | - Vinícius Silva Belo
- Universidade Federal de São João del-Rei, campus Centro Oeste Dona Lindu, Rua Sebastião Gonçalves Coelho, 400, Chanadour, Divinópolis, MG 35.501-296, Brazil
| | - Fernanda Nazaré Morgado
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Fabiano Borges Figueiredo
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Rua Professor Algacyr Munhoz Mader, 3.775, CIC, campus do Tecpar, bloco C, Curitiba, PR 81.350-010 Brazil
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34
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Mozzi A, Pontremoli C, Sironi M. Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches. INFECTION GENETICS AND EVOLUTION 2017; 66:286-307. [PMID: 28951201 PMCID: PMC7106304 DOI: 10.1016/j.meegid.2017.09.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes > 2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens. Relatively few GWASs for infectious diseases were performed. Phenotype heterogeneity and case/control misclassification can affect GWAS power. Adaptive and innate immunity loci were identified in several infectious disease GWASs. Unexpected loci (e.g., lncRNAs) were also associated with infection susceptibility. GWASs should integrate host and pathogen diversity and use complex association models.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy.
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35
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Marquet S, Bucheton B, Reymond C, Argiro L, El-Safi SH, Kheir MM, Desvignes JP, Béroud C, Mergani A, Hammad A, Dessein AJ. Exome Sequencing Identifies Two Variants of the Alkylglycerol Monooxygenase Gene as a Cause of Relapses in Visceral Leishmaniasis in Children, in Sudan. J Infect Dis 2017; 216:22-28. [PMID: 28586473 DOI: 10.1093/infdis/jix277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/02/2017] [Indexed: 01/01/2023] Open
Abstract
Background Visceral leishmaniasis (kala-azar, KA) is the most severe form of leishmaniasis, characterized by fever, weight loss, hepatosplenomegaly, and lymphadenopathy. During an outbreak of KA in Babar El Fugara (Sudan), 5.7% of cured patients displayed relapses, with familial clustering in half the cases. Methods We performed whole-exome sequencing on 10 relapsing individuals and 11 controls from 5 nuclear families. Results Rare homozygous and compound-heterozygous nonsense (c.1213C > T, rs139309795, p.Arg405*) and missense (c.701A > G, rs143439626, p.Lys234Arg) mutations of the alkylglycerol monooxygenase (AGMO) gene were associated with KA relapse in 3 families. Sequencing in additional family members confirmed the segregation of these mutations with relapse and revealed an autosomal dominant mode of transmission. These mutations were detected heterozygous in 2 subjects among 100 unrelated individuals with KA who never relapsed after cure, suggesting incomplete penetrance of AGMO deficiency. AGMO is expressed in hematopoietic cells, and is strongly expressed in the liver. AGMO modulates PAF production by mouse macrophages, suggesting that it may act through the PAF/PAF receptor pathway previously shown to have anti-Leishmania activity. Conclusions This is the first demonstration that relapses after a first episode of KA are due to differences in human genetic susceptibility and not to modifications of parasite pathogenicity.
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Affiliation(s)
- Sandrine Marquet
- INSERM UMR906, GIMP, Labex ParaFrap, Aix-Marseille University, Marseille
| | - Bruno Bucheton
- INSERM UMR906, GIMP, Labex ParaFrap, Aix-Marseille University, Marseille.,Institut de Recherche pour le Développement, Unité Mixte de Recherche IRD-CIRAD 177, Campus International de Baillarguet, Montpellier, France
| | - Camille Reymond
- INSERM UMR906, GIMP, Labex ParaFrap, Aix-Marseille University, Marseille
| | - Laurent Argiro
- INSERM UMR906, GIMP, Labex ParaFrap, Aix-Marseille University, Marseille
| | - Sayda Hassan El-Safi
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Musa Mohamed Kheir
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Christophe Béroud
- INSERM UMR910, GMGF, Aix-Marseille University.,AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, Marseille, France
| | - Adil Mergani
- College of Applied Medical Sciences, Taif University, Turabah, Saudi Arabia
| | - Awad Hammad
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Alain J Dessein
- INSERM UMR906, GIMP, Labex ParaFrap, Aix-Marseille University, Marseille
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36
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Salih MAM, Fakiola M, Lyons PA, Younis BM, Musa AM, Elhassan AM, Anderson D, Syn G, Ibrahim ME, Blackwell JM, Mohamed HS. Expression profiling of Sudanese visceral leishmaniasis patients pre- and post-treatment with sodium stibogluconate. Parasite Immunol 2017; 39. [PMID: 28370072 DOI: 10.1111/pim.12431] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/24/2017] [Indexed: 01/08/2023]
Abstract
Visceral leishmaniasis (VL) in Sudan caused by Leishmania donovani is fatal in susceptible individuals if untreated. Treatment with sodium stibogluconate (SSG) leads to post-kala-azar dermal leishmaniasis (PKDL) in 58% of patients. Here, Affymetrix microarrays were used to identify genes differentially expressed in lymph nodes (N=9 paired samples) pre- and post-treatment with SSG. Using the Bioconductor package limma, 438 genes from 28 869 post-quality-control probe sets were differentially expressed (Pnominal ≤.02) post- vs pretreatment. Canonical pathway analysis using Ingenuity Pathway Analysis™ identified "role of nuclear factor of activated T-cell in regulation of immune response" (Pnominal =1.35×10-5 ; PBH-adjusted =4.79×10-3 ), "B-cell development" (Pnominal =2.04×10-4 ; PBH-adjusted =.024), "Fcγ receptor-mediated phagocytosis in macrophages and monocytes" (Pnominal =2.04×10-4 ; PBH-adjusted =.024) and "OX40 signalling" (Pnominal =2.82×10-4 ; PBH-adjusted =.025) as pathways differentially regulated post- vs pretreatment. Major network hub genes included TP53, FN1, MYC, BCL2, JUN, SYK, RUNX2, MMP1 and ACTA2. Top endogenous upstream regulators included IL-7 (P=2.28×10-6 ), TNF (P=4.26×10-6 ), Amyloid Precursor Protein (P=4.23×10-5 ) and SPI1/PI.1 (P=1.17×10-7 ). Top predicted chemical drug regulators included the flavonoid genistein (P=4.56×10-7 ) and the quinoline alkaloid camptothecin (P=5.14×10-5 ). These results contribute to our understanding of immunopathology associated with VL and response to SSG treatment. Further replication could identify novel therapeutic strategies that improve on SSG treatment and reduce the likelihood of progression to PKDL.
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Affiliation(s)
- M A M Salih
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan.,Central Laboratory, Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - M Fakiola
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - P A Lyons
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - B M Younis
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - A M Musa
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - A M Elhassan
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - D Anderson
- Telethon Kids Institute, The University of Western Australia, Subiaco, WA, Australia
| | - G Syn
- Telethon Kids Institute, The University of Western Australia, Subiaco, WA, Australia
| | - M E Ibrahim
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - J M Blackwell
- Department of Pathology, University of Cambridge, Cambridge, UK.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, Australia
| | - H S Mohamed
- Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan.,Department of Biology, Taibah University, Kingdom of Saudi Arabia
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37
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017. [PMID: 28449694 DOI: 10.1186/s13059-017-1207-1.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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38
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017; 18:76. [PMID: 28449694 PMCID: PMC5406920 DOI: 10.1186/s13059-017-1207-1] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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39
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Weirather JL, Duggal P, Nascimento EL, Monteiro GR, Martins DR, Lacerda HG, Fakiola M, Blackwell JM, Jeronimo SMB, Wilson ME. Comprehensive candidate gene analysis for symptomatic or asymptomatic outcomes of Leishmania infantum infection in Brazil. Ann Hum Genet 2017; 81:41-48. [PMID: 28054334 DOI: 10.1111/ahg.12180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/22/2016] [Indexed: 12/17/2022]
Abstract
Genetic risk factors contribute to asymptomatic versus symptomatic visceral leishmaniasis (VL) outcomes following infection with Leishmania infantum. We therefore carried out a family-based (n = 918 post-quality control fully genotyped and phenotyped individuals) candidate gene study for symptomatic VL or asymptomatic delayed-type hypersensitivity (DTH) skin test phenotypes in highly endemic neighborhoods of northeast Brazil. A total of 248 SNPs were genotyped in 42 genes selected as candidates on the basis of prior genetic, immunological, and transcriptional profiling studies. The most significant association with the VL phenotype was with SNP rs6785358 (P = 5.7e-04; pcorrected = 0.026) 3.8 kb upstream of TGFBR2, the gene encoding the type 2 receptor for transforming growth factor beta (TGFβ). A second inhibitory member of the TGBβ superfamily signaling pathway, SMAD7, was associated with the DTH phenotype (SNP rs7238442: P = 0.001; pcorrected = 0.051). The most significant association for the DTH phenotype was with SNP rs10800309 (P = -8.4e-06; pcorrected = 3.9e-04) situated 3.1 kb upstream of FCGR2A, the gene encoding the low-affinity IIa receptor for the Fc fragment of IgG. Overall, our results imply a role for IgG-mediated inflammation in determining DTH associated with asymptomatic infection and contribute to growing evidence that the TGFβ pathway is important in the immunopathogenesis of VL.
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Affiliation(s)
- Jason L Weirather
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eliana L Nascimento
- Department of Infectious Diseases, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Gloria R Monteiro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniella R Martins
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Henio G Lacerda
- Department of Infectious Diseases, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Michaela Fakiola
- Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Jenefer M Blackwell
- Cambridge Institute for Medical Research, University of Cambridge, UK.,Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Selma M B Jeronimo
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN and the National Institute of Science and Technology of Tropical Diseases, Natal, Rio Grande do Norte, Brazil
| | - Mary E Wilson
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA, USA.,Departments of Internal Medicine and Microbiology, University of Iowa and the Iowa City Veterans' Affairs Medical Center, Iowa City, IA, USA
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40
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Gardinassi LG, Garcia GR, Costa CHN, Costa Silva V, de Miranda Santos IKF. Blood Transcriptional Profiling Reveals Immunological Signatures of Distinct States of Infection of Humans with Leishmania infantum. PLoS Negl Trop Dis 2016; 10:e0005123. [PMID: 27828962 PMCID: PMC5102635 DOI: 10.1371/journal.pntd.0005123] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/23/2016] [Indexed: 12/04/2022] Open
Abstract
Visceral leishmaniasis (VL) can be lethal if untreated; however, the majority of human infections with the etiological agents are asymptomatic. Using Illumina Bead Chip microarray technology, we investigated the patterns of gene expression in blood of active VL patients, asymptomatic infected individuals, patients under remission of VL and controls. Computational analyses based on differential gene expression, gene set enrichment, weighted gene co-expression networks and cell deconvolution generated data demonstrating discriminative transcriptional signatures. VL patients exhibited transcriptional profiles associated with pathways and gene modules reflecting activation of T lymphocytes via MHC class I and type I interferon signaling, as well as an overall down regulation of pathways and gene modules related to myeloid cells, mainly due to differences in the relative proportions of monocytes and neutrophils. Patients under remission of VL presented heterogeneous transcriptional profiles associated with activation of T lymphocytes via MHC class I, type I interferon signaling and cell cycle and, importantly, transcriptional activity correlated with activation of Notch signaling pathway and gene modules that reflected increased proportions of B cells after treatment of disease. Asymptomatic and uninfected individuals presented similar gene expression profiles, nevertheless, asymptomatic individuals exhibited particularities which suggest an efficient regulation of lymphocyte activation and a strong association with a type I interferon response. Of note, we validated a set of target genes by RT-qPCR and demonstrate the robustness of expression data acquired by microarray analysis. In conclusion, this study profiles the immune response during distinct states of infection of humans with Leishmania infantum with a novel strategy that indicates the molecular pathways that contribute to the progression of the disease, while also providing insights into transcriptional activity that can drive protective mechanisms. Infections of humans with the protozoan parasites L. donvani and L. infantum can lead to the development of the disease visceral leishmaniasis, but also to an asymptomatic status. However, the mechanisms that result in these clinical outcomes after infection are poorly understood. In this study, we applied a data-driven approach to obtain insights into the immunological processes linked to the progression of the disease or to protective mechanisms. For this purpose, we evaluated the patterns of expression for genes that code proteins from the entire human genome in the peripheral blood from patients with visceral leishmaniasis, from individuals who remained asymptomatic after infections with L. infantum, from patients who were recovering from disease after treatment and from uninfected individuals. By employing computational analysis to evaluate the blood transcriptional activity of each group, we identified transcriptional signatures that correlate with previous findings obtained through different analytical methods. Moreover, our analyses uncovered hitherto unidentified molecular pathways and gene networks associated with the transcriptional profiles of individuals recovering from disease or that did not develop symptoms after infection. This suggests that activation of protective responses can be useful targets for the development of new therapies for visceral leishmaniasis.
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Affiliation(s)
- Luiz Gustavo Gardinassi
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Gustavo Rocha Garcia
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Carlos Henrique Nery Costa
- Department of Community Medicine, Natan Portela Institute for Tropical Diseases, Federal University of Piauí, Teresina, Brazil
| | - Vladimir Costa Silva
- Department of Community Medicine, Natan Portela Institute for Tropical Diseases, Federal University of Piauí, Teresina, Brazil
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41
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Jerônimo SMB, Pearson RD. The challenges on developing vaccine against visceral leishmaniasis. Rev Soc Bras Med Trop 2016; 49:395-7. [DOI: 10.1590/0037-8682-0343-2016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 02/01/2023] Open
Affiliation(s)
- Selma Maria Bezerra Jerônimo
- Universidade Federal do Rio Grande do Norte, Brazil; Universidade Federal do Rio Grande do Norte, Brazil; Instituto Nacional de Ciências e Tecnologia de Doenças Tropicais, Brazil
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42
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Kashyap M, Farooq U, Jaiswal V. Homology modelling of frequent HLA class-II alleles: A perspective to improve prediction of HLA binding peptide and understand the HLA associated disease susceptibility. INFECTION GENETICS AND EVOLUTION 2016; 44:234-244. [PMID: 27421208 DOI: 10.1016/j.meegid.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/24/2016] [Accepted: 07/05/2016] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) plays significant role via the regulation of immune system and contribute in the progression and protection of many diseases. HLA molecules bind and present peptides to T- cell receptors which generate the immune response. HLA peptide interaction and molecular function of HLA molecule is the key to predict peptide binding and understanding its role in different diseases. The availability of accurate three dimensional (3D) structures is the initial step towards this direction. In the present work, homology modelling of important and frequent HLA-DRB1 alleles (07:01, 11:01 and 09:01) was done and acceptable models were generated. These modelled alleles were further refined and cross validated by using several methods including Ramachandran plot, Z-score, ERRAT analysis and root mean square deviation (RMSD) calculations. It is known that numbers of allelic variants are related to the susceptibility or protection of various infectious diseases. Difference in amino acid sequences and structures of alleles were also studied to understand the association of HLA with disease susceptibility and protection. Susceptible alleles showed more amino acid variations than protective alleles in three selected diseases caused by different pathogens. Amino acid variations at binding site were found to be more than other part of alleles. RMSD values were also higher at variable positions within binding site. Higher RMSD values indicate that mutations occurring at peptide binding site alter protein structure more than rest of the protein. Hence, these findings and modelled structures can be used to design HLA-DRB1 binding peptides to overcome low prediction accuracy of HLA class II binding peptides. Furthermore, it may help to understand the allele specific molecular mechanisms involved in susceptibility/resistance against pathogenic diseases.
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Affiliation(s)
- Manju Kashyap
- Faculty of Applied sciences and Biotechnology, Shoolini University, Solan, Himachal, Pradesh, India
| | - Umar Farooq
- Faculty of Applied sciences and Biotechnology, Shoolini University, Solan, Himachal, Pradesh, India
| | - Varun Jaiswal
- School of Electrical and Computer Science Engineering, Shoolini University, Solan, Himachal Pradesh, India.
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Samaranayake N, Fernando SD, Neththikumara NF, Rodrigo C, Karunaweera ND, Dissanayake VHW. Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review. BMC Infect Dis 2016; 16:292. [PMID: 27301744 PMCID: PMC4908677 DOI: 10.1186/s12879-016-1626-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 06/07/2016] [Indexed: 12/21/2022] Open
Abstract
Background The outcome of leishmaniasis is an interplay between Leishamania and the host. Identifying contributory host genetic factors is complicated by the variability in phenotype, ethnicity and parasite species. Leishmaniasis is caused exclusively by L. donovani in Sri Lanka with localized cutaneous leishmaniasis (LCL) being the predominant form. We report here an association study of human leucocyte antigen (HLA) class I and II genes with LCL in Sri Lanka, the first on HLA associations in cutaneous leishmaniasis in a South Asian population. Methods An existing DNA repository of 200 each of patients and controls was typed for HLA-DQ by PCR-SSP. Next generation sequencing-based typing for HLA-A, HLA-B and HLA-DRB1 alleles was done in a subset of 280 samples. Association tests were performed on 28,489 genotyped and imputed SNPs spanning a region of 1.4 Mb across the HLA genes. To compare our results with similar studies, we carried out a systematic review to document all HLA associations reported to-date for cutaneous and muco-cutaneous leishmaniasis. Results DRB1*04 DQB1*02 (P = 0.03; Pc = 0.09), DRB1*07 DQB1*02 (P = 0.03; Pc = 0.09) haplotypes were absent in patients. B*07 (P = 0.007; Pc = 0.13; OR = 0.36; 95 % CI = 0.17–0.77) allele and DRB1*15 DQB1*06 (P = 0.00; Pc < 0.01; OR = 0.3; 95 % CI = 0.2–.0.6) haplotype were over represented in controls and DRB1*15 (P = 0.002; Pc = 0.01) allele was over represented in patients. Two SNPs (rs281864595/rs1050517) in the antigen recognition region of HLA-B, comprised a haplotype more frequent in controls (P = 0.04). The alleles identified by the systematic review to predispose or to protect from cutaneous/mucocutaneous leishmaniasis remained highly heterogeneous in different populations studied. Conclusions Our preliminary findings suggest a role for some class I and class II HLA genes in determining predisposition to LCL in this population which should be corroborated with further studies. The systematic review reiterates this need, as the purported susceptibility or protection gained by certain HLA alleles or haplotypes has rarely been independently verified. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1626-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka
| | - Sumadhya D Fernando
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka.
| | | | - Chaturaka Rodrigo
- Department of Clinical Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka
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The Potential Use of Forensic DNA Methods Applied to Sand Fly Blood Meal Analysis to Identify the Infection Reservoirs of Anthroponotic Visceral Leishmaniasis. PLoS Negl Trop Dis 2016; 10:e0004706. [PMID: 27192489 PMCID: PMC4871566 DOI: 10.1371/journal.pntd.0004706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/21/2016] [Indexed: 01/05/2023] Open
Abstract
Background In the Indian sub-continent, visceral leishmaniasis (VL), also known as kala azar, is a fatal form of leishmaniasis caused by the kinetoplastid parasite Leishmania donovani and transmitted by the sand fly Phlebotomus argentipes. VL is prevalent in northeast India where it is believed to have an exclusive anthroponotic transmission cycle. There are four distinct cohorts of L. donovani exposed individuals who can potentially serve as infection reservoirs: patients with active disease, cured VL cases, patients with post kala azar dermal leishmaniasis (PKDL), and asymptomatic individuals. The relative contribution of each group to sustaining the transmission cycle of VL is not known. Methodology/Principal Findings To answer this critical epidemiological question, we have addressed the feasibility of an approach that would use forensic DNA methods to recover human DNA profiles from the blood meals of infected sand flies that would then be matched to reference DNA sampled from individuals living or working in the vicinity of the sand fly collections. We found that the ability to obtain readable human DNA fingerprints from sand flies depended entirely on the size of the blood meal and the kinetics of its digestion. Useable profiles were obtained from most flies within the first 24 hours post blood meal (PBM), with a sharp decline at 48 hours and no readable profiles at 72 hours. This early time frame necessitated development of a sensitive, nested-PCR method compatible with detecting L. donovani within a fresh, 24 hours blood meal in flies fed on infected hamsters. Conclusion/Significance Our findings establish the feasibility of the forensic DNA method to directly trace the human source of an infected blood meal, with constraints imposed by the requirement that the flies be recovered for analysis within 24 hours of their infective feed. Visceral leishmaniasis, also known as kala-azar, is a fatal form of leishmaniasis that is caused by the protozoan parasite Leishmania donovani. In the Indian sub-continent, the parasite is transmitted between people by the sand fly Phlebotomus argentipes. There are four different groups of infected people that can carry the parasite: active cases, cured cases, cases of post-kala azar dermal leishmanisis, and people with asymptomatic infections. The relative contribution of these different groups to sustaining the transmission cycle is not known. In the current work, we explore the feasibility of forensic DNA methods that could be applied to directly trace the human source of an infected blood meal in flies collected from high transmission areas. We report that a readable human DNA profile can be generated from the majority of sand flies so long as the flies are sampled within 24 hours after blood feeding. We developed a highly sensitive nested-PCR method that was able to detect parasites present in a fresh, 24 hour blood meal after feeding on an infected host.
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Weirather JL, Duggal P, Nascimento EL, Monteiro GR, Martins DR, Lacerda HG, Fakiola M, Blackwell JM, Jeronimo SMB, Wilson ME. Fine mapping under linkage peaks for symptomatic or asymptomatic outcomes of Leishmania infantum infection in Brazil. INFECTION GENETICS AND EVOLUTION 2016; 43:1-5. [PMID: 27155051 DOI: 10.1016/j.meegid.2016.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/08/2016] [Accepted: 05/04/2016] [Indexed: 01/08/2023]
Abstract
Infection with the protozoan Leishmania infantum can lead to asymptomatic infection and protective immunity, or to the progressive and potentially fatal disease visceral leishmaniasis (VL). Published studies show host genetic background determines in part whether infected individuals will develop a symptomatic or asymptomatic outcome. The purpose of the current study was to fine map chromosome regions previously linked with risk for symptomatic (chromosome 9) or asymptomatic (chromosomes 15 and 19) manifestations of L. infantum infection. We conducted a family-based genetic study of VL and asymptomatic infection (detected by a DTH skin test) with a final post quality control sample of 961 individuals with full genotype and phenotype information from highly endemic neighborhoods of northeast Brazil. A total of 5485 SNPs under the linkage peaks on chromosomes 9, 15 and 19 were genotyped. No strong SNP associations were observed for the DTH phenotype. The most significant associations with the VL phenotype were with SNP rs1470217 (p=5.9e-05; pcorrected=0.057) on chromosome 9, and with SNP rs8107014 (p=1.4e-05; pcorrected=0.013) on chromosome 19. SNP rs1470217 is situated in a 180kb intergenic region between TMEM215 (Transmembrane protein 215) and APTX (Aprataxin). SNP rs8107014 lies in the intron between exons 26 and 27 of a 34 exon transcript (ENST00000204005) of LTBP4, (Latent transforming growth factor-beta-binding protein 4a). The latter supports growing evidence that the transforming growth factor-beta pathway is important in the immunopathogenesis of VL.
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Affiliation(s)
- Jason L Weirather
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA, USA.
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Eliana L Nascimento
- Department of Infectious Diseases, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
| | - Gloria R Monteiro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
| | - Daniella R Martins
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
| | - Henio G Lacerda
- Department of Infectious Diseases, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
| | - Michaela Fakiola
- Cambridge Institute for Medical Research, University of Cambridge, UK.
| | - Jenefer M Blackwell
- Cambridge Institute for Medical Research, University of Cambridge, UK; Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - Selma M B Jeronimo
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Institute of Science and Technology of Tropical Diseases, Brazil.
| | - Mary E Wilson
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA, USA; Department of Microbiology, University of Iowa, Iowa City, IA, USA; Iowa City Veterans' Affairs Medical Center, Iowa City, IA, USA.
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Chen H, Wang C, Conomos MP, Stilp AM, Li Z, Sofer T, Szpiro AA, Chen W, Brehm JM, Celedón JC, Redline S, Papanicolaou GJ, Thornton TA, Laurie CC, Rice K, Lin X. Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models. Am J Hum Genet 2016; 98:653-66. [PMID: 27018471 DOI: 10.1016/j.ajhg.2016.02.012] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/17/2016] [Indexed: 11/17/2022] Open
Abstract
Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM's constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs.
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Affiliation(s)
- Han Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Chaolong Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Mathematics, Tsinghua University, Beijing 100084, P. R. China
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Adam A Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - John M Brehm
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - George J Papanicolaou
- Prevention and Population Sciences Program, Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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Joo JWJ, Hormozdiari F, Han B, Eskin E. Multiple testing correction in linear mixed models. Genome Biol 2016; 17:62. [PMID: 27039378 PMCID: PMC4818520 DOI: 10.1186/s13059-016-0903-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Multiple hypothesis testing is a major issue in genome-wide association studies (GWAS), which often analyze millions of markers. The permutation test is considered to be the gold standard in multiple testing correction as it accurately takes into account the correlation structure of the genome. Recently, the linear mixed model (LMM) has become the standard practice in GWAS, addressing issues of population structure and insufficient power. However, none of the current multiple testing approaches are applicable to LMM. RESULTS We were able to estimate per-marker thresholds as accurately as the gold standard approach in real and simulated datasets, while reducing the time required from months to hours. We applied our approach to mouse, yeast, and human datasets to demonstrate the accuracy and efficiency of our approach. CONCLUSIONS We provide an efficient and accurate multiple testing correction approach for linear mixed models. We further provide an intuition about the relationships between per-marker threshold, genetic relatedness, and heritability, based on our observations in real data.
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Affiliation(s)
- Jong Wha J Joo
- Bioinformatics IDP, University of California, Los Angeles, CA, USA
| | - Farhad Hormozdiari
- Computer Science Department, University of California, Los Angeles, CA, USA
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, 138-736, Republic of Korea.
| | - Eleazar Eskin
- Computer Science Department, University of California, Los Angeles, CA, USA. .,Department of Human Genetics, University of California, Los Angeles, CA, USA.
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Adem E, Tajebe F, Getahun M, Kiflie A, Diro E, Hailu A, Shkedy Z, Mengesha B, Mulaw T, Atnafu S, Deressa T, Mathewos B, Abate E, Modolell M, Munder M, Müller I, Takele Y, Kropf P. Successful Treatment of Human Visceral Leishmaniasis Restores Antigen-Specific IFN-γ, but not IL-10 Production. PLoS Negl Trop Dis 2016; 10:e0004468. [PMID: 26962865 PMCID: PMC4786308 DOI: 10.1371/journal.pntd.0004468] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/27/2016] [Indexed: 12/31/2022] Open
Abstract
One of the key immunological characteristics of active visceral leishmaniasis (VL) is a profound immunosuppression and impaired production of Interferon-γ (IFN-γ). However, recent studies from Bihar in India showed using a whole blood assay, that whole blood cells have maintained the capacity to produce IFN-γ. Here we tested the hypothesis that a population of low-density granulocytes (LDG) might contribute to T cell responses hyporesponsiveness via the release of arginase. Our results show that this population is affected by the anticoagulant used to collect blood: the frequency of LDGs is significantly lower when the blood is collected with heparin as compared to EDTA; however, the anticoagulant does not impact on the levels of arginase released. Next, we assessed the capacity of whole blood cells from patients with active VL to produce IFN-γ and IL-10 in response to antigen-specific and polyclonal activation. Our results show that whole blood cells produce low or levels below detection limit of IFN-γ and IL-10, however, after successful treatment of VL patients, these cells gradually regain their capacity to produce IFN-γ, but not IL-10, in response to activation. These results suggest that in contrast to VL patients from Bihar, India, whole blood cells from VL patients from Gondar, Ethiopia, have lost their ability to produce IFN-γ during active VL and that active disease is not associated with sustained levels of IL-10 production following stimulation. The leishmaniases, a group of diseases caused by Leishmania parasites, belong to the most neglected tropical diseases: they are mainly found in low-income countries and affect the poorest populations. These parasites infect cells of the immune system called macrophages, which can kill the intracellular parasites in response to soluble mediators they receive from other cells of the immune system, the lymphocytes. Visceral leishmaniasis is the most severe form of the leishmaniases and is characterized by enlarged liver and spleen, fever, weight-loss and anaemia and represents a major public health problem in Ethiopia. Currently there is no vaccine available, the existing treatment has many severe side effects and drug-resistance is increasing. In the present study, we worked with patients suffering from visceral leishmaniasis. This form of the disease is fatal if the patients are not treated. We studied the ability of lymphocytes isolated from their blood to produce soluble mediators before and at different times after the end of treatment. Our results show that the lymphocytes have an impaired capacity to produce the soluble mediator required to instruct infected cells to kill the intracellular parasites, but that this lack of response is gradually restored with time after successful treatment.
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Affiliation(s)
- Emebet Adem
- Department of Immunology, University of Gondar, Ethiopia
| | | | | | - Amare Kiflie
- Department of Immunology, University of Gondar, Ethiopia
| | - Ermias Diro
- Department of Internal Medicine, University of Gondar, Ethiopia
| | - Asrat Hailu
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Ziv Shkedy
- Department of Mathematics and Statistics, University of Hasselt, Belgium
| | - Bewketu Mengesha
- Leishmaniasis Research and Treatment Centre, Gondar University, Ethiopia
| | - Tadele Mulaw
- Leishmaniasis Research and Treatment Centre, Gondar University, Ethiopia
| | - Saba Atnafu
- Leishmaniasis Research and Treatment Centre, Gondar University, Ethiopia
| | | | | | - Ebba Abate
- Department of Immunology, University of Gondar, Ethiopia
| | - Manuel Modolell
- Department of Cellular Immunology, Max-Planck-Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Markus Munder
- Third Department of Medicine (Hematology, Oncology, and Pneumology), University Medical Center Mainz, Mainz, Germany
| | - Ingrid Müller
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Yegnasew Takele
- Leishmaniasis Research and Treatment Centre, Gondar University, Ethiopia
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Pascale Kropf
- Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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Price AL, Spencer CCA, Donnelly P. Progress and promise in understanding the genetic basis of common diseases. Proc Biol Sci 2015; 282:20151684. [PMID: 26702037 PMCID: PMC4707742 DOI: 10.1098/rspb.2015.1684] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/21/2015] [Indexed: 02/07/2023] Open
Abstract
Susceptibility to common human diseases is influenced by both genetic and environmental factors. The explosive growth of genetic data, and the knowledge that it is generating, are transforming our biological understanding of these diseases. In this review, we describe the technological and analytical advances that have enabled genome-wide association studies to be successful in identifying a large number of genetic variants robustly associated with common disease. We examine the biological insights that these genetic associations are beginning to produce, from functional mechanisms involving individual genes to biological pathways linking associated genes, and the identification of functional annotations, some of which are cell-type-specific, enriched in disease associations. Although most efforts have focused on identifying and interpreting genetic variants that are irrefutably associated with disease, it is increasingly clear that--even at large sample sizes--these represent only the tip of the iceberg of genetic signal, motivating polygenic analyses that consider the effects of genetic variants throughout the genome, including modest effects that are not individually statistically significant. As data from an increasingly large number of diseases and traits are analysed, pleiotropic effects (defined as genetic loci affecting multiple phenotypes) can help integrate our biological understanding. Looking forward, the next generation of population-scale data resources, linking genomic information with health outcomes, will lead to another step-change in our ability to understand, and treat, common diseases.
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Affiliation(s)
- Alkes L Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Chris C A Spencer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Donnelly
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
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Berthier D, Brenière SF, Bras-Gonçalves R, Lemesre JL, Jamonneau V, Solano P, Lejon V, Thévenon S, Bucheton B. Tolerance to Trypanosomatids: A Threat, or a Key for Disease Elimination? Trends Parasitol 2015; 32:157-168. [PMID: 26643519 DOI: 10.1016/j.pt.2015.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 12/20/2022]
Abstract
So far, research on trypanosomatid infections has been driven by 'disease by disease' approaches, leading to different concepts and control strategies. It is, however, increasingly clear that they share common features such as the ability to generate long-lasting asymptomatic infections in their mammalian hosts. Trypanotolerance, long integrated in animal African trypanosomiasis control, historically refers to the ability of cattle breeds to limit Trypanosoma infection and pathology, but has only recently been recognized in humans. Whilst trypanotolerance is absent from the vocabulary on leishmaniasis and Chagas disease, asymptomatic infections also occur. We review the concept of trypanotolerance across the trypanosomatids and discuss the importance of asymptomatic carriage in the current context of elimination.
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Affiliation(s)
| | | | | | | | - Vincent Jamonneau
- CIRDES Bobo-Dioulasso 01 BP 454, Burkina Faso; IPR, 01 BP 1500 Bouaké 01, Côte d'Ivoire
| | | | - Veerle Lejon
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France
| | | | - Bruno Bucheton
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France; PNLTHA, Ministère de la Santé, BP 851 Conakry, République de Guinée
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