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Holmes IA, Durso AM, Myers CR, Hendry TA. Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters. PeerJ 2024; 12:e16910. [PMID: 38436008 PMCID: PMC10909344 DOI: 10.7717/peerj.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.
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Affiliation(s)
- Iris A. Holmes
- Department of Microbiology, Cornell University, Ithaca, NY, United States
- Cornell Institute of Host Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Christopher R. Myers
- Center for Advanced Computing & Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, United States
| | - Tory A. Hendry
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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2
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Marraccini C, Merolle L, Schiroli D, Razzoli A, Gavioli G, Iotti B, Baricchi R, Ottone M, Mancuso P, Giorgi Rossi P. A cohort study on the biochemical and haematological parameters of Italian blood donors as possible risk factors of COVID-19 infection and severe disease in the pre- and post-Omicron period. PLoS One 2023; 18:e0294272. [PMID: 37988390 PMCID: PMC10662768 DOI: 10.1371/journal.pone.0294272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023] Open
Abstract
To investigate the association between biochemical and blood parameters collected before the pandemic in a large cohort of Italian blood donors with the risk of infection and severe disease. We also focused on the differences between the pre- and post-Omicron spread in Italy (i.e., pre- and post-January 01, 2022) on the observed associations. We conducted an observational cohort study on 13750 blood donors was conducted using data archived up to 5 years before the pandemic. A t-test or chi-squared test was used to compare differences between groups. Hazard ratios with 95% confidence intervals for SARS-CoV-2 infection and severe disease were estimated using Cox proportional hazards models. Subgroup analyses stratified by sex, age and epidemic phase of first infection (pre- and post-Omicron spread) were examined. We confirmed a protective effect of groups B and O, while groups A and AB had a higher likelihood of infection and severe disease. However, these associations were only significant in the pre-Omicron period. We found an opposite behavior after Omicron spread, with the O phenotype having a higher probability of infection. When stratified by variant, A antigen appeared to protect against Omicron infection, whereas it was associated with an increased risk of infection by earlier variants. We were able to stratify for the SARS CoV-2 dominant variant, which revealed a causal association between blood group and probability of infection, as evidenced by the strong effect modification observed between the pre- and post-Omicron spread. The mechanism by which group A acts on the probability of infection should consider this strong effect modification.
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Affiliation(s)
- Chiara Marraccini
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Lucia Merolle
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Davide Schiroli
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Agnese Razzoli
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Gaia Gavioli
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Barbara Iotti
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Roberto Baricchi
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Marta Ottone
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Pamela Mancuso
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Paolo Giorgi Rossi
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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3
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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4
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Almorish MA, Al-Absi B, Elkhalifa AME, Elamin E, Elderdery AY, Alhamidi AH. ABO, Lewis blood group systems and secretory status with H.pylori infection in yemeni dyspeptic patients: a cross- sectional study. BMC Infect Dis 2023; 23:520. [PMID: 37553651 PMCID: PMC10408178 DOI: 10.1186/s12879-023-08496-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The ABO and Lewis blood group antigens are potential factors in susceptibility to H. pylori infection. This research aimed to examine the prevalence of Helicobater pylori (H.pylori) infection and its association with ABO, Lewis blood group systems, and secretory status in Yemeni symptomatic patients. METHODS In a cross-sectional study, 103 patients referred for endoscopy due to dyspepsia were included. H pylori infection was assessed using stool antigen and serum antibody rapid tests. ABO and Lewis blood group systems were examined using hemagglutination assay. Saliva samples were investigated for identification of the secretory phenotype using hemagglutination inhibition test. RESULTS The prevalence of H. pylori infection was (80.6%), with a higher rate of infection in females than males. The ABO blood groups were found to be significantly different between males and females (p = 0.047). The O blood group was prevalent among H. pylori patients, especially secretors. There was a significant association between ABO blood groups and H. pylori infection (p = 0.001). The Le (a + b+) phenotype was the most common, followed by Le (a + b-), Le (a-b+), and Le (a-b-). Lewis blood group systems and secretory status of symptomatic patients were not associated with H. pylori infection. The results showed that serum Ab test for H. pylori achieved poor sensitivity (68%), specificity of 55%; positive predictive value (PPV) 86%, negative predictive value (NPV) 29% and accuracy 65.1%. CONCLUSION The prevalence of H. pylori infection was high in Yemeni patients. This infection was linked to the O and Le (a + b+) secretor phenotype. The H. pylori stool Ag test is the most reliable noninvasive diagnostic method for detecting H. pylori infection.
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Affiliation(s)
| | - Boshra Al-Absi
- Department of Hematology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - Ahmed M E Elkhalifa
- Public Heath Department, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
- Department of Hematology, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti, 1158, Sudan
| | - Elham Elamin
- Department of Hematology, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti, 1158, Sudan
| | - Abozer Y Elderdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, Jouf University, Sakaka, Saudi Arabia
| | - Abdulaziz H Alhamidi
- Clinical Laboratory Sciences Department, College of Applied Medical Science, King Saud University, Riyadh, Saudi Arabia
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5
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Sung C, An J, Lee S, Park J, Lee KS, Kim IH, Han JY, Park YH, Kim JH, Kang EJ, Hong MH, Kim TY, Lee JC, Lee JL, Yoon S, Choi CM, Lee DH, Yoo C, Kim SW, Jeong JH, Seo S, Kim SY, Kong SY, Choi JK, Park SR. Integrative analysis of risk factors for immune-related adverse events of checkpoint blockade therapy in cancer. NATURE CANCER 2023; 4:844-859. [PMID: 37308678 DOI: 10.1038/s43018-023-00572-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 05/05/2023] [Indexed: 06/14/2023]
Abstract
Immune-related adverse events (irAEs) induced by checkpoint inhibitors involve a multitude of different risk factors. Here, to interrogate the multifaceted underlying mechanisms, we compiled germline exomes and blood transcriptomes with clinical data, before and after checkpoint inhibitor treatment, from 672 patients with cancer. Overall, irAE samples showed a substantially lower contribution of neutrophils in terms of baseline and on-therapy cell counts and gene expression markers related to neutrophil function. Allelic variation of HLA-B correlated with overall irAE risk. Analysis of germline coding variants identified a nonsense mutation in an immunoglobulin superfamily protein, TMEM162. In our cohort and the Cancer Genome Atlas (TCGA) data, TMEM162 alteration was associated with higher peripheral and tumor-infiltrating B cell counts and suppression of regulatory T cells in response to therapy. We developed machine learning models for irAE prediction, validated using additional data from 169 patients. Our results provide valuable insights into risk factors of irAE and their clinical utility.
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Affiliation(s)
- Changhwan Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Soohyeon Lee
- Division of Oncology-Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaesoon Park
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Il-Hwan Kim
- Department of Oncology, Haeundae Paik Hospital, Cancer Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jee Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Eun Joo Kang
- Division of Oncology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae-Yong Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jae Lyun Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang-Min Choi
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dae Ho Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-We Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seyoung Seo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sun Young Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sun-Young Kong
- Targeted Therapy Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam, Republic of Korea.
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Vallier M, Suwandi A, Ehrhardt K, Belheouane M, Berry D, Čepić A, Galeev A, Johnsen JM, Grassl GA, Baines JF. Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice. Gut Microbes 2023; 15:2164448. [PMID: 36683151 PMCID: PMC9872957 DOI: 10.1080/19490976.2022.2164448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/15/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.
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Affiliation(s)
- Marie Vallier
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Meriem Belheouane
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Aleksa Čepić
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alibek Galeev
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jill M. Johnsen
- Bloodworks Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Kaur P, Gupta M, Sagar V. FUT2 gene as a genetic susceptible marker of infectious diseases: A Review. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2022; 13:1-14. [PMID: 35892094 PMCID: PMC9301175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Some blood group antigens are reported as a susceptibility marker for some diseases. For instance, HBGA (Histo-blood group antigen) which is controlled by gene FUT2 also considered as a susceptible marker. The FUT2 gene which exhibits the expression of alpha-1, 2-L-fucosyltransferase enzyme also leads to HBGA expression for the gut, and it provides a composition of the phenotypical profile that exists in some populations with unique histories of evolution and it can be considered as a marker of the genetic population. It is found to have an association with many diseases which is discussed in this review. Polymorphic mutations are known to inhibit and reduce its function which are population specific. Detailed understanding and deeper knowledge of its role in the pathogenesis and prevention of many diseases is required. FUT2 may also have a potential role in the case of COVID-19 as a susceptible marker due to its association with respiratory diseases and the ABO blood group. There is an utmost need for this kind of review knowing its importance and owing to limited collective information.
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Affiliation(s)
- Paramvir Kaur
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | - Madhu Gupta
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | - Vivek Sagar
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
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McGill S, Burchmore RJS, Pomeroy PP, Kennedy MW. Is a Little Enough? Paucity of Immune Proteins in Serum of Precocial Neonates of a Marine Carnivoran—the Atlantic Grey Seal. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.802510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mammalian mothers usually provide their offspring with large quantities of immunoglobulins (antibodies) for circulation in blood, either trans-placentally before birth, via colostrum briefly thereafter, or, less commonly, from milk. Neonates of true, phocid seals, however, are peculiarly impoverished in serum immunoglobulins, the levels of which slowly increase but do not reach adult levels by the time of weaning. We investigated whether grey seal (Halichoerus grypus) neonates compensate through an elevation or rapid maturation in levels of serum innate immune factors, namely acute phase and complement proteins. Instead, their sera contained remarkably low levels of acute phase proteins (including C-reactive protein, haptoglobin, hemopexin, ceruloplasmin, orosomucoid), compared to their mothers, that barely increased to adult levels by weaning. For complement, there was a strong demarcation between the early activation and amplification cascade components (present at normal adult levels in pups) and the late lytic membrane attack complex and regulatory proteins (consistently at low relative levels). Phocid neonates therefore differ dramatically from land Carnivorans, such as dogs and cats, in early life immune protection. That neonatal phocids survive this apparent vulnerability to infections between birth and weaning prompts questions as to what other mechanisms protect them, and the adaptive value of their seeming vulnerability.
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Francoeur R, Atuhaire A, Arinaitwe M, Adriko M, Ajambo D, Nankasi A, Babayan SA, Lamberton PHL. ABO Blood Groups Do Not Predict Schistosoma mansoni Infection Profiles in Highly Endemic Villages of Uganda. Microorganisms 2021; 9:microorganisms9122448. [PMID: 34946048 PMCID: PMC8705964 DOI: 10.3390/microorganisms9122448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 01/21/2023] Open
Abstract
Schistosoma mansoni is a parasite which causes significant public-health issues, with over 240 million people infected globally. In Uganda alone, approximately 11.6 million people are affected. Despite over a decade of mass drug administration in this country, hyper-endemic hotspots persist, and individuals who are repeatedly heavily and rapidly reinfected are observed. Human blood-type antigens are known to play a role in the risk of infection for a variety of diseases, due to cross-reactivity between host antibodies and pathogenic antigens. There have been conflicting results on the effect of blood type on schistosomiasis infection and pathology. Moreover, the effect of blood type as a potential intrinsic host factor on S. mansoni prevalence, intensity, clearance, and reinfection dynamics and on co-infection risk remains unknown. Therefore, the epidemiological link between host blood type and S. mansoni infection dynamics was assessed in three hyper-endemic communities in Uganda. Longitudinal data incorporating repeated pretreatment S. mansoni infection intensities and clearance rates were used to analyse associations between blood groups in school-aged children. Soil-transmitted helminth coinfection status and biometric parameters were incorporated in a generalised linear mixed regression model including age, gender, and body mass index (BMI), which have previously been established as significant factors influencing the prevalence and intensity of schistosomiasis. The analysis revealed no associations between blood type and S. mansoni prevalence, infection intensity, clearance, reinfection, or coinfection. Variations in infection profiles were significantly different between the villages, and egg burden significantly decreased with age. While blood type has proven to be a predictor of several diseases, the data collected in this study indicate that it does not play a significant role in S. mansoni infection burdens in these high-endemicity communities.
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Affiliation(s)
- Rachel Francoeur
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;
- Welcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
- Faculty of Science and Engineering, Department of Biological Sciences, University of Chester, Chester CH1 4BJ, UK
- Correspondence: (R.F.); (P.H.L.L.)
| | - Alon Atuhaire
- Vector Control Division, Ministry of Health, Kampala P.O. Box 1661, Uganda; (A.A.); (M.A.); (M.A.); (A.N.)
| | - Moses Arinaitwe
- Vector Control Division, Ministry of Health, Kampala P.O. Box 1661, Uganda; (A.A.); (M.A.); (M.A.); (A.N.)
| | - Moses Adriko
- Vector Control Division, Ministry of Health, Kampala P.O. Box 1661, Uganda; (A.A.); (M.A.); (M.A.); (A.N.)
| | - Diana Ajambo
- Vector Control Division, Ministry of Health, Kampala P.O. Box 1661, Uganda; (A.A.); (M.A.); (M.A.); (A.N.)
| | - Andrina Nankasi
- Vector Control Division, Ministry of Health, Kampala P.O. Box 1661, Uganda; (A.A.); (M.A.); (M.A.); (A.N.)
| | - Simon A. Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Poppy H. L. Lamberton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;
- Welcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
- Correspondence: (R.F.); (P.H.L.L.)
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Abstract
Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual’s entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.
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Galeev A, Suwandi A, Cepic A, Basu M, Baines JF, Grassl GA. The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease. Int J Med Microbiol 2021; 311:151487. [PMID: 33662872 DOI: 10.1016/j.ijmm.2021.151487] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The glycosylation profile of the gastrointestinal tract is an important factor mediating host-microbe interactions. Variation in these glycan structures is often mediated by blood group-related glycosyltransferases, and can lead to wide-ranging differences in susceptibility to both infectious- as well as chronic disease. In this review, we focus on the interplay between host glycosylation, the intestinal microbiota and susceptibility to gastrointestinal pathogens based on studies of two exemplary blood group-related glycosyltransferases that are conserved between mice and humans, namely FUT2 and B4GALNT2. We highlight that differences in susceptibility can arise due to both changes in direct interactions, such as bacterial adhesion, as well as indirect effects mediated by the intestinal microbiota. Although a large body of experimental work exists for direct interactions between host and pathogen, determining the more complex and variable mechanisms underlying three-way interactions involving the intestinal microbiota will be the subject of much-needed future research.
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Affiliation(s)
- Alibek Galeev
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Aleksa Cepic
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Meghna Basu
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany.
| | - Guntram A Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany.
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12
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Miłkowska K, Galbarczyk A, Mijas M, Jasienska G. Disgust Sensitivity Among Women During the COVID-19 Outbreak. Front Psychol 2021; 12:622634. [PMID: 33833715 PMCID: PMC8021948 DOI: 10.3389/fpsyg.2021.622634] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
The emotion of disgust is suggested to be an adaptation that evolved to keep us away from sources of infection. Therefore, individuals from populations with greater pathogen stress should have a greater disgust sensitivity. However, current evidence for a positive relationship between disgust sensitivity and the intensity of infectious diseases in the environment is limited. We tested whether disgust and contamination sensitivity changed in response to the COVID-19 pandemic. Disgust was assessed in 984 women in 2017 (before pandemic) and 633 women in 2020 (during pandemic) by a set of photographs depicting sources of infection and Pathogen and Moral of Three-Domain Disgust Scale. Further, contamination sensitivity among participants in two waves was measured by Contamination Obsessions and Washing Compulsions Subscale of Padua Inventory. State anxiety was measured with the Polish adaptation of the State-Trait Anxiety Inventory (STAI) only during the second wave of data collection. Women from the COVID-19 pandemic group assessed the photographs depicting sources of infection as more disgusting, scoring higher on Padua Inventory, but lower on Moral Disgust Domain as compared to women from before the pandemic. In addition, anxiety levels during pandemic positively correlated with scores from Pathogen Disgust Domain, Padua Inventory, and the ratings of the photographs. The participants of the study scored higher in state anxiety than the norms determined for the Polish population. Summarizing, we present evidence for differences in individual levels of disgust sensitivity in relation to pathogen stress, supporting the idea that disgust evolved to serve as protection from pathogens.
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Affiliation(s)
- Karolina Miłkowska
- Department of Environmental Health, Faculty of Health Science, Jagiellonian University Medical College, Krakow, Poland
| | - Andrzej Galbarczyk
- Department of Environmental Health, Faculty of Health Science, Jagiellonian University Medical College, Krakow, Poland
| | - Magdalena Mijas
- Department of Environmental Health, Faculty of Health Science, Jagiellonian University Medical College, Krakow, Poland
| | - Grazyna Jasienska
- Department of Environmental Health, Faculty of Health Science, Jagiellonian University Medical College, Krakow, Poland
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13
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Isildak U, Stella A, Fumagalli M. Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. Mol Ecol Resour 2021; 21:2706-2718. [PMID: 33749134 DOI: 10.1111/1755-0998.13379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022]
Abstract
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study, we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false-positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to familial Mediterranean fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterize signals of selection on intermediate frequency variants, an analysis currently inaccessible by commonly used strategies.
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Affiliation(s)
- Ulas Isildak
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Alessandro Stella
- Laboratory of Medical Genetics, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, London, UK
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14
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Ahluwalia TS, Eliasen AU, Sevelsted A, Pedersen CET, Stokholm J, Chawes B, Bork-Jensen J, Grarup N, Pedersen O, Hansen T, Linneberg A, Sharma A, Weiss ST, Evans MD, Jackson DJ, Morin A, Krogfelt KA, Schjørring S, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J, Bækvad-Hansen M, Mors O, Nordentoft M, Børglum AD, Werge T, Agerbo E, Gern JE, Lemanske RF, Ober C, Pedersen AG, Bisgaard H, Bønnelykke K. FUT2-ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses. Nat Commun 2020; 11:6398. [PMID: 33328473 PMCID: PMC7744576 DOI: 10.1038/s41467-020-19814-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Asthma with severe exacerbation is the most common cause of hospitalization among young children. We aim to increase the understanding of this clinically important disease entity through a genome-wide association study. The discovery analysis comprises 2866 children experiencing severe asthma exacerbation between ages 2 and 6 years, and 65,415 non-asthmatic controls, and we replicate findings in 918 children from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) birth cohorts. We identify rs281379 near FUT2/MAMSTR on chromosome 19 as a novel risk locus (OR = 1.18 (95% CI = 1.11-1.25), Pdiscovery = 2.6 × 10-9) as well as a biologically plausible interaction between functional variants in FUT2 and ABO. We further discover and replicate a potential causal mechanism behind this interaction related to S. pneumoniae respiratory illnesses. These results suggest a novel mechanism of early childhood asthma and demonstrates the importance of phenotype-specificity for discovery of asthma genes and epistasis.
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Affiliation(s)
- Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Anders U Eliasen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Astrid Sevelsted
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Casper-Emil T Pedersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael D Evans
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - Andreanne Morin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark, Aarhus C, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | | | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Anders G Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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15
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Flegr J, Toman J, Hůla M, Kaňková Š. The role of balancing selection in maintaining human RhD blood group polymorphism: A preregistered cross-sectional study. J Evol Biol 2020; 34:426-438. [PMID: 33244840 DOI: 10.1111/jeb.13745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
Maintenance of genetic polymorphism remains one of the big questions of evolutionary biology, which for a long time tended to be explained by balancing selection. This explanation was later criticized, but now is again accepted as an important mechanism in evolution. Human blood group systems seem affected by balancing selection especially strongly. In this preregistered study, we focused on stable coexistence of RhD-positive and RhD-negative subjects in a population. This is an evolutionary conundrum, because carriers of the less frequent negative allele suffer from lower fecundity due to haemolytic disease of the newborn affecting RhD-positive infants born to RhD-negative women. One explanation of persisting stability of RhD polymorphism points to heterozygote advantage. Over the past decade, numerous studies demonstrated that RhD-positive subjects score better than RhD-negative homozygotes in psychomotor tests and physical health-related variables. Still, evidence of better health and performance of heterozygotes is scarce and merely indirect. We compared the physical and mental health of 2,539 subjects whose RhD genotype was estimated based on their and their parents' RhD phenotype. We confirmed that RhD-negative homozygotes fare worse in terms of physical and mental health than subjects with RhD-positive phenotype and that RhD-positive heterozygotes enjoy better health than both homozygotes. For the first time, we demonstrated that RhD-positive homozygotes might suffer from worse health than RhD-negative homozygotes. Our results strongly support the hypothesis that RhD polymorphism is maintained by heterozygote advantage and that balancing selection may have played an important role in human evolution in this context and in general.
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Affiliation(s)
- Jaroslav Flegr
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Toman
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Hůla
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic
| | - Šárka Kaňková
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Applied Neuroscience and Neuroimaging, National Institute of Mental Health, Klecany, Czech Republic
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16
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Cheng X, DeGiorgio M. Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection. Mol Biol Evol 2020; 37:3267-3291. [PMID: 32462188 PMCID: PMC7820363 DOI: 10.1093/molbev/msaa134] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Long-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. Here, we employ mixture models to construct a set of five composite likelihood ratio test statistics, which we collectively term B statistics. These statistics are agnostic to window sizes and can operate on diverse forms of input data. Through simulations, we show that they exhibit comparable power to the best-performing current methods, and retain substantially high power regardless of window sizes. They also display considerable robustness to high mutation rates and uneven recombination landscapes, as well as an array of other common confounding scenarios. Moreover, we applied a specific version of the B statistics, termed B2, to a human population-genomic data set and recovered many top candidates from prior studies, including the then-uncharacterized STPG2 and CCDC169-SOHLH2, both of which are related to gamete functions. We further applied B2 on a bonobo population-genomic data set. In addition to the MHC-DQ genes, we uncovered several novel candidate genes, such as KLRD1, involved in viral defense, and SCN9A, associated with pain perception. Finally, we show that our methods can be extended to account for multiallelic balancing selection and integrated the set of statistics into open-source software named BalLeRMix for future applications by the scientific community.
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Affiliation(s)
- Xiaoheng Cheng
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
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17
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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18
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Ji L, Wu D, Xie H, Yao B, Chen Y, Irwin DM, Huang D, Xu J, Tang NLS, Zhang Y. Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:489-500. [PMID: 32822870 PMCID: PMC8377383 DOI: 10.1016/j.gpb.2019.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 08/22/2019] [Accepted: 11/29/2019] [Indexed: 01/22/2023]
Abstract
Solar energy, which is essential for the origin and evolution of all life forms on Earth, can be objectively recorded through attributes such as climatic ambient temperature (CAT), ultraviolet radiation (UVR), and sunlight duration (SD). These attributes have specific geographical variations and may cause different adaptation traits. However, the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive. Here, we performed a genome-wide adaptation study with respect to CAT, UVR, and SD using the Human Genome Diversity Project-Centre Etude Polymorphism Humain (HGDP-CEPH) panel data. We singled out CAT as the most important driving force with the highest number of adaptive loci (6 SNPs at the genome-wide 1 × 10−7 level; 401 at the suggestive 1 × 10−5 level). Five of the six genome-wide significant adaptation SNPs were successfully replicated in an independent Chinese population (N = 1395). The corresponding 316 CAT adaptation genes were mostly involved in development and immunity. In addition, 265 (84%) genes were related to at least one genome-wide association study (GWAS)-mapped human trait, being significantly enriched in anthropometric loci such as those associated with body mass index (χ2; P < 0.005), immunity, metabolic syndrome, and cancer (χ2; P < 0.05). For these adaptive SNPs, balancing selection was evident in Euro-Asians, whereas obvious positive and/or purifying selection was observed in Africans. Taken together, our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations. It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.
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Affiliation(s)
- Lindan Ji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Biochemistry, Medical School of Ningbo University, Ningbo 315211, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Haibing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Binbin Yao
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China
| | - Yanming Chen
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dan Huang
- Department of Chemical Pathology, and Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Jin Xu
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo 315211, China.
| | - Nelson L S Tang
- Department of Chemical Pathology, and Laboratory for Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
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19
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Mank M, Hauner H, Heck AJR, Stahl B. Targeted LC-ESI-MS 2 characterization of human milk oligosaccharide diversity at 6 to 16 weeks post-partum reveals clear staging effects and distinctive milk groups. Anal Bioanal Chem 2020; 412:6887-6907. [PMID: 32794008 PMCID: PMC7496073 DOI: 10.1007/s00216-020-02819-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022]
Abstract
Many molecular components in human milk (HM), such as human milk oligosaccharides (HMOs), assist in the healthy development of infants. It has been hypothesized that the functional benefits of HM may be highly dependent on the abundance and individual fine structures of contained HMOs and that distinctive HM groups can be defined by their HMO profiles. However, the structural diversity and abundances of individual HMOs may also vary between milk donors and at different stages of lactations. Improvements in efficiency and selectivity of quantitative HMO analysis are essential to further expand our understanding about the impact of HMO variations on healthy early life development. Hence, we applied here a targeted, highly selective, and semi-quantitative LC-ESI-MS2 approach by analyzing 2 × 30 mature human milk samples collected at 6 and 16 weeks post-partum. The analytical approach covered the most abundant HMOs up to hexasaccharides and, for the first time, also assigned blood group A and B tetrasaccharides. Principal component analysis (PCA) was employed and allowed for automatic grouping and assignment of human milk samples to four human milk groups which are related to the maternal Secretor (Se) and Lewis (Le) genotypes. We found that HMO diversity varied significantly between these four HM groups. Variations were driven by HMOs being either dependent or independent of maternal genetic Se and Le status. We found preliminary evidence for an additional HM subgroup within the Se- and Le-positive HM group I. Furthermore, the abundances of 6 distinct HMO structures (including 6'-SL and 3-FL) changed significantly with progression of lactation. Graphical abstract.
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Affiliation(s)
- Marko Mank
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, The Netherlands.
| | - Hans Hauner
- Else Kröner-Fresenius Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, Ismaninger Straße 22, 81675, Munich, Germany.,Nutritional Medicine Unit, Research Center for Nutrition and Food Sciences (ZIEL), Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Bernd Stahl
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, The Netherlands.,Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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20
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Rodrigues JKF, Crovella S, Celerino da Silva R. The HLA-G 14 bp allele frequency in different populations: A global meta-analysis. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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21
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Bioinformatics analysis of regulatory elements of the CD151 gene and insilico docking of CD151 with diallyl sulfide. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Colston JM, Francois R, Pisanic N, Peñataro Yori P, McCormick BJJ, Olortegui MP, Gazi MA, Svensen E, Ahmed MMM, Mduma E, Liu J, Houpt ER, Klapheke R, Schwarz JW, Atmar RL, Black RE, Kosek MN. Effects of Child and Maternal Histo-Blood Group Antigen Status on Symptomatic and Asymptomatic Enteric Infections in Early Childhood. J Infect Dis 2019; 220:151-162. [PMID: 30768135 PMCID: PMC6548901 DOI: 10.1093/infdis/jiz072] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/13/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Histo-blood group antigens (HBGAs) such as fucosyltransferase (FUT)2 and 3 may act as innate host factors that differentially influence susceptibility of individuals and their offspring to pediatric enteric infections. METHODS In 3 community-based birth cohorts, FUT2 and FUT3 statuses were ascertained for mother-child dyads. Quantitative polymerase chain reaction panels tested 3663 diarrheal and 18 148 asymptomatic stool samples for 29 enteropathogens. Cumulative diarrhea and infection incidence were compared by child (n = 520) and mothers' (n = 519) HBGA status and hazard ratios (HRs) derived for all-cause diarrhea and specific enteropathogens. RESULTS Children of secretor (FUT2 positive) mothers had a 38% increased adjusted risk of all-cause diarrhea (HR = 1.38; 95% confidence interval (CI), 1.15-1.66) and significantly reduced time to first diarrheal episode. Child FUT2 and FUT3 positivity reduced the risk for all-cause diarrhea by 29% (HR = 0.81; 95% CI, 0.71-0.93) and 27% (HR = 0.83; 95% CI, 0.74-0.92), respectively. Strong associations between HBGAs and pathogen-specific infection and diarrhea were observed, particularly for noroviruses, rotaviruses, enterotoxigenic Escherichia coli, and Campylobacter jejuni/coli. CONCLUSIONS Histo-blood group antigens affect incidence of all-cause diarrhea and enteric infections at magnitudes comparable to many common disease control interventions. Studies measuring impacts of interventions on childhood enteric disease should account for both child and mothers' HBGA status.
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Affiliation(s)
- Josh M Colston
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ruthly Francois
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | | | | | - Md Amran Gazi
- International Centre for Diarrhoeal Disease Research, Bangladesh
| | | | | | - Esto Mduma
- Haydom Global Health Institute, Haydom, Tanzania
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | | | | | | | - Robert E Black
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
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23
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Wilhelm I, Levit-Zerdoun E, Jakob J, Villringer S, Frensch M, Übelhart R, Landi A, Müller P, Imberty A, Thuenauer R, Claudinon J, Jumaa H, Reth M, Eibel H, Hobeika E, Römer W. Carbohydrate-dependent B cell activation by fucose-binding bacterial lectins. Sci Signal 2019; 12:12/571/eaao7194. [PMID: 30837305 DOI: 10.1126/scisignal.aao7194] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacterial lectins are typically multivalent and bind noncovalently to specific carbohydrates on host tissues to facilitate bacterial adhesion. Here, we analyzed the effects of two fucose-binding lectins, BambL from Burkholderia ambifaria and LecB from Pseudomonas aeruginosa, on specific signaling pathways in B cells. We found that these bacterial lectins induced B cell activation, which, in vitro, was dependent on the cell surface expression of the B cell antigen receptor (BCR) and its co-receptor CD19, as well as on spleen tyrosine kinase (Syk) activity. The resulting release of intracellular Ca2+ was followed by an increase in the cell surface abundance of the activation marker CD86, augmented cytokine secretion, and subsequent cell death, replicating all of the events that are observed in vitro upon canonical and antigen-mediated B cell activation. Moreover, injection of BambL in mice resulted in a substantial, BCR-independent loss of B cells in the bone marrow with simultaneous, transient enlargement of the spleen (splenomegaly), as well as an increase in the numbers of splenic B cells and myeloid cells. Together, these data suggest that bacterial lectins can initiate polyclonal activation of B cells through their sole capacity to bind to fucose.
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Affiliation(s)
- Isabel Wilhelm
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Ella Levit-Zerdoun
- Max Planck Institute of Immunology and Epigenetics Freiburg, 79108 Freiburg, Germany.,International Max Planck Research School (IMPRS), Max Planck Institute of Immunobiology and Epigenetics Freiburg, 79108 Freiburg, Germany.,German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Center (DKFZ), Heidelberg, Institute of Molecular Medicine and Cell Research, 79104 Freiburg, Germany
| | - Johanna Jakob
- Institute for Immunology, University Medical Centre Ulm, 89081 Ulm, Germany
| | - Sarah Villringer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Marco Frensch
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.,International Max Planck Research School (IMPRS), Max Planck Institute of Immunobiology and Epigenetics Freiburg, 79108 Freiburg, Germany
| | - Rudolf Übelhart
- Institute for Immunology, University Medical Centre Ulm, 89081 Ulm, Germany
| | - Alessia Landi
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Peter Müller
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Roland Thuenauer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Julie Claudinon
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Hassan Jumaa
- Institute for Immunology, University Medical Centre Ulm, 89081 Ulm, Germany
| | - Michael Reth
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.,Max Planck Institute of Immunology and Epigenetics Freiburg, 79108 Freiburg, Germany
| | - Hermann Eibel
- CCI-Center for Chronic Immunodeficiency (CCI), University Medical Centre, 79106 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Elias Hobeika
- Institute for Immunology, University Medical Centre Ulm, 89081 Ulm, Germany.
| | - Winfried Römer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany. .,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
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24
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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25
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Abstract
Trans-species polymorphism has been widely used as a key sign of long-term balancing selection across multiple species. However, such sites are often rare in the genome and could result from mutational processes or technical artifacts. Few methods are yet available to specifically detect footprints of trans-species balancing selection without using trans-species polymorphic sites. In this study, we develop summary- and model-based approaches that are each specifically tailored to uncover regions of long-term balancing selection shared by a set of species by using genomic patterns of intraspecific polymorphism and interspecific fixed differences. We demonstrate that our trans-species statistics have substantially higher power than single-species approaches to detect footprints of trans-species balancing selection, and are robust to those that do not affect all tested species. We further apply our model-based methods to human and chimpanzee whole-genome sequencing data. In addition to the previously established major histocompatibility complex and malaria resistance-associated FREM3/GYPE regions, we also find outstanding genomic regions involved in barrier integrity and innate immunity, such as the GRIK1/CLDN17 intergenic region, and the SLC35F1 and ABCA13 genes. Our findings not only echo the significance of pathogen defense but also reveal novel candidates in maintaining balanced polymorphisms across human and chimpanzee lineages. Finally, we show that these trans-species statistics can be applied to and work well for an arbitrary number of species, and integrate them into open-source software packages for ease of use by the scientific community.
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Affiliation(s)
- Xiaoheng Cheng
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA
- Department of Statistics, Pennsylvania State University, University Park, PA
- Institute for CyberScience, Pennsylvania State University, University Park, PA
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26
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The radial expansion of the Diego blood group system polymorphisms in Asia: mark of co-migration with the Mongol conquests. Eur J Hum Genet 2018; 27:125-132. [PMID: 30143806 PMCID: PMC6303257 DOI: 10.1038/s41431-018-0245-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/09/2018] [Accepted: 07/18/2018] [Indexed: 01/07/2023] Open
Abstract
Red cell polymorphisms can provide evidence of human migration and adaptation patterns. In Eurasia, the distribution of Diego blood group system polymorphisms remains unaddressed. To shed light on the dispersal of the Dia antigen, we performed analyses of correlations between the frequencies of DI*01 allele, C2-M217 and C2-M401 Y-chromosome haplotypes ascribed as being of Mongolian-origin and language affiliations, in 75 Eurasian populations including DI*01 frequency data from the HGDP-CEPH panel. We revealed that DI*01 reaches its highest frequency in Mongolia, Turkmenistan and Kyrgyzstan, expanding southward and westward across Asia with Altaic-speaking nomadic carriers of C2-M217, and even more precisely C2-M401, from their homeland presumably in Mongolia, between the third century BCE and the thirteenth century CE. The present study has highlighted the gene-culture co-migration with the demographic movements that occurred during the past two millennia in Central and East Asia. Additionally, this work contributes to a better understanding of the distribution of immunogenic erythrocyte polymorphisms with a view to improve transfusion safety.
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27
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Naret O, Chaturvedi N, Bartha I, Hammer C, Fellay J. Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes. Front Genet 2018; 9:266. [PMID: 30105048 PMCID: PMC6078058 DOI: 10.3389/fgene.2018.00266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 11/23/2022] Open
Abstract
Studies of host genetic determinants of pathogen sequence variations can identify sites of genomic conflicts, by highlighting variants that are implicated in immune response on the host side and adaptive escape on the pathogen side. However, systematic genetic differences in host and pathogen populations can lead to inflated type I (false positive) and type II (false negative) error rates in genome-wide association analyses. Here, we demonstrate through a simulation that correcting for both host and pathogen stratification reduces spurious signals and increases power to detect real associations in a variety of tested scenarios. We confirm the validity of the simulations by showing comparable results in an analysis of paired human and HIV genomes.
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Affiliation(s)
- Olivier Naret
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nimisha Chaturvedi
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian Hammer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland
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28
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Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, 96 Jonathan Lucas Street, Suite 816, Charleston, SC 29425, USA; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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29
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Taylor SL, McGuckin MA, Wesselingh S, Rogers GB. Infection's Sweet Tooth: How Glycans Mediate Infection and Disease Susceptibility. Trends Microbiol 2018; 26:92-101. [PMID: 29079498 PMCID: PMC7125966 DOI: 10.1016/j.tim.2017.09.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/10/2017] [Accepted: 09/29/2017] [Indexed: 12/21/2022]
Abstract
Glycans form a highly variable constituent of our mucosal surfaces and profoundly affect our susceptibility to infection and disease. The diversity and importance of these surface glycans can be seen in individuals who lack a functional copy of the fucosyltransferase gene, FUT2. Representing around one-fifth of the population, these individuals have an altered susceptibility to many bacterial and viral infections and diseases. The mediation of host-pathogen interactions by mucosal glycans, such as those added by FUT2, is poorly understood. We highlight, with specific examples, important mechanisms by which host glycans influence infection dynamics, including by: acting as pathogen receptors (or receptor-decoys), promoting microbial stability, altering the physical characteristics of mucus, and acting as immunological markers. We argue that the effect glycans have on infection dynamics has profound implications for many aspects of healthcare and policy, including clinical management, outbreak control, and vaccination policy.
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Affiliation(s)
- Steven L Taylor
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Michael A McGuckin
- Inflammatory Diseases Biology and Therapeutics, Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Steve Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
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30
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van der Lee R, Wiel L, van Dam TJP, Huynen MA. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. Nucleic Acids Res 2017; 45:10634-10648. [PMID: 28977405 PMCID: PMC5737536 DOI: 10.1093/nar/gkx704] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/02/2017] [Indexed: 12/17/2022] Open
Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus–host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus–human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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31
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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: 39] [Impact Index Per Article: 5.6] [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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32
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Vallier M, Abou Chakra M, Hindersin L, Linnenbrink M, Traulsen A, Baines JF. Evaluating the maintenance of disease-associated variation at the blood group-related gene B4galnt2 in house mice. BMC Evol Biol 2017; 17:187. [PMID: 28806915 PMCID: PMC5557512 DOI: 10.1186/s12862-017-1035-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022] Open
Abstract
Background B4galnt2 is a blood group-related glycosyltransferase that displays cis-regulatory variation for its tissue-specific expression patterns in house mice. The wild type allele, found e.g. in the C57BL/6 J strain, directs intestinal expression of B4galnt2, which is the pattern observed among vertebrates, including humans. An alternative allele class found in the RIIIS/J strain and other mice instead drives expression in blood vessels, which leads to a phenotype similar to type 1 von Willebrand disease (VWD), a common human bleeding disorder. We previously showed that alternative B4galnt2 alleles are subject to long-term balancing selection in mice and that variation in B4galnt2 expression influences host-microbe interactions in the intestine. This suggests that the costs of prolonged bleeding in RIIIS/J allele-bearing mice might be outweighed by benefits associated with resistance against gastrointestinal pathogens. However, the conditions under which such trade-offs could lead to the long-term maintenance of disease-associated variation at B4galnt2 are unclear. Results To explore the persistence of B4galnt2 alleles in wild populations of house mice, we combined B4galnt2 haplotype frequency data together with a mathematical model based on an evolutionary game framework with a modified Wright-Fisher process. In particular, given the potential for a heterozygote advantage as a possible explanation for balancing selection, we focused on heterozygous mice, which express B4galnt2 in both blood vessels and the gastrointestinal tract. We show that B4galnt2 displays an interesting spatial allelic distribution in Western Europe, likely due to the recent action of natural selection. Moreover, we found that the genotype frequencies observed in nature can be produced by pathogen-driven selection when both heterozygotes and RIIIS/J homozygotes are protected against infection and the fitness cost of bleeding is roughly half that of infection. Conclusion By comparing the results of our models to the patterns of polymorphism at B4galnt2 in natural populations, we are able to recognize the long-term maintenance of the RIIIS/J allele through host-pathogen interactions as a viable hypothesis. Further, our models identify that a putative dominant-, yet unknown protective function of the RIIIS/J allele appears to be more likely than a protective loss of intestinal B4galnt2 expression in RIIIS/J homozygotes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1035-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie Vallier
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany.,Institute for Experimental Medicine, Section of Evolutionary Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Maria Abou Chakra
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Laura Hindersin
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany
| | - Miriam Linnenbrink
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany. .,Institute for Experimental Medicine, Section of Evolutionary Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany.
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33
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Deschamps M, Quintana-Murci L. Immunité innée et maladies chez l’homme. Med Sci (Paris) 2017; 32:1079-1086. [DOI: 10.1051/medsci/20163212011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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34
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Galinsky KJ, Loh PR, Mallick S, Patterson NJ, Price AL. Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure. Am J Hum Genet 2016; 99:1130-1139. [PMID: 27773431 PMCID: PMC5097941 DOI: 10.1016/j.ajhg.2016.09.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/21/2016] [Indexed: 01/11/2023] Open
Abstract
Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses of ancient Eurasians revealed that populations in the northern UK have higher levels of Steppe ancestry and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along the top PCs identified a genome-wide-significant signal of selection at the coding variant rs601338 in FUT2 (p = 9.16 × 10-9). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified genome-wide-significant (p = 5 × 10-8) signals of recent selection at two additional loci: CYP1A2-CSK and F12. We detected strong associations between diastolic blood pressure in the UK Biobank and both the variants with selection signals at CYP1A2-CSK (p = 1.10 × 10-19) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10-33), implicating recent adaptation related to blood pressure.
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Affiliation(s)
- Kevin J Galinsky
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Swapan Mallick
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nick J Patterson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alkes L Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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35
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Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa. THE PHARMACOGENOMICS JOURNAL 2016; 17:112-120. [PMID: 27779243 PMCID: PMC5380847 DOI: 10.1038/tpj.2016.78] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/06/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.
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36
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Everest-Dass AV, Kolarich D, Pascovici D, Packer NH. Blood group antigen expression is involved in C. albicans interaction with buccal epithelial cells. Glycoconj J 2016; 34:31-50. [PMID: 27639389 DOI: 10.1007/s10719-016-9726-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/03/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022]
Abstract
Human blood group polymorphisms are known to be determined by the expression of A, B or H antigens and the Lewis antigens. Protection against microbial infections has been associated with inheritance of polymorphisms in genes encoding and regulating the expression of ABH and Lewis antigens in bodily secretions and epithelial tissue surfaces, subsequently resulting in the presentation of different glycosylated terminal antigens on the cell surface. We investigated the role of blood group antigens in diversifying the glycosylation of buccal epithelial cells (BEC) that line the oral cavity. Specifically, we characterized and statistically evaluated the expression of histo-blood group (A, B, O) antigens on N-and O-linked glycans from BEC membrane proteins of various individuals that represented different blood group type and secretor status using a porous graphitic carbon liquid chromatography electrospray ionization mass spectrometry (PGC-LC-ESI-MS) based glycomics approach. From these BEC membrane proteins a total of 77 N-glycan and 96 O-glycan structures were structurally characterized from 19 individuals and relatively quantitated. The N-glycans from the secretor individuals did not express any A/B blood group determinants, but contained several terminal H-antigens. Apart from the non-secretors, the N-glycan profiles of BEC from all blood groups displayed similar glycan types, while varying in their relative intensities between individuals. However, multivariate analysis of the O-glycans from individuals displayed segregation patterns clearly associated with their blood group type and secretor status. In adhesion assays the oral pathogen Candida albicans showed a significantly higher interaction to blood group O type BECs relative to other blood groups.
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Affiliation(s)
- Arun V Everest-Dass
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.,ARC Centre of Excellence in Nanoscale Biophotonics, Macquarie University, Sydney, Australia
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14428, Potsdam, Germany
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, Australia
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia. .,ARC Centre of Excellence in Nanoscale Biophotonics, Macquarie University, Sydney, Australia.
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37
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Rotimi CN, Tekola-Ayele F, Baker JL, Shriner D. The African diaspora: history, adaptation and health. Curr Opin Genet Dev 2016; 41:77-84. [PMID: 27644073 DOI: 10.1016/j.gde.2016.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/30/2016] [Accepted: 08/02/2016] [Indexed: 01/13/2023]
Abstract
The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities.
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Affiliation(s)
- Charles N Rotimi
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA.
| | - Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Jennifer L Baker
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
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38
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Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates. Rev Bras Hematol Hemoter 2016; 38:331-340. [PMID: 27863762 PMCID: PMC5119663 DOI: 10.1016/j.bjhh.2016.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/08/2016] [Accepted: 07/21/2016] [Indexed: 12/20/2022] Open
Abstract
ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of expression in tissue and exocrine secretions, little is known about their biological importance and potential applications in medicine. This review highlights the structural diversity, the biological importance and potential applications of ABO, H, Lewis and secretor histo-blood carbohydrates.
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39
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Sung MK, Jang J, Lee KS, Ghim CM, Choi JK. Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. Genome Biol 2016; 17:164. [PMID: 27468897 PMCID: PMC4964047 DOI: 10.1186/s13059-016-1027-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/13/2016] [Indexed: 12/28/2022] Open
Abstract
Background Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions. Results The single-nucleotide polymorphisms bearing the signatures of balancing selection are enriched in active cis-regulatory regions of immune cells and epithelial cells, the latter of which provide barrier function and innate immunity. Examples associated with ancient trans-specific balancing selection are also discovered. Allelic imbalance in chromatin accessibility and divergence in transcription factor motif sequences indicate that these balanced polymorphisms cause distinct regulatory variation. However, a majority of these variants show no association with the expression level of the target gene. Instead, single-cell experimental data for gene expression and chromatin accessibility demonstrate that heterozygous sequences can lower cell-to-cell variability in proportion to selection strengths. This negative correlation is more pronounced for highly expressed genes and consistently observed when using different data and methods. Based on mathematical modeling, we hypothesize that extrinsic noise from fluctuations in transcription factor activity may be amplified in homozygotes, whereas it is buffered in heterozygotes. While high expression levels are coupled with intrinsic noise reduction, regulatory heterozygosity can contribute to the suppression of extrinsic noise. Conclusions This mechanism may confer a selective advantage by increasing cell population homogeneity and thereby enhancing the collective action of the cells, especially of those involved in the defense systems in humans. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1027-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Kyung Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Juneil Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Cheol-Min Ghim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Mathematical Bioscience Institute, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea.
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40
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Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Mol Biol Evol 2016; 33:2555-64. [PMID: 27436009 PMCID: PMC5026253 DOI: 10.1093/molbev/msw127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.
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Affiliation(s)
- Tobias L Lenz
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Victor Spirin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Daniel M Jordan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Shamil R Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA
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41
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Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
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42
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Croze M, Živković D, Stephan W, Hutter S. Balancing selection on immunity genes: review of the current literature and new analysis in Drosophila melanogaster. ZOOLOGY 2016; 119:322-9. [PMID: 27106015 DOI: 10.1016/j.zool.2016.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/11/2016] [Accepted: 03/16/2016] [Indexed: 12/18/2022]
Abstract
Balancing selection has been widely assumed to be an important evolutionary force, yet even today little is known about its abundance and its impact on the patterns of genetic diversity. Several studies have shown examples of balancing selection in humans, plants or parasites, and many genes under balancing selection are involved in immunity. It has been proposed that host-parasite coevolution is one of the main forces driving immune genes to evolve under balancing selection. In this paper, we review the literature on balancing selection on immunity genes in several organisms, including Drosophila. Furthermore, we performed a genome scan for balancing selection in an African population of Drosophila melanogaster using coalescent simulations of a demographic model with and without selection. We find very few genes under balancing selection and only one novel candidate gene related to immunity. Finally, we discuss the possible causes of the low number of genes under balancing selection.
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Affiliation(s)
- Myriam Croze
- Department of Biology II, Ludwig Maximilian University Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany.
| | - Daniel Živković
- Department of Biology II, Ludwig Maximilian University Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
| | - Wolfgang Stephan
- Department of Biology II, Ludwig Maximilian University Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
| | - Stephan Hutter
- Department of Biology II, Ludwig Maximilian University Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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43
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Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, van Driem G, Jobling MA, de Knijff P, Tyler-Smith C, Ayub Q. Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas. Hum Genet 2016; 135:393-402. [PMID: 26883865 PMCID: PMC4796332 DOI: 10.1007/s00439-016-1641-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/23/2016] [Indexed: 12/19/2022]
Abstract
High-altitude adaptation in Tibetans is influenced by introgression of a 32.7-kb haplotype from the Denisovans, an extinct branch of archaic humans, lying within the endothelial PAS domain protein 1 (EPAS1), and has also been reported in Sherpa. We genotyped 19 variants in this genomic region in 1507 Eurasian individuals, including 1188 from Bhutan and Nepal residing at altitudes between 86 and 4550 m above sea level. Derived alleles for five SNPs characterizing the core Denisovan haplotype (AGGAA) were present at high frequency not only in Tibetans and Sherpa, but also among many populations from the Himalayas, showing a significant correlation with altitude (Spearman’s correlation coefficient = 0.75, p value 3.9 × 10−11). Seven East- and South-Asian 1000 Genomes Project individuals shared the Denisovan haplotype extending beyond the 32-kb region, enabling us to refine the haplotype structure and identify a candidate regulatory variant (rs370299814) that might be interacting in an additive manner with the derived G allele of rs150877473, the variant previously associated with high-altitude adaptation in Tibetans. Denisovan-derived alleles were also observed at frequencies of 3–14 % in the 1000 Genomes Project African samples. The closest African haplotype is, however, separated from the Asian high-altitude haplotype by 22 mutations whereas only three mutations, including rs150877473, separate the Asians from the Denisovan, consistent with distant shared ancestry for African and Asian haplotypes and Denisovan adaptive introgression.
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Affiliation(s)
- Sophie Hackinger
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern, CH 3012, Switzerland
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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44
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Ramos PS, Shedlock AM, Langefeld CD. Genetics of autoimmune diseases: insights from population genetics. J Hum Genet 2015; 60:657-64. [PMID: 26223182 PMCID: PMC4660050 DOI: 10.1038/jhg.2015.94] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/12/2015] [Accepted: 06/19/2015] [Indexed: 12/14/2022]
Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Autoimmune diseases (ADs) are a family of complex heterogeneous disorders with similar underlying mechanisms characterized by immune responses against self. Collectively, ADs are common, exhibit gender and ethnic disparities, and increasing incidence. As natural selection is an important influence on human genetic variation, and immune function genes are enriched for signals of positive selection, it is thought that the prevalence of AD risk alleles seen in different population is partially the result of differing selective pressures (for example, due to pathogens). With the advent of high-throughput technologies, new analytical methodologies and large-scale projects, evidence for the role of natural selection in contributing to the heritable component of ADs keeps growing. This review summarizes the genetic regions associated with susceptibility to different ADs and concomitant evidence for selection, including known agents of selection exerting selective pressure in these regions. Examples of specific adaptive variants with phenotypic effects are included as an evidence of natural selection increasing AD susceptibility. Many of the complexities of gene effects in different ADs can be explained by population genetics phenomena. Integrating AD susceptibility studies with population genetics to investigate how natural selection has contributed to genetic variation that influences disease risk will help to identify functional variants and elucidate biological mechanisms. As such, the study of population genetics in human population holds untapped potential for elucidating the genetic causes of human disease and more rapidly focusing to personalized medicine.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, and Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, SC, USA
- Hollings Marine Laboratory Center for Marine Biomedicine and College of Graduate Studies, Medical University of South Carolina, Charleston, SC, USA
| | - Carl D Langefeld
- Division of Public Health Sciences, Department of Biostatistical Sciences; and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
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45
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Forni D, Pozzoli U, Cagliani R, Tresoldi C, Menozzi G, Riva S, Guerini FR, Comi GP, Bolognesi E, Bresolin N, Clerici M, Sironi M. Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders. Genome Biol 2015; 15:499. [PMID: 25358694 PMCID: PMC4237747 DOI: 10.1186/s13059-014-0499-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 01/18/2023] Open
Abstract
Background The temporal coordination of biological processes into daily cycles is a common feature of most living organisms. In humans, disruption of circadian rhythms is commonly observed in psychiatric diseases, including schizophrenia, bipolar disorder, depression and autism. Light therapy is the most effective treatment for seasonal affective disorder and circadian-related treatments sustain antidepressant response in bipolar disorder patients. Day/night cycles represent a major circadian synchronizing signal and vary widely with latitude. Results We apply a geographically explicit model to show that out-of-Africa migration, which led humans to occupy a wide latitudinal area, affected the evolutionary history of circadian regulatory genes. The SNPs we identify using this model display consistent signals of natural selection using tests based on population genetic differentiation and haplotype homozygosity. Signals of natural selection driven by annual photoperiod variation are detected for schizophrenia, bipolar disorder, and restless leg syndrome risk variants, in line with the circadian component of these conditions. Conclusions Our results suggest that human populations adapted to life at different latitudes by tuning their circadian clock systems. This process also involves risk variants for neuropsychiatric conditions, suggesting possible genetic modulators for chronotherapies and candidates for interaction analysis with photoperiod-related environmental variables, such as season of birth, country of residence, shift-work or lifestyle habits. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0499-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy
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46
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Abstract
Blood group antigens represent polymorphic traits inherited among individuals and populations. At present, there are 34 recognized human blood groups and hundreds of individual blood group antigens and alleles. Differences in blood group antigen expression can increase or decrease host susceptibility to many infections. Blood groups can play a direct role in infection by serving as receptors and/or coreceptors for microorganisms, parasites, and viruses. In addition, many blood group antigens facilitate intracellular uptake, signal transduction, or adhesion through the organization of membrane microdomains. Several blood groups can modify the innate immune response to infection. Several distinct phenotypes associated with increased host resistance to malaria are overrepresented in populations living in areas where malaria is endemic, as a result of evolutionary pressures. Microorganisms can also stimulate antibodies against blood group antigens, including ABO, T, and Kell. Finally, there is a symbiotic relationship between blood group expression and maturation of the gastrointestinal microbiome.
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Affiliation(s)
- Laura Cooling
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
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47
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Rausch P, Steck N, Suwandi A, Seidel JA, Künzel S, Bhullar K, Basic M, Bleich A, Johnsen JM, Vallance BA, Baines JF, Grassl GA. Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection. PLoS Pathog 2015; 11:e1005008. [PMID: 26133982 PMCID: PMC4489644 DOI: 10.1371/journal.ppat.1005008] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/05/2015] [Indexed: 12/16/2022] Open
Abstract
Glycans play important roles in host-microbe interactions. Tissue-specific expression patterns of the blood group glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) are variable in wild mouse populations, and loss of B4galnt2 expression is associated with altered intestinal microbiota. We hypothesized that variation in B4galnt2 expression alters susceptibility to intestinal pathogens. To test this, we challenged mice genetically engineered to express different B4galnt2 tissue-specific patterns with a Salmonella Typhimurium infection model. We found B4galnt2 intestinal expression was strongly associated with bacterial community composition and increased Salmonella susceptibility as evidenced by increased intestinal inflammatory cytokines and infiltrating immune cells. Fecal transfer experiments demonstrated a crucial role of the B4galnt2-dependent microbiota in conferring susceptibility to intestinal inflammation, while epithelial B4galnt2 expression facilitated epithelial invasion of S. Typhimurium. These data support a critical role for B4galnt2 in gastrointestinal infections. We speculate that B4galnt2-specific differences in host susceptibility to intestinal pathogens underlie the strong signatures of balancing selection observed at the B4galnt2 locus in wild mouse populations.
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Affiliation(s)
- Philipp Rausch
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Natalie Steck
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Models of Inflammation, Research Center Borstel, Borstel, Germany
| | - Abdulhadi Suwandi
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Janice A. Seidel
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kirandeep Bhullar
- Department of Pediatrics, Division of Gastroenterology, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Jill M. Johnsen
- Research Institute, Puget Sound Blood Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Bruce A. Vallance
- Department of Pediatrics, Division of Gastroenterology, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - John F. Baines
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Guntram A. Grassl
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Models of Inflammation, Research Center Borstel, Borstel, Germany
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48
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Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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Teixeira JC, de Filippo C, Weihmann A, Meneu JR, Racimo F, Dannemann M, Nickel B, Fischer A, Halbwax M, Andre C, Atencia R, Meyer M, Parra G, Pääbo S, Andrés AM. Long-Term Balancing Selection in LAD1 Maintains a Missense Trans-Species Polymorphism in Humans, Chimpanzees, and Bonobos. Mol Biol Evol 2015; 32:1186-96. [PMID: 25605789 DOI: 10.1093/molbev/msv007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here, we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.
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Affiliation(s)
- João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Juan R Meneu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Fischer
- International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Michel Halbwax
- Clinique vétérinaire du Dr. Jacquemin, Maisons-Alfort, France
| | - Claudine Andre
- Lola Ya Bonobo sanctuary, Kinshasa, Democratic Republic Congo
| | - Rebeca Atencia
- Réserve Naturelle Sanctuaire à Chimpanzés de Tchimpounga, Jane Goodall Institute, Pointe-Noire, Republic of Congo
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Genís Parra
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Song Q, Zhang Z, Liu Y, Han S, Zhang X. The tag SNP rs10746463 in decay-accelerating factor is associated with the susceptibility to gastric cancer. Mol Immunol 2015; 63:473-8. [PMID: 25457880 DOI: 10.1016/j.molimm.2014.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/29/2014] [Accepted: 10/03/2014] [Indexed: 01/25/2023]
Abstract
BACKGROUND Complement activation involved in the innate immunity and adaptive immunity and further contributed to the development of tumor growth. This study aimed to investigate the association of genetic variants in complement 3 (C3) and decay-accelerating factor (DAF) genes with the risk of gastric cancer. METHODS This case-control study included 500 gastric cancer patients and 500 cancer-free controls. Based on the Chinese population data from HapMap database, we used Haploview 4.2 program to select candidate tag SNPs. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression to evaluate the association of each genetic variant with the risk of gastric cancer. RESULTS Among 12 tag SNPs of C3, no correlation was observed between C3 genetic variants and risk of gastric cancer. For tag SNPS of DAF, logistic regression analysis revealed that the carriers with DAF rs10746463 AA genotype had a significantly increased risk for developing gastric cancer (OR = 1.46, 95% CI = 1.01–2.10) when compared with GG genotype, but those carrying with rs10746463 AG genotype didn't (OR = 1.31, 95% CI = 0.98-1.75). When stratified by smoking status, we found that the risk of gastric cancer was associated with rs10746463 GA or AA genotype carriers among smoker with OR (95% CI) of 1.64 (1.06-2.54), but not among non-smoker (OR = 1.37, 95% CI = 0.97-1.94). CONCLUSION DAF rs10746463 polymorphism effects on the risk of developing gastric cancer in Chinese population.
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Affiliation(s)
- Qinqin Song
- Institute of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
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