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Shirizadeh A, Razavi Z, Saeedi V, Faradmal J, Roshanaei G, Hajilooi M, Morahan G, Solgi G. Family-based association of HLA-DRB1 and DQB1 alleles and haplotypes in a group of Iranian Type 1 diabetes children. HLA 2024; 103:e15446. [PMID: 38575369 DOI: 10.1111/tan.15446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 04/06/2024]
Abstract
This family-based study was conducted in a group of Iranians with Type 1 diabetes (T1D) to investigate the transmission from parents of risk and non-risk HLA alleles and haplotypes, and to estimate the genetic risk score for this disease within this population. A total of 240 T1D subjects including 111 parent-child trios (111 children with T1D, 133 siblings, and 222 parents) and 330 ethnically matched healthy individuals were recruited. High-resolution HLA typing for DRB1/DQB1 loci was performed for all study subjects (n = 925) using polymerase chain reaction-sequence-specific oligonucleotide probe method. The highest predisposing effect on developing T1D was conferred by the following haplotypes both in all subjects and in probands compared to controls: DRB1*04:05-DQB1*03:02 (Pc = 2.97e-06 and Pc = 6.04e-10, respectively), DRB1*04:02-DQB1*03:02 (Pc = 5.94e-17 and Pc = 3.86e-09, respectively), and DRB1*03:01-DQB1*02:01 (Pc = 8.26e-29 and Pc = 6.56e-16, respectively). Conversely, the major protective haplotypes included DRB1*13:01-DQB1*06:03 (Pc = 6.99e-08), DRB1*15:01-DQB1*06:02 (Pc = 2.97e-06) in the cases versus controls. Also, DRB1*03:01-DQB1*02:01/DRB1*04:02|05-DQB1*03:02 and DRB1*03:01-DQB1*02:01/DRB1*03:01-DQB1*02:01 diplotypes conferred the highest predisposing effect in the cases (Pc = 8.65e-17 and Pc = 6.26e-08, respectively) and in probands (Pc = 5.4e-15 and Pc = 0.001, respectively) compared to controls. Transmission disequilibrium test showed that the highest risk was conferred by DRB1*04:02-DQB1*03:02 (Pc = 3.26e-05) and DRB1*03:01-DQB1*02:01 (Pc = 1.78e-12) haplotypes and the highest protection by DRB1*14:01-DQB1*05:03 (Pc = 8.66e-05), DRB1*15:01-DQB1*06:02 (Pc = 0.002), and DRB1*11:01-DQB1*03:01 (Pc = 0.0003) haplotypes. Based on logistic regression analysis, carriage of risk haplotypes increased the risk of T1D development 24.5 times in the Iranian population (p = 5.61e-13). Also, receiver operating characteristic curve analysis revealed a high predictive power of those risk haplotypes in discrimination of susceptible from healthy individuals (area under curve: 0.88, p = 5.5e-32). Our study highlights the potential utility of genetic risk assessment based on HLA diplotypes for predicting T1D risk in individuals, particularly among family members of affected children in our population.
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Affiliation(s)
- Ata Shirizadeh
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Zahra Razavi
- Pediatrics Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Vahid Saeedi
- Pediatric Endocrinology and Metabolism Department, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javad Faradmal
- Biostatistics Department, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghodratollah Roshanaei
- Biostatistics Department, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdad Hajilooi
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Grant Morahan
- Centre for Medical Research, University of Western Australia, Perth, Western Australia, Australia
| | - Ghasem Solgi
- Immunology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Kambala A, Rajeh A, Joel MZ, Ma E, Cornman H, Zhang J, Kwatra SG. HLA DRB5∗01:01 is associated with pruritus in individuals with Fitzpatrick skin type IV-VI. J Am Acad Dermatol 2024; 90:855-857. [PMID: 38104778 DOI: 10.1016/j.jaad.2023.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Affiliation(s)
- Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marina Z Joel
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily Ma
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hannah Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeni Zhang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Al Agbar S, Sharma A, Cohoe E, Beaune D, Sidahmed AME. The novel HLA-DQA1*05:05:17:03 allele, identified in a potential organ donor. HLA 2024; 103:e15489. [PMID: 38647206 DOI: 10.1111/tan.15489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
HLA-DQA1*05:05:17:03 differs from HLA-DQA1*05:05:01:02 by a single base substitution in exon 1 and HLA-DQA1*05:05:17:01 within introns 1 and 2.
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Affiliation(s)
- Sabina Al Agbar
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Arpit Sharma
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Elsa Cohoe
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - David Beaune
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Abubaker M E Sidahmed
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
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Park K, Yoo SJ. Clinical application of a real-time polymerase chain reaction test for CYP2C19 genotyping based on genotype distribution in a healthy Korean population. Lab Med 2024; 55:234-237. [PMID: 37543868 DOI: 10.1093/labmed/lmad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023] Open
Abstract
OBJECTIVE With the recent reports of additional alleles of the CYP2C19 gene with decreased or no function, the clinical utility of real-time polymerase chain reaction (PCR)-based testing that detects only a small number of variant targets needs to be evaluated. METHOD We retrospectively reviewed 7-year data for real-time PCR test records from a single hospital and analyzed CYP2C19 genotypes from publicly available whole-genome or whole-exome data from a healthy Korean population. RESULTS Of the 2327 test results in this hospital, the *1 allele was most common (60.5%), followed by *2 (28.0%), *3 (10.1%), and *17 (1.4%). Among 5305 healthy Korean individuals, the frequencies of the *2, *3, and *17 alleles were 28.6%, 9.9%, and 1.0%, respectively, which were not statistically different from those of the hospital data (P = .4439, P = .6025, and P = .1142, respectively). Interestingly, the total frequency of additional nonfunctional alleles (*4, *6, *22, and *24) that could not be detected using real-time PCR was only 0.1%, with a total allele count of 8. CONCLUSION Our study shows that the clinical utility of real-time PCR for CYP2C19 genotyping remains satisfactory. However, caution should be exercised because the test can miss patients with decreased CYP2C19 function.
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Affiliation(s)
- Kuenyoul Park
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, Republic of Korea
| | - Soo Jin Yoo
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, Republic of Korea
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Beaune D, Sharma A, Cohoe E, Al Agbar S, Sidahmed AME. The novel HLA-C*06:372 allele, identified in a stem cell donor of an old order mennonite ethnicity. HLA 2024; 103:e15432. [PMID: 38470345 DOI: 10.1111/tan.15432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
HLA-C*06:372 differs from HLA-C*06:02:01:01 by a single substitution in exon 4.
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Affiliation(s)
- David Beaune
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Arpit Sharma
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Elsa Cohoe
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Sabina Al Agbar
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - Abubaker M E Sidahmed
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
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Bajpai D, Rajasekar A. Genetic Association of ICAM-1 (rs5498) Gene Polymorphism With Susceptibility to Stage II Grade B Periodontitis: A Case-Control Study in South Indian Population. Cureus 2024; 16:e56629. [PMID: 38650775 PMCID: PMC11034711 DOI: 10.7759/cureus.56629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION In the contemporary perspective, periodontitis is considered a complex issue triggered and perpetuated by bacteria but strongly influenced by the way the body reacts to bacterial plaque. Recent research has indicated that variations in genes might have an impact on the development of periodontitis. This study was conducted to explore a probable link between the genetic variations in intercellular adhesion molecule-1 (ICAM-1) represented by rs5498 and the occurrence of periodontitis. Methods: A total of 100 participants, 50 with periodontitis and 50 with periodontally healthy or mild gingivitis, were recruited for this study. Whole blood drawn from the participants was used to obtain genomic DNA. The ICAM-1 gene polymorphism (rs5498) was determined using polymerase chain reaction (PCR) amplification and digestion. The ICAM-1 gene's flanking primers were used to amp up the DNA. For statistical analysis, the genotype that was analyzed using the pattern of restriction fragment length polymorphism was recorded. The Chi-square test compared genotype and allele frequency distributions between both groups. The odds ratio with 95% confidence intervals with each individual allele or genotype was used to compute the risk. Statistical significance was established in all tests when the p-value was less than 0.05. RESULTS There was no discernible difference between the genotype frequencies of patients and controls χ2df (P = 0.6065). The findings demonstrated that no significant difference was present between the two groups for homozygous or heterozygous mutant genotypes (AA vs. AG+GG; P = 0.6854). There was no discernible difference in the detected frequencies of the A allele (58% vs. 61%), G allele (42% vs. 39%), TT (16% vs. 24%), AG (40% vs. 36%), and TT genotypes in the studied groups. CONCLUSION According to the results of the current investigation, the ICAM-1 (rs5498) gene polymorphism is not associated with periodontitis in the population investigated.
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Affiliation(s)
- Devika Bajpai
- Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Arvina Rajasekar
- Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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Stelet VN, Romero M, Cita RF, Binato R, Abdelhay E. A novel HLA-C*02:10 variant, HLA-C*02:10:09, identified in a healthy individual from Brazil. HLA 2024; 103:e15410. [PMID: 38372615 DOI: 10.1111/tan.15410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Identification of the novel HLA-C*02:10:09 allele that differs from HLA-C*02:10:01:01 at one position in exon 1.
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Affiliation(s)
- Vinícius N Stelet
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Matilde Romero
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Rafael F Cita
- Transplant Immunology Laboratory, Pio XII Foundation, Barretos, Brazil
| | - Renata Binato
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Eliana Abdelhay
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
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Sharma A, Beaune D, Fielder D, Al Agbar S, Sidahmed AME. The novel HLA-DRB1*08:127 allele, identified in a deceased organ donor of Scandinavian descent. HLA 2024; 103:e15376. [PMID: 38323708 DOI: 10.1111/tan.15376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
HLA-DRB1*08:127 differs from HLA-DRB1*08:01:01:01 by a single substitution in exon 4.
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Affiliation(s)
- A Sharma
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - D Beaune
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - D Fielder
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - S Al Agbar
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
| | - A M E Sidahmed
- Immunogenetics and Transplantation Laboratory, London Health Sciences Centre and Pathology and Laboratory Medicine, University Hospital, London, Ontario, Canada
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Abstract
The association of an individual's genetic makeup with their response to drugs is referred to as pharmacogenomics. By understanding the relationship between genetic variants and drug efficacy or toxicity, we are able to optimize pharmacological therapy according to an individual's genotype. Pharmacogenomics research has historically suffered from bias and underrepresentation of people from certain ancestry groups and of the female sex. These biases can arise from factors such as drugs and indications studied, selection of study participants, and methods used to collect and analyze data. To examine the representation of biogeographical populations in pharmacogenomic data sets, we describe individuals involved in gene-drug response studies from PharmGKB, a leading repository of drug-gene annotations, and showcaseCYP2D6, a gene that metabolizes approximately 25% of all prescribed drugs. We also show how the historical underrepresentation of females in clinical trials has led to significantly more adverse drug reactions in females than in males.
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Affiliation(s)
- Manuel Corpas
- School of Life Sciences, University of Westminster, London, United Kingdom
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, United Kingdom
| | - Moneeza K Siddiqui
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Opeyemi Soremekun
- African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Rohini Mathur
- Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Segun Fatumo
- African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom;
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Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet 2024; 14:1320652. [PMID: 38259621 PMCID: PMC10801239 DOI: 10.3389/fgene.2023.1320652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.
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Affiliation(s)
- Jana Biová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Ivana Kaňovská
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
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Grubic Z, Maskalan M, Stingl Jankovic K, Burek Kamenaric M, Zunec R. An intermediate-sized donor registry experience: HLA barriers in matching procedures. HLA 2024; 103:e15348. [PMID: 38265197 DOI: 10.1111/tan.15348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
The data enabling the estimation of the possibility of finding a matched unrelated donor (MUD) within a relatively short time is important for the success of hematopoietic stem cell transplantation (HSCT). In the present study, 738 unrelated Croatian patients in the program of unrelated HSCT were retrospectively analyzed for gender matching, donor origin (national or international), the distribution of HLA alleles and haplotypes, as well as for the probability of finding a 9-10/10 MUD. Almost 70% of the patients in our study group had a 10/10 MUD, while among the patients with a 9/10 MUD, a 1st field resolution level mismatched donor was selected for 55.0% of patients. The majority of pairs were HLA-A mismatched (33.8%). A comparison of HLA allele frequencies between two subgroups of patients revealed significant differences for 13 alleles. However, after p value correction, the difference in frequency remained significant only for four alleles; three HLA alleles (B*08:01, C*07:01, and DRB1*03:01) demonstrated a significantly higher frequency among patients with a 10/10 MUD (Pcorr < 0.0001, Pcorr = 0.0096, and Pcorr < 0.0001, respectively), while the B*35:08 allele was significantly more present among patients with a 9/10 MUD (Pcorr = 0.0328). The comparison of the distribution of HLA haplotypes between patients with a 10/10 MUD and patients with a 9/10 MUD showed significant differences for a number of two-locus and three-locus haplotypes, as well as for one five-locus haplotype (HLA-A*01:01~B*08:01~C*07:01~DRB1*03:01~DQB1*02:01), which was significantly more present in the group of patients with a 10/10 MUD. At least one HLA haplotype from the group of non-frequent HLA haplotypes (positions >1000) was carried by patients with a 9/10 MUD. The data obtained by the present study will contribute to a better estimation of the probability of finding a suitable 9-10/10 MUD for Croatian patients in need of HSCT.
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Affiliation(s)
- Zorana Grubic
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Maskalan
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Katarina Stingl Jankovic
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Burek Kamenaric
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Renata Zunec
- Tissue Typing Centre, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
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Petrea RE, Pinheiro A, Demissie S, Ekenze O, Aparicio HJ, Satizabal C, Maillard P, DeCarli C, Beiser AS, Seshadri S, Lioutas VA, Romero JR. Hypertension Trends and White Matter Brain Injury in the Offspring Framingham Heart Study Cohort. Hypertension 2024; 81:87-95. [PMID: 37855140 PMCID: PMC10896002 DOI: 10.1161/hypertensionaha.123.21264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/03/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Hypertension is the most potent stroke risk factor and is also related to cerebral small vessel disease. We studied the relation between mid-to-late-life hypertension trends and cerebral white matter injury in community-dwelling individuals from the FHS (Framingham Heart Study). METHODS FHS Offspring cohort participants with available mid-life and late-life blood pressure measurements and brain magnetic resonance imaging were included. Multiple regression analyses were used to relate hypertension trends (normotension-normotension [reference], normotension-hypertension, and hypertension-hypertension) to white matter injury metrics on diffusion tensor imaging (free water, fractional anisotropy, and peak skeletonized mean diffusivity) and Fluid Attenuated Inversion Recovery (white matter hyperintensity volume) by different blood pressure cutoffs (130/80, 140/90, and 150/90 mm Hg). RESULTS We included 1018 participants (mean age 47.3±7.4 years at mid-life and 73.2±7.3 at late-life). At the 140/90 mm Hg cutoff, the hypertension-hypertension trend was associated with higher free water (β, 0.16 [95% CI, 0.03-0.30]; P=0.021) and peak skeletonized mean diffusivity (β, 0.15 [95% CI, 0.01-0.29]; P=0.033). At a 130/80 mm Hg cutoff, the hypertension-hypertension trend had significantly higher free water (β, 0.16 [95% CI, 0.01-0.30]; P=0.035); and the normotension-hypertension (β, 0.24 [95% CI, 0.03-0.44]; P=0.027) and hypertension-hypertension (β, 0.22 [95% CI, 0.04-0.41]; P=0.022) trends had significantly increased white matter hyperintensity volume. Exploratory stratified analysis showed effect modifications by APOE ɛ4 allele and age. CONCLUSIONS Mid-to-late-life hypertension exposure is significantly associated with microstructural and to a lesser extent, visible white matter injury; the effects are observed at both conventional and lower blood pressure cutoffs and are associated with longer duration of hypertension.
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Affiliation(s)
- Rodica Elena Petrea
- Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
| | - Adlin Pinheiro
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Serkalem Demissie
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Oluchi Ekenze
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Graduate medical sciences, Boston University School of Medicine
| | - Hugo J. Aparicio
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Claudia Satizabal
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Pauline Maillard
- Alzheimer’s Disease Center and Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology and Center for Neuroscience, University of California at Davis School of Medicine, Sacramento, CA, USA
| | - Charles DeCarli
- Alzheimer’s Disease Center and Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology and Center for Neuroscience, University of California at Davis School of Medicine, Sacramento, CA, USA
| | - Alexa S Beiser
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Sudha Seshadri
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Vasileios-Arsenios Lioutas
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, MA, USA
| | - Jose Rafael Romero
- NHLBI’s Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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Sun B, Rouzbehani OM, Kramer RJ, Ghosh R, Perelli RM, Atkins S, Fatahian AN, Davis K, Szulik MW, Goodman MA, Hathaway MA, Chi E, Word TA, Tunuguntla H, Denfield SW, Wehrens XHT, Whitehead KJ, Abdelnasser HY, Warren JS, Wu M, Franklin S, Boudina S, Landstrom AP. Nonsense Variant PRDM16-Q187X Causes Impaired Myocardial Development and TGF-β Signaling Resulting in Noncompaction Cardiomyopathy in Humans and Mice. Circ Heart Fail 2023; 16:e010351. [PMID: 38113297 PMCID: PMC10752244 DOI: 10.1161/circheartfailure.122.010351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND PRDM16 plays a role in myocardial development through TGF-β (transforming growth factor-beta) signaling. Recent evidence suggests that loss of PRDM16 expression is associated with cardiomyopathy development in mice, although its role in human cardiomyopathy development is unclear. This study aims to determine the impact of PRDM16 loss-of-function variants on cardiomyopathy in humans. METHODS Individuals with PRDM16 variants were identified and consented. Induced pluripotent stem cell-derived cardiomyocytes were generated from a proband hosting a Q187X nonsense variant as an in vitro model and underwent proliferative and transcriptional analyses. CRISPR (clustered regularly interspaced short palindromic repeats)-mediated knock-in mouse model hosting the Prdm16Q187X allele was generated and subjected to ECG, histological, and transcriptional analysis. RESULTS We report 2 probands with loss-of-function PRDM16 variants and pediatric left ventricular noncompaction cardiomyopathy. One proband hosts a PRDM16-Q187X variant with left ventricular noncompaction cardiomyopathy and demonstrated infant-onset heart failure, which was selected for further study. Induced pluripotent stem cell-derived cardiomyocytes prepared from the PRDM16-Q187X proband demonstrated a statistically significant impairment in myocyte proliferation and increased apoptosis associated with transcriptional dysregulation of genes implicated in cardiac maturation, including TGF-β-associated transcripts. Homozygous Prdm16Q187X/Q187X mice demonstrated an underdeveloped compact myocardium and were embryonically lethal. Heterozygous Prdm16Q187X/WT mice demonstrated significantly smaller ventricular dimensions, heightened fibrosis, and age-dependent loss of TGF-β expression. Mechanistic studies were undertaken in H9c2 cardiomyoblasts to show that PRDM16 binds TGFB3 promoter and represses its transcription. CONCLUSIONS Novel loss-of-function PRDM16 variant impairs myocardial development resulting in noncompaction cardiomyopathy in humans and mice associated with altered TGF-β signaling.
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Affiliation(s)
- Bo Sun
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Omid M.T. Rouzbehani
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Ryan J. Kramer
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Rajeshwary Ghosh
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Robin M. Perelli
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Sage Atkins
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Amir Nima Fatahian
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Kathryn Davis
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - Marta W. Szulik
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - Michael A. Goodman
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Marissa A. Hathaway
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Ellenor Chi
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Tarah A. Word
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, Texas, United States
| | - Hari Tunuguntla
- Departments of Medicine and Pediatrics, Section of Cardiology, Baylor College of Medicine, Houston, Texas, United States
| | - Susan W. Denfield
- Departments of Medicine and Pediatrics, Section of Cardiology, Baylor College of Medicine, Houston, Texas, United States
| | - Xander H. T. Wehrens
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, Texas, United States
- Departments of Medicine and Pediatrics, Section of Cardiology, Baylor College of Medicine, Houston, Texas, United States
- Departments of Neuroscience, Cardiovascular Research Institute, and Center for Space Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Kevin J. Whitehead
- Division Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Hala Y. Abdelnasser
- Department of Pharmacological and Pharmaceutical Sciences, The University of Houston College of Pharmacy, Houston, Texas, United States
| | - Junco S. Warren
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
- Division of Cardiovascular Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Mingfu Wu
- Department of Pharmacological and Pharmaceutical Sciences, The University of Houston College of Pharmacy, Houston, Texas, United States
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - Sihem Boudina
- Department of Nutrition and Integrative Physiology, Program in Molecular Medicine, University of Utah, Salt Lake City, Utah, United States
| | - Andrew P. Landstrom
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, United States
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States
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Sarray S, Lamine LB, Dallel M, Ezzidi I, Sellami N, Turki A, Moustafa AEEA, Mtiraoui N. Association of matrix metalloproteinase-2 gene variants with diabetic nephropathy risk. J Gene Med 2023; 25:e3553. [PMID: 37312425 DOI: 10.1002/jgm.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/11/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Diabetic nephropathy is a highly destructive microvascular complication of diabetes. Genetic predisposition is involved in the pathogenesis of diabetic nephropathy, with multiple allelic polymorphisms associated with the development and progression of the disease, thereby increasing the overall risk. To date, no study is available that shows the association of matrix metalloproteinase-2 (MMP-2) gene polymorphisms with diabetic nephropathy risk. Thus, we investigated the potential genetic influence of MMP-2 promoter variants in the development of diabetic nephropathy in type 2 diabetic patients. METHODS In total, 726 type 2 diabetic patients and 310 healthy controls were included in the study and genotyped for MMP-2, -1306C/T, -790T/G, -1575G/T and -735C/T by real-time PCR. The analysis of the outcomes was performed assuming three genetic models. The threshold for statistical significance was set at 0.05. RESULTS The results showed that the minor allele frequency of the -790T/G variant was significantly higher in patients with and without nephropathy compared to controls. Furthermore, the distribution analysis revealed a significant association of the -790T/G variant, in all genetic models, with increased risk of diabetic nephropathy that persisted after adjusting for key covariates. No significant associations between MMP-2, -1306C/T, -1575G/T, -735C/T and the risk of diabetic nephropathy were detected. Haplotype analysis identified two risk haplotypes GCGC and GTAC associated with diabetic nephropathy. CONCLUSIONS The present study is the first to demonstrate the allelic and genotypic association of the MMP-2-790T/G variant and two haplotypes with an increased risk of diabetic nephropathy in a Tunisian population with type 2 diabetes.
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Affiliation(s)
- Sameh Sarray
- Arabian Gulf University, Manama, Bahrain
- Faculty of Sciences, University Tunis EL Manar, Tunis, Tunisia
| | - Laila Ben Lamine
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Meriem Dallel
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Intissar Ezzidi
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Nejla Sellami
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Amira Turki
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | | | - Nabil Mtiraoui
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
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Xie X, Jing J, Meng X, Claiborne Johnston S, Bath PM, Li Z, Zhao X, Liu L, Wang Y, Xu Q, Wang A, Jiang Y, Li H, Wang Y. Dual Antiplatelet Therapies and Causes in Minor Stroke or Transient Ischemic Attack: A Prespecified Analysis in the CHANCE-2 Trial. Stroke 2023; 54:2241-2250. [PMID: 37548009 DOI: 10.1161/strokeaha.122.042233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/25/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND It is unclear whether patients with different stroke/transient ischemic attack etiologies benefit differently from gene-directed dual antiplatelet therapy. This study explored the efficacy and safety of ticagrelor-aspirin versus clopidogrel-aspirin in transient ischemic attack or minor stroke with different causes in the CHANCE-2 trial (Clopidogrel in High-Risk Patients With Acute Nondisabling Cerebrovascular Events-II). METHODS This was a prespecified analysis of the CHANCE-2 trial, which enrolled 6412 patients with minor stroke or transient ischemic attack who carried CYP2C19 loss-of-function alleles. Patients with centralized evaluation of TOAST (Trial of ORG 10172 in Acute Stroke Treatment) classification of large-artery atherosclerosis, small-vessel occlusion, and stroke of undetermined cause were included. The primary efficacy outcome was new stroke, and the primary safety outcome was severe or moderate bleeding, both within 90 days. Cox proportional hazards models were used to assess the interaction of TOAST classification with the effects of dual antiplatelet therapy with ticagrelor-aspirin versus clopidogrel-aspirin. RESULTS A total of 6336 patients were included in this study. In patients administered ticagrelor-aspirin and clopidogrel-aspirin, respectively, stroke recurred in 85 (9.8%) and 88 (10.7%) patients with large-artery atherosclerosis (hazard ratio, 0.86 [95% CI, 0.63-1.18]; P=0.34); 32 (3.6%) and 61 (7.0%) patients with small-vessel occlusion (hazard ratio, 0.51 [95% CI, 0.33-0.79]; P=0.002); and 68 (4.8%) and 87 (5.9%) patients with stroke of undetermined cause (hazard ratio, 0.80 [95% CI, 0.58-1.10]; P=0.17), with P=0.08 for the treatment×cause subtype interaction effect. There were no significant differences in severe or moderate bleeding events in patients with different cause and different treatment. CONCLUSIONS In this prespecified analysis of the CHANCE-2 trial, the efficacy and safety of ticagrelor-aspirin versus clopidogrel-aspirin in preventing new stroke were consistent in patients with different causes. The influence of stroke cause on benefit of gene-guided antiplatelet therapy should be explored by further trials. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT04078737.
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Affiliation(s)
- Xuewei Xie
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Jing Jing
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Tiantan Neuroimaging Center of Excellence, Beijing, China (J.J.)
| | - Xia Meng
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | | | - Philip M Bath
- Stroke Trials Unit, Mental Health and Clinical Neuroscience, University of Nottingham, United Kingdom (P.M.B.)
| | - Zixiao Li
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Xingquan Zhao
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Liping Liu
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Yilong Wang
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Qin Xu
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Anxin Wang
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Yong Jiang
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Hao Li
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
| | - Yongjun Wang
- China National Clinical Research Center for Neurological Diseases, Beijing (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China (X.X., J.J., X.M., Z.L., X.Z., L.L., Yilong Wang, Q.X., A.W., Y.J., H.L., Yongjun Wang)
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Torres G, Mourad M, Iqbal S, Moses-Fynn E, Pandita A, Siddhartha SS, Sood RA, Srinivasan K, Subbaiah RT, Tiwari A, Leheste JR. Conceptualizing Epigenetics and the Environmental Landscape of Autism Spectrum Disorders. Genes (Basel) 2023; 14:1734. [PMID: 37761876 PMCID: PMC10531442 DOI: 10.3390/genes14091734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Complex interactions between gene variants and environmental risk factors underlie the pathophysiological pathways in major psychiatric disorders. Autism Spectrum Disorder is a neuropsychiatric condition in which susceptible alleles along with epigenetic states contribute to the mutational landscape of the ailing brain. The present work reviews recent evolutionary, molecular, and epigenetic mechanisms potentially linked to the etiology of autism. First, we present a clinical vignette to describe clusters of maladaptive behaviors frequently diagnosed in autistic patients. Next, we microdissect brain regions pertinent to the nosology of autism, as well as cell networks from the bilateral body plan. Lastly, we catalog a number of pathogenic environments associated with disease risk factors. This set of perspectives provides emerging insights into the dynamic interplay between epigenetic and environmental variation in the development of Autism Spectrum Disorders.
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Affiliation(s)
- German Torres
- Department of Counseling and Clinical Psychology, Medaille College, Buffalo, NY 14214, USA;
| | - Mervat Mourad
- Department of Clinical Specialties, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA;
| | - Saba Iqbal
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Emmanuel Moses-Fynn
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Ashani Pandita
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Shriya S. Siddhartha
- Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX 75275, USA;
| | - Riya A. Sood
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Kavya Srinivasan
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Riya T. Subbaiah
- Department of Arts and Sciences, Georgetown University, Washington, DC 20057, USA;
| | - Alisha Tiwari
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
| | - Joerg R. Leheste
- Department of Biomedical Sciences, New York College of Osteopathic Medicine, Old Westbury, NY 11568, USA; (S.I.); (E.M.-F.); (A.P.); (R.A.S.); (K.S.); (A.T.)
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17
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Al-Awadi AM, Saldhana FL, Bauyrzhanova Z, Nemr R, Mahmood NA, Almawi WY. Relation of resistin gene variants to resistin plasma levels and altered susceptibility to polycystic ovary syndrome: A case control study. Am J Reprod Immunol 2023; 90:e13731. [PMID: 37382171 DOI: 10.1111/aji.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND A role for resistin in the pathogenesis of polycystic ovarian syndrome (PCOS) and related features were described for various ethnicities. As its expression is partly inherited, a role for RETN polymorphisms in regulating resistin levels and PCOS risk was shown, but with varied results. AIM To investigate the association of rs34124816 (-537A>C), rs1862513 (-420C>G), rs3219175 (-358G>A), rs3745367 (+299G>A), rs3745369 (+1263G>C), and rs1423096 (+4965C>T) RETN SNPs with PCOS. METHODS Study subjects included 583 women with PCOS, and 713 eumenorrheic women serving as controls. Genotyping was done by real-time PCR. RESULTS Higher minor allele frequency (MAF) of rs34124816, rs3219175, and rs3745369, and lower MAF of rs1862513 and rs1423096 were seen in PCOS cases. Reduced PCOS risk was found with rs3745367 minor-allele homozygotes and rs1423096 minor-allele homozygotes, while increased risk was linked with rs3745367 heterozygotes, and with rs3745369 heterozygotes and minor-allele homozygotes. While it did not reach statistical significance, serum resistin levels were elevated in PCOS cases than in control women and major-allele homozygotes of rs34124816 and rs1862513, and in rs1423096 minor-allele-containing carriers. Carriage of rs34124816 correlated positively with age and LH, whereas rs1862513 positively and rs3745367 negatively correlated with fasting glucose. Six-locus (rs34124816-rs1862513-rs3219175-rs3745367-rs3745369-rs1423096) haplotype analysis demonstrated a significant reduction in AGGGGG and a marked increase in AGGGCG haplotypes between cases and controls, thus assigning PCOS protective and susceptible nature to these haplotypes, respectively. CONCLUSIONS This study is the first to document the contribution of rs34124816 and rs1423096 RETN variants to the risk of PCOS. The varied association of RETN gene variants with PCOS suggests an ethnic contribution of RETN association with PCOS.
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Affiliation(s)
- Aminah M Al-Awadi
- Department of Pediatrics, College of Medicine, Kuwait University, Kuwait
| | | | | | - Rita Nemr
- School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Naeema A Mahmood
- Department of Obstetrics and Gynecology, Salmaniya Medical Complex, Manama, Bahrain
| | - Wassim Y Almawi
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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18
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Zapata I, Eyre AW, Alvarez CE. Psychological Stress Is Associated with Increased Cancer Risk in Dogs. Animals (Basel) 2023; 13:1869. [PMID: 37889770 PMCID: PMC10251977 DOI: 10.3390/ani13111869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 10/29/2023] Open
Abstract
Although there is evidence that psychological stress may be associated with increased cancer risk, the effect of stress on cancer risk is difficult to study, both in humans, due to socioeconomic factors, and in animal models, due to questionable biological relevance. Here, we test whether heritable canine temperament that increases psychological stress is associated with cancer risk. The study data are breed-specific averages of incidences of multiple cancer types and of temperament classes. The latter are derived from a latent class analysis of behavioral questionnaires completed by owners (C-BARQ). We thus classified the dogs according to whether they are calm vs. reactive within and across breeds. Using meta-analysis approaches, we modeled the risk of multiple cancer types in calm vs. reactive dogs. We adjusted for breed averages of body mass and lifespan, which are common confounders that impact cancer. Our study confirms that body size has a significant effect of on risk of multiple types of cancers in dogs and shows for the first time that temperament also has a moderate effect. These findings suggest dog models of heritable psychological stress are suitable for molecular epidemiological and translational studies on its effects on cancer risk.
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Affiliation(s)
- Isain Zapata
- Department of Biomedical Sciences, Rocky Vista University College of Osteopathic Medicine, Englewood, CO 80112, USA
| | | | - Carlos E Alvarez
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA
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19
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Jang MY, Patel PN, Pereira AC, Willcox JA, Haghighi A, Tai AC, Ito K, Morton SU, Gorham JM, McKean DM, DePalma SR, Bernstein D, Brueckner M, Chung WK, Giardini A, Goldmuntz E, Kaltman JR, Kim R, Newburger JW, Shen Y, Srivastava D, Tristani-Firouzi M, Gelb BD, Porter GA, Seidman CE, Seidman JG. Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease. Circ Genom Precis Med 2023; 16:224-231. [PMID: 37165897 PMCID: PMC10404383 DOI: 10.1161/circgen.122.003924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/13/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Known genetic causes of congenital heart disease (CHD) explain <40% of CHD cases, and interpreting the clinical significance of variants with uncertain functional impact remains challenging. We aim to improve diagnostic classification of variants in patients with CHD by assessing the impact of noncanonical splice region variants on RNA splicing. METHODS We tested de novo variants from trio studies of 2649 CHD probands and their parents, as well as rare (allele frequency, <2×10-6) variants from 4472 CHD probands in the Pediatric Cardiac Genetics Consortium through a combined computational and in vitro approach. RESULTS We identified 53 de novo and 74 rare variants in CHD cases that alter splicing and thus are loss of function. Of these, 77 variants are in known dominant, recessive, and candidate CHD genes, including KMT2D and RBFOX2. In 1 case, we confirmed the variant's predicted impact on RNA splicing in RNA transcripts from the proband's cardiac tissue. Two probands were found to have 2 loss-of-function variants for recessive CHD genes HECTD1 and DYNC2H1. In addition, SpliceAI-a predictive algorithm for altered RNA splicing-has a positive predictive value of ≈93% in our cohort. CONCLUSIONS Through assessment of RNA splicing, we identified a new loss-of-function variant within a CHD gene in 78 probands, of whom 69 (1.5%; n=4472) did not have a previously established genetic explanation for CHD. Identification of splice-altering variants improves diagnostic classification and genetic diagnoses for CHD. REGISTRATION URL: https://clinicaltrials.gov; Unique identifier: NCT01196182.
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Affiliation(s)
- Min Young Jang
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Department of Medicine (M.Y.J., A.H.), Brigham and Women’s Hospital, Boston, MA
| | - Parth N. Patel
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Division of Cardiology, Massachusetts General Hospital, Boston, MA (P.N.P.)
| | - Alexandre C. Pereira
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Jon A.L. Willcox
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Alireza Haghighi
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Department of Medicine (M.Y.J., A.H.), Brigham and Women’s Hospital, Boston, MA
| | - Angela C. Tai
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Kaoru Ito
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan (K.I.)
| | - Sarah U. Morton
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Pediatrics (S.U.M.), Harvard Medical School, Boston, MA
| | - Joshua M. Gorham
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - David M. McKean
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
| | - Steven R. DePalma
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Division of Cardiology (S.R.D., C.E.S.), Brigham and Women’s Hospital, Boston, MA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA (D.B.)
| | - Martina Brueckner
- Departments of Genetics (M.B.), Yale University School of Medicine, New Haven, CT
- Pediatric Cardiology (M.B.), Yale University School of Medicine, New Haven, CT
| | - Wendy K. Chung
- Departments of Pediatrics (W.K.C.), Columbia University Medical Center, New York, NY
- Medicine (W.K.C.), Columbia University Medical Center, New York, NY
| | - Alessandro Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital, London, United Kingdom (A.G.)
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA (E.G.)
| | - Jonathan R. Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, National Institute of Heart, Lung, and Blood, National Institutes of Health, Bethesda, MD (J.R.K.)
| | - Richard Kim
- Department of Cardiac Surgery, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA (R.K.)
| | - Jane W. Newburger
- Department of Cardiology (J.W.N.), Boston Children’s Hospital, MA
- Department of Cardiology (J.W.N.), Boston Children’s Hospital, MA
| | - Yufeng Shen
- Systems Biology (Y.S.), Columbia University Medical Center, New York, NY
- Biomedical Informatics (Y.S.), Columbia University Medical Center, New York, NY
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (D.S.)
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT (M.T.-F.)
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute (B.D.G.), Icahn School of Medicine at Mount Sinai, New York
- Department of Pediatrics (B.D.G.), Icahn School of Medicine at Mount Sinai, New York
- Department of Genetics (B.D.G.), Icahn School of Medicine at Mount Sinai, New York
- Department of Genomic Sciences (B.D. co-occurrence G.), Icahn School of Medicine at Mount Sinai, New York
| | - George A. Porter
- Department of Pediatrics, University of Rochester Medical Center, NY (G.A.P.)
| | - Christine E. Seidman
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
- Division of Cardiology (S.R.D., C.E.S.), Brigham and Women’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Jonathan G. Seidman
- Departments of Genetics (M.Y.J., P.N.P., A.C.P., J.A.L.W., A.H., A.C.T., S.U.M., J.M.G., D.M.M., S.R.D., C.E.S., J.G.S.), Harvard Medical School, Boston, MA
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20
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Flipphi M, Márton A, Bíró V, Ág N, Sándor E, Fekete E, Karaffa L. Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains. J Fungi (Basel) 2023; 9:jof9050570. [PMID: 37233281 DOI: 10.3390/jof9050570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes-A. calidoustus and A. implicatus-as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species.
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Affiliation(s)
- Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Alexandra Márton
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Vivien Bíró
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
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21
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Frandsen PB, Hotaling S, Powell A, Heckenhauer J, Kawahara AY, Baker RH, Hayashi CY, Ríos-Touma B, Holzenthal R, Pauls SU, Stewart RJ. Allelic resolution of insect and spider silk genes reveals hidden genetic diversity. Proc Natl Acad Sci U S A 2023; 120:e2221528120. [PMID: 37094147 PMCID: PMC10161007 DOI: 10.1073/pnas.2221528120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we show that there is extensive variation-both in terms of length and repeat motif order-between alleles of silk genes within individual arthropods. Further, this variation exists across two deep, independent origins of silk which diverged more than 500 Mya: the insect clade containing caddisflies and butterflies and spiders. This remarkable convergence in previously overlooked patterns of allelic variation across multiple origins of silk suggests common mechanisms for the generation and maintenance of structural protein-coding genes. Future genomic efforts to connect genotypes to phenotypes should account for such allelic variation.
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Affiliation(s)
- Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
| | - Scott Hotaling
- Department of Watershed Sciences, Utah State University, Logan, UT 84322
| | - Ashlyn Powell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Richard H Baker
- Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Cheryl Y Hayashi
- Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Blanca Ríos-Touma
- Facultad de Ingenierías y Ciencias Aplicadas, Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud, Universidad de las Américas, Quito 170503, Ecuador
| | - Ralph Holzenthal
- Department of Entomology, University of Minnesota, St. Paul, MN 55108
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen 35390, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112
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22
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Chien TH, Lin CL, Chen LW, Chien CH, Hu CC. Patients with Non-Alcoholic Fatty Liver Disease and Alcohol Dehydrogenase 1B/Aldehyde Dehydrogenase 2 Mutant Gene Have Higher Values of Serum Alanine Transaminase. J Pers Med 2023; 13:jpm13050758. [PMID: 37240928 DOI: 10.3390/jpm13050758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Patients with non-alcoholic fatty liver disease (NAFLD) share similar pathophysiologies to those of patients with alcohol liver disease. Alcoholic metabolic enzyme-related genes (alcohol dehydrogenase 1B (ADH1B) and aldehyde dehydrogenase 2 (ALDH2)) may be associated with pathophysiology in NAFLD patients. In this study, the association between ADH1B/ALDH2 gene polymorphism and serum metabolic factors, body statures, and hepatic steatosis/fibrosis status was evaluated in patients with NAFLD. Using biochemistry data, abdominal ultrasonography, fibrosis evaluation (Kpa), and steatosis evaluation (CAP), ADH1B gene SNP rs1229984 and ALDH2 gene SNP rs671 polymorphism were analyzed in sixty-six patients from 1 January 2022 to 31 December 2022. The percentage of the mutant type (GA + AA) was 87.9% (58/66) in the ADH1B allele and 45.5% (30/66) in the ALDH2 allele. Patients with the mutant-type ADH1B/ALDH2 allele had higher values of alanine aminotransferase (ALT) than the wild type (β = 0.273, p = 0.04). No association was observed between body mass index, serum metabolic factors (sugar and lipid profile), CAP, kPa, and ADH1B/ALDH2. A high proportion of the mutant-type ADH1B allele (87.9%) and ALDH2 allele (45.5%) was observed in patients with NAFLD. No association was observed between ADH1B/ALDH2 allele, BMI, and hepatic steatosis/fibrosis. Patients with the mutant-type ADH1B/ALDH2 allele had higher values of ALT than those with the wild type.
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Affiliation(s)
- Tsuo-Hsuan Chien
- Department of Gastroenterology and Hepatology, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
| | - Chih-Lang Lin
- Department of Gastroenterology and Hepatology, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
- Community Medicine Research Center, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
| | - Li-Wei Chen
- Department of Gastroenterology and Hepatology, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
- Community Medicine Research Center, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
| | - Cheng-Hung Chien
- Department of Gastroenterology and Hepatology, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
- Community Medicine Research Center, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
| | - Ching-Chih Hu
- Department of Gastroenterology and Hepatology, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
- Community Medicine Research Center, Chang-Gung Memorial Hospital and University, Keelung Branch, Keelung 204, Taiwan
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23
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Yu M, Aguirre M, Jia M, Gjoni K, Cordova-Palomera A, Munger C, Amgalan D, Rosa Ma X, Pereira A, Tcheandjieu C, Seidman C, Seidman J, Tristani-Firouzi M, Chung W, Goldmuntz E, Srivastava D, Loos RJF, Chami N, Cordell H, Dreßen M, Mueller-Myhsok B, Lahm H, Krane M, Pollard KS, Engreitz JM, Gagliano Taliun SA, Gelb BD, Priest JR. Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes. Circ Genom Precis Med 2023:e003968. [PMID: 37026454 DOI: 10.1161/circgen.122.003968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND Congenital heart disease (CHD) is highly heritable, but the power to identify inherited risk has been limited to analyses of common variants in small cohorts. METHODS We performed reimputation of 4 CHD cohorts (n=55 342) to the TOPMed reference panel (freeze 5), permitting meta-analysis of 14 784 017 variants including 6 035 962 rare variants of high imputation quality as validated by whole genome sequencing. RESULTS Meta-analysis identified 16 novel loci, including 12 rare variants, which displayed moderate or large effect sizes (median odds ratio, 3.02) for 4 separate CHD categories. Analyses of chromatin structure link 13 of the genome-wide significant loci to key genes in cardiac development; rs373447426 (minor allele frequency, 0.003 [odds ratio, 3.37 for Conotruncal heart disease]; P=1.49×10-8) is predicted to disrupt chromatin structure for 2 nearby genes BDH1 and DLG1 involved in Conotruncal development. A lead variant rs189203952 (minor allele frequency, 0.01 [odds ratio, 2.4 for left ventricular outflow tract obstruction]; P=1.46×10-8) is predicted to disrupt the binding sites of 4 transcription factors known to participate in cardiac development in the promoter of SPAG9. A tissue-specific model of chromatin conformation suggests that common variant rs78256848 (minor allele frequency, 0.11 [odds ratio, 1.4 for Conotruncal heart disease]; P=2.6×10-8) physically interacts with NCAM1 (PFDR=1.86×10-27), a neural adhesion molecule acting in cardiac development. Importantly, while each individual malformation displayed substantial heritability (observed h2 ranging from 0.26 for complex malformations to 0.37 for left ventricular outflow tract obstructive disease) the risk for different CHD malformations appeared to be separate, without genetic correlation measured by linkage disequilibrium score regression or regional colocalization. CONCLUSIONS We describe a set of rare noncoding variants conferring significant risk for individual heart malformations which are linked to genes governing cardiac development. These results illustrate that the oligogenic basis of CHD and significant heritability may be linked to rare variants outside protein-coding regions conferring substantial risk for individual categories of cardiac malformation.
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Affiliation(s)
- Mengyao Yu
- Department of Pediatrics, Stanford University School of Medicine. (M.Y., M.A., A.C.-P., C.T., J.R.P.)
| | - Matthew Aguirre
- Department of Pediatrics, Stanford University School of Medicine. (M.Y., M.A., A.C.-P., C.T., J.R.P.)
- Department of Biomedical Data Science, Stanford University, CA (M.A.)
| | - Meiwen Jia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Germany (M.J., B.M.-M.)
| | - Ketrin Gjoni
- Gladstone Institutes; University of California San Francisco (K.G., C.T., D.S., K.S.P.)
| | - Aldo Cordova-Palomera
- Department of Pediatrics, Stanford University School of Medicine. (M.Y., M.A., A.C.-P., C.T., J.R.P.)
| | - Chad Munger
- Department of Genetics, Stanford University School of Medicine. (C.M., D.A., X.R.M., J.M.E.)
| | - Dulguun Amgalan
- Department of Genetics, Stanford University School of Medicine. (C.M., D.A., X.R.M., J.M.E.)
| | - X Rosa Ma
- Department of Genetics, Stanford University School of Medicine. (C.M., D.A., X.R.M., J.M.E.)
| | - Alexandre Pereira
- Department of Genetics, Harvard University, Cambridge, MA (A.P., C.S., J.S.)
| | - Catherine Tcheandjieu
- Department of Pediatrics, Stanford University School of Medicine. (M.Y., M.A., A.C.-P., C.T., J.R.P.)
- Gladstone Institutes; University of California San Francisco (K.G., C.T., D.S., K.S.P.)
| | - Christine Seidman
- Department of Genetics, Harvard University, Cambridge, MA (A.P., C.S., J.S.)
| | - Jonathan Seidman
- Department of Genetics, Harvard University, Cambridge, MA (A.P., C.S., J.S.)
| | | | - Wendy Chung
- Department of Pediatrics, Columbia University, NY (W.C.)
| | | | - Deepak Srivastava
- Gladstone Institutes; University of California San Francisco (K.G., C.T., D.S., K.S.P.)
| | - Ruth J F Loos
- Icahn School of Medicine at Mount Sinai, NY (R.J.F.L., N.C.)
| | - Nathalie Chami
- Icahn School of Medicine at Mount Sinai, NY (R.J.F.L., N.C.)
| | - Heather Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom (H.C.)
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich & Technical University of Munich, School of Medicine & Health, Germany (M.D., H.L., M.K.)
| | - Bertram Mueller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Germany (M.J., B.M.-M.)
| | - Harald Lahm
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich & Technical University of Munich, School of Medicine & Health, Germany (M.D., H.L., M.K.)
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich & Technical University of Munich, School of Medicine & Health, Germany (M.D., H.L., M.K.)
- Department of Cardiac Surgery, Yale School of Medicine, New Haven, CT (M.K.)
| | - Katherine S Pollard
- Gladstone Institutes; University of California San Francisco (K.G., C.T., D.S., K.S.P.)
- Chan Zuckerberg Biohub, San Francisco (K.S.P.)
| | - Jesse M Engreitz
- Department of Genetics, Stanford University School of Medicine. (C.M., D.A., X.R.M., J.M.E.)
- Basic Sciences and Engineering (BASE) Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA (J.M.E.)
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Faculty of Medicine, University ersité de Montréal (S.A.G.T.)
- Montreal Heart Institute, Montreal, Quebec, Canada (S.A.G.T.)
| | - Bruce D Gelb
- The Mindich Child Health & Development Institute at the Hess Center for Science & Medicine at Mount Sinai, NY (B.D.G.)
| | - James R Priest
- Department of Pediatrics, Stanford University School of Medicine. (M.Y., M.A., A.C.-P., C.T., J.R.P.)
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Otsu M, Tanabe Y, Iwakiri A, Arima K, Uchiyama A, Yamamoto M, Ohtani S, Endo H, Komoto M, Miyazaki K. A report on a modified protocol for flow cytometry-based assessment of blood group erythrocyte antigens potentially suitable for analysis of weak ABO subgroups. Transfusion 2023; 63:463-469. [PMID: 36597800 DOI: 10.1111/trf.17239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Flow cytometry (FC) has proven its utility in scrutinizing AB antigen expression in red blood cells (RBCs), cooperating with serological tests for accurate blood group typing. However, technical difficulties may impair the characterization of weak ABO subtypes when background noises appear at non-negligible levels. STUDY DESIGN AND METHODS We sought to establish an FC method that could prevent antibody-induced hemagglutination and an increase in cellular autofluorescence, two major issues inherent to RBC-FC analysis of AB expression. We optimized fixatives, multicolor-staining protocols, and sequential gating strategies. Blood samples from weak ABO subtype cases, Bm and Ael , were analyzed with the established protocol. RESULTS The optimized mixture of glutaraldehyde and formaldehyde successfully generated fixed RBCs resistant to agglutination while maintaining low autofluorescence. These features allowed co-staining of leukocyte- and erythrocyte-markers, which enabled sequential gating strategies facilitating the precise AB antigen analysis in purely single RBCs with minimum background noises. By the established FC analysis, we could detect in the Bm sample a small RBC population exhibiting weak B antigen expression. The assay also proved it feasible to identify a small population (0.04%) of RBCs weakly expressing the A antigen in the Ael sample confirmed as harboring a rare c.816dupG ABO variant allele. CONCLUSION The RBC-FC analysis described here allows the detection of AB antigens weakly expressed in RBCs while achieving minimum background noise levels in negative control samples. Overall, the modified protocol provides a quick and reliable assay valuable in transfusion medicine and is potentially applicable to the characterization of rare weak ABO variants.
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Affiliation(s)
- Makoto Otsu
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Japan
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Yuji Tanabe
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Ayako Iwakiri
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Kazuna Arima
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Anna Uchiyama
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Marina Yamamoto
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Shinichi Ohtani
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Japan
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Hiroshi Endo
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Mina Komoto
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
| | - Koji Miyazaki
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Japan
- Department of Clinical Laboratory, Kitasato University Hospital, Sagamihara, Japan
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Hajjej A, Abdrakhmanova S, Turganbekova A, Almawi WY. HLA allele and haplotype frequencies in Kazakhstani Russians and their relationship with other populations. HLA 2023; 101:249-261. [PMID: 36502279 DOI: 10.1111/tan.14937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/12/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
HLA class I and class II genotypes from 947 Kazakhstani individuals of Russian origin were analyzed for investigating their most likely origin. The results were compared with similar data from other Russians (East and West), and also Worldwide populations, using standard genetic distances, neighbor-joining dendrograms, correspondence and haplotype analysis. Of the five HLA loci analyzed (HLA-A, HLA-C, HLA-B, HLA-DRB1, and HLA-DQB1) genotyped, 216 HLA alleles were identified. The most frequent alleles were A*02:01 (26.5%), B*07:02 (11.1%), C*04:01 (13.5%) and C*06:02 (12.1%), DRB1*07:01 (13.8%) and DRB1*15:01 (12.2%), and DQB1*03:01 (19.7%). Significant linkage disequilibrium was noted between all HLA pairs. DRB1*15:01 ~ DQB1*06:02 (10.5%), B*07:02 ~ C*07:02 (10.0%), B*07:02 ~ DRB1*15:01 (6.3%), and A*01:01 ~ B*08:01 (4.5%) were the most frequent two-locus haplotypes identified. Subsequent analyses showed that Kazakhstani Russians were closely related to West Russia-residing populations (Northwest Slavic, Vologda, Chelyabinsk, Moscow), East Europeans (Belarus Brest, Ukraine, Poland) and Scandinavians (Swedish, Finns), but distinct from East Russia-residing populations (Tuvians, Siberians from Chukotka, Kamchatka, and Ulchi) and East Mediterraneans (Levantines, Turks, North Macedonians, Albanians), and East Asians (Koreans, Japanese, Taiwanese, Mongolians). These results are in accordance with historical data indicating that the Russians of central Asia originate mainly from European Russia during the migratory flow of 18th and 19th centuries.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan.,Faculty of Sciences, El-Manar University, Tunis, Tunisia
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Gulati A, Dahl NK, Hartung EA, Clark SL, Moudgil A, Goodwin J, Somlo S. Hypomorphic PKD1 Alleles Impact Disease Variability in Autosomal Dominant Polycystic Kidney Disease. Kidney360 2023; 4:387-392. [PMID: 36706243 PMCID: PMC10103195 DOI: 10.34067/kid.0000000000000064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) manifesting earlier than expected on the basis of family history can identify clinically tolerant PKD1 alleles with reduced expression. Hypomorphic PKD1 alleles can cause mild kidney disease or liver cysts in the absence of clinically manifest kidney involvement. The presented data highlight pleiotropic ADPKD clinical presentations and varying severity of kidney disease from PKD1 allele combinations.
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Affiliation(s)
- Ashima Gulati
- Division of Nephrology, Children's National Hospital, Washington, District of Columbia
- Children's National Research Institute, Washington, District of Columbia
| | - Neera K. Dahl
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Erum A. Hartung
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie L. Clark
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Asha Moudgil
- Division of Nephrology, Children's National Hospital, Washington, District of Columbia
| | - Julie Goodwin
- Division of Nephrology, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Stefan Somlo
- Section of Nephrology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
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Manini A, Casiraghi V, Brusati A, Maranzano A, Gentile F, Colombo E, Bonetti R, Peverelli S, Invernizzi S, Gentilini D, Messina S, Verde F, Poletti B, Fogh I, Morelli C, Silani V, Ratti A, Ticozzi N. Association of the risk factor UNC13A with survival and upper motor neuron involvement in amyotrophic lateral sclerosis. Front Aging Neurosci 2023; 15:1067954. [PMID: 36819716 PMCID: PMC9931189 DOI: 10.3389/fnagi.2023.1067954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Background The UNC13A gene is an established susceptibility locus for amyotrophic lateral sclerosis (ALS) and a determinant of shorter survival after disease onset, with up to 33.0 months difference in life expectancy for carriers of the rs12608932 risk genotype. However, its overall effect on other clinical features and ALS phenotypic variability is controversial. Methods Genotype data of the UNC13A rs12608932 SNP (A-major allele; C-minor allele) was obtained from a cohort of 972 ALS patients. Demographic and clinical variables were collected, including cognitive and behavioral profiles, evaluated through the Edinburgh Cognitive and Behavioral ALS Screen (ECAS) - Italian version and the Frontal Behavioral Inventory (FBI); upper and lower motor neuron involvement, assessed by the Penn Upper Motor Neuron Score (PUMNS) and the Lower Motor Neuron Score (LMNS)/Medical Research Council (MRC) scores, respectively; the ALS Functional Rating Scale Revised (ALSFRS-R) score at evaluation and progression rate; age and site of onset; survival. The comparison between the three rs12608932 genotypes (AA, AC, and CC) was performed using the additive, dominant, and recessive genetic models. Results The rs12608932 minor allele frequency was 0.31 in our ALS cohort, in comparison to 0.33-0.41 reported in other Caucasian ALS populations. Carriers of at least one minor C allele (AC + CC genotypes) had a shorter median survival than patients with the wild-type AA genotype (-11.7 months, p = 0.013), even after adjusting for age and site of onset, C9orf72 mutational status and gender. Patients harboring at least one major A allele (AA + AC genotypes) and particularly those with the wild-type AA genotype showed a significantly higher PUMNS compared to CC carriers (p = 0.015 and padj = 0.037, respectively), thus indicating a more severe upper motor neuron involvement. Our analysis did not detect significant associations with all the other clinical parameters considered. Conclusion Overall, our findings confirm the role of UNC13A as a determinant of survival in ALS patients and show the association of this locus also with upper motor neuron involvement.
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Affiliation(s)
- Arianna Manini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Neurology Residency Program, Università degli Studi di Milano, Milan, Italy
| | - Valeria Casiraghi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Medical Biotechnology and Molecular Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alberto Brusati
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Brain and Behavioral Sciences, Università degli Studi di Pavia, Pavia, Italy
| | - Alessio Maranzano
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Neurology Residency Program, Università degli Studi di Milano, Milan, Italy
| | - Francesco Gentile
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Neurology Residency Program, Università degli Studi di Milano, Milan, Italy
| | - Eleonora Colombo
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Ruggero Bonetti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Neurology Residency Program, Università degli Studi di Milano, Milan, Italy
| | - Silvia Peverelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Sabrina Invernizzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, Università degli Studi di Pavia, Pavia, Italy,Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Stefano Messina
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Federico Verde
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Barbara Poletti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, United Kingdom
| | - Claudia Morelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Medical Biotechnology and Molecular Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy,*Correspondence: Nicola Ticozzi, ✉
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28
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Stroeks SLVM, van Beek D, Adriaens ME, Verdonschot JAJ. Titin Allelic Expression and Protein Processing Pathways in Early-Stage Dilated Cardiomyopathy Patients With Truncating Titin Variants. Circ Genom Precis Med 2023; 16:e003901. [PMID: 36716182 DOI: 10.1161/circgen.122.003901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sophie L V M Stroeks
- Department of Cardiology, Cardiovascular Research Institute (CARIM), Maastricht, The Netherlands (S.L.V.M.S., J.A.J.V.).,KU Leuven, Cardiovascular Sciences, Belgium (S.L.V.M.S.)
| | - Daan van Beek
- Maastricht Centre for Systems Biology, Maastricht University, The Netherlands (D.v.B., M.E.A.)
| | - Michiel E Adriaens
- Maastricht Centre for Systems Biology, Maastricht University, The Netherlands (D.v.B., M.E.A.)
| | - Job A J Verdonschot
- Department of Cardiology, Cardiovascular Research Institute (CARIM), Maastricht, The Netherlands (S.L.V.M.S., J.A.J.V.).,Department of Clinical Genetics, Maastricht University Medical Center, The Netherlands (J.A.J.V.)
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29
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Milani A, Panozzo S, Pinton S, Danielis RA, Sattin M, Scarabel L. Diversity and Spread of Acetolactate Synthase Allelic Variants at Position 574 Endowing Resistance in Amaranthus hybridus in Italy. Plants (Basel) 2023; 12:332. [PMID: 36679045 PMCID: PMC9860533 DOI: 10.3390/plants12020332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Poor control of Amaranthus spp. with herbicides inhibiting acetolactate synthase (ALS) has been observed for several years in soybean fields in north-eastern Italy, but to date only a few ALS-resistant populations have been confirmed. An extensive sampling of putatively resistant Amaranthus accessions was completed in the Friuli Venezia Giulia region, across an arable land area of about 3000 km2. In total, 58 accessions were tested to confirm their resistance status, recognize the Amaranthus species, identify the mutant ALS alleles endowing the resistance and determine the efficacy of 3 pre-emergence herbicides. Most accessions resulted in cross-resistance to thifensulfuron-methyl and imazamox. Genomic DNA were extracted from single seeds with a newly developed protocol; an allele-specific PCR assay revealed the presence of the 574-leucine in 20 accessions, of the 574-methionine in 22, and of both alleles in 9 accessions. The two variants showed a different spatial distribution. All resistant populations were ascribed to A. hybridus. A. hybridus resistant to ALS herbicides is well-established in this Italian region and its resistance is due to two ALS mutant alleles. Metribuzin, clomazone and metobromuron can be used as alternative herbicides to be applied in pre-emergence and they should be integrated into the management strategies to limit the spread of resistance.
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Affiliation(s)
- Andrea Milani
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Silvia Panozzo
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Samuele Pinton
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Renato Antonio Danielis
- Regional Agency for Rural Development of Friuli Venezia Giulia (ERSA), 33050 Pozzuolo del Friuli, Italy
| | - Maurizio Sattin
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
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30
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Amin MM, Husada MS, Idaiani S, Effendy E, Nasution S, Purnama SD. The Effect of Interleukin-2 -330 T/G Polymorphism in People with Schizophrenia Among The Batak and Javanese Ethnic Groups. Med Arch 2023; 77:363-369. [PMID: 38299092 PMCID: PMC10825752 DOI: 10.5455/medarh.2023.77.363-369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/29/2023] [Indexed: 02/02/2024] Open
Abstract
Background Schizophrenia is a complex disorder involving multiple genes with mild to moderate effects and non-genetic risk factors such as environmental and psychological influences that alter brain chemistry. Significant reduction in interleukin-2 production by peripheral lymphocytes is an immunological finding replicated in schizophrenia across various countries. Investigations on the interleukin-2 -330 T/G polymorphism in people with schizophrenia (PWS) are still minimal, and the study location involves only a few countries with different results. Therefore, this study aims to examine the effect of interleukin-2 -330 T/G polymorphisms in people with schizophrenia among the Batak and Javanese ethnic groups in Indonesia, particularly in North Sumatra. Method This study used purposive non-probability sampling to recruit people with schizophrenia with 120 Batak and 120 Javanese subjects who were hospitalized at Prof. M. Ildrem Mental Hospital, Medan, Indonesia. The interleukin-2 -330 T/G polymorphism was examined by the PCR method. Result The results showed that the genotype frequency of the Batak people with schizophrenia is as follows: GG 11.7%, TG 53.3% and TT 35%. Furthermore, the group of Javanese people with schizophrenia is as follows: GG 23.3%, TG 44.2% and TT 32.5%. The OR for the genotypic comparison of GG was found to be 2.154 with 95% CI 0.992-4.678, p=0.053, while that of the TG genotype was 0.892 with 95% CI 0.505-1.574 and p=0.693. The T allele was higher than the G allele in Batak and Javanese ethnic groups, as demonstrated by p=0.713, OR=0.919 with 95% CI 0.641-1.318. Conclusion There is no statistically significant difference between the occurrence frequency of alleles. In addition, there is no significant relationship between the GG and the TG genotype of the interleukin-2 - 330T/G polymorphism in people with schizophrenia among the Batak and the Javanese ethnic groups.
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Affiliation(s)
- Mustafa M. Amin
- Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
| | | | - Sri Idaiani
- Centre of Preclinical and Clinical Medicine Research National Research and Innovation Agency
| | - Elmeida Effendy
- Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
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Vivekanandam R, Rajagopalan K, Jeevanandam M, Ganesan H, Jagannathan V, Selvan Christyraj JD, Kalimuthu K, Selvan Christyraj JRS, Mohan M. Designing of cytotoxic T lymphocyte-based multi-epitope vaccine against SARS-CoV2: a reverse vaccinology approach. J Biomol Struct Dyn 2022; 40:13711-13726. [PMID: 34696708 DOI: 10.1080/07391102.2021.1993338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV2 is a single-stranded RNA virus, gaining much attention after it out broke in China in December 2019. The virus rapidly spread to several countries around the world and caused severe respiratory illness to humans. Since the outbreak, researchers around the world have devoted maximum resources and effort to develop a potent vaccine that would offer protection to uninfected individuals against SARS-CoV2. Reverse vaccinology is a relatively new approach that thrives faster in vaccine research. In this study, we constructed Cytotoxic T Lymphocytes (CTL)-based multi-epitope vaccine using hybrid epitope prediction methods. A total of 121 immunogenic CTL epitopes were screened by various sequence-based prediction methods and docked with their respective HLA alleles using the AutoDock Vina v1.1.2. In all, 17 epitopes were selected based on their binding affinity, followed by the construction of multi-epitope vaccine by placing the appropriate linkers between the epitopes and tuberculosis heparin-binding hemagglutinin (HBHA) adjuvant. The final vaccine construct was modeled by the I-TASSER server and the best model was further validated by ERRAT, ProSA, and PROCHECK servers. Furthermore, the molecular interaction of the constructed vaccine with TLR4 was assessed by ClusPro 2.0 and PROtein binDIng enerGY prediction (PRODIGY) server. The immune simulation analysis confirms that the constructed vaccine was capable of inducing long-lasting memory T helper (Th) and CTL responses. Finally, the nucleotide sequence was codon-optimized by the JCAT tool and cloned into the pET21a (+) vector. The current results reveal that the candidate vaccine is capable of provoking robust CTL response against the SARS-CoV2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore, Tamilnadu, India
| | - Kamarajan Rajagopalan
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Madesh Jeevanandam
- Department of Biochemistry, PSG college of Arts and Science, Coimbatore, Tamilnadu, India
| | - Harsha Ganesan
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, Tamilnadu, India
| | - Vaishnavi Jagannathan
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, Tamilnadu, India
| | - Jackson Durairaj Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Kalishwaralal Kalimuthu
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Manikandan Mohan
- Vaxigen International Research Center Private Limited, Coimbatore, Tamilnadu, India.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
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Wang J, Yin Y, Gao H, Sheng L. Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch. Genes (Basel) 2022; 14:68. [PMID: 36672809 PMCID: PMC9859318 DOI: 10.3390/genes14010068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The cultivated strawberry (Fragaria × ananassa Duch.) is an important horticultural crop. The economic values of strawberry cultivars are decided by their fruit qualities including taste, color and aroma. The important role of MYB transcription factors in fruit quality regulation is recognized increasingly with the identification of MYB genes involved in metabolism. A total of 407 MYB genes of F. × ananassa (FaMYBs) were identified in the genome-wide scale and named according to subgenome locations. The 407 FaMYBs were clustered into 36 groups based on phylogenetic analysis. According to synteny analysis, whole genome duplication and segmental duplication contributed over 90% of the expansion of the FaMYBs family. A total of 101 FaMYB loci with 1-6 alleles were identified by the homologous gene groups on homologous chromosomes. The differentially expressed FaMYB profiles of three cultivars with different fruit quality and fruit ripe processes provided the 8 candidate loci involved in fruit quality regulation. In this experiment, 7, 5, and 4 FaMYBs were screeded as candidate genes involved in the regulation of metabolism/transportation of anthocyanins, sugars or organic acids and 4-hydroxy-2, 5-dimethyl-3(2H)-furanone, respectively. These results pointed out the key FaMYBs for further functional analysis of gene regulation of strawberry fruit quality and would be helpful in the clarification on ofe roles of MYBs in the metabolism of fruit crops.
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Affiliation(s)
| | | | | | - Lixia Sheng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Moyeh MN, Fankem SN, Ali IM, Sofeu D, Sandie SM, Njimoh DL, Ghogomu SM, Kimbi HK, Mbacham WF. Current status of 4-aminoquinoline resistance markers 18 years after cessation of chloroquine use for the treatment of uncomplicated falciparum malaria in the littoral coastline region of Cameroon. Pathog Glob Health 2022; 116:509-514. [PMID: 35357271 PMCID: PMC9639544 DOI: 10.1080/20477724.2022.2056674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The onset and rapid spread of chloroquine resistance and the introduction of amodiaquine for the treatment of uncomplicated malaria in Cameroon have influenced the proportion of Plasmodium falciparum sensitive and resistant alleles related to 4-aminoquinoline drugs. This study was undertaken to determine the prevalence of resistance markers to antimalarial 4-aminoquinolines in Douala in the Littoral Region, and Buea in the South West Region in June 2020. Dry blood spots were prepared from malaria microscopy positive cases and used for parasite DNA extraction by chelex-100 method. Plasmodium species identification was carried out by PCR amplification/agarose gel electrophoresis of 18srRNA. The Pfcrt and Pfmdr1 genes were amplified by PCR followed by restriction digestion. The prevalence of single nucleotide polymorphisms (SNPs) was compared between study sites and with previous studies carried out between 2003-2005 and 2009-2011 using the Chi square test. The results showed that Plasmodium falciparum was the dominant species occurring as mono-infections (84.6%). The wild type K76 allele of the Pfcrt gene was found in 74.9% of isolates while the wild N86, Y184 and D1246 alleles of the Pfmdr1 gene were found respectively in 87.2%, 89.6% and 100% of field isolates. The results showed a significant reduction in the mutant alleles compared to results obtained in 2003-2005 and 2009-2013. The KNYD haplotype was observed to be the most prevalent. The results indicated that there is a gradual erosion of the mutant Pfcrt and Pfmdr1 genotype and a gradual return to the sensitive P. falciparum genotype in Cameroon.
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Affiliation(s)
- Marcel Nyuylam Moyeh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
- MARCAD Program, The Biotechnology Centre, University of Yaoundé 1, BP 8094, Yaoundé, Centre Region, Cameroon
- Department of Chemical and Biological Engineering, School of Engineering, University of Bamenda, Bambili, North West Region
| | - Sandra Noukimi Fankem
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
| | - Innocent Mbulli Ali
- MARCAD Program, The Biotechnology Centre, University of Yaoundé 1, BP 8094, Yaoundé, Centre Region, Cameroon
- Department of Biochemistry, Faculty of Science, BP 67, University of Dschang. West Region, Cameroon
| | - Denis Sofeu
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
| | - Sorelle Mekachie Sandie
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
| | - Dieudonne Lemuh Njimoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, University of Buea, Buea South West Region, Cameroon
| | - Helen Kuokuo Kimbi
- Department of Zoology and Animal Physiology, University of Buea, Buea South West Region, Cameroon
- Department of Biomedical Sciences, The University of Bamenda, Bambili North West Region, Cameroon
| | - Wilfred Fon Mbacham
- MARCAD Program, The Biotechnology Centre, University of Yaoundé 1, BP 8094, Yaoundé, Centre Region, Cameroon
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Asenjo J, Moraru M, Al‐Akioui‐Sanz K, Altadill M, Muntasell A, López‐Botet M, Vilches C. Diversity of NKG2C genotypes in a European population: Conserved and recombinant haplotypes in the coding, promoter, and 3'-untranslated regions. HLA 2022; 100:469-478. [PMID: 35802353 PMCID: PMC9796621 DOI: 10.1111/tan.14734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 07/05/2022] [Indexed: 01/01/2023]
Abstract
NK cells monitor altered molecular patterns in tumors and infected cells through an ample array of receptors. Two families of evolutionarily distant receptors have converged to enable human NK cells to sense levels of HLA class I ligands, frequently abnormal in altered cells. Whilst different forms of polymorphism are a hallmark of killer-cell immunoglobulin-like receptors and their classic HLA-A, B, and C ligands, genetic diversity of killer-cell lectin-like receptors for the non-classical HLA-E (CD94/NKG2 heterodimers) is less conspicuous and has attracted less attention. A common pattern of diversification in both receptor families is evolution of pairs of inhibitory and activating homologs for a common ligand, the genes encoding activating receptors being more frequently affected by copy number variation (CNV). This is exemplified by the gene encoding the activating NKG2C subunit (KLRC2 or NKG2C), which marks an NK-cell subpopulation that differentiates or expands in response to cytomegalovirus. We have studied NKG2C diversity in 240 South European individuals, using polymerase chain reaction and sequencing methods to assess both gene CNV and single-nucleotide polymorphisms (SNPs) affecting its promoter, coding and 3'-untranslated (3'UT) regions. Sequence analysis revealed eight common SNPs-one in the promoter, two in the coding sequence, and five in the 3'UT region. These SNPs associate strongly with each other, forming three conserved extended haplotypes (frequencies: 0.456, 0.221, and 0.117). Homo- and heterozygous combination of these, together with complete gene deletion (0.175) and additional haplotypes with frequencies lower than 0.015, generate a diversity of NKG2C genotypes of potential immunological importance.
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Affiliation(s)
- Judit Asenjo
- Immunogenetics and Histocompatibility LabInstituto de Investigación Sanitaria Puerta de Hierro ‐ Segovia de AranaMadridSpain
| | - Manuela Moraru
- Immunogenetics and Histocompatibility LabInstituto de Investigación Sanitaria Puerta de Hierro ‐ Segovia de AranaMadridSpain
| | - Karima Al‐Akioui‐Sanz
- Immunogenetics and Histocompatibility LabInstituto de Investigación Sanitaria Puerta de Hierro ‐ Segovia de AranaMadridSpain
| | - Mireia Altadill
- Medicine and Life SciencesUniversity Pompeu FabraBarcelonaSpain
| | - Aura Muntasell
- Immunology, Department of PathologyHospital del Mar Medical Research Institute (IMIM)BarcelonaSpain,Department of Cell Biology, Physiology and ImmunologyUniversitat Autonòma de BarcelonaBellaterraCataloniaSpain
| | - Miguel López‐Botet
- Medicine and Life SciencesUniversity Pompeu FabraBarcelonaSpain,Immunology, Department of PathologyHospital del Mar Medical Research Institute (IMIM)BarcelonaSpain
| | - Carlos Vilches
- Immunogenetics and Histocompatibility LabInstituto de Investigación Sanitaria Puerta de Hierro ‐ Segovia de AranaMadridSpain
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Prasad N, Yadav B, Prakash S, Yadav D, Singh A, Gautam S, Bhadauria D, Kaul A, Patel MR, Behera MR, Kushwaha RS, Yachha M. Association of Human Leucocyte Antigen Polymorphism with Coronavirus Disease 19 in Renal Transplant Recipients. Vaccines (Basel) 2022; 10:1840. [PMID: 36366349 PMCID: PMC9697220 DOI: 10.3390/vaccines10111840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 08/30/2023] Open
Abstract
Human leucocyte antigens (HLAs) are highly polymorphic glycoproteins expressed at the surface of all nucleated cells. It is required for the SARS-CoV-2 peptide antigen presentation to immune cells for their effector response. However, polymorphism in HLA significantly impacts the binding of SARS-CoV-2 antigenic peptide to the HLA pocket and regulates immune activation. In this study, 514 renal transplant recipients (RTRs) were recruited from the outpatient department and categorized either into symptomatic (n = 173) or asymptomatic groups (n = 341) based on Coronavirus disease-19 (COVID-19) symptoms. The anti-SARS-CoV-2 spike protein-specific IgG antibody titer was measured by chemiluminescent microparticle immune-assay methods in 310 RTRs. The HLA details of 514 patients were retrieved from the electronic medical records and analyzed retrospectively. We found that HLA antigen allele A*24 was significantly associated with asymptomatic infection in 22.78%, HLA C*02 in 4.51%, DRB1*12 in 10.85%, and HLA DQA1*02 in 27.74% of RTRs. Whereas HLA A*29 in 3.46%, A*33 in 26.01%, B*13 in 10.40%, DRB1*10 in 4.62%, DRB1*15 in 39.30%, DRB1*30 in 1.15%, and DQA1*60 in 3.57% of RTRs were associated with symptomatic infection. HLA DRB1*13 and DRB1*15 were associated with moderate to severe degrees of COVID-19 disease. The seroconversion rate in asymptomatic patients was 118/137 (86.13%), had a median titer of 647.80 au/ml, compared to symptomatic patients 148/173 (85.54%) with a median titer of 400.00 au/ml, which was not significant between the two groups (P = 0.88 and 0.13). In conclusion, HLA alleles A*24, C*02, DRB1*12, and DQA1*02 were significantly associated with asymptomatic infection, and A*29, A*33, B*13, DRB1*10, DRB*15, and DRB1*30 were significantly associated with symptomatic infection. HLA DRB1*13 and DRB1*15 were associated with moderate to severe degrees of COVID-19 disease.
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Affiliation(s)
- Narayan Prasad
- Department of Nephrology and Renal Transplantation, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
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Crowl AA, Fritsch PW, Tiley GP, Lynch NP, Ranney TG, Ashrafi H, Manos PS. A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus). Am J Bot 2022; 109:1596-1606. [PMID: 36109839 DOI: 10.1002/ajb2.16065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries. METHODS We used flow cytometry to verify the ploidy of putative diploid taxa and a target-enrichment approach to obtain a genomic data set for phylogenetic analyses. RESULTS Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of V. boreale was consistently nested in the V. myrtilloides clade and V. caesariense was nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is implicated as having a homoploid hybrid origin. CONCLUSIONS This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.
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Affiliation(s)
- Andrew A Crowl
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107, USA
| | - George P Tiley
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | - Nathan P Lynch
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, 28759, USA
| | - Thomas G Ranney
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, 28759, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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Roy P, Sidney J, Lindestam Arlehamn CS, Phillips E, Mallal S, Suthahar SSA, Billitti M, Rubiro P, Marrama D, Drago F, Vallejo J, Suryawanshi V, Orecchioni M, Makings J, Kim PJ, McNamara CA, Peters B, Sette A, Ley K. Immunodominant MHC-II (Major Histocompatibility Complex II) Restricted Epitopes in Human Apolipoprotein B. Circ Res 2022; 131:258-276. [PMID: 35766025 PMCID: PMC9536649 DOI: 10.1161/circresaha.122.321116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND CD (cluster of differentiation) 4+ T-cell responses to APOB (apolipoprotein B) are well characterized in atherosclerotic mice and detectable in humans. CD4+ T cells recognize antigenic peptides displayed on highly polymorphic HLA (human leukocyte antigen)-II. Immunogenicity of individual APOB peptides is largely unknown in humans. Only 1 HLA-II-restricted epitope was validated using the DRB1*07:01-APOB3036-3050 tetramer. We hypothesized that human APOB may contain discrete immunodominant CD4+ T-cell epitopes that trigger atherosclerosis-related autoimmune responses in donors with diverse HLA alleles. METHODS We selected 20 APOB-derived peptides (APOB20) from an in silico screen and experimentally validated binding to the most commonly occurring human HLA-II alleles. We optimized a restimulation-based workflow to evaluate antigenicity of multiple candidate peptides in HLA-typed donors. This included activation-induced marker assay, intracellular cytokine staining, IFNγ (interferon gamma) enzyme-linked immunospot and cytometric bead array. High-throughput sequencing revealed TCR (T-cell receptor) clonalities of APOB-reactive CD4+ T cells. RESULTS Using stringent positive, negative, and crossover stimulation controls, we confirmed specificity of expansion-based protocols to detect CD4+ T cytokine responses to the APOB20 pool. Ex vivo assessment of AIM+CD4+ T cells revealed a statistically significant autoimmune response to APOB20 but not to a ubiquitously expressed negative control protein, actin. Resolution of CD4+ T responses to the level of individual peptides using IFNγ enzyme-linked immunospot led to the discovery of 6 immunodominant epitopes (APOB6) that triggered robust CD4+ T activation in most donors. APOB6-specific responding CD4+ T cells were enriched in unique expanded TCR clonotypes and preferentially expressed memory markers. Cytometric bead array analysis detected APOB6-induced secretion of both proinflammatory and regulatory cytokines. In clinical samples from patients with angiographically verified coronary artery disease, APOB6 stimulation induced higher activation and memory phenotypes and augmented secretion of proinflammatory cytokines TNF (tumor necrosis factor) and IFNγ, compared with patients with low coronary artery disease. CONCLUSIONS Using 3 cohorts, each with ≈20 donors, we discovered and validated 6 immunodominant, HLA-II-restricted APOB epitopes. The immune response to these APOB epitopes correlated with coronary artery disease severity.
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Affiliation(s)
- Payel Roy
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Sujit Silas Armstrong Suthahar
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Monica Billitti
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Daniel Marrama
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Fabrizio Drago
- Cardiovascular Research Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville
| | - Jenifer Vallejo
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Vasantika Suryawanshi
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Marco Orecchioni
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Jeffrey Makings
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Paul J. Kim
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Coleen A. McNamara
- Cardiovascular Research Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Klaus Ley
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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Matthews S, Levy PD. A sociogenomic paradigm to replace the racial paradigm. Per Med 2022; 19:377-382. [PMID: 35758011 DOI: 10.2217/pme-2021-0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Sajith Matthews
- Department of Internal Medicine, Division of General Medicine, Wayne State University, 4201 St Antoine Street, UHC 5C, Detroit, MI 48201, USA
| | - Phillip D Levy
- Department of Emergency Medicine & Integrative Biosciences Center, Wayne State University, Detroit, MI 48201, USA
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Karshovska E, Mohibullah R, Zhu M, Zahedi F, Thomas D, Magkrioti C, Geissler C, Megens RTA, Bianchini M, Nazari-Jahantigh M, Ferreirós N, Aidinis V, Schober A. ENPP2 (Endothelial Ectonucleotide Pyrophosphatase/Phosphodiesterase 2) Increases Atherosclerosis in Female and Male Mice. Arterioscler Thromb Vasc Biol 2022; 42:1023-1036. [PMID: 35708027 DOI: 10.1161/atvbaha.122.317682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Maladapted endothelial cells (ECs) secrete ENPP2 (ectonucleotide pyrophosphatase/phosphodiesterase 2; autotaxin)-a lysophospholipase D that generates lysophosphatidic acids (LPAs). ENPP2 derived from the arterial wall promotes atherogenic monocyte adhesion induced by generating LPAs, such as arachidonoyl-LPA (LPA20:4), from oxidized lipoproteins. Here, we aimed to determine the role of endothelial ENPP2 in the production of LPAs and atherosclerosis. METHODS We quantified atherosclerosis in mice harboring loxP-flanked Enpp2 alleles crossed with Apoe-/- mice expressing tamoxifen-inducible Cre recombinase under the control of the EC-specific bone marrow X kinase promoter after 12 weeks of high-fat diet feeding. RESULTS A tamoxifen-induced EC-specific Enpp2 knockout decreased atherosclerosis, accumulation of lesional macrophages, monocyte adhesion, and expression of endothelial CXCL (C-X-C motif chemokine ligand) 1 in male and female Apoe-/- mice. In vitro, ENPP2 mediated the mildly oxidized LDL (low-density lipoprotein)-induced expression of CXCL1 in aortic ECs by generating LPA20:4, palmitoyl-LPA (LPA16:0), and oleoyl-LPA (LPA18:1). ENPP2 and its activity were detected on the endothelial surface by confocal imaging. The expression of endothelial Enpp2 established a strong correlation between the plasma levels of LPA16:0, stearoyl-LPA (LPA18:0), and LPA18:1 and plaque size and a strong negative correlation between the LPA levels and ENPP2 activity in the plasma. Moreover, endothelial Enpp2 knockout increased the weight of high-fat diet-fed male Apoe-/- mice. CONCLUSIONS We demonstrated that the expression of ENPP2 in ECs promotes atherosclerosis and endothelial inflammation in a sex-independent manner. This might be due to the generation of LPA20:4, LPA16:0, and LPA18:1 from mildly oxidized lipoproteins on the endothelial surface.
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Affiliation(s)
- Ela Karshovska
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.)
| | - Rokia Mohibullah
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.)
| | - Mengyu Zhu
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.).,Cardiovascular Research Institute Maastricht, Maastricht University, the Netherlands (M.Z., R.T.A.M.)
| | - Farima Zahedi
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.).,Now with Department of Biomedical Science and Mari Lowe Center for Comparative Oncology, University of Pennsylvania, Philadelphia (F.Z.)
| | - Dominique Thomas
- Institute of Clinical Pharmacology, Johann Wolfgang Goethe-University, Frankfurt, Germany (D.T., N.F.).,Fraunhofer Institute for Translational Medicine and Pharmacology, Frankfurt, Germany (D.T.)
| | - Christiana Magkrioti
- Division of Immunology, Biomedical Science Research, Center Alexander Fleming, Athens, Greece (C.M., V.A.)
| | - Claudia Geissler
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.)
| | - Remco T A Megens
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.).,Cardiovascular Research Institute Maastricht, Maastricht University, the Netherlands (M.Z., R.T.A.M.)
| | - Mariaelvy Bianchini
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.)
| | - Maliheh Nazari-Jahantigh
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.).,German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Germany (M.N.-J., A.S.)
| | - Nerea Ferreirós
- Institute of Clinical Pharmacology, Johann Wolfgang Goethe-University, Frankfurt, Germany (D.T., N.F.)
| | - Vassilis Aidinis
- Division of Immunology, Biomedical Science Research, Center Alexander Fleming, Athens, Greece (C.M., V.A.)
| | - Andreas Schober
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, Munich, Germany (E.K., R.M., M.Z., F.Z., C.G., R.T.A.M., M.B., M.N.-J., A.S.).,German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Germany (M.N.-J., A.S.)
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Mekata H, Yamamoto M. Single-Nucleotide Polymorphism on Spermatogenesis Associated 16 Gene-Coding Region Affecting Bovine Leukemia Virus Proviral Load. Vet Sci 2022; 9. [PMID: 35737328 DOI: 10.3390/vetsci9060275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Bovine leukemia virus (BLV) is an etiological agent of malignant lymphoma in cattle and is endemic in many cattle-breeding countries. Thus, the development of cattle genetically resistant to BLV is desirable. The purpose of this study was to identify novel single-nucleotide polymorphisms (SNPs) related to resistance to BLV. A total of 146 DNA samples from cattle with high BLV proviral loads (PVLs) and 142 samples from cattle with low PVLs were used for a genome-wide association study (GWAS). For the verification of the GWAS results, an additional 1342 and 456 DNA samples from BLV-infected Japanese Black and Holstein cattle, respectively, were used for an SNP genotyping PCR to compare the genotypes for the identified SNPs and PVLs. An SNP located on the spermatogenesis associated 16 (SPATA16)-coding region on bovine chromosome 1 was found to exceed the moderate threshold (p < 1.0 × 10−5) in the Additive and Dominant models of the GWAS. The SNP genotyping PCR revealed that the median values of the PVL were 1278 copies/50 ng of genomic DNA for the major homozygous, 843 for the heterozygous, and 621 for the minor homozygous genotypes in the Japanese Black cattle (p < 0.0001). A similar tendency was also observed in the Holstein cattle. We found that cattle with the minor allele for this SNP showed 20−25% lower PVLs. Although the mechanisms through which this SNP impacts the PVL remain unknown, we found a novel SNP related to BLV resistance located on the SPATA16 gene-coding region on bovine chromosome 1.
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Agbla JM, Esona MD, Jaimes J, Gautam R, Agbankpé AJ, Katz E, Dougnon TV, Capo-Chichi A, Ouedraogo N, Razack O, Bankolé HS, Bowen MD. Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018. Virus Res 2022;:198715. [PMID: 35247484 DOI: 10.1016/j.virusres.2022.198715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Species A Rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016-2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3=1 new allele and G12=2 new alleles) and VP4 (P[4]=1 new allele and P[6]=2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.
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42
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McLean BS, Bell KC, Cook JA. SNP-based Phylogenomic Inference in Holarctic Ground Squirrels (Urocitellus). Mol Phylogenet Evol 2022; 169:107396. [PMID: 35031463 DOI: 10.1016/j.ympev.2022.107396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022]
Abstract
Resolution of rapid evolutionary radiations requires harvesting maximal signal from phylogenomic datasets. However, studies of non-model clades often target conserved loci that are characterized by reduced information content, which can negatively affect gene tree precision and species tree accuracy. Single nucleotide polymorphism (SNP)-based methods are an underutilized but potentially valuable tool for estimating phylogeny and divergence times because they do not rely on resolved gene trees, allowing information from many or all variant loci to be leveraged in species tree reconstruction. We evaluated the utility of SNP-based methods in resolving phylogeny of Holarctic ground squirrels (Urocitellus), a radiation that has been difficult to disentangle, even in prior phylogenomic studies. We inferred phylogeny from a dataset of >3,000 ultraconserved element loci (UCEs) using two methods (SNAPP, SVDquartets) and compared our results with a new mitogenome phylogeny. We also systematically evaluated how phasing of UCEs improves per-locus information content, and inference of topology and other parameters within each of these SNP-based methods. Phasing improved topological resolution and branch length estimation at shallow levels (within species complexes), but less so at deeper levels, likely reflecting true uncertainty due to ancestral polymorphisms segregating in these rapidly diverging lineages. We resolved several key clades in Urocitellus and present targeted opportunities for future phylogenomic inquiry. Our results extend the roadmap for use of SNPs to address vertebrate radiations and support comparative analyses at multiple temporal scales.
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Affiliation(s)
- Bryan S McLean
- University of North Carolina Greensboro, Department of Biology, Greensboro, NC 27402 USA.
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, Department of Mammalogy, Los Angeles, CA 90007 USA.
| | - Joseph A Cook
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM 87131 USA.
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Abstract
Genome-wide association studies identified various loci associated with periodontal diseases, but assigning causal alleles remains difficult. Likewise, the generation of biological meaning underlying a statistical association has been challenging. Here, we characterized the genetic association at the gene ST8SIA1 that increases the risk for severe periodontitis in smokers. We used CRISPR/dCas9 activation and RNA-sequencing to identify genetic interaction partners of ST8SIA1 and to determine its function in the cell. We used reporter gene assays to identify regulatory elements at the associated single-nucleotide polymorphisms (SNPs) and to determine effect directions and allele-specific changes of enhancer activity. Antibody electrophoretic mobility shift assays proved allele-specific transcription factor binding at the putative causal SNPs. We found the reported periodontitis risk gene ABCA1 as the top upregulated gene following ST8SIA1 activation. Gene set enrichment analysis showed highest effects on integrin cell surface interactions (area under the curve [AUC] = 0.85; q = 4.9 × 10-6) and cell cycle regulation (AUC = 0.89; q = 1.6 × 10-5). We identified 2 associated repressor elements in the introns of ST8SIA1 that bind the transcriptional repressor BACH1. The putative causative variant rs2012722 decreased BACH1 binding by 40%. We also pinpointed ST8SIA1 as the target gene of the association. ST8SIA1 inhibits cell adhesion with extracellular matrix proteins, integrins, and cell cycle, as well as enhances apoptosis. Likewise, tobacco smoke reportedly results in an inhibition of cell adhesion and a decrease in integrin-positive cells and cell growth. We conclude that impaired ST8SIA1 repression, independently caused by reduced BACH1 binding at the effect T allele, as well as by tobacco smoke, contributes to higher ST8SIA1 levels, and in smokers who carry the effect T allele, both factors would be additive with damaging effects on the gingival barrier integrity. The activity of ST8SIA1 is also linked with the periodontitis risk gene ABCA1.
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Affiliation(s)
- A. Chopra
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - R. Mueller
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - J. Weiner
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - J. Rosowski
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - H. Dommisch
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - E. Grohmann
- Department of Microbiology, Faculty of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, Berlin, Germany
| | - A.S. Schaefer
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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44
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Lyzenga WJ, Kagale S. Wheat improvement using genome editing technology. Biotechniques 2021; 71:577-9. [PMID: 34809487 DOI: 10.2144/btn-2021-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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45
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Schwartz JC, Maccari G, Heimeier D, Hammond JA. Highly-contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I. HLA 2021; 99:167-182. [PMID: 34802191 DOI: 10.1111/tan.14494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3' end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3' coding sequence, we identified distinct subgroups of BoLA-3 and BoLA-6 that represent distinct genetic loci. We further examined allele-specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, UK.,Anthony Nolan Research Institute, London, UK
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46
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Stelet VN, Cita RF, Mendes MF, Romero M, Abdelhay E. The novel HLA-DQB1*05:240 allele was likely generated by recombination between DQB1*05:01 and DQB1*03:02. HLA 2021; 99:144-145. [PMID: 34418318 DOI: 10.1111/tan.14418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Identification of the novel HLA-DQB1*05:240 allele that differs from HLA-DQB1*05:01:09 at three positions in exon 2.
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Affiliation(s)
- Vinícius N Stelet
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Rafael F Cita
- Transplant Immunology Laboratory, Pio XII Foundation, Barretos, Brazil
| | | | - Matilde Romero
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Eliana Abdelhay
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
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Güere ME, Våge J, Tharaldsen H, Kvie KS, Bårdsen BJ, Benestad SL, Vikøren T, Madslien K, Rolandsen CM, Tranulis MA, Røed KH. Chronic wasting disease in Norway-A survey of prion protein gene variation among cervids. Transbound Emerg Dis 2021; 69:e20-e31. [PMID: 34346562 DOI: 10.1111/tbed.14258] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022]
Abstract
Susceptibility of cervids to Chronic Wasting Disease (CWD), a prion disease, can be modulated by variations in the prion protein gene (PRNP), encoding the cellular prion protein (PrPC ). In prion diseases, PrPC is conformationally converted to pathogenic conformers (PrPSc ), aggregates of which comprise infectious prions. CWD has recently been observed in its contagious form in Norwegian reindeer (Rangifer tarandus) and in novel, potentially sporadic forms, here called 'atypical CWD', in moose (Alces alces) and red deer (Cervus elaphus). To estimate relative susceptibility of different Norwegian cervid species to CWD, their non-synonymous PRNP variants were analyzed. In reindeer, seven PRNP alleles were observed and in red deer and moose two alleles were present, whereas roe deer (Capreolus capreolus) PRNP was monomorphic. One 'archetypal' PRNP allele associated with susceptibility was common to all four cervid species. The distribution of PRNP alleles differed between wild and semi-domesticated reindeer, with alleles associated with a high susceptibility occurring, on average, above 55% in wild reindeer and below 20% in semi-domesticated reindeer. This difference may reflect the diverse origins of the populations and/or selection processes during domestication and breeding. Overall, PRNP genetic data indicate considerable susceptibility to CWD among Norwegian cervids and suggest that PRNP homozygosity may be a risk factor for the atypical CWD observed in moose. The CWD isolates found in the Norwegian cervid species differ from those previously found in Canada and USA. Our study provides an overview of the PRNP genetics in populations exposed to these emerging strains that will provide a basis for understanding these strains' dynamics in relation to PRNP variability.
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Affiliation(s)
- Mariella Evelyn Güere
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Jørn Våge
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Helene Tharaldsen
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Kjersti Sternang Kvie
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Bård-Jørgen Bårdsen
- Arctic Ecology Department, Fram Centre, Norwegian Institute for Nature Research, Tromsø, Norway
| | | | - Turid Vikøren
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Knut Madslien
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Christer Moe Rolandsen
- Terrestrial Ecology Department, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Michael Andreas Tranulis
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Knut Håkon Røed
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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48
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Al-Akioui-Sanz K, Moraru M, Vilches C. A simple genotyping method for CD247 3'-untranslated region polymorphism rs1052231 and characterization of a reference cell panel. HLA 2021; 98:218-222. [PMID: 34233083 PMCID: PMC9291556 DOI: 10.1111/tan.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
CD247 (or CD3‐ζ chain) is an essential adaptor and signal‐transducing molecule of the T‐cell antigen receptor (TCR) complex, and it also couples to NK‐cell activating receptors such as NKp46, NKp30 and CD16A (FcγRIII). Noncoding sequence polymorphisms and variations in CD247 expression, a tightly regulated process, have been related with an altered immune response in multiple health conditions. A single nucleotide polymorphism (T > A) at nucleotide 844 of the CD247 3′‐untranslated region, rs1052231, has been related with lower CD247 gene expression and it has been investigated as a potential biomarker of autoimmune disease. We present here a simple, accurate, reliable, time‐efficient, and cost‐effective method for CD247‐rs1052231 genotyping. Using this method, based on polymerase chain reaction with confronting two‐pair primers (PCR‐CTPP), we have also characterized the CD247‐rs1052231 genotypes in a panel of worldwide available cell lines, which should facilitate study of the role of this polymorphism in immunity and human health.
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Affiliation(s)
- Karima Al-Akioui-Sanz
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Manuela Moraru
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Carlos Vilches
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
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49
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Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets. Appl Plant Sci 2021; 9:APS311441. [PMID: 34336402 PMCID: PMC8312746 DOI: 10.1002/aps3.11441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 05/24/2023]
Abstract
PREMISE Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.
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Affiliation(s)
- Lars Nauheimer
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Nicholas Weigner
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Elizabeth Joyce
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Charles Clarke
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Cairns Botanic GardensCollins AvenueEdge HillQueensland4870Australia
| | - Katharina Nargar
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- National Research Collections AustraliaCommonwealth Industrial and Scientific Research Organisation (CSIRO)GPO Box 1700CanberraAustralian Capital Territory2601Australia
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50
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Abstract
[Figure: see text].
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Affiliation(s)
- Qiongxin Wang
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center (Q.W., S.W., Z.S.)
| | - Shirley Wang
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center (Q.W., S.W., Z.S.).,Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Memphis (S.W., Z.S.)
| | - Zhongjie Sun
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center (Q.W., S.W., Z.S.).,Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Memphis (S.W., Z.S.)
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