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Zhang K, Wang S, Qiu Y, Bai B, Zhang Q, Xie X. Retrospective studies and quantitative proteomics reveal that abnormal expression of blood pressure, blood lipids, and coagulation related proteins is associated with hypospadias. Hum Genet 2024:10.1007/s00439-024-02676-z. [PMID: 38850429 DOI: 10.1007/s00439-024-02676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/04/2024] [Indexed: 06/10/2024]
Abstract
Hypospadias refers to the abnormal position of the male urethral orifice, which not only leads to urination disorder but also causes sexual dysfunction in adulthood. However, the complex and diverse pathogenic factors of hypospadias are still unclear. To study the pathogenesis and prognosis of hypospadias, we counted the serological indexes of children with hypospadias, and found that sSBP, TC and LDL increased in children with mild, moderate and severe hypospadias. Subsequently, we used quantitative proteomics to find differential proteins in mild, moderate and severe hypospadias. After bioinformatics analysis and biochemical experiments on the screened DEPs, we found that the expression of proteins related to immune inflammation, coagulation, blood pressure and inflammation, and blood lipid were differential expressed in the prepuce tissue of children with hypospadias. We further confirmed that the proteins FGB, FGG, SERPINA1, and AGT involved in the angiotensin system, cholesterol metabolism, and coagulation were significantly up-regulated by biochemical experiments. In particular, the AGT protein of the angiotensin system involved in blood pressure regulation, we have shown that it increases with the severity of hypospadias. This study suggests that children with hypospadias are more likely to suffer from hyperlipidemia and cardiovascular disease (CVD). Our findings provide a theoretical basis for early monitoring of blood lipids and blood pressure to prevent CVD in children with hypospadias.
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Affiliation(s)
- Kexin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shengxiong Wang
- Department of Urology, Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Ying Qiu
- Department of Urology, Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Baoling Bai
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Qin Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Xianghui Xie
- Department of Urology, Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, 100020, China.
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2
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Pokrovac I, Rohner N, Pezer Ž. The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization. Mol Ecol 2024; 33:e17339. [PMID: 38556927 DOI: 10.1111/mec.17339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.
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Affiliation(s)
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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3
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Soejima M, Koda Y. Identification and Diagnosis of Complete Haptoglobin Gene Deletion, One of the Genes Responsible for Adverse Posttransfusion Reactions. Biomedicines 2024; 12:790. [PMID: 38672145 PMCID: PMC11048176 DOI: 10.3390/biomedicines12040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Allergic reactions are the most frequent adverse events in blood transfusion, and anaphylactic shock, although less frequent, is systemic and serious. The cause of allergic reactions to blood transfusions are largely unknown, but deficiencies in serum proteins such as haptoglobin (Hp) can lead to anaphylactic shock. A complete deletion of the haptoglobin gene (HPdel) was first identified in families with anomalous inheritance and then verified as a genetic variant that can cause anaphylactic shock because homozygotes for HPdel have complete Hp deficiency. Thereby, they may produce antibodies against Hp from blood transfusions. HPdel is found in East and Southeast Asian populations, with a frequency of approximately 0.9% to 4%, but not in other populations. Diagnosis of Hp deficiency due to HPdel prior to transfusion is advisable because severe adverse reactions can be prevented by washing the red blood cells and/or platelets with saline or by administering plasma products obtained from an Hp-deficient donor pool. This review outlines the background of the identification of HPdel and several genetic and immunological methods developed for diagnosing Hp deficiency caused by HPdel.
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Affiliation(s)
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan;
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4
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Mohsen Y, Shami A, Edsfeldt A, Sun J, Gonçalves I. Haptoglobin Gene Polymorphism Is Associated With Lower Postoperative Cardiovascular Risk in Carotid Stenosis Patients. J Stroke 2024; 26:125-128. [PMID: 38246719 PMCID: PMC10850447 DOI: 10.5853/jos.2023.03349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024] Open
Affiliation(s)
- Yazan Mohsen
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Electrophysiology and Rhythmology, Hospital Porz am Rhein, Cologne, Germany
| | - Annelie Shami
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Andreas Edsfeldt
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Jiangming Sun
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Isabel Gonçalves
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden
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5
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Margoliash J, Fuchs S, Li Y, Zhang X, Massarat A, Goren A, Gymrek M. Polymorphic short tandem repeats make widespread contributions to blood and serum traits. CELL GENOMICS 2023; 3:100458. [PMID: 38116119 PMCID: PMC10726533 DOI: 10.1016/j.xgen.2023.100458] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/09/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023]
Abstract
Short tandem repeats (STRs) are genomic regions consisting of repeated sequences of 1-6 bp in succession. Single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) do not fully capture STR effects. To study these effects, we imputed 445,720 STRs into genotype arrays from 408,153 White British UK Biobank participants and tested for association with 44 blood phenotypes. Using two fine-mapping methods, we identify 119 candidate causal STR-trait associations and estimate that STRs account for 5.2%-7.6% of causal variants identifiable from GWASs for these traits. These are among the strongest associations for multiple phenotypes, including a coding CTG repeat associated with apolipoprotein B levels, a promoter CGG repeat with platelet traits, and an intronic poly(A) repeat with mean platelet volume. Our study suggests that STRs make widespread contributions to complex traits, provides stringently selected candidate causal STRs, and demonstrates the need to consider a more complete view of genetic variation in GWASs.
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Affiliation(s)
- Jonathan Margoliash
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shai Fuchs
- Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Yang Li
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuan Zhang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arya Massarat
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alon Goren
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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6
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Bai H, Naj AC, Benchek P, Dumitrescu L, Hohman T, Hamilton-Nelson K, Kallianpur AR, Griswold AJ, Vardarajan B, Martin ER, Beecham GW, Below JE, Schellenberg G, Mayeux R, Farrer L, Pericak-Vance MA, Haines JL, Bush WS. A haptoglobin (HP) structural variant alters the effect of APOE alleles on Alzheimer's disease. Alzheimers Dement 2023; 19:4886-4895. [PMID: 37051669 DOI: 10.1002/alz.13050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND Haptoglobin (HP) is an antioxidant of apolipoprotein E (APOE), and previous reports have shown HP binds with APOE and amyloid beta (Aβ) to aid its clearance. A common structural variant of the HP gene distinguishes it into two alleles: HP1 and HP2. METHODS HP genotypes were imputed in 29 cohorts from the Alzheimer's Disease Genetics Consortium (N = 20,512). Associations between the HP polymorphism and Alzheimer's disease (AD) risk and age of onset through APOE interactions were investigated using regression models. RESULTS The HP polymorphism significantly impacts AD risk in European-descent individuals (and in meta-analysis with African-descent individuals) by modifying both the protective effect of APOE ε2 and the detrimental effect of APOE ε4. The effect is particularly significant among APOE ε4 carriers. DISCUSSION The effect modification of APOE by HP suggests adjustment and/or stratification by HP genotype is warranted when APOE risk is considered. Our findings also provided directions for further investigations on potential mechanisms behind this association.
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Affiliation(s)
- Haimeng Bai
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Systems Biology and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Asha R Kallianpur
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
- Department of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Badri Vardarajan
- Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard Mayeux
- Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Lindsay Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | | | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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7
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Liu Z, Duan T, Zhang Y, Weng S, Xu H, Ren Y, Zhang Z, Han X. Radiogenomics: a key component of precision cancer medicine. Br J Cancer 2023; 129:741-753. [PMID: 37414827 PMCID: PMC10449908 DOI: 10.1038/s41416-023-02317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/02/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Radiogenomics, focusing on the relationship between genomics and imaging phenotypes, has been widely applied to address tumour heterogeneity and predict immune responsiveness and progression. It is an inevitable consequence of current trends in precision medicine, as radiogenomics costs less than traditional genetic sequencing and provides access to whole-tumour information rather than limited biopsy specimens. By providing voxel-by-voxel genetic information, radiogenomics can allow tailored therapy targeting a complete, heterogeneous tumour or set of tumours. In addition to quantifying lesion characteristics, radiogenomics can also be used to distinguish benign from malignant entities, as well as patient characteristics, to better stratify patients according to disease risk, thereby enabling more precise imaging and screening. Here, we have characterised the radiogenomic application in precision medicine using a multi-omic approach. we outline the main applications of radiogenomics in diagnosis, treatment planning and evaluations in the field of oncology with the aim of developing quantitative and personalised medicine. Finally, we discuss the challenges in the field of radiogenomics and the scope and clinical applicability of these methods.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Tian Duan
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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8
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Mukamel RE, Handsaker RE, Sherman MA, Barton AR, Hujoel MLA, McCarroll SA, Loh PR. Repeat polymorphisms underlie top genetic risk loci for glaucoma and colorectal cancer. Cell 2023; 186:3659-3673.e23. [PMID: 37527660 PMCID: PMC10528368 DOI: 10.1016/j.cell.2023.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/07/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023]
Abstract
Many regions in the human genome vary in length among individuals due to variable numbers of tandem repeats (VNTRs). To assess the phenotypic impact of VNTRs genome-wide, we applied a statistical imputation approach to estimate the lengths of 9,561 autosomal VNTR loci in 418,136 unrelated UK Biobank participants and 838 GTEx participants. Association and statistical fine-mapping analyses identified 58 VNTRs that appeared to influence a complex trait in UK Biobank, 18 of which also appeared to modulate expression or splicing of a nearby gene. Non-coding VNTRs at TMCO1 and EIF3H appeared to generate the largest known contributions of common human genetic variation to risk of glaucoma and colorectal cancer, respectively. Each of these two VNTRs associated with a >2-fold range of risk across individuals. These results reveal a substantial and previously unappreciated role of non-coding VNTRs in human health and gene regulation.
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Affiliation(s)
- Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Kachuri L, Mak ACY, Hu D, Eng C, Huntsman S, Elhawary JR, Gupta N, Gabriel S, Xiao S, Keys KL, Oni-Orisan A, Rodríguez-Santana JR, LeNoir MA, Borrell LN, Zaitlen NA, Williams LK, Gignoux CR, Burchard EG, Ziv E. Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture. Nat Genet 2023; 55:952-963. [PMID: 37231098 PMCID: PMC10260401 DOI: 10.1038/s41588-023-01377-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/21/2023] [Indexed: 05/27/2023]
Abstract
We explored ancestry-related differences in the genetic architecture of whole-blood gene expression using whole-genome and RNA sequencing data from 2,733 African Americans, Puerto Ricans and Mexican Americans. We found that heritability of gene expression significantly increased with greater proportions of African genetic ancestry and decreased with higher proportions of Indigenous American ancestry, reflecting the relationship between heterozygosity and genetic variance. Among heritable protein-coding genes, the prevalence of ancestry-specific expression quantitative trait loci (anc-eQTLs) was 30% in African ancestry and 8% for Indigenous American ancestry segments. Most anc-eQTLs (89%) were driven by population differences in allele frequency. Transcriptome-wide association analyses of multi-ancestry summary statistics for 28 traits identified 79% more gene-trait associations using transcriptome prediction models trained in our admixed population than models trained using data from the Genotype-Tissue Expression project. Our study highlights the importance of measuring gene expression across large and ancestrally diverse populations for enabling new discoveries and reducing disparities.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer R Elhawary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
| | - Kevin L Keys
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA
| | - Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Luisa N Borrell
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Esteban González Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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10
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Singh P, Crossman DK, Zhou L, Wang X, Sharafeldin N, Hageman L, Blanco JG, Burridge PW, Armenian SH, Balis FM, Hawkins DS, Keller FG, Hudson MM, Neglia JP, Ritchey AK, Ginsberg JP, Landier W, Bhatia S. Haptoglobin Gene Expression and Anthracycline-Related Cardiomyopathy in Childhood Cancer Survivors: A COG-ALTE03N1 Report. JACC CardioOncol 2023; 5:392-401. [PMID: 37397079 PMCID: PMC10308004 DOI: 10.1016/j.jaccao.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 02/10/2023] Open
Abstract
Background Anthracycline-related cardiomyopathy is a leading cause of premature death in childhood cancer survivors. The high interindividual variability in risk suggests the need to understand the underlying pathogenesis. Objectives The authors interrogated differentially expressed genes (DEGs) to identify genetic variants serving regulatory functions or genetic variants not easily identified when using genomewide array platforms. Using leads from DEGs, candidate copy number variants (CNVs) and single-nucleotide variants (SNVs) were genotyped. Methods Messenger RNA sequencing was performed on total RNA from peripheral blood of 40 survivors with cardiomyopathy (cases) and 64 matched survivors without cardiomyopathy (control subjects). Conditional logistic regression analysis adjusting for sex, age at cancer diagnosis, anthracycline dose, and chest radiation was used to assess the associations between gene expression and cardiomyopathy and between CNVs and SNVs and cardiomyopathy. Results Haptoglobin (HP) was identified as the top DEG. Participants with higher HP gene expression had 6-fold greater odds of developing cardiomyopathy (OR: 6.4; 95% CI: 1.4-28.6). The HP2-specific allele among the HP genotypes (HP1-1, HP1-2, and HP2-2) had higher transcript levels, as did the G allele among SNVs previously reported to be associated with HP gene expression (rs35283911 and rs2000999). The HP1-2 and HP2-2 genotypes combined with the G/G genotype for rs35283911 and/or rs2000999 placed the survivors at 4-fold greater risk (OR: 3.9; 95% CI: 1.0-14.5) for developing cardiomyopathy. Conclusions These findings provide evidence of a novel association between HP2 allele and cardiomyopathy. HP binds to free hemoglobin to form an HP-hemoglobin complex, thereby preventing oxidative damage from free heme iron, thus providing biological plausibility to the mechanistic basis of the present observation.
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Affiliation(s)
- Purnima Singh
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Liting Zhou
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Xuexia Wang
- Department of Mathematics, University of North Texas, Denton, Texas, USA
| | - Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lindsey Hageman
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Javier G. Blanco
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Paul W. Burridge
- Department of Pharmacology, Northwestern University, Chicago, Illinois, USA
| | - Saro H. Armenian
- Department of Population Sciences, City of Hope, Duarte, California
| | - Frank M. Balis
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Frank G. Keller
- Children’s Healthcare of Atlanta, Emory University, Atlanta, Georgia, USA
| | | | | | - A. Kim Ritchey
- Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jill P. Ginsberg
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wendy Landier
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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11
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Zhang Q, Zhao Q, Li T, Lu L, Wang F, Zhang H, Liu Z, Ma H, Zhu Q, Wang J, Zhang X, Pei Y, Liu Q, Xu Y, Qie J, Luan X, Hu Z, Liu X. Lactobacillus plantarum-derived indole-3-lactic acid ameliorates colorectal tumorigenesis via epigenetic regulation of CD8 + T cell immunity. Cell Metab 2023:S1550-4131(23)00141-9. [PMID: 37192617 DOI: 10.1016/j.cmet.2023.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/10/2023] [Accepted: 04/14/2023] [Indexed: 05/18/2023]
Abstract
Previous studies have shown that Lactobacillus species play a role in ameliorating colorectal cancer (CRC) in a mouse model. However, the underlying mechanisms remain largely unknown. Here, we found that administration of a probiotic strain, Lactobacillus plantarumL168 and its metabolite, indole-3-lactic acid, ameliorated intestinal inflammation, tumor growth, and gut dysbiosis. Mechanistically, we indicated that indole-3-lactic acid accelerated IL12a production in dendritic cells by enhancing H3K27ac binding at the enhancer regions of IL12a that contributed to priming CD8+ T cell immunity against tumor growth. Furthermore, indole-3-lactic acid was found to transcriptionally inhibit Saa3 expression related to cholesterol metabolism of CD8+ T cells through changing chromatin accessibility and subsequent enhancing function of tumor-infiltrating CD8+ T cells. Together, our findings provide new insights into the epigenetic regulation of probiotics-mediated anti-tumor immunity and suggest the potential of L. plantarumL168 and indole-3-lactic acid to develop therapeutic strategies for patients with CRC.
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Affiliation(s)
- Qingqing Zhang
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Qing Zhao
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Tao Li
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Longya Lu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Fei Wang
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Hong Zhang
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Zhi Liu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Huihui Ma
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Qihui Zhu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Jingjing Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuemei Zhang
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Yang Pei
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Qisha Liu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Yuyu Xu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Jinlong Qie
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoting Luan
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 211166, China; State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China; Department of Microbiota Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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12
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Langlois AWR, El-Boraie A, Pouget JG, Cox LS, Ahluwalia JS, Fukunaga K, Mushiroda T, Knight J, Chenoweth MJ, Tyndale RF. Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data. J Hum Genet 2023:10.1038/s10038-023-01148-y. [PMID: 37059825 DOI: 10.1038/s10038-023-01148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023]
Abstract
CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. The CYP2A6 gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1 × 2), and hybrids with the CYP2A7 pseudogene (CYP2A6*12, CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility of CYP2A6 SV imputation from SNP array data in two ancestry populations. European- (EUR; n = 935) and African- (AFR; n = 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and for CYP2A6 SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility of CYP2A6 SV imputation. A minimal protocol requiring three Taqman CN assays for CYP2A6 SV genotyping was developed and known SV associations with activity were replicated. The first domain swap CYP2A6-CYP2A7 hybrid SV, CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm that CYP2A6 SV imputation can identify most SV alleles, including a novel SV.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Lisa Sanderson Cox
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Jasjit S Ahluwalia
- Departments of Behavioral and Social Sciences and Medicine, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisei Mushiroda
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jo Knight
- Data Science Institute and Medical School, Lancaster University, Lancaster, UK
| | - Meghan J Chenoweth
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada.
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13
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Shwan NAA, Moise EC, Necsoiu PE, Farr AJ, Gale DP, Barratt J, Armour JAL. Segregation analysis identifies specific alpha-defensin (DEFA1A3) SNP-CNV haplotypes in predisposition to IgA nephropathy. Ann Hum Genet 2023; 87:1-8. [PMID: 36214424 DOI: 10.1111/ahg.12481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Immunoglobulin A (IgA) nephropathy is a disorder of the immune system affecting kidney function, and genome-wide association studies (GWAS) have defined numerous loci with associated variation, all implicating components of innate or adaptive immunity. Among these, single nucleotide polymorphisms (SNPs) in a region including the multiallelic copy number variation (CNV) of DEFA1A3 are associated with IgA nephropathy in both European and Asian populations. At present, the precise factors underlying the observed associations at DEFA1A3 have not been defined, although the key alleles differ between Asian and European populations, and multiple independent factors may be involved even within a single population. METHODS In this study, we measured DEFA1A3 copy number in UK family trios with an offspring affected by IgA nephropathy, used the population distributions of joint SNP-CNV haplotypes to infer the likely segregation in trios, and applied transmission disequilibrium tests (TDT) to examine joint SNP-CNV haplotypes for over- or undertransmission into affected offspring from heterozygous parents. RESULTS AND CONCLUSIONS We observed overtransmission of 3-copy class 2 haplotypes (raw p = 0.029) and some evidence for under-transmission of 3-copy class 1 haplotypes (raw p = 0.051), although these apparent effects were not statistically significant after correction for testing of multiple haplotypes.
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Affiliation(s)
- Nzar A A Shwan
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Erbil Technical Health and Medical College, Erbil Polytechnic University, Erbil, Kurdistan Region, Iraq
| | - Eric C Moise
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paula E Necsoiu
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Amy J Farr
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Daniel P Gale
- Department of Renal Medicine, Division of Medicine, University College London, London, UK
| | - Jonathan Barratt
- Department of Cardiovascular Medicine, University of Leicester, Leicester, UK
| | - John A L Armour
- School of Life Sciences, University of Nottingham, Nottingham, UK
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14
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Sun YH, Cui H, Song C, Shen JT, Zhuo X, Wang RH, Yu X, Ndamba R, Mu Q, Gu H, Wang D, Murthy GG, Li P, Liang F, Liu L, Tao Q, Wang Y, Orlowski S, Xu Q, Zhou H, Jagne J, Gokcumen O, Anthony N, Zhao X, Li XZ. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 2023; 14:812. [PMID: 36781861 PMCID: PMC9925758 DOI: 10.1038/s41467-023-36354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hongxiao Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiafei Teng Shen
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, 322000, China
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ruoqiao Huiyi Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rudo Ndamba
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Qian Mu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hanwen Gu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Duolin Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gayathri Guru Murthy
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Pidong Li
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Fan Liang
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Lei Liu
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Qing Tao
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Sara Orlowski
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Qi Xu
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, NY, 14850, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Nick Anthony
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada.
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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15
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Meegan JE, Kerchberger VE, Fortune NL, McNeil JB, Bastarache JA, Austin ED, Ware LB, Hemnes AR, Brittain EL. Transpulmonary generation of cell-free hemoglobin contributes to vascular dysfunction in pulmonary arterial hypertension via dysregulated clearance mechanisms. Pulm Circ 2023; 13:e12185. [PMID: 36743426 PMCID: PMC9841468 DOI: 10.1002/pul2.12185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/12/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
Circulating cell-free hemoglobin (CFH) is elevated in pulmonary arterial hypertension (PAH) and associated with poor outcomes but the mechanisms are unknown. We hypothesized that CFH is generated from the pulmonary circulation and inadequately cleared in PAH. Transpulmonary CFH (difference between wedge and pulmonary artery positions) and lung hemoglobin α were analyzed in patients with PAH and healthy controls. Haptoglobin genotype and plasma hemoglobin processing proteins were analyzed in patients with PAH, unaffected bone morphogenetic protein receptor type II mutation carriers (UMCs), and control subjects. Transpulmonary CFH was increased in patients with PAH (p = 0.04) and correlated with pulmonary vascular resistanc (PVR) (r s = 0.75, p = 0.02) and mean pulmonary arterial pressure (mPAP) (r s = 0.78, p = 0.02). Pulmonary vascular hemoglobin α protein was increased in patients with PAH (p = 0.006), especially in occluded vessels (p = 0.04). Haptoglobin genotype did not differ between groups. Plasma haptoglobin was higher in UMCs compared with both control subjects (p = 0.03) and patients with HPAH (p < 0.0001); patients with IPAH had higher circulating haptoglobin levels than patients with HPAH (p = 0.006). Notably, circulating CFH to haptoglobin ratio was elevated in patients with HPAH compared to control subjects (p = 0.02) and UMCs (p = 0.006). Moreover, in patients with PAH, CFH: haptoglobin correlated with PVR (r s = 0.37, p = 0.0004) and mPAP (r s = 0.25, p = 0.02). Broad alterations in other plasma hemoglobin processing proteins (hemopexin, heme oxygenase-1, and sCD163) were observed. In conclusion, pulmonary vascular CFH is associated with increased PVR and mPAP in PAH and dysregulated CFH clearance may contribute to PAH pathology. Further study is needed to determine whether targeting CFH is a viable therapeutic for pulmonary vascular dysfunction in PAH.
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Affiliation(s)
- Jamie E. Meegan
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Vern Eric Kerchberger
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Niki L. Fortune
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Joel Brennan McNeil
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Julie A. Bastarache
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Pathology, Microbiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Cell and Developmental BiologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Eric D. Austin
- Department of Pediatrics, Division of Allergy, Immunology, and Pulmonary MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Lorraine B. Ware
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Pathology, Microbiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Anna R. Hemnes
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Pulmonary Circulation CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Evan L. Brittain
- Vanderbilt Pulmonary Circulation CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Medicine, Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
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16
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Mendelian randomization and genetic colocalization infer the effects of the multi-tissue proteome on 211 complex disease-related phenotypes. Genome Med 2022; 14:140. [PMID: 36510323 PMCID: PMC9746220 DOI: 10.1186/s13073-022-01140-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human proteins are widely used as drug targets. Integration of large-scale protein-level genome-wide association studies (GWAS) and disease-related GWAS has thus connected genetic variation to disease mechanisms via protein. Previous proteome-by-phenome-wide Mendelian randomization (MR) studies have been mainly focused on plasma proteomes. Previous MR studies using the brain proteome only reported protein effects on a set of pre-selected tissue-specific diseases. No studies, however, have used high-throughput proteomics from multiple tissues to perform MR on hundreds of phenotypes. METHODS Here, we performed MR and colocalization analysis using multi-tissue (cerebrospinal fluid (CSF), plasma, and brain from pre- and post-meta-analysis of several disease-focus cohorts including Alzheimer disease (AD)) protein quantitative trait loci (pQTLs) as instrumental variables to infer protein effects on 211 phenotypes, covering seven broad categories: biological traits, blood traits, cancer types, neurological diseases, other diseases, personality traits, and other risk factors. We first implemented these analyses with cis pQTLs, as cis pQTLs are known for being less prone to horizontal pleiotropy. Next, we included both cis and trans conditionally independent pQTLs that passed the genome-wide significance threshold keeping only variants associated with fewer than five proteins to minimize pleiotropic effects. We compared the tissue-specific protein effects on phenotypes across different categories. Finally, we integrated the MR-prioritized proteins with the druggable genome to identify new potential targets. RESULTS In the MR and colocalization analysis including study-wide significant cis pQTLs as instrumental variables, we identified 33 CSF, 13 plasma, and five brain proteins to be putative causal for 37, 18, and eight phenotypes, respectively. After expanding the instrumental variables by including genome-wide significant cis and trans pQTLs, we identified a total of 58 CSF, 32 plasma, and nine brain proteins associated with 58, 44, and 16 phenotypes, respectively. For those protein-phenotype associations that were found in more than one tissue, the directions of the associations for 13 (87%) pairs were consistent across tissues. As we were unable to use methods correcting for horizontal pleiotropy given most of the proteins were only associated with one valid instrumental variable after clumping, we found that the observations of protein-phenotype associations were consistent with a causal role or horizontal pleiotropy. Between 66.7 and 86.3% of the disease-causing proteins overlapped with the druggable genome. Finally, between one and three proteins, depending on the tissue, were connected with at least one drug compound for one phenotype from both DrugBank and ChEMBL databases. CONCLUSIONS Integrating multi-tissue pQTLs with MR and the druggable genome may open doors to pinpoint novel interventions for complex traits with no effective treatments, such as ovarian and lung cancers.
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17
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Bjarni V Halldórsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavík, Iceland
| | | | - Jia Wen
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna V Mihkaylova
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Min-Zhi Jiang
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Goo Jun
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Joshua B Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yan Gao
- Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS, 39216, USA
| | - Kai Kammers
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Laura Almasy
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, 5446, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, 1702, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Unnur Þorsteinsdóttir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Magnús K Magnússon
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Nathan D Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98105, USA.
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18
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Syreeni A, Dahlström EH, Hägg-Holmberg S, Forsblom C, Eriksson MI, Harjutsalo V, Putaala J, Groop PH, Sandholm N, Thorn LM. Haptoglobin Genotype Does Not Confer a Risk of Stroke in Type 1 Diabetes. Diabetes 2022; 71:2728-2738. [PMID: 36409784 DOI: 10.2337/db22-0327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023]
Abstract
The exon copy number variant in the haptoglobin gene is associated with cardiovascular and kidney disease. For stroke, previous research is inconclusive. We aimed to study the relationship between the haptoglobin Hp1/2 genotype and stroke in individuals with type 1 diabetes from the Finnish Diabetic Nephropathy Study. We included two partially overlapping cohorts: one with haptoglobin genotypes determined using genotyping for 179 individuals with stroke and 517 matched control subjects, and the other using haptoglobin genotype imputation for a larger cohort of 500 individuals with stroke and 3,806 individuals without stroke. We observed no difference in the Hp1-1, Hp2-1, and Hp2-2 genotype frequencies between individuals with or without stroke, neither in the genotyping nor the imputation cohorts. Haptoglobin genotypes were also not associated with the ischemic or hemorrhagic stroke subtypes. In our imputed haptoglobin cohort, 61% of individuals with stroke died during follow-up. However, the risk of death was not related to the haptoglobin genotype. Diabetic kidney disease and cardiovascular events were common in the cohort, but the haptoglobin genotypes were not associated with stroke when stratified by these complications. To conclude, the Hp1/2 genotypes did not affect the risk of stroke or survival after stroke in our cohort with type 1 diabetes.
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Affiliation(s)
- Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Stefanie Hägg-Holmberg
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marika I Eriksson
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jukka Putaala
- Department of Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lena M Thorn
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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19
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Pokrovac I, Pezer Ž. Recent advances and current challenges in population genomics of structural variation in animals and plants. Front Genet 2022; 13:1060898. [PMID: 36523759 PMCID: PMC9745067 DOI: 10.3389/fgene.2022.1060898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 05/02/2024] Open
Abstract
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.
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Affiliation(s)
| | - Željka Pezer
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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20
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Genetic Factors Associated with Response to Vitamin E Treatment in NAFLD. Antioxidants (Basel) 2022; 11:antiox11071284. [PMID: 35883775 PMCID: PMC9311784 DOI: 10.3390/antiox11071284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 12/07/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is becoming the predominant liver disease worldwide, and vitamin E has been clinically shown to improve histological parameters in a subset of patients. In this narrative review, we investigate whether genetic factors may help to explain why some patients show histological improvements upon high-dose alpha-tocopherol (αT) treatment while others do not. In summary, we identified two factors that are associated with treatment response, including genetic variations in haptoglobin as well as fatty acid desaturase 1/2 (FADS1/FADS2). Other genetic variants such as in alpha-tocopherol transfer protein (αTTP), tocopherol associated protein (TAP), transmembrane 6 superfamily 2 (TM6SF2), cluster of differentiation 36 (CD36), and proteins involved in lipoprotein metabolism may also play a role, but have not yet been investigated in a clinical context. We propose to further validate these associations in larger populations, to then use them as a clinical tool to identify the subset of patients that will benefit the most from vitamin E supplementation.
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21
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Bai H, Kaur H, Kallianpur AR, Hulgan T, Franklin DR, Letendre SL, Ellis RJ, Bush WS. A Haptoglobin Exon Copy Number Variant Associates With HIV-Associated Neurocognitive Impairment in European and African-Descent Populations. Front Genet 2022; 12:756685. [PMID: 35003209 PMCID: PMC8727522 DOI: 10.3389/fgene.2021.756685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
A common two-exon deletion distinguishes the gene encoding the free hemoglobin capturing protein—haptoglobin (HP)–into two alleles: HP1 and HP2. To evaluate the impact of this copy number variant (CNV) on neurocognitive impairment (NCI) in people living with HIV, we imputed this variant in 432 European-descent (EUR) and 491 African-descent (AFR) participants from the CNS HIV Antiretroviral Therapy Effects Research Study using an optimized imputation pipeline and evaluated its associations with NCI. At baseline, in AFR, the HP2 allele decreased the odds of NCI (defined by a global deficit score, GDS, ⩾0.5; Odds Ratio, OR = 0.584, p = 0.022). However, in EUR, HP2 increased the odds (OR = 2.081, p = 0.040) of NCI suggesting a detrimental effect. These effects were extended to longitudinal analyses using repeated measurements where the protective effect of the HP2 allele in AFR became marginally significant (p = 0.054) and in EUR the detrimental effect increased in significance (p = 0.037). In EUR, the HP2 allele slightly reduced the risk of NCI over time (OR = 0.028 per allele per year, p = 0.024). Further analyses of cognitive domain-specific impairment revealed that the HP-NCI effect was based on changes in learning, speed of information processing, and verbal domains over time differing by ancestry groups. Overall, these findings suggest that these functional HP CNV alleles influence the likelihood of NCI and contribute to changes in neurocognitive function over time in people living with HIV.
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Affiliation(s)
- Haimeng Bai
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States.,Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Harpreet Kaur
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Asha R Kallianpur
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States.,Department of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Todd Hulgan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Donald R Franklin
- Department of Psychiatry, HIV Neurobehavioral Research Center, University of California, San Diego, San Diego, CA, United States
| | - Scott L Letendre
- Departments of Medicine and Psychiatry, University of California, San Diego, San Diego, CA, United States
| | - Ronald J Ellis
- Departments of Neurosciences and Psychiatry, University of California, San Diego, San Diego, CA, United States
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States
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22
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Perrot N, Pelletier W, Bourgault J, Couture C, Li Z, Mitchell PL, Ghodsian N, Bossé Y, Thériault S, Mathieu P, Arsenault BJ. A trans-omic Mendelian randomization study of parental lifespan uncovers novel aging biology and therapeutic candidates for chronic diseases. Aging Cell 2021; 20:e13497. [PMID: 34704651 PMCID: PMC8590095 DOI: 10.1111/acel.13497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/20/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
The study of parental lifespan has emerged as an innovative tool to advance aging biology and our understanding of the genetic architecture of human longevity and aging-associated diseases. Here, we leveraged summary statistics of a genome-wide association study including over one million parental lifespans to identify genetically regulated genes from the Genotype-Tissue Expression project. Through a combination of multi-tissue transcriptome-wide association analyses and genetic colocalization, we identified novel genes that may be associated with parental lifespan. Mendelian randomization (MR) analyses also identified circulating proteins and metabolites causally associated with parental lifespan and chronic diseases offering new drug repositioning opportunities such as those targeting apolipoprotein-B-containing lipoproteins. Liver expression of HP, the gene encoding haptoglobin, and plasma haptoglobin levels were causally linked with parental lifespan. Phenome-wide MR analyses were used to map genetically regulated genes, proteins and metabolites with other human traits as well as the disease-related phenome in the FinnGen cohorts (n = 135,638). Altogether, this study identified new candidate genes, circulating proteins and metabolites that may influence human aging as well as potential therapeutic targets for chronic diseases that warrant further investigation.
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Affiliation(s)
- Nicolas Perrot
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of MedicineFaculty of MedicineUniversité LavalQuébecQCCanada
| | - William Pelletier
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of MedicineFaculty of MedicineUniversité LavalQuébecQCCanada
| | - Jérôme Bourgault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
| | - Christian Couture
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
| | - Zhonglin Li
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
| | - Patricia L. Mitchell
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
| | - Nooshin Ghodsian
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
| | - Yohan Bossé
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of Molecular MedicineFaculty of MedicineUniversité LavalQuébecQCCanada
| | - Sébastien Thériault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of Molecular Biology, Medical Biochemistry and PathologyFaculty of MedicineUniversité LavalQuébecQCCanada
| | - Patrick Mathieu
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of SurgeryFaculty of MedicineUniversité LavalQuébecQCCanada
| | - Benoit J. Arsenault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de QuébecQuébecQCCanada
- Department of MedicineFaculty of MedicineUniversité LavalQuébecQCCanada
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23
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Saitou M, Masuda N, Gokcumen O. Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Mol Biol Evol 2021; 39:6413645. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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Affiliation(s)
- Marie Saitou
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Currently at the Faculty of Biosciences, Norwegian University of Life Sciences, Universitetstunet 3, 1430 Ås, Norway.,Dept. of Medicine, The University of Chicago. Section of Genetic Medicine, 5841 S. Maryland Ave., Chicago, IL, 60637-1447, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY 14260-5030, USA
| | - Omer Gokcumen
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA
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24
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Buzzi RM, Owczarek CM, Akeret K, Tester A, Pereira N, Butcher R, Brügger-Verdon V, Hardy MP, Illi M, Wassmer A, Vallelian F, Humar R, Hugelshofer M, Buehler PW, Gentinetta T, Schaer DJ. Modular Platform for the Development of Recombinant Hemoglobin Scavenger Biotherapeutics. Mol Pharm 2021; 18:3158-3170. [PMID: 34292741 DOI: 10.1021/acs.molpharmaceut.1c00433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free hemoglobin (Hb) is a driver of disease progression in conditions with intravascular or localized hemolysis. Genetic and acquired anemias or emergency medical conditions such as aneurysmal subarachnoid hemorrhage involve tissue Hb exposure. Haptoglobin (Hp) captures Hb in an irreversible protein complex and prevents its pathophysiological contributions to vascular nitric oxide depletion and tissue oxidation. Preclinical proof-of-concept studies suggest that human plasma-derived Hp is a promising therapeutic candidate for several Hb-driven diseases. Optimizing the efficacy and safety of Hb-targeting biotherapeutics may require structural and functional modifications for specific indications. Improved Hp variants could be designed to achieve the desired tissue distribution, metabolism, and elimination to target hemolytic disease states effectively. However, it is critical to ensure that these modifications maintain the function of Hp. Using transient mammalian gene expression of Hp combined with co-transfection of the pro-haptoglobin processing protease C1r-LP, we established a platform for generating recombinant Hp-variants. We designed an Hpβ-scaffold, which was expressed in this system at high levels as a monomeric unit (mini-Hp) while maintaining the key protective functions of Hp. We then used this Hpβ-scaffold as the basis to develop an initial proof-of-concept Hp fusion protein using human serum albumin as the fusion partner. Next, a hemopexin-Hp fusion protein with bispecific heme and Hb detoxification capacity was generated. Further, we developed a Hb scavenger devoid of CD163 scavenger receptor binding. The functions of these proteins were then characterized for Hb and heme-binding, binding of the Hp-Hb complexes with the clearance receptor CD163, antioxidant properties, and vascular nitric oxide sparing capacity. Our platform is designed to support the generation of innovative Hb scavenger biotherapeutics with novel modes of action and potentially improved formulation characteristics, function, and pharmacokinetics.
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Affiliation(s)
- Raphael M Buzzi
- Division of Internal Medicine, Universitätsspital and University of Zurich, Zurich 8091, Switzerland
| | | | - Kevin Akeret
- Department of Neurosurgery, Clinical Neuroscience Center, Universitätsspital und University of Zurich, Zurich 8091, Switzerland
| | - Andrea Tester
- CSL Limited, Bio21 Institute, Parkville, Victoria 3010, Australia
| | - Natasha Pereira
- CSL Limited, Bio21 Institute, Parkville, Victoria 3010, Australia
| | - Rebecca Butcher
- CSL Limited, Bio21 Institute, Parkville, Victoria 3010, Australia
| | | | - Matthew P Hardy
- CSL Limited, Bio21 Institute, Parkville, Victoria 3010, Australia
| | - Marlies Illi
- Research and Development, CSL Behring AG, Bern 3014, Switzerland
| | - Andreas Wassmer
- Research and Development, CSL Behring AG, Bern 3014, Switzerland
| | - Florence Vallelian
- Division of Internal Medicine, Universitätsspital and University of Zurich, Zurich 8091, Switzerland
| | - Rok Humar
- Division of Internal Medicine, Universitätsspital and University of Zurich, Zurich 8091, Switzerland
| | - Michael Hugelshofer
- Department of Neurosurgery, Clinical Neuroscience Center, Universitätsspital und University of Zurich, Zurich 8091, Switzerland
| | - Paul W Buehler
- Department of Pathology, The University of Maryland School of Medicine, Baltimore, Maryland 21201, United States.,The Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, The University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | | | - Dominik J Schaer
- Division of Internal Medicine, Universitätsspital and University of Zurich, Zurich 8091, Switzerland
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Abstract
Haptoglobin (Hp) is a blood plasma glycoprotein that binds free hemoglobin (Hb) and plays a critical role in tissue protection and the prevention of oxidative damage. In addition, it has a number of regulatory functions. Haptoglobin is an acute phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. Only in humans, the Hp gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of Hp, homozygous Hp1-1 and Hp2-2, and heterozygous Hp2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual's predisposition to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting of the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the Hp β-chain has become the main direction in the study of pathological processes, including malignant neoplasms. Many studies are focused on the identification of PTM and changes in the level of the α2-chain of this protein in pathology. These characteristics of Hp indicate the possibility of the existence of this protein as different proteoforms, probably with different functions. This review is devoted to the description of the structural and functional diversity of Hp and its potential use as a biomarker of various pathologies.
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Affiliation(s)
- S N Naryzhny
- Institute of Biomedical Chemistry, Moscow, Russia; Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
| | - O K Legina
- Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
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26
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Chen L, Abel HJ, Das I, Larson DE, Ganel L, Kanchi KL, Regier AA, Young EP, Kang CJ, Scott AJ, Chiang C, Wang X, Lu S, Christ R, Service SK, Chiang CWK, Havulinna AS, Kuusisto J, Boehnke M, Laakso M, Palotie A, Ripatti S, Freimer NB, Locke AE, Stitziel NO, Hall IM. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 2021; 108:583-596. [PMID: 33798444 PMCID: PMC8059371 DOI: 10.1016/j.ajhg.2021.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/03/2021] [Indexed: 02/08/2023] Open
Abstract
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.
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Affiliation(s)
- Lei Chen
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Indraniel Das
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica P Young
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Alexandra J Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Colby Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ryan Christ
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Finnish Institute for Health and Welfare (THL), Helsinki 00271, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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27
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Power N, Turpin W, Espin-Garcia O, Smith MI, Croitoru K. Serum Zonulin Measured by Commercial Kit Fails to Correlate With Physiologic Measures of Altered Gut Permeability in First Degree Relatives of Crohn's Disease Patients. Front Physiol 2021; 12:645303. [PMID: 33841181 PMCID: PMC8027468 DOI: 10.3389/fphys.2021.645303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/26/2021] [Indexed: 12/22/2022] Open
Abstract
Intestinal epithelial cell tight junctions (TJs) contribute to the integrity of the intestinal barrier allowing for control of the physical barrier between external antigens or bacterial products and the internal environment. Zonula occludens-1 (ZO-1) is a protein that modulates intestinal TJs, and serum levels of ZO-1 has been suggested as a biomarker of disrupted barrier function in humans. Previous studies suggested that increased intestinal permeability was associated with evidence of TJ abnormalities. However, there is limited information on the serological measurement of ZO-1 and its relation to other tests of barrier function in healthy subjects. We investigated the correlation of serum ZO-1, with physiologic measures of intestinal permeability (as the ratio of the fractional excretion of lactulose-mannitol or LMR) in a cohort of 39 healthy FDRs of Crohn's disease (CD) patients. No significant correlation was found between LMR and ZO-1 levels (r2 = 0.004, P < 0.71), or intestinal fatty acid binding proteins (I-FABP) (r2 = 0.004, P < 0.71). In conclusion, our data show that ZO-1 and I-FABP are not a marker of gut permeability as defined by LMR.
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Affiliation(s)
- Namita Power
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Gastroenterology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Gastroenterology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | | | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Gastroenterology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
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28
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Chmielińska M, Olesińska M, Romanowska-Próchnicka K, Szukiewicz D. Haptoglobin and Its Related Protein, Zonulin-What Is Their Role in Spondyloarthropathy? J Clin Med 2021; 10:jcm10051131. [PMID: 33800376 PMCID: PMC7962838 DOI: 10.3390/jcm10051131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022] Open
Abstract
Haptoglobin (Hp) is an acute phase protein which supports the immune response and protects tissues from free radicals. Its concentration correlates with disease activity in spondyloarthropathies (SpAs). The Hp polymorphism determines the functional differences between Hp1 and Hp2 protein products. The role of the Hp polymorphism has been demonstrated in many diseases. In particular, the Hp 2-2 phenotype has been associated with the unfavorable course of some inflammatory and autoimmune disorders. Its potential role in modulating the immune system in SpA is still unknown. This article contains pathophysiological considerations on the potential relationship between Hp, its polymorphism and SpA.
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Affiliation(s)
- Magdalena Chmielińska
- Department of Biophysics and Human Physiology, Medical University of Warsaw, Chałubińskiego 5, 02-004 Warsaw, Poland; (K.R.-P.); (D.S.)
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland;
- Correspondence:
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland;
| | - Katarzyna Romanowska-Próchnicka
- Department of Biophysics and Human Physiology, Medical University of Warsaw, Chałubińskiego 5, 02-004 Warsaw, Poland; (K.R.-P.); (D.S.)
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland;
| | - Dariusz Szukiewicz
- Department of Biophysics and Human Physiology, Medical University of Warsaw, Chałubińskiego 5, 02-004 Warsaw, Poland; (K.R.-P.); (D.S.)
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29
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Beaudoin JJ, Liang T, Tang Q, Banini BA, Shah VH, Sanyal AJ, Chalasani NP, Gawrieh S. Role of candidate gene variants in modulating the risk and severity of alcoholic hepatitis. Alcohol Clin Exp Res 2021; 45:709-719. [PMID: 33616244 DOI: 10.1111/acer.14581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Alcoholic hepatitis (AH) is a severe and life-threatening alcohol-associated liver disease. Only a minority of heavy drinkers acquires AH and severity varies among affected individuals, suggesting a genetic basis for the susceptibility to and severity of AH. METHODS A cohort consisting of 211 patients with AH and 176 heavy drinking controls was genotyped for five variants in five candidate genes that have been associated with chronic liver diseases: rs738409 in patatin-like phospholipase domain-containing protein 3 (PNPLA3), rs72613567 in hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13), rs58542926 in transmembrane 6 superfamily member 2 (TM6SF2), rs641738 in membrane bound O-acyltransferase domain containing 7 (MBOAT7), and a copy number variant in the haptoglobin (HP) gene. We tested the effects of individual variants and the combined/interacting effects of variants on AH risk and severity. RESULTS We found significant associations between AH risk and the risk alleles of rs738409 (p = 0.0081) and HP (p = 0.0371), but not rs72613567 (p = 0.3132), rs58542926 (p = 0.2180), or rs641738 (p = 0.7630), after adjusting for patient's age and sex. A multiple regression model indicated that PNPLA3 rs738409:G [OR = 1.59 (95% CI: 1.15-2.22), p = 0.0055] and HP*2 [OR = 1.38 (95% CI: 1.04-1.82), p = 0.0245], when combined and adjusted for age and sex also had a large influence on AH risk among heavy drinkers. In the entire cohort, variants in PNPLA3 and HP were associated with increased total bilirubin and Model for End-stage Liver Disease (MELD) score, both measures of AH severity. The HSD17B13 rs72613567:AA allele was not found to reduce risk of AH in patients carrying the G allele of PNPLA3 rs738409 (p = 0.0921). CONCLUSION PNPLA3 and HP genetic variants increase AH risk and are associated with total bilirubin and MELD score, surrogates of AH severity.
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Affiliation(s)
- James J Beaudoin
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Tiebing Liang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qing Tang
- Department of Biostatistics, Indiana University School of Medicine and Richard M. Fairbanks School of Public Health, Indianapolis, IN, USA
| | - Bubu A Banini
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, Richmond, VA, USA
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Arun J Sanyal
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, Richmond, VA, USA
| | - Naga P Chalasani
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Samer Gawrieh
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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30
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Naryzny SN, Legina OK. Haptoglobin as a Biomarker. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES B, BIOMEDICAL CHEMISTRY 2021; 15:184-198. [PMID: 34422226 PMCID: PMC8365284 DOI: 10.1134/s1990750821030069] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Haptoglobin (Hp) is a glycoprotein that binds free hemoglobin (Hb) in plasma and plays a critical role in tissue protection and prevention of oxidative damage. Besides, it has some regulatory functions. Haptoglobin is an acute-phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. The human Нр gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of haptoglobin: homozygous Нр1-1 and Нр2-2, and heterozygous Нр2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual predisposition of a person to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting off the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the β-chain of Hp has become the main direction in the study of pathological processes, including malignant neoplasms. These characteristics indicate the possibility of the existence of Hp in the form of a multitude of proteoforms, probably performing different functions. This review is devoted to the description of the structural and functional diversity and the potential use of Hp as a biomarker of various pathologies.
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Affiliation(s)
- S. N. Naryzny
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia ,St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
| | - O. K. Legina
- St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
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31
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Carew AS, Levy AP, Ginsberg HN, Coca S, Lache O, Ransom T, Byington R, Rimm EB, Sapp J, Gardner M, Cahill LE. Haptoglobin Phenotype Modifies the Influence of Intensive Glycemic Control on Cardiovascular Outcomes. J Am Coll Cardiol 2020; 75:512-521. [PMID: 32029134 DOI: 10.1016/j.jacc.2019.11.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 02/09/2023]
Abstract
BACKGROUND Whereas there exists a direct relationship between glycated hemoglobin and cardiovascular disease (CVD), clinical trials targeting glycated hemoglobin to near-normal levels using intensive therapy have failed to prevent CVD and have even increased mortality, making clinical decision making difficult. A common polymorphism at the haptoglobin (Hp) genetic locus is associated with CVD, especially coronary heart disease, in the setting of hyperglycemia. OBJECTIVES This study sought to determine whether the treatment difference of intensive versus standard glucose-lowering therapy on risk of CVD events in the ACCORD (Action to Control Cardiovascular Risk in Diabetes) study depended on Hp phenotype. METHODS Hp phenotype was measured within 5,806 non-Hispanic white ACCORD participants using a validated assay. Adjusted hazard ratios (aHR) with 95% confidence intervals (CI) estimated from stratified Cox regression models were used to quantify the association between intensive therapy and incident CVD for the 2 different Hp phenotype groups (Hp2-2, Hp1 carriers). RESULTS Compared with standard therapy, intensive therapy was associated with a lower risk of incident coronary heart disease among participants with the Hp2-2 phenotype (n = 2,133; aHR: 0.71; 95% CI: 0.55 to 0.91; p = 0.006), but not among the other 2 phenotypes (Hp1 allele carriers) (n = 3,673; aHR: 0.95; 95% CI: 0.79 to 1.13; p = 0.550). The same pattern was observed for CVD. Conversely, intensive therapy was associated with an increased risk of fatal CVD (aHR: 1.50; 95% CI: 1.00 to 2.25; p = 0.049) and total mortality (aHR: 1.40; 95% CI: 1.08 to 1.81; p = 0.011) among the Hp1 carriers, whereas this risk was not increased in the Hp2-2 phenotype (fatal CVD: aHR: 1.02; 95% CI: 0.59 to 1.77; p = 0.931; total mortality: aHR: 0.98; 95% CI: 0.68 to 1.41; p = 0.908). CONCLUSIONS Intensive glucose-lowering therapy was effective at preventing incident coronary heart disease and CVD events in ACCORD study participants with the Hp2-2 phenotype but not in Hp1 carriers, who had increased mortality risk from intensive therapy.
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Affiliation(s)
- Allie S Carew
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Andrew P Levy
- Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | | | - Steven Coca
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Orit Lache
- Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Thomas Ransom
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Robert Byington
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Eric B Rimm
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - John Sapp
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Martin Gardner
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Leah E Cahill
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority, Halifax, Nova Scotia, Canada; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
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32
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Chang X, Dorajoo R, Han Y, Wang L, Liu J, Khor CC, Low AF, Chan MYY, Yuan JM, Koh WP, Friedlander Y, Heng CK. Interaction between a haptoglobin genetic variant and coronary artery disease (CAD) risk factors on CAD severity in Singaporean Chinese population. Mol Genet Genomic Med 2020; 8:e1450. [PMID: 32794371 PMCID: PMC7549588 DOI: 10.1002/mgg3.1450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 11/11/2022] Open
Abstract
Background Haptoglobin (Hp) is a plasma protein with strong anti‐inflammation and antioxidant activities. Its plasma level is known to be inversely associated with many inflammatory diseases, including cardiovascular diseases. However, the association of HP genetic variants with coronary artery disease (CAD) severity/mortality, and how they interact with common CAD risk factors are largely unknown. Methods We conducted the analysis in a Singaporean Chinese CAD population with Gensini severity scores (N = 582) and subsequently evaluated the significant findings in an independent cohort with cardiovascular mortality (excluding stroke) as outcome (917 cases and 19,093 controls). CAD risk factors were ascertained from questionnaires, and stenosis information from medical records. Mortality was identified through linkage with the nationwide registry of births and deaths in Singapore. Linear regression analysis between HP genetic variant (rs217181) and disease outcome were performed. Interaction analyses were performed by introducing an interaction term in the same regression models. Results Although rs217181 was not significantly associated with CAD severity and cardiovascular mortality (excluding stroke) in all subjects, when stratified by hypertension status, hypertensive individuals with the minor T allele have more severe CAD (β = 0.073, SE = 0.030, p = 0.015) and non‐hypertensive individuals with the T allele have lower risk for mortality (odds ratio = 0.771 (0.607–0.980), p = 0.033). Conclusion HP genetic variant is not associated with CAD severity and mortality in the general population. However, hypertensive individuals with the rs217181 T allele associated with higher Hp levels had more severe CAD while non‐hypertensive individuals with the same allele had lower risk for mortality in the Chinese population.
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Affiliation(s)
- Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yi Han
- Departments of Preventive Medicine and Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Adrian F Low
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,National University Heart Centre, National University Health System, Singapore, Singapore
| | - Mark Yan-Yee Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Health Systems and Services Research, Duke-NUS Medical School Singapore, Singapore, Singapore
| | - Yechiel Friedlander
- School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
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Haptoglobin polymorphisms in Latin American populations. Sci Rep 2020; 10:13780. [PMID: 32792581 PMCID: PMC7426911 DOI: 10.1038/s41598-020-70755-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022] Open
Abstract
Several genetic polymorphisms of the haptoglobin gene (HP) or haptoglobin-related gene (HPR) were reported to show a population-specific distribution and to be associated with not only serum haptoglobin (HP) but also cholesterol levels. For such association studies, it is important to know the distribution of polymorphisms or their haplotypes in the populations concerned. However, no comprehensive genetic studies have explored this in Latin Americans, and not every human variation or genotype is available in a database. In this study, we determined the genotypes of common HP (HP1 and HP2), HPdel, rs5471, rs5472, and rs2000999 in several Latin American populations. Haplotypes of rs5472-common HP-rs2000999 polymorphisms were estimated. We did not encounter any HPdel, and the frequencies of rs5471 A, rs5472 A, HP1, and rs2000999 G were higher than their counterpart alleles in studied populations. All of the alleles with higher frequency in the Latin Americans are associated with higher serum HP and lower cholesterol levels. Both A-1-G (probably HP1S) and G-1-G (probably HP1F) haplotypes were higher in Latin American populations than those in other geographic regions. In addition, the genetic influx from populations of other continents into Peruvians seems to be relatively lower than that into other Latin Americans.
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di Masi A, De Simone G, Ciaccio C, D'Orso S, Coletta M, Ascenzi P. Haptoglobin: From hemoglobin scavenging to human health. Mol Aspects Med 2020; 73:100851. [PMID: 32660714 DOI: 10.1016/j.mam.2020.100851] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
Haptoglobin (Hp) belongs to the family of acute-phase plasma proteins and represents the most important plasma detoxifier of hemoglobin (Hb). The basic Hp molecule is a tetrameric protein built by two α/β dimers. Each Hp α/β dimer is encoded by a single gene and is synthesized as a single polypeptide. Following post-translational protease-dependent cleavage of the Hp polypeptide, the α and β chains are linked by disulfide bridge(s) to generate the mature Hp protein. As human Hp gene is characterized by two common Hp1 and Hp2 alleles, three major genotypes can result (i.e., Hp1-1, Hp2-1, and Hp2-2). Hp regulates Hb clearance from circulation by the macrophage-specific receptor CD163, thus preventing Hb-mediated severe consequences for health. Indeed, the antioxidant and Hb binding properties of Hp as well as its ability to stimulate cells of the monocyte/macrophage lineage and to modulate the helper T-cell type 1 and type 2 balance significantly associate with a variety of pathogenic disorders (e.g., infectious diseases, diabetes, cardiovascular diseases, and cancer). Alternative functions of the variants Hp1 and Hp2 have been reported, particularly in the susceptibility and protection against infectious (e.g., pulmonary tuberculosis, HIV, and malaria) and non-infectious (e.g., diabetes, cardiovascular diseases and obesity) diseases. Both high and low levels of Hp are indicative of clinical conditions: Hp plasma levels increase during infections, inflammation, and various malignant diseases, and decrease during malnutrition, hemolysis, hepatic disease, allergic reactions, and seizure disorders. Of note, the Hp:Hb complexes display heme-based reactivity; in fact, they bind several ferrous and ferric ligands, including O2, CO, and NO, and display (pseudo-)enzymatic properties (e.g., NO and peroxynitrite detoxification). Here, genetic, biochemical, biomedical, and biotechnological aspects of Hp are reviewed.
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Affiliation(s)
- Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Silvia D'Orso
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146, Roma, Italy.
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Johnson AA, Shokhirev MN, Wyss-Coray T, Lehallier B. Systematic review and analysis of human proteomics aging studies unveils a novel proteomic aging clock and identifies key processes that change with age. Ageing Res Rev 2020; 60:101070. [PMID: 32311500 DOI: 10.1016/j.arr.2020.101070] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/23/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022]
Abstract
The development of clinical interventions that significantly improve human healthspan requires robust markers of biological age as well as thoughtful therapeutic targets. To promote these goals, we performed a systematic review and analysis of human aging and proteomics studies. The systematic review includes 36 different proteomics analyses, each of which identified proteins that significantly changed with age. We discovered 1,128 proteins that had been reported by at least two or more analyses and 32 proteins that had been reported by five or more analyses. Each of these 32 proteins has known connections relevant to aging and age-related disease. GDF15, for example, extends both lifespan and healthspan when overexpressed in mice and is additionally required for the anti-diabetic drug metformin to exert beneficial effects on body weight and energy balance. Bioinformatic enrichment analyses of our 1,128 commonly identified proteins heavily implicated processes relevant to inflammation, the extracellular matrix, and gene regulation. We additionally propose a novel proteomic aging clock comprised of proteins that were reported to change with age in plasma in three or more different studies. Using a large patient cohort comprised of 3,301 subjects (aged 18-76 years), we demonstrate that this clock is able to accurately predict human age.
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A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin. Proc Natl Acad Sci U S A 2020; 117:15554-15564. [PMID: 32561649 PMCID: PMC7355005 DOI: 10.1073/pnas.2002483117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Haptoglobin (Hp) is one of the most abundant plasma proteins; it binds with high affinity to hemoglobin (Hb). Thereby Hp protects against the toxic effects of the heme when Hb leaks into plasma from damaged red blood cells. Therefore, serum Hp is an important antioxidant and a clinically important protein, often used as a protein biomarker. Here, we address in detail what proteoforms and proteoform assemblies co-occur in serum, and show how they differ in individuals with distinct genotypes. Our data, obtained by a range of state-of-the-art analytical methods, reveal in unprecedented detail how these hundreds of Hp proteoforms influence the scavenging of Hb through several distinctive molecular features of Hp genotypes. The serum haptoglobin protein (Hp) scavenges toxic hemoglobin (Hb) leaked into the bloodstream from erythrocytes. In humans, there are two frequently occurring allelic forms of Hp, resulting in three genotypes: Homozygous Hp 1-1 and Hp 2-2, and heterozygous Hp 2-1. The Hp genetic polymorphism has an intriguing effect on the quaternary structure of Hp. The simplest form, Hp 1-1, forms dimers consisting of two α1β units, connected by disulfide bridges. Hp 2-1 forms mixtures of linear (α1)2(α2)n-2(β)n oligomers (n > 1) while Hp 2-2 occurs in cyclic (α2)n(β)n oligomers (n > 2). Different Hp genotypes bind Hb with different affinities, with Hp 2-2 being the weakest binder. This behavior has a significant influence on Hp’s antioxidant capacity, with potentially distinctive personalized clinical consequences. Although Hp has been studied extensively in the past, the finest molecular details of the observed differences in interactions between Hp and Hb are not yet fully understood. Here, we determined the full proteoform profiles and proteoform assemblies of all three most common genetic Hp variants. We combined several state-of-the-art analytical methods, including various forms of chromatography, mass photometry, and different tiers of mass spectrometry, to reveal how the tens to hundreds distinct proteoforms and their assemblies influence Hp’s capacity for Hb binding. We extend the current knowledge by showing that Hb binding does not just depend on the donor’s genotype, but is also affected by variations in Hp oligomerization, glycosylation, and proteolytic processing of the Hp α-chain.
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Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR. Genome Res 2020; 30:724-735. [PMID: 32424072 PMCID: PMC7263195 DOI: 10.1101/gr.255273.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Despite the interest in characterizing genomic variation, the presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, since there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different genome-wide techniques. In addition, we obtained new experimental human population information across 95 African, European, and East Asian individuals for 16 inversions, including four already validated variants without high-throughput genotyping methods. Through comparison with previous data, independent replicates and both inversion breakpoints, we demonstrate that the technique is highly accurate and reproducible. Most studied inversions are widespread across continents, and their frequency is negatively correlated with genetic length. Moreover, all except two show clear signs of being recurrent, and we could better define the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, the generated genotypes have allowed us to check inversion functional effects, validating gene expression differences reported before for two inversions and finding new candidate associations. Therefore, the developed methodology makes it possible to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
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Olatunya OS, Albuquerque DM, Santos MNN, Kayode TS, Adekile A, Costa FF. Haptoglobin Gene Polymorphism in Patients with Sickle Cell Anemia: Findings from a Nigerian Cohort Study. Appl Clin Genet 2020; 13:107-114. [PMID: 32440193 PMCID: PMC7217459 DOI: 10.2147/tacg.s246607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/26/2020] [Indexed: 01/12/2023] Open
Abstract
PURPOSE To determine the various haptoglobin genotypes and their influence on the clinico-laboratory manifestations among young Nigerian sickle cell anemia (SCA) patients. PATIENTS AND METHODS A total of 101 SCA patients and 64 controls were studied. SCA was diagnosed by polymerase chain reaction (PCR). Haptoglobin genotype was determined by PCR followed by agarose gel electrophoresis. The patients' laboratory and clinical parameters were differentiated by haptoglobin genotypes. RESULTS The Hp1 and Hp2 alleles frequencies were 0.62 and 0.38 in the patients and 0.73 and 0.27 in the controls, respectively, and these did not differ significantly (p>0.05). The haptoglobin genotype distribution among the patients and controls were Hp1-1, 43 (42.6%); Hp2-1, 40 (39.6%); Hp2-2, 18 (17.8%) and Hp1-1, 35 (54.7%); Hp2-1, 24 (37.5%); Hp2-2, 5 (7.8%), respectively, with no difference between the two groups (P>0.05). No significant difference was found in the clinical events and laboratory parameters of the patients when partitioned according to the various haptoglobin genotypes (P> 0.05). CONCLUSION This study found that haptoglobin gene polymorphism does not have a significant influence on the clinico-laboratory manifestations among SCA patients.
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Affiliation(s)
- Oladele Simeon Olatunya
- Hematology and Hemotherapy Center, University of Campinas, Campinas, São Paulo State, Brazil
- Department of Paediatrics, College of Medicine, Ekiti State University, Ado Ekiti, Ekiti State, Nigeria
| | | | - Magnun Nueldo Nunes Santos
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Campinas, São Paulo State, Brazil
| | - Tolorunju Segun Kayode
- Department of Chemical Pathology, Ekiti State University Teaching Hospital, Ado Ekiti, Ekiti State, Nigeria
| | - Adekunle Adekile
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Fernando Ferreira Costa
- Hematology and Hemotherapy Center, University of Campinas, Campinas, São Paulo State, Brazil
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Assessment of haptoglobin alleles in autism spectrum disorders. Sci Rep 2020; 10:7758. [PMID: 32385356 PMCID: PMC7210291 DOI: 10.1038/s41598-020-64679-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Gene-environment interactions, by means of abnormal macromolecular intestinal adsorption, is one of the possible causes of autism spectrum disorders (ASD) predominantly in patients with gastrointestinal disorders. Pre-haptoglobin-2 (zonulin), encoded by the Haptoglobin (HP) allele-2 gene, enhances the intestinal permeability by modulation of intercellular tight junctions. The two alleles of HP, HP1 and HP2, differ for 2 extra exons in HP2 that result in exon duplication undetectable by classic genome-wide association studies. To evaluate the role of HP2 in ASD pathogenesis and to set up a method to discriminate HP alleles, Italian subjects with ASD (n = 398) and healthy controls (n = 379) were genotyped by PCR analysis; subsequently, the PCR results were integrated with microarray genotypes (Illumina Human Omni 1S-8), obtained using a subset from the same subjects, and then we developed a computational method to predict HP alleles. On the contrary to our expectations, there was no association between HP2 and ASD (P > 0.05), and there was no significant allele association in subjects with ASD with or without gastrointestinal disorders (P > 0.05). With the aid of bioinformatics analysis, from a window frame of ~2 Mb containing 314 SNPs, we obtain imputation accuracy (r2) between 0.4 and 0.9 (median 0.7) and correct predictions were between 70% and 100% (median 90%). The conclusions endorse that enhanced intestinal permeability in subjects with ASD should not be imputed to HP2 but to other members of the zonulin family and/or to environmental factors.
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40
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Willen SM, McNeil JB, Rodeghier M, Kerchberger VE, Shaver CM, Bastarache JA, Steinberg MH, DeBaun MR, Ware LB. Haptoglobin genotype predicts severe acute vaso-occlusive pain episodes in children with sickle cell anemia. Am J Hematol 2020; 95:E92-E95. [PMID: 31919880 PMCID: PMC7343605 DOI: 10.1002/ajh.25728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Shaina M. Willen
- Division of Pulmonary Medicine, Department of Pediatrics, UCSF Benioff Children’s Hospital San Francisco, CA, USA
| | - J. Brennan McNeil
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - V. Eric Kerchberger
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Julie A. Bastarache
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Martin H. Steinberg
- Division of Hematology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Michael R. DeBaun
- Division of Hematology/Oncology, Department of Pediatrics, Vanderbilt-Meharry Center for Excellence in Sickle Cell Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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Buehler PW, Humar R, Schaer DJ. Haptoglobin Therapeutics and Compartmentalization of Cell-Free Hemoglobin Toxicity. Trends Mol Med 2020; 26:683-697. [PMID: 32589936 DOI: 10.1016/j.molmed.2020.02.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Abstract
Hemolysis and accumulation of cell-free hemoglobin (Hb) in the circulation or in confined tissue compartments such as the subarachnoid space is an important driver of disease. Haptoglobin is the Hb binding and clearance protein in human plasma and an efficient antagonist of Hb toxicity resulting from physiological red blood cell turnover. However, endogenous concentrations of haptoglobin are insufficient to provide protection against Hb-driven disease processes in conditions such as sickle cell anemia, sepsis, transfusion reactions, medical-device associated hemolysis, or after a subarachnoid hemorrhage. As a result, there is increasing interest in developing haptoglobin therapeutics to target 'toxic' cell-free Hb exposures. Here, we discuss key concepts of Hb toxicity and provide a perspective on the use of haptoglobin as a therapeutic protein.
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Affiliation(s)
- Paul W Buehler
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Rok Humar
- Division of Internal Medicine, University Hospital, Zurich, Switzerland
| | - Dominik J Schaer
- Division of Internal Medicine, University Hospital, Zurich, Switzerland.
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Soejima M, Munkhtulga L, Furukawa K, Iwamoto S, Koda Y. Serum haptoglobin correlates positively with cholesterol and triglyceride concentrations in an obese Mongolian population. Clin Chim Acta 2020; 505:176-182. [PMID: 32156606 DOI: 10.1016/j.cca.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent studies revealed that several genetic polymorphisms of haptoglobin gene (HP) and the haptoglobin-related protein gene (HPR) associated not only with haptoglobin (HP) but total, non-HDL, and/or LDL cholesterol concentrations in various populations. METHODS Association between serum HP concentrations and polymorphisms of HP and the HPR gene, or anthropometric and metabolic factors were examined in Mongolian participants (n = 927) using linear regression analyses. RESULTS The association of HP and HPR polymorphisms with serum HP concentration but not serum lipids concentrations was observed. However, subgroup analysis revealed that the association of HP and HPR polymorphisms with serum HP concentration was weakened in subgroup of obese (BMI ≥ 30) subjects and positive correlations between serum HP and non-HDL cholesterol, HDL cholesterol or triglyceride concentrations were observed in the obese subjects as compared with in subgroups of normal weight (BMI < 25) and overweight (25 ≤ BMI < 30) subjects. CONCLUSION The degree of obesity strongly affects the relationships between serum HP concentrations and several genetic, anthropometric and metabolic factors. These results suggested that we need to take into account the degree of obesity when considering the HP polymorphisms as predictive markers for clinical states.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Lkhagvasuren Munkhtulga
- Department of Pathophysiology, Biomedical School, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Sadahiko Iwamoto
- Division of Human Genetics, Center for Community Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan.
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Morton MJ, Hostettler IC, Kazmi N, Alg VS, Bonner S, Brown MM, Durnford A, Gaastra B, Garland P, Grieve J, Kitchen N, Walsh D, Zolnourian A, Houlden H, Gaunt TR, Bulters DO, Werring DJ, Galea I. Haptoglobin genotype and outcome after aneurysmal subarachnoid haemorrhage. J Neurol Neurosurg Psychiatry 2020; 91:305-313. [PMID: 31937585 PMCID: PMC7116595 DOI: 10.1136/jnnp-2019-321697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022]
Abstract
OBJECTIVE After aneurysmal subarachnoid haemorrhage (aSAH), extracellular haemoglobin (Hb) in the subarachnoid space is bound by haptoglobin, neutralising Hb toxicity and helping its clearance. Two exons in the HP gene (encoding haptoglobin) exhibit copy number variation (CNV), giving rise to HP1 and HP2 alleles, which influence haptoglobin expression level and possibly haptoglobin function. We hypothesised that the HP CNV associates with long-term outcome beyond the first year after aSAH. METHODS The HP CNV was typed using quantitative PCR in 1299 aSAH survivors in the Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study, a retrospective multicentre cohort study with a median follow-up of 18 months. To investigate mediation of the HP CNV effect by haptoglobin expression level, as opposed to functional differences, we used rs2000999, a single nucleotide polymorphism associated with haptoglobin expression independent of the HP CNV. Outcome was assessed using modified Rankin and Glasgow Outcome Scores. SAH volume was dichotomised on the Fisher grade. Haemoglobin-haptoglobin complexes were measured in cerebrospinal fluid (CSF) of 44 patients with aSAH and related to the HP CNV. RESULTS The HP2 allele associated with a favourable long-term outcome after high-volume but not low-volume aSAH (multivariable logistic regression). However rs2000999 did not predict outcome. The HP2 allele associated with lower CSF haemoglobin-haptoglobin complex levels. The CSF Hb concentration after high-volume and low-volume aSAH was, respectively, higher and lower than the Hb-binding capacity of CSF haptoglobin. CONCLUSION The HP2 allele carries a favourable long-term prognosis after high-volume aSAH. Haptoglobin and the Hb clearance pathway are therapeutic targets after aSAH.
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Affiliation(s)
- Matthew J Morton
- Clinical Neurosciences, Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - Isabel C Hostettler
- Stroke Research Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Varinder S Alg
- Stroke Research Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Stephen Bonner
- Department of Anaesthesia, James Cook University Hospital, Middlesbrough, UK
| | - Martin M Brown
- Stroke Research Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Andrew Durnford
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Benjamin Gaastra
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Patrick Garland
- Clinical Neurosciences, Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - Joan Grieve
- Department of Neurosurgery, The National Hospital of Neurology and Neurosurgery, London, UK
| | - Neil Kitchen
- Department of Neurosurgery, The National Hospital of Neurology and Neurosurgery, London, UK
| | - Daniel Walsh
- Department of Neurosurgery, King's College Hospital NHS Foundation Trust, London, UK
| | - Ardalan Zolnourian
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Henry Houlden
- Neurogenetics Laboratory, The National Hospital of Neurology and Neurosurgery, London, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Diederik O Bulters
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - David J Werring
- Stroke Research Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ian Galea
- Clinical Neurosciences, Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
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Mostaza JM, de Dios O, Lahoz C, Arribas M, Pérez Arroyo A, Salinero-Fort MA, Laguna F, Estirado E, García-Iglesias F, González Alegre T, Sabín C, López S, Sánchez V, Cornejo V, Garcés C. Phenotype of haptoglobin and presence of subclinical vascular disease: Population study. CLINICA E INVESTIGACION EN ARTERIOSCLEROSIS : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ARTERIOSCLEROSIS 2020; 32:1-7. [PMID: 31221534 DOI: 10.1016/j.arteri.2019.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
INTRODUCTION AND OBJECTIVES Haptoglobin is a protein involved in the protection against oxidative damage caused by iron in haemoglobin. This protein is polymorphic, with 3 isomorphs prevalent in the population. The carriers of the Hp2-2 isoform have a lower antioxidant capacity and, in the population with diabetes, an increased risk of subclinical vascular disease and cardiovascular complications. The objective of this study was to evaluate whether this isomorphy is associated with an increased risk of carotid arteriosclerosis in subjects with and without diabetes, and free of cardiovascular disease. PATIENTS AND METHODS A study was conducted in a population between 45 and 74years of age, randomly selected from the northwest area of Madrid. The participants were characterised in terms of their glycaemic status by oral glucose overload and the determination of the concentration of Hb1Ac. The haptoglobin phenotypes in all of them were determined by means of an immunoenzymatic assay, and the presence of carotid arteriosclerosis by ultrasound. RESULTS Of the 1,256 participants included in the present analysis (mean age 61.6±6years, 41.8% males), the distribution of the isoforms of haptoglobin was as follows: Hp1-1: 13.3%, Hp1-2: 48.5%, and Hp2-2: 38.2%. In comparison with subjects Hp1-1 and Hp1-2, those with the Hp2-2 phenotype had a higher prevalence of dyslipidaemia (53.3% vs 43%; P<.0001) and arterial hypertension (39.2% vs. 32.2%, P=.012), and they more frequently received treatment with statins (31.5% vs 21.6%, P<.0001), and with antihypertensive agents (38.4% vs 30.8%, P=.006). The carriers of the Hp2-2 isoform had a higher prevalence of carotid plaques (OR: 1.35, 95%CI: 1.07-1.69, P=.011), with no differences in that prevalence as regards the glycaemic status. There were no differences in the intima-media thickness between the different phenotypes. The relationship of the Hp2-2 phenotype with the presence of plaques in the carotid was independent of age, gender, presence of risk factors (dyslipidaemia, hypertension and diabetes), the concentration of LDL-cholesterol, C-reactive protein and uric acid, blood pressure, and treatment with statins, and hypertensive drugs (OR: 1.31, 95%CI 1.01-1.70, P=.044). CONCLUSION Subjects with the Hp2-2 phenotype of haptoglobin have a higher prevalence of carotid arteriosclerosis, which is independent of the presence of other cardiovascular risk factors and their glycaemic status.
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Affiliation(s)
- Jose M Mostaza
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España.
| | - Olaya de Dios
- Laboratorio de Lípidos, IIS-Fundación Jiménez Díaz, UAM, Madrid, España
| | - Carlos Lahoz
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | - Marta Arribas
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | | | - Miguel A Salinero-Fort
- Gerencia Adjunta de Planificación y Calidad Atención Primaria, Servicio Madrileño de Salud, Madrid, España
| | - Fernando Laguna
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | - Eva Estirado
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | - Francisca García-Iglesias
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | - Teresa González Alegre
- Unidad de Lípidos y Riesgo Cardiovascular, Servicio de Medicina Interna, Hospital Carlos III, Madrid, España
| | | | - Silvia López
- Unidad de día, Hospital Carlos III, Madrid, España
| | | | | | - Carmen Garcés
- Laboratorio de Lípidos, IIS-Fundación Jiménez Díaz, UAM, Madrid, España
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Lempiäinen J, Ijäs P, Niiranen TJ, Kaste M, Karhunen PJ, Lindsberg PJ, Erkinjuntti T, Melkas S. Haptoglobin Hp1 Variant Does Not Associate with Small Vessel Disease. Brain Sci 2019; 10:brainsci10010018. [PMID: 31905636 PMCID: PMC7016682 DOI: 10.3390/brainsci10010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Haptoglobin (Hp) is a plasma protein that binds free hemoglobin and protects tissues from oxidative damage. An Hp2 allele has been associated with an increased risk of cardiovascular complications. On the other hand, recent studies have suggested that Hp1 allele increases risk to develop severe cerebral small vessel disease. We aimed to replicate this finding in a first-ever stroke patient cohort. Hp was genotyped by PCR and gel electrophoresis in the Helsinki Stroke Aging Memory Study in patients with DNA and magnetic resonance imaging (MRI) available (SAM; n = 316). Lacunar infarcts and white matter lesions (WML) classified by Fazekas grading from brain MRI were associated with Hp genotypes. As population controls, we used participants of Cardiovascular diseases—a sub study of Health 2000 Survey (n = 1417). In the SAM cohort, 63.0% of Hp1-1 carriers (n = 46), 52.5% of Hp1-2 carriers (n = 141) and 51.2% of Hp2-2 carriers (n = 129) had severe WML (p = 0.372). There was no difference in severe WMLs between Hp1-1 vs. Hp1-2 and Hp2-2 carriers (p = 0.201). In addition, 68.9% of Hp1-1 carriers (n = 45), 58.5% of Hp1-2 carriers (n = 135), and 61.8% of Hp2-2 carriers (n = 126) had one or more lacunar lesions (p = 0.472). There was no difference in the number of patients with at least one lacunar infarct between Hp1-1 vs. Hp1-2 and Hp2-2 groups (p = 0.322). Neither was there any difference when diabetic patients (type I and II) were examined separately. Hp1 allele is not associated with an increased risk for cerebral small vessel disease in a well-characterized Finnish stroke patient cohort.
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Affiliation(s)
- Juha Lempiäinen
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Correspondence: ; Tel.: +358-407-787-278; Fax: +358-947-185-957
| | - Petra Ijäs
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Teemu J. Niiranen
- Department of Public Health Solutions, National institute for Health and Welfare, Mannerheimintie 166, 00300 Helsinki, Finland;
- Division of Medicine, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Markku Kaste
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Pekka J. Karhunen
- School of Medicine, University of Tampere, 33014 Tampere, Finland;
- FimLab Laboratories Ltd., Tampere University Hospital Region, 33014 Tampere, Finland
| | - Perttu J. Lindsberg
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Timo Erkinjuntti
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Susanna Melkas
- Clinical Neurosciences, University of Helsinki, 00014 Helsinki, Finland; (P.I.); (M.K.); (P.J.L.); (T.E.); (S.M.)
- Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
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Kerchberger VE, Bastarache JA, Shaver CM, Nagata H, McNeil JB, Landstreet SR, Putz ND, Yu WK, Jesse J, Wickersham NE, Sidorova TN, Janz DR, Parikh CR, Siew ED, Ware LB. Haptoglobin-2 variant increases susceptibility to acute respiratory distress syndrome during sepsis. JCI Insight 2019; 4:131206. [PMID: 31573976 DOI: 10.1172/jci.insight.131206] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/20/2019] [Indexed: 01/15/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is an inflammatory lung disorder that frequently complicates critical illness and commonly occurs in sepsis. Although numerous clinical and environmental risk factors exist, not all patients with risk factors develop ARDS, raising the possibility of genetic underpinnings for ARDS susceptibility. We have previously reported that circulating cell-free hemoglobin (CFH) is elevated during sepsis, and higher levels predict worse outcomes. Excess CFH is rapidly scavenged by haptoglobin (Hp). A common HP genetic variant, HP2, is unique to humans and is common in many populations worldwide. HP2 haptoglobin has reduced ability to inhibit CFH-mediated inflammation and oxidative stress compared with the alternative HP1. We hypothesized that HP2 increases ARDS susceptibility during sepsis when plasma CFH levels are elevated. In a murine model of sepsis with elevated CFH, transgenic mice homozygous for Hp2 had increased lung inflammation, pulmonary vascular permeability, lung apoptosis, and mortality compared with wild-type mice. We then tested the clinical relevance of our findings in 496 septic critically ill adults, finding that HP2 increased ARDS susceptibility after controlling for clinical risk factors and plasma CFH. These observations identify HP2 as a potentially novel genetic ARDS risk factor during sepsis and may have important implications in the study and treatment of ARDS.
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Affiliation(s)
- V Eric Kerchberger
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine.,Department of Biomedical Informatics
| | - Julie A Bastarache
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine.,Department of Cell and Developmental Biology, and.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ciara M Shaver
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Hiromasa Nagata
- Department of Anesthesiology, Keio University School of Medicine, Tokyo, Japan
| | - J Brennan McNeil
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Stuart R Landstreet
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Nathan D Putz
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Wen-Kuang Yu
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine.,Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jordan Jesse
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Nancy E Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - Tatiana N Sidorova
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | - David R Janz
- Section of Pulmonary and Critical Care Medicine, Louisiana State University School of Medicine, New Orleans, Louisiana, USA
| | - Chirag R Parikh
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Edward D Siew
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lorraine B Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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47
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The impact of short tandem repeat variation on gene expression. Nat Genet 2019; 51:1652-1659. [PMID: 31676866 PMCID: PMC6917484 DOI: 10.1038/s41588-019-0521-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022]
Abstract
Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and provide insights into putative mechanisms. Here, we leverage whole-genome sequencing and expression data for 17 tissues from the Genotype-Tissue Expression Project to identify more than 28,000 STRs for which repeat number is associated with expression of nearby genes (eSTRs). We use fine-mapping to quantify the probability that each eSTR is causal and characterize the top 1,400 fine-mapped eSTRs. We identify hundreds of eSTRs linked with published genome-wide association study signals and implicate specific eSTRs in complex traits, including height, schizophrenia, inflammatory bowel disease and intelligence. Overall, our results support the hypothesis that eSTRs contribute to a range of human phenotypes, and our data should serve as a valuable resource for future studies of complex traits.
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48
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An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 2019; 88:104-119. [PMID: 31522275 DOI: 10.1007/s00239-019-09911-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Copy number variants (CNVs), deletions and duplications of segments of DNA, account for at least five times more variable base pairs in humans than single-nucleotide variants. Several common CNVs were shown to change coding and regulatory sequences and thus dramatically affect adaptive phenotypes involving immunity, perception, metabolism, skin structure, among others. Some of these CNVs were also associated with susceptibility to cancer, infection, and metabolic disorders. These observations raise the possibility that CNVs are a primary contributor to human phenotypic variation and consequently evolve under selective pressures. Indeed, locus-specific haplotype-level analyses revealed signatures of natural selection on several CNVs. However, more traditional tests of selection which are often applied to single-nucleotide variation often have diminished statistical power when applied to CNVs because they often do not show strong linkage disequilibrium with nearby variants. Recombination-based formation mechanisms of CNVs lead to frequent recurrence and gene conversion events, breaking the linkage disequilibrium involving CNVs. Similar methodological challenges also prevent routine genome-wide association studies to adequately investigate the impact of CNVs on heritable human disease. Thus, we argue that the full relevance of CNVs to human health and evolution is yet to be elucidated. We further argue that a holistic investigation of formation mechanisms within an evolutionary framework would provide a powerful framework to understand the functional and biomedical impact of CNVs. In this paper, we review several cases where studies reveal diverse evolutionary histories and unexpected functional consequences of CNVs. We hope that this review will encourage further work on CNVs by both evolutionary and medical geneticists.
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49
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Suarez-Sanchez F, Vazquez-Moreno M, Herrera-Lopez E, Gomez-Zamudio JH, Peralta-Romero JJ, Castelan-Martinez OD, Cruz M, Parra EJ, Valladares-Salgado A. Association of rs2000999 in the haptoglobin gene with total cholesterol, HDL-C, and LDL-C levels in Mexican type 2 diabetes patients. Medicine (Baltimore) 2019; 98:e17298. [PMID: 31574854 PMCID: PMC6775401 DOI: 10.1097/md.0000000000017298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Recently, studies have shown significant association between the rs2000999 polymorphism in the haptoglobin-encoding gene (HP) and low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) levels, which are important risk factors for cardiovascular diseases. However, the association of rs2000999 with serum lipids in Latin American diabetic populations is still uncharacterized. Here, we analyzed the association of rs2000999 with TC, high-density lipoprotein cholesterol (HDL-C), and LDL-C levels in 546 Mexican adults with type 2 diabetes (T2D) and in 654 controls without T2D. In this observational case-control study we included adults from 4 centers of the Mexican Social Security Institute in Mexico City recruited from 2012 to 2015. TC, HDL-C, LDL-C, triglycerides (TG), and glucose levels were measured by an enzymatic colorimetric method. The variant rs2000999 was genotyped using TaqMan real time polymerase chain reaction. The percentage of Native-American ancestry showed a negative association with the rs2000999 A allele. In contrast, the rs2000999 A allele had a strong positive association with European ancestry, and to a lesser extent, with African ancestry. Linear regression was used to estimate the association between the variant rs2000999 and lipid concentrations, using different genetic models. Under codominant and recessive models, rs2000999 was significantly associated with TC and LDL-C levels in the T2D group and in controls without T2D. In addition, the group with T2D showed a significant association between the variant and HDL-C levels. In summary, the rs2000999 A allele in Mexican population is positively associated with the percentage of European and negatively associated with Native American ancestry. Carriers of the A allele have increased levels of TC and LDL-C, independently of T2D diagnosis, and also increased concentrations of HDL-C in the T2D sample.
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Affiliation(s)
- Fernando Suarez-Sanchez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | - Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | - Ema Herrera-Lopez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | - Jaime H. Gomez-Zamudio
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | - José J. Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | | | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social
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50
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Kazmi N, Koda Y, Ndiaye NC, Visvikis-Siest S, Morton MJ, Gaunt TR, Galea I. Genetic determinants of circulating haptoglobin concentration. Clin Chim Acta 2019; 494:138-142. [PMID: 30898509 PMCID: PMC6541910 DOI: 10.1016/j.cca.2019.03.1617] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 03/17/2019] [Indexed: 01/15/2023]
Abstract
Haptoglobin (Hp) is a major plasma acute-phase glycoprotein, which binds free haemoglobin to neutralize its toxicity. The HP gene exists as two copy number variants (CNV), Hp1 and HP2, which differ in two ways: serum Hp level and functional differences in Hp protein products. Both mechanisms may underlie the HP CNV's influence on susceptibility and/or outcome in several diseases. A single nucleotide polymorphism rs2000999 has also been associated with serum Hp level. In a meta-analysis of three studies from England, France and Japan, with a combined sample size of 1210 participants, we show that rs2000999's effect on circulating Hp level is independent from that of the HP CNV. The combined use of rs2000999 and the HP CNV can be an important genetic epidemiological tool to discriminate between the two potential mechanisms underlying differences between HP1 and HP2 alleles.
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Affiliation(s)
- Nabila Kazmi
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | | | | | - Matthew J Morton
- Clinical Neurosciences, Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ian Galea
- Clinical Neurosciences, Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, UK.
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